diff --git a/envi/envi.h b/envi/envi.h
index aa545e2..b0775a3 100644
--- a/envi/envi.h
+++ b/envi/envi.h
@@ -47,7 +47,7 @@ struct envi
 	std::vector<std::string> band_names;	//name for each band in the image
 	std::vector<double> wavelength;		//wavelength for each band
 
-	envi(){
+	void init(){
         name = "";
 
 		//specify default values for a new or empty ENVI file
@@ -68,6 +68,14 @@ struct envi
 		z_plot_titles[0] = z_plot_titles[1] = "Unknown";
 	}
 
+	envi(){
+		init();
+	}
+	envi(std::string name){
+		init();
+		load(name);
+	}
+
 	std::string trim(std::string line){
 		//trims whitespace from the beginning and end of line
 		unsigned int start_i, end_i;
diff --git a/legacy/CHECK_OPENGL_ERROR.h b/legacy/CHECK_OPENGL_ERROR.h
deleted file mode 100755
index d9324ef..0000000
--- a/legacy/CHECK_OPENGL_ERROR.h
+++ /dev/null
@@ -1,15 +0,0 @@
-#ifndef RTS_OPENGL_ERROR
-#define RTS_OPENGL_ERROR
-
-#include <stdio.h>
-#include <GL/gl.h>
-#include <GL/glu.h>
-
-#define CHECK_OPENGL_ERROR \
-{ GLenum error; \
-   while ( (error = glGetError()) != GL_NO_ERROR) { \
-   printf( "OpenGL ERROR: %s\nCHECK POINT: %s (line %d)\n", gluErrorString(error), __FILE__, __LINE__ ); \
-   } \
-}
-
-#endif
\ No newline at end of file
diff --git a/legacy/PerformanceDataTemplate.h b/legacy/PerformanceDataTemplate.h
deleted file mode 100755
index 9b5684e..0000000
--- a/legacy/PerformanceDataTemplate.h
+++ /dev/null
@@ -1,138 +0,0 @@
-// add the following to a cpp file:
-// PerformanceData PD;
-
-
-#pragma once
-#include <ostream>
-using namespace std;
-
-enum PerformanceDataType
-{
-	PD_DISPLAY=0,
-	PD_SPS,
-	PD_UNUSED0,
-
-	//my stuff
-	SIMULATE_SPECTRUM,
-	SIMULATE_GPU,
-	KRAMERS_KRONIG,
-
-	
-
-	//end my stuff
-	PERFORMANCE_DATA_TYPE_COUNT
-};
-
-static char PDTypeNames[][255] = {
-		"Display            ",
-		"Simulation Total   ",
-		" ----------------- ",
-		//my stuff
-		"Simulate Spectrum  ",
-		"      GPU Portion  ",
-		"Kramers-Kronig     ",
-
-		//end my stuff
-		
-};
-#ifdef WIN32
-#include <stdio.h>
-#include <windows.h>
-#include <float.h>
-
-#include <iostream>
-#include <iomanip>
-
-//-------------------------------------------------------------------------------
-
-class PerformanceData
-{
-public:
-	PerformanceData() { ClearAll(); QueryPerformanceFrequency(&cps); }
-	~PerformanceData(){}
-
-	void ClearAll()
-	{
-		for ( int i=0; i<PERFORMANCE_DATA_TYPE_COUNT; i++ ) {
-			for ( int j=0; j<256; j++ ) times[i][j] = 0;
-			pos[i] = 0;
-			minTime[i] = 0xFFFFFFFF;
-			maxTime[i] = 0;
-			totalTime[i] = 0;
-			dataReady[i] = false;
-		}
-	}
-
-	void StartTimer( int type ) { QueryPerformanceCounter( &startTime[type] );}
-	void EndTimer( int type ) {
-		LARGE_INTEGER endTime;
-		QueryPerformanceCounter( &endTime );
-		double t = (double)(endTime.QuadPart - startTime[type].QuadPart);
-		//unsigned int t = GetTickCount() - startTime[type];
-		if ( t < minTime[type] ) minTime[type] = t;
-		if ( t > maxTime[type] ) maxTime[type] = t;
-		totalTime[type] -= times[type][ pos[type] ];
-		times[type][ pos[type] ] = t;
-		totalTime[type] += t;
-		pos[type]++;
-		if ( pos[type] == 0 ) dataReady[type] = true;
-	}
-
-	void PrintResult( ostream &os,int i=PERFORMANCE_DATA_TYPE_COUNT)
-	{
-		os.setf(ios::fixed);
-		if ((i<PERFORMANCE_DATA_TYPE_COUNT)&&(i>=0)){
-			double a = GetAvrgTime(i);
-			if ( a ) 
-				os<< PDTypeNames[i]<<" :  avrg="<<setw(8)<<setprecision(3)<<a<<"\tmin="<<setw(8)<<setprecision(3)<< GetMinTime(i) <<"\tmax="<<setw(8)<<setprecision(3)<< GetMaxTime(i) <<endl ;
-			else 
-				os<< PDTypeNames[i]<<" :  avrg=   -----\tmin=   -----\tmax=   -----"<<endl;
-		}
-	}
-
-	void PrintResults( ostream &os)
-	{
-		for ( int i=0; i<PERFORMANCE_DATA_TYPE_COUNT; i++ ) 
-			PrintResult(os,i);
-	}
-
-	double	GetLastTime( int type ) { return times[type][pos[type]]; }
-	double	GetAvrgTime( int type ) { double a = 1000.0 * totalTime[type] / (float)cps.QuadPart / ( (dataReady[type]) ? 256.0 : (double)pos[type] ); return (_finite(a))? a:0; }
-	double	GetMinTime( int type ) { return 1000.0 * minTime[type] / (float)cps.LowPart; }
-	double	GetMaxTime( int type ) { return 1000.0 * maxTime[type] / (float)cps.LowPart; }
-
-private:
-	double times[PERFORMANCE_DATA_TYPE_COUNT][256];
-	unsigned char pos[PERFORMANCE_DATA_TYPE_COUNT];
-	LARGE_INTEGER startTime[PERFORMANCE_DATA_TYPE_COUNT];
-	double minTime[ PERFORMANCE_DATA_TYPE_COUNT ];
-	double maxTime[ PERFORMANCE_DATA_TYPE_COUNT ];
-	double totalTime[ PERFORMANCE_DATA_TYPE_COUNT ];
-	bool dataReady[ PERFORMANCE_DATA_TYPE_COUNT ];
-	LARGE_INTEGER cps;
-};
-
-//-------------------------------------------------------------------------------
-#else	
-
-class PerformanceData{
-public:
-	PerformanceData() {;};
-	~PerformanceData(){;};
-	void ClearAll(){;};
-	void StartTimer( int type ) {;};
-	void EndTimer( int type ) {;};
-	void PrintResults( ostream &os){;};
-	void PrintResult( ostream &os, int i=PERFORMANCE_DATA_TYPE_COUNT){;};
-	double	GetLastTime( int type ) { return 0.0; };
-	double	GetAvrgTime( int type ) { return 0.0; };
-	double	GetMinTime( int type ) { return 0.0; };
-	double	GetMaxTime( int type ) { return 0.0; };
-};
-
-#endif
-//-------------------------------------------------------------------------------
-
-extern PerformanceData PD;
-
-//-------------------------------------------------------------------------------
diff --git a/legacy/README.md b/legacy/README.md
deleted file mode 100644
index 2dad741..0000000
--- a/legacy/README.md
+++ /dev/null
@@ -1,12 +0,0 @@
-rts
-===
-
-Real-Time Scraps is my codebase.  I use it for a lot of stuff.  It mostly has a bunch of functions helpful for writing simulation, visualization, and GPU-based code.
-
-Revisions-----
-
-[2013-8-24] - Started re-writing this library. The new stuff will be in the rts subdirectory and I'll remove individual deprecated files over time as they are re-written.
-
-[2013-8-24] - Re-committed this repository.  It was time for a nice refresh since I'm going to be re-building it.
-
-[2013-8-23] - Started using Boost for my command-line processing.
diff --git a/legacy/cudaHandleError.h b/legacy/cudaHandleError.h
deleted file mode 100755
index 68df6f6..0000000
--- a/legacy/cudaHandleError.h
+++ /dev/null
@@ -1,41 +0,0 @@
-#include <stdio.h>
-#include "cuda_runtime.h"
-#include "device_launch_parameters.h"
-
-#ifndef CUDA_HANDLE_ERROR_H
-#define CUDA_HANDLE_ERROR_H
-
-//handle error macro
-static void HandleError( cudaError_t err, const char *file,  int line ) {
-   	if (err != cudaSuccess) {
-			FILE* outfile = fopen("cudaErrorLog.txt", "w");
-      		fprintf(outfile,  "%s in %s at line %d\n", cudaGetErrorString( err ),  file, line );
-			fclose(outfile);
-       		exit( EXIT_FAILURE );
-			printf("%s in %s at line %d\n", cudaGetErrorString( err ),  file, line );
-   	}
-}
-#define HANDLE_ERROR( err ) (HandleError( err, __FILE__, __LINE__ ))
-
-static cudaEvent_t tStartEvent;
-static cudaEvent_t tStopEvent;
-static void gpuStartTimer()
-{
-	//set up timing events
-	cudaEventCreate(&tStartEvent);
-	cudaEventCreate(&tStopEvent);
-	cudaEventRecord(tStartEvent, 0);
-}
-
-static float gpuStopTimer()
-{
-	cudaEventRecord(tStopEvent, 0);
-	cudaEventSynchronize(tStopEvent);
-	float elapsedTime;
-	cudaEventElapsedTime(&elapsedTime, tStartEvent, tStopEvent);
-	cudaEventDestroy(tStartEvent);
-	cudaEventDestroy(tStopEvent);
-	return elapsedTime;
-}
-
-#endif
diff --git a/legacy/cuda_callable.h b/legacy/cuda_callable.h
deleted file mode 100644
index eefc437..0000000
--- a/legacy/cuda_callable.h
+++ /dev/null
@@ -1,10 +0,0 @@
-#ifndef CUDA_CALLABLE
-
-//define the CUDA_CALLABLE macro (will prefix all members)
-#ifdef __CUDACC__
-#define CUDA_CALLABLE __host__ __device__
-#else
-#define CUDA_CALLABLE
-#endif
-
-#endif
diff --git a/legacy/objJedi.cpp b/legacy/objJedi.cpp
deleted file mode 100755
index 8b87934..0000000
--- a/legacy/objJedi.cpp
+++ /dev/null
@@ -1,1531 +0,0 @@
-/*BUG NOTES
-The standard function calls for inserting vertices don't work anymore.  I've fixed points
-but everything beyond that has to be updated.
-*/
-
-#include "objJedi.h"
-#include "rtsvector3D.h"
-#include "rtspoint3D.h"
-#include <string>
-//variable for use in global functions
-rtsOBJ g_OBJ;
-
-/********UTILITY METHODS*******************************/
-void rtsOBJ::Scale(float scale_x, float scale_y, float scale_z)
-{
-	vector<vertex_position>::iterator i;
-	for(i = v_list.begin(); i!= v_list.end(); i++)
-	{
-		(*i).x *= scale_x;
-		(*i).y *= scale_y;
-		(*i).z *= scale_z;
-	}
-}
-
-void rtsOBJ::Translate(float trans_x, float trans_y, float trans_z)
-{
-	vector<vertex_position>::iterator i;
-	for(i = v_list.begin(); i!= v_list.end(); i++)
-	{
-		(*i).x += trans_x;
-		(*i).y += trans_y;
-		(*i).z += trans_z;
-	}
-	
-}
-
-float rtsOBJ::GetDistance(float x, float y, float z)
-{
-	//gets the distance between the specified point and the nearest surface of the OBJ
-	//currently only works for lines
-
-	//cout<<"Primitives: "<<primitives.size()<<endl;
-	int num_primitives = primitives.size();
-	point3D<double> p0, p1, p2;
-	double min_dist = 255;
-	double dist, numerator, denominator;
-	int p, l;
-	vector3D<double> v, w;
-	double c1, c2, b;
-	point3D<double> Pb;
-
-	//for each line
-	for(l=0; l<num_primitives; l++)
-	{
-		if(primitives[l].type & OBJ_LINES)
-		{
-			//for each point
-			for(p = 1; p<primitives[l].p.size(); p++)
-			{
-				
-				vertex_position v1 = v_list[primitives[l].p[p-1].v];
-				vertex_position v2 = v_list[primitives[l].p[p].v];
-				p1.x = v1.x;
-				p1.y = v1.y;
-				p1.z = v1.z;
-				p2.x = v2.x;
-				p2.y = v2.y;
-				p2.z = v2.z;
-				
-				p0.x = x;
-				p0.y = y;
-				p0.z = z;
-
-				v = p2 - p1;
-				w = p0 - p1;
-				if((c1 = w*v) <= 0)
-					dist = (p1 - p0).Length();
-				else if((c2 = v*v) <= c1)
-					dist = (p2 - p0).Length();
-				else
-				{
-					b = c1/c2;
-					Pb = p1 + b*v;
-					dist = (Pb - p0).Length();
-				}
-				if(dist < min_dist)
-					min_dist = dist;
-				
-
-		
-			}
-		}
-	}
-	//cout<<"---------------------------------------------"<<endl;
-
-	return min_dist;
-				
-
-}
-
-/********CLASS METHOD DEFINITIONS**********************/
-//constructors
-
-//constructor
-rtsOBJ::rtsOBJ()
-{
-	g_CurrentMode = OBJ_NONE;
-	g_NumVertices = 0;
-	g_AttributeMask = 0x0;
-	g_AttributeResetMask = 0x0;
-	g_LatestVT = 0;
-	g_LatestVN = 0;
-
-	m_bounds.min.x = m_bounds.min.y = m_bounds.min.z = 99999;
-	m_bounds.max.x = m_bounds.max.y = m_bounds.max.z = -99999;
-
-	current_primitive_mask = 0x0;
-}
-
-void rtsOBJ::CopyOBJ(const rtsOBJ& obj)
-{
-	current_vt = obj.current_vt;
-	current_vn = obj.current_vn;
-	vt_changed = obj.vt_changed;				//true if a new vt or vn was inserted since the last vertex
-	vn_changed = obj.vn_changed;
-	current_primitive_mask = obj.current_primitive_mask;	//defines what coordinates are being used by the current primitive
-	//global variable storing the current render mode
-	g_CurrentMode = obj.g_CurrentMode;
-	//output file stream
-	//g_objFile = obj.g_objFile;
-	//obj file object
-	//objData g_OBJ;
-	//number of vertices since the last BEGIN
-	g_NumVertices = obj.g_NumVertices;
-	/*Attribute mask.  This indicates what attributes are stored for each vertex.
-	Only a single mask applies to each vertex between objBegin() and objEnd().  The
-	attribute mask is flipped the first time an attribute is set but it is fixed after
-	the first vertex is passed.*/
-	g_AttributeMask = obj.g_AttributeMask;
-	/*Attribute reset mask.  This indicates whether or not an attribute has been
-	reset since the last vertex was rendered.  This applies to OBJ_VT and OBJ_VN*/
-	g_AttributeResetMask = obj.g_AttributeResetMask;
-	//latest texture coordinate sent
-	g_LatestVT = obj.g_LatestVT;
-	//latest vertex normal sent
-	g_LatestVN = obj.g_LatestVN;
-	m_bounds = obj.m_bounds;
-
-
-	v_list = obj.v_list;
-	vt_list = obj.vt_list;
-	vn_list = obj.vn_list;
-	primitives = obj.primitives;
-
-	points = obj.points;
-	lines = obj.lines;
-	faces = obj.faces;
-}
-
-//opens an obj file for rendering
-OBJint rtsOBJ::objOpen(const char* filename)
-{
-	g_objFile.open(filename);
-	return OBJ_OK;
-}
-
-//close the obj file
-OBJint rtsOBJ::objClose()
-{
-	//TODO: write obj data
-	f_OutputVertices();
-	f_OutputTextureCoordinates();
-	f_OutputVertexNormals();
-	f_OutputPoints();
-	f_OutputLines();
-	f_OutputFaces();
-
-	//close the file
-	g_objFile.close();
-
-	//delete all of the data from the global object
-	f_ClearAll();
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::objBegin(OBJint mode)
-{
-	//make sure that we aren't currently rendering
-	if(g_CurrentMode != OBJ_NONE)
-		return OBJ_ERROR;
-	//make sure that the given mode is valid
-	if(mode < OBJ_POINTS || mode > OBJ_POLYGON)
-		return OBJ_ERROR;
-
-	//otherwise, go ahead and set the mode
-	g_CurrentMode = mode;
-	//set the number of vertices to zero
-	g_NumVertices = 0;
-
-	//reset the current state primitive state
-	current_primitive_mask = 0x0;
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::objEnd()
-{
-	OBJint error = OBJ_OK;
-	//check to make sure the number of rendered vertices is valid for the current mode
-	switch(g_CurrentMode)
-	{
-	case OBJ_NONE:
-		//can't quit if we haven't started
-		error = OBJ_ERROR;
-		break;
-	case OBJ_LINES:
-		//if less than two vertices or an odd number of vertices
-		if(g_NumVertices < 2 || g_NumVertices%2 != 0)
-		{
-			//if there wasn't a vertex at all
-			if(g_NumVertices == 0)
-				error = OBJ_ERROR;
-			//if there was at least one vertex
-			else
-			{
-				//pop the last line off the list
-				primitives.pop_back();
-				lines.pop_back();
-				error = OBJ_ERROR;
-			}
-		}
-		break;
-	case OBJ_LINE_STRIP:
-		//if less than two vertices
-		if(g_NumVertices < 2)
-		{
-			//if there wasn't a vertex at all
-			if(g_NumVertices == 0)
-				error = OBJ_ERROR;
-			//if there was at least one vertex
-			else
-			{
-				//pop the last line off the list
-				primitives.pop_back();
-				lines.pop_back();
-				error = OBJ_ERROR;
-			}
-		}
-		break;
-	case OBJ_LINE_LOOP:
-		//if less than three vertices
-		if(g_NumVertices < 3)
-		{
-			//pop the last line off the list
-			primitives.pop_back();
-			lines.pop_back();
-			error = OBJ_ERROR;
-		}
-		//connect the first and last points
-		else
-		{
-			error = f_TerminateLineLoop();
-		}
-		break;
-	case OBJ_TRIANGLES:
-		//if less than three vertices or not a power of three
-		if(g_NumVertices < 3 || g_NumVertices%3 !=0)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_TRIANGLE_STRIP:
-		//if less than three vertices
-		if(g_NumVertices < 3)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_TRIANGLE_FAN:
-		//if less than three vertices
-		if(g_NumVertices < 3)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_QUADS:
-		if(g_NumVertices < 4 || g_NumVertices%4 != 0)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_QUAD_STRIP:
-		//has to be at least 4 vertices and an even number
-		if(g_NumVertices < 4 || g_NumVertices%2 != 0)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_POLYGON:
-		//has to be at least three vertices
-		if(g_NumVertices < 3)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	}
-
-	//reset the attribute mask
-	g_AttributeMask = 0x0;
-	//just for closure, reset the attribute reset mask
-	g_AttributeResetMask = 0x0;
-	//stop rendering
-	g_CurrentMode = OBJ_NONE;
-	return error;
-}
-
-OBJint rtsOBJ::f_InsertVertexf(float x, float y, float z, float w, unsigned char mask)
-{
-	//make sure we're rendering
-	if(g_CurrentMode == OBJ_NONE)
-		return OBJ_ERROR;
-
-	//insert the vertex into the vertex vector
-	vertex_position v; 
-	v.x = x; v.y = y; v.z=z; v.w=w; v.mask = mask;
-	v_list.push_back(v);
-	f_AdjustExtents(v);			//set the bounding box
-	//insert texture coordinate and normal if specified for this primitive
-	if((current_primitive_mask & OBJ_VT)  && (vt_changed))
-		vt_list.push_back(current_vt);
-	if((current_primitive_mask & OBJ_VN) && (vn_changed))
-		vn_list.push_back(current_vn);
-
-
-	//increment the number of vertices inserted
-	g_NumVertices++;
-
-	//handle each case of the vertex creation individually
-	OBJint error = OBJ_OK;
-	switch(g_CurrentMode)
-	{
-	case OBJ_POINTS:
-		error = f_InsertPointVertex();
-		break;
-	case OBJ_LINES:
-		error = f_InsertLineVertex();
-		break;
-	case OBJ_LINE_LOOP:
-		error = f_InsertLineLoopVertex();
-		break;
-	case OBJ_LINE_STRIP:
-		error = f_InsertLineStripVertex();
-		break;
-	case OBJ_TRIANGLES:
-		error = f_InsertTriangleVertex();
-		break;
-	case OBJ_TRIANGLE_STRIP:
-		error = f_InsertTriangleStripVertex();
-		break;
-	case OBJ_TRIANGLE_FAN:
-		error = f_InsertTriangleFanVertex();
-		break;
-	case OBJ_QUADS:
-		error = f_InsertQuadVertex();
-		break;
-	case OBJ_QUAD_STRIP:
-		error = f_InsertQuadStripVertex();
-		break;
-	case OBJ_POLYGON:
-		error = f_InsertPolygonVertex();
-		break;
-	}
-	//set the reset mask to zero
-	g_AttributeResetMask = 0x0;
-	
-	//set the attribute mask to include vertex position
-	g_AttributeMask = g_AttributeMask | OBJ_V;
-
-	//return the result of the insertion
-	return error;
-}
-
-OBJint rtsOBJ::objVertex1f(float x)
-{
-	return f_InsertVertexf(x, 0.0, 0.0, 0.0, OBJ_V_X);
-}
-
-OBJint rtsOBJ::objVertex2f(float x, float y)
-{
-	return f_InsertVertexf(x, y, 0.0, 0.0, OBJ_V_X | OBJ_V_Y);
-}
-
-OBJint rtsOBJ::objVertex3f(float x, float y, float z)
-{
-	return f_InsertVertexf(x, y, z, 0.0, OBJ_V_X | OBJ_V_Y | OBJ_V_Z);
-	
-}
-
-OBJint rtsOBJ::objVertex4f(float x, float y, float z, float w)
-{
-	return f_InsertVertexf(x, y, z, w, OBJ_V_X | OBJ_V_Y | OBJ_V_Z | OBJ_V_W);
-}
-
-OBJint rtsOBJ::objNormal3f(float i, float j, float k)
-{
-	return f_InsertNormalf(i, j, k, OBJ_VN_I | OBJ_VN_J | OBJ_VN_K);
-}
-OBJint rtsOBJ::objNormal2f(float i, float j)
-{
-	return f_InsertNormalf(i, j, 0.0, OBJ_VN_I | OBJ_VN_J);
-}
-
-OBJint rtsOBJ::objNormal1f(float i)
-{
-	return f_InsertNormalf(i, 0.0, 0.0, OBJ_VN_I);
-}
-
-OBJint rtsOBJ::f_InsertNormalf(float i, float j, float k, unsigned char mask)
-{
-	/*DEPRECATED
-	//if the mode is not rendering faces, there is an error
-	if(g_CurrentMode < OBJ_TRIANGLES)
-		return OBJ_ERROR;
-	//if the normal attribute flag is not set, set it (as long as a vertex hasn't been written)
-	if(!(g_AttributeMask & OBJ_VN))
-	{
-		//if a vertex has been rendered, then we can't change the attribute, so exit
-		if(g_NumVertices > 0)
-			return OBJ_ERROR;
-		else
-			//otherwise, just set the attribute flag
-			g_AttributeMask = g_AttributeMask | OBJ_VN;
-	}
-
-
-	//insert the new normal into the normal list for the file
-	vertex_normal new_vn;
-	new_vn.i = i;  new_vn.j = j;  new_vn.k = k;
-	new_vn.mask = mask;
-	vn_list.push_back(new_vn);
-	*/
-	current_vn.i = i;											//set the current texture state to the given coordinates
-	current_vn.j = j;		
-	current_vn.k = k;
-	current_vn.mask = mask;										//set the mask as appropriate
-	vn_changed = true;											//the texture coordinate state has changed
-	current_primitive_mask = current_primitive_mask | OBJ_VN;	//the current primitive now uses texture coordinates (if it didn't previously)
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::objTexCoord3f(float u, float v, float w)
-{
-	return f_InsertTexCoordf(u, v, w, OBJ_VT_U | OBJ_VT_V | OBJ_VT_W);
-}
-
-OBJint rtsOBJ::objTexCoord2f(float u, float v)
-{
-	return f_InsertTexCoordf(u, v, 0.0, OBJ_VT_U | OBJ_VT_V);
-}
-
-OBJint rtsOBJ::objTexCoord1f(float u)
-{
-	return f_InsertTexCoordf(u, 0.0, 0.0, OBJ_VT_U);
-}
-
-OBJint rtsOBJ::f_InsertTexCoordf(float u, float v, float w, unsigned char mask)
-{
-	/*
-	DEPRECATED
-	//if the normal attribute flag is not set, set it (as long as a vertex hasn't been written)
-	if(!(g_AttributeMask & OBJ_VT))
-	{
-		//if a vertex has been rendered, then we can't change the attribute, so exit
-		if(g_NumVertices > 0)
-			return OBJ_ERROR;
-		else
-			//otherwise, just set the attribute flag
-			g_AttributeMask = g_AttributeMask | OBJ_VT;
-	}
-
-	//insert the new texture coordinate into the list for the file
-	vertex_texture new_vt;
-	new_vt.u = u;  new_vt.v = v;  new_vt.w = w;
-	new_vt.mask = mask;
-	vt_list.push_back(new_vt);
-	*/
-	current_vt.u = u;											//set the current texture state to the given coordinates
-	current_vt.v = v;		
-	current_vt.w = w;
-	current_vt.mask = mask;										//set the mask as appropriate
-	vt_changed = true;											//the texture coordinate state has changed
-	current_primitive_mask = current_primitive_mask | OBJ_VT;	//the current primitive now uses texture coordinates (if it didn't previously)
-
-	return OBJ_OK;
-}
-
-
-void rtsOBJ::insertVertexPosition(float x, float y, float z, unsigned char mask)
-{
-	vertex_position v;
-	v.x = x;
-	v.y = y;
-	v.z = z;
-	v.mask = mask;
-
-	v_list.push_back(v);
-}
-
-void rtsOBJ::insertLine(unsigned int num_points, unsigned int* pointlist, unsigned int* normallist, unsigned int* texturelist)
-{
-	//create the new primitive
-	primitive line;
-	line.type = OBJ_LINES;
-	line.mask = 0;
-
-	//set the mask based on the passed data
-	if(pointlist != NULL)
-		line.mask = line.mask | OBJ_V;
-	if(normallist != NULL)
-		line.mask = line.mask | OBJ_VN;
-	if(texturelist != NULL)
-		line.mask = line.mask | OBJ_VT;
-
-	//insert the line
-	int v;
-	vertex new_vert;
-	for(v=0; v<num_points; v++)
-	{
-		if(pointlist)
-			new_vert.v = pointlist[v];
-		if(normallist)
-			new_vert.vn = normallist[v];
-		if(texturelist)
-			new_vert.vt = texturelist[v];
-		line.p.push_back(new_vert);
-	}
-	//insert the new primitive into the list
-	primitives.push_back(line);
-}
-OBJint rtsOBJ::f_InsertPointVertex()
-{
-	//insert the most recent point into the most recent point list
-	//if this is the first vertex, create the point list
-	if(g_NumVertices == 1)
-	{
-		primitive new_p;						//create the new point
-		new_p.type = OBJ_POINTS;
-		new_p.mask = current_primitive_mask;
-		points.push_back(primitives.size());	//store the primitive id in the points list
-		primitives.push_back(new_p);
-	}
-
-	//find the id of the most recent primitive
-	unsigned int p_index = primitives.size() - 1;
-	//find the index of the recent point
-	vertex p;
-	p.v = v_list.size() - 1;
-	//insert the indices for texture coordinates and normal if necessary
-	if(primitives[p_index].mask & OBJ_VT)
-		p.vt = vt_list.size() - 1;
-	if(primitives[p_index].mask & OBJ_VN)
-		p.vn = vn_list.size() - 1;
-
-	//insert the vertex index into the primitive's point list
-	primitives[p_index].p.push_back(p);
-
-	//push the point into the points list if it is not the only point in the primitive
-	if(g_NumVertices > 1)
-		points.push_back(p_index);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertLineVertex()
-{
-	//if this is an odd vertex, create a new line
-	if(g_NumVertices%2 == 1)
-	{
-		f_CreateNewLine();
-	}
-
-	f_InsertNewLineVertex();
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertLineLoopVertex()
-{
-	//technically, this is the same as inserting a line strip vertex
-	f_InsertLineStripVertex();
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertLineStripVertex()
-{
-	if(g_NumVertices == 1)
-	{
-		f_CreateNewLine();
-	}
-
-	f_InsertNewLineVertex();
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertTriangleVertex()
-{
-	//if this is the first vertex in a triangle, create a new triangle
-	if(g_NumVertices%3 == 1)
-	{
-		f_CreateNewFace();
-	}
-
-
-	f_InsertNewFaceVertex();
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertTriangleStripVertex()
-{
-	//in the special case of the first three vertices, just create a triangle
-	if(g_NumVertices <4)
-		f_InsertTriangleVertex();
-	else
-	{
-		
-		//create a new face for the new triangle
-		f_CreateNewFace();
-
-		//insert the last two vertices from the previous triangle
-		f_InsertPreviousFaceVertex(1);
-		f_InsertPreviousFaceVertex(2);
-		//insert the new vertex
-		f_InsertNewFaceVertex();
-	}
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertTriangleFanVertex()
-{
-	//in the special case of the first three vertices, just create a triangle
-	if(g_NumVertices <4)
-		f_InsertTriangleVertex();
-	else
-	{
-		//create a new face for the new triangle
-		f_CreateNewFace();
-		//add the previous vertices to the face
-		f_InsertFirstFaceVertex(0);
-		f_InsertPreviousFaceVertex(2);
-		//insert the current vertex
-		f_InsertNewFaceVertex();
-	}
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertQuadVertex()
-{
-	//if this is the first vertex in a quad, create a new quad
-	if(g_NumVertices%4 == 1)
-	{
-		f_CreateNewFace();
-	}
-
-	f_InsertNewFaceVertex();
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertQuadStripVertex()
-{
-	//in the case of one of the first four vertices, just create a quad
-	if(g_NumVertices < 5)
-		f_InsertQuadVertex();
-	//if the vertex is odd (it will be the third vertex of a quad)
-	else if(g_NumVertices%2 == 1)
-	{
-		//create a new face for the new quad
-		f_CreateNewFace();
-		//add the previous two vertices
-		f_InsertPreviousFaceVertex(2);
-		f_InsertPreviousFaceVertex(3);
-		//add the current vertex
-		f_InsertNewFaceVertex();
-	}
-	else
-	{
-		//if this is the last vertex of the quad, just add it
-		f_InsertNewFaceVertex();
-
-	}
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertPolygonVertex()
-{
-	//if this is the first vertex, create the quad
-	if(g_NumVertices == 1)
-	{
-		f_CreateNewFace();
-	}
-	f_InsertNewFaceVertex();
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertPreviousFaceVertex(unsigned int v_index)
-{
-	/*Finds the vertex used in the previous face with the given index and
-	inserts it into the current face.  This limits the redundancy in the file
-	for re-used vertices (in strips and fans).  This also transfers texture
-	and normal information.*/
-
-	//find the index of the previous face
-	unsigned int prev_f_index = primitives.size() - 2;
-	//find the index of the current face
-	unsigned int f_index = prev_f_index +1;
-	//add the vertex information from the previous face to this face
-	primitives[f_index].p.push_back(primitives[prev_f_index].p[v_index]);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertFirstFaceVertex(unsigned int v_index)
-{
-	/*Finds the vertex used in the first face (since the last objBegin())
-	with the given index and inserts it at the end of the current face.
-	This includes texture and normal information.*/
-
-	//The result depends on the type of face being rendered
-	//So far, this function only applies to triangle fans
-	if(g_CurrentMode != OBJ_TRIANGLE_FAN)
-		return OBJ_ERROR;
-
-	//calculate the number of faces that have been rendered
-	unsigned int num_faces = g_NumVertices - 2;
-	//find the index of the first face
-	unsigned int first_f_index = primitives.size() - num_faces;
-	//find the index of the current face
-	unsigned int f_index = primitives.size() - 1;
-	//transfer the vertex information from the first face to this one
-	primitives[f_index].p.push_back(primitives[first_f_index].p[v_index]);
-
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertNewFaceVertex()
-{
-	/*This inserts information about the current vertex into the current face*/
-	//find the new vertex index
-	vertex p;
-	p.v = v_list.size() -1;
-	p.vt = vt_list.size() - 1;
-	p.vn = vn_list.size() -1;
-	//find the face index
-	unsigned int f_index = primitives.size() -1;
-	//INSERT VERTEX AND ATTRIBUTE DATA
-	//just add the vertex to the face
-	primitives[f_index].p.push_back(p);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertNewLineVertex()
-{
-	/*This inserts information about the current vertex into the current line*/
-	//find the new vertex index
-	vertex p;
-	p.v = v_list.size() -1;
-	p.vt = vt_list.size() - 1;
-	//find the line index
-	unsigned int l_index = primitives.size() -1;
-
-	//ADD VERTEX AND ATTRIBUTE INFORMATION
-	//add the vertex to the line
-	primitives[l_index].p.push_back(p);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_CreateNewFace()
-{
-	primitive new_f;
-	new_f.type = OBJ_FACE;
-	new_f.mask = g_AttributeMask;
-	faces.push_back(primitives.size());
-	primitives.push_back(new_f);
-
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_CreateNewLine()
-{
-	primitive new_l;
-	new_l.type = OBJ_LINES;
-	new_l.mask = g_AttributeMask;
-	lines.push_back(primitives.size());
-	primitives.push_back(new_l);
-
-	return OBJ_OK;
-}
-
-
-OBJint rtsOBJ::f_TerminateLineLoop()
-{
-	/*This function just terminates the line loop by setting the last vertex
-	to the first vertex.*/
-	if(g_CurrentMode != OBJ_LINE_LOOP)
-		return OBJ_ERROR;
-	//find the index for the current line
-	unsigned int l_index = lines.size() -1;
-	//insert the first vertex as the last vertex
-	primitives[l_index].p.push_back(primitives[l_index].p[0]);
-
-	return OBJ_OK;
-}
-
-void rtsOBJ::f_OutputVertices()
-{
-	//get the number of vertices in the object
-	unsigned int v_num = v_list.size();
-	for(unsigned int i=0; i<v_num; i++)
-	{
-		g_objFile<<"v";
-		if(v_list[i].mask & OBJ_V_X)
-			g_objFile<<" "<<v_list[i].x;
-		if(v_list[i].mask & OBJ_V_Y)
-			g_objFile<<" "<<v_list[i].y;
-		if(v_list[i].mask & OBJ_V_Z)
-			g_objFile<<" "<<v_list[i].z;
-		if(v_list[i].mask & OBJ_V_W)
-			g_objFile<<" "<<v_list[i].w;
-		g_objFile<<endl;
-	}
-
-}
-
-void rtsOBJ::f_OutputVertexNormals()
-{
-	//get the number of normals in the object
-	unsigned int vn_num = vn_list.size();
-	for(unsigned int i=0; i<vn_num; i++)
-	{
-		g_objFile<<"vn ";
-		if(vn_list[i].mask & OBJ_VN_I)
-		{
-			g_objFile<<vn_list[i].i;
-			if(vn_list[i].mask & OBJ_VN_J)
-			{
-				g_objFile<<" "<<vn_list[i].j;
-				if(vn_list[i].mask & OBJ_VN_K)
-					g_objFile<<" "<<vn_list[i].k;
-			}
-		}
-		g_objFile<<endl;
-	}
-}
-
-void rtsOBJ::f_OutputTextureCoordinates()
-{
-	//get the number of vertices in the object
-	unsigned int vt_num = vt_list.size();
-	for(unsigned int i=0; i<vt_num; i++)
-	{
-		g_objFile<<"vt ";
-		if(vt_list[i].mask & OBJ_VT_U)
-		{
-			g_objFile<<vt_list[i].u;
-			if(vt_list[i].mask & OBJ_VT_V)
-			{
-				g_objFile<<" "<<vt_list[i].v;
-				if(vt_list[i].mask & OBJ_VT_W)
-					g_objFile<<" "<<vt_list[i].w;
-			}
-		}
-		g_objFile<<endl;
-	}
-}
-
-void rtsOBJ::f_OutputPoints()
-{
-	/*
-	//get the number of point vectors
-	unsigned int p_num = points.size();
-
-	//for each point vector, output the points
-	for(unsigned int i=0; i<p_num; i++)
-	{
-		g_objFile<<"p";
-		unsigned int v_num = points[i].p.size();
-		for(unsigned int j=0; j<v_num; j++)
-		{
-			g_objFile<<" "<<points[i].p[j].v+1;
-		}
-		g_objFile<<endl;
-	}
-	*/
-}
-
-void rtsOBJ::f_OutputLines()
-{
-	/*
-	//get the number of line vectors
-	unsigned int l_num = lines.size();
-
-	//for each line vector, output the associated points
-	for(unsigned int i=0; i<l_num; i++)
-	{
-		g_objFile<<"l";
-		unsigned int v_num = lines[i].p.size();
-		for(unsigned int j=0; j<v_num; j++)
-		{
-			g_objFile<<" "<<lines[i].p[j].v+1;
-			//output texture coordinate if there are any
-			if(lines[i].mask & OBJ_VT)
-				g_objFile<<"/"<<lines[i].p[j].vt+1;
-		}
-		g_objFile<<endl;
-	}
-	*/
-}
-
-void rtsOBJ::f_OutputFaces()
-{
-	/*
-	//get the number of faces
-	unsigned int f_num = faces.size();
-
-	//for each face, output the associated points
-	for(unsigned int i=0; i<f_num; i++)
-	{
-		g_objFile<<"f";
-		//get the number of face vertices
-		unsigned int v_num = faces[i].p.size();
-		for(unsigned int j=0; j<v_num; j++)
-		{
-			g_objFile<<" "<<faces[i].p[j].v+1;
-			//if there are texture coordinates
-			if(faces[i].mask & OBJ_VT)
-				g_objFile<<"/"<<faces[i].p[j].vt+1;
-			//if there is a normal
-			if(faces[i].mask & OBJ_VN)
-			{
-				//but no texture coordinates, put an extra slash
-				if(!(faces[i].mask & OBJ_VT))
-					g_objFile<<"/";
-				g_objFile<<"/"<<faces[i].p[j].vn+1;
-			}
-
-		}
-		g_objFile<<endl;
-	}
-	*/
-}
-
-void rtsOBJ::f_ClearAll()
-{
-	rtsOBJ();
-	//clear all data from the global obj function
-	faces.clear();
-	lines.clear();
-	points.clear();
-	v_list.clear();
-	vn_list.clear();
-	vt_list.clear();
-	primitives.clear();
-}
-
-/*GLOBAL FUNCTION DEFINITIONS*/
-//initialize the OBJ file
-OBJint objOpen(char* filename)
-{
-	return g_OBJ.objOpen(filename);
-}
-//close the obj file
-OBJint objClose()
-{
-	return g_OBJ.objClose();
-}
-
-//start rendering in a certain mode
-OBJint objBegin(OBJint mode)
-{
-	return g_OBJ.objBegin(mode);
-}
-//stop the current rendering sequence
-OBJint objEnd(void)
-{
-	return g_OBJ.objEnd();
-}
-//render a vertex to the file
-OBJint objVertex1f(float x)
-{
-	return g_OBJ.objVertex1f(x);
-}
-
-OBJint objVertex2f(float x, float y)
-{
-	return g_OBJ.objVertex2f(x, y);
-}
-
-OBJint objVertex3f(float x, float y, float z)
-{
-	return g_OBJ.objVertex3f(x, y, z);
-}
-
-OBJint objVertex4f(float x, float y, float z, float w)
-{
-	return g_OBJ.objVertex4f(x, y, z, w);
-}
-//set a normal vector for a vertex
-OBJint objNormal3f(float i, float j, float k)
-{
-	return g_OBJ.objNormal3f(i, j, k);
-}
-OBJint objNormal2f(float i, float j)
-{
-	return g_OBJ.objNormal2f(i, j);
-}
-OBJint objNormal1f(float i)
-{
-	return g_OBJ.objNormal1f(i);
-}
-//set a texture coordinate for a vertex
-OBJint objTexCoord3f(float u, float v, float w)
-{
-	return g_OBJ.objTexCoord3f(u, v, w);
-}
-
-OBJint objTexCoord2f(float u, float v)
-{
-	return g_OBJ.objTexCoord2f(u,v);
-}
-
-OBJint objTexCoord1f(float u)
-{
-	return g_OBJ.objTexCoord1f(u);
-}
-
-OBJint rtsOBJ::f_ReadPosition(ifstream &infile)
-{
-	vertex_position new_vertex;
-	//get each coordinate
-	infile>>new_vertex.x;
-	new_vertex.mask = OBJ_V_X;
-
-	if(infile.peek() == ' ')
-	{
-		infile>>new_vertex.y;
-		new_vertex.mask = new_vertex.mask | OBJ_V_Y;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_vertex.z;
-		new_vertex.mask = new_vertex.mask | OBJ_V_Z;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_vertex.w;
-		new_vertex.mask = new_vertex.mask | OBJ_V_W;
-	}
-	int c = infile.peek();
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-	c = infile.peek();
-	
-	//cout<<"vertex read: "<<new_vertex.x<<","<<new_vertex.y<<","<<new_vertex.z<<","<<new_vertex.w<<endl;
-	//insert the vertex into the list
-	v_list.push_back(new_vertex);
-
-	//adjust the extents of the model
-	f_AdjustExtents(new_vertex);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_ReadNormal(ifstream &infile)
-{
-	vertex_normal new_normal;
-	infile>>new_normal.i;
-	new_normal.mask = OBJ_VN_I;
-	//get every other component
-	if(infile.peek() == ' ')
-	{
-		infile>>new_normal.j;
-		new_normal.mask = new_normal.mask | OBJ_VN_J;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_normal.k;
-		new_normal.mask = new_normal.mask | OBJ_VN_K;
-	}
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-	//insert the normal
-	vn_list.push_back(new_normal);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_ReadTexCoord(ifstream &infile)
-{
-	vertex_texture new_texcoord;
-	infile>>new_texcoord.u;
-	new_texcoord.mask = OBJ_VT_U;
-	//get every other component
-	if(infile.peek() == ' ')
-	{
-		infile>>new_texcoord.v;
-		new_texcoord.mask = new_texcoord.mask | OBJ_VT_V;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_texcoord.w;
-		new_texcoord.mask = new_texcoord.mask | OBJ_VT_W;
-	}
-
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-	//insert the texture coordinate
-	vt_list.push_back(new_texcoord);
-
-	return OBJ_OK;
-
-}
-
-OBJint rtsOBJ::f_ReadVertex(ifstream &infile, vertex &new_point, unsigned char &mask)
-{
-	//store the line vertex
-	infile>>new_point.v;
-	new_point.v--;
-	mask = OBJ_V;
-	//new_face.v.push_back(new_v - 1);
-	if(infile.peek() == '/')
-	{
-		infile.get();
-		//if there actually is a texcoord
-		if(infile.peek() != '/')
-		{
-			infile>>new_point.vt;						//get the index
-			new_point.vt--;
-			mask = mask | OBJ_VT;				//update the mask
-			//new_face.vt.push_back(new_vt - 1);	
-		}
-	}
-	//check for a normal
-	if(infile.peek() == '/')
-	{
-		infile.get();
-		infile>>new_point.vn;							//get the index
-		new_point.vn--;
-		mask = mask | OBJ_VN;	//update the mask
-	}
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_ReadPrimitive(ifstream &infile, primitive_type type)
-{
-	//create a new point list
-	primitive new_primitive;
-	new_primitive.type = type;
-	//until the end of the line
-	while(infile.peek() != '\n')
-	{
-		//read each point
-		if(infile.peek() == ' ')
-			infile.get();
-		else
-		{
-			vertex new_point;
-			f_ReadVertex(infile, new_point, new_primitive.mask);
-			new_primitive.p.push_back(new_point);
-		}
-	}
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-
-	//push the id of the primitive into the new list
-	//:DEBUG:
-	if(type == OBJ_POINTS)
-		points.push_back(primitives.size());
-	else if(type == OBJ_LINES)
-		lines.push_back(primitives.size());
-	else if(type == OBJ_FACE)
-		faces.push_back(primitives.size());
-
-	primitives.push_back(new_primitive);	//push the new primitive
-
-	return OBJ_OK;
-}
-
-
-OBJint rtsOBJ::f_AdjustExtents(vertex_position v)
-{
-	if(v.x < m_bounds.min.x) 
-		m_bounds.min.x = v.x;
-	if(v.y < m_bounds.min.y) 
-		m_bounds.min.y = v.y;
-	if(v.z < m_bounds.min.z) 
-		m_bounds.min.z = v.z;
-
-	if(v.x > m_bounds.max.x) m_bounds.max.x = v.x;
-	if(v.y > m_bounds.max.y) m_bounds.max.y = v.y;
-	if(v.z > m_bounds.max.z) m_bounds.max.z = v.z;
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_LoadOBJ(const char* filename)
-{
-	f_ClearAll();
-	//open the file as a stream
-	ifstream infile;
-	infile.open(filename);
-	if(!infile.is_open())
-		return OBJ_ERROR;
-
-	unsigned int vertices = 0;
-
-	string token;
-	infile>>token;
-	while(!infile.eof())
-	{
-		//if the token is some vertex property
-		if(token == "v")
-			f_ReadPosition(infile);
-		else if(token == "vn")
-			f_ReadNormal(infile);
-		else if(token == "vt")
-			f_ReadTexCoord(infile);
-		else if(token == "p")
-			f_ReadPrimitive(infile, OBJ_POINTS);
-		else if(token == "l")
-			f_ReadPrimitive(infile, OBJ_LINES);
-		else if(token == "f")
-			f_ReadPrimitive(infile, OBJ_FACE);
-		else
-			infile.ignore(9999, '\n');
-		//vertices++;
-
-		infile>>token;
-	}
-
-}
-
-OBJint rtsOBJ::f_LoadSWC(const char* filename)
-{
-	f_ClearAll();
-	//open the file as a stream
-	ifstream infile;
-	infile.open(filename);
-	if(!infile.is_open())
-		return OBJ_ERROR;
-
-	vector<vertex_position> swcVertices;
-	float token;
-	objBegin(OBJ_LINES);
-	while(!infile.eof())
-	{
-		vertex_position v;
-		infile>>token;			//get the id
-		infile>>token;			//get the fiber type
-		infile>>v.x;			//get the node position
-		infile>>v.y;
-		infile>>v.z;
-		infile>>token;			//get the radius
-		infile>>token;			//get the parent
-
-		//insert the node into the swc vector
-		swcVertices.push_back(v);
-		//now draw the line from the parent to the current node
-		if(token != -1)
-		{
-			objVertex3f(swcVertices[token-1].x, swcVertices[token-1].y, swcVertices[token-1].z);
-			objVertex3f(v.x, v.y, v.z);
-		}
-	}
-	objEnd();
-
-
-	return OBJ_OK;
-
-}
-OBJint rtsOBJ::LoadFile(const char* filename)
-{
-	string strFilename = filename;
-	int length = strFilename.length();
-	string extension = strFilename.substr(strFilename.length() - 3, 3);
-	if(!extension.compare(string("obj")))
-		return f_LoadOBJ(filename);
-	else if(!extension.compare(string("swc")))
-		return f_LoadSWC(filename);
-	else return f_LoadOBJ(filename);
-
-}
-
-OBJint rtsOBJ::SaveFile(const char* filename)
-{
-	//open the file as a stream
-	ofstream outfile;
-	outfile.open(filename);
-	if(!outfile.is_open())
-		return OBJ_ERROR;
-
-	//output vertex positions
-	vector<vertex_position>::iterator v;
-	for(v=v_list.begin(); v!= v_list.end(); v++)
-	{
-		outfile<<"v";
-		if((*v).mask & OBJ_V_X)
-		{
-			outfile<<' '<<(*v).x;
-			if((*v).mask & OBJ_V_Y)
-			{
-				outfile<<' '<<(*v).y;
-				if((*v).mask & OBJ_V_Z)
-				{
-					outfile<<' '<<(*v).z;
-					if((*v).mask & OBJ_V_W)
-						outfile<<' '<<(*v).w;
-				}
-			}
-		}
-		outfile<<'\n';
-	}
-
-	//output vertex texture coordinates
-	vector<vertex_texture>::iterator vt;
-	for(vt=vt_list.begin(); vt!= vt_list.end(); vt++)
-	{
-		outfile<<"vt";
-		if((*vt).mask & OBJ_VT_U)
-		{
-			outfile<<' '<<(*vt).u;
-			if((*vt).mask & OBJ_VT_V)
-			{
-				outfile<<' '<<(*vt).v;
-				if((*vt).mask & OBJ_VT_W)
-					outfile<<' '<<(*vt).w;
-			}
-		}
-		outfile<<'\n';
-	}
-
-	//output vertex normal coordinates
-	vector<vertex_normal>::iterator vn;
-	for(vn=vn_list.begin(); vn!= vn_list.end(); vn++)
-	{
-		outfile<<"vn";
-		if((*vn).mask & OBJ_VN_I)
-		{
-			outfile<<' '<<(*vn).i;
-			if((*vn).mask & OBJ_VN_J)
-			{
-				outfile<<' '<<(*vn).j;
-				if((*vn).mask & OBJ_VN_K)
-					outfile<<' '<<(*vn).k;
-			}
-		}
-		outfile<<'\n';
-	}
-
-	//output each primitive
-	vector<primitive>::iterator p;
-	vector<vertex>::iterator vert;
-	for(p=primitives.begin(); p!= primitives.end(); p++)
-	{
-		switch((*p).type)
-		{
-		case OBJ_POINTS:
-			outfile<<"p";			//output the points token
-			break;
-		case OBJ_LINES:
-			outfile<<"l";			//output the lines token
-			break;
-		case OBJ_FACE:
-			outfile<<"f";			//output the face token
-			break;
-		}
-
-		//for each vertex in the list for the primitive
-		for(vert = (*p).p.begin(); vert != (*p).p.end(); vert++)
-		{
-			outfile<<' '<<(*vert).v + 1;
-			if((*p).mask & OBJ_VT)
-				outfile<<'/'<<(*vert).vt + 1;
-			if((*p).mask & OBJ_VN)
-			{
-				if(!((*p).mask & OBJ_VT))
-					outfile<<'/';
-				outfile<<'/'<<(*vert).vn + 1;
-			}
-		}
-		outfile<<'\n';
-			
-	}
-
-
-
-}
-
-//get methods
-unsigned int rtsOBJ::getNumVertices(){return v_list.size();}
-unsigned int rtsOBJ::getNumLines(){return lines.size();}
-unsigned int rtsOBJ::getNumFaces(){return faces.size();}
-unsigned int rtsOBJ::getNumPointLists(){return points.size();}
-unsigned int rtsOBJ::getNumTexCoords(){return vt_list.size();}
-unsigned int rtsOBJ::getNumNormals(){return vn_list.size();}
-
-//these functions return the coordinate index as well as the value
-unsigned int rtsOBJ::getNumFaceVertices(unsigned int face){return primitives[face].p.size();}
-unsigned int rtsOBJ::getFaceVertex(unsigned int face, unsigned int vertex){return primitives[face].p[vertex].v;}
-unsigned int rtsOBJ::getFaceNormal(unsigned int face, unsigned int normal){return primitives[face].p[normal].vn;}
-unsigned int rtsOBJ::getFaceTexCoord(unsigned int face, unsigned int texcoord){return primitives[face].p[texcoord].vt;}
-unsigned int rtsOBJ::getNumLineVertices(unsigned int line){return primitives[line].p.size();}
-unsigned int rtsOBJ::getLineVertex(unsigned int line, unsigned int vertex){return primitives[line].p[vertex].v;}
-unsigned int rtsOBJ::getLineTexCoord(unsigned int line, unsigned int texcoord){return primitives[line].p[texcoord].vt;}
-point3D<float> rtsOBJ::getVertex3d(unsigned int index)
-{
-	return point3D<float>(v_list[index].x, v_list[index].y, v_list[index].z);
-}
-point3D<float> rtsOBJ::getTexCoord3d(unsigned int index)
-{
-	return point3D<float>(vt_list[index].u, vt_list[index].v, vt_list[index].w);
-}
-point3D<float> rtsOBJ::getNormal3d(unsigned int index)
-{
-	return point3D<float>(vn_list[index].i, vn_list[index].j, vn_list[index].k);
-}
-vertex_position rtsOBJ::getVertex(unsigned int index){return v_list[index];}
-vertex_texture rtsOBJ::getTexCoord(unsigned int index){return vt_list[index];}
-vertex_normal rtsOBJ::getNormal(unsigned int index){return vn_list[index];}
-
-
-unsigned int rtsOBJ::getPrimitiveType(unsigned int primitive)
-{
-	/*
-	switch(primitives[i].type)
-	{
-	case OBJ_POINTS:
-		return OBJ_POINTS;
-		break;
-	case OBJ_LINES:
-		return OBJ_LINES;
-		break;
-	case OBJ_FACE:
-		f_RenderFace(i);
-		break;
-	}*/
-	return 0;
-}
-/****************************************************/
-/*******Iterator Methods*****************************/
-/****************************************************/
-
-rtsOBJ::iterator rtsOBJ::begin()
-{
-	//create an iterator that will be returned and assign it to this OBJ
-	iterator result;
-	result.obj = this;
-	result.end_object = false;
-	result.end_primitive = false;
-
-	//if there are no primitives, return the end iterator
-	if(primitives.size() == 0)
-		return end();
-	
-	//start at the beginning of the primitive array
-	result.primitive_index = 0;
-
-	return result;
-}
-
-rtsOBJ::iterator rtsOBJ::end()
-{
-	//create an end iterator to return
-	iterator result;
-	result.obj = this;
-	result.end_primitive = true;
-	result.primitive_index = result.obj->primitives.size();
-
-	return result;
-}
-
-void rtsOBJ::iterator::operator++()
-{
-	primitive_index++;
-	if(primitive_index >= obj->primitives.size())
-		(*this) = obj->end();
-
-}
-
-bool rtsOBJ::iterator::operator ==(rtsOBJ::iterator operand)
-{
-	if(operand.primitive_index == primitive_index)
-	   return true;
-	else return false;
-}
-
-bool rtsOBJ::iterator::operator !=(rtsOBJ::iterator operand)
-{
-	if(operand.primitive_index != primitive_index)
-	   return true;
-	else return false;
-}
-
-unsigned int rtsOBJ::iterator::operator*()
-{
-	return primitive_index;
-}
-
-void rtsOBJ::iterator::print()
-{
-	cout<<"This is a test"<<endl;	
-}
-
-	
-	
\ No newline at end of file
diff --git a/legacy/objJedi.h b/legacy/objJedi.h
deleted file mode 100755
index 932e6fb..0000000
--- a/legacy/objJedi.h
+++ /dev/null
@@ -1,1856 +0,0 @@
-#ifndef OBJJEDI_H
-#define OBJJEDI_H
-
-/*OBJ reader and writer.
-
-One aspect of the writer is based on OpenGL output commands.  You can send OpenGL commands
-(replacing "gl" and "GL" with "obj" and "OBJ" respectively to render to an Wavefront OBJ file
-*/
-
-//#include "rtsMath.h"
-#include "rtsLinearAlgebra.h"
-#include <vector>
-#include <fstream>
-#include <iostream>
-#include <string.h>
-using namespace std;
-
-//masks for valid vertex components
-#define OBJ_V_X		0x1
-#define OBJ_V_Y		0x2
-#define OBJ_V_Z		0x4
-#define OBJ_V_W		0x8
-
-#define OBJ_VT_U	0x1
-#define OBJ_VT_V	0x2
-#define OBJ_VT_W	0x4
-
-#define OBJ_VN_I	0x1
-#define OBJ_VN_J	0x2
-#define OBJ_VN_K	0x4
-
-#define OBJ_V		0x1
-#define OBJ_VT		0x2
-#define OBJ_VN		0x4
-
-//primitive types
-typedef unsigned char primitive_type;
-
-#define OBJ_END				0x0
-#define OBJ_POINTS			0x1
-#define OBJ_LINES			0x2
-#define OBJ_FACE			0x3
-
-
-#define OBJ_INVALID		ULONG_MAX
-//define the point structures
-struct vertex_position{float x,y,z,w; unsigned char mask;};
-struct vertex_texture{float u,v,w; unsigned char mask;};
-struct vertex_normal{float i,j,k; unsigned char mask;};
-//the point structure contains indices to the relative 3-vectors in the lists
-struct vertex
-{
-	unsigned int v;
-	unsigned int vt;
-	unsigned int vn;
-};
-
-struct primitive
-{
-	vector<vertex> p;		//indices to the point
-	unsigned char mask;		//mask describing which features (v, vt, vn) are used
-	primitive_type type;	//the type of primitive (points, lines, face)
-};
-
-//axis-aligned bounding box
-struct AABB
-{
-	vertex_position min;
-	vertex_position max;
-};
-
-//create variable types
-typedef unsigned int OBJint;
-
-//define the OBJ data class
-class rtsOBJ
-{
-private:
-
-	/*Current state variables.  These variables are committed to the OBJ object
-	when a vertex is added.  However, we are careful to only add them once (if they don't
-	change with every vertex.
-	*/
-	vertex_texture current_vt;
-	vertex_normal current_vn;
-	bool vt_changed;				//true if a new vt or vn was inserted since the last vertex
-	bool vn_changed;
-	unsigned char current_primitive_mask;	//defines what coordinates are being used by the current primitive
-	//global variable storing the current render mode
-	OBJint g_CurrentMode;
-	//output file stream
-	ofstream g_objFile;
-	//obj file object
-	//objData g_OBJ;
-	//number of vertices since the last BEGIN
-	unsigned int g_NumVertices;
-	/*Attribute mask.  This indicates what attributes are stored for each vertex.
-	Only a single mask applies to each vertex between objBegin() and objEnd().  The
-	attribute mask is flipped the first time an attribute is set but it is fixed after
-	the first vertex is passed.*/
-	unsigned char g_AttributeMask;
-	/*Attribute reset mask.  This indicates whether or not an attribute has been
-	reset since the last vertex was rendered.  This applies to OBJ_VT and OBJ_VN*/
-	unsigned char g_AttributeResetMask;
-	//latest texture coordinate sent
-	unsigned int g_LatestVT;
-	//latest vertex normal sent
-	unsigned int g_LatestVN;
-
-	//extents of the points in the OBJ file
-	AABB m_bounds;
-
-	OBJint f_InsertPointVertex();
-	OBJint f_InsertLineVertex();
-	OBJint f_InsertLineLoopVertex();
-	OBJint f_InsertLineStripVertex();
-	OBJint f_InsertTriangleVertex();
-	OBJint f_InsertTriangleStripVertex();
-	OBJint f_InsertTriangleFanVertex();
-	OBJint f_InsertQuadVertex();
-	OBJint f_InsertQuadStripVertex();
-	OBJint f_InsertPolygonVertex();
-	OBJint f_InsertPreviousFaceVertex(unsigned int v_index);
-	OBJint f_InsertFirstFaceVertex(unsigned int v_index);
-	OBJint f_InsertNewFaceVertex();
-	OBJint f_InsertNewLineVertex();
-	OBJint f_CreateNewFace();
-	OBJint f_CreateNewLine();
-	OBJint f_TerminateLineLoop();
-	OBJint f_LoadOBJ(const char* filename);
-	OBJint f_LoadSWC(const char* filename);
-
-	//insert coordinate commands
-	//these are used to handle coordinates of different dimensions (and are called by the associated public function)
-	OBJint f_InsertVertexf(float x, float y, float z, float w, unsigned char mask);
-	OBJint f_InsertTexCoordf(float u, float v, float w, unsigned char mask);
-	OBJint f_InsertNormalf(float i, float j, float k, unsigned char mask);
-	//output functions
-	void f_OutputVertices();
-	void f_OutputPoints();
-	void f_OutputLines();
-	void f_OutputFaces();
-	void f_OutputVertexNormals();
-	void f_OutputTextureCoordinates();
-	void f_ClearAll();
-
-	//methods for reading from a file
-	OBJint f_ReadPosition(ifstream &infile);
-	OBJint f_ReadNormal(ifstream &infile);
-	OBJint f_ReadTexCoord(ifstream &infile);
-	OBJint f_ReadVertex(ifstream &infile, vertex &new_point, unsigned char &mask);
-	OBJint f_ReadPrimitive(ifstream &infile, primitive_type type);
-	OBJint f_AdjustExtents(vertex_position v);
-
-public:
-	/*These vectors store the vertex and primitive data from the obj file.
-	All vertices, texture coordinates, and normals are stored in m_v, m_vt, m_vn
-	respectively.  The vectors for each primitive store an index into m_v, m_vt,
-	and m_vn identifying the associated coordinate.  Basically, the data is stored
-	in a structure very similar to the OBJ file itself.
-	*/
-	vector<vertex_position> v_list;
-	vector<vertex_texture> vt_list;
-	vector<vertex_normal> vn_list;
-	vector<primitive> primitives;
-
-	vector<unsigned int> points;
-	vector<unsigned int> lines;
-	vector<unsigned int> faces;
-
-public:
-
-	OBJint objOpen(const char* filename);
-	OBJint objBegin(OBJint obj_mode);
-	OBJint objEnd();
-	OBJint objClose();
-	OBJint objNormal3f(float i, float j, float k);
-	OBJint objNormal2f(float i, float j);
-	OBJint objNormal1f(float i);
-	OBJint objTexCoord3f(float u, float v, float w);
-	OBJint objTexCoord2f(float u, float v);
-	OBJint objTexCoord1f(float u);
-	OBJint objVertex1f(float x);
-	OBJint objVertex2f(float x, float y);
-	OBJint objVertex3f(float x, float y, float z);
-	OBJint objVertex4f(float x, float y, float z, float w);
-	OBJint LoadFile(const char* filename);
-	OBJint SaveFile(const char* filename);
-
-	//direct insertion methods
-	void insertVertexPosition(float x, float y, float z, unsigned char mask = OBJ_V_X | OBJ_V_Y | OBJ_V_Z);
-	void insertLine(unsigned int num_points, unsigned int* pointlist, unsigned int* normallist, unsigned int* texturelist);
-
-	//get methods
-	unsigned int getNumVertices();
-	unsigned int getNumLines();
-	unsigned int getNumFaces();
-	unsigned int getNumPointLists();
-	unsigned int getNumTexCoords();
-	unsigned int getNumNormals();
-
-	//these functions return the coordinate index as well as the value
-	unsigned int getNumFaceVertices(unsigned int face);
-	unsigned int getFaceVertex(unsigned int face, unsigned int vertex);
-	unsigned int getFaceNormal(unsigned int face, unsigned int normal);
-	unsigned int getFaceTexCoord(unsigned int face, unsigned int texcoord);
-	unsigned int getNumLineVertices(unsigned int line);
-	unsigned int getLineVertex(unsigned int line, unsigned int vertex);
-	unsigned int getLineTexCoord(unsigned int line, unsigned int texcoord);
-	point3D<float> getVertex3d(unsigned int index);
-	point3D<float> getTexCoord3d(unsigned int index);
-	point3D<float> getNormal3d(unsigned int index);
-	vertex_position getVertex(unsigned int index);
-	vertex_texture getTexCoord(unsigned int index);
-	vertex_normal getNormal(unsigned int index);
-	AABB getBoundingBox(){return m_bounds;}
-	void Scale(float scale_x, float scale_y, float scale_z);
-	void Translate(float trans_x, float trans_y, float trans_z);
-
-	float GetDistance(float x, float y, float z);
-
-	//return data about primitives
-	unsigned int getPrimitiveType(unsigned int primitive);
-
-	//constructors
-	rtsOBJ();
-	void CopyOBJ(const rtsOBJ& obj);
-	//assignment
-	rtsOBJ& operator=(const rtsOBJ& obj)
-	{
-		CopyOBJ(obj);
-		return *this;
-	}
-	//copy
-	rtsOBJ(const rtsOBJ& obj)
-	{
-		CopyOBJ(obj);
-		//return *this;
-	}
-
-
-
-	//Iterator stuff
-	class iterator
-	{
-		friend class rtsOBJ;
-	private:
-		rtsOBJ* obj;
-		bool end_primitive;
-		bool end_object;
-		unsigned int primitive_index;
-	public:
-		unsigned int operator*();
-		void operator++();
-		bool operator==(rtsOBJ::iterator operand);
-		bool operator!=(rtsOBJ::iterator operand);
-		unsigned int size(){return obj->primitives[primitive_index].p.size();};
-		void print();
-	};
-
-	iterator begin();
-	iterator end();
-};
-
-//define error codes
-#define OBJ_OK				0x0100
-#define OBJ_ERROR			0x0101
-
-//define the different modes
-#define OBJ_NONE			0x0
-#define OBJ_POINTS			0x1
-#define OBJ_LINES			0x2
-#define OBJ_LINE_STRIP		0x3
-#define OBJ_LINE_LOOP		0x4
-#define OBJ_TRIANGLES		0x5
-#define OBJ_TRIANGLE_STRIP	0x6
-#define OBJ_TRIANGLE_FAN	0x7
-#define OBJ_QUADS			0x8
-#define OBJ_QUAD_STRIP		0x9
-#define OBJ_POLYGON			0x10
-
-
-
-
-
-
-//initialize the OBJ file
-OBJint objOpen(char* filename);
-//close the obj file
-OBJint objClose();
-
-//start rendering in a certain mode
-OBJint objBegin(OBJint mode);
-//stop the current rendering sequence
-OBJint objEnd(void);
-//render a vertex to the file
-OBJint objVertex1f(float x);
-OBJint objVertex2f(float x, float y);
-OBJint objVertex3f(float x, float y, float z);
-OBJint objVertex4f(float x, float y, float z, float w);
-//set a normal vector for a vertex
-OBJint objNormal3f(float i, float j, float k);
-OBJint objNormal2f(float i, float j);
-OBJint objNormal1f(float i);
-//set a texture coordinate for a vertex
-OBJint objTexCoord3f(float u, float v, float w);
-OBJint objTexCoord2f(float u, float v);
-OBJint objTexCoord1f(float u);
-
-//global variable for global functions
-extern rtsOBJ g_OBJ;
-
-/*BUG NOTES
-The standard function calls for inserting vertices don't work anymore.  I've fixed points
-but everything beyond that has to be updated.
-*/
-
-#include "objJedi.h"
-#include "rtsVector3d.h"
-#include "rtsPoint3d.h"
-#include <string>
-//variable for use in global functions
-rtsOBJ g_OBJ;
-
-/********UTILITY METHODS*******************************/
-void rtsOBJ::Scale(float scale_x, float scale_y, float scale_z)
-{
-	vector<vertex_position>::iterator i;
-	for(i = v_list.begin(); i!= v_list.end(); i++)
-	{
-		(*i).x *= scale_x;
-		(*i).y *= scale_y;
-		(*i).z *= scale_z;
-	}
-}
-
-void rtsOBJ::Translate(float trans_x, float trans_y, float trans_z)
-{
-	vector<vertex_position>::iterator i;
-	for(i = v_list.begin(); i!= v_list.end(); i++)
-	{
-		(*i).x += trans_x;
-		(*i).y += trans_y;
-		(*i).z += trans_z;
-	}
-
-}
-
-float rtsOBJ::GetDistance(float x, float y, float z)
-{
-	//gets the distance between the specified point and the nearest surface of the OBJ
-	//currently only works for lines
-
-	//cout<<"Primitives: "<<primitives.size()<<endl;
-	unsigned int num_primitives = primitives.size();
-	point3D<float> p0, p1, p2;
-	float min_dist = 255;
-	float dist;
-	unsigned int p, l;
-	vector3D<float> v, w;
-	float c1, c2, b;
-	point3D<float> Pb;
-
-	//for each line
-	for(l=0; l<num_primitives; l++)
-	{
-		if(primitives[l].type & OBJ_LINES)
-		{
-			//for each point
-			for(p = 1; p<primitives[l].p.size(); p++)
-			{
-
-				vertex_position v1 = v_list[primitives[l].p[p-1].v];
-				vertex_position v2 = v_list[primitives[l].p[p].v];
-				p1.x = v1.x;
-				p1.y = v1.y;
-				p1.z = v1.z;
-				p2.x = v2.x;
-				p2.y = v2.y;
-				p2.z = v2.z;
-
-				p0.x = x;
-				p0.y = y;
-				p0.z = z;
-
-				v = p2 - p1;
-				w = p0 - p1;
-				if((c1 = w*v) <= 0)
-					dist = (p1 - p0).Length();
-				else if((c2 = v*v) <= c1)
-					dist = (p2 - p0).Length();
-				else
-				{
-					b = c1/c2;
-					Pb = p1 + b*v;
-					dist = (Pb - p0).Length();
-				}
-				if(dist < min_dist)
-					min_dist = dist;
-
-
-
-			}
-		}
-	}
-	//cout<<"---------------------------------------------"<<endl;
-
-	return min_dist;
-
-
-}
-
-/********CLASS METHOD DEFINITIONS**********************/
-//constructors
-
-//constructor
-rtsOBJ::rtsOBJ()
-{
-	g_CurrentMode = OBJ_NONE;
-	g_NumVertices = 0;
-	g_AttributeMask = 0x0;
-	g_AttributeResetMask = 0x0;
-	g_LatestVT = 0;
-	g_LatestVN = 0;
-
-	m_bounds.min.x = m_bounds.min.y = m_bounds.min.z = 99999;
-	m_bounds.max.x = m_bounds.max.y = m_bounds.max.z = -99999;
-
-	current_primitive_mask = 0x0;
-}
-
-void rtsOBJ::CopyOBJ(const rtsOBJ& obj)
-{
-	current_vt = obj.current_vt;
-	current_vn = obj.current_vn;
-	vt_changed = obj.vt_changed;				//true if a new vt or vn was inserted since the last vertex
-	vn_changed = obj.vn_changed;
-	current_primitive_mask = obj.current_primitive_mask;	//defines what coordinates are being used by the current primitive
-	//global variable storing the current render mode
-	g_CurrentMode = obj.g_CurrentMode;
-	//output file stream
-	//g_objFile = obj.g_objFile;
-	//obj file object
-	//objData g_OBJ;
-	//number of vertices since the last BEGIN
-	g_NumVertices = obj.g_NumVertices;
-	/*Attribute mask.  This indicates what attributes are stored for each vertex.
-	Only a single mask applies to each vertex between objBegin() and objEnd().  The
-	attribute mask is flipped the first time an attribute is set but it is fixed after
-	the first vertex is passed.*/
-	g_AttributeMask = obj.g_AttributeMask;
-	/*Attribute reset mask.  This indicates whether or not an attribute has been
-	reset since the last vertex was rendered.  This applies to OBJ_VT and OBJ_VN*/
-	g_AttributeResetMask = obj.g_AttributeResetMask;
-	//latest texture coordinate sent
-	g_LatestVT = obj.g_LatestVT;
-	//latest vertex normal sent
-	g_LatestVN = obj.g_LatestVN;
-	m_bounds = obj.m_bounds;
-
-
-	v_list = obj.v_list;
-	vt_list = obj.vt_list;
-	vn_list = obj.vn_list;
-	primitives = obj.primitives;
-
-	points = obj.points;
-	lines = obj.lines;
-	faces = obj.faces;
-}
-
-//opens an obj file for rendering
-OBJint rtsOBJ::objOpen(const char* filename)
-{
-	g_objFile.open(filename);
-	return OBJ_OK;
-}
-
-//close the obj file
-OBJint rtsOBJ::objClose()
-{
-	//TODO: write obj data
-	f_OutputVertices();
-	f_OutputTextureCoordinates();
-	f_OutputVertexNormals();
-	f_OutputPoints();
-	f_OutputLines();
-	f_OutputFaces();
-
-	//close the file
-	g_objFile.close();
-
-	//delete all of the data from the global object
-	f_ClearAll();
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::objBegin(OBJint mode)
-{
-	//make sure that we aren't currently rendering
-	if(g_CurrentMode != OBJ_NONE)
-		return OBJ_ERROR;
-	//make sure that the given mode is valid
-	if(mode < OBJ_POINTS || mode > OBJ_POLYGON)
-		return OBJ_ERROR;
-
-	//otherwise, go ahead and set the mode
-	g_CurrentMode = mode;
-	//set the number of vertices to zero
-	g_NumVertices = 0;
-
-	//reset the current state primitive state
-	current_primitive_mask = 0x0;
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::objEnd()
-{
-	OBJint error = OBJ_OK;
-	//check to make sure the number of rendered vertices is valid for the current mode
-	switch(g_CurrentMode)
-	{
-	case OBJ_NONE:
-		//can't quit if we haven't started
-		error = OBJ_ERROR;
-		break;
-	case OBJ_LINES:
-		//if less than two vertices or an odd number of vertices
-		if(g_NumVertices < 2 || g_NumVertices%2 != 0)
-		{
-			//if there wasn't a vertex at all
-			if(g_NumVertices == 0)
-				error = OBJ_ERROR;
-			//if there was at least one vertex
-			else
-			{
-				//pop the last line off the list
-				primitives.pop_back();
-				lines.pop_back();
-				error = OBJ_ERROR;
-			}
-		}
-		break;
-	case OBJ_LINE_STRIP:
-		//if less than two vertices
-		if(g_NumVertices < 2)
-		{
-			//if there wasn't a vertex at all
-			if(g_NumVertices == 0)
-				error = OBJ_ERROR;
-			//if there was at least one vertex
-			else
-			{
-				//pop the last line off the list
-				primitives.pop_back();
-				lines.pop_back();
-				error = OBJ_ERROR;
-			}
-		}
-		break;
-	case OBJ_LINE_LOOP:
-		//if less than three vertices
-		if(g_NumVertices < 3)
-		{
-			//pop the last line off the list
-			primitives.pop_back();
-			lines.pop_back();
-			error = OBJ_ERROR;
-		}
-		//connect the first and last points
-		else
-		{
-			error = f_TerminateLineLoop();
-		}
-		break;
-	case OBJ_TRIANGLES:
-		//if less than three vertices or not a power of three
-		if(g_NumVertices < 3 || g_NumVertices%3 !=0)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_TRIANGLE_STRIP:
-		//if less than three vertices
-		if(g_NumVertices < 3)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_TRIANGLE_FAN:
-		//if less than three vertices
-		if(g_NumVertices < 3)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_QUADS:
-		if(g_NumVertices < 4 || g_NumVertices%4 != 0)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_QUAD_STRIP:
-		//has to be at least 4 vertices and an even number
-		if(g_NumVertices < 4 || g_NumVertices%2 != 0)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	case OBJ_POLYGON:
-		//has to be at least three vertices
-		if(g_NumVertices < 3)
-		{
-			primitives.pop_back();
-			faces.pop_back();
-			error = OBJ_ERROR;
-		}
-		break;
-	}
-
-	//reset the attribute mask
-	g_AttributeMask = 0x0;
-	//just for closure, reset the attribute reset mask
-	g_AttributeResetMask = 0x0;
-	//stop rendering
-	g_CurrentMode = OBJ_NONE;
-	return error;
-}
-
-OBJint rtsOBJ::f_InsertVertexf(float x, float y, float z, float w, unsigned char mask)
-{
-	//make sure we're rendering
-	if(g_CurrentMode == OBJ_NONE)
-		return OBJ_ERROR;
-
-	//insert the vertex into the vertex vector
-	vertex_position v;
-	v.x = x; v.y = y; v.z=z; v.w=w; v.mask = mask;
-	v_list.push_back(v);
-	f_AdjustExtents(v);			//set the bounding box
-	//insert texture coordinate and normal if specified for this primitive
-	if((current_primitive_mask & OBJ_VT)  && (vt_changed))
-		vt_list.push_back(current_vt);
-	if((current_primitive_mask & OBJ_VN) && (vn_changed))
-		vn_list.push_back(current_vn);
-
-
-	//increment the number of vertices inserted
-	g_NumVertices++;
-
-	//handle each case of the vertex creation individually
-	OBJint error = OBJ_OK;
-	switch(g_CurrentMode)
-	{
-	case OBJ_POINTS:
-		error = f_InsertPointVertex();
-		break;
-	case OBJ_LINES:
-		error = f_InsertLineVertex();
-		break;
-	case OBJ_LINE_LOOP:
-		error = f_InsertLineLoopVertex();
-		break;
-	case OBJ_LINE_STRIP:
-		error = f_InsertLineStripVertex();
-		break;
-	case OBJ_TRIANGLES:
-		error = f_InsertTriangleVertex();
-		break;
-	case OBJ_TRIANGLE_STRIP:
-		error = f_InsertTriangleStripVertex();
-		break;
-	case OBJ_TRIANGLE_FAN:
-		error = f_InsertTriangleFanVertex();
-		break;
-	case OBJ_QUADS:
-		error = f_InsertQuadVertex();
-		break;
-	case OBJ_QUAD_STRIP:
-		error = f_InsertQuadStripVertex();
-		break;
-	case OBJ_POLYGON:
-		error = f_InsertPolygonVertex();
-		break;
-	}
-	//set the reset mask to zero
-	g_AttributeResetMask = 0x0;
-
-	//set the attribute mask to include vertex position
-	g_AttributeMask = g_AttributeMask | OBJ_V;
-
-	//return the result of the insertion
-	return error;
-}
-
-OBJint rtsOBJ::objVertex1f(float x)
-{
-	return f_InsertVertexf(x, 0.0, 0.0, 0.0, OBJ_V_X);
-}
-
-OBJint rtsOBJ::objVertex2f(float x, float y)
-{
-	return f_InsertVertexf(x, y, 0.0, 0.0, OBJ_V_X | OBJ_V_Y);
-}
-
-OBJint rtsOBJ::objVertex3f(float x, float y, float z)
-{
-	return f_InsertVertexf(x, y, z, 0.0, OBJ_V_X | OBJ_V_Y | OBJ_V_Z);
-
-}
-
-OBJint rtsOBJ::objVertex4f(float x, float y, float z, float w)
-{
-	return f_InsertVertexf(x, y, z, w, OBJ_V_X | OBJ_V_Y | OBJ_V_Z | OBJ_V_W);
-}
-
-OBJint rtsOBJ::objNormal3f(float i, float j, float k)
-{
-	return f_InsertNormalf(i, j, k, OBJ_VN_I | OBJ_VN_J | OBJ_VN_K);
-}
-OBJint rtsOBJ::objNormal2f(float i, float j)
-{
-	return f_InsertNormalf(i, j, 0.0, OBJ_VN_I | OBJ_VN_J);
-}
-
-OBJint rtsOBJ::objNormal1f(float i)
-{
-	return f_InsertNormalf(i, 0.0, 0.0, OBJ_VN_I);
-}
-
-OBJint rtsOBJ::f_InsertNormalf(float i, float j, float k, unsigned char mask)
-{
-	/*DEPRECATED
-	//if the mode is not rendering faces, there is an error
-	if(g_CurrentMode < OBJ_TRIANGLES)
-		return OBJ_ERROR;
-	//if the normal attribute flag is not set, set it (as long as a vertex hasn't been written)
-	if(!(g_AttributeMask & OBJ_VN))
-	{
-		//if a vertex has been rendered, then we can't change the attribute, so exit
-		if(g_NumVertices > 0)
-			return OBJ_ERROR;
-		else
-			//otherwise, just set the attribute flag
-			g_AttributeMask = g_AttributeMask | OBJ_VN;
-	}
-
-
-	//insert the new normal into the normal list for the file
-	vertex_normal new_vn;
-	new_vn.i = i;  new_vn.j = j;  new_vn.k = k;
-	new_vn.mask = mask;
-	vn_list.push_back(new_vn);
-	*/
-	current_vn.i = i;											//set the current texture state to the given coordinates
-	current_vn.j = j;
-	current_vn.k = k;
-	current_vn.mask = mask;										//set the mask as appropriate
-	vn_changed = true;											//the texture coordinate state has changed
-	current_primitive_mask = current_primitive_mask | OBJ_VN;	//the current primitive now uses texture coordinates (if it didn't previously)
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::objTexCoord3f(float u, float v, float w)
-{
-	return f_InsertTexCoordf(u, v, w, OBJ_VT_U | OBJ_VT_V | OBJ_VT_W);
-}
-
-OBJint rtsOBJ::objTexCoord2f(float u, float v)
-{
-	return f_InsertTexCoordf(u, v, 0.0, OBJ_VT_U | OBJ_VT_V);
-}
-
-OBJint rtsOBJ::objTexCoord1f(float u)
-{
-	return f_InsertTexCoordf(u, 0.0, 0.0, OBJ_VT_U);
-}
-
-OBJint rtsOBJ::f_InsertTexCoordf(float u, float v, float w, unsigned char mask)
-{
-	/*
-	DEPRECATED
-	//if the normal attribute flag is not set, set it (as long as a vertex hasn't been written)
-	if(!(g_AttributeMask & OBJ_VT))
-	{
-		//if a vertex has been rendered, then we can't change the attribute, so exit
-		if(g_NumVertices > 0)
-			return OBJ_ERROR;
-		else
-			//otherwise, just set the attribute flag
-			g_AttributeMask = g_AttributeMask | OBJ_VT;
-	}
-
-	//insert the new texture coordinate into the list for the file
-	vertex_texture new_vt;
-	new_vt.u = u;  new_vt.v = v;  new_vt.w = w;
-	new_vt.mask = mask;
-	vt_list.push_back(new_vt);
-	*/
-	current_vt.u = u;											//set the current texture state to the given coordinates
-	current_vt.v = v;
-	current_vt.w = w;
-	current_vt.mask = mask;										//set the mask as appropriate
-	vt_changed = true;											//the texture coordinate state has changed
-	current_primitive_mask = current_primitive_mask | OBJ_VT;	//the current primitive now uses texture coordinates (if it didn't previously)
-
-	return OBJ_OK;
-}
-
-
-void rtsOBJ::insertVertexPosition(float x, float y, float z, unsigned char mask)
-{
-	vertex_position v;
-	v.x = x;
-	v.y = y;
-	v.z = z;
-	v.mask = mask;
-
-	v_list.push_back(v);
-}
-
-void rtsOBJ::insertLine(unsigned int num_points, unsigned int* pointlist, unsigned int* normallist, unsigned int* texturelist)
-{
-	//create the new primitive
-	primitive line;
-	line.type = OBJ_LINES;
-	line.mask = 0;
-
-	//set the mask based on the passed data
-	if(pointlist != NULL)
-		line.mask = line.mask | OBJ_V;
-	if(normallist != NULL)
-		line.mask = line.mask | OBJ_VN;
-	if(texturelist != NULL)
-		line.mask = line.mask | OBJ_VT;
-
-	//insert the line
-	unsigned int v;
-	vertex new_vert;
-	for(v=0; v<num_points; v++)
-	{
-		if(pointlist)
-			new_vert.v = pointlist[v];
-		if(normallist)
-			new_vert.vn = normallist[v];
-		if(texturelist)
-			new_vert.vt = texturelist[v];
-		line.p.push_back(new_vert);
-	}
-	//insert the new primitive into the list
-	primitives.push_back(line);
-}
-OBJint rtsOBJ::f_InsertPointVertex()
-{
-	//insert the most recent point into the most recent point list
-	//if this is the first vertex, create the point list
-	if(g_NumVertices == 1)
-	{
-		primitive new_p;						//create the new point
-		new_p.type = OBJ_POINTS;
-		new_p.mask = current_primitive_mask;
-		points.push_back(primitives.size());	//store the primitive id in the points list
-		primitives.push_back(new_p);
-	}
-
-	//find the id of the most recent primitive
-	unsigned int p_index = primitives.size() - 1;
-	//find the index of the recent point
-	vertex p;
-	p.v = v_list.size() - 1;
-	//insert the indices for texture coordinates and normal if necessary
-	if(primitives[p_index].mask & OBJ_VT)
-		p.vt = vt_list.size() - 1;
-	if(primitives[p_index].mask & OBJ_VN)
-		p.vn = vn_list.size() - 1;
-
-	//insert the vertex index into the primitive's point list
-	primitives[p_index].p.push_back(p);
-
-	//push the point into the points list if it is not the only point in the primitive
-	if(g_NumVertices > 1)
-		points.push_back(p_index);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertLineVertex()
-{
-	//if this is an odd vertex, create a new line
-	if(g_NumVertices%2 == 1)
-	{
-		f_CreateNewLine();
-	}
-
-	f_InsertNewLineVertex();
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertLineLoopVertex()
-{
-	//technically, this is the same as inserting a line strip vertex
-	f_InsertLineStripVertex();
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertLineStripVertex()
-{
-	if(g_NumVertices == 1)
-	{
-		f_CreateNewLine();
-	}
-
-	f_InsertNewLineVertex();
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertTriangleVertex()
-{
-	//if this is the first vertex in a triangle, create a new triangle
-	if(g_NumVertices%3 == 1)
-	{
-		f_CreateNewFace();
-	}
-
-
-	f_InsertNewFaceVertex();
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertTriangleStripVertex()
-{
-	//in the special case of the first three vertices, just create a triangle
-	if(g_NumVertices < 4)
-		f_InsertTriangleVertex();
-	else
-	{
-
-		//create a new face for the new triangle
-		f_CreateNewFace();
-
-		//make sure to get the ordering right:
-		//		Even vertices provide the previous two vertices "in order": (v2, v3, v4)
-		//		Odd vertices provide the previous two vertices in reverse order: (v1, v3, v2)
-		if(g_NumVertices % 2 == 1)
-		{
-			f_InsertPreviousFaceVertex(2);
-			f_InsertPreviousFaceVertex(1);
-			f_InsertNewFaceVertex();
-		}
-		else
-		{
-			f_InsertPreviousFaceVertex(1);
-			f_InsertNewFaceVertex();
-			f_InsertPreviousFaceVertex(2);
-		}
-	}
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertTriangleFanVertex()
-{
-	//in the special case of the first three vertices, just create a triangle
-	if(g_NumVertices <4)
-		f_InsertTriangleVertex();
-	else
-	{
-		//create a new face for the new triangle
-		f_CreateNewFace();
-		//add the previous vertices to the face
-		f_InsertFirstFaceVertex(0);
-		f_InsertPreviousFaceVertex(2);
-		//insert the current vertex
-		f_InsertNewFaceVertex();
-	}
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertQuadVertex()
-{
-	//if this is the first vertex in a quad, create a new quad
-	if(g_NumVertices%4 == 1)
-	{
-		f_CreateNewFace();
-	}
-
-	f_InsertNewFaceVertex();
-
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertQuadStripVertex()
-{
-	//in the case of one of the first four vertices, just create a quad
-	if(g_NumVertices < 5)
-		f_InsertQuadVertex();
-	//if the vertex is odd (it will be the third vertex of a quad)
-	else if(g_NumVertices%2 == 1)
-	{
-		//create a new face for the new quad
-		f_CreateNewFace();
-		//add the previous two vertices
-		f_InsertPreviousFaceVertex(2);
-		f_InsertPreviousFaceVertex(3);
-		//add the current vertex
-		f_InsertNewFaceVertex();
-	}
-	else
-	{
-		//if this is the last vertex of the quad, just add it
-		f_InsertNewFaceVertex();
-
-	}
-	return OBJ_OK;
-}
-OBJint rtsOBJ::f_InsertPolygonVertex()
-{
-	//if this is the first vertex, create the quad
-	if(g_NumVertices == 1)
-	{
-		f_CreateNewFace();
-	}
-	f_InsertNewFaceVertex();
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertPreviousFaceVertex(unsigned int v_index)
-{
-	/*Finds the vertex used in the previous face with the given index and
-	inserts it into the current face.  This limits the redundancy in the file
-	for re-used vertices (in strips and fans).  This also transfers texture
-	and normal information.*/
-
-	//find the index of the previous face
-	unsigned int prev_f_index = primitives.size() - 2;
-	//find the index of the current face
-	unsigned int f_index = prev_f_index +1;
-	//add the vertex information from the previous face to this face
-	primitives[f_index].p.push_back(primitives[prev_f_index].p[v_index]);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertFirstFaceVertex(unsigned int v_index)
-{
-	/*Finds the vertex used in the first face (since the last objBegin())
-	with the given index and inserts it at the end of the current face.
-	This includes texture and normal information.*/
-
-	//The result depends on the type of face being rendered
-	//So far, this function only applies to triangle fans
-	if(g_CurrentMode != OBJ_TRIANGLE_FAN)
-		return OBJ_ERROR;
-
-	//calculate the number of faces that have been rendered
-	unsigned int num_faces = g_NumVertices - 2;
-	//find the index of the first face
-	unsigned int first_f_index = primitives.size() - num_faces;
-	//find the index of the current face
-	unsigned int f_index = primitives.size() - 1;
-	//transfer the vertex information from the first face to this one
-	primitives[f_index].p.push_back(primitives[first_f_index].p[v_index]);
-
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertNewFaceVertex()
-{
-	/*This inserts information about the current vertex into the current face*/
-	//find the new vertex index
-	vertex p;
-	p.v = v_list.size() -1;
-	p.vt = vt_list.size() - 1;
-	p.vn = vn_list.size() -1;
-	//find the face index
-	unsigned int f_index = primitives.size() -1;
-	//INSERT VERTEX AND ATTRIBUTE DATA
-	//just add the vertex to the face
-	primitives[f_index].p.push_back(p);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_InsertNewLineVertex()
-{
-	/*This inserts information about the current vertex into the current line*/
-	//find the new vertex index
-	vertex p;
-	p.v = v_list.size() -1;
-	p.vt = vt_list.size() - 1;
-	//find the line index
-	unsigned int l_index = primitives.size() -1;
-
-	//ADD VERTEX AND ATTRIBUTE INFORMATION
-	//add the vertex to the line
-	primitives[l_index].p.push_back(p);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_CreateNewFace()
-{
-	primitive new_f;
-	new_f.type = OBJ_FACE;
-	new_f.mask = g_AttributeMask;
-	faces.push_back(primitives.size());
-	primitives.push_back(new_f);
-
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_CreateNewLine()
-{
-	primitive new_l;
-	new_l.type = OBJ_LINES;
-	new_l.mask = g_AttributeMask;
-	lines.push_back(primitives.size());
-	primitives.push_back(new_l);
-
-	return OBJ_OK;
-}
-
-
-OBJint rtsOBJ::f_TerminateLineLoop()
-{
-	/*This function just terminates the line loop by setting the last vertex
-	to the first vertex.*/
-	if(g_CurrentMode != OBJ_LINE_LOOP)
-		return OBJ_ERROR;
-	//find the index for the current line
-	unsigned int l_index = lines.size() -1;
-	//insert the first vertex as the last vertex
-	primitives[l_index].p.push_back(primitives[l_index].p[0]);
-
-	return OBJ_OK;
-}
-
-void rtsOBJ::f_OutputVertices()
-{
-	//get the number of vertices in the object
-	unsigned int v_num = v_list.size();
-	for(unsigned int i=0; i<v_num; i++)
-	{
-		g_objFile<<"v";
-		if(v_list[i].mask & OBJ_V_X)
-			g_objFile<<" "<<v_list[i].x;
-		if(v_list[i].mask & OBJ_V_Y)
-			g_objFile<<" "<<v_list[i].y;
-		if(v_list[i].mask & OBJ_V_Z)
-			g_objFile<<" "<<v_list[i].z;
-		if(v_list[i].mask & OBJ_V_W)
-			g_objFile<<" "<<v_list[i].w;
-		g_objFile<<endl;
-	}
-
-}
-
-void rtsOBJ::f_OutputVertexNormals()
-{
-	//get the number of normals in the object
-	unsigned int vn_num = vn_list.size();
-	for(unsigned int i=0; i<vn_num; i++)
-	{
-		g_objFile<<"vn ";
-		if(vn_list[i].mask & OBJ_VN_I)
-		{
-			g_objFile<<vn_list[i].i;
-			if(vn_list[i].mask & OBJ_VN_J)
-			{
-				g_objFile<<" "<<vn_list[i].j;
-				if(vn_list[i].mask & OBJ_VN_K)
-					g_objFile<<" "<<vn_list[i].k;
-			}
-		}
-		g_objFile<<endl;
-	}
-}
-
-void rtsOBJ::f_OutputTextureCoordinates()
-{
-	//get the number of vertices in the object
-	unsigned int vt_num = vt_list.size();
-	for(unsigned int i=0; i<vt_num; i++)
-	{
-		g_objFile<<"vt ";
-		if(vt_list[i].mask & OBJ_VT_U)
-		{
-			g_objFile<<vt_list[i].u;
-			if(vt_list[i].mask & OBJ_VT_V)
-			{
-				g_objFile<<" "<<vt_list[i].v;
-				if(vt_list[i].mask & OBJ_VT_W)
-					g_objFile<<" "<<vt_list[i].w;
-			}
-		}
-		g_objFile<<endl;
-	}
-}
-
-void rtsOBJ::f_OutputPoints()
-{
-	/*
-	//get the number of point vectors
-	unsigned int p_num = points.size();
-
-	//for each point vector, output the points
-	for(unsigned int i=0; i<p_num; i++)
-	{
-		g_objFile<<"p";
-		unsigned int v_num = points[i].p.size();
-		for(unsigned int j=0; j<v_num; j++)
-		{
-			g_objFile<<" "<<points[i].p[j].v+1;
-		}
-		g_objFile<<endl;
-	}
-	*/
-}
-
-void rtsOBJ::f_OutputLines()
-{
-	/*
-	//get the number of line vectors
-	unsigned int l_num = lines.size();
-
-	//for each line vector, output the associated points
-	for(unsigned int i=0; i<l_num; i++)
-	{
-		g_objFile<<"l";
-		unsigned int v_num = lines[i].p.size();
-		for(unsigned int j=0; j<v_num; j++)
-		{
-			g_objFile<<" "<<lines[i].p[j].v+1;
-			//output texture coordinate if there are any
-			if(lines[i].mask & OBJ_VT)
-				g_objFile<<"/"<<lines[i].p[j].vt+1;
-		}
-		g_objFile<<endl;
-	}
-	*/
-}
-
-void rtsOBJ::f_OutputFaces()
-{
-	/*
-	//get the number of faces
-	unsigned int f_num = faces.size();
-
-	//for each face, output the associated points
-	for(unsigned int i=0; i<f_num; i++)
-	{
-		g_objFile<<"f";
-		//get the number of face vertices
-		unsigned int v_num = faces[i].p.size();
-		for(unsigned int j=0; j<v_num; j++)
-		{
-			g_objFile<<" "<<faces[i].p[j].v+1;
-			//if there are texture coordinates
-			if(faces[i].mask & OBJ_VT)
-				g_objFile<<"/"<<faces[i].p[j].vt+1;
-			//if there is a normal
-			if(faces[i].mask & OBJ_VN)
-			{
-				//but no texture coordinates, put an extra slash
-				if(!(faces[i].mask & OBJ_VT))
-					g_objFile<<"/";
-				g_objFile<<"/"<<faces[i].p[j].vn+1;
-			}
-
-		}
-		g_objFile<<endl;
-	}
-	*/
-}
-
-void rtsOBJ::f_ClearAll()
-{
-	rtsOBJ();
-	//clear all data from the global obj function
-	faces.clear();
-	lines.clear();
-	points.clear();
-	v_list.clear();
-	vn_list.clear();
-	vt_list.clear();
-	primitives.clear();
-}
-
-/*GLOBAL FUNCTION DEFINITIONS*/
-//initialize the OBJ file
-OBJint objOpen(char* filename)
-{
-	return g_OBJ.objOpen(filename);
-}
-//close the obj file
-OBJint objClose()
-{
-	return g_OBJ.objClose();
-}
-
-//start rendering in a certain mode
-OBJint objBegin(OBJint mode)
-{
-	return g_OBJ.objBegin(mode);
-}
-//stop the current rendering sequence
-OBJint objEnd(void)
-{
-	return g_OBJ.objEnd();
-}
-//render a vertex to the file
-OBJint objVertex1f(float x)
-{
-	return g_OBJ.objVertex1f(x);
-}
-
-OBJint objVertex2f(float x, float y)
-{
-	return g_OBJ.objVertex2f(x, y);
-}
-
-OBJint objVertex3f(float x, float y, float z)
-{
-	return g_OBJ.objVertex3f(x, y, z);
-}
-
-OBJint objVertex4f(float x, float y, float z, float w)
-{
-	return g_OBJ.objVertex4f(x, y, z, w);
-}
-//set a normal vector for a vertex
-OBJint objNormal3f(float i, float j, float k)
-{
-	return g_OBJ.objNormal3f(i, j, k);
-}
-OBJint objNormal2f(float i, float j)
-{
-	return g_OBJ.objNormal2f(i, j);
-}
-OBJint objNormal1f(float i)
-{
-	return g_OBJ.objNormal1f(i);
-}
-//set a texture coordinate for a vertex
-OBJint objTexCoord3f(float u, float v, float w)
-{
-	return g_OBJ.objTexCoord3f(u, v, w);
-}
-
-OBJint objTexCoord2f(float u, float v)
-{
-	return g_OBJ.objTexCoord2f(u,v);
-}
-
-OBJint objTexCoord1f(float u)
-{
-	return g_OBJ.objTexCoord1f(u);
-}
-
-OBJint rtsOBJ::f_ReadPosition(ifstream &infile)
-{
-	vertex_position new_vertex;
-	//get each coordinate
-	infile>>new_vertex.x;
-	new_vertex.mask = OBJ_V_X;
-
-	if(infile.peek() == ' ')
-	{
-		infile>>new_vertex.y;
-		new_vertex.mask = new_vertex.mask | OBJ_V_Y;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_vertex.z;
-		new_vertex.mask = new_vertex.mask | OBJ_V_Z;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_vertex.w;
-		new_vertex.mask = new_vertex.mask | OBJ_V_W;
-	}
-	int c = infile.peek();
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-	c = infile.peek();
-
-	//cout<<"vertex read: "<<new_vertex.x<<","<<new_vertex.y<<","<<new_vertex.z<<","<<new_vertex.w<<endl;
-	//insert the vertex into the list
-	v_list.push_back(new_vertex);
-
-	//adjust the extents of the model
-	f_AdjustExtents(new_vertex);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_ReadNormal(ifstream &infile)
-{
-	vertex_normal new_normal;
-	infile>>new_normal.i;
-	new_normal.mask = OBJ_VN_I;
-	//get every other component
-	if(infile.peek() == ' ')
-	{
-		infile>>new_normal.j;
-		new_normal.mask = new_normal.mask | OBJ_VN_J;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_normal.k;
-		new_normal.mask = new_normal.mask | OBJ_VN_K;
-	}
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-	//insert the normal
-	vn_list.push_back(new_normal);
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_ReadTexCoord(ifstream &infile)
-{
-	vertex_texture new_texcoord;
-	infile>>new_texcoord.u;
-	new_texcoord.mask = OBJ_VT_U;
-	//get every other component
-	if(infile.peek() == ' ')
-	{
-		infile>>new_texcoord.v;
-		new_texcoord.mask = new_texcoord.mask | OBJ_VT_V;
-	}
-	if(infile.peek() == ' ')
-	{
-		infile>>new_texcoord.w;
-		new_texcoord.mask = new_texcoord.mask | OBJ_VT_W;
-	}
-
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-	//insert the texture coordinate
-	vt_list.push_back(new_texcoord);
-
-	return OBJ_OK;
-
-}
-
-OBJint rtsOBJ::f_ReadVertex(ifstream &infile, vertex &new_point, unsigned char &mask)
-{
-	//store the line vertex
-	infile>>new_point.v;
-	new_point.v--;
-	mask = OBJ_V;
-	//new_face.v.push_back(new_v - 1);
-	if(infile.peek() == '/')
-	{
-		infile.get();
-		//if there actually is a texcoord
-		if(infile.peek() != '/')
-		{
-			infile>>new_point.vt;						//get the index
-			new_point.vt--;
-			mask = mask | OBJ_VT;				//update the mask
-			//new_face.vt.push_back(new_vt - 1);
-		}
-	}
-	//check for a normal
-	if(infile.peek() == '/')
-	{
-		infile.get();
-		infile>>new_point.vn;							//get the index
-		new_point.vn--;
-		mask = mask | OBJ_VN;	//update the mask
-	}
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_ReadPrimitive(ifstream &infile, primitive_type type)
-{
-	//create a new point list
-	primitive new_primitive;
-	new_primitive.type = type;
-	//until the end of the line
-	while(infile.peek() != '\n')
-	{
-		//read each point
-		if(infile.peek() == ' ')
-			infile.get();
-		else
-		{
-			vertex new_point;
-			f_ReadVertex(infile, new_point, new_primitive.mask);
-			new_primitive.p.push_back(new_point);
-		}
-	}
-	//ignore the rest of the line
-	infile.ignore(1000, '\n');
-
-	//push the id of the primitive into the new list
-	//:DEBUG:
-	if(type == OBJ_POINTS)
-		points.push_back(primitives.size());
-	else if(type == OBJ_LINES)
-		lines.push_back(primitives.size());
-	else if(type == OBJ_FACE)
-		faces.push_back(primitives.size());
-
-	primitives.push_back(new_primitive);	//push the new primitive
-
-	return OBJ_OK;
-}
-
-
-OBJint rtsOBJ::f_AdjustExtents(vertex_position v)
-{
-	if(v.x < m_bounds.min.x)
-		m_bounds.min.x = v.x;
-	if(v.y < m_bounds.min.y)
-		m_bounds.min.y = v.y;
-	if(v.z < m_bounds.min.z)
-		m_bounds.min.z = v.z;
-
-	if(v.x > m_bounds.max.x) m_bounds.max.x = v.x;
-	if(v.y > m_bounds.max.y) m_bounds.max.y = v.y;
-	if(v.z > m_bounds.max.z) m_bounds.max.z = v.z;
-
-	return OBJ_OK;
-}
-
-OBJint rtsOBJ::f_LoadOBJ(const char* filename)
-{
-	f_ClearAll();
-	//open the file as a stream
-	ifstream infile;
-	infile.open(filename);
-	if(!infile)
-		exit(1);
-
-	unsigned int vertices = 0;
-
-	string token;
-	infile>>token;
-	while(!infile.eof())
-	{
-		//if the token is some vertex property
-		if(token == "v")
-			f_ReadPosition(infile);
-		else if(token == "vn")
-			f_ReadNormal(infile);
-		else if(token == "vt")
-			f_ReadTexCoord(infile);
-		else if(token == "p")
-			f_ReadPrimitive(infile, OBJ_POINTS);
-		else if(token == "l")
-			f_ReadPrimitive(infile, OBJ_LINES);
-		else if(token == "f")
-			f_ReadPrimitive(infile, OBJ_FACE);
-		else
-			infile.ignore(9999, '\n');
-		//vertices++;
-
-		infile>>token;
-	}
-
-}
-
-OBJint rtsOBJ::f_LoadSWC(const char* filename)
-{
-	f_ClearAll();
-	//open the file as a stream
-	ifstream infile;
-	infile.open(filename);
-	if(!infile.is_open())
-		return OBJ_ERROR;
-
-	vector<vertex_position> swcVertices;
-	float token;
-	objBegin(OBJ_LINES);
-	while(!infile.eof())
-	{
-		vertex_position v;
-		infile>>token;			//get the id
-		infile>>token;			//get the fiber type
-		infile>>v.x;			//get the node position
-		infile>>v.y;
-		infile>>v.z;
-		infile>>token;			//get the radius
-		infile>>token;			//get the parent
-
-		//insert the node into the swc vector
-		swcVertices.push_back(v);
-		//now draw the line from the parent to the current node
-		if(token != -1)
-		{
-			unsigned int i = (unsigned int)token - 1;
-			objVertex3f(swcVertices[i].x, swcVertices[i].y, swcVertices[i].z);
-			objVertex3f(v.x, v.y, v.z);
-		}
-	}
-	objEnd();
-
-
-	return OBJ_OK;
-
-}
-OBJint rtsOBJ::LoadFile(const char* filename)
-{
-	string strFilename = filename;
-	int length = strFilename.length();
-	string extension = strFilename.substr(strFilename.length() - 3, 3);
-	if(!extension.compare(string("obj")))
-		return f_LoadOBJ(filename);
-	else if(!extension.compare(string("swc")))
-		return f_LoadSWC(filename);
-	else return f_LoadOBJ(filename);
-
-}
-
-OBJint rtsOBJ::SaveFile(const char* filename)
-{
-	//open the file as a stream
-	ofstream outfile;
-	outfile.open(filename);
-	if(!outfile.is_open())
-		return OBJ_ERROR;
-
-	//output vertex positions
-	vector<vertex_position>::iterator v;
-	for(v=v_list.begin(); v!= v_list.end(); v++)
-	{
-		outfile<<"v";
-		if((*v).mask & OBJ_V_X)
-		{
-			outfile<<' '<<(*v).x;
-			if((*v).mask & OBJ_V_Y)
-			{
-				outfile<<' '<<(*v).y;
-				if((*v).mask & OBJ_V_Z)
-				{
-					outfile<<' '<<(*v).z;
-					if((*v).mask & OBJ_V_W)
-						outfile<<' '<<(*v).w;
-				}
-			}
-		}
-		outfile<<'\n';
-	}
-
-	//output vertex texture coordinates
-	vector<vertex_texture>::iterator vt;
-	for(vt=vt_list.begin(); vt!= vt_list.end(); vt++)
-	{
-		outfile<<"vt";
-		if((*vt).mask & OBJ_VT_U)
-		{
-			outfile<<' '<<(*vt).u;
-			if((*vt).mask & OBJ_VT_V)
-			{
-				outfile<<' '<<(*vt).v;
-				if((*vt).mask & OBJ_VT_W)
-					outfile<<' '<<(*vt).w;
-			}
-		}
-		outfile<<'\n';
-	}
-
-	//output vertex normal coordinates
-	vector<vertex_normal>::iterator vn;
-	for(vn=vn_list.begin(); vn!= vn_list.end(); vn++)
-	{
-		outfile<<"vn";
-		if((*vn).mask & OBJ_VN_I)
-		{
-			outfile<<' '<<(*vn).i;
-			if((*vn).mask & OBJ_VN_J)
-			{
-				outfile<<' '<<(*vn).j;
-				if((*vn).mask & OBJ_VN_K)
-					outfile<<' '<<(*vn).k;
-			}
-		}
-		outfile<<'\n';
-	}
-
-	//output each primitive
-	vector<primitive>::iterator p;
-	vector<vertex>::iterator vert;
-	for(p=primitives.begin(); p!= primitives.end(); p++)
-	{
-		switch((*p).type)
-		{
-		case OBJ_POINTS:
-			outfile<<"p";			//output the points token
-			break;
-		case OBJ_LINES:
-			outfile<<"l";			//output the lines token
-			break;
-		case OBJ_FACE:
-			outfile<<"f";			//output the face token
-			break;
-		}
-
-		//for each vertex in the list for the primitive
-		for(vert = (*p).p.begin(); vert != (*p).p.end(); vert++)
-		{
-			outfile<<' '<<(*vert).v + 1;
-			if((*p).mask & OBJ_VT)
-				outfile<<'/'<<(*vert).vt + 1;
-			if((*p).mask & OBJ_VN)
-			{
-				if(!((*p).mask & OBJ_VT))
-					outfile<<'/';
-				outfile<<'/'<<(*vert).vn + 1;
-			}
-		}
-		outfile<<'\n';
-
-	}
-
-
-
-}
-
-//get methods
-unsigned int rtsOBJ::getNumVertices(){return v_list.size();}
-unsigned int rtsOBJ::getNumLines(){return lines.size();}
-unsigned int rtsOBJ::getNumFaces(){return faces.size();}
-unsigned int rtsOBJ::getNumPointLists(){return points.size();}
-unsigned int rtsOBJ::getNumTexCoords(){return vt_list.size();}
-unsigned int rtsOBJ::getNumNormals(){return vn_list.size();}
-
-//these functions return the coordinate index as well as the value
-unsigned int rtsOBJ::getNumFaceVertices(unsigned int face){return primitives[face].p.size();}
-unsigned int rtsOBJ::getFaceVertex(unsigned int face, unsigned int vertex){return primitives[face].p[vertex].v;}
-unsigned int rtsOBJ::getFaceNormal(unsigned int face, unsigned int normal){return primitives[face].p[normal].vn;}
-unsigned int rtsOBJ::getFaceTexCoord(unsigned int face, unsigned int texcoord){return primitives[face].p[texcoord].vt;}
-unsigned int rtsOBJ::getNumLineVertices(unsigned int line){return primitives[line].p.size();}
-unsigned int rtsOBJ::getLineVertex(unsigned int line, unsigned int vertex){return primitives[line].p[vertex].v;}
-unsigned int rtsOBJ::getLineTexCoord(unsigned int line, unsigned int texcoord){return primitives[line].p[texcoord].vt;}
-point3D<float> rtsOBJ::getVertex3d(unsigned int index)
-{
-	return point3D<float>(v_list[index].x, v_list[index].y, v_list[index].z);
-}
-point3D<float> rtsOBJ::getTexCoord3d(unsigned int index)
-{
-	return point3D<float>(vt_list[index].u, vt_list[index].v, vt_list[index].w);
-}
-point3D<float> rtsOBJ::getNormal3d(unsigned int index)
-{
-	return point3D<float>(vn_list[index].i, vn_list[index].j, vn_list[index].k);
-}
-vertex_position rtsOBJ::getVertex(unsigned int index){return v_list[index];}
-vertex_texture rtsOBJ::getTexCoord(unsigned int index){return vt_list[index];}
-vertex_normal rtsOBJ::getNormal(unsigned int index){return vn_list[index];}
-
-
-unsigned int rtsOBJ::getPrimitiveType(unsigned int primitive)
-{
-	/*
-	switch(primitives[i].type)
-	{
-	case OBJ_POINTS:
-		return OBJ_POINTS;
-		break;
-	case OBJ_LINES:
-		return OBJ_LINES;
-		break;
-	case OBJ_FACE:
-		f_RenderFace(i);
-		break;
-	}*/
-	return 0;
-}
-/****************************************************/
-/*******Iterator Methods*****************************/
-/****************************************************/
-
-rtsOBJ::iterator rtsOBJ::begin()
-{
-	//create an iterator that will be returned and assign it to this OBJ
-	iterator result;
-	result.obj = this;
-	result.end_object = false;
-	result.end_primitive = false;
-
-	//if there are no primitives, return the end iterator
-	if(primitives.size() == 0)
-		return end();
-
-	//start at the beginning of the primitive array
-	result.primitive_index = 0;
-
-	return result;
-}
-
-rtsOBJ::iterator rtsOBJ::end()
-{
-	//create an end iterator to return
-	iterator result;
-	result.obj = this;
-	result.end_primitive = true;
-	result.primitive_index = result.obj->primitives.size();
-
-	return result;
-}
-
-void rtsOBJ::iterator::operator++()
-{
-	primitive_index++;
-	if(primitive_index >= obj->primitives.size())
-		(*this) = obj->end();
-
-}
-
-bool rtsOBJ::iterator::operator ==(rtsOBJ::iterator operand)
-{
-	if(operand.primitive_index == primitive_index)
-	   return true;
-	else return false;
-}
-
-bool rtsOBJ::iterator::operator !=(rtsOBJ::iterator operand)
-{
-	if(operand.primitive_index != primitive_index)
-	   return true;
-	else return false;
-}
-
-unsigned int rtsOBJ::iterator::operator*()
-{
-	return primitive_index;
-}
-
-void rtsOBJ::iterator::print()
-{
-	cout<<"This is a test"<<endl;
-}
-
-
-
-
-#endif
diff --git a/legacy/rect.h b/legacy/rect.h
deleted file mode 100644
index e69de29..0000000
--- a/legacy/rect.h
+++ /dev/null
diff --git a/legacy/rtsCamera.h b/legacy/rtsCamera.h
deleted file mode 100755
index 0b2e4b5..0000000
--- a/legacy/rtsCamera.h
+++ /dev/null
@@ -1,191 +0,0 @@
-#include "rtsVector3d.h"
-#include "rtsPoint3d.h"
-#include "rtsQuaternion.h"
-
-#ifndef RTS_CAMERA_H
-#define RTS_CAMERA_H
-
-class rtsCamera
-{
-	vector3D<float> d;	//direction that the camera is pointing
-	point3D<float> p;	//position of the camera
-	vector3D<float> up;	//"up" direction
-	float focus;		//focal length of the camera
-	float fov;
-
-	//private function makes sure that the up vector is orthogonal to the direction vector and both are normalized
-	void stabalize()
-	{
-		vector3D<float> side = up.X(d);
-		up = d.X(side);
-		up.Normalize();
-		d.Normalize();
-	}
-
-public:
-	void setPosition(point3D<float> pos)
-	{
-		p = pos;
-	}
-	void setPosition(float x, float y, float z){setPosition(point3D<float>(x, y, z));}
-
-	void setFocalDistance(float distance){focus = distance;}
-	void setFOV(float field_of_view){fov = field_of_view;}
-
-	void LookAt(point3D<float> pos)
-	{
-		//find the new direction
-		d = pos - p;
-	
-		//find the distance from the look-at point to the current position
-		focus = d.Length();
-
-		//stabalize the camera
-		stabalize();
-	}
-	void LookAt(float px, float py, float pz){LookAt(point3D<float>(px, py, pz));}
-	void LookAt(point3D<float> pos, vector3D<float> new_up){up = new_up; LookAt(pos);}
-	void LookAt(float px, float py, float pz, float ux, float uy, float uz){LookAt(point3D<float>(px, py, pz), vector3D<float>(ux, uy, uz));}
-	void LookAtDolly(float lx, float ly, float lz)
-	{
-		//find the current focus point
-		point3D<float> f = p + focus*d;
-		vector3D<float> T = point3D<float>(lx, ly, lz) - f;
-		p = p + T;
-	}
-
-	void Dolly(vector3D<float> direction)
-	{
-		p = p+direction;
-	}
-	void Dolly(float x, float y, float z){Dolly(vector3D<float>(x, y, z));}
-	void Push(float delta)
-	{
-		if(delta > focus)
-			delta = focus;
-
-		focus -= delta;
-
-		Dolly(d*delta);
-	}
-
-	void Pan(float theta_x, float theta_y, float theta_z)
-	{
-		//x rotation is around the up axis
-		rtsQuaternion<float> qx;
-		qx.CreateRotation(theta_x, up.x, up.y, up.z);
-
-		//y rotation is around the side axis
-		vector3D<float> side = up.X(d);
-		rtsQuaternion<float> qy;
-		qy.CreateRotation(theta_y, side.x, side.y, side.z);
-
-		//z rotation is around the direction vector
-		rtsQuaternion<float> qz;
-		qz.CreateRotation(theta_z, d.x, d.y, d.z);
-
-		//combine the rotations in x, y, z order
-		rtsQuaternion<float> final = qz*qy*qx;
-
-		//get the rotation matrix
-		matrix4x4<float> rot_matrix = final.toMatrix();
-
-		//apply the rotation
-		d = rot_matrix*d;
-		up = rot_matrix*up;
-
-		//stabalize the camera
-		stabalize();
-
-	}
-	void Pan(float theta_x){Pan(theta_x, 0, 0);}
-	void Tilt(float theta_y){Pan(0, theta_y, 0);}
-	void Twist(float theta_z){Pan(0, 0, theta_z);}
-
-	void Zoom(float delta)
-	{
-		fov -= delta;
-		if(fov < 0.5)
-			fov = 0.5;
-		if(fov > 180)
-			fov = 180;
-	}
-
-	void OrbitFocus(float theta_x, float theta_y)
-	{
-		//find the focal point
-		point3D<float> focal_point = p + focus*d;
-
-		//center the coordinate system on the focal point
-		point3D<float> centered = p - (focal_point - point3D<float>(0, 0, 0));
-
-		//create the x rotation (around the up vector)
-		rtsQuaternion<float> qx;
-		qx.CreateRotation(theta_x, up.x, up.y, up.z);
-		centered = qx.toMatrix()*centered;
-
-		//get a side vector for theta_y rotation
-		vector3D<float> side = up.X((point3D<float>(0, 0, 0) - centered).Normalize());
-
-		rtsQuaternion<float> qy;
-		qy.CreateRotation(theta_y, side.x, side.y, side.z);
-		centered = qy.toMatrix()*centered;
-
-		//perform the rotation on the centered camera position
-		//centered = final.toMatrix()*centered;
-
-		//re-position the camera
-		p = centered + (focal_point - point3D<float>(0, 0, 0));
-
-		//make sure we are looking at the focal point
-		LookAt(focal_point);
-
-		//stabalize the camera
-		stabalize();	
-
-	}
-
-	void Slide(float u, float v)
-	{
-		vector3D<float> V = up.Normalize();
-		vector3D<float> U = up.X(d).Normalize();
-
-		p = p + (V * v) + (U * u);
-	}
-
-	//accessor methods
-	point3D<float> getPosition(){return p;}
-	vector3D<float> getUp(){return up;}
-	vector3D<float> getDirection(){return d;}
-	point3D<float> getLookAt(){return p + focus*d;}
-	float getFOV(){return fov;}
-
-	//output the camera settings
-	const void print(ostream& output)
-	{
-		output<<"Position: "<<p<<endl;
-
-	}
-	friend ostream& operator<<(ostream& out, const rtsCamera& c)
-	{
-		out<<"Position: "<<c.p<<endl;
-		out<<"Direction: "<<c.d<<endl;
-		out<<"Up: "<<c.up<<endl;
-		out<<"Focal Distance: "<<c.focus<<endl;
-		return out;
-	}
-
-	//constructor
-	rtsCamera()
-	{
-		p = point3D<float>(0, 0, 0);
-		d = vector3D<float>(0, 0, 1);
-		up = vector3D<float>(0, 1, 0);
-		focus = 1;
-
-	}
-};
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsCameraController.cpp b/legacy/rtsCameraController.cpp
deleted file mode 100755
index d53af24..0000000
--- a/legacy/rtsCameraController.cpp
+++ /dev/null
@@ -1,407 +0,0 @@
-#include "rtsCameraController.h"
-#include <math.h>
-rtsCamera::rtsCamera()
-{
-	m_camera_state.position = point3D<float>(10, 10, 10);
-	m_camera_state.lookat = point3D<float>(0, 0, 0);
-	m_camera_state.up = vector3D<float>(0, 1, 0);
-	m_camera_state.pers_view_angle = 60;
-	m_camera_state.near_plane = 1;
-	m_camera_state.far_plane = 100;
-}
-
-rtsCamera::~rtsCamera()
-{
-
-}
-
-rtsCamera::rtsCamera(rtsCameraState initial_state)
-{
-	m_camera_state = initial_state;
-
-	//make sure that the view and lookat vectors are orthogonal
-	vector3D<float> lookat = m_camera_state.lookat - m_camera_state.position;
-	vector3D<float> up = m_camera_state.up;
-	vector3D<float> side = lookat.X(up);
-	up = side.X(lookat);
-	up.Normalize();
-	m_camera_state.up = up;
-}
-
-rtsCameraState rtsCamera::getState()
-{
-	return m_camera_state;
-}
-
-vector3D<float> rtsCamera::getViewVector()
-{
-	vector3D<float> result = m_camera_state.lookat - m_camera_state.position;
-	result.Normalize();
-	return result;
-}
-
-vector3D<float> rtsCamera::getUpVector()
-{
-	return m_camera_state.up;
-}
-
-point3D<float> rtsCamera::getPosition()
-{
-	return m_camera_state.position;
-}
-
-void rtsCamera::setState(rtsCameraState camera_state)
-{
-	m_camera_state = camera_state;
-	
-	//re-orthogonalize the vectors
-	vector3D<float> view = m_camera_state.lookat - m_camera_state.position;
-	vector3D<float> side = view.X(m_camera_state.up);
-	m_camera_state.up = side.X(view);
-	m_camera_state.up.Normalize();
-}
-
-void rtsCamera::LookAt(point3D<float> point)
-{
-	//looks at a point
-
-	//find the new view vector
-	vector3D<float> view = point - m_camera_state.position;
-
-	//normalize the view vector
-	view.Normalize();
-
-	//prepare a new side vector and up vector
-	vector3D<float> side;
-	vector3D<float> up;
-
-	//get the up vector
-	//if the new viewvector is at 0 or 180 degrees to the up vector
-	float cos_angle = view*m_camera_state.up;
-	if(cos_angle == 1.0f || cos_angle == -1.0f)
-	{
-		//re-calculate the up vector
-		up = m_camera_state.up.X(m_camera_state.lookat - m_camera_state.position);
-	}
-	else
-	{
-		//otherwise, just get the current up vector
-		up = m_camera_state.up;
-	}
-	
-
-	//correct the up vector based on the new view vector
-	side = up.X(view);
-	up = view.X(side);
-	up.Normalize();
-
-	//change the camera state
-	m_camera_state.up = up;
-	m_camera_state.lookat = point;
-}
-
-void rtsCamera::Position(point3D<float> p)
-{
-	m_camera_state.position = p;
-}
-
-void rtsCamera::Up(vector3D<float> up)
-{
-	m_camera_state.up = up;
-}
-
-void rtsCamera::DollyPosition(point3D<float> p)
-{
-	vector3D<float> adjustment = p-m_camera_state.position;
-	m_camera_state.position = p;
-	m_camera_state.lookat = m_camera_state.lookat + adjustment;
-}
-
-point3D<float> rtsCamera::getLookAtPoint()
-{
-	return m_camera_state.lookat;
-}
-
-
-
-void rtsCamera::Pan(double x, double y)
-{
-	//first calculate the lookat and side vectors
-	vector3D<float> lookatvector=m_camera_state.lookat - m_camera_state.position;
-	vector3D<float> sidevector = lookatvector.X(m_camera_state.up);
-	sidevector.Normalize();
-
-	m_camera_state.position=m_camera_state.position+sidevector*x;
-	m_camera_state.lookat=m_camera_state.lookat+sidevector*x;
-
-	vector3D<float> upvector = lookatvector.X(sidevector);
-	upvector.Normalize();
-	m_camera_state.position=m_camera_state.position+upvector*y;
-	m_camera_state.lookat=m_camera_state.lookat+upvector*y;
-}
-
-void rtsCamera::RotateUpDown(double degrees)
-{
-	//first calculate the lookat and side vectors
-	vector3D<float> lookatvector=m_camera_state.lookat-m_camera_state.position;
-	vector3D<float> sidevector = lookatvector.X(m_camera_state.up);
-	m_camera_state.up=sidevector.X(lookatvector);
-	m_camera_state.up.Normalize();
-	sidevector.Normalize();
-
-	//translate the look-at point to the origin (and the camera with it)
-	point3D<float> origin = point3D<float>(0.0, 0.0, 0.0);
-	vector3D<float> translateCamera = origin-m_camera_state.lookat;
-
-	point3D<float> translatedCamera=m_camera_state.position+translateCamera;
-
-	//the next step is to rotate the side vector so that it lines up with the z axis
-	double a=sidevector.x;
-	double b=sidevector.y;
-	double c=sidevector.z;
-
-	double d=sqrt(b*b + c*c);
-
-	//error correction for when we are already looking down the z-axis
-	if(d==0)
-		return;
-
-	vector3D<float> XZplane = vector3D<float>(translatedCamera.x, 
-								(translatedCamera.y*c/d - translatedCamera.z*b/d), 
-								(translatedCamera.y*b/d + translatedCamera.z*c/d));
-
-	vector3D<float> Zaxis = vector3D<float>(XZplane.x*d - XZplane.z*a,
-								XZplane.y,
-								XZplane.x*a + XZplane.z*d);
-
-	vector3D<float> rotated = vector3D<float>(Zaxis.x*cos(TORADIANS(degrees)) - Zaxis.y*sin(TORADIANS(degrees)),
-								Zaxis.x*sin(TORADIANS(degrees)) + Zaxis.y*cos(TORADIANS(degrees)),
-								Zaxis.z);
-
-	vector3D<float> XZout = vector3D<float>( rotated.x*(d/(a*a + d*d)) + rotated.z*(a/(a*a + d*d)),
-								rotated.y,
-								rotated.x*(-a/(a*a+d*d)) + rotated.z*(d/(a*a + d*d)));
-
-	vector3D<float> result = vector3D<float>( XZout.x,
-								XZout.y*(c*d/(b*b + c*c)) + XZout.z*(b*d/(b*b + c*c)),
-								XZout.y*(-b*d/(b*b + c*c)) + XZout.z*(c*d/(b*b + c*c)));
-
-	result=result-translateCamera;
-
-	m_camera_state.position.x=result.x;
-	m_camera_state.position.y=result.y;
-	m_camera_state.position.z=result.z;
-
-}
-
-void rtsCamera::Yaw(double degrees)
-{
-	//basically, we have to rotate the look-at point around the up vector
-	//first, translate the look-at point so that the camera is at the origin
-	point3D<float> origin(0.0, 0.0, 0.0);
-	point3D<float> temp_lookat = m_camera_state.lookat - (m_camera_state.position - origin);
-	
-	//create a rotation matrix to rotate the lookat point around the up vector
-	float x=m_camera_state.up.x;
-	float y=m_camera_state.up.y;
-	float z=m_camera_state.up.z;
-	float c=cos(TORADIANS(-degrees));
-	float s=sin(TORADIANS(-degrees));
-	float t=1.0 - cos(TORADIANS(-degrees));
-	float m00 = t*x*x + c;
-	float m01 = t*x*y + s*z;
-	float m02 = t*x*z - s*y;
-	float m03 = 0;
-	float m10 = t*x*y - s*z;
-	float m11 = t*y*y + c;
-	float m12 = t*y*z + s*x;
-	float m13 = 0;
-	float m20 = t*x*z + s*y;
-	float m21 = t*y*z - s*x;
-	float m22 = t*z*z + c;
-	float m23 = 0;
-	float m30 = 0;
-	float m31 = 0;
-	float m32 = 0;
-	float m33 = 1;
-	matrix4x4<float> rotation(m00, m01, m02, m03,
-					   m10, m11, m12, m13,
-					   m20, m21, m22, m23,
-					   m30, m31, m32, m33);
-	point3D<float> result = rotation*temp_lookat + (m_camera_state.position - origin);
-	m_camera_state.lookat = result;
-}
-
-void rtsCamera::Pitch(double degrees)
-{
-	//basically, we have to rotate the look-at point and up vector around the side vector
-	//first, translate the look-at point so that the camera is at the origin
-	point3D<float> origin(0.0, 0.0, 0.0);
-	
-	//find all three necessary vectors
-	vector3D<float> temp_lookat = m_camera_state.lookat - m_camera_state.position;
-	double lookat_length = temp_lookat.Length();
-	vector3D<float> temp_up = m_camera_state.up;
-	vector3D<float> temp_side = temp_lookat.X(temp_up);
-	temp_lookat.Normalize();
-	temp_up.Normalize();
-	temp_side.Normalize();
-
-
-	//create a rotation matrix to rotate around the side vector
-	float x=temp_side.x;
-	float y=temp_side.y;
-	float z=temp_side.z;
-	float c=cos(TORADIANS(degrees));
-	float s=sin(TORADIANS(degrees));
-	float t=1.0 - cos(TORADIANS(degrees));
-	float m00 = t*x*x + c;
-	float m01 = t*x*y + s*z;
-	float m02 = t*x*z - s*y;
-	float m03 = 0;
-	float m10 = t*x*y - s*z;
-	float m11 = t*y*y + c;
-	float m12 = t*y*z + s*x;
-	float m13 = 0;
-	float m20 = t*x*z + s*y;
-	float m21 = t*y*z - s*x;
-	float m22 = t*z*z + c;
-	float m23 = 0;
-	float m30 = 0;
-	float m31 = 0;
-	float m32 = 0;
-	float m33 = 1;
-	matrix4x4<float> rotation(m00, m01, m02, m03,
-					   m10, m11, m12, m13,
-					   m20, m21, m22, m23,
-					   m30, m31, m32, m33);
-	
-	//rotate the up and look-at vectors around the side vector
-	vector3D<float> result_lookat = rotation*temp_lookat;
-	vector3D<float> result_up = rotation*temp_up;
-	result_lookat.Normalize();
-	result_up.Normalize();
-
-	m_camera_state.lookat = m_camera_state.position + result_lookat * lookat_length;
-	m_camera_state.up = result_up;
-}
-	
-
-void rtsCamera::RotateLeftRight(double degrees)
-//this function rotates the camera around the up vector (which always points along hte positive
-//Y world axis).
-{
-	//translate the look-at point to the origin (and the camera with it)
-	point3D<float> origin = point3D<float>(0.0, 0.0, 0.0);
-	vector3D<float> translateCamera = origin-m_camera_state.lookat;
-
-	point3D<float> translatedCamera=m_camera_state.position+translateCamera;
-
-
-	//perform the rotation around the look-at point
-	//using the y-axis as the rotation axis
-	point3D<float> newcamera;
-	newcamera.x=translatedCamera.x*cos(TORADIANS(degrees)) - translatedCamera.z*sin(TORADIANS(degrees));
-	newcamera.z=translatedCamera.x*sin(TORADIANS(degrees)) + translatedCamera.z*cos(TORADIANS(degrees));
-	newcamera.y=translatedCamera.y;
-
-	vector3D<float> newup;
-	newup.x=m_camera_state.up.x*cos(TORADIANS(degrees)) - m_camera_state.up.z*sin(TORADIANS(degrees));
-	newup.z=m_camera_state.up.x*sin(TORADIANS(degrees)) + m_camera_state.up.z*cos(TORADIANS(degrees));
-	newup.y=m_camera_state.up.y;
-
-	//translate the lookat point back to it's original position (along with the camera)
-	newcamera=newcamera-translateCamera;
-
-    m_camera_state.position.x=newcamera.x;
-	m_camera_state.position.y=newcamera.y;
-	m_camera_state.position.z=newcamera.z;
-
-	m_camera_state.up.x=newup.x;
-	m_camera_state.up.y=newup.y;
-	m_camera_state.up.z=newup.z;
-	m_camera_state.up.Normalize();
-
-}
-
-void rtsCamera::Forward(double distance)
-{
-	//calculate the lookat vector (direction of travel)
-	vector3D<float> old_lookat=m_camera_state.lookat-m_camera_state.position;
-	old_lookat.Normalize();
-
-	//calculate the new position of the camera
-	point3D<float> new_position = m_camera_state.position+old_lookat*distance;
-	//now calculate the new lookat vector
-	vector3D<float> new_lookat=m_camera_state.lookat-new_position;
-	//find the length of the new lookat vector
-	/*double newlength=lookatvector.length();
-	//if the length is 0 or the camera flipped
-	if((newlength <= 0.0))
-	{
-		//recalculate the lookat vector using the old position
-		lookatvector=m_camera_state.lookat-m_camera_state.position;
-		lookatvector.Normalize();
-		//adjust the lookat point appropriately
-		m_camera_state.lookat = new_position + lookatvector;
-	}*/
-	//move the camera to the new position
-	m_camera_state.position = new_position;
-}
-
-void rtsCamera::ScaleForward(double factor, double min, double max)
-{
-	/*This function moves the camera forward, scaling the magnitude
-	of the motion by the length of the view vector.  Basically, the closer
-	the camera is to the lookat point, the slower the camera moves.*/
-
-	//calculate the lookat vector (direction of travel)
-	vector3D<float> lookatvector=m_camera_state.lookat-m_camera_state.position;
-	//find the length of the view vector
-	double length = lookatvector.Length();
-	//normalize
-	lookatvector.Normalize();
-
-	//prevent motion if the bounds would be passed
-	double new_distance = length - (factor*length);
-	if(new_distance < min || new_distance > max)
-		factor = 0;
-	//move the camera
-	m_camera_state.position=m_camera_state.position+lookatvector*factor*length;
-	lookatvector=m_camera_state.lookat-m_camera_state.position;
-	/*double newlength=lookatvector.length();
-	if((newlength < 2))
-	{
-		lookatvector.Normalize();
-		m_camera_state.lookat = m_camera_state.position + lookatvector*2;
-	}*/
-
-
-}
-
-void rtsCamera::DollyLeftRight(double distance)
-{
-	//calculate the side vector vector (direction of travel)
-	vector3D<float> lookatvector=m_camera_state.lookat-m_camera_state.position;
-	vector3D<float> side = lookatvector.X(m_camera_state.up);
-	side.Normalize();	
-
-	m_camera_state.position=m_camera_state.position+side*distance;
-	m_camera_state.lookat = m_camera_state.lookat + side*distance;
-	//lookatvector=m_camera_state.lookat-m_camera_state.position;
-}
-
-void rtsCamera::DollyUpDown(double distance)
-{
-	//move along the up vector
-	m_camera_state.up.Normalize();	
-
-	m_camera_state.position=m_camera_state.position+m_camera_state.up*distance;
-	m_camera_state.lookat = m_camera_state.lookat + m_camera_state.up*distance;
-	//lookatvector=m_camera_state.lookat-m_camera_state.position;
-}
-
-void rtsCamera::Zoom(double angle)
-{
-	m_camera_state.pers_view_angle += angle;
-}
\ No newline at end of file
diff --git a/legacy/rtsCameraController.h b/legacy/rtsCameraController.h
deleted file mode 100755
index d17c2b0..0000000
--- a/legacy/rtsCameraController.h
+++ /dev/null
@@ -1,77 +0,0 @@
-#include "rtsLinearAlgebra.h"
-
-#ifndef _RTSMATH_H
-#define _RTSMATH_H
-
-#define	CAMERA_UP		-1
-#define CAMERA_DOWN		 1
-#define CAMERA_LEFT		-1
-#define CAMERA_RIGHT	 1
-
-struct rtsCameraState
-{
-	point3D<float> position;
-	point3D<float> lookat;
-	vector3D<float> up;
-	float pers_view_angle;
-	float ortho_width;
-	float ortho_height;
-	float near_plane;
-	float far_plane;
-};
-
-class rtsCamera
-{
-	//members
-	rtsCameraState m_camera_state;
-
-public:
-
-	//methods
-	void RotateUpDown(double degrees);		
-	void RotateLeftRight(double degrees);	
-	void Pan(double x, double y);
-	void Yaw(double degrees);
-	void Pitch(double degrees);
-	void Forward(double distance);
-	void ScaleForward(double factor, double min = 0, double max = 999999);
-	void DollyLeftRight(double distance);
-	void DollyUpDown(double distance);
-	void Zoom(double angle);
-	void LookAt(point3D<float> point);
-	void Position(point3D<float> point);
-	void Up(vector3D<float> up);
-	void DollyPosition(point3D<float> point);		//moves the camera but keeps the current orientation
-
-	//get methods
-	rtsCameraState getState();
-	vector3D<float> getViewVector();
-	vector3D<float> getUpVector();
-	point3D<float> getPosition();
-	point3D<float> getLookAtPoint();
-	double getViewAngle(){return m_camera_state.pers_view_angle;}
-	double getNearPlane(){return m_camera_state.near_plane;}
-	double getFarPlane(){return m_camera_state.far_plane;}
-	double getOrthoWidth(){return m_camera_state.ortho_width;}
-	double getOrthoHeight(){return m_camera_state.ortho_height;}
-
-	//set methods
-	void setState(rtsCameraState camera_state);
-
-	//initialization methods
-	//int SetPosition(double x, double y, double z);
-	//int OrthogonalCamera(double width, double height, double near, double far);
-	//int LookAt(double x, double y, double z);		//looks at a point in space
-	//int SetUpVector(double x, double y, double z);
-	/*int InitializePerspectiveCamera(double position_x, double position_y, double position_z,
-						 double lookat_x, double lookat_y, double lookat_z,
-						 double up_x, double up_y, double up_z, 
-						 double angle, double near_dist, double far_dist);*/
-	//int InitializeCamera();							//initializes a camera to defaults
-
-	rtsCamera();
-	rtsCamera(rtsCameraState initial_state);
-	~rtsCamera();
-};
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsConstants.h b/legacy/rtsConstants.h
deleted file mode 100755
index 70e683f..0000000
--- a/legacy/rtsConstants.h
+++ /dev/null
@@ -1,15 +0,0 @@
-#define RTS_OK							0
-#define RTS_ERROR						99
-
-
-#define RTS_EMPTY						1	//an element can't be deleted if it contains no data
-#define RTS_INVALID_ID					2	//an object with this identifier does not exist
-#define RTS_INVALID_CONSTANT			3	//an invalid constant passed as a parameter
-
-//objects
-#define RTS_END_OBJECT					4	//reached the end of an object's elements
-
-//utility constants
-#define RTS_NULL								0
-
-#define RTS_NO_INTERSECTION				1	//there is no intersection in intersection calculations
\ No newline at end of file
diff --git a/legacy/rtsCubeSampler.cpp b/legacy/rtsCubeSampler.cpp
deleted file mode 100755
index eab89b1..0000000
--- a/legacy/rtsCubeSampler.cpp
+++ /dev/null
@@ -1,56 +0,0 @@
-#include "rtsCubeSampler.h"
-
-vector<vector3D> rtsCubeSampler::Evaluate()
-{
-	/*This function evaluates the cube with the given parameters and returns
-	a vector of sample normalized sample vectors.*/
-
-	//find a valid up vector
-	vector3D u(0.0, 1.0, 0.0);
-	//calculate the side vector
-	vector3D s = u.cross(m_main_vector);
-	//orthogonalize the up vector
-	u = m_main_vector.cross(s);
-	//normalize all three vectors
-	m_main_vector.normalize();
-	u.normalize();
-	s.normalize();
-
-	//create a vector representing each side of the cube
-	vector3D sides[6];
-	sides[0] = m_main_vector;
-	sides[1] = (m_main_vector)*(-1);
-	sides[2] = u;
-	sides[3] = u*(-1);
-	sides[4] = s;
-	sides[5] = s*(-1);
-
-	//calculate the step size along the basis vectors for a side
-	double step = 1.0/((double)m_squared_samples_per_side);
-
-	//evaluate the cube, storing the result in an STL vector
-	vector<vector3D> result;
-	for(int k=0; k<6; k++)
-		for(int i=0; i<m_squared_samples_per_side; i++)
-			for(int j=0; j<m_squared_samples_per_side; j++)
-			{
-				//find the indices for the vectors representing the edges of the current side
-				unsigned int u_vector_index = (k+2)%6;
-				unsigned int v_vector_index = (k+4)%6;
-				//get two basis vectors for the side
-				vector3D u = sides[u_vector_index];
-				vector3D v = sides[v_vector_index];
-
-				//calculate a vector
-				vector3D adjustment = (u*2*(i*step+0.5*step) - u) + (v*2*(j*step + 0.5*step) - v);
-				vector3D final_vector = sides[k] + adjustment;
-				final_vector.normalize();
-				//test the angle and eliminate the vector if it is too large
-				double cosine_angle = final_vector*m_main_vector;
-				if(cosine_angle >= cos(TORADIANS(max_angle)))
-					result.push_back(final_vector);
-			}
-
-	//return the vector of results
-	return result;
-}
\ No newline at end of file
diff --git a/legacy/rtsCubeSampler.h b/legacy/rtsCubeSampler.h
deleted file mode 100755
index 9d92b3c..0000000
--- a/legacy/rtsCubeSampler.h
+++ /dev/null
@@ -1,32 +0,0 @@
-/*This class returns a series of normalized vectors that sample the surface of a cube*/
-/*TODO:
--)Implement random sampling
--)Allow the user to provide a total number of samples
-
-*/
-#ifndef RTSCUBESAMPLER_H
-#define RTSCUBESAMPLER_H
-
-#include <vector>
-#include "rtsMath.h"
-
-using namespace std;
-
-//definitions for sample types
-#define RTS_RANDOM_UNIFORM	0x00001001
-#define RTS_RANDOM_GAUSSIAN	0x00001002
-#define RTS_REGULAR			0x00001003
-
-class rtsCubeSampler
-{
-public:
-
-	unsigned int m_sample_type;
-	unsigned int m_squared_samples_per_side;
-	double max_angle;
-	vector3D m_main_vector;
-
-	vector<vector3D> Evaluate();
-};
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsDTGrid1D.h b/legacy/rtsDTGrid1D.h
deleted file mode 100755
index 8ec59b8..0000000
--- a/legacy/rtsDTGrid1D.h
+++ /dev/null
@@ -1,624 +0,0 @@
-#ifndef _RTS_DTGRID1D_H
-#define _RTS_DTGRID1D_H
-
-#include <vector>
-#include <iostream>
-using namespace std;
-
-struct ConnectedComponent
-{
-	int toValue;
-	int coordMin;
-	int coordMax;
-};
-
-
-
-
-template<typename T>
-class rtsDTGrid1D
-{
-	
-private:
-	//main arrays
-	vector<T> value;
-	vector<ConnectedComponent> conn;
-
-	//variables to keep track of insertion
-	int max_coord;
-	bool insertion_started;
-	bool randomIndex(int &v, int &c, int x1);
-
-
-public:
-	T background;
-	rtsDTGrid1D<T>()
-	{
-		insertion_started = false;
-		max_coord = 0;
-	}
-	int getMaxX1(){return max_coord;}
-	
-	T random(int x1);
-	T& back();
-	bool push(int x1, T value);
-	void insert(rtsDTGrid1D<T> toInsert);
-	void getBounds(int &min_x1, int &max_x1);
-	void dilate(int H);
-	template<typename P> rtsDTGrid1D<P> getStorage()
-	{
-		//create the resulting grid
-		rtsDTGrid1D<P> result;
-		//create an iterator to run over the existing grid
-		P* new_value = (P*)calloc(1, sizeof(P));		
-		for(iterator i = begin(); i!=end(); i.increment())
-		{
-			result.push(i.X1(), *new_value);
-		}
-		return result;
-		
-	}
-	void operator=(T rhs);
-	void print();
-
-	//iterator
-	class iterator;
-	friend class iterator;
-	class stencil_iterator;
-	iterator randomIterator(int x1);
-	iterator begin();
-	iterator end();
-	iterator before();
-	iterator after();
-
-};
-
-/***************ITERATOR*************************/
-template<typename T>
-class rtsDTGrid1D<T>::iterator
-{
-	friend class rtsDTGrid1D;
-	
-
-protected:
-	rtsDTGrid1D<T>* parent;
-	int iv;
-	int ic;
-	int x1;
-
-public:
-	T Value(){return parent->value[iv];}
-	int X1(){return x1;}
-	void SetValue(T val){parent->value[iv] = val;}
-
-	iterator(){parent = NULL;}
-
-	void p()
-	{
-		//increment the current coordinate and value
-		x1++;
-		iv++;
-		//if we are outside of the current connected component
-		if(x1 > parent->conn[ic].coordMax)
-		{
-			//if this is the last connected component, set the iterator to END and return
-			if(ic == parent->conn.size() - 1)
-			{
-				(*this) = parent->after();
-				return;
-			}
-			//otherwise move to the next connected component and update the coordinate
-			ic++;
-			x1 = parent->conn[ic].coordMin;
-		}
-	}
-	void n()
-	{
-		//increment the current coordinate and value
-		x1--;
-		iv--;
-		//if we are outside of the current connected component
-		if(x1 < parent->conn[ic].coordMin)
-		{
-			//if this is the last connected component, set the iterator to END and return
-			if(ic <= 0)
-			{
-				(*this) = parent->before();
-				return;
-			}
-			//otherwise move to the next connected component and update the coordinate
-			ic--;
-			x1 = parent->conn[ic].coordMax;
-		}
-
-
-	}
-	//boolean operators for comparing iterators
-	bool operator==(iterator &rhs)
-	{
-		if(parent == rhs.parent && iv == rhs.iv)
-			return true;
-		//if(x1 == rhs.x1)
-		//	return true;
-		return false;
-	}
-	bool operator!=(iterator &rhs){return !((*this) == rhs);}
-	bool operator<(iterator &rhs)
-	{
-		if(parent == rhs.parent && iv == rhs.iv)
-			return true;
-		//if the parents are the same, test value indices
-		//if(parent == rhs.parent && iv < rhs.iv)
-		//	return true;
-		//otherwise test coordinates
-		//if(parent != rhs.parent && x1 < rhs.x1)
-		//	return true;
-		return false;
-	}
-	bool operator<=(iterator &rhs)
-	{
-		if(parent == rhs.parent && iv <= rhs.iv)
-			return true;
-		//if(x1 <= rhs.x1)
-		//	return true;
-		return false;
-	}
-	void operator++(){p();}
-	void operator--(){n();}
-
-	void increment_until(int pos)
-	{
-		while(x1 < pos && (*this) != parent->after())
-		{
-			p();
-		}
-	}
-};
-
-
-/************STENCIL ITERATOR********************/
-template<typename T>
-class rtsDTGrid1D<T>::stencil_iterator : public iterator
-{
-private:
-	//list of iterators that make up the template
-	vector<iterator> iterator_list;
-	//iterator positions (relative to the position of the stencil iterator)
-	vector<int> position_list;
-	//list containing the values for each position in the stencil
-	vector<T> value_list;
-
-	void refresh_iterators();
-	void set_values();
-	void increment_all();
-
-public:
-	typename rtsDTGrid1D<T>::stencil_iterator operator=(const iterator rhs);
-	void addPosition(int p);
-	void operator++(){p();}
-	void p();
-	T getValue(int id){return value_list[id];}
-	bool exists(int id);
-	
-};
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::increment_all()
-{
-	//run through each iterator and increment to the correct position
-	int i;
-	int dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest = x1 + position_list[i];
-		//iterate until that position is reached
-		iterator_list[i].increment_until(dest);
-		set_values();
-	}
-
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::p()
-{
-	//increment the current position
-	rtsDTGrid1D<T>::iterator::p();
-
-	increment_all();
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::refresh_iterators()
-{
-	//make sure that the iterator position has been set
-	if(parent == NULL)
-	{
-		cout<<"Iterator location not set."<<endl;
-		return;
-	}
-	
-	//initialize all of the other iterators
-	int i;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//for each iterator, set the iterator to the beginning of the grid
-		iterator_list[i] = parent->begin();
-	}
-	increment_all();
-	//set the values for all of the iterators
-	set_values();
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::set_values()
-{
-	int i;
-	int dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest = x1 + position_list[i];
-		//now add the value to the value list
-		if(iterator_list[i].X1() == dest)
-			value_list[i] = iterator_list[i].Value();
-		else
-			value_list[i] = parent->background;
-	}
-
-
-}
-
-template<typename T>
-typename rtsDTGrid1D<T>::stencil_iterator rtsDTGrid1D<T>::stencil_iterator::operator=(const iterator rhs)
-{
-	parent = rhs.parent;
-	iv = rhs.iv;
-	ic = rhs.ic;
-	x1 = rhs.x1;
-
-	refresh_iterators();
-
-	return (*this);
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::addPosition(int p)
-{
-	position_list.push_back(p);
-	rtsDTGrid1D<T>::iterator new_iter;
-	/*If the parent variable is valid (the current iterator is assigned to
-	a grid), assign the position just added to the same grid.
-	If the parent isn't set, all iterators are assigned to the appropriate grid
-	later on when the operator= is used to assign the grid to the stencil.
-	*/
-	if(parent != NULL)
-	{
-		new_iter = parent->begin();
-		refresh_iterators();
-	}
-
-	iterator_list.push_back(new_iter);
-	value_list.resize(value_list.size() + 1);
-}
-
-template<typename T>
-bool rtsDTGrid1D<T>::stencil_iterator::exists(int id)
-{
-	//returns true if the iterator defined by id points to an actual grid node
-	
-	//determine the appropriate position for the iterator
-	int dest = x1 + position_list[id];
-
-	if(iterator_list[id].X1() == dest)
-		return true;
-	else
-		return false;
-
-}
-
-
-/**************ITERATOR METHODS IN DT GRID*******************/
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::begin()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = 0;
-	result.x1 = conn[0].coordMin;
-	return result;
-}
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::before()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = -1;
-	//result.x1 = conn[0].coordMin;
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::end()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size() - 1;
-	result.x1 = conn[result.ic].coordMax;
-	return result;
-}
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::after()
-{
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size();
-	//result.x1 = conn[result.ic].coordMax;
-	return result;
-}
-
-
-
-
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::randomIterator(int x1)
-{
-	//if the grid is empty return a "after" iterator
-	if(value.size() == 0)
-		return after();
-
-	rtsDTGrid1D<T>::iterator result;
-	result.parent = this;
-	int v_i, c_i;
-
-	//if the value exists in the grid, create the iterator and return
-	if(randomIndex(v_i, c_i, x1))
-	{
-		result.iv = v_i;
-		result.ic = c_i;
-		int offset = v_i - conn[c_i].toValue;
-		result.x1 = conn[c_i].coordMin + offset;
-	}
-	//if the value doesn't exist
-	else
-	{
-		//if the value lies before the current column
-		if(x1 < conn[c_i].coordMin)
-		{
-			result.ic = c_i;
-
-		}
-		else
-		{
-			//if this is the last connected component
-			if(c_i >= conn.size() - 1)
-				return after();
-			else
-			{
-				c_i++;
-				result.ic = c_i;
-			}
-		}
-		result.iv = conn[c_i].toValue;
-		result.x1 = conn[c_i].coordMin;
-	}
-	return result;
-
-}
-template<typename T>
-void rtsDTGrid1D<T>::print()
-{
-	rtsDTGrid1D<T>::iterator i;
-	i = begin();
-	while(i != after())
-	{
-		cout<<i.X1()<<":"<<i.Value()<<endl;
-		i++;
-	}
-	
-
-}
-
-/**************DT GRID**************************/
-template<typename T>
-bool rtsDTGrid1D<T>::push(int x1, T v)
-{
-	//test to make sure the insertion is happening in the right order
-	if(insertion_started && x1 <= max_coord)
-	{
-		cout<<"Out-of-order insertion in D = 1: X1 = "<<x1<<endl;
-		return false;
-	}
-	
-
-	//run this code if we have to start a new connected component.  This happens when:
-	//(a) We insert the first value into the grid
-	//(b) There is empty space between the last insertion and this one
-	if(insertion_started == false || x1 > (max_coord + 1))
-	{
-		//start a new connected component
-		ConnectedComponent new_conn;
-		new_conn.toValue = value.size();
-		new_conn.coordMin = x1;
-		new_conn.coordMax = x1;
-		conn.push_back(new_conn);
-		insertion_started = true;
-	}
-
-	//insert the value into the grid:
-	//(a) Insert the value at the end of the coord array
-	//(b) Increment the coordMax value of the current connected component
-	//(c) Change the maximum inserted coordinate to the new value
-	value.push_back(v);
-	conn[conn.size() - 1].coordMax = x1;
-	//change max_coord to the new coordinate
-	max_coord = x1;
-	return true;
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::insert(rtsDTGrid1D<T> toInsert)
-{
-	//create source and destination iterators
-	rtsDTGrid1D<T>::iterator source = toInsert.begin();
-	rtsDTGrid1D<T>::iterator dest = begin();
-
-	while(source != toInsert.after())
-	{
-		//move the destination iterator to the current source position
-		dest.increment_until(source.X1());
-		//if the position exists in dest
-		if(dest.X1() == source.X1())
-			dest.SetValue(source.Value());
-		source++;
-	}
-
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::getBounds(int &min_x1, int &max_x1)
-{
-	//return an empty bounding volume if the grid is empty
-	if(value.size() == 0)
-	{
-		min_x1 = 0;
-		max_x1 = 0;
-		return;
-	}
-
-	//get the minimum and maximum coordinates
-	min_x1 = conn[0].coordMin;
-	max_x1 = conn.back().coordMax;
-}
-template<typename T>
-void rtsDTGrid1D<T>::dilate(int H)
-{
-	//this function creates a new DT grid dilated by H and copies
-	//the original grid into the new grid
-
-	//create a new grid
-	rtsDTGrid1D<T> new_grid;
-
-	//determine the dilated values for the first connected component
-	int numValues = 0;
-	int start = conn[0].coordMin - H;
-	int end = conn[0].coordMax + H;
-
-	//run through each remaining connected component
-	for(int i=1; i<conn.size(); i++)
-	{
-		//if the new component and the i'th ones overlap, combine them
-		//cout<<conn[i].coordMin - H<<endl;
-		if(conn[i].coordMin - H <= end)
-			end = conn[i].coordMax + H;
-		else
-		{
-			//store the dilated connected component
-			ConnectedComponent cc;
-			cc.coordMin = start;
-			cc.coordMax = end;
-			cc.toValue = numValues;
-			numValues += end - start + 1;
-			new_grid.conn.push_back(cc);
-
-			//start a new dilated connected component
-			start = conn[i].coordMin - H;
-			end = conn[i].coordMax + H;
-		}
-	}
-	//add the last dilated connected component
-	ConnectedComponent cc;
-	cc.coordMin = start;
-	cc.coordMax = end;
-	cc.toValue = numValues;
-	numValues += end - start + 1;
-	new_grid.conn.push_back(cc);
-	//allocate space in the value array, fill it with the background value
-	new_grid.value.resize(numValues, background);
-
-	//insert this grid into the new one
-	new_grid.insert(*this);
-	
-	//copy the new grid to this grid
-	conn = new_grid.conn;
-	value = new_grid.value;
-}
-
-template<typename T>
-bool rtsDTGrid1D<T>::randomIndex(int &v, int &c, int x1)
-{
-	//if the grid is empty return false
-	if(value.size() == 0)
-		return false;
-
-	int low = 0;
-	int high = conn.size()-1;
-	int mid;
-	do
-	{
-		mid = low + (high - low)/2;
-		if(x1 > conn[mid].coordMax)
-			low = mid + 1;
-		//else if(x1 < conn[mid].coordMin)
-		else if(x1 < conn[mid].coordMin)
-			high = mid - 1;
-		else break;
-	}
-	while(low <= high);
-
-	//at this point, mid is either at the appropriate connected component,
-	//or x1 is not in the grid
-	int offset = x1 - conn[mid].coordMin;
-	v = conn[mid].toValue + offset;
-	c = mid;
-	if(x1 >= conn[mid].coordMin && x1 <= conn[mid].coordMax)
-	{		
-		return true;
-	}
-	else
-	{
-		return false;
-	}
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::operator=(T rhs)
-{
-	for(int i=0; i<value.size(); i++)
-		value[i] = rhs;
-}
-template<typename T>
-T& rtsDTGrid1D<T>::back()
-{
-	return value[value.size()-1];
-}
-
-template<typename T>
-T rtsDTGrid1D<T>::random(int x1)
-{
-	int v_i, c_i;
-	
-	if(randomIndex(v_i, c_i, x1))
-		return value[v_i];
-	else
-		return background;
-}
-
-
-#endif
diff --git a/legacy/rtsDTGrid1D_v1.h b/legacy/rtsDTGrid1D_v1.h
deleted file mode 100755
index ab5b9bb..0000000
--- a/legacy/rtsDTGrid1D_v1.h
+++ /dev/null
@@ -1,594 +0,0 @@
-
-#include <vector>
-#include <iostream>
-using namespace std;
-
-#ifndef _RTS_DTGRID1D_H
-#define _RTS_DTGRID1D_H
-
-struct ConnectedComponent
-{
-	int toValue;
-	int coordMin;
-	int coordMax;
-};
-
-
-
-
-template<typename T>
-class rtsDTGrid1D
-{
-	
-private:
-	//main arrays
-	vector<T> value;
-	vector<ConnectedComponent> conn;
-
-	//variables to keep track of insertion
-	int max_coord;
-	bool insertion_started;
-	bool randomIndex(int &v, int &c, int x1);
-
-
-public:
-	T background;
-	rtsDTGrid1D<T>()
-	{
-		insertion_started = false;
-		max_coord = 0;
-	}
-	int getMaxX1(){return max_coord;}
-	
-	T random(int x1);
-	T& back();
-	bool push(int x1, T value);
-	void insert(rtsDTGrid1D<T> toInsert);
-	void getBounds(int &min_x1, int &max_x1);
-	void dilate(int H);
-	template<typename P> rtsDTGrid1D<P> getStorage()
-	{
-		//create the resulting grid
-		rtsDTGrid1D<P> result;
-		//create an iterator to run over the existing grid
-		P* new_value = (P*)calloc(1, sizeof(P));		
-		for(iterator i = begin(); i!=end(); i.increment())
-		{
-			result.push(i.X1(), *new_value);
-		}
-		return result;
-		
-	}
-	void operator=(T rhs);
-	void print();
-
-	//iterator
-	class iterator;
-	friend class iterator;
-	class stencil_iterator;
-	iterator randomIterator(int x1);
-	iterator begin();
-	iterator end();
-	iterator before();
-	iterator after();
-
-};
-
-/***************ITERATOR*************************/
-template<typename T>
-class rtsDTGrid1D<T>::iterator
-{
-	friend class rtsDTGrid1D;
-	
-
-protected:
-	rtsDTGrid1D<T>* parent;
-	int iv;
-	int ic;
-	int x1;
-
-public:
-	T Value(){return parent->value[iv];}
-	int X1(){return x1;}
-	void SetValue(T val){parent->value[iv] = val;}
-
-	iterator(){parent = NULL;}
-
-	void increment()
-	{
-		//increment the current coordinate and value
-		x1++;
-		iv++;
-		//if we are outside of the current connected component
-		if(x1 > parent->conn[ic].coordMax)
-		{
-			//if this is the last connected component, set the iterator to END and return
-			if(ic == parent->conn.size() - 1)
-			{
-				(*this) = parent->after();
-				return;
-			}
-			//otherwise move to the next connected component and update the coordinate
-			ic++;
-			x1 = parent->conn[ic].coordMin;
-		}
-	}
-
-	//boolean operators for comparing iterators
-	bool operator==(iterator rhs)
-	{
-		if(parent == rhs.parent && iv == rhs.iv)
-			return true;
-		return false;
-	}
-	bool operator!=(iterator rhs){return !((*this) == rhs);}
-	friend bool operator<(iterator &left, iterator &right)
-	{
-		if(left.iv < right.iv)
-			return true;
-		return false;
-	}
-	friend bool operator<=(iterator &left, iterator &right)
-	{
-		if(left.iv <= right.iv)
-			return true;
-		return false;
-	}
-	void operator++(){increment();}
-
-	void increment_until(int pos)
-	{
-		while(x1 < pos && (*this) != parent->after())
-		{
-			p();
-		}
-	}
-};
-
-
-/************STENCIL ITERATOR********************/
-template<typename T>
-class rtsDTGrid1D<T>::stencil_iterator : public iterator
-{
-private:
-	//list of iterators that make up the template
-	vector<iterator> iterator_list;
-	//iterator positions (relative to the position of the stencil iterator)
-	vector<int> position_list;
-	//list containing the values for each position in the stencil
-	vector<T> value_list;
-
-	void refresh_iterators();
-	void set_values();
-	void increment_all();
-
-public:
-	typename rtsDTGrid1D<T>::stencil_iterator operator=(const iterator rhs);
-	void addPosition(int p);
-	void operator++(){p();}
-	void p();
-	T getValue(int id){return value_list[id];}
-	bool exists(int id);
-	
-};
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::increment_all()
-{
-	//run through each iterator and increment to the correct position
-	int i;
-	int dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest = x1 + position_list[i];
-		//iterate until that position is reached
-		iterator_list[i].increment_until(dest);
-		set_values();
-	}
-
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::increment()
-{
-	//increment the current position
-	rtsDTGrid1D<T>::iterator::increment();
-
-	increment_all();
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::refresh_iterators()
-{
-	//make sure that the iterator position has been set
-	if(parent == NULL)
-	{
-		cout<<"Iterator location not set."<<endl;
-		return;
-	}
-	
-	//initialize all of the other iterators
-	int i;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//for each iterator, set the iterator to the beginning of the grid
-		iterator_list[i] = parent->begin();
-	}
-	increment_all();
-	//set the values for all of the iterators
-	set_values();
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::set_values()
-{
-	int i;
-	int dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest = x1 + position_list[i];
-		//now add the value to the value list
-		if(iterator_list[i].X1() == dest)
-			value_list[i] = iterator_list[i].Value();
-		else
-			value_list[i] = parent->background;
-	}
-
-
-}
-
-template<typename T>
-typename rtsDTGrid1D<T>::stencil_iterator rtsDTGrid1D<T>::stencil_iterator::operator=(const iterator rhs)
-{
-	parent = rhs.parent;
-	iv = rhs.iv;
-	ic = rhs.ic;
-	x1 = rhs.x1;
-
-	refresh_iterators();
-
-	return (*this);
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::stencil_iterator::addPosition(int p)
-{
-	position_list.push_back(p);
-	rtsDTGrid1D<T>::iterator new_iter;
-	/*If the parent variable is valid (the current iterator is assigned to
-	a grid), assign the position just added to the same grid.
-	If the parent isn't set, all iterators are assigned to the appropriate grid
-	later on when the operator= is used to assign the grid to the stencil.
-	*/
-	if(parent != NULL)
-	{
-		new_iter = parent->begin();
-		refresh_iterators();
-	}
-
-	iterator_list.push_back(new_iter);
-	value_list.resize(value_list.size() + 1);
-}
-
-template<typename T>
-bool rtsDTGrid1D<T>::stencil_iterator::exists(int id)
-{
-	//returns true if the iterator defined by id points to an actual grid node
-	
-	//determine the appropriate position for the iterator
-	int dest = x1 + position_list[id];
-
-	if(iterator_list[id].X1() == dest)
-		return true;
-	else
-		return false;
-
-}
-
-
-/**************ITERATOR METHODS IN DT GRID*******************/
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::begin()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = 0;
-	result.x1 = conn[0].coordMin;
-	return result;
-}
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::before()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = -1;
-	//result.x1 = conn[0].coordMin;
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::end()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size() - 1;
-	result.x1 = conn[result.ic].coordMax;
-	return result;
-}
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::after()
-{
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size();
-	//result.x1 = conn[result.ic].coordMax;
-	return result;
-}
-
-
-
-
-template<typename T>
-typename rtsDTGrid1D<T>::iterator rtsDTGrid1D<T>::randomIterator(int x1)
-{
-	//if the grid is empty return a "after" iterator
-	if(value.size() == 0)
-		return after();
-
-	rtsDTGrid1D<T>::iterator result;
-	result.parent = this;
-	int v_i, c_i;
-
-	//if the value exists in the grid, create the iterator and return
-	if(randomIndex(v_i, c_i, x1))
-	{
-		result.iv = v_i;
-		result.ic = c_i;
-		int offset = v_i - conn[c_i].toValue;
-		result.x1 = conn[c_i].coordMin + offset;
-	}
-	//if the value doesn't exist
-	else
-	{
-		//if the value lies before the current column
-		if(x1 < conn[c_i].coordMin)
-		{
-			result.ic = c_i;
-
-		}
-		else
-		{
-			//if this is the last connected component
-			if(c_i >= conn.size() - 1)
-				return after();
-			else
-			{
-				c_i++;
-				result.ic = c_i;
-			}
-		}
-		result.iv = conn[c_i].toValue;
-		result.x1 = conn[c_i].coordMin;
-	}
-	return result;
-
-}
-template<typename T>
-void rtsDTGrid1D<T>::print()
-{
-	rtsDTGrid1D<T>::iterator i;
-	i = begin();
-	while(i != after())
-	{
-		cout<<i.X1()<<":"<<i.Value()<<endl;
-		i++;
-	}
-	
-
-}
-
-/**************DT GRID**************************/
-template<typename T>
-bool rtsDTGrid1D<T>::push(int x1, T v)
-{
-	//test to make sure the insertion is happening in the right order
-	if(insertion_started && x1 <= max_coord)
-	{
-		cout<<"Out-of-order insertion in D = 1: X1 = "<<x1<<endl;
-		return false;
-	}
-	
-
-	//run this code if we have to start a new connected component.  This happens when:
-	//(a) We insert the first value into the grid
-	//(b) There is empty space between the last insertion and this one
-	if(insertion_started == false || x1 > (max_coord + 1))
-	{
-		//start a new connected component
-		ConnectedComponent new_conn;
-		new_conn.toValue = value.size();
-		new_conn.coordMin = x1;
-		new_conn.coordMax = x1;
-		conn.push_back(new_conn);
-		insertion_started = true;
-	}
-
-	//insert the value into the grid:
-	//(a) Insert the value at the end of the coord array
-	//(b) Increment the coordMax value of the current connected component
-	//(c) Change the maximum inserted coordinate to the new value
-	value.push_back(v);
-	conn[conn.size() - 1].coordMax = x1;
-	//change max_coord to the new coordinate
-	max_coord = x1;
-	return true;
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::insert(rtsDTGrid1D<T> toInsert)
-{
-	//create source and destination iterators
-	rtsDTGrid1D<T>::iterator source = toInsert.begin();
-	rtsDTGrid1D<T>::iterator dest = begin();
-
-	while(source != toInsert.after())
-	{
-		//move the destination iterator to the current source position
-		dest.increment_until(source.X1());
-		//if the position exists in dest
-		if(dest.X1() == source.X1())
-			dest.SetValue(source.Value());
-		source++;
-	}
-
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::getBounds(int &min_x1, int &max_x1)
-{
-	//return an empty bounding volume if the grid is empty
-	if(value.size() == 0)
-	{
-		min_x1 = 0;
-		max_x1 = 0;
-		return;
-	}
-
-	//get the minimum and maximum coordinates
-	min_x1 = conn[0].coordMin;
-	max_x1 = conn.back().coordMax;
-}
-template<typename T>
-void rtsDTGrid1D<T>::dilate(int H)
-{
-	//this function creates a new DT grid dilated by H and copies
-	//the original grid into the new grid
-
-	//create a new grid
-	rtsDTGrid1D<T> new_grid;
-
-	//determine the dilated values for the first connected component
-	int numValues = 0;
-	int start = conn[0].coordMin - H;
-	int end = conn[0].coordMax + H;
-
-	//run through each remaining connected component
-	for(int i=1; i<conn.size(); i++)
-	{
-		//if the new component and the i'th ones overlap, combine them
-		//cout<<conn[i].coordMin - H<<endl;
-		if(conn[i].coordMin - H <= end)
-			end = conn[i].coordMax + H;
-		else
-		{
-			//store the dilated connected component
-			ConnectedComponent cc;
-			cc.coordMin = start;
-			cc.coordMax = end;
-			cc.toValue = numValues;
-			numValues += end - start + 1;
-			new_grid.conn.push_back(cc);
-
-			//start a new dilated connected component
-			start = conn[i].coordMin - H;
-			end = conn[i].coordMax + H;
-		}
-	}
-	//add the last dilated connected component
-	ConnectedComponent cc;
-	cc.coordMin = start;
-	cc.coordMax = end;
-	cc.toValue = numValues;
-	numValues += end - start + 1;
-	new_grid.conn.push_back(cc);
-	//allocate space in the value array, fill it with the background value
-	new_grid.value.resize(numValues, background);
-
-	//insert this grid into the new one
-	new_grid.insert(*this);
-	
-	//copy the new grid to this grid
-	conn = new_grid.conn;
-	value = new_grid.value;
-}
-
-template<typename T>
-bool rtsDTGrid1D<T>::randomIndex(int &v, int &c, int x1)
-{
-	//if the grid is empty return false
-	if(value.size() == 0)
-		return false;
-
-	int low = 0;
-	int high = conn.size()-1;
-	int mid;
-	do
-	{
-		mid = low + (high - low)/2;
-		if(x1 > conn[mid].coordMax)
-			low = mid + 1;
-		//else if(x1 < conn[mid].coordMin)
-		else if(x1 < conn[mid].coordMin)
-			high = mid - 1;
-		else break;
-	}
-	while(low <= high);
-
-	//at this point, mid is either at the appropriate connected component,
-	//or x1 is not in the grid
-	int offset = x1 - conn[mid].coordMin;
-	v = conn[mid].toValue + offset;
-	c = mid;
-	if(x1 >= conn[mid].coordMin && x1 <= conn[mid].coordMax)
-	{		
-		return true;
-	}
-	else
-	{
-		return false;
-	}
-}
-
-template<typename T>
-void rtsDTGrid1D<T>::operator=(T rhs)
-{
-	for(int i=0; i<value.size(); i++)
-		value[i] = rhs;
-}
-template<typename T>
-T& rtsDTGrid1D<T>::back()
-{
-	return value[value.size()-1];
-}
-
-template<typename T>
-T rtsDTGrid1D<T>::random(int x1)
-{
-	int v_i, c_i;
-	
-	if(randomIndex(v_i, c_i, x1))
-		return value[v_i];
-	else
-		return background;
-}
-
-
-#endif
diff --git a/legacy/rtsDTGrid2D.h b/legacy/rtsDTGrid2D.h
deleted file mode 100755
index 568f6fc..0000000
--- a/legacy/rtsDTGrid2D.h
+++ /dev/null
@@ -1,1072 +0,0 @@
-
-#ifndef _RTS_DTGRID2D_H
-#define _RTS_DTGRID2D_H
-
-#include <vector>
-#include <iostream>
-using namespace std;
-
-#include "rtsDTGrid1D.h"
-
-
-
-struct IndexPair
-{
-	//int toValue;
-	int toConn;
-	int numConn;
-};
-
-
-struct Coord2D
-{
-	int x1;
-	int x2;
-};
-
-#include <list>
-using namespace std;
-
-class ColumnUnion
-{
-private:
-	list<IndexPair> Q;
-	vector<ConnectedComponent>* toConn;
-
-public:
-	void InsertColumn(IndexPair col)
-	{
-		Q.push_back(col);
-	}
-	void RemoveColumn()
-	{
-		Q.pop_front();
-	}
-	vector<ConnectedComponent> MergeColumns(vector<ConnectedComponent> *Pc,
-											vector<ConnectedComponent> *n,
-											int H)
-	{
-		int i_Pc = 0;
-		int i_n = 0;
-		int smallest_column;
-		ConnectedComponent smallest_cc;
-		vector<ConnectedComponent> result;
-
-		//iterate while there are remaining connected components in each column
-		while(i_Pc < Pc->size() || i_n < n->size())
-		{
-			//find the smallest coordMin value at the two index locations
-
-			//if the index is at the end of the primary array
-			if(i_Pc == Pc->size())
-			{
-				smallest_cc = n->at(i_n);
-				smallest_cc.coordMin -= H;
-				smallest_cc.coordMax += H;
-				i_n++;
-			}
-			//if n is at the end of the array
-			else if(i_n == n->size())
-			{
-				smallest_cc = Pc->at(i_Pc);
-				i_Pc++;
-			}
-			else if(n->at(i_n).coordMin - H < Pc->at(i_Pc).coordMin)
-			{
-				smallest_cc = n->at(i_n);
-				smallest_cc.coordMin -= H;
-				smallest_cc.coordMax += H;
-				i_n++;
-			}
-			else
-			{
-				smallest_cc = Pc->at(i_Pc);
-				i_Pc++;
-			}
-
-			//merge the connected component into result
-			//if the result array is empty or the last connected component doesn't overlap with smallest_cc
-			if(result.size() == 0 || result.back().coordMax + 1 < smallest_cc.coordMin)
-				result.push_back(smallest_cc);
-			else if(result.back().coordMax < smallest_cc.coordMax)
-				result.back().coordMax = smallest_cc.coordMax;
-		}
-		return result;
-
-	}
-
-	vector<ConnectedComponent> ComputeUnion(int H)
-	{
-		//create a vector to store the result
-		vector<ConnectedComponent> result;
-
-		//for each column in the list, merge it with the result vector
-		list<IndexPair>::iterator i;
-		vector<ConnectedComponent>::iterator start;
-		vector<ConnectedComponent>::iterator end;
-		for(i = Q.begin(); i != Q.end(); i++)
-		{
-			start = toConn->begin() + (*i).toConn;
-			end = start + (*i).numConn;
-			vector<ConnectedComponent> column(start, end);
-			result = MergeColumns(&result, &column, H);
-		}
-
-		//output result
-		//for(int i=0; i<result.size(); i++)
-		//	cout<<i<<": "<<result[i].coordMin<<"--"<<result[i].coordMax<<endl;
-
-		return result;
-	}
-	void ConnectToGrid(vector<ConnectedComponent> *cc_list)
-	{
-		toConn = cc_list;
-	}
-};
-
-
-/*vector<ConnectedComponent> ColumnUnion::MergeColumns(vector<ConnectedComponent> *Pc, vector<ConnectedComponent> *n, int H)
-{
-	int i_Pc = 0;
-	int i_n = 0;
-	int smallest_column;
-	ConnectedComponent smallest_cc;
-	vector<ConnectedComponent> result;
-
-	//iterate while there are remaining connected components in each column
-	while(i_Pc < Pc->size() || i_n < n->size())
-	{
-		//find the smallest coordMin value at the two index locations
-
-		//if the index is at the end of the primary array
-		if(i_Pc == Pc->size())
-		{
-			smallest_cc = n->at(i_n);
-			smallest_cc.coordMin -= H;
-			smallest_cc.coordMax += H;
-			i_n++;
-		}
-		//if n is at the end of the array
-		else if(i_n == n->size())
-		{
-			smallest_cc = Pc->at(i_Pc);
-			i_Pc++;
-		}
-		else if(n->at(i_n).coordMin - H < Pc->at(i_Pc).coordMin)
-		{
-			smallest_cc = n->at(i_n);
-			smallest_cc.coordMin -= H;
-			smallest_cc.coordMax += H;
-			i_n++;
-		}
-		else
-		{
-			smallest_cc = Pc->at(i_Pc);
-			i_Pc++;
-		}
-
-		//merge the connected component into result
-		//if the result array is empty or the last connected component doesn't overlap with smallest_cc
-		if(result.size() == 0 || result.back().coordMax + 1 < smallest_cc.coordMin)
-			result.push_back(smallest_cc);
-		else if(result.back().coordMax < smallest_cc.coordMax)
-			result.back().coordMax = smallest_cc.coordMax;
-	}
-	return result;
-}*/
-
-/*vector<ConnectedComponent> ColumnUnion::ComputeUnion(int H)
-{
-
-	//create a vector to store the result
-	vector<ConnectedComponent> result;
-
-	//for each column in the list, merge it with the result vector
-	list<IndexPair>::iterator i;
-	vector<ConnectedComponent>::iterator start;
-	vector<ConnectedComponent>::iterator end;
-	for(i = Q.begin(); i != Q.end(); i++)
-	{
-		start = toConn->begin() + (*i).toConn;
-		end = start + (*i).numConn;
-		vector<ConnectedComponent> column(start, end);
-		result = MergeColumns(&result, &column, H);
-	}
-
-	//output result
-	//for(int i=0; i<result.size(); i++)
-	//	cout<<i<<": "<<result[i].coordMin<<"--"<<result[i].coordMax<<endl;
-
-	return result;
-}
-*/
-
-
-template<typename T>
-class rtsDTGrid2D
-{
-private:
-	//main arrays
-	vector<T> value;
-	vector<ConnectedComponent> conn;
-	rtsDTGrid1D<IndexPair> proj1D;
-	bool randomIndex(rtsDTGrid1D<IndexPair>::iterator &iter1D, int &v_i, int &c_i, int x1, int x2);
-
-	
-
-	//variables to keep track of insertion
-	int max_coord;
-	bool grid_insertion_started;
-	bool column_insertion_started;
-
-
-public:
-	rtsDTGrid2D<T>()
-	{
-		grid_insertion_started = false;
-		column_insertion_started = false;
-		proj1D.background.toConn = -1;
-		max_coord = 0;
-	}
-
-	bool push(int x1, int x2, T v);
-	T random(int x1, int x2);
-	T& back();
-	T background;
-	void print();
-
-	friend class ColumnUnion;
-	void dilate(int H);
-	void insert(rtsDTGrid2D<T> toInsert);
-	void operator=(T rhs);
-	void getBounds(int &min_x1, int &min_x2, int &max_x1, int &max_x2);
-
-	void dumpValue();
-	void dumpConn();
-
-	//iterator
-	class iterator;
-	friend class iterator;
-	class stencil_iterator;
-	iterator randomIterator(int x1, int x2);
-	iterator begin();
-	iterator before();
-	iterator end();
-	iterator after();
-
-	//other types of iteration
-	iterator begin_pn();
-	iterator end_pn();
-	iterator begin_np();
-	iterator end_np();
-};
-
-/**********ITERATOR***********************/
-template<typename T>
-class rtsDTGrid2D<T>::iterator
-{
-	friend class rtsDTGrid2D;
-	rtsDTGrid2D<T>* parent;
-	rtsDTGrid1D<IndexPair>::iterator loc1D;
-	int iv;
-	int ic;
-	int x2;
-
-public:
-	
-
-	T Value(){return parent->value[iv];}
-	int X1(){return loc1D.X1();}
-	int X2(){return x2;}
-	iterator(){parent = NULL;}
-	void SetValue(T value){parent->value[iv] = value;}
-	
-
-	void pp()
-	{
-		//increment the value
-		iv++;
-		//if this exceeds the length of the value array, we are at the end of the grid
-		if(iv == parent->value.size())
-		{
-			(*this) = parent->after();
-			return;
-		}
-
-		//increment the current coordinate
-		x2++;
-		//if we are outside of the current connected component
-		if(x2 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is the last connected component in the column
-			if(ic == loc1D.Value().toConn + loc1D.Value().numConn)
-				loc1D++;
-			//if there are no more connected components
-			if(ic == parent->conn.size())
-			{
-				//we're at the end, return end
-				(*this) = parent->end();
-				return;
-			}
-			x2 = parent->conn[ic].coordMin;
-		}
-	}
-
-	void nn()
-	{
-		//decrement the value
-		iv--;
-		//if this is less than 0, we are at the beginning of the grid
-		if(iv < 0)
-		{
-			(*this) = parent->before();
-			return;
-		}
-
-		//decrement the current coordinate
-		x2--;
-		//if we are outside of the current connected component
-		if(x2 < parent->conn[ic].coordMin)
-		{
-			//move to the previous connected component
-			ic--;
-			//if this is the first connected component in the column
-			if(ic < loc1D.Value().toConn)
-				loc1D--;
-			//if there are no more connected components
-			if(ic < 0)
-			{
-				//we're at the beginning, return begin
-				(*this) = parent->before();
-				return;
-			}
-			x2 = parent->conn[ic].coordMax;
-		}
-
-	}
-
-	void pn()
-	{
-		//for the most part we will be going backwards through the array
-		//so first decrement iv
-		iv--;
-		x2--;
-		//if iv is less than the current connected component
-		if(iv < parent->conn[ic].toValue)
-		{
-			//go to the previous connected component
-			ic--;
-			//if we are before the first connected component in the column
-			if(ic < loc1D.Value().toConn)
-			{
-				//increment the 1D iterator
-				loc1D++;
-				//reset ic to the last component of the new column
-				ic = loc1D.Value().toConn + loc1D.Value().numConn - 1;
-				//find the new value identifier
-				iv = parent->conn[ic].toValue + (parent->conn[ic].coordMax - parent->conn[ic].coordMin);
-			}
-			//compute the currect coordinate
-			x2 = parent->conn[ic].coordMax;
-		}
-	}
-
-	void np()
-	{
-		//for the most part we will be going forward through the grid
-		//increment iv
-		iv++;
-		x2++;
-		
-		//if we are outside of the current connected component
-		if(x2 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is the last connected component in the column
-			if(ic == loc1D.Value().toConn + loc1D.Value().numConn)
-			{
-				loc1D--;
-				ic = loc1D.Value().toConn;
-				iv = parent->conn[ic].toValue;
-			}
-
-			x2 = parent->conn[ic].coordMin;
-		}
-
-	}
-
-	//boolean operators for comparing iterators
-	bool operator==(iterator &rhs)
-	{
-		if(parent == rhs.parent && iv == rhs.iv)
-			return true;
-		//if(loc1D == rhs.loc1D && x2 == rhs.x2)
-		//	return true;
-		return false;
-	}
-	bool operator!=(iterator &rhs){return !((*this) == rhs);}
-
-	bool operator<(iterator &rhs)
-	{
-		if(parent == rhs.parent && iv < rhs.iv)
-			return true;
-		//if(loc1D < rhs.loc1D)
-		//	return true;
-		//else if(loc1D == rhs.loc1D && x2 < rhs.x2)
-		//	return true;
-		return false;
-	}
-	bool operator<=(iterator &rhs)
-	{
-		if(parent == rhs.parent && iv <= rhs.iv)
-			return true;
-		//if(loc1D <= rhs.loc1D)
-		//	return true;
-		//else if(loc1D == rhs.loc1D && x2 <= rhs.x2)
-		//	return true;
-		return false;
-	}
-	void operator++(){pp();}
-	void operator--(){nn();}
-	void increment_until(int p1, int p2)
-	{
-		while((*this) != parent->end())
-		{
-			if(X1() > p1)
-				return;
-			else if(X1() == p1 && X2() >= p2)
-				return;
-
-			pp();
-		}
-	}
-};
-
-/********STENCIL ITERATOR*****************/
-template<typename T>
-class rtsDTGrid2D<T>::stencil_iterator : public iterator
-{
-private:
-	//list of iterators that make up the template
-	vector<iterator> iterator_list;
-	//iterator positions (relative to the position of the stencil iterator)
-	vector<Coord2D> position_list;
-	//list containing the values for each position in the stencil
-	vector<T> value_list;
-
-	void refresh_iterators();
-	void set_values();
-	void increment_all();
-
-public:
-	typename rtsDTGrid2D<T>::stencil_iterator operator=(const iterator rhs);
-	void addPosition(int p1, int p2);
-	void increment();
-	void operator++()
-	{
-		increment();
-	}
-	T getValue(int id){return value_list[id];}
-	bool exists(int id);
-	
-};
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::increment_all()
-{
-	//run through each iterator and increment to the correct position
-	int i;
-	Coord2D dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest.x1 = X1() + position_list[i].x1;
-		dest.x2 = X2() + position_list[i].x2;
-		//iterate until that position is reached
-		iterator_list[i].increment_until(dest.x1, dest.x2);
-	}
-	set_values();
-
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::increment()
-{
-	//increment the current position
-	rtsDTGrid2D<T>::iterator::pp();
-
-	increment_all();
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::refresh_iterators()
-{
-	//make sure that the iterator position has been set
-	if(parent == NULL)
-	{
-		cout<<"Iterator location not set."<<endl;
-		return;
-	}
-	
-	//initialize all of the other iterators
-	int i;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//for each iterator, set the iterator to the beginning of the grid
-		//iterator_list[i] = parent->begin();
-		iterator_list[i] = parent->randomIterator(X1() + position_list[i].x1,
-												  X2() + position_list[i].x2);
-	}
-	//increment_all();
-	//set the values for all of the iterators
-	set_values();
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::set_values()
-{
-	int i;
-	Coord2D dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest.x1 = X1() + position_list[i].x1;
-		dest.x2 = X2() + position_list[i].x2;
-		//now add the value to the value list
-		if(iterator_list[i].X1() == dest.x1 && iterator_list[i].X2() == dest.x2)
-			value_list[i] = iterator_list[i].Value();
-		else
-			value_list[i] = parent->background;
-	}
-
-
-}
-
-template<typename T>
-typename rtsDTGrid2D<T>::stencil_iterator rtsDTGrid2D<T>::stencil_iterator::operator=(const iterator rhs)
-{
-	parent = rhs.parent;
-	loc1D = rhs.loc1D;
-	iv = rhs.iv;
-	ic = rhs.ic;
-	x2 = rhs.x2;
-
-	refresh_iterators();
-
-	return (*this);
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::addPosition(int p1, int p2)
-{
-	//add a position to the position list and add a new iterator to the iterator list
-	Coord2D p;
-	p.x1 = p1;
-	p.x2 = p2;
-	position_list.push_back(p);
-	rtsDTGrid2D<T>::iterator new_iter;
-
-
-	iterator_list.push_back(new_iter);
-	T empty;
-	value_list.push_back(empty);
-}
-
-template<typename T>
-bool rtsDTGrid2D<T>::stencil_iterator::exists(int id)
-{
-	int i;
-	Coord2D dest;
-
-	//determine the appropriate position for the iterator
-	dest.x1 = X1() + position_list[id].x1;
-	dest.x2 = X2() + position_list[id].x2;
-	//now add the value to the value list
-	if(iterator_list[id].X1() == dest.x1 && iterator_list[id].X2() == dest.x2)
-		return true;
-	else
-		return false;
-	
-}
-
-/**************ITERATOR METHODS IN DT GRID*******************/
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::begin()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = 0;
-	result.x2 = conn[0].coordMin;
-	result.loc1D = proj1D.begin();
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::before()
-{
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = -1;
-	//result.x2 = conn[0].coordMin;
-	result.loc1D = proj1D.before();
-
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::end()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size() - 1;
-	result.x2 = conn[result.ic].coordMax;
-	result.loc1D = proj1D.end();
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::randomIterator(int x1, int x2)
-{
-	rtsDTGrid2D<T>::iterator result;
-	result.parent = this;
-
-	//perform the random search
-	int v_i, c_i;
-	rtsDTGrid1D<IndexPair>::iterator iter1D;
-
-	//if the value exists in the grid, create the iterator and return
-	if(randomIndex(iter1D, v_i, c_i, x1, x2))
-	{
-		result.loc1D = iter1D;
-		result.iv = v_i;
-		result.ic = c_i;
-		int offset = v_i - conn[c_i].toValue;
-		result.x2 = conn[c_i].coordMin + offset;
-	}
-	//if the value doesn't exist
-	else
-	{
-		//if the 1D iterator is at the end of the grid, return after()
-		if(iter1D == proj1D.after())
-			return after();
-		
-		//if the value lies before the current column
-		if(x1 < iter1D.X1() || (x1 == iter1D.X1() && x2 < conn[c_i].coordMin) )
-		{
-			result.ic = c_i;
-		}
-		//else if the value lies after the current column
-		else
-		{
-			//increment the 1D iterator
-			iter1D++;
-			//if this is the last connected component
-			if(c_i >= conn.size() - 1)
-				return after();
-			else
-			{
-				c_i++;
-				result.ic = c_i;
-			}
-		}
-		
-
-		result.loc1D = iter1D;
-		result.iv = conn[c_i].toValue;
-		result.x2 = conn[c_i].coordMin;
-	}
-	return result;
-
-
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::after()
-{
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size();
-	//result.x2 = conn[result.ic].coordMax;
-	result.loc1D = proj1D.after();
-	return result;
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::begin_pn()
-{
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.loc1D = proj1D.begin();
-	result.ic = result.loc1D.Value().toConn + result.loc1D.Value().numConn - 1;
-	result.iv = conn[result.ic].toValue + (conn[result.ic].coordMax - conn[result.ic].coordMin);
-	result.x2 = conn[result.ic].coordMax;
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::begin_np()
-{
-	//this is the opposite corner of pn
-	return end_pn();
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::end_pn()
-{
-	if(value.size() == 0)
-		return after();
-	iterator result;
-	result.parent = this;
-	result.loc1D = proj1D.end();
-	result.ic = result.loc1D.Value().toConn;
-	result.iv = conn[result.ic].toValue;
-	result.x2 = conn[result.ic].coordMin;
-	
-	return result;
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::end_np()
-{
-	//this is the opposite corner of pn
-	return begin_pn();
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::print()
-{
-	rtsDTGrid2D<T>::iterator i;
-	i = begin();
-	while(i!=end())
-	{
-		cout<<i.X1()<<","<<i.X2()<<":"<<i.Value()<<endl;
-		i.increment();
-	}
-	
-
-}
-
-/**************DT GRID**************************/
-template<typename T>
-bool rtsDTGrid2D<T>::push(int x1, int x2, T v)
-{
-	//run this code if we have to start a new column in X1.  This happens when:
-	//(a) we have just inserted the first value into the grid
-	//(b) the value of x1 is greater than the last value of x1	
-	if(grid_insertion_started == false || x1 != proj1D.getMaxX1())
-	{
-		//assume that a new column is being created
-		//create the column in proj1D
-		IndexPair newPair;
-		newPair.toConn = conn.size();
-		//newPair.toValue = value.size();
-		newPair.numConn = 0;
-
-		//if this insertion throws an error, the value was inserted incorrectly
-		//the error will get thrown by DTGrid1D, so just return
-		if(!proj1D.push(x1, newPair))
-		{
-			cout<<"Out-of-order insertion in D = 2: X1 = "<<x1<<" X2 = "<<x2<<endl;
-			return false;
-		}
-
-		column_insertion_started = false;
-		grid_insertion_started = true;
-	}
-	//If there is no new column, we still have to check to make sure the value is inserted
-	//in the correct order in X2:
-	else
-	{
-		if(column_insertion_started && x2 <= max_coord)
-		{
-			cout<<"Out-of-order insertion in D = 2: X1 = "<<x1<<" X2 = "<<x2<<endl;
-			return false;
-		}
-	}
-	
-
-	//run this code if we have to start a new connected component.  This happens when:
-	//(a) We insert the first value into the column
-	//(b) There is empty space between the last insertion and this one
-	if(column_insertion_started == false || x2 > (max_coord + 1))
-	{
-		//start a new connected component
-		ConnectedComponent new_conn;
-		new_conn.toValue = value.size();
-		new_conn.coordMin = x2;
-		new_conn.coordMax = x2;
-		conn.push_back(new_conn);
-		//increment the number of connected components for the column in X1
-		proj1D.back().numConn++;
-		column_insertion_started = true;
-	}
-
-	//insert the value into the grid:
-	//(a) Insert the value at the end of the coord array
-	//(b) Increment the coordMax value of the current connected component
-	//(c) Change the maximum inserted coordinate to the new value
-	value.push_back(v);
-	conn[conn.size() - 1].coordMax = x2;
-	//change max_coord to the new coordinate
-	max_coord = x2;
-	return true;
-}
-
-template<typename T>
-bool rtsDTGrid2D<T>::randomIndex(rtsDTGrid1D<IndexPair>::iterator &iter1D, int &v_i, int &c_i, int x1, int x2)
-{
-	//search along the first dimension
-	//get an iterator
-	iter1D = proj1D.randomIterator(x1);
-
-	//if the after() iterator is returned, exit
-	if(iter1D == proj1D.after())
-	{
-		c_i = conn.size();
-		v_i = value.size();
-		return false;
-	}
-
-	IndexPair i = iter1D.Value();
-
-	//if the 1D column does not exist
-	if(iter1D.X1() != x1)
-	{
-		//get the appropriate values from the 1D iterator
-		//(which points to the next valid column)
-		c_i = i.toConn;
-		v_i = conn[c_i].toValue;
-		return false;
-	}
-	
-
-	int high, low, mid;
-	low = i.toConn;
-	high = i.toConn + i.numConn - 1;
-
-	do
-	{
-		mid = low + (high - low)/2;
-		if(x2 > conn[mid].coordMax)
-			low = mid + 1;
-		else if(x2 < conn[mid].coordMin)
-			high = mid - 1;
-		else break;
-	}
-	while(low <= high);
-
-	//at this point, mid is either at the appropriate connected component,
-	//or x2 is not in the grid
-	if(x2 >= conn[mid].coordMin && x2 <= conn[mid].coordMax)
-	{
-		int offset = x2 - conn[mid].coordMin;
-		c_i = mid;
-		v_i = conn[mid].toValue + offset;
-		return true;
-	}
-	else
-	{
-		c_i = mid;
-		v_i = conn[c_i].toValue;
-		return false;
-	}
-}
-
-template<typename T>
-T rtsDTGrid2D<T>::random(int x1, int x2)
-{
-	int v_i, c_i;
-	rtsDTGrid1D<IndexPair>::iterator iter1D;
-	if(randomIndex(iter1D, v_i, c_i, x1, x2))
-		return value[v_i];
-	else
-		return background;
-}
-
-template<typename T>
-T& rtsDTGrid2D<T>::back()
-{
-	return value[value.size()-1];
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::dilate(int H)
-{
-	//if the grid is empty, return unchanged
-	if(value.size() == 0)
-		return;
-
-	ColumnUnion CUqueue;
-	CUqueue.ConnectToGrid(&conn);
-
-
-	//dilate the N-1 DT-Grid constituent
-	rtsDTGrid1D<IndexPair> dilated_proj1D = proj1D;
-	
-	//an empty pair has a number of connected components equal to zero
-	//this should not happen in reality and can therefore be used to check for new columns
-	IndexPair empty_pair;
-	empty_pair.numConn = 0;
-
-	//set the background node to the empty node and dilate the 1D projection
-	dilated_proj1D.background = empty_pair;
-	dilated_proj1D.dilate(H);
-
-	//create a new DT Grid that will replace this one
-	rtsDTGrid2D<T> new_grid;
-	new_grid.proj1D = dilated_proj1D;
-	new_grid.proj1D.background.toConn = -1;
-
-	//create iteratorDilate that iterates along the dilated N-1 grid
-	rtsDTGrid1D<IndexPair>::stencil_iterator iteratorDilate;
-	iteratorDilate.addPosition(-H);
-	iteratorDilate.addPosition(H);
-
-	//create an iterator to set the new proj1D values
-	rtsDTGrid1D<IndexPair>::iterator iteratorNew;
-
-
-	//variables for each iteration
-	IndexPair new_pair;
-	vector<ConnectedComponent>::iterator ccIterator;
-	unsigned int numValues = 0;
-	for(iteratorNew = new_grid.proj1D.begin(),
-		iteratorDilate = dilated_proj1D.begin();
-		iteratorDilate != dilated_proj1D.after();
-		iteratorNew++,
-		iteratorDilate++)
-		{
-			//cout<<"1D position: "<<iteratorNew.X1()<<endl;
-			//if a column is entering the stencil
-			if(iteratorDilate.getValue(1).numConn)
-				CUqueue.InsertColumn(iteratorDilate.getValue(1));
-			
-			//compute the union of all columns in the queue
-			vector<ConnectedComponent> result = CUqueue.ComputeUnion(H);
-
-			//compute the new IndexPair representing the column
-			new_pair.toConn = new_grid.conn.size();
-			new_pair.numConn = result.size();
-			//store the index pair
-			iteratorNew.SetValue(new_pair);
-
-			//insert each of the connected components
-			for(ccIterator = result.begin(); ccIterator!=result.end(); ccIterator++)
-			{
-				new_grid.conn.push_back(*ccIterator);
-				new_grid.conn.back().toValue = numValues;
-				numValues += (*ccIterator).coordMax - (*ccIterator).coordMin + 1;
-			}
-
-			//if a column is leaving the stencil
-			if(iteratorDilate.getValue(0).numConn)
-				CUqueue.RemoveColumn();
-		}
-
-	//allocate space for the new value array
-	new_grid.value.resize(numValues, background);
-
-	//copy the data from this grid into the new grid
-	new_grid.insert(*this);
-
-	//replace this grid with the new grid
-	conn = new_grid.conn;
-	value = new_grid.value;
-	proj1D = new_grid.proj1D;
-
-	
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::insert(rtsDTGrid2D<T> toInsert)
-{
-	//create source and destination iterators
-	rtsDTGrid2D<T>::iterator source = toInsert.begin();
-	rtsDTGrid2D<T>::iterator dest = begin();
-
-	for(source = toInsert.begin(); source != toInsert.after(); source++)
-	{
-		//move the destination iterator to the current source position
-		dest.increment_until(source.X1(), source.X2());
-		//cout<<"source: "<<source.X1()<<" "<<source.X2()<<": "<<source.Value()<<endl;
-		//cout<<"dest: "<<dest.X1()<<" "<<dest.X2()<<": "<<dest.Value()<<endl;
-		//if the position exists in dest
-		if(dest.X1() == source.X1() && dest.X2() == source.X2())
-			dest.SetValue(source.Value());
-		//cout<<"dest: "<<dest.X1()<<" "<<dest.X2()<<": "<<dest.Value()<<endl;
-	}
-
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::getBounds(int &min_x1, int &min_x2, int &max_x1, int &max_x2)
-{
-	//if the grid is empty, return an empty bounding volume
-	if(value.size() == 0)
-	{
-		min_x1 = min_x2 = max_x1 = max_x2 = 0;
-		return;
-	}
-
-	//get the min and max values for the 1D grid (x1 coordinate)
-	proj1D.getBounds(min_x1, max_x1);
-
-	//initialize the min and max values
-	min_x2 = conn[0].coordMin;
-	max_x2 = conn.back().coordMax;
-
-	//iterate through all columns finding the smallest and largest coordinate values
-	rtsDTGrid1D<IndexPair>::iterator i;
-	IndexPair col;
-	for(i=proj1D.begin(); i!=proj1D.after(); i++)
-	{
-		col = i.Value();
-		if(conn[col.toConn].coordMin < min_x2)
-			min_x2 = conn[col.toConn].coordMin;
-		if(conn[col.toConn + col.numConn - 1].coordMax > max_x2)
-			max_x2 = conn[col.toConn + col.numConn - 1].coordMax;
-	}
-		
-
-}
-template<typename T>
-void rtsDTGrid2D<T>::operator =(T rhs)
-{
-	for(int i=0; i<value.size(); i++)
-		value[i] = rhs;
-}
-
-
-template<typename T>
-void rtsDTGrid2D<T>::dumpValue()
-{
-	for(int i=0; i<value.size(); i++)
-		cout<<value[i]<<endl;
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::dumpConn()
-{
-	for(int i=0; i<conn.size(); i++)
-		cout<<conn[i].toValue<<","<<conn[i].coordMin<<","<<conn[i].coordMax<<endl;
-
-
-}
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsDTGrid2D_v1.h b/legacy/rtsDTGrid2D_v1.h
deleted file mode 100755
index 538f69a..0000000
--- a/legacy/rtsDTGrid2D_v1.h
+++ /dev/null
@@ -1,740 +0,0 @@
-
-#include <vector>
-#include <iostream>
-using namespace std;
-
-#include "rtsDTGrid1D.h"
-
-#ifndef _RTS_DTGRID2D_H
-#define _RTS_DTGRID2D_H
-
-struct IndexPair
-{
-	//int toValue;
-	int toConn;
-	int numConn;
-};
-
-#include "ColumnUnion.h"
-
-struct Coord2D
-{
-	int x1;
-	int x2;
-};
-
-
-
-template<typename T>
-class rtsDTGrid2D
-{
-private:
-	//main arrays
-	vector<T> value;
-	vector<ConnectedComponent> conn;
-	rtsDTGrid1D<IndexPair> proj1D;
-	bool randomIndex(rtsDTGrid1D<IndexPair>::iterator &iter1D, int &v_i, int &c_i, int x1, int x2);
-
-	
-
-	//variables to keep track of insertion
-	int max_coord;
-	bool grid_insertion_started;
-	bool column_insertion_started;
-
-
-public:
-	rtsDTGrid2D<T>()
-	{
-		grid_insertion_started = false;
-		column_insertion_started = false;
-		proj1D.background.toConn = -1;
-		max_coord = 0;
-	}
-
-	bool push(int x1, int x2, T v);
-	T random(int x1, int x2);
-	T& back();
-	T background;
-	void print();
-
-	friend class ColumnUnion;
-	void dilate(int H);
-	void insert(rtsDTGrid2D<T> toInsert);
-	void operator=(T rhs);
-	void getBounds(int &min_x1, int &min_x2, int &max_x1, int &max_x2);
-
-	void dumpValue();
-	void dumpConn();
-
-	//iterator
-	class iterator;
-	friend class iterator;
-	class stencil_iterator;
-	iterator randomIterator(int x1, int x2);
-	iterator begin();
-	iterator before();
-	iterator end();
-	iterator after();
-};
-
-/**********ITERATOR***********************/
-template<typename T>
-class rtsDTGrid2D<T>::iterator
-{
-	friend class rtsDTGrid2D;
-	rtsDTGrid2D<T>* parent;
-	rtsDTGrid1D<IndexPair>::iterator loc1D;
-	int iv;
-	int ic;
-	int x2;
-
-public:
-	
-
-	T Value(){return parent->value[iv];}
-	int X1(){return loc1D.X1();}
-	int X2(){return x2;}
-	iterator(){parent = NULL;}
-	void SetValue(T value){parent->value[iv] = value;}
-	
-
-	void increment()
-	{
-		//increment the value
-		iv++;
-		//if this exceeds the length of the value array, we are at the end of the grid
-		if(iv == parent->value.size())
-		{
-			(*this) = parent->after();
-			return;
-		}
-
-		//increment the current coordinate
-		x2++;
-		//if we are outside of the current connected component
-		if(x2 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is the last connected component in the column
-			if(ic == loc1D.Value().toConn + loc1D.Value().numConn)
-				loc1D++;
-			//if there are no more connected components
-			if(ic == parent->conn.size())
-			{
-				//we're at the end, return end
-				(*this) = parent->end();
-				return;
-			}
-			x2 = parent->conn[ic].coordMin;
-		}
-	}
-
-
-	//boolean operators for comparing iterators
-	bool operator==(iterator rhs)
-	{
-		if(parent == rhs.parent && iv == rhs.iv)
-			return true;
-		return false;
-	}
-	bool operator!=(iterator rhs){return !((*this) == rhs);}
-
-	friend bool operator<(iterator &left, iterator &right)
-	{
-		if(left.iv < right.iv)
-			return true;
-		return false;
-	}
-	friend bool operator<=(iterator &left, iterator &right)
-	{
-		if(left.iv <= right.iv)
-			return true;
-		return false;
-	}
-	void operator++(){increment();}
-	void increment_until(int p1, int p2)
-	{
-		while((*this) != parent->end())
-		{
-			if(X1() > p1)
-				return;
-			else if(X1() == p1 && X2() >= p2)
-				return;
-
-			increment();
-		}
-	}
-};
-
-/********STENCIL ITERATOR*****************/
-template<typename T>
-class rtsDTGrid2D<T>::stencil_iterator : public iterator
-{
-private:
-	//list of iterators that make up the template
-	vector<iterator> iterator_list;
-	//iterator positions (relative to the position of the stencil iterator)
-	vector<Coord2D> position_list;
-	//list containing the values for each position in the stencil
-	vector<T> value_list;
-
-	void refresh_iterators();
-	void set_values();
-	void increment_all();
-
-public:
-	typename rtsDTGrid2D<T>::stencil_iterator operator=(const iterator rhs);
-	void addPosition(int p1, int p2);
-	void increment();
-	void operator++()
-	{
-		increment();
-	}
-	T getValue(int id){return value_list[id];}
-	bool exists(int id);
-	
-};
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::increment_all()
-{
-	//run through each iterator and increment to the correct position
-	int i;
-	Coord2D dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest.x1 = X1() + position_list[i].x1;
-		dest.x2 = X2() + position_list[i].x2;
-		//iterate until that position is reached
-		iterator_list[i].increment_until(dest.x1, dest.x2);
-	}
-	set_values();
-
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::increment()
-{
-	//increment the current position
-	rtsDTGrid2D<T>::iterator::increment();
-
-	increment_all();
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::refresh_iterators()
-{
-	//make sure that the iterator position has been set
-	if(parent == NULL)
-	{
-		cout<<"Iterator location not set."<<endl;
-		return;
-	}
-	
-	//initialize all of the other iterators
-	int i;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//for each iterator, set the iterator to the beginning of the grid
-		//iterator_list[i] = parent->begin();
-		iterator_list[i] = parent->randomIterator(X1() + position_list[i].x1,
-												  X2() + position_list[i].x2);
-	}
-	//increment_all();
-	//set the values for all of the iterators
-	set_values();
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::set_values()
-{
-	int i;
-	Coord2D dest;
-	for(i=0; i<iterator_list.size(); i++)
-	{
-		//determine the appropriate position for the iterator
-		dest.x1 = X1() + position_list[i].x1;
-		dest.x2 = X2() + position_list[i].x2;
-		//now add the value to the value list
-		if(iterator_list[i].X1() == dest.x1 && iterator_list[i].X2() == dest.x2)
-			value_list[i] = iterator_list[i].Value();
-		else
-			value_list[i] = parent->background;
-	}
-
-
-}
-
-template<typename T>
-typename rtsDTGrid2D<T>::stencil_iterator rtsDTGrid2D<T>::stencil_iterator::operator=(const iterator rhs)
-{
-	parent = rhs.parent;
-	loc1D = rhs.loc1D;
-	iv = rhs.iv;
-	ic = rhs.ic;
-	x2 = rhs.x2;
-
-	refresh_iterators();
-
-	return (*this);
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::stencil_iterator::addPosition(int p1, int p2)
-{
-	//add a position to the position list and add a new iterator to the iterator list
-	Coord2D p;
-	p.x1 = p1;
-	p.x2 = p2;
-	position_list.push_back(p);
-	rtsDTGrid2D<T>::iterator new_iter;
-
-
-	iterator_list.push_back(new_iter);
-	T empty;
-	value_list.push_back(empty);
-}
-
-template<typename T>
-bool rtsDTGrid2D<T>::stencil_iterator::exists(int id)
-{
-	int i;
-	Coord2D dest;
-
-	//determine the appropriate position for the iterator
-	dest.x1 = X1() + position_list[id].x1;
-	dest.x2 = X2() + position_list[id].x2;
-	//now add the value to the value list
-	if(iterator_list[id].X1() == dest.x1 && iterator_list[id].X2() == dest.x2)
-		return true;
-	else
-		return false;
-	
-}
-
-/**************ITERATOR METHODS IN DT GRID*******************/
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::begin()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = 0;
-	result.x2 = conn[0].coordMin;
-	result.loc1D = proj1D.begin();
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::before()
-{
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = -1;
-	//result.x2 = conn[0].coordMin;
-	result.loc1D = proj1D.before();
-
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::end()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size() - 1;
-	result.x2 = conn[result.ic].coordMax;
-	result.loc1D = proj1D.end();
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::randomIterator(int x1, int x2)
-{
-	rtsDTGrid2D<T>::iterator result;
-	result.parent = this;
-
-	//perform the random search
-	int v_i, c_i;
-	rtsDTGrid1D<IndexPair>::iterator iter1D;
-
-	//if the value exists in the grid, create the iterator and return
-	if(randomIndex(iter1D, v_i, c_i, x1, x2))
-	{
-		result.loc1D = iter1D;
-		result.iv = v_i;
-		result.ic = c_i;
-		int offset = v_i - conn[c_i].toValue;
-		result.x2 = conn[c_i].coordMin + offset;
-	}
-	//if the value doesn't exist
-	else
-	{
-		//if the 1D iterator is at the end of the grid, return after()
-		if(iter1D == proj1D.after())
-			return after();
-		
-		//if the value lies before the current column
-		if(x1 < iter1D.X1() || (x1 == iter1D.X1() && x2 < conn[c_i].coordMin) )
-		{
-			result.ic = c_i;
-		}
-		//else if the value lies after the current column
-		else
-		{
-			//increment the 1D iterator
-			iter1D++;
-			//if this is the last connected component
-			if(c_i >= conn.size() - 1)
-				return after();
-			else
-			{
-				c_i++;
-				result.ic = c_i;
-			}
-		}
-		
-
-		result.loc1D = iter1D;
-		result.iv = conn[c_i].toValue;
-		result.x2 = conn[c_i].coordMin;
-	}
-	return result;
-
-
-}
-template<typename T>
-typename rtsDTGrid2D<T>::iterator rtsDTGrid2D<T>::after()
-{
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size();
-	//result.x2 = conn[result.ic].coordMax;
-	result.loc1D = proj1D.after();
-	return result;
-}
-
-/**************DT GRID**************************/
-template<typename T>
-bool rtsDTGrid2D<T>::push(int x1, int x2, T v)
-{
-	//run this code if we have to start a new column in X1.  This happens when:
-	//(a) we have just inserted the first value into the grid
-	//(b) the value of x1 is greater than the last value of x1	
-	if(grid_insertion_started == false || x1 != proj1D.getMaxX1())
-	{
-		//assume that a new column is being created
-		//create the column in proj1D
-		IndexPair newPair;
-		newPair.toConn = conn.size();
-		//newPair.toValue = value.size();
-		newPair.numConn = 0;
-
-		//if this insertion throws an error, the value was inserted incorrectly
-		//the error will get thrown by DTGrid1D, so just return
-		if(!proj1D.push(x1, newPair))
-		{
-			cout<<"Out-of-order insertion in D = 2: X1 = "<<x1<<" X2 = "<<x2<<endl;
-			return false;
-		}
-
-		column_insertion_started = false;
-		grid_insertion_started = true;
-	}
-	//If there is no new column, we still have to check to make sure the value is inserted
-	//in the correct order in X2:
-	else
-	{
-		if(column_insertion_started && x2 <= max_coord)
-		{
-			cout<<"Out-of-order insertion in D = 2: X1 = "<<x1<<" X2 = "<<x2<<endl;
-			return false;
-		}
-	}
-	
-
-	//run this code if we have to start a new connected component.  This happens when:
-	//(a) We insert the first value into the column
-	//(b) There is empty space between the last insertion and this one
-	if(column_insertion_started == false || x2 > (max_coord + 1))
-	{
-		//start a new connected component
-		ConnectedComponent new_conn;
-		new_conn.toValue = value.size();
-		new_conn.coordMin = x2;
-		new_conn.coordMax = x2;
-		conn.push_back(new_conn);
-		//increment the number of connected components for the column in X1
-		proj1D.back().numConn++;
-		column_insertion_started = true;
-	}
-
-	//insert the value into the grid:
-	//(a) Insert the value at the end of the coord array
-	//(b) Increment the coordMax value of the current connected component
-	//(c) Change the maximum inserted coordinate to the new value
-	value.push_back(v);
-	conn[conn.size() - 1].coordMax = x2;
-	//change max_coord to the new coordinate
-	max_coord = x2;
-	return true;
-}
-
-template<typename T>
-bool rtsDTGrid2D<T>::randomIndex(rtsDTGrid1D<IndexPair>::iterator &iter1D, int &v_i, int &c_i, int x1, int x2)
-{
-	//search along the first dimension
-	//get an iterator
-	iter1D = proj1D.randomIterator(x1);
-
-	//if the after() iterator is returned, exit
-	if(iter1D == proj1D.after())
-	{
-		c_i = conn.size();
-		v_i = value.size();
-		return false;
-	}
-
-	IndexPair i = iter1D.Value();
-
-	//if the 1D column does not exist
-	if(iter1D.X1() != x1)
-	{
-		//get the appropriate values from the 1D iterator
-		//(which points to the next valid column)
-		c_i = i.toConn;
-		v_i = conn[c_i].toValue;
-		return false;
-	}
-	
-
-	int high, low, mid;
-	low = i.toConn;
-	high = i.toConn + i.numConn - 1;
-
-	do
-	{
-		mid = low + (high - low)/2;
-		if(x2 > conn[mid].coordMax)
-			low = mid + 1;
-		else if(x2 < conn[mid].coordMin)
-			high = mid - 1;
-		else break;
-	}
-	while(low <= high);
-
-	//at this point, mid is either at the appropriate connected component,
-	//or x2 is not in the grid
-	if(x2 >= conn[mid].coordMin && x2 <= conn[mid].coordMax)
-	{
-		int offset = x2 - conn[mid].coordMin;
-		c_i = mid;
-		v_i = conn[mid].toValue + offset;
-		return true;
-	}
-	else
-	{
-		c_i = mid;
-		v_i = conn[c_i].toValue;
-		return false;
-	}
-}
-
-template<typename T>
-T rtsDTGrid2D<T>::random(int x1, int x2)
-{
-	int v_i, c_i;
-	rtsDTGrid1D<IndexPair>::iterator iter1D;
-	if(randomIndex(iter1D, v_i, c_i, x1, x2))
-		return value[v_i];
-	else
-		return background;
-}
-
-template<typename T>
-T& rtsDTGrid2D<T>::back()
-{
-	return value[value.size()-1];
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::dilate(int H)
-{
-	//if the grid is empty, return unchanged
-	if(value.size() == 0)
-		return;
-
-	ColumnUnion CUqueue;
-	CUqueue.ConnectToGrid(&conn);
-
-
-	//dilate the N-1 DT-Grid constituent
-	rtsDTGrid1D<IndexPair> dilated_proj1D = proj1D;
-	
-	//an empty pair has a number of connected components equal to zero
-	//this should not happen in reality and can therefore be used to check for new columns
-	IndexPair empty_pair;
-	empty_pair.numConn = 0;
-
-	//set the background node to the empty node and dilate the 1D projection
-	dilated_proj1D.background = empty_pair;
-	dilated_proj1D.dilate(H);
-
-	//create a new DT Grid that will replace this one
-	rtsDTGrid2D<T> new_grid;
-	new_grid.proj1D = dilated_proj1D;
-	new_grid.proj1D.background.toConn = -1;
-
-	//create iteratorDilate that iterates along the dilated N-1 grid
-	rtsDTGrid1D<IndexPair>::stencil_iterator iteratorDilate;
-	iteratorDilate.addPosition(-H);
-	iteratorDilate.addPosition(H);
-
-	//create an iterator to set the new proj1D values
-	rtsDTGrid1D<IndexPair>::iterator iteratorNew;
-
-
-	//variables for each iteration
-	IndexPair new_pair;
-	vector<ConnectedComponent>::iterator ccIterator;
-	unsigned int numValues = 0;
-	for(iteratorNew = new_grid.proj1D.begin(),
-		iteratorDilate = dilated_proj1D.begin();
-		iteratorDilate != dilated_proj1D.after();
-		iteratorNew++,
-		iteratorDilate++)
-		{
-			//cout<<"1D position: "<<iteratorNew.X1()<<endl;
-			//if a column is entering the stencil
-			if(iteratorDilate.getValue(1).numConn)
-				CUqueue.InsertColumn(iteratorDilate.getValue(1));
-			
-			//compute the union of all columns in the queue
-			vector<ConnectedComponent> result = CUqueue.ComputeUnion(H);
-
-			//compute the new IndexPair representing the column
-			new_pair.toConn = new_grid.conn.size();
-			new_pair.numConn = result.size();
-			//store the index pair
-			iteratorNew.SetValue(new_pair);
-
-			//insert each of the connected components
-			for(ccIterator = result.begin(); ccIterator!=result.end(); ccIterator++)
-			{
-				new_grid.conn.push_back(*ccIterator);
-				new_grid.conn.back().toValue = numValues;
-				numValues += (*ccIterator).coordMax - (*ccIterator).coordMin + 1;
-			}
-
-			//if a column is leaving the stencil
-			if(iteratorDilate.getValue(0).numConn)
-				CUqueue.RemoveColumn();
-		}
-
-	//allocate space for the new value array
-	new_grid.value.resize(numValues, background);
-
-	//copy the data from this grid into the new grid
-	new_grid.insert(*this);
-
-	//replace this grid with the new grid
-	conn = new_grid.conn;
-	value = new_grid.value;
-	proj1D = new_grid.proj1D;
-
-	
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::insert(rtsDTGrid2D<T> toInsert)
-{
-	//create source and destination iterators
-	rtsDTGrid2D<T>::iterator source = toInsert.begin();
-	rtsDTGrid2D<T>::iterator dest = begin();
-
-	for(source = toInsert.begin(); source != toInsert.after(); source++)
-	{
-		//move the destination iterator to the current source position
-		dest.increment_until(source.X1(), source.X2());
-		//cout<<"source: "<<source.X1()<<" "<<source.X2()<<": "<<source.Value()<<endl;
-		//cout<<"dest: "<<dest.X1()<<" "<<dest.X2()<<": "<<dest.Value()<<endl;
-		//if the position exists in dest
-		if(dest.X1() == source.X1() && dest.X2() == source.X2())
-			dest.SetValue(source.Value());
-		//cout<<"dest: "<<dest.X1()<<" "<<dest.X2()<<": "<<dest.Value()<<endl;
-	}
-
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::getBounds(int &min_x1, int &min_x2, int &max_x1, int &max_x2)
-{
-	//if the grid is empty, return an empty bounding volume
-	if(value.size() == 0)
-	{
-		min_x1 = min_x2 = max_x1 = max_x2 = 0;
-		return;
-	}
-
-	//get the min and max values for the 1D grid (x1 coordinate)
-	proj1D.getBounds(min_x1, max_x1);
-
-	//initialize the min and max values
-	min_x2 = conn[0].coordMin;
-	max_x2 = conn.back().coordMax;
-
-	//iterate through all columns finding the smallest and largest coordinate values
-	rtsDTGrid1D<IndexPair>::iterator i;
-	IndexPair col;
-	for(i=proj1D.begin(); i!=proj1D.after(); i++)
-	{
-		col = i.Value();
-		if(conn[col.toConn].coordMin < min_x2)
-			min_x2 = conn[col.toConn].coordMin;
-		if(conn[col.toConn + col.numConn - 1].coordMax > max_x2)
-			max_x2 = conn[col.toConn + col.numConn - 1].coordMax;
-	}
-		
-
-}
-template<typename T>
-void rtsDTGrid2D<T>::operator =(T rhs)
-{
-	for(int i=0; i<value.size(); i++)
-		value[i] = rhs;
-}
-
-
-template<typename T>
-void rtsDTGrid2D<T>::dumpValue()
-{
-	for(int i=0; i<value.size(); i++)
-		cout<<value[i]<<endl;
-}
-
-template<typename T>
-void rtsDTGrid2D<T>::dumpConn()
-{
-	for(int i=0; i<conn.size(); i++)
-		cout<<conn[i].toValue<<","<<conn[i].coordMin<<","<<conn[i].coordMax<<endl;
-
-
-}
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsDTGrid3D.h b/legacy/rtsDTGrid3D.h
deleted file mode 100755
index 2f559fb..0000000
--- a/legacy/rtsDTGrid3D.h
+++ /dev/null
@@ -1,1098 +0,0 @@
-#ifndef RTS_DTGRID_3D_H
-#define RTS_DTGRID_3D_H
-
-#include <vector>
-#include <iostream>
-using namespace std;
-
-#include "rtsDTGrid2D.h"
-
-struct Coord3D
-{
-	int x1;
-	int x2;
-	int x3;
-
-	bool operator==(Coord3D &rhs)
-	{
-		if( (x1 == rhs.x1) && (x2 == rhs.x2) && (x3 == rhs.x3) )
-			return true;
-		return false;
-	}
-
-	bool operator<(Coord3D &rhs)
-	{
-		if(x1 < rhs.x1)
-			return true;
-		else if( (x1 == rhs.x1) && (x2 < rhs.x2) )
-			return true;
-		else if( (x1 == rhs.x1) && (x2 == rhs.x2) && (x3 < rhs.x3) )
-			return true;
-		return false;
-
-	}
-
-};
-
-
-
-
-/**************DT GRID**************************/
-template<typename T>
-class rtsDTGrid3D
-{
-private:
-	//main arrays
-	vector<T> value;
-	vector<ConnectedComponent> conn;
-	rtsDTGrid2D<IndexPair> proj2D;
-	Coord2D current_column;
-	bool randomIndex(rtsDTGrid2D<IndexPair>::iterator &iter2D, int &v_i, int &c_i, int x1, int x2, int x3);
-
-	
-
-	//variables to keep track of insertion
-	int max_coord;
-	bool grid_insertion_started;
-	bool column_insertion_started;
-
-
-public:
-	rtsDTGrid3D<T>()
-	{
-		grid_insertion_started = false;
-		column_insertion_started = false;
-		proj2D.background.toConn = -1;
-		max_coord = 0;
-	}
-
-	bool push(int x1, int x2, int x3, T v);
-	T random(int x1, int x2, int x3);
-	T background;
-
-	
-	T& back();
-	
-	void print();
-	void operator=(T rhs);
-	void getBounds(int &min_x1, int &min_x2, int &min_x3, int &max_x1, int &max_x2, int &max_x3);
-	int getNumNodes(){return value.size();}
-	void insert(rtsDTGrid3D<T> toInsert);
-
-	//arithmetic
-	rtsDTGrid3D<T> operator+(rtsDTGrid3D<T> &rhs);
-	rtsDTGrid3D<T> operator-(rtsDTGrid3D<T> &rhs);
-
-
-	//dilation
-	friend class ColumnUnion;
-	void dilate(int H);
-
-	/*
-	
-	
-	
-
-
-	//other types of iteration
-	iterator begin_pn();
-	iterator end_pn();
-	iterator begin_np();
-	iterator end_np();
-	*/
-
-	//iterator
-	class iterator;
-	friend class iterator;
-	class stencil_iterator;
-	//iterator randomIterator(int x1, int x2);
-	iterator begin();
-	iterator before();
-	iterator end();
-	iterator after();
-
-	//other types of iteration
-	iterator begin_ppn();
-	iterator begin_nnp();
-	iterator begin_pnp();
-	iterator begin_npn();
-	iterator begin_pnn();
-	iterator begin_npp();
-
-
-	iterator end_ppn(){return begin_nnp();}
-	iterator end_nnp(){return begin_ppn();}
-	iterator end_pnp(){return begin_npn();}
-	iterator end_npn(){return begin_pnp();}
-	iterator end_pnn(){return begin_npp();}
-	iterator end_npp(){return begin_pnn();}
-};
-
-
-/**********ITERATOR***********************/
-template<typename T>
-class rtsDTGrid3D<T>::iterator
-{
-	friend class rtsDTGrid3D;
-	rtsDTGrid3D<T>* parent;
-	rtsDTGrid2D<IndexPair>::iterator loc2D;
-	int iv;
-	int ic;
-	int x3;
-
-public:
-	
-
-	T Value(){return parent->value[iv];}
-	int X1(){return loc2D.X1();}
-	int X2(){return loc2D.X2();}
-	int X3(){return x3;}
-	Coord3D Coord()
-	{
-		Coord3D result;
-		result.x1 = X1();
-		result.x2 = X2();
-		result.x3 = X3();
-		return result;
-	}
-	iterator(){parent = NULL;}
-	void SetValue(T value){parent->value[iv] = value;}
-	
-
-	void ppp()
-	{
-		//increment the value
-		iv++;
-		//if this exceeds the length of the value array, we are at the end of the grid
-		if(iv == parent->value.size())
-		{
-			(*this) = parent->after();
-			return;
-		}
-
-		//increment the current coordinate
-		x3++;
-		//if we are outside of the current connected component
-		if(x3 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is the last connected component in the column
-			if(ic == loc2D.Value().toConn + loc2D.Value().numConn)
-				loc2D++;
-			//if there are no more connected components
-			if(ic == parent->conn.size())
-			{
-				//we're at the end, return end
-				(*this) = parent->end();
-				return;
-			}
-			x3 = parent->conn[ic].coordMin;
-		}
-	}
-	void ppn()
-	{
-		//decrement the value
-		iv--;
-
-		//decrement the current coordinate
-		x3--;
-		//if we are outside of the current connected component
-		if(x3 < parent->conn[ic].coordMin)
-		{
-			//move to the previous connected component
-			ic--;
-			//if this is before the first connected component in the column
-			if(ic < loc2D.Value().toConn)
-			{
-				//increment to the next column
-				loc2D++;
-				//set the connected component to the last one in the column
-				ic = loc2D.Value().toConn + loc2D.Value().numConn - 1;
-				int num_values = parent->conn[ic].coordMax - parent->conn[ic].coordMin + 1;
-				iv = parent->conn[ic].toValue + num_values - 1;
-			}
-
-			x3 = parent->conn[ic].coordMax;
-		}
-
-
-	}
-
-	void nnp()
-	{
-		//increment the value
-		iv++;
-
-		//increment the current coordinate
-		x3++;
-		//if we are outside of the current connected component
-		if(x3 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is after the last connected component in the column
-			if(ic == loc2D.Value().toConn + loc2D.Value().numConn)
-			{
-				//decrement to the previous column
-				loc2D--;
-				//set the connected component to the first one in the column
-				ic = loc2D.Value().toConn;
-				iv = parent->conn[ic].toValue;
-			}
-
-			x3 = parent->conn[ic].coordMin;
-		}
-
-
-	}
-
-	
-	void nnn()
-	{
-		//decrement the value
-		iv--;
-		//if this is less than 0, we are at the beginning of the grid
-		if(iv < 0)
-		{
-			(*this) = parent->before();
-			return;
-		}
-
-		//decrement the current coordinate
-		x3--;
-		//if we are outside of the current connected component
-		if(x3 < parent->conn[ic].coordMin)
-		{
-			//move to the previous connected component
-			ic--;
-			//if this is the first connected component in the column
-			if(ic < loc2D.Value().toConn)
-				loc2D--;
-			//if there are no more connected components
-			if(ic < 0)
-			{
-				//we're at the beginning, return begin
-				(*this) = parent->before();
-				return;
-			}
-			x3 = parent->conn[ic].coordMax;
-		}
-
-	}
-
-	void pnp()
-	{
-		//increment the value
-		iv++;
-
-		//increment the current coordinate
-		x3++;
-		//if we are outside of the current connected component
-		if(x3 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is after the last connected component in the column
-			if(ic == loc2D.Value().toConn + loc2D.Value().numConn)
-			{
-				//decrement to the previous column
-				loc2D.pn();
-				//set the connected component to the first one in the column
-				ic = loc2D.Value().toConn;
-				iv = parent->conn[ic].toValue;
-			}
-
-			x3 = parent->conn[ic].coordMin;
-		}
-
-
-	}
-	void npn()
-	{
-		//decrement the value
-		iv--;
-
-		//decrement the current coordinate
-		x3--;
-		//if we are outside of the current connected component
-		if(x3 < parent->conn[ic].coordMin)
-		{
-			//move to the previous connected component
-			ic--;
-			//if this is before the first connected component in the column
-			if(ic < loc2D.Value().toConn)
-			{
-				//increment to the next column
-				loc2D.np();
-				//set the connected component to the last one in the column
-				ic = loc2D.Value().toConn + loc2D.Value().numConn - 1;
-				int num_values = parent->conn[ic].coordMax - parent->conn[ic].coordMin + 1;
-				iv = parent->conn[ic].toValue + num_values - 1;
-			}
-
-			x3 = parent->conn[ic].coordMax;
-		}
-
-
-	}
-	void pnn()
-	{
-		//decrement the value
-		iv--;
-
-		//decrement the current coordinate
-		x3--;
-		//if we are outside of the current connected component
-		if(x3 < parent->conn[ic].coordMin)
-		{
-			//move to the previous connected component
-			ic--;
-			//if this is before the first connected component in the column
-			if(ic < loc2D.Value().toConn)
-			{
-				//increment to the next column
-				loc2D.pn();
-				//set the connected component to the last one in the column
-				ic = loc2D.Value().toConn + loc2D.Value().numConn - 1;
-				int num_values = parent->conn[ic].coordMax - parent->conn[ic].coordMin + 1;
-				iv = parent->conn[ic].toValue + num_values - 1;
-			}
-
-			x3 = parent->conn[ic].coordMax;
-		}
-
-
-	}
-	void npp()
-	{
-		//increment the value
-		iv++;
-
-		//increment the current coordinate
-		x3++;
-		//if we are outside of the current connected component
-		if(x3 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is after the last connected component in the column
-			if(ic == loc2D.Value().toConn + loc2D.Value().numConn)
-			{
-				//decrement to the previous column
-				loc2D.np();
-				//set the connected component to the first one in the column
-				ic = loc2D.Value().toConn;
-				iv = parent->conn[ic].toValue;
-			}
-
-			x3 = parent->conn[ic].coordMin;
-		}
-
-
-	}
-
-	/*
-	void pn()
-	{
-		//for the most part we will be going backwards through the array
-		//so first decrement iv
-		iv--;
-		x2--;
-		//if iv is less than the current connected component
-		if(iv < parent->conn[ic].toValue)
-		{
-			//go to the previous connected component
-			ic--;
-			//if we are before the first connected component in the column
-			if(ic < loc1D.Value().toConn)
-			{
-				//increment the 1D iterator
-				loc1D++;
-				//reset ic to the last component of the new column
-				ic = loc1D.Value().toConn + loc1D.Value().numConn - 1;
-				//find the new value identifier
-				iv = parent->conn[ic].toValue + (parent->conn[ic].coordMax - parent->conn[ic].coordMin);
-			}
-			//compute the currect coordinate
-			x2 = parent->conn[ic].coordMax;
-		}
-	}
-
-	void np()
-	{
-		//for the most part we will be going forward through the grid
-		//increment iv
-		iv++;
-		x2++;
-		
-		//if we are outside of the current connected component
-		if(x2 > parent->conn[ic].coordMax)
-		{
-			//move to the next connected component
-			ic++;
-			//if this is the last connected component in the column
-			if(ic == loc1D.Value().toConn + loc1D.Value().numConn)
-			{
-				loc1D--;
-				ic = loc1D.Value().toConn;
-				iv = parent->conn[ic].toValue;
-			}
-
-			x2 = parent->conn[ic].coordMin;
-		}
-
-	}
-	
-
-	
-
-	friend bool operator<(iterator &left, iterator &right)
-	{
-		if(left.iv < right.iv)
-			return true;
-		return false;
-	}
-	friend bool operator<=(iterator &left, iterator &right)
-	{
-		if(left.iv <= right.iv)
-			return true;
-		return false;
-	}
-	
-	*/
-	
-	void increment_until(int p1, int p2, int p3)
-	{
-		while((*this) != parent->end())
-		{
-			if(X1() > p1)
-				return;
-			if(X1() == p1 && X2() > p2)
-				return;
-			else if(X1() == p1 && X2() == p2 && X3() >= p3)
-				return;
-
-			ppp();
-		}
-	}
-	void operator++(){ppp();}
-	void operator--(){nnn();}
-
-	//boolean operators for comparing iterators
-	bool operator==(iterator &rhs)
-	{
-		if(parent == rhs.parent && iv == rhs.iv)
-			return true;
-	
-		//if(loc2D == rhs.loc2D && x3 == rhs.x3)
-		//	return true;
-		return false;
-	}
-	bool operator!=(iterator &rhs){return !((*this) == rhs);}
-	bool operator<(iterator rhs)
-	{
-		if(parent == rhs.parent && iv < rhs.iv)
-			return true;
-		//if(loc2D < rhs.loc2D && x3 < rhs.x3)
-		//	return true;
-		return false;
-
-	}
-};
-
-/**************ITERATOR METHODS IN DT GRID*******************/
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::begin()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = 0;
-	result.x3 = conn[0].coordMin;
-	result.loc2D = proj2D.begin();
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::end()
-{
-	//if the grid is empty, return after()
-	if(value.size() == 0)
-		return after();
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size() - 1;
-	result.x3 = conn[result.ic].coordMax;
-	result.loc2D = proj2D.end();
-	return result;
-}
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::after()
-{
-	iterator result;
-	result.parent = this;
-	result.ic = conn.size() - 1;
-	result.iv = value.size();
-	//result.x2 = conn[result.ic].coordMax;
-	result.loc2D = proj2D.after();
-	return result;
-}
-
-
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::before()
-{
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.ic = 0;
-	result.iv = -1;
-	//result.x2 = conn[0].coordMin;
-	result.loc2D = proj2D.before();
-
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::begin_ppn()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.loc2D = proj2D.begin();
-	//find the index of the last connected component in the first column
-	int last_conn = result.loc2D.Value().toConn + result.loc2D.Value().numConn - 1;
-	result.ic = last_conn;
-	result.iv = conn[last_conn].toValue + conn[last_conn].coordMax - conn[last_conn].coordMin;
-	result.x3 = conn[last_conn].coordMax;
-	
-
-	return result;
-}
-
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::begin_nnp()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.loc2D = proj2D.end();
-	//find the index of the first connected component in the last column
-	int first_conn = result.loc2D.Value().toConn;
-	result.ic = first_conn;
-	result.iv = conn[first_conn].toValue;
-	result.x3 = conn[first_conn].coordMin;
-	
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::begin_pnp()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.loc2D = proj2D.begin_pn();
-	//find the index of the first connected component in the column
-	int first_conn = result.loc2D.Value().toConn;
-	result.ic = first_conn;
-	result.iv = conn[first_conn].toValue;
-	result.x3 = conn[first_conn].coordMin;
-	
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::begin_npn()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.loc2D = proj2D.begin_np();
-	//find the index of the last connected component in the column
-	int last_conn = result.loc2D.Value().toConn + result.loc2D.Value().numConn - 1;
-	result.ic = last_conn;
-	result.iv = conn[last_conn].toValue + conn[last_conn].coordMax - conn[last_conn].coordMin;
-	result.x3 = conn[last_conn].coordMax;
-	
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::begin_pnn()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.loc2D = proj2D.begin_pn();
-	//find the index of the last connected component in the column
-	int last_conn = result.loc2D.Value().toConn + result.loc2D.Value().numConn - 1;
-	result.ic = last_conn;
-	result.iv = conn[last_conn].toValue + conn[last_conn].coordMax - conn[last_conn].coordMin;
-	result.x3 = conn[last_conn].coordMax;
-	
-
-	return result;
-}
-template<typename T>
-typename rtsDTGrid3D<T>::iterator rtsDTGrid3D<T>::begin_npp()
-{
-	//if the grid is empty, return an iterator to "after"
-	if(value.size() == 0)
-		return after();
-
-	iterator result;
-	result.parent = this;
-	result.loc2D = proj2D.begin_np();
-	//find the index of the first connected component in the column
-	int first_conn = result.loc2D.Value().toConn;
-	result.ic = first_conn;
-	result.iv = conn[first_conn].toValue;
-	result.x3 = conn[first_conn].coordMin;
-	
-
-	return result;
-}
-/**************DT GRID METHODS**************************/
-template<typename T>
-bool rtsDTGrid3D<T>::push(int x1, int x2, int x3, T v)
-{
-	//run this code if we have to start a new column.  This happens when:
-	//(a) we have just inserted the first value into the grid
-	//(b) the insertion takes place in a different column
-	if(grid_insertion_started == false || x1 != current_column.x1 || x2 != current_column.x2)
-	{
-		//assume that a new column is being created
-		//create the column in proj1D
-		IndexPair newPair;
-		newPair.toConn = conn.size();
-		//newPair.toValue = value.size();
-		newPair.numConn = 0;
-
-		//if this insertion throws an error, the value was inserted incorrectly
-		//the error will get thrown by DTGrid2D, so just return
-		if(!proj2D.push(x1, x2, newPair))
-		{
-			cout<<"Out-of-order insertion in D = 3: X1 = "<<x1<<" X2 = "<<x2<<" X3 = "<<x3<<endl;
-			return false;
-		}
-
-		column_insertion_started = false;
-		grid_insertion_started = true;
-	}
-	//If there is no new column, we still have to check to make sure the value is inserted
-	//in the correct order in X3:
-	else
-	{
-		if(column_insertion_started && x3 <= max_coord)
-		{
-			cout<<"Out-of-order insertion in D = 3: X1 = "<<x1<<" X2 = "<<x2<<" X3 = "<<x3<<endl;
-			return false;
-		}
-	}
-	
-
-	//run this code if we have to start a new connected component.  This happens when:
-	//(a) We insert the first value into the column
-	//(b) There is empty space between the last insertion and this one
-	if(column_insertion_started == false || x3 > (max_coord + 1))
-	{
-		//start a new connected component
-		ConnectedComponent new_conn;
-		new_conn.toValue = value.size();
-		new_conn.coordMin = x3;
-		new_conn.coordMax = x3;
-		conn.push_back(new_conn);
-		//increment the number of connected components for the column in X1
-		proj2D.back().numConn++;
-		column_insertion_started = true;
-	}
-
-	//insert the value into the grid:
-	//(a) Insert the value at the end of the coord array
-	//(b) Increment the coordMax value of the current connected component
-	//(c) Change the maximum inserted coordinate to the new value
-	value.push_back(v);
-	conn[conn.size() - 1].coordMax = x3;
-	//change max_coord to the new coordinate
-	max_coord = x3;
-	//set the current column
-	current_column.x1 = x1;
-	current_column.x2 = x2;
-	return true;
-}
-
-
-template<typename T>
-bool rtsDTGrid3D<T>::randomIndex(rtsDTGrid2D<IndexPair>::iterator &iter2D, int &v_i, int &c_i, int x1, int x2, int x3)
-{
-	//search along the 2nd dimension
-	//get an iterator
-	iter2D = proj2D.randomIterator(x1, x2);
-
-	//if the after() iterator is returned, exit
-	if(iter2D == proj2D.after())
-	{
-		c_i = conn.size();
-		v_i = value.size();
-		return false;
-	}
-
-	IndexPair i = iter2D.Value();
-
-	//if the column does not exist
-	if(iter2D.X1() != x1 || iter2D.X2() != x2)
-	{
-		//get the appropriate values from the 2D iterator
-		//(which points to the next valid column)
-		c_i = i.toConn;
-		v_i = conn[c_i].toValue;
-		return false;
-	}
-	
-	//otherwise perform the binary search within the column
-	int high, low, mid;
-	low = i.toConn;
-	high = i.toConn + i.numConn - 1;
-
-	do
-	{
-		mid = low + (high - low)/2;
-		if(x3 > conn[mid].coordMax)
-			low = mid + 1;
-		else if(x3 < conn[mid].coordMin)
-			high = mid - 1;
-		else break;
-	}
-	while(low <= high);
-
-	//at this point, mid is either at the appropriate connected component,
-	//or x2 is not in the grid
-	if(x3 >= conn[mid].coordMin && x3 <= conn[mid].coordMax)
-	{
-		int offset = x3 - conn[mid].coordMin;
-		c_i = mid;
-		v_i = conn[mid].toValue + offset;
-		return true;
-	}
-	else
-	{
-		c_i = mid;
-		v_i = conn[c_i].toValue;
-		return false;
-	}
-}
-
-template<typename T>
-T rtsDTGrid3D<T>::random(int x1, int x2, int x3)
-{
-	int v_i, c_i;
-	rtsDTGrid2D<IndexPair>::iterator iter2D;
-	if(randomIndex(iter2D, v_i, c_i, x1, x2, x3))
-		return value[v_i];
-	else
-		return background;
-}
-
-
-
-template<typename T>
-T& rtsDTGrid3D<T>::back()
-{
-	return value[value.size()-1];
-}
-template<typename T>
-void rtsDTGrid3D<T>::print()
-{
-	rtsDTGrid3D<T>::iterator i;
-	for(i = begin(); i != after(); i++)
-	{
-		cout<<i.X1()<<","<<i.X2()<<","<<i.X3()<<":"<<i.Value()<<endl;
-	}
-	
-
-}
-template<typename T>
-void rtsDTGrid3D<T>::operator =(T rhs)
-{
-	for(int i=0; i<value.size(); i++)
-		value[i] = rhs;
-}
-
-template<typename T>
-void rtsDTGrid3D<T>::getBounds(int &min_x1, int &min_x2, int &min_x3, int &max_x1, int &max_x2, int &max_x3)
-{
-	//if the grid is empty, return an empty bounding volume
-	if(value.size() == 0)
-	{
-		min_x1 = min_x2 = min_x3 = max_x1 = max_x2 = max_x3 = 0;
-		return;
-	}
-
-	//get the min and max values for the 1D grid (x1 coordinate)
-	proj2D.getBounds(min_x1, min_x2, max_x1, max_x2);
-
-	//initialize the min and max values
-	min_x3 = conn[0].coordMin;
-	max_x3 = conn.back().coordMax;
-
-	//iterate through all columns finding the smallest and largest coordinate values
-	rtsDTGrid2D<IndexPair>::iterator i;
-	IndexPair col;
-	for(i=proj2D.begin(); i!=proj2D.after(); i++)
-	{
-		col = i.Value();
-		if(conn[col.toConn].coordMin < min_x3)
-			min_x3 = conn[col.toConn].coordMin;
-		if(conn[col.toConn + col.numConn - 1].coordMax > max_x3)
-			max_x3 = conn[col.toConn + col.numConn - 1].coordMax;
-	}
-		
-
-}
-template<typename T>
-void rtsDTGrid3D<T>::insert(rtsDTGrid3D<T> toInsert)
-{
-	//create source and destination iterators
-	rtsDTGrid3D<T>::iterator source = toInsert.begin();
-	rtsDTGrid3D<T>::iterator dest = begin();
-
-	for(source = toInsert.begin(); source != toInsert.after(); source++)
-	{
-		//move the destination iterator to the current source position
-		dest.increment_until(source.X1(), source.X2(), source.X3());
-		//cout<<"source: "<<source.X1()<<" "<<source.X2()<<": "<<source.Value()<<endl;
-		//cout<<"dest: "<<dest.X1()<<" "<<dest.X2()<<": "<<dest.Value()<<endl;
-		//if the position exists in dest
-		if(dest.X1() == source.X1() && dest.X2() == source.X2() && dest.X3() == source.X3())
-			dest.SetValue(source.Value());
-		//cout<<"dest: "<<dest.X1()<<" "<<dest.X2()<<": "<<dest.Value()<<endl;
-	}
-
-}
-
-template<typename T>
-void rtsDTGrid3D<T>::dilate(int H)
-{
-	//if the grid is empty, return unchanged
-	if(value.size() == 0)
-		return;
-
-	ColumnUnion CUqueue;
-	CUqueue.ConnectToGrid(&conn);
-
-
-	//dilate the N-1 DT-Grid constituent
-	rtsDTGrid2D<IndexPair> dilated_proj2D = proj2D;
-	
-	//an empty pair has a number of connected components equal to zero
-	//this should not happen in reality and can therefore be used to check for new columns
-	IndexPair empty_pair;
-	empty_pair.numConn = 0;
-
-	//set the background node to the empty node and dilate the 2D projection
-	dilated_proj2D.background = empty_pair;
-	dilated_proj2D.dilate(H);
-
-	//create a new DT Grid that will replace this one
-	rtsDTGrid3D<T> new_grid;
-	new_grid.proj2D = dilated_proj2D;
-	new_grid.proj2D.background.toConn = -1;
-
-	//create iteratorDilate that iterates along the dilated N-1 grid
-	rtsDTGrid2D<IndexPair>::stencil_iterator iteratorDilate;
-	
-	//create the template entrance nodes
-	int n;
-	for(n=-H; n<=H; n++)
-		iteratorDilate.addPosition(n, H);
-	//create the template exit nodes
-	for(n=-H; n<=H; n++)
-		iteratorDilate.addPosition(n, -H);
-	
-	//create an iterator to set the new proj2D values
-	rtsDTGrid2D<IndexPair>::iterator iteratorNew;
-
-
-	//variables for each iteration
-	IndexPair new_pair;
-	vector<ConnectedComponent>::iterator ccIterator;
-	unsigned int numValues = 0;
-	for(iteratorNew = new_grid.proj2D.begin(),
-		iteratorDilate = dilated_proj2D.begin();
-		iteratorDilate != dilated_proj2D.after();
-		iteratorNew++,
-		iteratorDilate++)
-		{
-			//if a column is entering the stencil
-			for(n=0; n<=(2*H); n++)
-				if(iteratorDilate.getValue(n).numConn)
-					CUqueue.InsertColumn(iteratorDilate.getValue(n));
-			
-			//compute the union of all columns in the queue
-			vector<ConnectedComponent> result = CUqueue.ComputeUnion(H);
-
-			//compute the new IndexPair representing the column
-			new_pair.toConn = new_grid.conn.size();
-			new_pair.numConn = result.size();
-			//store the index pair
-			iteratorNew.SetValue(new_pair);
-
-			//insert each of the connected components
-			for(ccIterator = result.begin(); ccIterator!=result.end(); ccIterator++)
-			{
-				new_grid.conn.push_back(*ccIterator);
-				new_grid.conn.back().toValue = numValues;
-				numValues += (*ccIterator).coordMax - (*ccIterator).coordMin + 1;
-			}
-
-			//if a column is leaving the stencil
-			for(n=(2*H + 1); n<=(4*H + 1); n++)
-				if(iteratorDilate.getValue(n).numConn)
-					CUqueue.RemoveColumn();
-		}
-
-	//allocate space for the new value array
-	new_grid.value.resize(numValues, background);
-
-	//copy the data from this grid into the new grid
-	new_grid.insert(*this);
-
-	//replace this grid with the new grid
-	conn = new_grid.conn;
-	value = new_grid.value;
-	proj2D = new_grid.proj2D;
-
-	
-}
-
-
-
-/***************ARITHMETIC********************************/
-template<typename T>
-rtsDTGrid3D<T> rtsDTGrid3D<T>::operator+(rtsDTGrid3D<T> &rhs)
-{
-	rtsDTGrid3D<T> result;
-
-	//create an iterator for each DT Grid
-	rtsDTGrid3D<T>::iterator left = begin();
-	rtsDTGrid3D<T>::iterator right = rhs.begin();
-
-	//iterate both until one iterator has hit after()
-	while(left != after() && right != rhs.after())
-	{
-		//if the iterators are at the same coordinate
-		if(left.Coord() == right.Coord())
-		{
-			//insert their sum into the new grid
-			result.push(left.X1(), left.X2(), left.X3(), left.Value() + right.Value());
-			//increment both
-			left++; right++;
-		}
-		//add the lowest (lexicographically) value to the background, insert the result, and increment
-		else if( (left.Coord() < right.Coord()) )
-		{
-			result.push(left.X1(), left.X2(), left.X3(), left.Value() + rhs.background);
-			left++;
-		}
-		else if( (right.Coord() < left.Coord()) )
-		{
-			result.push(right.X1(), right.X2(), right.X3(), right.Value() + background);
-			right++;
-		}
-	}
-
-	//if the left iterator hasn't finished, iterate to finish it off
-	while(left != after())
-	{
-		result.push(left.X1(), left.X2(), left.X3(), left.Value() + rhs.background);
-		left++;
-	}
-
-	while(right != rhs.after())
-	{
-		result.push(right.X1(), right.X2(), right.X3(), right.Value() + rhs.background);
-		right++;
-	}
-
-
-	return result;
-
-
-}
-
-template<typename T>
-rtsDTGrid3D<T> rtsDTGrid3D<T>::operator-(rtsDTGrid3D<T> &rhs)
-{
-	rtsDTGrid3D<T> result;
-
-	//create an iterator for each DT Grid
-	rtsDTGrid3D<T>::iterator left = begin();
-	rtsDTGrid3D<T>::iterator right = rhs.begin();
-
-	//iterate both until one iterator has hit after()
-	while(left != after() && right != rhs.after())
-	{
-		//if the iterators are at the same coordinate
-		if(left.Coord() == right.Coord())
-		{
-			//insert their sum into the new grid
-			result.push(left.X1(), left.X2(), left.X3(), left.Value() - right.Value());
-			//increment both
-			left++; right++;
-		}
-		//add the lowest (lexicographically) value to the background, insert the result, and increment
-		else if( (left.Coord() < right.Coord()) )
-		{
-			result.push(left.X1(), left.X2(), left.X3(), left.Value() - rhs.background);
-			left++;
-		}
-		else if( (right.Coord() < left.Coord()) )
-		{
-			result.push(right.X1(), right.X2(), right.X3(), background - right.Value());
-			right++;
-		}
-	}
-
-	//if the left iterator hasn't finished, iterate to finish it off
-	while(left != after())
-	{
-		result.push(left.X1(), left.X2(), left.X3(), left.Value() - rhs.background);
-		left++;
-	}
-
-	while(right != rhs.after())
-	{
-		result.push(right.X1(), right.X2(), right.X3(), background - right.Value());
-		right++;
-	}
-
-
-	return result;
-
-
-}
-#endif
diff --git a/legacy/rtsFilamentNetwork.cpp b/legacy/rtsFilamentNetwork.cpp
deleted file mode 100755
index 0806f8e..0000000
--- a/legacy/rtsFilamentNetwork.cpp
+++ /dev/null
@@ -1,92 +0,0 @@
-#include "rtsFilamentNetwork.h"
-
-int rtsFilamentNetwork::LoadFIB(const char* filename)
-{
-	 return fib_load(filename);
-}
-
-int rtsFilamentNetwork::fib_load(const char* filename)
-{
-	//open the input file
-	ifstream infile;
-	infile.open(filename);
-	if(!infile) return 0;
-
-	//temporary vector storing points
-	vector<point3D<float>> vertices;
-	vector<float> radii;
-	point3D<float> input;
-	point3D<float> max(0.0, 0.0, 0.0);	//maximum extents of the points in the file
-
-	float r;
-
-	int i,j;
-	//get all of the nodes from the file
-	int num_nodes;
-	infile>>num_nodes;	
-	int id;
-	for(i=0; i<num_nodes; i++)
-	{
-		infile>>id;
-		infile>>input.x;  infile>>input.y;  infile>>input.z;  infile>>r;
-
-		//update the maximum
-		if(input.x > max.x) max.x = input.x;
-		if(input.y > max.y) max.y = input.y;
-		if(input.z > max.z) max.z = input.z;
-
-		vertices.push_back(input);
-		radii.push_back(r);
-	}
-
-	/*Scale the node values based on the maximum value.  I do this so that
-	every node is between 0 - 1 rather than the original scale.  In the long run,
-	it should make rendering easier.
-	*/
-	for(i=0; i<num_nodes; i++)
-	{
-		vertices[i].x = vertices[i].x/max.x;
-		vertices[i].y = vertices[i].y/max.y;
-		vertices[i].z = vertices[i].z/max.z;
-
-		vertices.push_back(input);
-		radii.push_back(r);
-	}
-
-	//get each fiber
-	int num_filaments;
-	int num_edges;
-	infile>>num_filaments;
-
-	for(i=0; i<num_filaments; i++)
-	{
-		network->objBegin(OBJ_LINE_STRIP);	//begin the filament
-		infile>>num_edges;
-		for(j = 1; j<num_edges; j++)	//get the index of each edge
-		{
-			infile>>id; id--;
-			network->objVertex3f(vertices[id].x, vertices[id].y, vertices[id].z);
-			//this final read is required because of redundancy in the input file
-			infile>>id;
-		}
-		infile>>id;		//this final read is also required due to redundancy in the input file
-		id--;
-		network->objVertex3f(vertices[id].x, vertices[id].y, vertices[id].z);
-		infile>>id;
-		id--;
-		network->objVertex3f(vertices[id].x, vertices[id].y, vertices[id].z);
-		network->objEnd();
-	}
-	return 1;
-}
-
-void rtsFilamentNetwork::PrintProperties()
-{
-
-	cout<<"Number of Filaments: "<<network->getNumLines();
-}
-
-void rtsFilamentNetwork::PrintNetwork()
-{
-
-}
\ No newline at end of file
diff --git a/legacy/rtsFilamentNetwork.h b/legacy/rtsFilamentNetwork.h
deleted file mode 100755
index f9a3144..0000000
--- a/legacy/rtsFilamentNetwork.h
+++ /dev/null
@@ -1,35 +0,0 @@
-#ifndef RTSFILAMENTNETWORK_H
-#define RTSFILAMENTNETWORK_H
-
-#include "rtsLinearAlgebra.h"
-#include "objJedi.h"
-#include <vector>
-#include <fstream>
-
-using namespace std;
-
-
-class rtsFilamentNetwork
-{
-protected:
-	rtsOBJ* network;
-	int fib_load(const char* filename);
-
-public:
-	rtsFilamentNetwork(){network = new rtsOBJ();}
-
-	virtual int LoadFIB(const char* filename);
-	void PrintProperties();
-	void PrintNetwork();
-
-};
-	
-
-
-#endif
-
-		
-
-
-
-	
\ No newline at end of file
diff --git a/legacy/rtsFilename.h b/legacy/rtsFilename.h
deleted file mode 100755
index 414bbca..0000000
--- a/legacy/rtsFilename.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#include <string>
-
-using namespace std;
-
-#ifndef RTS_FILENAME_H
-#define RTS_FILENAME_H
-
-class rtsFilename
-{
-private:
-	string filename;
-
-public:
-	string getFilename()
-	{
-		int pos = filename.find_last_of("/\\");
-		string name = filename.substr(pos+1, filename.size());
-		return name;
-	}
-
-	rtsFilename& operator=(const string str)
-	{
-		filename = str;
-		return *this;
-	}
-	rtsFilename(const string str){filename = str;}
-	rtsFilename(){filename = "";}
-
-	string getExtension()
-	{
-		int pos = filename.find_last_of(".");
-		string ext = filename.substr(pos+1, filename.size() - pos);
-		return ext;
-	}
-
-	string getDirectory()
-	{
-		int pos = filename.find_last_of("/\\");
-		string directory;
-		if(pos != -1)
-			directory = filename.substr(0, pos);
-		else
-			directory = "";
-		return directory;
-	}
-
-	string getPrefix()
-	{
-		int slash = filename.find_last_of("/\\");
-		int dot = filename.find_last_of(".");
-
-		string prefix;
-		prefix = filename.substr(slash+1, dot - slash - 1);
-		return prefix;
-
-	}
-
-	string getString()
-	{
-		return filename;
-	}
-
-
-
-};
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsFunction3D.h b/legacy/rtsFunction3D.h
deleted file mode 100755
index 3711979..0000000
--- a/legacy/rtsFunction3D.h
+++ /dev/null
@@ -1,913 +0,0 @@
-#ifndef RTSFUNCTION3D_H
-#define RTSFUNCTION3D_H
-
-#define DIST_MAX	255
-
-#include "rtsLinearAlgebra.h"
-//#include "rtsDTGrid3D.h"
-#include <fstream>
-//#include <iostream>
-//#include <math.h>
-//#include <queue>
-//#include <algorithm>
-using namespace std;
-
-typedef int indextype;
-
-///This class represents a 3D implicit function as a grid.  It provides methods for accessing values, interpolation, and several utilities.
-
-template <class T> class rtsFunction3D
-{
-private:
-	//pointer to store the data
-	T* m_data;
-	//resolution of the data (x, y, z) dimensional extents
-	vector3D<indextype> m_resolution;
-	T m_boundary;			//boundary condition
-	point3D<double> m_domain_min;	//min and max range values (used for parametric access)
-	point3D<double> m_domain_max;
-	vector3D<double> m_voxel_size;
-	
-	//bit-blit function copies 3D data quickly from source to dest
-	void blit3D(const T* source,
-				   indextype s_px, indextype s_py, indextype s_pz,
-				   indextype s_sx, indextype s_sy, indextype s_sz,
-				   T* dest,
-				   indextype d_px, indextype d_py, indextype d_pz,
-				   indextype d_sx, indextype d_sy, indextype d_sz,
-				   indextype blit_size_x, indextype blit_size_y, indextype blit_size_z);
-
-	void shallow_copy(const rtsFunction3D<T> source, rtsFunction3D<T> &dest);
-	inline point3D<double> getParameter(indextype i);
-	void initialize_empty(indextype res_x, indextype res_y, indextype res_z);
-
-public:
-	//construct an implicit function with a size of 1
-	rtsFunction3D();			///<Create an empty implicit function
-	//construct an implicit function of the specified resolution
-	rtsFunction3D(indextype res_x, indextype res_y, indextype res_z);	///<Create an implicit function with the specified resolution
-	//construct an implicit function from sample data and a specified size
-	rtsFunction3D(T* data, indextype res_x, indextype res_y, indextype res_z);	///<Create an implicit function from previous data at the specified resolution
-	//shallow-copy constructor, defines all shallow variables
-	rtsFunction3D(vector3D<int> resolution, T boundary, point3D<double> min_domain, point3D<double> max_domain);
-	//full copy constructor, defines all variables
-	rtsFunction3D(T* data, vector3D<int> resolution, T boundary, point3D<double> min_domain, point3D<double> max_domain);
-	rtsFunction3D(const rtsFunction3D<T> &original);	//copy constructor
-	~rtsFunction3D();		//destructor
-	void Init(indextype res_x, indextype res_y, indextype res_z);
-
-	//overloaded operators
-	rtsFunction3D<T>& operator=(const rtsFunction3D<T>& original);		///<Overloaded operator creates a copy of an implicit function
-	rtsFunction3D<T>& operator=(const T constant);						///<Overloaded operator sets all points in an implicit function to the given constant value
-	inline T& operator()(indextype x, indextype y, indextype z);		///<Allows access to the sample point indexed by x, y, and z using the parenthesis operator
-	inline T operator()(double i, double j, double k);					///<Allows access to the implicit function (based on the domain boundaries) at the position (i, j, k).  This class uses linear interpolation.
-	rtsFunction3D<T>& operator*=(const T constant);						///<Multiplies the values at all sample points by a constant.
-	rtsFunction3D<T>& operator+=(const T constant);						///<Adds a constant to the values at all sample points.
-	rtsFunction3D<T>& operator-=(const T constant);						///<Subtracts a constant from the values at all sample points.
-	rtsFunction3D<T>& operator/=(const T constant);						///<Divides all values by a constant.
-	const rtsFunction3D<T> operator+(const T constant);					///<Adds a constant to an implicit function and returns a new function.
-	const rtsFunction3D<T> operator-(const T constant);					///<Subtracts a constant from an implicit function and returns a new function.
-	const rtsFunction3D<T> operator*(const T constant);					///<Multiplies an implicit function by a constant and returns a new function.
-	const rtsFunction3D<T> operator/(const T constant);					///<Divides an implicit function by a constant and returns a new function.
-
-	//casting operator
-	//template <class U> friend class rtsFunction3D<U>;
-	template <class U> operator rtsFunction3D<U>();						///<Casts between data types.
-
-	//friend classes for overloading "backwards" operations (like 3*function)
-	friend rtsFunction3D<T> operator*(const T lhs, rtsFunction3D<T> rhs){return rhs*lhs;}	///<Allows associative multiplication.
-	friend rtsFunction3D<T> operator+(const T lhs, rtsFunction3D<T> rhs){return rhs+lhs;}	///<Allows associative addition.
-	friend rtsFunction3D<T> operator-(const T lhs, rtsFunction3D<T> rhs)					///<Allows associative subtraction.
-	{
-		rtsFunction3D<T> result;
-		rhs.shallow_copy(rhs, result);	//make a copy of all of the shallow variables and allocate memory
-		indextype size = rhs.m_resolution.x * rhs.m_resolution.y * rhs.m_resolution.z;
-		//iterate and subtract
-		for(indextype i=0; i<size; i++)
-			result.m_data[i] = lhs - rhs.m_data[i];
-
-		return result;
-	}
-	//friend rtsFunction3D<T> operator/(const T lhs, rtsFunction3D<T> rhs);
-
-	//loading/saving data to disk
-	void LoadRAW(indextype header_size, indextype data_x, indextype data_y, indextype data_z, const char* filename);	///<Loads RAW data from a file with the specified header size and data size.
-	void SaveRAW(const char* filename);							///<Save the data as RAW data to disk.
-	void LoadVOL(const char* filename);							///<Load a VOL file from disk.
-	void SaveVOL(const char* filename);							///<Save a VOL file to disk.
-
-	rtsFunction3D<T> Project2D();			//<Projects the data along the z-axis using a maximum-intensity projection.
-
-	//data access methods
-	inline T& xyz(indextype x, indextype y, indextype z);
-	inline T ijk(double i, double j, double k);
-	void Parameterize(double x_min, double x_max, double y_min, double y_max, double z_min, double z_max);
-	void setBoundary(T boundary){m_boundary = boundary;}
-	T getBoundary(){return m_boundary;}
-	T* GetBits();
-	indextype DimX(){return m_resolution.x;}
-	indextype DimY(){return m_resolution.y;}
-	indextype DimZ(){return m_resolution.z;}
-	inline point3D<double> getParameter(indextype x, indextype y, indextype z);
-	inline point3D<indextype> getNearestIndex(double i, double j, double k);
-	inline point3D<double> getFractionalIndex(double i, double j, double k);
-	inline point3D<indextype> getNearestIndex(indextype i);
-	point3D<double> getMinDomain(){return m_domain_min;}
-	point3D<double> getMaxDomain(){return m_domain_max;}
-
-	//data input methods
-	void Insert(rtsFunction3D<T>* source, indextype x, indextype y, indextype z);
-
-	//data massaging
-	
-	void Scale(T min, T max);
-	void Crop(indextype x, indextype y, indextype z, indextype size_x, indextype size_y, indextype size_z);
-	void Binary(T threshold, T true_value);		///<Turns the image into a binary image based on a threshold value T.  All values below T are set to 0, all values above are set to true_value.
-	void Threshold(T min, T value);
-	void Threshold(T min, T max, T value);
-	void Threshold(T min, T max, T inside, T outside);
-	void ClampMax(T max);		///<Clamps the function to the given maximum value.
-	void ClampMin(T min);
-	T getMin();
-	T getMax();
-
-	//create new data
-	rtsFunction3D<T>* Resample(indextype newres_x, indextype newres_y, indextype newres_z);
-
-	//output functions
-	void toConsole();
-
-};
-
-template <class T>
-void rtsFunction3D<T>::blit3D(const T* source,
-				   indextype s_px, indextype s_py, indextype s_pz,
-				   indextype s_sx, indextype s_sy, indextype s_sz,
-				   T* dest,
-				   indextype d_px, indextype d_py, indextype d_pz,
-				   indextype d_sx, indextype d_sy, indextype d_sz,
-				   indextype blit_size_x, indextype blit_size_y, indextype blit_size_z)
-{
-	indextype ps, pd;		//stores the mapping for the source point to the dest point
-	//find the maximum points that can be blit to (in case source overlaps the edges of dest)
-	blit_size_x = min(blit_size_x, min(s_sx - s_px, d_sx - d_px));
-	blit_size_y = min(blit_size_y, min(s_sy - s_py, d_sy - d_py));
-	blit_size_z = min(blit_size_z, min(s_sz - s_pz, d_sz - d_pz));
-
-	indextype source_z_offset = s_sx * s_sy;
-	indextype dest_z_offset = d_sx * d_sy;
-
-	indextype z,y;
-	for(z=0; z<blit_size_z; z++)
-		for(y=0; y<blit_size_y; y++)
-		{
-			ps = (z + s_pz) * source_z_offset + (y + s_py) * s_sx + s_px;
-			pd = (z + d_pz) * dest_z_offset + (y + d_py) * d_sx + d_px;
-			memcpy((void*)(&dest[pd]), (void*)(&source[ps]), sizeof(T)*blit_size_x);
-		}
-}
-
-template <class T>
-void rtsFunction3D<T>::shallow_copy(const rtsFunction3D<T> source, rtsFunction3D<T> &dest)
-{
-	dest = rtsFunction3D<T>(source.m_resolution.x, source.m_resolution.y, source.m_resolution.z);
-	dest.m_boundary = source.m_boundary;
-	dest.m_domain_max = source.m_domain_max;
-	dest.m_domain_min = source.m_domain_max;
-	dest.m_voxel_size = source.m_voxel_size;
-}
-
-template <class T>
-rtsFunction3D<T>::rtsFunction3D(vector3D<int> resolution, T boundary, point3D<double> domain_min, point3D<double> domain_max)
-{
-	//This function creates an implicit function based on all of the shallow variables
-	m_resolution = resolution;
-	m_boundary = boundary;
-	m_domain_min = domain_min;
-	m_domain_max = domain_max;
-	m_voxel_size = domain_max - domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-
-	//allocate the data
-	m_data = new T[m_resolution.x * m_resolution.y * m_resolution.z];
-}
-
-template <class T>
-rtsFunction3D<T>::rtsFunction3D(T* data, vector3D<int> resolution, T boundary, point3D<double> domain_min, point3D<double> domain_max)
-{
-	//This function creates an implicit function based on ALL of the variables
-	m_resolution = resolution;
-	m_boundary = boundary;
-	m_domain_min = domain_min;
-	m_domain_max = domain_max;
-	m_voxel_size = domain_max - domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-
-	//allocate the data
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	m_data = new T[size];
-	memcpy(m_data, data, sizeof(T)*size);
-	//for(int i=0; i<size; i++)
-	//	m_data[i] = data[i];
-}
-
-
-
-template <class T>
-rtsFunction3D<T>::rtsFunction3D()
-{
-	m_resolution.x = 1;
-	m_resolution.y = 1;
-	m_resolution.z = 1;
-	m_data = new T[1];
-	memset(&m_boundary, 0, sizeof(T));							//initialize boundary condition
-	m_domain_min = point3D<double>(0.0, 0.0, 0.0);	//set range parameters
-	m_domain_max = point3D<double>(1.0, 1.0, 1.0);
-	m_voxel_size = vector3D<double>(1.0, 1.0, 1.0);
-}
-
-template <class T>
-void rtsFunction3D<T>::initialize_empty(indextype res_x, indextype res_y, indextype res_z)
-{
-	m_resolution.x = res_x;					//set resolution vector
-	m_resolution.y = res_y;
-	m_resolution.z = res_z;
-	m_data = (T*)calloc(res_x*res_y*res_z, sizeof(T));		//allocate data
-}
-
-template <class T>
-rtsFunction3D<T>::rtsFunction3D(indextype res_x, indextype res_y, indextype res_z)
-{
-	initialize_empty(res_x, res_y, res_z);
-	memset(&m_boundary, 0, sizeof(T));							//initialize boundary condition
-	m_domain_min = point3D<double>(0.0, 0.0, 0.0);	//set range parameters
-	m_domain_max = point3D<double>(1.0, 1.0, 1.0);
-
-	m_voxel_size = m_domain_max - m_domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-}
-
-template <class T>
-void rtsFunction3D<T>::Init(indextype res_x, indextype res_y, indextype res_z)
-{
-	initialize_empty(res_x, res_y, res_z);
-	m_domain_min = point3D<double>(0.0, 0.0, 0.0);	//set range parameters
-	m_domain_max = point3D<double>(1.0, 1.0, 1.0);
-	memset(&m_boundary, 0, sizeof(T));							//initialize boundary condition
-
-	m_voxel_size = m_domain_max - m_domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-}
-
-template <class T>
-rtsFunction3D<T>::rtsFunction3D(T* data, indextype res_x, indextype res_y, indextype res_z)
-{
-	m_resolution.x = res_x;					//set resolution vector
-	m_resolution.y = res_y;
-	m_resolution.z = res_z;
-	m_data = new T[res_x*res_y*res_z];		//allocate data
-	//copy the sample data into the data array
-	indextype size = res_x*res_y*res_z;
-	for(indextype i=0; i<size; i++)
-		m_data[i] = data[i];
-	memset(&m_boundary, 0, sizeof(T));							//initialize boundary condition
-	m_domain_min = point3D<double>(0.0, 0.0, 0.0);	//set range parameters
-	m_domain_max = point3D<double>(1.0, 1.0, 1.0);
-
-	m_voxel_size = domain_max - domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-}
-
-template <class T>
-rtsFunction3D<T>::rtsFunction3D(const rtsFunction3D<T>& original)
-{
-	//copy the shallow variables
-	m_resolution = original.m_resolution;
-	m_boundary = original.m_boundary;
-	m_domain_min = original.m_domain_min;
-	m_domain_max = original.m_domain_max;
-	m_voxel_size = original.m_voxel_size;
-
-	//allocate space for the data
-	m_data = new T[m_resolution.x * m_resolution.y * m_resolution.z];
-	//copy the data
-	blit3D(original.m_data,
-		   0, 0, 0,
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_data,
-		   0, 0, 0,
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_resolution.x, m_resolution.y, m_resolution.z);
-}
-
-template <class T>
-rtsFunction3D<T>::~rtsFunction3D()
-{
-	delete m_data;
-}
-
-template <class T>
-typename rtsFunction3D<T>& rtsFunction3D<T>::operator=(const T rhs)
-{
-	indextype size = m_resolution.x*m_resolution.y*m_resolution.z;
-	for(int i=0; i<size; i++)
-		m_data[i] = rhs;
-
-	return *this;
-}
-
-template <class T>
-typename rtsFunction3D<T>& rtsFunction3D<T>::operator=(const rtsFunction3D<T>& rhs)
-{
-	//check for self-assignment
-	if(this == &rhs)
-		return *this;
-
-	//deallocate memory
-	if(m_data != NULL)
-		delete m_data;
-
-	//copy the shallow variables
-	m_resolution = rhs.m_resolution;
-	m_boundary = rhs.m_boundary;
-	m_domain_min = rhs.m_domain_min;
-	m_domain_max = rhs.m_domain_max;
-	m_voxel_size = rhs.m_voxel_size;
-
-	//allocate and copy memory
-	m_data = new T[m_resolution.x * m_resolution.y * m_resolution.z];
-	//copy the data
-	blit3D(rhs.m_data,
-		   0,0,0,
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_data, 
-		   0, 0, 0, 
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_resolution.x, m_resolution.y, m_resolution.z);
-
-	//return the left hand side
-	return *this;
-}
-
-template <class T>
-inline T& rtsFunction3D<T>::operator ()(indextype x, indextype y, indextype z)
-{
-	return xyz(x, y, z);
-}
-
-template <class T>
-inline T rtsFunction3D<T>::operator()(double i, double j, double k)
-{
-	return ijk(i, j, k);
-}
-
-template <class T>
-rtsFunction3D<T>& rtsFunction3D<T>::operator *=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] *= constant;
-
-	return *this;
-}
-
-template <class T>
-rtsFunction3D<T>& rtsFunction3D<T>::operator +=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] += constant;
-
-	return *this;
-}
-template <class T>
-rtsFunction3D<T>& rtsFunction3D<T>::operator -=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] -= constant;
-
-	return *this;
-}
-template <class T>
-rtsFunction3D<T>& rtsFunction3D<T>::operator /=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] /= constant;
-
-	return *this;
-}
-template <class T>
-const rtsFunction3D<T> rtsFunction3D<T>::operator *(const T constant)
-{
-	rtsFunction3D<T> result = (*this);
-	result *= constant;
-
-	return result;
-}
-
-template <class T>
-const rtsFunction3D<T> rtsFunction3D<T>::operator +(const T constant)
-{
-	rtsFunction3D<T> result = (*this);
-	result += constant;
-
-	return result;
-}
-
-template <class T>
-const rtsFunction3D<T> rtsFunction3D<T>::operator -(const T constant)
-{
-	rtsFunction3D<T> result = (*this);
-	result -= constant;
-
-	return result;
-}
-
-template <class T>
-const rtsFunction3D<T> rtsFunction3D<T>::operator /(const T constant)
-{
-	rtsFunction3D<T> result = (*this);
-	result /= constant;
-
-	return result;
-}
-
-template <class T>
-template <class U>
-rtsFunction3D<T>::operator rtsFunction3D<U>()
-{
-	//cast one type to another
-	//create the data pointer from the current function
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	U* new_data = new U[size];
-	for(int i=0; i<size; i++)
-		new_data[i] = m_data[i];
-	rtsFunction3D<U> cast_result(new_data, m_resolution, m_boundary, m_domain_min, m_domain_max);
-
-	return cast_result;
-}
-
-template <class T>
-inline T& rtsFunction3D<T>::xyz(indextype x, indextype y, indextype z)
-{
-	if(x<0 || y<0 || z<0 || x>=m_resolution.x || y>=m_resolution.y || z>=m_resolution.z)
-		return m_boundary;
-	//return m_data[(z * m_resolution.x * m_resolution.y) + (y * m_resolution.x) + x];
-	return m_data[x + m_resolution.x * (y + z * m_resolution.y)];
-
-}
-
-template <class T>
-inline point3D<indextype> rtsFunction3D<T>::getNearestIndex(indextype i)
-{
-	point3D<indextype> result;
-	result.z = i/(m_resolution.x*m_resolution.y);
-	indextype mod = i%(m_resolution.x*m_resolution.y);
-	result.y = mod/m_resolution.x;
-	result.x = mod%m_resolution.x;
-
-	return result;
-
-}
-
-template <class T>
-void rtsFunction3D<T>::LoadRAW(indextype header_size, indextype size_x,
-							   indextype size_y, indextype size_z, const char *filename)
-{
-	//set the data size
-	m_resolution = vector3D<indextype>(size_x, size_y, size_z);
-	//delete any previous data
-	if(m_data != NULL)
-	{
-		delete m_data;
-		m_data = NULL;
-	}
-
-	ifstream infile(filename, ios::in | ios::binary);
-
-	//load the header
-	unsigned char* header = new unsigned char[header_size];
-	infile.read((char*)header, header_size);
-
-	//load the actual data
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	//m_data = (T*)malloc(size*sizeof(T));
-	initialize_empty(m_resolution.x, m_resolution.y, m_resolution.z);
-	infile.read((char*)m_data, size*sizeof(T));
-
-	//calculate min and maxes
-	infile.close();
-}
-
-template <class T>
-void rtsFunction3D<T>::LoadVOL(const char *filename)
-{
-	ifstream infile(filename, ios::in | ios::binary);	//create the files stream
-	if(!infile)
-		return;
-
-	indextype size_x, size_y, size_z;				//create variables to store the size of the data set
-	//load the dimensions of the data set
-	infile.read((char*)&size_x, sizeof(int));			//load the file header
-	infile.read((char*)&size_y, sizeof(int));
-	infile.read((char*)&size_z, sizeof(int));
-
-	//close the file
-	infile.close();
-	//load the raw data
-	LoadRAW(12, size_x, size_y, size_z, filename);
-}
-
-template <class T>
-void rtsFunction3D<T>::SaveVOL(const char *filename)
-{
-	ofstream outfile(filename, ios::out | ios::binary);	//create the binary file stream
-
-	//write the volume size to the file
-	vector3D<int> vol_size = m_resolution;
-	outfile.write((char*)&vol_size.x, sizeof(int));
-	outfile.write((char*)&vol_size.y, sizeof(int));
-	outfile.write((char*)&vol_size.z, sizeof(int));
-
-	outfile.write((char*)m_data, sizeof(T)*vol_size.x*vol_size.y*vol_size.z);
-}
-
-template <class T>
-void rtsFunction3D<T>::SaveRAW(const char *filename)
-{
-	ofstream outfile(filename, ios::out | ios::binary);	//create the binary file stream
-
-	//write the volume data
-	outfile.write((char*)m_data, sizeof(T)*m_resolution.x*m_resolution.y*m_resolution.z);
-}
-
-template <class T>
-inline T rtsFunction3D<T>::ijk(double i, double j, double k)
-{
-	/*This function determines the value at the specified parametric points
-	defined by the m_domain_min and m_domain_max parameter values.*/
-
-	//if the parameter is outside the range, return the boundary value
-	if(i<m_domain_min.x || j<m_domain_min.y || k<m_domain_min.z ||
-	   i>m_domain_max.x || j>m_domain_max.y || k>m_domain_max.z)
-	   return m_boundary;
-	
-	point3D<double> index = getFractionalIndex(i, j, k);
-
-	//cout<<index.x<<","<<index.y<<","<<index.z<<endl;
-
-	//interpolate the values
-	int f_x = (int)floor(index.x);				//calculate floor and ceiling values
-	int f_y = (int)floor(index.y);
-	int f_z = (int)floor(index.z);
-	int c_x = (int)ceil(index.x);
-	int c_y = (int)ceil(index.y);
-	int c_z = (int)ceil(index.z);
-
-	double x_d = index.x - f_x;			//find the point within the voxel
-	double y_d = index.y - f_y;
-	double z_d = index.z - f_z;
-
-	T i_1 = xyz(f_x, f_y, f_z)*(1.0 - z_d) + xyz(f_x, f_y, c_z)*(z_d);	//interpolate along z
-	T i_2 = xyz(f_x, c_y, f_z)*(1.0 - z_d) + xyz(f_x, c_y, c_z)*(z_d);
-	T j_1 = xyz(c_x, f_y, f_z)*(1.0 - z_d) + xyz(c_x, f_y, c_z)*(z_d);
-	T j_2 = xyz(c_x, c_y, f_z)*(1.0 - z_d) + xyz(c_x, c_y, c_z)*(z_d);
-
-	T w_1 = i_1*(1.0 - y_d) + i_2*(y_d);
-	T w_2 = j_1*(1.0 - y_d) + j_2*(y_d);
-
-	return w_1*(1.0 - x_d) + w_2*(x_d);
-}
-
-
-template <class T>
-void rtsFunction3D<T>::Parameterize(double x_min, double x_max, double y_min, double y_max, double z_min, double z_max)
-{
-	m_domain_min = point3D<double>(x_min, y_min, z_min);
-	m_domain_max = point3D<double>(x_max, y_max, z_max);
-	m_voxel_size = m_domain_max - m_domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-}
-
-template <class T>
-inline point3D<double> rtsFunction3D<T>::getParameter(indextype x, indextype y, indextype z)
-{
-	//get the value between 0 and 1
-	point3D<double> normalized((double)x / (double)(m_resolution.x) + (1.0/(m_resolution.x*2.0)),
-							   (double)y / (double)(m_resolution.y) + (1.0/(m_resolution.y*2.0)),
-							   (double)z/(double)(m_resolution.z) + (1.0/(m_resolution.z*2.0)));
-
-	point3D<double> result(normalized.x * (m_domain_max.x - m_domain_min.x) + m_domain_min.x,
-						   normalized.y * (m_domain_max.y - m_domain_min.y) + m_domain_min.y,
-						   normalized.z * (m_domain_max.z - m_domain_min.z) + m_domain_min.z);
-
-	return result;
-}
-
-template <class T>
-inline point3D<indextype> rtsFunction3D<T>::getNearestIndex(double i, double j, double k)
-{
-	//this function returns the index of the voxel containing the specified parameter point
-	point3D<double> normalized((i - m_domain_min.x)/(m_domain_max.x-m_domain_min.x),
-							   (j - m_domain_min.y)/(m_domain_max.y-m_domain_min.y),
-							   (k - m_domain_min.z)/(m_domain_max.z-m_domain_min.z));
-	
-	point3D<indextype> result((normalized.x - (1.0/(m_resolution.x*2.0)))*(double)m_resolution.x+0.5,
-							  (normalized.y - (1.0/(m_resolution.y*2.0)))*(double)m_resolution.y+0.5,
-							  (normalized.z - (1.0/(m_resolution.z*2.0)))*(double)m_resolution.z+0.5);
-
-	return result;
-}
-
-template <class T>
-inline point3D<double> rtsFunction3D<T>::getFractionalIndex(double i, double j, double k)
-{
-	//this function returns the index of the voxel containing the specified parameter point
-	point3D<double> normalized((i - m_domain_min.x)/(m_domain_max.x-m_domain_min.x),
-							   (j - m_domain_min.y)/(m_domain_max.y-m_domain_min.y),
-							   (k - m_domain_min.z)/(m_domain_max.z-m_domain_min.z));
-	
-	point3D<double> result((normalized.x - (1.0/(m_resolution.x*2.0)))*(double)m_resolution.x,
-							  (normalized.y - (1.0/(m_resolution.y*2.0)))*(double)m_resolution.y,
-							  (normalized.z - (1.0/(m_resolution.z*2.0)))*(double)m_resolution.z);
-	return result;
-}
-
-
-template <class T>
-T* rtsFunction3D<T>::GetBits()
-{
-	/*Returns bit data in lexocographical order (possibly for 3D texture mapping)*/
-	return m_data;
-}
-
-template <class T>
-rtsFunction3D<T>* rtsFunction3D<T>::Resample(indextype newres_x, indextype newres_y, indextype newres_z)
-{
-	/*This function resamples the current function at the specified resolution.
-	No convolution is done for reducing he resolution.
-	*/
-
-	rtsFunction3D<T>* result = new rtsFunction3D<T>(vector3D<indextype>(newres_x, newres_y, newres_z),
-						    m_boundary, m_domain_min, m_domain_max);
-
-	//run through the entire resolution of the new function, sampling the current function
-	int x, y, z;
-	point3D<double> parametric;
-	for(x = 0; x<newres_x; x++)
-		for(y=0; y<newres_y; y++)
-			for(z=0; z<newres_z; z++)
-			{
-				//compute the parametric point for the sample point
-				parametric = result->getParameter(x, y, z);
-				(*result)(x, y, z) = ijk(parametric.x, parametric.y, parametric.z);
-			}
-
-	return result;
-}
-
-template <class T>
-void rtsFunction3D<T>::Scale(T new_min, T new_max)
-{
-	/*This function scales all values of the implicit function to within a specified range
-	*/
-
-	//find the minimum and maximum values in this function
-	indextype data_size = m_resolution.x * m_resolution.y * m_resolution.z;
-	T min = m_data[0];
-	T max = m_data[0];
-	for(indextype i=0; i<data_size; i++)
-	{
-		if(m_data[i] < min)
-			min = m_data[i];
-		if(m_data[i] > max)
-			max = m_data[i];
-	}
-
-	//scale all values to the specified range
-	T current_range = max - min;
-	T new_range = new_max - new_min;
-	for(indextype i=0; i<data_size; i++)
-		m_data[i] = ((m_data[i] - min)/current_range)*(new_range) + new_min;
-}
-
-template <class T>
-void rtsFunction3D<T>::Crop(indextype x, indextype y, indextype z, 
-							indextype size_x, indextype size_y, indextype size_z)
-{
-	/*This function crops the implicit function at the specified nodes
-	*/
-	//create a pointer for the new data
-	T* new_data = new T[size_x*size_y*size_z];
-
-	//blit from the old data to the new data
-	blit3D(m_data,
-			x, y, z,
-			m_resolution.x, m_resolution.y, m_resolution.z,
-			new_data,
-			0, 0, 0,
-			size_x, size_y, size_z,
-			size_x, size_y, size_z);
-
-	//change the shallow variables
-	vector3D<indextype> new_resolution = vector3D<indextype>(size_x, size_y, size_z);
-	vector3D<double> voxel_size = getParameter(0,0,0) - getParameter(1,1,1);
-	point3D<double> new_domain_min = getParameter(x, y, z) - 0.5*voxel_size;
-	point3D<double> new_domain_max = getParameter(size_x-1, size_y - 1, size_z-1) + 0.5*voxel_size;
-	//copy new shallow variables
-	m_resolution = new_resolution;
-	m_domain_min = new_domain_min;
-	m_domain_max = new_domain_max;
-
-	//copy data
-	delete m_data;
-	m_data = new_data;
-
-}
-
-template <class T>
-void rtsFunction3D<T>::Threshold(T min, T value)
-{
-	/*This function sets all values between min and max to value.
-	*/
-	int x, y, z;
-	T test_value;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				test_value = xyz(x, y, z);
-				if(test_value >= min)
-					xyz(x, y, z) = value;
-			}
-}
-
-template <class T>
-void rtsFunction3D<T>::Threshold(T min, T max, T value)
-{
-	/*This function sets all values between min and max to value.
-	*/
-	int x, y, z;
-	T test_value;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				test_value = xyz(x, y, z);
-				if(test_value >= min && test_value <= max)
-					xyz(x, y, z) = value;
-			}
-}
-
-template <class T>
-void rtsFunction3D<T>::Threshold(T min, T max, T inside, T outside)
-{
-	/*This function sets all values between min and max to value.
-	*/
-	int x, y, z;
-	T test_value;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				test_value = xyz(x, y, z);
-				if(test_value >= min && test_value <= max)
-					xyz(x, y, z) = inside;
-				else
-					xyz(x, y, z) = outside;
-			}
-}
-
-template <class T>
-void rtsFunction3D<T>::Insert(rtsFunction3D<T>* source, indextype x, indextype y, indextype z)
-{
-	blit3D(source->m_data, 0, 0, 0, source->m_resolution.x, source->m_resolution.y, source->m_resolution.z,
-			m_data, x, y, z, m_resolution.x, m_resolution.y, m_resolution.z,
-			source->m_resolution.x, source->m_resolution.y, source->m_resolution.z);
-}
-
-
-
-
-template <class T>
-void rtsFunction3D<T>::Binary(T threshold, T true_value)
-{
-	/**
-	This function converts an implicit function into a binary or characteristic function describing the solid represented by the level
-	set at isovalue "threshold".  All values below threshold are set to zero while all values above threshold are set to the specified
-	"true_value".  In order to use this function, the data type T must be able to be set to 0.
-	**/
-	int max_index = m_resolution.x * m_resolution.y * m_resolution.z;	//find the size of the data array
-	int i;
-	for(i=0; i<max_index; i++)
-		if(m_data[i] >= threshold)
-			m_data[i] = true_value;
-		else
-			m_data[i] = 0;
-}
-
-
-
-template <class T>
-void rtsFunction3D<T>::ClampMax(T max)
-{
-	int i;
-	int elements = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(i=0; i<elements; i++)
-		if(m_data[i] > max)
-			m_data[i] = max;
-}
-
-template <class T>
-void rtsFunction3D<T>::ClampMin(T min)
-{
-	int i;
-	int elements = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(i=0; i<elements; i++)
-		if(m_data[i] < min)
-			m_data[i] = min;
-}
-
-template <class T>
-T rtsFunction3D<T>::getMin()
-{
-	int i;
-	int elements = m_resolution.x * m_resolution.y * m_resolution.z;
-	T current = m_data[0];
-	for(i=1; i<elements; i++)
-		if(m_data[i] < current)
-			current = m_data[i];
-	return current;
-}
-
-template <class T>
-T rtsFunction3D<T>::getMax()
-{
-	int i;
-	int elements = m_resolution.x * m_resolution.y * m_resolution.z;
-	T current = m_data[0];
-	for(i=1; i<elements; i++)
-		if(m_data[i] > current)
-			current = m_data[i];
-	return current;
-}
-
-
-template <class T>
-void rtsFunction3D<T>::toConsole()
-{
-	cout<<endl;
-	int x, y, z;
-	for(z=0; z<m_resolution.z; z++)
-	{
-		for(y=0; y<m_resolution.y; y++)
-		{
-			for(x=0; x<m_resolution.x; x++)
-			{
-				cout.width(7);
-				cout.precision(3);
-				cout<<(double)xyz(x, y, z);
-			}
-			cout<<endl;
-		}
-		cout<<"-----------------------------"<<endl;
-	}
-
-}
-
-template <class T>
-rtsFunction3D<T> rtsFunction3D<T>::Project2D()
-{
-	/**
-	This function projects the entire 3D function onto a 2D function along the z-axis.
-	**/
-	rtsFunction3D<T> result(m_resolution.x, m_resolution.y, 1);
-	result = 0;
-	
-	indextype x, y, z;
-	for(x = 0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				if(result(x, y, 0) < xyz(x, y, z))
-					result(x, y, 0) = xyz(x, y, z);
-			}
-	return result;
-}
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsGUIConsole.h b/legacy/rtsGUIConsole.h
deleted file mode 100755
index 32057db..0000000
--- a/legacy/rtsGUIConsole.h
+++ /dev/null
@@ -1,72 +0,0 @@
-#ifndef __GUICON_H__
-#define __GUICON_H__
-
-//void RedirectIOToConsole(int Xpos = 0, int Ypos = 0, int Width = 700, int Height = 400);
-
-#ifdef WIN32
-#include <windows.h>
-#include <stdio.h>
-#include <fcntl.h>
-#include <io.h>
-#include <iostream>
-#include <fstream>
-
-#ifndef _USE_OLD_IOSTREAMS
-
-using namespace std;
-#endif
-
-// maximum mumber of lines the output console should have
-
-static const WORD MAX_CONSOLE_LINES = 500;
-//#ifdef _DEBUG
-
-void RedirectIOToConsole(int Xpos = 0, int Ypos = 0, int Width = 700, int Height = 400)
-{
-	int hConHandle;
-	long lStdHandle;
-	CONSOLE_SCREEN_BUFFER_INFO coninfo;
-	FILE *fp;
-	// allocate a console for this app
-	AllocConsole();
-	// set the screen buffer to be big enough to let us scroll text
-	GetConsoleScreenBufferInfo(GetStdHandle(STD_OUTPUT_HANDLE), &coninfo);
-	coninfo.dwSize.Y = MAX_CONSOLE_LINES;
-	SetConsoleScreenBufferSize(GetStdHandle(STD_OUTPUT_HANDLE),
-	coninfo.dwSize);
-	// redirect unbuffered STDOUT to the console
-	lStdHandle = (long)GetStdHandle(STD_OUTPUT_HANDLE);
-	hConHandle = _open_osfhandle(lStdHandle, _O_TEXT);
-	fp = _fdopen( hConHandle, "w" );
-	*stdout = *fp;
-	setvbuf( stdout, NULL, _IONBF, 0 );
-	// redirect unbuffered STDIN to the console
-	lStdHandle = (long)GetStdHandle(STD_INPUT_HANDLE);
-	hConHandle = _open_osfhandle(lStdHandle, _O_TEXT);
-	fp = _fdopen( hConHandle, "r" );
-	*stdin = *fp;
-	setvbuf( stdin, NULL, _IONBF, 0 );
-
-	// redirect unbuffered STDERR to the console
-	lStdHandle = (long)GetStdHandle(STD_ERROR_HANDLE);
-	hConHandle = _open_osfhandle(lStdHandle, _O_TEXT);
-	fp = _fdopen( hConHandle, "w" );
-	*stderr = *fp;
-	setvbuf( stderr, NULL, _IONBF, 0 );
-
-	// make cout, wcout, cin, wcin, wcerr, cerr, wclog and clog
-	// point to console as well
-	ios::sync_with_stdio();
-	//position
-	MoveWindow(GetConsoleWindow(), Xpos, Ypos, Width, Height, true);
-}
-
-#else
-void RedirectIOToConsole(int Xpos = 0, int Ypos = 0, int Width = 700, int Height = 400)
-{
-}
-#endif
-
-#endif
-
-/* End of File */
\ No newline at end of file
diff --git a/legacy/rtsGraph.h b/legacy/rtsGraph.h
deleted file mode 100755
index f18efea..0000000
--- a/legacy/rtsGraph.h
+++ /dev/null
@@ -1,142 +0,0 @@
-#ifndef RTS_GRAPH_H
-#define RTS_GRAPH_H
-
-#include <list>
-#include <algorithm>
-
-using namespace std;
-
-template<typename T>
-class rtsGraph
-{
-	unsigned int current_id;
-public:
-	class rtsGraphNode;
-	typedef typename list<rtsGraphNode>::iterator rtsGraphNodePtr;
-	
-	class rtsGraphNode
-	{
-	public:
-		list<rtsGraphNodePtr> ConnectionList;
-		unsigned int ID;
-		T Data;
-	};
-
-	list<rtsGraphNode> NodeList;
-
-	rtsGraphNodePtr addNode(T data)
-	{
-		//Adds a node to the graph.  This node is unconnected by default.
-
-		//create the new node
-		rtsGraphNode new_node;
-		//set the data to the data provided
-		new_node.Data = data;
-		//set the id
-		new_node.ID = current_id++;
-
-		//add the node to the node list
-		NodeList.push_back(new_node);
-		rtsGraphNodePtr result = NodeList.end();
-		result--;
-		return result;
-	}
-	bool cmpPtr(const rtsGraphNodePtr a, const rtsGraphNodePtr b)
-	{
-		return (*a).ID < (*b).ID;
-	}
-
-	void addConnection(rtsGraphNodePtr n0, rtsGraphNodePtr n1)
-	{
-		//adds a connection between two nodes
-		//connect n0 to n1
-		(*n0).ConnectionList.push_back(n1);
-		(*n1).ConnectionList.push_back(n0);
-
-	}
-
-	void removeNode(rtsGraphNodePtr n)
-	{
-		
-		typename list<rtsGraphNodePtr>::iterator i;
-		typename list<rtsGraphNodePtr>::iterator j;
-		typename list<rtsGraphNodePtr>::iterator temp;
-		rtsGraphNodePtr m;
-		rtsGraphNodePtr k;
-		/*Remove all of the connections TO n*/
-
-		//for each node m connected to n
-		for(i = (*n).ConnectionList.begin(); i != (*n).ConnectionList.end(); i++)
-		{
-			m = (*i);
-			//for each node k connected to m
-			j = (*m).ConnectionList.begin();
-			while(j != (*m).ConnectionList.end())
-			{
-				k = (*j);
-				//if k is the same as n, remove it
-				if(k == n)
-				{
-					temp = j;
-					j++;
-					(*m).ConnectionList.erase(temp);
-				}
-				else
-					j++;
-
-			}
-		}
-
-		/*Add all connections to neighboring nodes*/
-
-		//for each node m connected to n
-		for(i = (*n).ConnectionList.begin(); i != (*n).ConnectionList.end(); i++)
-		{
-			m = (*i);
-			//for each node k connected to n
-			for(j = (*n).ConnectionList.begin(); j != (*n).ConnectionList.end(); j++) 
-			{
-				k = (*j);
-				if(k != m)
-					(*m).ConnectionList.push_back(k);				
-
-			}
-			//(*m).ConnectionList.sort(&rtsGraph<T>::cmpPtr);
-			//sort((*m).ConnectionList.begin(), (*m).ConnectionList.end(), rtsGraph<T>::cmpPtr);
-			(*m).ConnectionList.unique();
-		}
-
-
-
-
-
-
-
-	}
-
-
-	void PrintGraph()
-	{
-		rtsGraphNodePtr i;
-		typename list<rtsGraphNodePtr>::iterator c;
-		for(i = NodeList.begin(); i != NodeList.end(); i++)
-		{
-			cout<<(*i).Data<<": ";
-			for(c = (*i).ConnectionList.begin(); c != (*i).ConnectionList.end(); c++)
-			{
-				if(c != (*i).ConnectionList.begin())
-					cout<<"--";
-				cout<<(*(*c)).Data;
-			}
-			cout<<endl;		
-
-		}
-
-	}
-	
-	
-
-
-};
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsImage.h b/legacy/rtsImage.h
deleted file mode 100755
index bbc0b8b..0000000
--- a/legacy/rtsImage.h
+++ /dev/null
@@ -1,136 +0,0 @@
-#include "rtsFunction3D.h"
-#include "cimg/cimg.h"
-#include <string>
-#include <sstream>
-#include <iomanip>
-
-using namespace std;
-using namespace cimg_library;
-
-
-///This file contains a series of functions useful for loading images into other structures.  These function use the CImg header file.
-
-void rts_cimgLoadImage(rtsFunction3D<unsigned char>& result, const char* filename)	///<This function loads an image and store it in an Implicit3D object.
-{
-	CImg<unsigned char> image(filename), visu(500,400,1,3,0);
-
-	result = rtsFunction3D<unsigned char>(image.width, image.height, 1);
-	unsigned int x, y;
-	for(x=0; x<image.width; x++)
-		for(y=0; y<image.height; y++)
-		{
-			result(x, y, 0) = image(x, y);
-		}
-}
-
-void rts_cimgSaveImage(rtsFunction3D<unsigned char>& result, int z, const char* filename)
-{
-	CImg<unsigned char> image(result.DimX(), result.DimY());
-	unsigned int x, y;
-	for(x=0; x<image.width; x++)
-		for(y=0; y<image.height; y++)
-			image(x, y) = result(x, y, z);
-
-	image.save(filename);
-}
-
-void rts_cimgLoadImageSequence(rtsFunction3D<unsigned char>& result, const char* filename, unsigned int min, unsigned int max, unsigned int color = 0)
-{
-	/**
-	This function loads a sequence of images into a 3D implicit function.  The filename is passed using the '?' wild
-	card.  The wild cards are then replaced with the given min through max values in order to construct the names
-	for the image files to be loaded.  The files are then loaded and placed in sequential order along the z-axis
-	of the implicit function.
-	**/
-	string sequence_name = filename;							//turn the filename into a string
-	unsigned int wild_card_begin = sequence_name.find_first_of('?');		//find the start and end indices of the wild card
-	unsigned int wild_card_end = sequence_name.find_last_of('?');
-
-	unsigned int max_number_length = wild_card_end - wild_card_begin + 1;	//find the maximum number of characters in the image number
-	unsigned int max_number = (unsigned int)pow((double)10, (double)max_number_length) - 1;				//find the maximum possible number
-
-	//make sure that the data is given correctly
-	if(max < min) return;
-	if(max > max_number) max = max_number;
-
-	//create an array of file names
-	int num_images = max - min + 1;					//compute the number of images
-	bool implicit_created = false;
-	for(int i=0; i<num_images; i++)
-	{
-		ostringstream format_stream;			//create a stream for number formatting
-		format_stream.fill('0');				//the frame name will be right justified with proceeding zeroes
-		format_stream<<setw(max_number_length);	//specify the length of the frame name (based on the wild cards)
-		format_stream<<i+min;							//put the number in the stream, convert it to a string
-		string frame_name = format_stream.str();
-
-		string file_name = sequence_name;		//create the file name for the current frame
-		file_name.replace(wild_card_begin, max_number_length, frame_name);
-
-		CImg<unsigned char> image(file_name.c_str());	//load the frame
-		if(implicit_created == false)			//create the implicit function for the first frame
-		{
-			result = rtsFunction3D<unsigned char>(image.width, image.height, num_images);
-			implicit_created = true;
-		}
-
-		//place the frame in the implicit function
-		unsigned int x, y;
-		for(x=0; x<image.width; x++)
-		for(y=0; y<image.height; y++)
-			result(x, y, i) = image(x, y, color);
-	}	
-}
-
-void rts_cimgSaveImageSequence(rtsFunction3D<unsigned char>& result, const char* filename)
-{
-	string sequence_name = filename;							//turn the filename into a string
-	unsigned int wild_card_begin = sequence_name.find_first_of('?');		//find the start and end indices of the wild card
-	unsigned int wild_card_end = sequence_name.find_last_of('?');
-
-	unsigned int max_number_length = wild_card_end - wild_card_begin + 1;	//find the maximum number of characters in the image number
-	unsigned int max_number = (unsigned int)pow((double)10, (double)max_number_length) - 1;				//find the maximum possible number
-
-	//make sure that the data is given correctly
-	unsigned int max = result.DimZ();
-	if(max > max_number) max = max_number;
-
-	//save each individual file
-	int num_images = max;					//compute the number of images
-	CImg<unsigned char> image(result.DimX(), result.DimY());	//create an image for saving
-	for(int i=0; i<num_images; i++)			//determine the filename and save the image
-	{
-		ostringstream format_stream;			//create a stream for number formatting
-		format_stream.fill('0');				//the frame name will be right justified with proceeding zeroes
-		format_stream<<setw(max_number_length);	//specify the length of the frame name (based on the wild cards)
-		format_stream<<i;							//put the number in the stream, convert it to a string
-		string frame_name = format_stream.str();
-
-		string file_name = sequence_name;		//create the file name for the current frame
-		file_name.replace(wild_card_begin, max_number_length, frame_name);
-
-		//fill the image with the implicit data at the current z coordinate
-		unsigned int x, y;
-		for(x=0; x<image.width; x++)
-			for(y=0; y<image.height; y++)
-				image(x, y) = result(x, y, i);
-
-		//save the file
-		image.save(file_name.c_str());
-	}
-
-}
-
-void rts_cimgDisplayFunction3D(rtsFunction3D<unsigned char> source, unsigned int z)
-{
-	CImg<unsigned char> image(source.DimX(), source.DimY());
-
-	int x, y;
-	for(x=0; x<image.width; x++)
-		for(y=0; y<image.height; y++)
-			image(x, y) = source(x, y, z);
-
-	CImgDisplay main_disp(image,"loaded image");
-	while (!main_disp.is_closed)
-      main_disp.wait();
-}
\ No newline at end of file
diff --git a/legacy/rtsImplicit3D.h b/legacy/rtsImplicit3D.h
deleted file mode 100755
index 67364d8..0000000
--- a/legacy/rtsImplicit3D.h
+++ /dev/null
@@ -1,2091 +0,0 @@
-#ifndef RTSIMPLICIT3D_H
-#define RTSIMPLICIT3D_H
-
-#define DIST_MAX	255
-
-#include "rtsLinearAlgebra.h"
-#include "rtsDTGrid3D.h"
-#include <fstream>
-#include <iostream>
-#include <math.h>
-#include <queue>
-#include <algorithm>
-using namespace std;
-
-typedef int indextype;
-
-///This class represents a 3D implicit function as a grid.  It provides methods for accessing values, interpolation, and several utilities.
-
-template <class T> class rtsImplicit3D
-{
-private:
-	//pointer to store the data
-	T* m_data;
-	//resolution of the data (x, y, z) dimensional extents
-	vector3D<indextype> m_resolution;
-	T m_boundary;			//boundary condition
-	point3D<double> m_domain_min;	//min and max range values (used for parametric access)
-	point3D<double> m_domain_max;
-	vector3D<double> m_voxel_size;
-	
-	//bit-blit function copies 3D data quickly from source to dest
-	void blit3D(const T* source,
-				   indextype s_px, indextype s_py, indextype s_pz,
-				   indextype s_sx, indextype s_sy, indextype s_sz,
-				   T* dest,
-				   indextype d_px, indextype d_py, indextype d_pz,
-				   indextype d_sx, indextype d_sy, indextype d_sz,
-				   indextype blit_size_x, indextype blit_size_y, indextype blit_size_z);
-
-	void shallow_copy(const rtsImplicit3D<T> source, rtsImplicit3D<T> &dest);
-	inline point3D<double> getParameter(indextype i);
-
-	inline float isosurface_distance(point3D<double> p0, point3D<double> p1, T isovalue);
-	inline float manhattan_distance(rtsImplicit3D<float>* function, point3D<indextype> p, bool sdf = false);
-	void compute_distance_function_boundary(T isovalue, rtsImplicit3D<float>* &result, rtsImplicit3D<bool>* &mask, bool sdf = false);
-
-
-public:
-	//construct an implicit function with a size of 1
-	rtsImplicit3D();			///<Create an empty implicit function
-	//construct an implicit function of the specified resolution
-	rtsImplicit3D(indextype res_x, indextype res_y, indextype res_z);	///<Create an implicit function with the specified resolution
-	//construct an implicit function from sample data and a specified size
-	rtsImplicit3D(T* data, indextype res_x, indextype res_y, indextype res_z);	///<Create an implicit function from previous data at the specified resolution
-	//shallow-copy constructor, defines all shallow variables
-	rtsImplicit3D(vector3D<int> resolution, T boundary, point3D<double> min_domain, point3D<double> max_domain);
-	//full copy constructor, defines all variables
-	rtsImplicit3D(T* data, vector3D<int> resolution, T boundary, point3D<double> min_domain, point3D<double> max_domain);
-	rtsImplicit3D(const rtsImplicit3D<T> &original);	//copy constructor
-	~rtsImplicit3D();		//destructor
-
-	//overloaded operators
-	rtsImplicit3D<T>& operator=(const rtsImplicit3D<T>& original);		///<Overloaded operator creates a copy of an implicit function
-	rtsImplicit3D<T>& operator=(const T constant);						///<Overloaded operator sets all points in an implicit function to the given constant value
-	inline T& operator()(indextype x, indextype y, indextype z);		///<Allows access to the sample point indexed by x, y, and z using the parenthesis operator
-	inline T operator()(double i, double j, double k);					///<Allows access to the implicit function (based on the domain boundaries) at the position (i, j, k).  This class uses linear interpolation.
-	rtsImplicit3D<T>& operator*=(const T constant);						///<Multiplies the values at all sample points by a constant.
-	rtsImplicit3D<T>& operator+=(const T constant);						///<Adds a constant to the values at all sample points.
-	rtsImplicit3D<T>& operator-=(const T constant);						///<Subtracts a constant from the values at all sample points.
-	rtsImplicit3D<T>& operator/=(const T constant);						///<Divides all values by a constant.
-	const rtsImplicit3D<T> operator+(const T constant);					///<Adds a constant to an implicit function and returns a new function.
-	const rtsImplicit3D<T> operator-(const T constant);					///<Subtracts a constant from an implicit function and returns a new function.
-	const rtsImplicit3D<T> operator*(const T constant);					///<Multiplies an implicit function by a constant and returns a new function.
-	const rtsImplicit3D<T> operator/(const T constant);					///<Divides an implicit function by a constant and returns a new function.
-
-	//casting operator
-	//template <class U> friend class rtsImplicit3D<U>;
-	template <class U> operator rtsImplicit3D<U>();						///<Casts between data types.
-
-	//friend classes for overloading "backwards" operations (like 3*function)
-	friend rtsImplicit3D<T> operator*(const T lhs, rtsImplicit3D<T> rhs){return rhs*lhs;}	///<Allows associative multiplication.
-	friend rtsImplicit3D<T> operator+(const T lhs, rtsImplicit3D<T> rhs){return rhs+lhs;}	///<Allows associative addition.
-	friend rtsImplicit3D<T> operator-(const T lhs, rtsImplicit3D<T> rhs)					///<Allows associative subtraction.
-	{
-		rtsImplicit3D<T> result;
-		rhs.shallow_copy(rhs, result);	//make a copy of all of the shallow variables and allocate memory
-		indextype size = rhs.m_resolution.x * rhs.m_resolution.y * rhs.m_resolution.z;
-		//iterate and subtract
-		for(indextype i=0; i<size; i++)
-			result.m_data[i] = lhs - rhs.m_data[i];
-
-		return result;
-	}
-	//friend rtsImplicit3D<T> operator/(const T lhs, rtsImplicit3D<T> rhs);
-
-	//loading/saving data to disk
-	void LoadRAW(indextype header_size, indextype data_x, indextype data_y, indextype data_z, const char* filename);	///<Loads RAW data from a file with the specified header size and data size.
-	void SaveRAW(const char* filename);							///<Save the data as RAW data to disk.
-	void LoadVOL(const char* filename);							///<Load a VOL file from disk.
-	void SaveVOL(const char* filename);							///<Save a VOL file to disk.
-
-	//data access methods
-	inline T& xyz(indextype x, indextype y, indextype z);
-	inline T ijk(double i, double j, double k);
-	void Parameterize(double x_min, double x_max, double y_min, double y_max, double z_min, double z_max);
-	void setBoundary(T boundary){m_boundary = boundary;}
-	T getBoundary(){return m_boundary;}
-	T* GetBits();
-	indextype DimX(){return m_resolution.x;}
-	indextype DimY(){return m_resolution.y;}
-	indextype DimZ(){return m_resolution.z;}
-	inline point3D<double> getParameter(indextype x, indextype y, indextype z);
-	inline point3D<indextype> getNearestIndex(double i, double j, double k);
-	inline point3D<double> getFractionalIndex(double i, double j, double k);
-	inline point3D<indextype> getNearestIndex(indextype i);
-	point3D<double> getMinDomain(){return m_domain_min;}
-	point3D<double> getMaxDomain(){return m_domain_max;}
-	vector<point3D<indextype>> getEdgeNodes(T isovalue, bool protrusions = true); ///<Returns a vector nodes lying on the edge of an implicit surface.
-	rtsImplicit3D<T> Project2D();			//<Projects the data along the z-axis using a maximum-intensity projection.
-	unsigned int BackgroundComponents6(indextype x, indextype y, indextype z, T threshold, int n=18);	///<Returns the number of background components 6-connected to the specified node.
-	unsigned int Neighbors6(indextype x, indextype y, indextype z, T threshold); //<Returns the number of 6-connected neighbors above threshold.
-
-	//data input methods
-	void Insert(rtsDTGrid3D<T>* dt_grid, double factor, indextype x, indextype y, indextype z);
-	void Insert(rtsImplicit3D<T>* source, indextype x, indextype y, indextype z);
-
-	//data massaging
-	
-	void Scale(T min, T max);
-	void Crop(indextype x, indextype y, indextype z, indextype size_x, indextype size_y, indextype size_z);
-	void Binary(T threshold, T true_value);		///<Turns the image into a binary image based on a threshold value T.  All values below T are set to 0, all values above are set to true_value.
-	void Threshold(T min, T value);
-	void Threshold(T min, T max, T value);
-	void Threshold(T min, T max, T inside, T outside);
-	void Erode(T isovalue, T fill_value);			///<Erodes the image around the edges defined by an isovalue.
-	unsigned int Thin(T isovalue);		///<Finds the skeleton of the given isosurface using erosion.
-	bool TestTopology(T isovalue, unsigned int x, unsigned int y, unsigned int z);	///<Tests if the specified voxel is necessary to the topology of the specified isosurface.
-	int Neighbors26(indextype x, indextype y, indextype z, T isovalue);		///<Returns the number of neighbors above the given isovalue.
-	void FloodFill26(indextype x, indextype y, indextype z, T new_value);	///<Fills the connected component at (x, y, z) with the new value.
-	void FloodFill6(indextype x, indextype y, indextype z, T new_value);	///<Performs a 6-connected flood-fill operation starting at the specified node.
-	void MedianFilter(int dist_x, int dist_y, int dist_z, double factor = 0.5);		///<Performs a median filter on the data set.
-	void ClampMax(T max);		///<Clamps the function to the given maximum value.
-	void ClampMin(T min);
-	void ClampMin(T min, T value);	///<Sets all function values below min to value.
-
-	//create new data
-	rtsImplicit3D<T>* Resample(indextype newres_x, indextype newres_y, indextype newres_z);
-	rtsImplicit3D<float>* Isodistance_Manhattan(T isovalue, bool sdf = false);
-	rtsImplicit3D<vector3D<T>>* Gradient();
-	rtsImplicit3D<float>* EstimateAmbient(T threshold);
-	rtsImplicit3D<float>* EstimateAttenuatedAmbient(T surface, T transparent, float attenuation);
-
-	//implicit shapes
-	//(these functions create some basic implicit shapes just for fun)
-	void Sphere(double center_i, double center_j, double center_k, double radius, T in_value);
-
-	//output functions
-	void toConsole();
-
-};
-
-template <class T>
-void rtsImplicit3D<T>::blit3D(const T* source,
-				   indextype s_px, indextype s_py, indextype s_pz,
-				   indextype s_sx, indextype s_sy, indextype s_sz,
-				   T* dest,
-				   indextype d_px, indextype d_py, indextype d_pz,
-				   indextype d_sx, indextype d_sy, indextype d_sz,
-				   indextype blit_size_x, indextype blit_size_y, indextype blit_size_z)
-{
-	indextype ps, pd;		//stores the mapping for the source point to the dest point
-	//find the maximum points that can be blit to (in case source overlaps the edges of dest)
-	blit_size_x = min(blit_size_x, min(s_sx - s_px, d_sx - d_px));
-	blit_size_y = min(blit_size_y, min(s_sy - s_py, d_sy - d_py));
-	blit_size_z = min(blit_size_z, min(s_sz - s_pz, d_sz - d_pz));
-
-	indextype source_z_offset = s_sx * s_sy;
-	indextype dest_z_offset = d_sx * d_sy;
-
-	indextype z,y;
-	for(z=0; z<blit_size_z; z++)
-		for(y=0; y<blit_size_y; y++)
-		{
-			ps = (z + s_pz) * source_z_offset + (y + s_py) * s_sx + s_px;
-			pd = (z + d_pz) * dest_z_offset + (y + d_py) * d_sx + d_px;
-			memcpy((void*)(&dest[pd]), (void*)(&source[ps]), sizeof(T)*blit_size_x);
-		}
-}
-
-template <class T>
-void rtsImplicit3D<T>::shallow_copy(const rtsImplicit3D<T> source, rtsImplicit3D<T> &dest)
-{
-	dest = rtsImplicit3D<T>(source.m_resolution.x, source.m_resolution.y, source.m_resolution.z);
-	dest.m_boundary = source.m_boundary;
-	dest.m_domain_max = source.m_domain_max;
-	dest.m_domain_min = source.m_domain_max;
-	dest.m_voxel_size = source.m_voxel_size;
-}
-
-template <class T>
-rtsImplicit3D<T>::rtsImplicit3D(vector3D<int> resolution, T boundary, point3D<double> domain_min, point3D<double> domain_max)
-{
-	//This function creates an implicit function based on all of the shallow variables
-	m_resolution = resolution;
-	m_boundary = boundary;
-	m_domain_min = domain_min;
-	m_domain_max = domain_max;
-	m_voxel_size = domain_max - domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-
-	//allocate the data
-	m_data = new T[m_resolution.x * m_resolution.y * m_resolution.z];
-}
-
-template <class T>
-rtsImplicit3D<T>::rtsImplicit3D(T* data, vector3D<int> resolution, T boundary, point3D<double> domain_min, point3D<double> domain_max)
-{
-	//This function creates an implicit function based on ALL of the variables
-	m_resolution = resolution;
-	m_boundary = boundary;
-	m_domain_min = domain_min;
-	m_domain_max = domain_max;
-	m_voxel_size = domain_max - domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-
-	//allocate the data
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	m_data = new T[size];
-	memcpy(m_data, data, sizeof(T)*size);
-	//for(int i=0; i<size; i++)
-	//	m_data[i] = data[i];
-}
-
-
-
-template <class T>
-rtsImplicit3D<T>::rtsImplicit3D()
-{
-	m_resolution.x = 1;
-	m_resolution.y = 1;
-	m_resolution.z = 1;
-	m_data = new T[1];
-	//m_boundary = 0;				//initialize boundary condition
-	m_domain_min = point3D<double>(0.0, 0.0, 0.0);	//set range parameters
-	m_domain_max = point3D<double>(1.0, 1.0, 1.0);
-	m_voxel_size = vector3D<double>(1.0, 1.0, 1.0);
-}
-
-template <class T>
-rtsImplicit3D<T>::rtsImplicit3D(indextype res_x, indextype res_y, indextype res_z)
-{
-	m_resolution.x = res_x;					//set resolution vector
-	m_resolution.y = res_y;
-	m_resolution.z = res_z;
-	m_data = new T[res_x*res_y*res_z];		//allocate data
-	memset(&m_boundary, 0, sizeof(T));							//initialize boundary condition
-	m_domain_min = point3D<double>(0.0, 0.0, 0.0);	//set range parameters
-	m_domain_max = point3D<double>(1.0, 1.0, 1.0);
-
-	m_voxel_size = m_domain_max - m_domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-}
-
-template <class T>
-rtsImplicit3D<T>::rtsImplicit3D(T* data, indextype res_x, indextype res_y, indextype res_z)
-{
-	m_resolution.x = res_x;					//set resolution vector
-	m_resolution.y = res_y;
-	m_resolution.z = res_z;
-	m_data = new T[res_x*res_y*res_z];		//allocate data
-	//copy the sample data into the data array
-	indextype size = res_x*res_y*res_z;
-	for(indextype i=0; i<size; i++)
-		m_data[i] = data[i];
-	m_boundary = 0;							//initialize boundary condition
-	m_domain_min = point3D<double>(0.0, 0.0, 0.0);	//set range parameters
-	m_domain_max = point3D<double>(1.0, 1.0, 1.0);
-
-	m_voxel_size = domain_max - domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-}
-
-template <class T>
-rtsImplicit3D<T>::rtsImplicit3D(const rtsImplicit3D<T>& original)
-{
-	//copy the shallow variables
-	m_resolution = original.m_resolution;
-	m_boundary = original.m_boundary;
-	m_domain_min = original.m_domain_min;
-	m_domain_max = original.m_domain_max;
-	m_voxel_size = original.m_voxel_size;
-
-	//allocate space for the data
-	m_data = new T[m_resolution.x * m_resolution.y * m_resolution.z];
-	//copy the data
-	blit3D(original.m_data,
-		   0, 0, 0,
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_data,
-		   0, 0, 0,
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_resolution.x, m_resolution.y, m_resolution.z);
-}
-
-template <class T>
-rtsImplicit3D<T>::~rtsImplicit3D()
-{
-	delete m_data;
-}
-
-template <class T>
-typename rtsImplicit3D<T>& rtsImplicit3D<T>::operator=(const T rhs)
-{
-	indextype size = m_resolution.x*m_resolution.y*m_resolution.z;
-	for(int i=0; i<size; i++)
-		m_data[i] = rhs;
-
-	return *this;
-}
-
-template <class T>
-typename rtsImplicit3D<T>& rtsImplicit3D<T>::operator=(const rtsImplicit3D<T>& rhs)
-{
-	//check for self-assignment
-	if(this == &rhs)
-		return *this;
-
-	//deallocate memory
-	if(m_data != NULL)
-		delete m_data;
-
-	//copy the shallow variables
-	m_resolution = rhs.m_resolution;
-	m_boundary = rhs.m_boundary;
-	m_domain_min = rhs.m_domain_min;
-	m_domain_max = rhs.m_domain_max;
-	m_voxel_size = rhs.m_voxel_size;
-
-	//allocate and copy memory
-	m_data = new T[m_resolution.x * m_resolution.y * m_resolution.z];
-	//copy the data
-	blit3D(rhs.m_data,
-		   0,0,0,
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_data, 
-		   0, 0, 0, 
-		   m_resolution.x, m_resolution.y, m_resolution.z,
-		   m_resolution.x, m_resolution.y, m_resolution.z);
-
-	//return the left hand side
-	return *this;
-}
-
-template <class T>
-inline T& rtsImplicit3D<T>::operator ()(indextype x, indextype y, indextype z)
-{
-	return xyz(x, y, z);
-}
-
-template <class T>
-inline T rtsImplicit3D<T>::operator()(double i, double j, double k)
-{
-	return ijk(i, j, k);
-}
-
-template <class T>
-rtsImplicit3D<T>& rtsImplicit3D<T>::operator *=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] *= constant;
-
-	return *this;
-}
-
-template <class T>
-rtsImplicit3D<T>& rtsImplicit3D<T>::operator +=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] += constant;
-
-	return *this;
-}
-template <class T>
-rtsImplicit3D<T>& rtsImplicit3D<T>::operator -=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] -= constant;
-
-	return *this;
-}
-template <class T>
-rtsImplicit3D<T>& rtsImplicit3D<T>::operator /=(const T constant)
-{
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(indextype i = 0; i<size; i++)
-		m_data[i] /= constant;
-
-	return *this;
-}
-template <class T>
-const rtsImplicit3D<T> rtsImplicit3D<T>::operator *(const T constant)
-{
-	rtsImplicit3D<T> result = (*this);
-	result *= constant;
-
-	return result;
-}
-
-template <class T>
-const rtsImplicit3D<T> rtsImplicit3D<T>::operator +(const T constant)
-{
-	rtsImplicit3D<T> result = (*this);
-	result += constant;
-
-	return result;
-}
-
-template <class T>
-const rtsImplicit3D<T> rtsImplicit3D<T>::operator -(const T constant)
-{
-	rtsImplicit3D<T> result = (*this);
-	result -= constant;
-
-	return result;
-}
-
-template <class T>
-const rtsImplicit3D<T> rtsImplicit3D<T>::operator /(const T constant)
-{
-	rtsImplicit3D<T> result = (*this);
-	result /= constant;
-
-	return result;
-}
-
-template <class T>
-template <class U>
-rtsImplicit3D<T>::operator rtsImplicit3D<U>()
-{
-	//cast one type to another
-	//create the data pointer from the current function
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	U* new_data = new U[size];
-	for(int i=0; i<size; i++)
-		new_data[i] = m_data[i];
-	rtsImplicit3D<U> cast_result(new_data, m_resolution, m_boundary, m_domain_min, m_domain_max);
-
-	return cast_result;
-}
-
-template <class T>
-inline T& rtsImplicit3D<T>::xyz(indextype x, indextype y, indextype z)
-{
-	if(x<0 || y<0 || z<0 || x>=m_resolution.x || y>=m_resolution.y || z>=m_resolution.z)
-		return m_boundary;
-	//return m_data[(z * m_resolution.x * m_resolution.y) + (y * m_resolution.x) + x];
-	return m_data[x + m_resolution.x * (y + z * m_resolution.y)];
-
-}
-
-template <class T>
-inline point3D<indextype> rtsImplicit3D<T>::getNearestIndex(indextype i)
-{
-	point3D<indextype> result;
-	result.z = i/(m_resolution.x*m_resolution.y);
-	indextype mod = i%(m_resolution.x*m_resolution.y);
-	result.y = mod/m_resolution.x;
-	result.x = mod%m_resolution.x;
-
-	return result;
-
-}
-
-template <class T>
-void rtsImplicit3D<T>::LoadRAW(indextype header_size, indextype size_x,
-							   indextype size_y, indextype size_z, const char *filename)
-{
-	//set the data size
-	m_resolution = vector3D<indextype>(size_x, size_y, size_z);
-	//delete any previous data
-	if(m_data != NULL)
-		delete m_data;
-
-	ifstream infile(filename, ios::in | ios::binary);
-
-	//load the header
-	unsigned char* header = new unsigned char[header_size];
-	infile.read((char*)header, header_size);
-
-	//load the actual data
-	indextype size = m_resolution.x * m_resolution.y * m_resolution.z;
-	m_data = new T[size];
-	infile.read((char*)m_data, size*sizeof(T));
-
-	//calculate min and maxes
-	infile.close();
-}
-
-template <class T>
-void rtsImplicit3D<T>::LoadVOL(const char *filename)
-{
-	ifstream infile(filename, ios::in | ios::binary);	//create the files stream
-	if(!infile)
-		return;
-
-	indextype size_x, size_y, size_z;				//create variables to store the size of the data set
-	//load the dimensions of the data set
-	infile.read((char*)&size_x, sizeof(int));			//load the file header
-	infile.read((char*)&size_y, sizeof(int));
-	infile.read((char*)&size_z, sizeof(int));
-
-	//close the file
-	infile.close();
-	//load the raw data
-	LoadRAW(12, size_x, size_y, size_z, filename);
-}
-
-template <class T>
-void rtsImplicit3D<T>::SaveVOL(const char *filename)
-{
-	ofstream outfile(filename, ios::out | ios::binary);	//create the binary file stream
-
-	//write the volume size to the file
-	vector3D<int> vol_size = m_resolution;
-	outfile.write((char*)&vol_size.x, sizeof(int));
-	outfile.write((char*)&vol_size.y, sizeof(int));
-	outfile.write((char*)&vol_size.z, sizeof(int));
-
-	outfile.write((char*)m_data, sizeof(char)*vol_size.x*vol_size.y*vol_size.z);
-}
-
-template <class T>
-void rtsImplicit3D<T>::SaveRAW(const char *filename)
-{
-	ofstream outfile(filename, ios::out | ios::binary);	//create the binary file stream
-
-	//write the volume data
-	outfile.write((char*)m_data, sizeof(T)*m_resolution.x*m_resolution.y*m_resolution.z);
-}
-
-template <class T>
-inline T rtsImplicit3D<T>::ijk(double i, double j, double k)
-{
-	/*This function determines the value at the specified parametric points
-	defined by the m_domain_min and m_domain_max parameter values.*/
-
-	//if the parameter is outside the range, return the boundary value
-	if(i<m_domain_min.x || j<m_domain_min.y || k<m_domain_min.z ||
-	   i>m_domain_max.x || j>m_domain_max.y || k>m_domain_max.z)
-	   return m_boundary;
-	
-	point3D<double> index = getFractionalIndex(i, j, k);
-
-	//cout<<index.x<<","<<index.y<<","<<index.z<<endl;
-
-	//interpolate the values
-	int f_x = (int)floor(index.x);				//calculate floor and ceiling values
-	int f_y = (int)floor(index.y);
-	int f_z = (int)floor(index.z);
-	int c_x = (int)ceil(index.x);
-	int c_y = (int)ceil(index.y);
-	int c_z = (int)ceil(index.z);
-
-	double x_d = index.x - f_x;			//find the point within the voxel
-	double y_d = index.y - f_y;
-	double z_d = index.z - f_z;
-
-	T i_1 = xyz(f_x, f_y, f_z)*(1.0 - z_d) + xyz(f_x, f_y, c_z)*(z_d);	//interpolate along z
-	T i_2 = xyz(f_x, c_y, f_z)*(1.0 - z_d) + xyz(f_x, c_y, c_z)*(z_d);
-	T j_1 = xyz(c_x, f_y, f_z)*(1.0 - z_d) + xyz(c_x, f_y, c_z)*(z_d);
-	T j_2 = xyz(c_x, c_y, f_z)*(1.0 - z_d) + xyz(c_x, c_y, c_z)*(z_d);
-
-	T w_1 = i_1*(1.0 - y_d) + i_2*(y_d);
-	T w_2 = j_1*(1.0 - y_d) + j_2*(y_d);
-
-	return w_1*(1.0 - x_d) + w_2*(x_d);
-}
-
-
-template <class T>
-void rtsImplicit3D<T>::Parameterize(double x_min, double x_max, double y_min, double y_max, double z_min, double z_max)
-{
-	m_domain_min = point3D<double>(x_min, y_min, z_min);
-	m_domain_max = point3D<double>(x_max, y_max, z_max);
-	m_voxel_size = m_domain_max - m_domain_min;
-	m_voxel_size.x /= m_resolution.x;
-	m_voxel_size.y /= m_resolution.y;
-	m_voxel_size.z /= m_resolution.z;
-}
-
-template <class T>
-inline point3D<double> rtsImplicit3D<T>::getParameter(indextype x, indextype y, indextype z)
-{
-	//get the value between 0 and 1
-	point3D<double> normalized((double)x / (double)(m_resolution.x) + (1.0/(m_resolution.x*2.0)),
-							   (double)y / (double)(m_resolution.y) + (1.0/(m_resolution.y*2.0)),
-							   (double)z/(double)(m_resolution.z) + (1.0/(m_resolution.z*2.0)));
-
-	point3D<double> result(normalized.x * (m_domain_max.x - m_domain_min.x) + m_domain_min.x,
-						   normalized.y * (m_domain_max.y - m_domain_min.y) + m_domain_min.y,
-						   normalized.z * (m_domain_max.z - m_domain_min.z) + m_domain_min.z);
-
-	return result;
-}
-
-template <class T>
-inline point3D<indextype> rtsImplicit3D<T>::getNearestIndex(double i, double j, double k)
-{
-	//this function returns the index of the voxel containing the specified parameter point
-	point3D<double> normalized((i - m_domain_min.x)/(m_domain_max.x-m_domain_min.x),
-							   (j - m_domain_min.y)/(m_domain_max.y-m_domain_min.y),
-							   (k - m_domain_min.z)/(m_domain_max.z-m_domain_min.z));
-	
-	point3D<indextype> result((normalized.x - (1.0/(m_resolution.x*2.0)))*(double)m_resolution.x+0.5,
-							  (normalized.y - (1.0/(m_resolution.y*2.0)))*(double)m_resolution.y+0.5,
-							  (normalized.z - (1.0/(m_resolution.z*2.0)))*(double)m_resolution.z+0.5);
-
-	return result;
-}
-
-template <class T>
-inline point3D<double> rtsImplicit3D<T>::getFractionalIndex(double i, double j, double k)
-{
-	//this function returns the index of the voxel containing the specified parameter point
-	point3D<double> normalized((i - m_domain_min.x)/(m_domain_max.x-m_domain_min.x),
-							   (j - m_domain_min.y)/(m_domain_max.y-m_domain_min.y),
-							   (k - m_domain_min.z)/(m_domain_max.z-m_domain_min.z));
-	
-	point3D<double> result((normalized.x - (1.0/(m_resolution.x*2.0)))*(double)m_resolution.x,
-							  (normalized.y - (1.0/(m_resolution.y*2.0)))*(double)m_resolution.y,
-							  (normalized.z - (1.0/(m_resolution.z*2.0)))*(double)m_resolution.z);
-	return result;
-}
-
-
-template <class T>
-T* rtsImplicit3D<T>::GetBits()
-{
-	/*Returns bit data in lexocographical order (possibly for 3D texture mapping)*/
-	return m_data;
-}
-
-template <class T>
-rtsImplicit3D<T>* rtsImplicit3D<T>::Resample(indextype newres_x, indextype newres_y, indextype newres_z)
-{
-	/*This function resamples the current function at the specified resolution.
-	No convolution is done for reducing he resolution.
-	*/
-
-	rtsImplicit3D<T>* result = new rtsImplicit3D<T>(vector3D<indextype>(newres_x, newres_y, newres_z),
-						    m_boundary, m_domain_min, m_domain_max);
-
-	//run through the entire resolution of the new function, sampling the current function
-	int x, y, z;
-	point3D<double> parametric;
-	for(x = 0; x<newres_x; x++)
-		for(y=0; y<newres_y; y++)
-			for(z=0; z<newres_z; z++)
-			{
-				//compute the parametric point for the sample point
-				parametric = result->getParameter(x, y, z);
-				(*result)(x, y, z) = ijk(parametric.x, parametric.y, parametric.z);
-			}
-
-	return result;
-}
-
-template <class T>
-void rtsImplicit3D<T>::Scale(T new_min, T new_max)
-{
-	/*This function scales all values of the implicit function to within a specified range
-	*/
-
-	//find the minimum and maximum values in this function
-	indextype data_size = m_resolution.x * m_resolution.y * m_resolution.z;
-	T min = m_data[0];
-	T max = m_data[0];
-	for(indextype i=0; i<data_size; i++)
-	{
-		if(m_data[i] < min)
-			min = m_data[i];
-		if(m_data[i] > max)
-			max = m_data[i];
-	}
-
-	//scale all values to the specified range
-	T current_range = max - min;
-	T new_range = new_max - new_min;
-	for(indextype i=0; i<data_size; i++)
-		m_data[i] = ((m_data[i] - min)/current_range)*(new_range) + new_min;
-}
-
-template <class T>
-void rtsImplicit3D<T>::Crop(indextype x, indextype y, indextype z, 
-							indextype size_x, indextype size_y, indextype size_z)
-{
-	/*This function crops the implicit function at the specified nodes
-	*/
-	//create a pointer for the new data
-	T* new_data = new T[size_x*size_y*size_z];
-
-	//blit from the old data to the new data
-	blit3D(m_data,
-			x, y, z,
-			m_resolution.x, m_resolution.y, m_resolution.z,
-			new_data,
-			0, 0, 0,
-			size_x, size_y, size_z,
-			size_x, size_y, size_z);
-
-	//change the shallow variables
-	vector3D<indextype> new_resolution = vector3D<indextype>(size_x, size_y, size_z);
-	vector3D<double> voxel_size = getParameter(0,0,0) - getParameter(1,1,1);
-	point3D<double> new_domain_min = getParameter(x, y, z) - 0.5*voxel_size;
-	point3D<double> new_domain_max = getParameter(size_x-1, size_y - 1, size_z-1) + 0.5*voxel_size;
-	//copy new shallow variables
-	m_resolution = new_resolution;
-	m_domain_min = new_domain_min;
-	m_domain_max = new_domain_max;
-
-	//copy data
-	delete m_data;
-	m_data = new_data;
-
-}
-
-template <class T>
-void rtsImplicit3D<T>::Threshold(T min, T value)
-{
-	/*This function sets all values between min and max to value.
-	*/
-	int x, y, z;
-	T test_value;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				test_value = xyz(x, y, z);
-				if(test_value >= min)
-					xyz(x, y, z) = value;
-			}
-}
-
-template <class T>
-void rtsImplicit3D<T>::Threshold(T min, T max, T value)
-{
-	/*This function sets all values between min and max to value.
-	*/
-	int x, y, z;
-	T test_value;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				test_value = xyz(x, y, z);
-				if(test_value >= min && test_value <= max)
-					xyz(x, y, z) = value;
-			}
-}
-
-template <class T>
-void rtsImplicit3D<T>::Threshold(T min, T max, T inside, T outside)
-{
-	/*This function sets all values between min and max to value.
-	*/
-	int x, y, z;
-	T test_value;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				test_value = xyz(x, y, z);
-				if(test_value >= min && test_value <= max)
-					xyz(x, y, z) = inside;
-				else
-					xyz(x, y, z) = outside;
-			}
-}
-
-template <class T>
-void rtsImplicit3D<T>::Insert(rtsDTGrid3D<T>* dt_grid, double factor, indextype pos_x, indextype pos_y, indextype pos_z)
-{
-/*	This function copies a 3D DT-Grid into the implicit function at the specified position.
-*/
-	rtsDTGrid3D<T>::iterator i;
-	indextype x, y, z;
-	for(i=dt_grid->begin(); i != dt_grid->end(); i.increment())	//for each node in the grid
-	{
-		x = pos_x + i.getX();
-		y = pos_y + i.getY();
-		z = pos_z + i.getZ();
-		if(x >= 0 || x < m_resolution.x ||
-			y >= 0 || y < m_resolution.y ||
-			y >= 0 || y < m_resolution.z)
-			xyz(x, y, z) = max(i.value* factor, (double)xyz(x, y, z));
-	}
-}
-
-template <class T>
-void rtsImplicit3D<T>::Insert(rtsImplicit3D<T>* source, indextype x, indextype y, indextype z)
-{
-	blit3D(source->m_data, 0, 0, 0, source->m_resolution.x, source->m_resolution.y, source->m_resolution.z,
-			m_data, x, y, z, m_resolution.x, m_resolution.y, m_resolution.z,
-			source->m_resolution.x, source->m_resolution.y, source->m_resolution.z);
-}
-
-
-template <class T>
-inline float rtsImplicit3D<T>::manhattan_distance(rtsImplicit3D<float>* function, point3D<indextype> point, bool sdf)
-{
-	/*This function updates the manhattan distance from a surface using the manhattan
-	distance of its neighboring points.
-	*/
-	indextype x, y, z;
-	x=point.x; y=point.y, z=point.z;
-	int sign = 1;
-	float result = DIST_MAX;
-	float near_value;				//the value of the neighbor being considered
-	float possible_value;			
-	if(x!=0)
-	{ 
-		near_value = (*function)(x-1, y, z);
-		if(!sdf)
-			result = min(result, near_value + (float)m_voxel_size.x);
-		else
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + m_voxel_size.x);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-
-	}
-	if(x!=function->DimX()-1)
-	{
-		near_value = (*function)(x+1, y, z);
-		if(!sdf)
-			result = min(result, near_value + (float)m_voxel_size.x);
-		else
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + m_voxel_size.x);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(y!=0)
-	{
-		near_value = (*function)(x, y-1, z);
-		if(!sdf)
-			result = min(result, near_value + (float)m_voxel_size.y);
-		else
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + m_voxel_size.y);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(y!=function->DimY()-1)
-	{
-		near_value = (*function)(x, y+1, z);
-		if(!sdf)
-			result = min(result, near_value + (float)m_voxel_size.y);
-		else
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + m_voxel_size.y);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(z!=0)
-	{
-		near_value = (*function)(x, y, z-1);
-		if(!sdf)
-			result = min(result, near_value + (float)m_voxel_size.z);
-		else
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + m_voxel_size.z);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(z!=function->DimZ()-1)
-	{
-		near_value = (*function)(x, y, z+1);
-		if(!sdf)
-			result = min(result, near_value + (float)m_voxel_size.z);
-		else
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + m_voxel_size.z);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	return result;
-}
-
-template <class T>
-inline float rtsImplicit3D<T>::isosurface_distance(point3D<double> p0, point3D<double> p1, T isovalue)
-{
-	/*This function computes the distance from p0 to the surface, given two points p0 and p1
-	on either side of the surface.  isovalue specifies
-	the value at the surface.  Right now, this function returns a float.  I'll have to think
-	of something better to do in the future.
-	*/
-
-	//compute the normalized position of the surface between p0 and p1
-	float val0 = ijk(p0.x, p0.y, p0.z);
-	float val1 = ijk(p1.x, p1.y, p1.z);
-	float isovalue_norm_pos = (isovalue - val0) / (val1 - val0);
-	//compute the actual position of the surface
-	point3D<double> s_pos = p0 + isovalue_norm_pos * (p1 - p0);
-	//compute the distance from p0 to the surface
-	float result = (s_pos - p0).Length();
-	//cout<<"distance: "<<result<<endl;
-	return result;
-}
-
-template <class T>
-void rtsImplicit3D<T>::compute_distance_function_boundary(T isovalue, 
-														  rtsImplicit3D<float>* &result, 
-														  rtsImplicit3D<bool>* &mask, bool sdf)
-{
-	/*This function creates an initial signed distance function from a threshold image.
-	All voxels adjacent to the surface specified by the threshold are initialized with a
-	distance value.  Low values are inside, high values are outside.
-	*/
-	//current and neighboring voxel flags (false = inside, true = outside)
-	bool c, x_p, x_n, y_p, y_n, z_p, z_n;
-	float d_xp, d_xn, d_yp, d_yn, d_zp, d_zn;
-	float in_out = 1;
-
-	//boundary condition function and the mask
-	result = new rtsImplicit3D<float>(m_resolution.x, m_resolution.y, m_resolution.z);
-	//get the parameterization
-	result->Parameterize(m_domain_min.x, m_domain_max.x, m_domain_min.y, m_domain_max.y, m_domain_min.z, m_domain_max.z);
-	(*result) = DIST_MAX;
-	result->setBoundary(DIST_MAX);	
-	//create a mask
-	mask = new rtsImplicit3D<bool>(m_resolution.x, m_resolution.y, m_resolution.z);
-	(*mask) = false;
-
-	cout<<"done making boundary condition function"<<endl;
-	//for each voxel
-	int x, y, z;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				//reset flags
-				c=x_p=x_n=y_p=y_n=z_p=z_n=true;
-				in_out = 1.0;
-				//look at the current voxel
-				if(xyz(x, y, z) < isovalue)
-					c=false;
-				else c=true;
-				//if the voxel is outside the domain, assume that it is equal to the current voxel
-				if(x-1 < 0) x_n = c;	//X
-				else if(xyz(x-1, y, z) < isovalue) x_n = false;
-				if(x+1 >= m_resolution.x) x_p = c;
-				else if(xyz(x+1, y, z) < isovalue) x_p = false;
-				if(y-1 < 0) y_n = c;	//Y
-				else if(xyz(x, y-1, z) < isovalue) y_n = false;
-				if(y+1 >= m_resolution.y) y_p = c;
-				else if(xyz(x, y+1, z) < isovalue) y_p = false;
-				if(z-1 < 0) z_n = c;	//Z
-				else if(xyz(x, y, z-1) < isovalue) z_n = false;
-				if(z+1 >= m_resolution.z) z_p = c;
-				else if(xyz(x, y, z+1) < isovalue) z_p = false;
-
-				//set the distance from the isosurface
-				if(c == false && sdf)
-					in_out = -1.0;
-				if(x_n != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-										 isosurface_distance(getParameter(x, y, z), 
-													  getParameter(x-1, y, z),
-													  isovalue) * in_out);
-				if(x_p != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											isosurface_distance(getParameter(x, y, z), 
-													  getParameter(x+1, y, z),
-													  isovalue) * in_out);
-				if(y_n != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											isosurface_distance(getParameter(x, y, z), 
-													  getParameter(x, y-1, z),
-													  isovalue) * in_out);
-				if(y_p != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											isosurface_distance(getParameter(x, y, z), 
-													  getParameter(x, y+1, z),
-													  isovalue) * in_out);
-				if(z_n != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											isosurface_distance(getParameter(x, y, z-1), 
-													  getParameter(x, y, z),
-													  isovalue) * in_out);
-				if(z_p != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											isosurface_distance(getParameter(x, y, z), 
-													  getParameter(x, y, z+1),
-													  isovalue) * in_out);
-
-				//set the mask to 1 if the voxel is on an edge node
-				if(x_n != c || x_p != c || y_n != c || y_p != c || z_n != c || z_p != c)
-					(*mask)(x, y, z) = true;
-			}
-				
-
-	//if a line between the two voxels crosses the surface
-		//find the distance between the voxel center and the surface
-
-
-			cout<<"done computing boundary conditions"<<endl;
-}
-
-template <class T>
-rtsImplicit3D<float>* rtsImplicit3D<T>::EstimateAmbient(T threshold)
-{
-	rtsImplicit3D<float>* result = new rtsImplicit3D<float>(m_resolution.x, m_resolution.y, m_resolution.z);		//create a new implicit function
-	(*result) = 0.0f;
-	rtsImplicit3D<float>* temp = new rtsImplicit3D<float>(m_resolution.x, m_resolution.y, m_resolution.z);	//temp buffer for current lighting iteration
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	
-	cout<<"first iteration..."<<endl;
-	int x,y,z;
-	float ambient;
-	
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y, z-1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"second iteration..."<<endl;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"third iteration..."<<endl;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z);
-				if(xyz(x, y, z-1) < threshold)
-					ambient += (*temp)(x, y, z-1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"fourth iteration..."<<endl;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"fifth iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z);
-				if(xyz(x, y, z-1) < threshold)
-					ambient += (*temp)(x, y, z-1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"sixth iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"seventh iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z);
-				if(xyz(x, y, z-1) < threshold)
-					ambient += (*temp)(x, y, z-1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"eighth iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	(*result)/=8.0;
-	
-	return result;
-}
-
-
-template <class T>
-rtsImplicit3D<float>* rtsImplicit3D<T>::EstimateAttenuatedAmbient(T threshold, T transparent, float attenuation)
-{
-	rtsImplicit3D<float>* result = new rtsImplicit3D<float>(m_resolution.x, m_resolution.y, m_resolution.z);		//create a new implicit function
-	(*result) = 0.0f;
-	rtsImplicit3D<float>* temp = new rtsImplicit3D<float>(m_resolution.x, m_resolution.y, m_resolution.z);	//temp buffer for current lighting iteration
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	
-	cout<<"first iteration..."<<endl;
-	int x,y,z;
-	float ambient;
-	
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z)*(1.0 - (xyz(x-1, y, z)/255.0)*attenuation);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z)*(1.0 - (xyz(x, y-1, z)/255.0)*attenuation);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y, z-1)*(1.0 - (xyz(x, y, z-1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += min(1.0, ambient/3.0);
-				//if(ambient > 3.0)
-				//	cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"second iteration..."<<endl;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z)*(1.0 - (xyz(x-1, y, z)/255.0)*attenuation);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z)*(1.0 - (xyz(x, y-1, z)/255.0)*attenuation);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1)*(1.0 - (xyz(x, y, z+1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"third iteration..."<<endl;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z)*(1.0 - (xyz(x-1, y, z)/255.0)*attenuation);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z)*(1.0 - (xyz(x, y+1, z)/255.0)*attenuation);
-				if(xyz(x, y, z-1) < threshold)
-					ambient += (*temp)(x, y, z-1)*(1.0 - (xyz(x, y, z-1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"fourth iteration..."<<endl;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x-1, y, z) < threshold)
-					ambient += (*temp)(x-1, y, z)*(1.0 - (xyz(x-1, y, z)/255.0)*attenuation);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z)*(1.0 - (xyz(x, y+1, z)/255.0)*attenuation);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1)*(1.0 - (xyz(x, y, z+1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"fifth iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z)*(1.0 - (xyz(x+1, y, z)/255.0)*attenuation);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z)*(1.0 - (xyz(x, y-1, z)/255.0)*attenuation);
-				if(xyz(x, y, z-1) < threshold)
-					ambient += (*temp)(x, y, z-1)*(1.0 - (xyz(x, y, z-1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"sixth iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z)*(1.0 - (xyz(x+1, y, z)/255.0)*attenuation);
-				if(xyz(x, y-1, z) < threshold)
-					ambient += (*temp)(x, y-1, z)*(1.0 - (xyz(x, y-1, z)/255.0)*attenuation);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1)*(1.0 - (xyz(x, y, z+1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"seventh iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z)*(1.0 - (xyz(x+1, y, z)/255.0)*attenuation);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z)*(1.0 - (xyz(x, y+1, z)/255.0)*attenuation);
-				if(xyz(x, y, z-1) < threshold)
-					ambient += (*temp)(x, y, z-1)*(1.0 - (xyz(x, y, z-1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	cout<<"eighth iteration..."<<endl;
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=m_resolution.z-1; z>=0; z--)
-			{
-				ambient = 0.0;
-				if(xyz(x+1, y, z) < threshold)
-					ambient += (*temp)(x+1, y, z)*(1.0 - (xyz(x+1, y, z)/255.0)*attenuation);
-				if(xyz(x, y+1, z) < threshold)
-					ambient += (*temp)(x, y+1, z)*(1.0 - (xyz(x, y+1, z)/255.0)*attenuation);
-				if(xyz(x, y, z+1) < threshold)
-					ambient += (*temp)(x, y, z+1)*(1.0 - (xyz(x, y, z+1)/255.0)*attenuation);
-
-				(*temp)(x, y, z) += ambient/3.0;
-				(*result)(x, y, z) += ambient/3.0;
-				if(ambient > 3.0)
-					cout<<"error"<<endl;
-			}
-	(*temp) = 0.0f;
-	temp->setBoundary(1.0);
-	cout<<"done."<<endl;
-
-	(*result)/=8.0;
-	
-	return result;
-}
-
-template <class T>
-rtsImplicit3D<float>* rtsImplicit3D<T>::Isodistance_Manhattan(T isovalue, bool sdf)
-{
-	rtsImplicit3D<float>* function;
-	rtsImplicit3D<bool>* mask;
-	compute_distance_function_boundary(isovalue, function, mask, sdf);
-
-	//compute the manhattan distance for the entire function
-	//use fast sweeping to compute the manhattan distance
-	//0:X  0:Y  0:Z
-	cout<<"first iteration..."<<endl;
-	int x,y,z;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	cout<<"second iteration..."<<endl;
-	//0:X 0:Y Z:0
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=m_resolution.z-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	cout<<"third iteration..."<<endl;
-	//0:X Y:0 0:Z
-	for(x=0; x<m_resolution.x; x++)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=0; z<m_resolution.z; z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	cout<<"fourth iteration..."<<endl;
-	//0:X Y:0 Z:0
-	for(x=0; x<m_resolution.x; x++)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=m_resolution.z-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	cout<<"fifth iteration..."<<endl;
-	//X:0 0:Y 0:Z
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	cout<<"sixth iteration..."<<endl;
-	//X:0 0:Y Z:0
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=m_resolution.z-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	cout<<"seventh iteration..."<<endl;
-	//X:0 Y:0 0:Z
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=0; z<m_resolution.z; z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	cout<<"eighth iteration..."<<endl;
-	//X:0 Y:0 Z:0
-	for(x=m_resolution.x-1; x>=0; x--)
-		for(y=m_resolution.y-1; y>=0; y--)
-			for(z=m_resolution.z-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = manhattan_distance(function, point3D<indextype>(x, y, z), sdf);
-	cout<<"done."<<endl;
-	
-
-	return function;
-}
-
-//computes the gradient along all three dimensions and returns a vector field
-template <class T>
-rtsImplicit3D<vector3D<T>>* rtsImplicit3D<T>::Gradient()
-{
-	int x, y, z;
-	rtsImplicit3D<vector3D<T>>* result = new rtsImplicit3D<vector3D<T>>(m_resolution.x, m_resolution.y, m_resolution.z);
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				result->xyz(x, y, z).x = xyz(x-1, y, z) - xyz(x, y, z);
-				result->xyz(x, y, z).y = xyz(x, y-1, z) - xyz(x, y, z);
-				result->xyz(x, y, z).z = xyz(x, y, z-1) - xyz(x, y, z);
-			}
-	return result;
-}
-
-
-template <class T>
-int rtsImplicit3D<T>::Neighbors26(indextype x, indextype y, indextype z, T isovalue)
-{
-	int neighbors = 0;
-	int u,v,w;
-
-	for(u=-1; u<=1; u++)
-		for(v=-1; v<=1; v++)
-			for(w=-1; w<=1; w++)
-				if(xyz(x+u, y+v, z+w) >= isovalue)
-					neighbors++;
-	if(xyz(x, y, z) > isovalue)
-		neighbors--;
-
-	return neighbors;
-}
-
-template <class T>
-unsigned int rtsImplicit3D<T>::Neighbors6(indextype x, indextype y, indextype z, T threshold)
-{
-
-	unsigned int neighbors = 0;
-	if(xyz(x+1, y, z) >= threshold)
-		neighbors++;
-	if(xyz(x-1, y, z) >= threshold)
-		neighbors++;
-	if(xyz(x, y+1, z) >= threshold)
-		neighbors++;
-	if(xyz(x, y-1, z) >= threshold)
-		neighbors++;
-	if(xyz(x, y, z+1) >= threshold)
-		neighbors++;
-	if(xyz(x, y, z-1) >= threshold)
-		neighbors++;
-
-	return neighbors;
-}
-
-template <class T>
-bool rtsImplicit3D<T>::TestTopology(T isovalue, unsigned int x, unsigned int y, unsigned int z)
-{
-	if(xyz(x,y,z) < isovalue)
-		return false;
-	//This function returns true if a voxel is necessary, otherwise it returns false
-	unsigned int neighbors = Neighbors(x, y, z, isovalue);
-
-	if(neighbors == 3)
-		return false;
-	if(neighbors == 0 || neighbors == 1 || neighbors == 4)
-		return true;
-	if(neighbors == 2)
-	{
-		if(xyz(x-1, y, z) >= isovalue && xyz(x+1, y, z) >= isovalue)
-			return true;
-		if(xyz(x, y-1, z) >= isovalue && xyz(x, y+1, z) >= isovalue)
-			return true;
-		return false;
-	}
-	
-}
-
-template <class T>
-void rtsImplicit3D<T>::FloodFill6(indextype x, indextype y, indextype z, T target_value)
-{
-	T old_value = xyz(x, y, z);					//find the old value (the value being flood-filled)
-	if(target_value == old_value)				//if the target value is the same as the old value, nothing to do
-		return;
-
-	queue<point3D<indextype>> Q;				//create a queue for neighboring points
-	point3D<indextype> current(x, y, z);		//start with the current point
-	xyz(current.x, current.y, current.z) = target_value;
-	point3D<indextype> next;
-	Q.push(current);
-	indextype u, v, w;
-
-	while(!Q.empty())							//continue until the queue is empty
-	{
-		current = Q.front();					//get the first element from the queue
-		Q.pop();							
-		
-		if(current.x != m_resolution.x - 1)
-			if(xyz(current.x + 1, current.y, current.z) == old_value)
-			{
-				xyz(current.x + 1, current.y, current.z) = target_value;
-				Q.push(point3D<indextype>(current.x + 1, current.y, current.z));
-			}
-		if(current.x != 0)
-			if(xyz(current.x - 1, current.y, current.z) == old_value)
-			{
-				xyz(current.x - 1, current.y, current.z) = target_value;
-				Q.push(point3D<indextype>(current.x - 1, current.y, current.z));
-			}
-		if(current.y != m_resolution.y - 1)
-			if(xyz(current.x, current.y +1, current.z) == old_value)
-			{
-				xyz(current.x, current.y+1, current.z) = target_value;
-				Q.push(point3D<indextype>(current.x, current.y+1, current.z));
-			}
-		if(current.y != 0)
-			if(xyz(current.x, current.y-1, current.z) == old_value)
-			{
-				xyz(current.x, current.y-1, current.z) = target_value;
-				Q.push(point3D<indextype>(current.x, current.y-1, current.z));
-			}
-		if(current.z != m_resolution.z - 1)
-			if(xyz(current.x, current.y, current.z+1) == old_value)
-			{
-				xyz(current.x, current.y, current.z+1) = target_value;
-				Q.push(point3D<indextype>(current.x, current.y, current.z+1));
-			}
-		if(current.z != 0)
-			if(xyz(current.x, current.y, current.z-1) == old_value)
-			{
-				xyz(current.x, current.y, current.z-1) = target_value;
-				Q.push(point3D<indextype>(current.x, current.y, current.z-1));
-			}
-
-	}
-
-}
-
-template <class T>
-void rtsImplicit3D<T>::FloodFill26(int x, int y, int z, T target_value)
-{
-	T old_value = xyz(x, y, z);
-	if(target_value == old_value)
-		return;
-
-	queue<point3D<indextype>> Q;
-	point3D<indextype> current(x, y, z);
-	point3D<indextype> next;
-	Q.push(current);
-	indextype u, v, w;
-	while(!Q.empty())
-	{
-		current = Q.front();
-		if(xyz(current.x, current.y, current.z) == old_value)
-			xyz(current.x, current.y, current.z) = target_value;
-		Q.pop();
-		for(u=-1; u<=1; u++)
-			for(v=-1; v<=1; v++)
-				for(w=-1; w<=1; w++)
-				{
-					next.x = current.x + u;
-					next.y = current.y + v;
-					next.z = current.z + w;
-
-					if(next.x >= 0 && next.x < m_resolution.x &&
-						next.y >= 0 && next.y < m_resolution.y &&
-						next.z >= 0 && next.z < m_resolution.z &&
-						xyz(next.x, next.y, next.z) == old_value)
-						{
-							xyz(next.x, next.y, next.z) = target_value;
-							Q.push(next);
-						}
-				}
-	}
-
-				
-}
-
-template <class T>
-void rtsImplicit3D<T>::Binary(T threshold, T true_value)
-{
-	/**
-	This function converts an implicit function into a binary or characteristic function describing the solid represented by the level
-	set at isovalue "threshold".  All values below threshold are set to zero while all values above threshold are set to the specified
-	"true_value".  In order to use this function, the data type T must be able to be set to 0.
-	**/
-	int max_index = m_resolution.x * m_resolution.y * m_resolution.z;	//find the size of the data array
-	int i;
-	for(i=0; i<max_index; i++)
-		if(m_data[i] >= threshold)
-			m_data[i] = true_value;
-		else
-			m_data[i] = 0;
-}
-
-template <class T>
-vector<point3D<indextype>> rtsImplicit3D<T>::getEdgeNodes(T isovalue, bool protrusions = true)
-{
-	vector<point3D<indextype>> result;
-	indextype x, y, z;
-	int neighbors;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				if(xyz(x, y, z) >= isovalue)
-				{
-					neighbors = Neighbors26(x, y, z, isovalue);
-					if(protrusions == false && neighbors < 1)
-						continue;
-					if(neighbors < 26)
-						result.push_back(point3D<indextype>(x, y, z));
-				}
-			}
-
-	return result;
-
-}
-
-template <class T>
-unsigned int rtsImplicit3D<T>::BackgroundComponents6(indextype x, indextype y, indextype z, T threshold, int n = 18)
-{
-	/**
-	This function computes the number of 6-connected background components in the local region of (x, y, z).
-	This computation is performed by testing all 6 possible voxels that can connect to the specified node.  If
-	a background node is found, the entire background component associated with that node is filled and the counter
-	is incremented by 1.  The value n specifies the connectivity domain for the flood fill.
-	The definition of background components is that specified by He, Kischell, Rioult and Holmes.
-	**/
-
-	//see if there is at least one BG component
-	if(Neighbors6(x, y, z, threshold) == 6)
-		return 0;
-
-	
-	//retrieve the local region of the function
-	rtsImplicit3D<T> local(3, 3, 3);
-	point3D<indextype> corner(x-1, y-1, z-1);
-	indextype u, v, w;
-	for(u=0; u<3; u++)
-		for(v=0; v<3; v++)
-			for(w=0; w<3; w++)
-				local(u, v, w) = xyz(corner.x + u, corner.y + v, corner.z + w);
-
-	//threshold the background to find inside/outside points
-	local.Binary(threshold, 1);
-	//fill points that are not in the connectivity domain
-	if(n == 18)
-	{
-		local(0, 0, 0) = 1;
-		local(0, 0, 2) = 1;
-		local(0, 2, 0) = 1;
-		local(0, 2, 2) = 1;
-		local(2, 0, 0) = 1;
-		local(2, 0, 2) = 1;
-		local(2, 2, 0) = 1;
-		local(2, 2, 2) = 1;
-	}
-	//local.toConsole();
-
-	//search all 6 possible connected points.  If a background node is found, fill the component
-	unsigned int components = 0;
-	if(local(0, 1, 1) == 0)
-	{
-		components++;
-		local.FloodFill6(0, 1, 1, 1);
-	}
-	if(local(2, 1, 1) == 0)
-	{
-		components++;
-		local.FloodFill6(2, 1, 1, 1);
-	}
-	if(local(1, 0, 1) == 0)
-	{
-		components++;
-		local.FloodFill6(1, 0, 1, 1);
-	}
-	if(local(1, 2, 1) == 0)
-	{
-		components++;
-		local.FloodFill6(1, 2, 1, 1);
-	}
-	if(local(1, 1, 0) == 0)
-	{
-		components++;
-		local.FloodFill6(1, 1, 0, 1);
-	}
-	if(local(1, 1, 2) == 0)
-	{
-		components++;
-		local.FloodFill6(1, 1, 2, 1);
-	}
-
-	return components;
-}
-
-template <class T>
-rtsImplicit3D<T> rtsImplicit3D<T>::Project2D()
-{
-	/**
-	This function projects the entire 3D function onto a 2D function along the z-axis.
-	**/
-	rtsImplicit3D<T> result(m_resolution.x, m_resolution.y, 1);
-	result = 0;
-	
-	indextype x, y, z;
-	for(x = 0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				if(result(x, y, 0) < xyz(x, y, z))
-					result(x, y, 0) = xyz(x, y, z);
-			}
-	return result;
-}
-
-template <class T>
-void rtsImplicit3D<T>::Erode(T isovalue, T fill_value)
-{
-	vector<point3D<indextype>> border_nodes;	//get the border nodes for the image
-	indextype x, y, z;
-	int condition;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-				if(xyz(x, y, z) >= isovalue && BackgroundComponents6(x, y, z, isovalue) == 1)
-				{
-					condition = 0;
-					//now find the border pairs.  A border point must meet two of the following conditions to be a border pair.
-					//south border: s(p) is background
-					if(xyz(x, y-1, z) < isovalue)
-						condition++;
-					//north border: n(p) is background, s(p) and s(s(p)) are foreground
-					if(xyz(x, y+1, z) < isovalue && xyz(x, y-1, z) >= isovalue && xyz(x, y-2, z) >= isovalue)
-						condition++;
-					//west border: w(p) is background
-					if(xyz(x-1, y, z) < isovalue)
-						condition++;
-					//east border: e(p) is background, w(p) and w(w(p)) are foreground
-					if(xyz(x+1, y, z) < isovalue && xyz(x-1, y, z) >= isovalue && xyz(x-2, y, z) >= isovalue)
-						condition++;
-					//up border: u(p) is background
-					if(xyz(x, y, z-1) < isovalue)
-						condition++;
-					//down border: d(p) is background, u(p) and u(u(p)) are foreground
-					if(xyz(x, y, z+1) < isovalue && xyz(x, y, z-1) >= isovalue && xyz(x, y, z-2) >= isovalue)
-						condition++;
-					
-					if(condition > 1)
-						border_nodes.push_back(point3D<indextype>(x, y, z));
-				}
-	cout<<"Number of border nodes: "<<border_nodes.size()<<endl;
-	
-	vector<point3D<indextype>>::iterator i;
-	for(i=border_nodes.begin(); i!= border_nodes.end(); i++)
-		xyz((*i).x, (*i).y, (*i).z) = fill_value;
-
-
-}
-
-template <class T>
-void rtsImplicit3D<T>::ClampMax(T max)
-{
-	int i;
-	int elements = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(i=0; i<elements; i++)
-		if(m_data[i] > max)
-			m_data[i] = max;
-}
-
-template <class T>
-void rtsImplicit3D<T>::ClampMin(T min)
-{
-	int i;
-	int elements = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(i=0; i<elements; i++)
-		if(m_data[i] < min)
-			m_data[i] = min;
-}
-
-template <class T>
-void rtsImplicit3D<T>::ClampMin(T min, T value)
-{
-	int i;
-	int elements = m_resolution.x * m_resolution.y * m_resolution.z;
-	for(i=0; i<elements; i++)
-		if(m_data[i] < min)
-			m_data[i] = value;
-}
-
-template <class T>
-void rtsImplicit3D<T>::MedianFilter(int dist_x, int dist_y, int dist_z, double factor = 0.5)
-{
-	rtsImplicit3D<T> result = (*this);
-	indextype x, y, z;
-	indextype min_x, min_y, min_z;
-	indextype max_x, max_y, max_z;
-	indextype u, v, w;
-	vector<T> region;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				region.clear();
-				min_x = x - dist_x;
-				min_y = y - dist_y;
-				min_z = z - dist_z;
-				max_x = x + dist_x;
-				max_y = y + dist_y;
-				max_z = z + dist_z;
-
-				for(u=min_x; u<=max_x; u++)
-					for(v=min_y; v<=max_y; v++)
-						for(w=min_z; w<=max_z; w++)
-						{
-							region.push_back(xyz(u, v, w));
-						}
-				sort(region.begin(), region.end());
-				result(x, y, z) = region[(int)(region.size()*factor)];
-			}
-	(*this) = result;
-}
-
-template <class T>
-unsigned int rtsImplicit3D<T>::Thin(T isovalue)
-{
-	/**
-	This function computes the skeleton of an isosurface embedded in the implicit function and
-	described by the "isovalue" parameter.
-	**/
-
-	vector<point3D<indextype>> border_nodes;	//get the border nodes for the image
-	indextype x, y, z;
-	int condition;
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-				//find the border nodes
-				if(xyz(x, y, z) >= isovalue && BackgroundComponents6(x, y, z, isovalue) == 1 && Neighbors26(x, y, z, isovalue) != 1)
-				{
-					condition = 0;
-					//now find the border pairs.  A border point must meet two of the following conditions to be a border pair.
-					//south border: s(p) is background
-					if(xyz(x, y-1, z) < isovalue)
-						condition++;
-					//north border: n(p) is background, s(p) and s(s(p)) are foreground
-					if(xyz(x, y+1, z) < isovalue && xyz(x, y-1, z) >= isovalue && xyz(x, y-2, z) >= isovalue)
-						condition++;
-					//west border: w(p) is background
-					if(xyz(x-1, y, z) < isovalue)
-						condition++;
-					//east border: e(p) is background, w(p) and w(w(p)) are foreground
-					if(xyz(x+1, y, z) < isovalue && xyz(x-1, y, z) >= isovalue && xyz(x-2, y, z) >= isovalue)
-						condition++;
-					//up border: u(p) is background
-					if(xyz(x, y, z-1) < isovalue)
-						condition++;
-					//down border: d(p) is background, u(p) and u(u(p)) are foreground
-					if(xyz(x, y, z+1) < isovalue && xyz(x, y, z-1) >= isovalue && xyz(x, y, z-2) >= isovalue)
-						condition++;
-					
-					if(condition > 1)
-						border_nodes.push_back(point3D<indextype>(x, y, z));
-				}
-	cout<<"Number of border nodes: "<<border_nodes.size()<<endl;
-
-	//determine if each edge node can be removed without changing the topology of the model
-	//declare some initial variables
-	rtsImplicit3D<T> local(3, 3, 3);	//store the region local to the current voxel
-	int nodes_before, nodes_after;		//number of neighboring nodes before and after the filling operation
-	point3D<indextype> fill_start;
-	vector<point3D<indextype>>::iterator i;
-
-	/*
-	Here we determine if a point can be removed by looking at the number of foreground connected
-	components in the local region.  If there is more than one connected component
-	*/
-	unsigned int removed = 0;
-	for(i=border_nodes.begin(); i<border_nodes.end(); i++)
-	{
-		//get the local region around the current point
-		for(x=-1; x<=1; x++)
-			for(y=-1; y<=1; y++)
-				for(z=-1; z<=1; z++)
-					local(x+1, y+1, z+1) = xyz((*i).x + x, (*i).y + y, (*i).z + z);
-
-		//deal with the degenerate case of all four sides being internal
-		//if(local(0, 1, 0) >= isovalue && local(1, 0, 0) >= isovalue && local(1, 2, 0) >= isovalue && local(2, 1, 0) >= isovalue)
-		//	continue;
-		local(1, 1, 1) = 0;				//remove the center voxel
-		local.Binary(isovalue, 1);
-		nodes_before = local.Neighbors26(1, 1, 1, 1);
-		//if(nodes_before == 1)			//prevent reducing ends
-		//	continue;
-
-		//find an interior voxel to fill
-		for(x=0; x<3; x++)
-			for(y=0; y<3; y++)
-				for(z=0; z<3; z++)
-					if(local(x, y, z) > 0)
-						fill_start = point3D<indextype>(x, y, z);
-
-		//fill the local region
-		local.FloodFill26(fill_start.x, fill_start.y, fill_start.z, 2);
-		//get the number of filled neighbors
-		nodes_after = local.Neighbors26(1, 1, 1, 2);
-		if(nodes_after == nodes_before)
-		{
-			xyz((*i).x, (*i).y, (*i).z) = 0;
-			removed++;
-			//cout<<"removed"<<endl;
-		}
-		//else
-		//{
-			/*for(x=-1; x<=1; x++)
-			for(y=-1; y<=1; y++)
-				for(z=-1; z<=1; z++)
-					local(x+1, y+1, z+1) = xyz((*i).x + x, (*i).y + y, (*i).z + z);
-			local.toConsole();
-			cout<<"not removed:  "<<nodes_before<<"  "<<nodes_after<<endl;
-			xyz((*i).x, (*i).y, (*i).z) = 100;
-			char c;
-			cin>>c;*/
-		//}
-	}
-	return removed;
-}
-
-/*Shape functions*/
-/*These functions create implicit shapes in the function.
-Generally, the shape is based on the parameterization.*/
-template <class T>
-void rtsImplicit3D<T>::Sphere(double center_i, double center_j, double center_k, double radius, T in_value)
-{
-	point3D<double> center(center_i, center_j, center_k);
-	//for each point in the function
-	indextype x, y, z;
-	double radius_squared = radius*radius;
-	vector3D<double> point_to_point;
-	point3D<double> result;
-	double distance_squared;
-
-	for(x=0; x<m_resolution.x; x++)
-		for(y=0; y<m_resolution.y; y++)
-			for(z=0; z<m_resolution.z; z++)
-			{
-				//get the parameterized value
-				result = getParameter(x, y, z);
-				//find the distance between the center of the sphere and the resulting point
-				//double distance = (result - center).Length();
-				point_to_point = result - center;
-				distance_squared = point_to_point*point_to_point;
-				//if the distance is less than the radius, the point is inside the sphere
-				if(distance_squared < radius_squared)
-					xyz(x, y, z) = in_value;
-			}
-			
-}
-
-
-template <class T>
-void rtsImplicit3D<T>::toConsole()
-{
-	cout<<endl;
-	int x, y, z;
-	for(z=0; z<m_resolution.z; z++)
-	{
-		for(y=0; y<m_resolution.y; y++)
-		{
-			for(x=0; x<m_resolution.x; x++)
-			{
-				cout.width(7);
-				cout.precision(3);
-				cout<<(double)xyz(x, y, z);
-			}
-			cout<<endl;
-		}
-		cout<<"-----------------------------"<<endl;
-	}
-
-}
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsInputState.h b/legacy/rtsInputState.h
deleted file mode 100755
index cb55e15..0000000
--- a/legacy/rtsInputState.h
+++ /dev/null
@@ -1,59 +0,0 @@
-#ifndef INPUTSTATE_H
-#define INPUTSTATE_H
-
-class rtsInputState
-{
-private:
-	//mouse states
-	bool m_left_button;
-	bool m_right_button;
-	bool m_middle_button;
-
-	//keyboard keys
-	char* m_keys_pressed;
-
-	//mouse position
-	int m_mouse_x;
-	int m_mouse_y;
-
-	//some cool states for general use
-	bool m_selection_state;
-
-	//modifier keys
-	bool m_alt_key;
-	bool m_ctrl_key;
-	bool m_shift_key;
-
-public:
-	void PressLeftButton() {m_left_button = true;}
-	void ReleaseLeftButton() {m_left_button = false;}
-	void PressMiddleButton() {m_middle_button = true;}
-	void ReleaseMiddleButton() {m_middle_button = false;}
-	void PressRightButton() {m_right_button = true;}
-	void ReleaseRightButton() {m_right_button = false;}
-	void SetMousePosition(int x, int y) {m_mouse_x = x; m_mouse_y = y;}
-	
-	
-	bool getRightButton() {return m_right_button;}
-	bool getLeftButton() {return m_left_button;}
-	bool getMiddleButton() {return m_middle_button;}
-	int getMouseX()	{return m_mouse_x;}
-	int getMouseY()	{return m_mouse_y;}
-
-	//modifier keys
-	bool getShiftState(){return m_shift_key;}
-	bool getAltState(){return m_alt_key;}
-	bool getCtrlState(){return m_ctrl_key;}
-	void setShiftState(bool val){m_shift_key = val;}
-	void setCtrlState(bool val){m_ctrl_key = val;}
-	void setAltState(bool val){m_alt_key = val;}
-
-	//other useful states
-	bool getSelectionState(){return m_selection_state;}
-	void StartSelection(){m_selection_state = true;}
-	void EndSelection(){m_selection_state = false;}
-};
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsLinearAlgebra.h b/legacy/rtsLinearAlgebra.h
deleted file mode 100755
index beee5f1..0000000
--- a/legacy/rtsLinearAlgebra.h
+++ /dev/null
@@ -1,15 +0,0 @@
-/** \file
-    \brief Used to load common 3D linear algebra classes such as matrices, vectors, and points.
-
-The rtsLinearAlgebra.h file is used to load linear algebra objects commonly used in 3D graphics.
-This includes the 3D versions of the vector, point, and matrix classes.
-*/
-
-#define RTS_PI			3.14159				/**<Defines the value of PI used in RTS algorithms*/
-#define TORADIANS(a)	(a)*RTS_PI/180.0	/**<Defines a macro that converts a from degrees to radians*/
-#define TODEGREES(a)	(a)*180.0/RTS_PI	/**<Defines a macro that converts a from radians to degrees*/
-
-#include <math.h>
-#include "rtsVector3d.h"
-#include "rtsPoint3d.h"
-#include "rtsMatrix4x4.h"
\ No newline at end of file
diff --git a/legacy/rtsMath.cpp b/legacy/rtsMath.cpp
deleted file mode 100755
index a8d14e9..0000000
--- a/legacy/rtsMath.cpp
+++ /dev/null
@@ -1,757 +0,0 @@
-/*These files contain basic structures used frequently in the program and in computer
-graphics in general.  For more information, see the header file.
-
--David Mayerich, 8/20/05*/
-
-#include "rtsMath.h"
-
-//#include<iostream>
-
-//using namespace std;
-
-
-
-point3D::point3D()
-{
-	x=0; y=0; z=0;
-}
-
-point3D::point3D(double newx, double newy, double newz)
-{
-	x=newx; y=newy; z=newz;
-}
-
-point3D point3D::operator +(vector3D param)
-{
-	point3D result;
-	result.x=x+param.x;
-	result.y=y+param.y;
-	result.z=z+param.z;
-
-	return result;
-}
-
-point3D point3D::operator -(vector3D param)
-{
-	point3D result;
-	result.x=x-param.x;
-	result.y=y-param.y;
-	result.z=z-param.z;
-
-	return result;
-}
-
-vector3D point3D::operator -(point3D param)
-{
-	vector3D result;
-	result.x=x-param.x;
-	result.y=y-param.y;
-	result.z=z-param.z;
-
-	return result;
-}
-
-void point3D::print()
-{
-	cout<<x<<","<<y<<","<<z<<endl;
-}
-
-vector3D vector3D::operator+(vector3D param)
-{
-	vector3D result;
-	result.x=x+param.x;
-	result.y=y+param.y;
-	result.z=z+param.z;
-
-	return result;
-}
-
-vector3D vector3D::operator -(vector3D param)
-{
-	vector3D result;
-	result.x=x-param.x;
-	result.y=y-param.y;
-	result.z=z-param.z;
-
-	return result;
-}
-double vector3D::operator*(vector3D param)
-{
-	return x*param.x + y*param.y + z*param.z;
-}
-	
-vector3D::vector3D()
-{
-	x=0; y=0; z=0;
-}
-
-vector3D::vector3D(double newx, double newy, double newz)
-{
-	x=newx;
-	y=newy;
-	z=newz;
-}
-
-int vector3D::normalize()
-{
-	double length=sqrt(x*x + y*y + z*z);
-	if(length == 0)
-	{
-		x=0.0;
-		y=0.0;
-		z=0.0;
-	}
-	else
-	{
-		x=x/length;
-		y=y/length;
-		z=z/length;
-	}
-	
-	return 1;
-}
-
-double vector3D::length()
-{
-	return sqrt(x*x + y*y + z*z);
-}
-
-vector3D vector3D::cross(vector3D param)
-{
-	vector3D result;
-	result.x=y*param.z - z*param.y;
-	result.y=z*param.x - x*param.z;
-	result.z=x*param.y - y*param.x;
-
-	return result;
-}
-
-vector3D vector3D::operator *(double param)
-{
-	vector3D result;
-	result.x=x*param;
-	result.y=y*param;
-	result.z=z*param;
-
-	return result;
-}
-
-void vector3D::print()
-{
-	cout<<x<<","<<y<<","<<z<<endl;
-}
-
-matrix4x4::matrix4x4()
-{
-	//initialize to the identity matrix
-	for(int i=0; i<16; i++)
-		matrix[i] = 0.0;
-	matrix[0] = matrix[5] = matrix[10] = matrix[15] = 1.0;
-}
-
-matrix4x4::matrix4x4(float m00, float m01, float m02, float m03,
-			  float m10, float m11, float m12, float m13,
-			  float m20, float m21, float m22, float m23,
-			  float m30, float m31, float m32, float m33)
-{
-	float new_matrix[16] = {m00, m01, m02, m03,m10, m11, m12, m13, m20, m21, m22, m23,m30, m31, m32, m33};
-	for(int i=0; i<16; i++)
-		matrix[i] = new_matrix[i];
-}
-
-matrix4x4::matrix4x4(vector3D basis_x, vector3D basis_y, vector3D basis_z)
-{
-	//initialize to the identity matrix
-	for(int i=0; i<16; i++)
-		matrix[i] = 0.0;
-	matrix[0] = matrix[5] = matrix[10] = matrix[15] = 1.0;
-	//insert the vectors
-	matrix[0] = basis_x.x;
-	matrix[1] = basis_x.y;
-	matrix[2] = basis_x.z;
-
-	matrix[4] = basis_y.x;
-	matrix[5] = basis_y.y;
-	matrix[6] = basis_y.z;
-
-	matrix[8] = basis_z.x;
-	matrix[9] = basis_z.y;
-	matrix[10] = basis_z.z;
-}
-
-double matrix4x4::operator()(unsigned int row, unsigned int col)
-{
-	return matrix[row*4 + col];
-}
-
-void matrix4x4::gl_set_matrix(float* gl_matrix)
-{
-	//for(int row = 0; row<4; row++)
-	//	for(int col = 0; col<4; col++)
-	//		matrix[row*4 + col] = gl_matrix[col*4 + row];
-	for(int i=0; i<16; i++)
-		matrix[i] = gl_matrix[i];
-}
-
-
-void matrix4x4::gl_get_matrix(float* gl_matrix)
-{
-	//for(int row = 0; row<4; row++)
-	//	for(int col = 0; col<4; col++)
-	//		gl_matrix[col*4 + row] = matrix[row*4 + col];
-	for(int i=0; i<16; i++)
-		gl_matrix[i] = matrix[i];
-
-}
-
-matrix4x4 matrix4x4::submatrix(unsigned int start_col, unsigned int start_row, unsigned int end_col, unsigned int end_row)
-{
-	matrix4x4 result;
-	int col, row;
-	for(row = start_row; row<=end_row; row++)
-		for(col = start_col; col <= end_col; col++)
-			result.matrix[col*4 + row] = matrix[col*4 + row];
-	return result;
-
-}
-
-matrix4x4 matrix4x4::transpose()
-{
-	matrix4x4 result;
-	int col, row;
-	for(row = 0; row <4; row++)
-		for(col=0; col<4; col++)
-			result.matrix[col*4 + row] = matrix[row*4+ col];
-	return result;
-}
-
-
-
-vector3D matrix4x4::basis_x()
-{
-	vector3D basis(matrix[0], matrix[1], matrix[2]);
-	return basis;
-}
-
-vector3D matrix4x4::basis_y()
-{
-	vector3D basis(matrix[4], matrix[5], matrix[6]);
-	return basis;
-}
-
-vector3D matrix4x4::basis_z()
-{
-	vector3D basis(matrix[8], matrix[9], matrix[10]);
-	return basis;
-}
-
-
-
-point3D matrix4x4::operator *(point3D param)
-{
-	point3D result;
-	//result.x = matrix[0][0]*param.x + matrix[1][0]*param.y + matrix[2][0]*param.z + matrix[3][0];
-	//result.y = matrix[0][1]*param.x + matrix[1][1]*param.y + matrix[2][1]*param.z + matrix[3][1];
-	//result.z = matrix[0][2]*param.x + matrix[1][2]*param.y + matrix[2][2]*param.z + matrix[3][2];
-	//float homogeneous = matrix[0][3] + matrix[1][3] + matrix[2][3] + matrix[3][3];
-	result.x = matrix[0]*param.x + matrix[4]*param.y + matrix[8]*param.z + matrix[12];
-	result.y = matrix[1]*param.x + matrix[5]*param.y + matrix[9]*param.z + matrix[13];
-	result.z = matrix[2]*param.x + matrix[6]*param.y + matrix[10]*param.z + matrix[14];
-	float homogeneous = matrix[3] + matrix[7] + matrix[11] + matrix[15];
-	result.x/=homogeneous;
-	result.y/=homogeneous;
-	result.z/=homogeneous;
-	
-	return result;
-}
-
-vector3D matrix4x4::operator*(vector3D param)
-{
-	vector3D result;
-	result.x = matrix[0]*param.x + matrix[4]*param.y + matrix[8]*param.z;
-	result.y = matrix[1]*param.x + matrix[5]*param.y + matrix[9]*param.z;
-	result.z = matrix[2]*param.x + matrix[6]*param.y + matrix[10]*param.z;
-	
-	return result;
-}
-
-void matrix4x4::print()
-{
-	for(int row = 0; row<4; row++)
-	{
-		for(int col = 0; col<4; col++)
-		{
-			cout<<matrix[col*4 + row]<<" ";
-		}
-		cout<<endl;
-	}
-}
-		
-
-RGBA::RGBA(double red, double green, double blue, double ambient)
-{
-	r=red;
-	g=green;
-	b=blue;
-	a=ambient;
-}
-
-RGBA::RGBA()
-{
-	r=1.0;
-	g=1.0;
-	b=1.0;
-	a=1.0;
-}
-
-int quaternion::normalize()
-{
-	double length=sqrt(w*w + x*x + y*y + z*z);
-	w=w/length;
-	x=x/length;
-	y=y/length;
-	z=z/length;
-
-	return 1;
-}
-
-quaternion quaternion::operator *(quaternion param)
-{
-	float A, B, C, D, E, F, G, H;
-
-
-	A = (w + x)*(param.w + param.x);
-	B = (z - y)*(param.y - param.z);
-	C = (w - x)*(param.y + param.z); 
-	D = (y + z)*(param.w - param.x);
-	E = (x + z)*(param.x + param.y);
-	F = (x - z)*(param.x - param.y);
-	G = (w + y)*(param.w - param.z);
-	H = (w - y)*(param.w + param.z);
-
-	quaternion result;
-	result.w = B + (-E - F + G + H) /2;
-	result.x = A - (E + F + G + H)/2; 
-	result.y = C + (E - F + G - H)/2; 
-	result.z = D + (E - F - G + H)/2;
-
-	return result;
-}
-
-double* quaternion::toMatrix()
-{
-
-
-    double wx, wy, wz, xx, yy, yz, xy, xz, zz, x2, y2, z2;
-
-
-    // calculate coefficients
-    x2 = x + x; y2 = y + y;
-    z2 = z + z;
-    xx = x * x2; xy = x * y2; xz = x * z2;
-    yy = y * y2; yz = y * z2; zz = z * z2;
-    wx = w * x2; wy = w * y2; wz = w * z2;
-
-	double m[4][4];
-    m[0][0] = 1.0 - (yy + zz); m[1][0] = xy - wz;
-    m[2][0] = xz + wy; m[3][0] = 0.0;
-
-    m[0][1] = xy + wz; m[1][1] = 1.0 - (xx + zz);
-    m[2][1] = yz - wx; m[3][1] = 0.0;
-
-
-    m[0][2] = xz - wy; m[1][2] = yz + wx;
-    m[2][2] = 1.0 - (xx + yy); m[3][2] = 0.0;
-
-
-    m[0][3] = 0; m[1][3] = 0;
-    m[2][3] = 0; m[3][3] = 1;
-
-	double* orientationmatrix=(double*)m;
-	char c;
-
-
-	double* result=new double[16];
-	double* array=(double*)m;
-	for(int i=0; i<16; i++)
-		result[i]=array[i];
-
-	return result;
-}
-
-quaternion::quaternion()
-{
-	w=0.0; x=0.0; y=0.0; z=0.0;
-}
-
-quaternion::quaternion(double c, double i, double j, double k)
-{
-	w=c;  x=i;  y=j;  z=k;
-}
-
-ray3D::ray3D(point3D start_point, vector3D dir)
-{
-	point=start_point;
-	direction=dir;
-	direction.normalize();
-}
-
-ray3D::ray3D(point3D pointA, point3D pointB)
-{
-	point = pointA;
-	direction = pointB - pointA;
-	direction.normalize();
-}
-
-ray3D::ray3D()
-{
-	point = point3D(0, 0, 0);
-	direction = vector3D(0, 0, 1);
-}
-
-int ray3D::intersect(plane3D plane, point3D& intersection_point)
-{
-	double NdotD = plane.normal * direction;		//determine the angle between the plane normal and the ray direction
-	if(NdotD == 0.0)								//if they are orthogonal, the ray is parallel to the plane
-		return RTS_NO_INTERSECTION;
-
-	vector3D E = point - plane.point;			//determine the vector from the ray point to the plane point
-	double NdotE = plane.normal * E;			//find the angle between the plane normal and the above calculated E
-	double t = -NdotE/NdotD;					//the intersection occurrs at time t
-
-	if(t<0)
-		return RTS_NO_INTERSECTION;
-
-	intersection_point = point + direction*t;	//find the intersection point
-	return RTS_OK;
-}
-
-
-
-plane3D::plane3D()
-{
-	point = point3D(0.0, 0.0, 0.0);
-	normal = vector3D(0.0, 0.0, 1.0);
-	normal.normalize();
-}
-
-plane3D::plane3D(point3D point_on_plane, vector3D plane_normal)
-{
-	point = point_on_plane;
-	normal = plane_normal;
-	normal.normalize();
-}
-
-
-function2D::function2D(const function2D &copy)
-{
-	m_x0 = copy.m_x0;
-	m_y0 = copy.m_y0;
-	m_x1 = copy.m_x1;
-	m_y1 = copy.m_y1;
-	m_x_resolution = copy.m_x_resolution;
-	m_y_resolution = copy.m_y_resolution;
-	m_values = new float[m_x_resolution*m_y_resolution];
-
-	for(int i=0; i < m_x_resolution*m_y_resolution; i++)
-		m_values[i] = copy.m_values[i];
-}
-function2D& function2D::operator=(const function2D& f)
-{
-    if (this != &f)							// make sure not same object
-	{						
-        delete m_values;
-		m_x0 = f.m_x0;
-		m_x1 = f.m_x1;
-		m_y0 = f.m_y0;
-		m_y1 = f.m_y1;
-		m_x_resolution = f.m_x_resolution;
-		m_y_resolution = f.m_y_resolution;
-		m_values = new float[m_x_resolution*m_y_resolution];
-		for(int i=0; i<m_x_resolution * m_y_resolution; i++)
-			m_values[i] = f.m_values[i];
-    }
-    return *this;    // Return ref for multiple assignment
-}//end operator=
-
-function2D function2D::operator*(function2D param)
-{
-	//this is a quick and dirty multiplication method (mostly for images)
-
-	if((m_x_resolution != param.m_x_resolution) || (m_y_resolution != param.m_y_resolution))
-		exit(0);
-
-	float* a_bits = m_values;
-	float* b_bits = param.getBits();
-
-	function2D result(m_x0, m_x1, m_y0, m_y1, m_x_resolution, m_y_resolution);
-	//result.m_values = new T[m_x_resolution * m_y_resolution];
-
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-		result.m_values[i] = a_bits[i]*b_bits[i];
-
-	//result.setBits((T*)result_bits);
-	return result;
-}
-function2D function2D::operator*(float param)
-{
-	function2D result(m_x0, m_x1, m_y0, m_y1, m_x_resolution, m_y_resolution);
-	for(int i = 0; i<m_x_resolution*m_y_resolution; i++)
-		result.m_values[i] = m_values[i]*param;
-
-	return result;
-}
-
-function2D function2D::operator+(function2D param)
-{
-	function2D result(m_x0, m_x1, m_y0, m_y1, m_x_resolution, m_y_resolution);
-	for(int i=0; i<m_x_resolution * m_y_resolution; i++)
-		result.m_values[i] = m_values[i] + param.m_values[i];
-	return result;
-}
-
-function2D function2D::operator+(float param)
-{
-	function2D result(m_x0, m_x1, m_y0, m_y1, m_x_resolution, m_y_resolution);
-	for(int i=0; i<m_x_resolution * m_y_resolution; i++)
-		result.m_values[i] = m_values[i] + param;
-	return result;
-}
-
-function2D function2D::operator-(function2D param)
-{
-	function2D result(m_x0, m_x1, m_y0, m_y1, m_x_resolution, m_y_resolution);
-	for(int i=0; i<m_x_resolution * m_y_resolution; i++)
-		result.m_values[i] = m_values[i] - param.m_values[i];
-	return result;
-}
-
-function2D::function2D(float domain_x0, float domain_x1, float domain_y0, float domain_y1,
-											 int x_resolution, int y_resolution)
-{
-	//set all of the member variables describing the size of the function domain
-	m_x0=domain_x0;
-	m_y0=domain_y0;
-	m_x1=domain_x1;
-	m_y1=domain_y1;
-
-	m_x_resolution = x_resolution;
-	m_y_resolution = y_resolution;
-
-	//allocate memory for the function
-	m_values = new float[x_resolution * y_resolution];
-}
-
-function2D::function2D()
-{
-	m_x0 = 0;
-	m_x1 = 0;
-	m_y0 = 0;
-	m_y1 = 0;
-	m_x_resolution = 0;
-	m_y_resolution = 0;
-	m_values = NULL;
-}
-float function2D::operator ()(float x, float y)
-{
-	if(x < m_x0 || x > m_x1)
-		return 0.0f;
-	if(y < m_y0 || y > m_y1)
-		return 0.0f;
-
-	float x_size = m_x1 - m_x0;
-	float y_size = m_y1 - m_y0;
-	float scaled_x = (x-m_x0)/x_size;
-	float scaled_y = (y-m_y0)/y_size;
-	int x_index = scaled_x * m_x_resolution;
-	int y_index = scaled_y * m_y_resolution;
-	return m_values[y_index * m_x_resolution + x_index];
-}
-
-float* function2D::getBits()
-{
-	return m_values;
-}
-
-void function2D::setBits(unsigned char* bits)
-{
-	//copy the given bits to the current function
-	//the member m_values can't just be set to bits because the datatypes may be different
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-		m_values[i] = bits[i];
-}
-
-void function2D::setBits(float* bits)
-{
-	//copy the given bits to the current function
-	//the member m_values can't just be set to bits because the datatypes may be different
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-			m_values[i] = bits[i];
-}
-
-void function2D::setBits(double* bits)
-{
-	//copy the given bits to the current function
-	//the member m_values can't just be set to bits because the datatypes may be different
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-			m_values[i] = bits[i];
-}
-void function2D::setBits(int* bits)
-{
-	//copy the given bits to the current function
-	//the member m_values can't just be set to bits because the datatypes may be different
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-		m_values[i] = bits[i];
-}
-
-
-
-function2D::~function2D()
-{
-	delete m_values;
-}
-
-void function2D::CreateGaussian(float mean_x, float mean_y, float std_dev)
-{
-	//this function creates a 2D gaussian with a mean at the center of the image
-	//and a standard deviation as specified
-	//unsigned char* gaussian = new unsigned char[width*height];
-	//create a few variables to store details about the function domain
-	float domain_x;
-	float domain_y;
-	float x_domain_length = m_x1 - m_x0;
-	float y_domain_length = m_y1 - m_y0;
-	//double high_value = (1.0/(2.0*PI*std_dev*std_dev))*exp(0.0);
-	//cucle through all values in the functions resolution
-	for(int x = 0; x<m_x_resolution; x++)
-		for(int y=0; y<m_y_resolution; y++)
-		{
-			//find the appropriate domain values associated with the array index
-			domain_x = ((x/(double)m_x_resolution)*(x_domain_length))+m_x0;
-			domain_y = ((y/(double)m_y_resolution)*(y_domain_length))+m_y0;
-			double exponent = exp(-((domain_x-mean_x)*(domain_x-mean_x) + (domain_y-mean_y)*(domain_y-mean_y))/(2.0*std_dev*std_dev));
-			m_values[y*m_x_resolution+x] = (1.0/(2.0*RTS_PI*std_dev*std_dev))*exponent;
-		}
-}
-
-void function2D::CreateConstant(float value)
-{
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-	{
-		m_values[i] = value;
-	}
-}
-
-void function2D::CreateCircleMask(float center_x, float center_y, float radius)
-{
-	float domain_x;
-	float domain_y;
-	float x_domain_length = m_x1 - m_x0;
-	float y_domain_length = m_y1 - m_y0;
-
-	//cycle through all values in the functions resolution
-	for(int x = 0; x<m_x_resolution; x++)
-		for(int y=0; y<m_y_resolution; y++)
-		{
-			//find the appropriate domain values associated with the array index
-			domain_x = ((x/(double)m_x_resolution)*(x_domain_length))+m_x0;
-			domain_y = ((y/(double)m_y_resolution)*(y_domain_length))+m_y0;
-			//find the distance between the current point and the circle center
-			point3D center(center_x, center_y, 0.0);
-			point3D current(domain_x, domain_y, 0.0);
-			vector3D difference = current - center;
-			float distance = difference.length();
-
-			//if the pixel is inside the circle, set it to 1.0
-			//otherwise, set the pixel to 0.0
-			if(distance < radius)
-				m_values[y*m_x_resolution+x] = 1.0f;
-			else
-				m_values[y*m_x_resolution+x] = 0.0f;
-		}
-}
-
-void function2D::Scale(float min, float max)
-{
-	//this method scales the function so that it exists between the values min and max
-
-	//first, find the minimum and maximum values for the function
-	int current_min_index = 0;
-	int current_max_index = 0;
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-	{
-		if(m_values[i] < m_values[current_min_index])
-			current_min_index = i;
-		if(m_values[i] > m_values[current_max_index])
-			current_max_index = i;
-	}
-		//cout<<"current max: "<<m_values[current_max_index]<<endl;
-		//cout<<"current min: "<<m_values[current_min_index]<<endl;
-		//char c;cin>>c;
-	float current_min = m_values[current_min_index];
-	float current_max = m_values[current_max_index];
-	//now loop through the function again and scale to the appropriate values
-	float scaled;
-	for(int i=0; i<m_x_resolution * m_y_resolution; i++)
-	{
-		scaled = ((m_values[i] - current_min) / (current_max - current_min));
-		m_values[i] = (scaled *(max-min)) + min;
-	}
-}
-
-void function2D::Clip(float min, float max)
-{
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-	{
-		if(m_values[i] < min)
-			m_values[i] = min;
-		else if(m_values[i] > max)
-			m_values[i] = max;
-	}
-}
-
-void function2D::Abs()
-{
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-	{
-		m_values[i] = fabs(m_values[i]);
-	}
-}
-
-float function2D::Integral()
-{
-	//this function returns the sum of all values of the function
-	float result=0.0f;
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-		result+= m_values[i];
-	return result;
-}
-
-float function2D::Average()
-{
-	//this function returns the average of all of the values of the function
-	float result=0.0f;
-	for(int i=0; i<m_x_resolution*m_y_resolution; i++)
-		result+= m_values[i];
-	result = result/(m_x_resolution*m_y_resolution);
-	return result;
-}
-
-
-line3D::line3D()
-{
-	m_p0 = point3D(0.0, 0.0, 0.0);
-	m_p1 = point3D(0.0, 0.0, 0.0);
-}
-
-line3D::line3D(point3D p0, point3D p1)
-{
-	m_p0 = p0;
-	m_p1 = p1;
-}
-
-point3D line3D::get_point(double pos)
-{
-	return m_p0 + (m_p1 - m_p0)*pos;
-}
-										 
diff --git a/legacy/rtsMath.h b/legacy/rtsMath.h
deleted file mode 100755
index 4c19f56..0000000
--- a/legacy/rtsMath.h
+++ /dev/null
@@ -1,233 +0,0 @@
-/*These files contain basic structures used frequently in the program and in computer
-graphics in general.
-vector3D -	A 3D vector class that contains 3 double values and overloaded methods for
-			most vector operations such as euclidean and cross products.
-point3D	-	A 3D point structure that contains 3 values and overloads functions for
-			point-vector arithmetic.
-These two classes are designed to work together and different methods may require operands
-of both types.
-
-RGBA and RGB -	Color storage and associated methods, although they are not fully implemented yet
-
--David Mayerich, 8/20/05*/
-
-#ifndef _RTS_MATH_H
-#define _RTS_MATH_H
-
-#define RTS_PI			3.14159
-#define TORADIANS(a)	(a)*RTS_PI/180.0
-#define TODEGREES(a)	(a)*180.0/RTS_PI
-
-#include "rtsConstants.h"
-#include <math.h>
-#include <iostream>
-using namespace std;
-
-class vector3D
-{
-public:
-	float x;
-	float y;
-	float z;
-	
-	vector3D();
-	vector3D(double newx, double newy, double newz);
-	vector3D operator+(vector3D param);
-	vector3D operator-(vector3D param);
-	double operator*(vector3D param);	//inner product
-	vector3D cross(vector3D param);
-	vector3D operator*(double param);
-	
-	int normalize();
-	double length();
-
-	void print();
-};
-
-
-class point3D
-{
-public:
-	float x;
-	float y;
-	float z;
-
-	point3D();
-	point3D(double newx, double newy, double newz);
-
-	//support for vector arithmetic
-	point3D operator+(vector3D param);
-	point3D operator-(vector3D param);
-
-	vector3D operator-(point3D param);
-
-	void print();
-};
-
-class matrix4x4
-{
-
-	/*stored as:
-	| 0  4  8  12 |
-    |             |
-    | 1  5  9  13 |
-    |             |
-    | 2  6  10 14 |
-    |             |
-    | 3  7  11 15 |
-	*/
-public:
-	float matrix[16];
-	matrix4x4();
-	matrix4x4(float m00, float m01, float m02, float m03,
-			  float m10, float m11, float m12, float m13,
-			  float m20, float m21, float m22, float m23,
-			  float m30, float m31, float m32, float m33);
-	matrix4x4(vector3D basis_x, vector3D basis_y, vector3D basis_z);
-	vector3D basis_x();
-	vector3D basis_y();
-	vector3D basis_z();
-	point3D operator*(point3D param);
-	vector3D operator*(vector3D param);
-	double operator()(unsigned int row, unsigned int col);
-	void gl_set_matrix(float* gl_matrix);
-	void gl_get_matrix(float* gl_matrix);
-	matrix4x4 submatrix(unsigned int start_col, unsigned int start_row, unsigned int end_col, unsigned int end_row);
-	matrix4x4 transpose();
-	void print();
-};
-
-
-class RGB
-{
-public:
-	float r;
-	float g;
-	float b;
-};
-
-class RGBA
-{
-public:
-	float r;
-	float g;
-	float b;
-	float a;
-
-	RGBA();
-	RGBA(double red, double green, double blue, double ambient);
-};
-
-class quaternion
-{
-public:
-	float w;
-	float x;
-	float y;
-	float z;
-
-	int normalize();
-	quaternion operator*(quaternion param);
-	double* toMatrix();
-
-	quaternion();
-	quaternion(double w, double x, double y, double z);
-
-};
-
-class plane3D
-{
-public:
-	point3D point;
-	vector3D normal;
-
-	plane3D();
-	plane3D(point3D point_on_plane, vector3D plane_normal);
-};
-
-class ray3D
-{
-public:
-	point3D point;
-	vector3D direction;
-
-	ray3D();
-	ray3D(point3D start_point, vector3D direction);
-	ray3D(point3D first_point, point3D second_point);
-
-	int intersect(plane3D plane, point3D& intersection_point);
-};
-
-class line3D
-{
-private:
-	point3D m_p0;
-	point3D m_p1;
-
-public:
-	line3D();
-	line3D(point3D p0, point3D p1);
-
-	point3D get_point(double pos);	//returns a point at pos = [0.0, 1.0]
-};
-
-
-//at this point, this template class is only really working with floating point numbers (and doubles)
-#define RTS_UNSIGNED_BYTE		1
-#define RTS_FLOAT				2
-#define RTS_DOUBLE				3
-
-typedef unsigned int rtsBitType;	
-
-class function2D
-{
-public:
-
-	function2D(float domain_x0, float domain_x1, float domain_y0, float domain_y1, int x_resolution, int y_resolution);
-	function2D();
-	~function2D();
-	function2D(const function2D &copy);		//copy constructor
-	function2D& operator=(const function2D& f);
-	
-	void CreateGaussian(float mean_x, float mean_y, float std_dev);
-	void CreateConstant(float value);
-	void CreateCircleMask(float center_x, float center_y, float radius);
-	void Scale(float min, float max);		//scales the function so that the range exists only in the specified bounds
-	void Clip(float min, float max);		//clips the function so that the range exists only in the specified bounds
-	void Abs();								//sets every sample point to the absolute value
-	float Integral();						//returns the sum of the function
-	float Average();
-	float operator ()(float x, float y);
-
-	function2D operator*(function2D param);
-	function2D operator*(float param);
-	function2D operator+(function2D param);
-	function2D operator+(float param);
-	function2D operator-(function2D param);
-	
-	float* getBits();
-	void setBits(float* bits);
-	void setBits(unsigned char* bits);
-	void setBits(double* bits);
-	void setBits(int* bits);
-
-
-private:
-	float m_x0;
-	float m_x1;
-	float m_y0;
-	float m_y1;
-	int m_x_resolution;
-	int m_y_resolution;
-	float* m_values;
-};
-
-
-
-
-
-
-
-
-
-#endif
diff --git a/legacy/rtsMatrix4x4.h b/legacy/rtsMatrix4x4.h
deleted file mode 100755
index 4f053a5..0000000
--- a/legacy/rtsMatrix4x4.h
+++ /dev/null
@@ -1,196 +0,0 @@
-#include <iostream>
-#include <iomanip>
-#include <stdio.h>
-#include <string.h>
-
-#include "rtsVector3d.h"
-#include "rtsPoint3d.h"
-
-using namespace std;
-#ifndef RTSMATRIX4X4_H
-#define RTSMATRIX4X4_H
-
-#define RTS_PI	3.14159
-
-///This class represents a 4x4 matrix, which is often used to represent affine transformations on 3D points and vectors.
-
-///
-///This class is designed to work with point3d<T> and vector3d<T>.  Data is stored internally in a column-major form which is compatible with OpenGL.
-///
-
-template <class T>
-class matrix4x4
-{
-	/*stored as:
-	| 0  4  8  12 |
-    |             |
-    | 1  5  9  13 |
-    |             |
-    | 2  6  10 14 |
-    |             |
-    | 3  7  11 15 |
-	*/
-public:
-	T m_matrix[16];
-
-	//constructors
-	matrix4x4();								///<Constructor initializes all values to zero.
-	matrix4x4(T c0r0, T c0r1, T c0r2, T c0r3, 
-			  T c1r0, T c1r1, T c1r2, T c1r3, 
-			  T c2r0, T c2r1, T c2r2, T c2r3, 
-			  T c3r0, T c3r1, T c3r2, T c3r3);	///<Constructor initializes all values to those specified as parameters. c=column, r=row
-	
-	//overloaded operators
-	T& operator()(int row, int column){return m_matrix[column*4 + row];}	///<Returns the value at the specified position.  This function can be used as both m(0, 0) = x and x = m(0, 0)
-	vector3D<T> operator*(vector3D<T> rhs);		///<Overloaded arithmetic operator.  This function multiplies a vector by the current matrix, returning the transformed vector3D.
-	point3D<T> operator*(point3D<T> rhs);		///<Overloaded arithmetic operator.  This function multiplies a point by the current matrix, returning the transformed point3D.
-	matrix4x4<T> operator*(matrix4x4<T> rhs);	///<Overloaded arithmetic operator.  Computes the result of a matrix x matrix multiplication.
-
-	//methods
-	void SetIdentity();							///<Sets the current matrix to the identity matrix.
-	void SetRotation(T angle, T x, T y, T z);	///<Creates a matrix that represents a rotation of "angle" degrees around the axis given by (x, y, z).
-	void SetTranslation(T x, T y, T z);			///<Creates a matrix that represents a translation specified by the vector (x, y, z).
-	void SetScale(T x, T y, T z);				///<Creates a matrix that represents a scale along each axis given by the scalars x, y, and z.
-
-	//output
-	void Print(int width = 7, int precision = 2);///<Sends the current matrix to the standard output.
-
-};
-
-
-template <class T>
-matrix4x4<T>::matrix4x4()
-{
-	memset(m_matrix, 0, sizeof(T)*16);
-}
-
-template <class T>
-matrix4x4<T>::matrix4x4(T c0r0, T c0r1, T c0r2, T c0r3, 
-						T c1r0, T c1r1, T c1r2, T c1r3, 
-						T c2r0, T c2r1, T c2r2, T c2r3, 
-						T c3r0, T c3r1, T c3r2, T c3r3)
-{
-
-	T new_matrix[16] = {c0r0,c0r1,c0r2,c0r3,c1r0,c1r1,c1r2,c1r3,c2r0,c2r1,c2r2,c2r3,c3r0,c3r1,c3r2,c3r3};
-	memcpy(m_matrix, new_matrix, 16*sizeof(T));
-}
-
-template <class T>
-vector3D<T> matrix4x4<T>::operator*(vector3D<T> rhs)
-{
-	vector3D<T> result;
-	result.x = m_matrix[0] * rhs.x + m_matrix[4] * rhs.y + m_matrix[8] * rhs.z;
-	result.y = m_matrix[1] * rhs.x + m_matrix[5] * rhs.y + m_matrix[9] * rhs.z;
-	result.z = m_matrix[2] * rhs.x + m_matrix[6] * rhs.y + m_matrix[10] * rhs.z;
-	return result;
-}
-
-template <class T>
-point3D<T> matrix4x4<T>::operator *(point3D<T> rhs)
-{
-	point3D<T> result;
-	result.x = m_matrix[0] * rhs.x + m_matrix[4] * rhs.y + m_matrix[8] * rhs.z + m_matrix[12];
-	result.y = m_matrix[1] * rhs.x + m_matrix[5] * rhs.y + m_matrix[9] * rhs.z + m_matrix[13];
-	result.z = m_matrix[2] * rhs.x + m_matrix[6] * rhs.y + m_matrix[10] * rhs.z + m_matrix[14];
-	T w = m_matrix[3] + m_matrix[7] + m_matrix[11] + m_matrix[15];
-	result.x/=w;
-	result.y/=w;
-	result.z/=w;
-	return result;
-}
-
-template <class T>
-matrix4x4<T> matrix4x4<T>::operator *(matrix4x4<T> rhs)
-{
-	matrix4x4<T> result;
-	int i,j,r;
-	for(i = 0; i<4; i++)
-		for(j = 0; j<4; j++)
-			for(r=0; r<4; r++)
-				result(i, j) += (*this)(i, r) * rhs(r, j);
-
-	return result;
-}
-
-
-
-
-template <class T>
-void matrix4x4<T>::SetIdentity()
-{
-	T new_matrix[16] = {1,0,0,0,0,1,0,0,0,0,1,0,0,0,0,1};
-	memcpy(m_matrix, new_matrix, 16*sizeof(T));
-}
-
-template <class T>
-void matrix4x4<T>::SetTranslation(T x, T y, T z)
-{
-	T new_matrix[16] = {1,0,0,0,0,1,0,0,0,0,1,0,x,y,z,1};
-	memcpy(m_matrix, new_matrix, 16*sizeof(T));
-}
-
-template <class T>
-void matrix4x4<T>::SetScale(T x, T y, T z)
-{
-	T new_matrix[16] = {x,0,0,0,0,y,0,0,0,0,z,0,0,0,0,1};
-	memcpy(m_matrix, new_matrix, 16*sizeof(T));
-}
-
-template <class T>
-void matrix4x4<T>::SetRotation(T angle, T x, T y, T z)
-{
-	//create the axis of rotation
-	vector3D<T> axis(x, y, z);
-	T length = axis.Length();	//make sure that it is normalized
-	if(length != 1)
-		axis.Normalize();
-
-	T c = cos(angle*RTS_PI/180.0);			//compute the sine and cosine of angle
-	T s = sin(angle*RTS_PI/180.0);
-
-	//create the matrix
-	m_matrix[0] = x*x*(1-c) + c;
-	m_matrix[1] = y*x*(1-c) + z*s;
-	m_matrix[2] = x*z*(1-c) - y*s;
-	m_matrix[4] = x*y*(1-c) - z*s;
-	m_matrix[5] = y*y*(1-c) + c;
-	m_matrix[6] = y*z*(1-c) + x*s;
-	m_matrix[8] = x*z*(1-c) + y*s;
-	m_matrix[9] = y*z*(1-c) - x*s;
-	m_matrix[10]= z*z*(1-c) + c;
-	m_matrix[15]= 1;
-}
-
-
-template <class T>
-void matrix4x4<T>::Print(int width, int precision)
-{
-	cout<<setiosflags(ios::fixed);
-	cout<<setprecision(precision);
-	cout<<setw(width)<<m_matrix[0]
-		<<setw(width)<<m_matrix[4]
-		<<setw(width)<<m_matrix[8]
-		<<setw(width)<<m_matrix[12]<<endl
-		<<setw(width)<<m_matrix[1]
-		<<setw(width)<<m_matrix[5]
-		<<setw(width)<<m_matrix[9]
-		<<setw(width)<<m_matrix[13]<<endl
-		<<setw(width)<<m_matrix[2]
-		<<setw(width)<<m_matrix[6]
-		<<setw(width)<<m_matrix[10]
-		<<setw(width)<<m_matrix[14]<<endl
-		<<setw(width)<<m_matrix[3]
-		<<setw(width)<<m_matrix[7]
-		<<setw(width)<<m_matrix[11]
-		<<setw(width)<<m_matrix[15]<<endl;
-}
-
-	
-	
-
-
-
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsNetwork.h b/legacy/rtsNetwork.h
deleted file mode 100755
index b220f1c..0000000
--- a/legacy/rtsNetwork.h
+++ /dev/null
@@ -1,1902 +0,0 @@
-#include "objJedi.h"
-#include <list>
-#include <vector>
-#include <limits.h>
-#include <fstream>
-
-//itk includes
-#include "../../VesselAnalysis/VesselAnalysis/VOL_to_ITK.h"
-#include "itkDanielssonDistanceMapImageFilter.h"
-#include "itkBinaryThresholdImageFilter.h"
-#include "itkConstNeighborhoodIterator.h"
-#include "itkExpandImageFilter.h"
-#include "itkDiscreteGaussianImageFilter.h"
-#include "itkCastImageFilter.h"
-
-
-/* This code uses the octree library designed by Simon Perreault (http://nomis80.org/code/octree.html)*/
-#include "octree/octree.h"
-
-#define OCTREE_SIZE		1024
-#define BUFFER_ZONE		0
-
-
-using namespace std;
-
-
-
-//definitions for simple structures
-typedef vector<point3D<float>> FilamentType;
-typedef point3D<float> CoordType;
-typedef vector<FilamentType> NetworkType;
-
-struct EdgeType
-{
-	unsigned int v0;
-	unsigned int v1;
-	float avg_radius;
-	float min_radius;
-	float max_radius;
-	float volume;
-	float length;
-	bool valid;
-};
-
-struct NodeType
-{
-	CoordType p;
-	vector<unsigned int> edges;
-	bool valid;
-};
-
-struct ConnectType				//this structures stores the info necessary to combine two fibers
-{			
-	unsigned int edge0;
-	unsigned int edge1;
-	unsigned int node0;
-	unsigned int node1;
-	list<FilamentType>::iterator fiber0;
-	list<FilamentType>::iterator fiber1;
-};
-
-struct ConnectableType
-{
-	FilamentType fiber;
-	bool front;
-	bool back;
-	unsigned int id;
-};
-
-struct AttributeType
-{
-	float TotalFiberLength;
-	int NumFibers;
-	int NumPoints;
-	float TotalVolume;
-	int NumDisconnectedFibers;
-	int NumBoundaryFibers;
-	int NumBifurcations;
-};
-
-struct BranchType
-{
-	float angle;
-	unsigned int branch_id;
-};
-
-
-class rtsNetwork
-{
-private:
-	int id;							//used for swc output
-	ofstream outfile;				//also for swc
-	NetworkType network;			//list of filaments that make up the network
-	vector<NodeType> NodeList;		//vector of endpoints
-	vector<EdgeType> EdgeList;		//vector of vessels as edges
-	vector3D<unsigned int> boundary;
-	vector3D<float> position;
-	
-
-	float calcFiberLength(unsigned int f);
-	float calcFiberBend(unsigned int f);
-	float calcTotalLength();
-	bool isBoundaryNode(unsigned int node);
-	vector3D<float> calcTrajectory(FilamentType f, bool end);
-	bool compareTrajectories(CoordType p0, vector3D<float> v0, CoordType p1, vector3D<float> v1, float distance, float cosine_angle);
-	void calcGraph();
-	vector<unsigned int> getConnections(unsigned int node);
-	CoordType toTissue(CoordType grid_coord);
-	FilamentType combineFibers(FilamentType f0, bool endpoint0, FilamentType f1, bool endpoint1);
-	bool isConnectable(ConnectableType c0, ConnectableType c1, bool& c0_end, bool& c1_end, float distance, float cosine_angle);
-	void traverseGraph(int node, int parent_id);
-	void outputFiberToSWC(int edge, int node_from, int parent_id);
-
-	vector<BranchType> getFiberAngles(unsigned int fiber);
-	void reset();
-	
-public:
-	//attribute variables
-	AttributeType Attributes;
-
-	//control variables
-	point3D<float> voxel_size;
-
-	//cleaning
-	int cleanDegenerateEdges(float length);
-	int cleanRedundantEdges();
-	int cleanBarbs(float length);
-
-	//methods
-	rtsOBJ LoadOBJModel(const char* filename);
-	void AddOBJModel(const char* filename);
-	void SaveSWCModel(const char *filename, float root_x, float root_y);
-	void SaveSWCModel(const char *filename);
-	void Clean(float degenerate_length, float barb_length);
-	void CalculateAttributes();
-	rtsOBJ Repair(float max_distance, float cos_angle);
-	rtsOBJ CreateModel();
-	void printFiberStats(unsigned int fiber);
-	void ReMesh(float resample_length);
-	void SaveAngles(const char* filename);
-	void SaveBends(const char* filename);
-	void SaveLengths(const char* filename);
-	void SaveMathematicaGraph(const char* filename);
-	void SaveMathematicaNodeDistances(const char* filename);
-	void SetVoxelSize(float dx, float dy, float dz){voxel_size.x = dx; voxel_size.y = dy; voxel_size.z = dz;}
-	void RemoveTerminalComponents();
-	void RemoveBoundaryComponents();
-	void GetRadiusFromVolume(const char* filename, unsigned int threshold, unsigned int range);
-	void GetRadiusFromDistanceMap(const char *filename, int range);
-	point3D<float> GetFiberRadius(unsigned int fiber);
-	void ScaleNetwork(float x, float y, float z);
-	void SetOutputPosition(float x, float y, float z);
-	
-
-};
-//private
-void rtsNetwork::reset()
-{
-	vector<EdgeType>::iterator e;
-	for(e=EdgeList.begin(); e!=EdgeList.end(); e++)
-		(*e).valid = true;
-
-	vector<NodeType>::iterator n;
-	for(n=NodeList.begin(); n!=NodeList.end(); n++)
-		(*n).valid = true;
-}
-
-float rtsNetwork::calcFiberBend(unsigned int f)
-{
-	/*calculates the bend of a fiber.*/
-
-	//find the line connecting the two endpoints
-	point3D<float> p1 = toTissue(NodeList[EdgeList[f].v0].p);
-	point3D<float> p2 = toTissue(NodeList[EdgeList[f].v1].p);
-
-	//find the largest distance between the filament and the line between endpoints
-	FilamentType::iterator i;
-	float max_distance = 0;
-	for(i = network[f].begin(); i!= network[f].end(); i++)
-	{
-		point3D<float> p0 = toTissue((*i));
-
-		//find the distance between the current point and the line made by the endpoints
-		float d = ((p0 - p1).X(p0-p2).Length())/(p2-p1).Length();
-		if(d > max_distance)
-			max_distance = d;
-	}
-	float fiber_length = calcFiberLength(f);
-	if(max_distance/fiber_length > 0.5)
-	{
-		cout<<"Something's wrong."<<endl;
-		cout<<max_distance<<"---"<<fiber_length<<endl;
-	}
-
-	return max_distance/calcFiberLength(f);	
-
-}
-int rtsNetwork::cleanRedundantEdges()
-{
-	
-	//redundant edges are edges with nodes of valence-2
-
-	int combined = 0;
-
-	//combine all valence-2 fibers
-	NetworkType newNetwork;
-	unsigned int numNodes = NodeList.size();
-	unsigned int n;
-	unsigned int e0, e1;
-	for(n=0; n<numNodes; n++)
-	{
-		//if the node is valence-2
-		if(getConnections(n).size() == 2)
-		{
-			//get both edges
-			e0 = NodeList[n].edges[0];
-			e1 = NodeList[n].edges[1];
-
-			//if both edges are valid
-			if(EdgeList[e0].valid && EdgeList[e1].valid)
-			{
-				//combine them
-				if(EdgeList[e0].v0 == n)
-				{
-					if(EdgeList[e1].v0 == n)
-						newNetwork.push_back(combineFibers(network[e0], 0, network[e1], 0));
-					else
-						newNetwork.push_back(combineFibers(network[e0], 0, network[e1], 1));
-				}
-				else if(EdgeList[e0].v1 == n)
-				{
-					if(EdgeList[e1].v0 == n)
-						newNetwork.push_back(combineFibers(network[e0], 1, network[e1], 0));
-					else
-						newNetwork.push_back(combineFibers(network[e0], 1, network[e1], 1));
-				}
-				EdgeList[e0].valid = false;
-				EdgeList[e1].valid = false;
-				combined++;
-			}
-
-		}
-	}
-
-	unsigned int numEdges = network.size();
-	unsigned int e;
-	for(e=0; e<numEdges; e++)
-	{
-		if(EdgeList[e].valid)
-			newNetwork.push_back(network[e]);
-	}
-
-	network = newNetwork;
-	calcGraph();
-	return combined;
-
-
-}
-int rtsNetwork::cleanBarbs(float length)
-{
-	int removed = EdgeList.size();
-	//removes fibers that are shorter than the specified length
-	NetworkType newNetwork;
-
-	unsigned int numEdges, e;
-	numEdges = EdgeList.size();
-	unsigned int numVertices, v;
-	float e_length;
-
-	for(e=0; e<numEdges; e++)
-	{
-		//if the fiber is an end fiber (one vertex has valence 1)
-		if(getConnections(EdgeList[e].v0).size() ==1 || getConnections(EdgeList[e].v1).size() ==1)
-		{
-			e_length = calcFiberLength(e);
-			//if the fiber is larger than the given length
-			if(e_length > length)
-			{
-				newNetwork.push_back(network[e]);
-				removed--;
-			}
-			
-		}
-		//if the fiber is not an end fiber
-		else
-		{
-			newNetwork.push_back(network[e]);
-			removed--;
-		}
-
-	}
-
-	network.clear();
-	network = newNetwork;
-	calcGraph();
-
-	cout<<"Barbs removed: "<<removed<<endl;
-
-	return removed;
-
-}
-
-int rtsNetwork::cleanDegenerateEdges(float length)
-{
-	/*This function cleans unnecessary edges with length less than <length>*/
-
-	//form lists of degenerate and non-degenerate edges
-	int removed = 0;
-
-	list<ConnectableType> degenerate;
-	list<ConnectableType> complete;
-
-	//iterate through each fiber and put it in the appropriate list
-	int numFibers = network.size();
-	int f;
-	ConnectableType c;
-	for(f=0; f<numFibers; f++)
-	{
-		c.fiber = network[f];
-		c.id = f;
-		if(calcFiberLength(f) <= length)
-			degenerate.push_back(c);
-		else
-			complete.push_back(c);
-	}
-
-	
-	vector<unsigned int> connected_edges;
-	vector<unsigned int> shared_vertices;
-	int numEdges, numVerts, e, e0, e1, v;
-	int connectedEdge;
-	//for each degenerate edge
-	list<ConnectableType>::iterator i;
-	for(i=degenerate.begin(); i!=degenerate.end(); i++)
-	{
-/*DEGENERATE CASE 1
-In this case, we remove edges that are parts of very small cycles (ex short edges that
-bridge between a bifurcation, forming a small triangle).
-*/
-		//get all of the edges connected to that edge
-		connected_edges.clear();
-		//add edges connected to v0
-		v = EdgeList[(*i).id].v0;
-		numEdges = NodeList[v].edges.size();
-		for(e=0; e<numEdges; e++)
-		{
-			connectedEdge = NodeList[v].edges[e];
-			if(connectedEdge != (*i).id && EdgeList[connectedEdge].valid)
-				connected_edges.push_back(connectedEdge);
-		}
-		//add edges connected to v1
-		v = EdgeList[(*i).id].v1;
-		numEdges = NodeList[v].edges.size();
-		for(e=0; e<numEdges; e++)
-		{
-			connectedEdge = NodeList[v].edges[e];
-			if(connectedEdge != (*i).id && EdgeList[connectedEdge].valid)
-				connected_edges.push_back(connectedEdge);
-		}
-
-		//find all of the shared vertices
-		shared_vertices.clear();
-		numEdges = connected_edges.size();
-		for(e0=0; e0<numEdges; e0++)
-		{
-			for(e1 = e0; e1<numEdges; e1++)
-			{
-				if(e0 != e1)
-				{
-					if(EdgeList[connected_edges[e0]].v0 == EdgeList[connected_edges[e1]].v0 ||
-					   EdgeList[connected_edges[e0]].v0 == EdgeList[connected_edges[e1]].v1)
-						shared_vertices.push_back(EdgeList[connected_edges[e0]].v0);
-					else if(EdgeList[connected_edges[e0]].v1 == EdgeList[connected_edges[e1]].v0 ||
-							EdgeList[connected_edges[e0]].v1 == EdgeList[connected_edges[e1]].v1)
-						shared_vertices.push_back(EdgeList[connected_edges[e0]].v1);
-				}
-			}
-		}
-
-		//are any of these vertices not part of the original edge?
-		numVerts = shared_vertices.size();
-		bool delete_fiber = false;
-		for(v = 0; v<numVerts; v++)
-		{
-			if(shared_vertices[v] != EdgeList[(*i).id].v0 &&
-			   shared_vertices[v] != EdgeList[(*i).id].v1)
-			{
-				if(getConnections(EdgeList[(*i).id].v0).size() ==1 ||
-				   getConnections(EdgeList[(*i).id].v0).size() ==1)
-				   cout<<"error  "<<(*i).id<<endl;
-				delete_fiber = true;
-				removed++;
-				EdgeList[(*i).id].valid = false;
-			}
-		}
-/*DEGENERATE CASE 2
-In this case, we remove edges that are equal to each other (ex both ends are connected to the
-same outside fiber).
-*/
-		
-		//find the number of branches in v0
-		int v0 = EdgeList[(*i).id].v0;
-		int v1 = EdgeList[(*i).id].v1;
-
-		int numV0 = NodeList[v0].edges.size();
-		int numV1 = NodeList[v1].edges.size();
-
-		//go through each fiber connected to both nodes
-		for(int vi=0; vi<numV0; vi++)
-			for(int vj=0; vj<numV1; vj++)
-			{
-				//if there is a match and it isn't the current fiber, delete it
-				if(NodeList[v0].edges[vi] == NodeList[v1].edges[vj])
-					if(NodeList[v0].edges[vi] != (*i).id && EdgeList[NodeList[v0].edges[vi]].valid)
-					{
-						delete_fiber = true;
-						removed++;
-						EdgeList[(*i).id].valid = false;
-					}
-			}
-
-/*DEGENERATE CASE 3
-Delete fibers that are less than length and have degree-4 connections
-*/
-		if(calcFiberLength((*i).id) < length && 
-			NodeList[EdgeList[(*i).id].v1].edges.size() >3 &&
-			NodeList[EdgeList[(*i).id].v0].edges.size() >3)
-		{
-			delete_fiber = true;
-			removed++;
-			EdgeList[(*i).id].valid = false;
-		}
-
-
-
-
-		if(!delete_fiber)
-			complete.push_back((*i));
-
-	}
-
-	//re-create the network from <complete>
-	NetworkType newNetwork;
-	for(i = complete.begin(); i!=complete.end(); i++)
-		newNetwork.push_back((*i).fiber);
-
-	network = newNetwork;
-	calcGraph();
-
-	return removed;
-
-
-
-
-}
-bool rtsNetwork::isBoundaryNode(unsigned int node)
-{
-	CoordType p;
-
-	p = NodeList[node].p;
-	if(NodeList[node].edges.size() > 1)
-		return false;
-	if(p.x > BUFFER_ZONE && p.y > BUFFER_ZONE && p.z > BUFFER_ZONE &&
-	   p.x < boundary.x - BUFFER_ZONE && p.y < boundary.y - BUFFER_ZONE && p.z < boundary.z - BUFFER_ZONE)
-		return false;
-	else
-		return true;
-}
-
-
-bool rtsNetwork::isConnectable(ConnectableType c0, ConnectableType c1, bool& c0_end, bool& c1_end, float distance, float cosine_angle)
-{
-	//tests to see if two ConnectableType fibers can be connected.  If so, the function
-	//returns true as well as the optimal connected endpoints as <c0_end> and <c1_end>.
-	//For these parameters, 0 = the first point on the fiber and 1 = the last point.
-
-	if(c0.id == 1381 && c1.id == 1407)
-		cout<<"here"<<endl;
-
-
-	vector3D<float> t0;
-	vector3D<float> t1;
-	if(c0.front == 0)
-	{
-		t0 = calcTrajectory(c0.fiber, 0);
-		if(c1.front == 0)
-		{
-			t1 = calcTrajectory(c1.fiber, 0);
-			if(compareTrajectories(c0.fiber.front(), t0, c1.fiber.front(), t1, distance, cosine_angle))
-			{
-				c0_end = 0;
-				c1_end = 0;
-				return true;
-			}
-		}
-		if(c1.back == 0)
-		{
-			t1 = calcTrajectory(c1.fiber, 1);
-			if(compareTrajectories(c0.fiber.front(), t0, c1.fiber.back(), t1, distance, cosine_angle))
-			{
-				c0_end = 0;
-				c1_end = 1;
-				return true;
-			}
-		}
-	}
-	if(c0.back == 0)
-	{
-		t0 = calcTrajectory(c0.fiber, 1);
-		if(c1.front == 0)
-		{
-			t1 = calcTrajectory(c1.fiber, 0);
-			if(compareTrajectories(c0.fiber.back(), t0, c1.fiber.front(), t1, distance, cosine_angle))
-			{
-				c0_end = 1;
-				c1_end = 0;
-				return true;
-			}
-		}
-		if(c1.back == 0)
-		{
-			t1 = calcTrajectory(c1.fiber, 1);
-			if(compareTrajectories(c0.fiber.back(), t0, c1.fiber.back(), t1, distance, cosine_angle))
-			{
-				c0_end = 1;
-				c1_end = 1;
-				return true;
-			}
-		}
-	}
-
-
-	return false;
-
-}
-FilamentType rtsNetwork::combineFibers(FilamentType f0, bool endpoint0, FilamentType f1, bool endpoint1)
-{
-
-	//create the new filament
-	FilamentType newFilament;
-	//insert the first filament
-	//if the valence-1 vertex is at the beginning
-	if(endpoint0 == 0)
-	{
-		//add the edge backwards
-		for(int v=f0.size() - 1; v>=0; v--)
-			newFilament.push_back(f0[v]);
-	}
-	else
-	{
-		//otherwise we can just copy the filament over
-		newFilament = f0;
-	}
-
-	//insert the second filament
-	//if the valence-1 vertex is at the beginning
-	if(endpoint1 == 0)
-	{
-		//add the edge in forwards
-		for(int v=0; v<f1.size(); v++)
-			newFilament.push_back(f1[v]);
-	}
-	else
-	{
-		for(int v=f1.size() - 1; v>=0; v--)
-			newFilament.push_back(f1[v]);
-	}
-
-	return newFilament;
-}
-vector3D<float> rtsNetwork::calcTrajectory(FilamentType f, bool end)
-{
-	//calculates the trajectory of a fiber at the given endpoint (0 = first, 1 = last)
-
-	CoordType pEndpoint;
-	CoordType pPrevpoint;
-	if(end == 0)
-	{
-		pEndpoint = f.front();
-		pPrevpoint = f[1];
-		//pPrevpoint = f[ceil(f.size()/4.0)];
-	}
-	else
-	{
-		pEndpoint = f.back();
-		pPrevpoint = f[f.size() - 2];
-		//pPrevpoint = f[floor(f.size()*3.0/4.0)];
-	}
-
-	//pPrevpoint = f[f.size()/2];
-	
-
-	vector3D<float> result = toTissue(pEndpoint) - toTissue(pPrevpoint);
-	result.Normalize();
-	return result;
-}
-bool rtsNetwork::compareTrajectories(CoordType p0, vector3D<float> v0, CoordType p1, vector3D<float> v1, float distance, float cosine_angle)
-{
-	//determines of two points/trajectory pairs are compatible for connection
-	vector3D<float> difference = p1 - p0;
-	//test distance
-	if(difference.Length() <= distance)
-	{
-		difference.Normalize();
-		if(v0*difference >= cosine_angle && v1*difference <= -cosine_angle)
-			return true;
-	}
-	return false;
-}
-vector<unsigned int> rtsNetwork::getConnections(unsigned int node)
-{
-	return NodeList[node].edges;
-
-}
-point3D<float> rtsNetwork::toTissue(CoordType grid_coord)
-{
-	//converts a coordinate from the original voxel grid coordinates to tissue-space coordinates
-	return CoordType(grid_coord.x * voxel_size.x,
-					 grid_coord.y * voxel_size.y,
-				     grid_coord.z * voxel_size.z);
-					 
-	//return grid_coord;
-}
-
-float rtsNetwork::calcFiberLength(unsigned int f)
-{
-	//This function calculates the total length of the given fiber
-
-	float result = 0.0;
-
-	//find the length of each fiber
-	int vertNum, v;
-
-	vertNum = network[f].size();
-	for(v=1; v<vertNum; v++)
-	{
-		result += (toTissue(network[f][v-1]) - toTissue(network[f][v])).Length();
-	}
-
-	return result;
-
-}
-
-float rtsNetwork::calcTotalLength()
-{
-	float result = 0.0;
-
-	//find the length of each fiber
-	int numFibers = network.size();
-	int f;
-
-	for(f = 0; f < numFibers; f++)
-	{
-		result += calcFiberLength(f);		
-	}
-	return result;
-
-}
-
-rtsOBJ rtsNetwork::LoadOBJModel(const char *filename)
-{
-	rtsOBJ model;
-	model.LoadFile(filename);
-
-	//empty the current network if it isn't already
-	network.clear();
-
-	//get the number of filaments
-	int lineNum = model.getNumLines();
-
-	int vertexNum, v, vIndex;		//for keeping track of the vertices in each line
-
-	for(int l=0; l<lineNum; l++)
-	{
-		FilamentType fiber;							//create a new fiber
-		vertexNum = model.getNumLineVertices(l);	//get the number of vertices in the line
-
-		for(v = 0; v<vertexNum; v++)				//convert the line to a fiber
-		{
-			vIndex = model.getLineVertex(l, v);
-			fiber.push_back(model.getVertex3d(vIndex));
-		}
-		network.push_back(fiber);					//store the converted fiber in the network
-	}
-
-	//calculate the graph components
-	calcGraph();
-
-	//set the boundary
-	AABB bound = model.getBoundingBox();
-	boundary.x = ceil(bound.max.x);
-	boundary.y = ceil(bound.max.y);
-	boundary.z = ceil(bound.max.z);
-
-	return model;
-	
-}
-
-void rtsNetwork::AddOBJModel(const char *filename)
-{
-	rtsOBJ model;
-	model.LoadFile(filename);
-
-	//get the number of filaments
-	int lineNum = model.getNumLines();
-
-	int vertexNum, v, vIndex;		//for keeping track of the vertices in each line
-
-	for(int l=0; l<lineNum; l++)
-	{
-		FilamentType fiber;							//create a new fiber
-		vertexNum = model.getNumLineVertices(l);	//get the number of vertices in the line
-
-		for(v = 0; v<vertexNum; v++)				//convert the line to a fiber
-		{
-			vIndex = model.getLineVertex(l, v);
-			fiber.push_back(model.getVertex3d(vIndex));
-		}
-		network.push_back(fiber);					//store the converted fiber in the network
-	}
-
-	//calculate the graph components
-	calcGraph();
-
-	/*//set the boundary
-	AABB bound = model.getBoundingBox();
-	boundary.x = ceil(bound.max.x);
-	boundary.y = ceil(bound.max.y);
-	boundary.z = ceil(bound.max.z);
-	*/
-
-}
-
-void rtsNetwork::outputFiberToSWC(int e, int node_from, int parent_id)
-{
-	EdgeList[e].valid = false;
-	int p;
-	point3D<float> outPoint;
-	//if we are traversing the fiber front-to-back
-	if(EdgeList[e].v0 == node_from)
-	{
-		if(parent_id == -1)
-		{
-			p=0;
-			outPoint = network[e][p] + position;
-			outfile<<id<<" "<<2<<" "<<outPoint.x<<" "<<outPoint.y<<" "<<outPoint.z<<" "<<1.0<<" "<<parent_id<<endl;
-		}
-		else
-		{
-			p=1;
-			outPoint = network[e][p] + position;
-			outfile<<id<<" "<<2<<" "<<outPoint.x<<" "<<outPoint.y<<" "<<outPoint.z<<" "<<1.0<<" "<<parent_id<<endl;
-		}
-		p++;
-		id++;
-		for(; p<network[e].size(); p++)
-		{
-			outPoint = network[e][p] + position;
-			outfile<<id<<" "<<2<<" "<<outPoint.x<<" "<<outPoint.y<<" "<<outPoint.z<<" "<<1.0<<" "<<id-1<<endl;
-			id++;
-		}
-	}
-	//if we are traversing the fiber back-to-front
-	else
-	{
-		if(parent_id == -1)
-		{
-			p=network[e].size()-1;
-			outPoint = network[e][p] + position;
-			outfile<<id<<" "<<2<<" "<<outPoint.x<<" "<<outPoint.y<<" "<<outPoint.z<<" "<<1.0<<" "<<parent_id<<endl;
-		}
-		else
-		{
-			p=network[e].size()-2;
-			outPoint = network[e][p] + position;
-			outfile<<id<<" "<<2<<" "<<outPoint.x<<" "<<outPoint.y<<" "<<outPoint.z<<" "<<1.0<<" "<<parent_id<<endl;
-		}
-		p--;
-		id++;
-		for(; p>=0; p--)
-		{
-			outPoint = network[e][p] + position;
-			outfile<<id<<" "<<2<<" "<<outPoint.x<<" "<<outPoint.y<<" "<<outPoint.z<<" "<<1.0<<" "<<id-1<<endl;
-			id++;
-		}
-	}
-
-}
-void rtsNetwork::traverseGraph(int node, int parent_id)
-{
-	//if the node is valid
-	if(NodeList[node].valid)
-	{
-		NodeList[node].valid = false;
-		int num_edges = NodeList[node].edges.size();
-		for(int e = 0; e<num_edges; e++)
-		{
-			if(EdgeList[NodeList[node].edges[e]].valid)
-			{
-				outputFiberToSWC(NodeList[node].edges[e], node, parent_id);
-				int newNode = EdgeList[NodeList[node].edges[e]].v0;
-				if(newNode != node)
-					traverseGraph(newNode, id-1);
-				else
-					traverseGraph(EdgeList[NodeList[node].edges[e]].v1, id-1);
-			}
-		}
-	}
-
-
-}
-
-void rtsNetwork::SetOutputPosition(float x, float y, float z)
-{
-	position.x = x;
-	position.y = y;
-	position.z = z;
-}
-void rtsNetwork::SaveSWCModel(const char *filename, float root_x, float root_y)
-{
-	cout<<filename<<endl;
-	outfile.open(filename);
-	//recursively iterate through the network saving the elements to an SWC file
-	int node;
-	id = 1;
-
-	//set the root seed point
-	point3D<float> rootSeed(root_x, root_y, 0);
-	float distance = 9999999;
-	int closest_node;
-
-	//find the closest node to the root seed
-	for(node = 0; node != NodeList.size(); node++)
-	{
-		float length = (NodeList[node].p - rootSeed).Length();
-		if(length < distance)
-		{
-			closest_node = node;
-			distance = length;
-			cout<<length<<endl;
-		}
-	}
-	traverseGraph(closest_node, -1);
-
-	outfile.close();
-	
-}
-
-void rtsNetwork::SaveSWCModel(const char* filename)
-{
-	cout<<filename<<endl;
-	outfile.open(filename);
-	//recursively iterate through the network saving the elements to an SWC file
-	int node;
-	id = 1;
-
-	//set the root seed point
-	
-	//find the closest node to the root seed
-	for(node = 0; node != NodeList.size(); node++)
-	{
-		if(NodeList[node].valid)
-			traverseGraph(node, -1);
-	}
-	
-
-	outfile.close();
-}
-
-void rtsNetwork::ScaleNetwork(float x, float y, float z)
-{
-
-	NetworkType::iterator f;
-	FilamentType::iterator p;
-
-	for(f = network.begin(); f!=network.end(); f++)
-		for(p = (*f).begin(); p!= (*f).end(); p++)
-		{
-			(*p).x = (*p).x * x;
-			(*p).y = (*p).y * y;
-			(*p).z = (*p).z * z;
-		}
-
-	calcGraph();
-}
-rtsOBJ rtsNetwork::CreateModel()
-{
-	rtsOBJ model;
-	/*
-	NetworkType::iterator f;
-	unsigned int numVerts, v;
-	for(f=network.begin(); f!=network.end(); f++)
-	{
-		model.objBegin(OBJ_LINE_STRIP);
-		
-		numVerts = (*f).size();
-		for(v=0; v<numVerts; v++)
-		{
-			model.objVertex3f((*f)[v].x, (*f)[v].y, (*f)[v].z);
-		}
-		
-		model.objEnd();
-	}
-	*/
-
-	//add all of the vertices to the OBJ
-	int num_vertices = NodeList.size();
-	int v;
-	for(v=0; v<num_vertices; v++)
-	{
-		model.insertVertexPosition(NodeList[v].p.x, NodeList[v].p.y, NodeList[v].p.z);
-	}
-
-	//for each edge
-	int num_edges = EdgeList.size();
-	int e;
-	unsigned int* buffer = new unsigned int[10000];
-	
-	for(e=1; e<num_edges-1; e++)
-	{	
-		buffer[0] = EdgeList[e].v0;
-		
-		//walk along the fiber
-		num_vertices = network[e].size()-1;
-		for(v=1; v<num_vertices; v++)
-		{
-			buffer[v] = model.getNumVertices();
-			model.insertVertexPosition(network[e][v].x, network[e][v].y, network[e][v].z);
-		}
-		
-		buffer[v] = EdgeList[e].v1;
-
-		model.insertLine(v+1, buffer, NULL, NULL);
-	}
-	
-
-	return model;
-
-}
-
-
-
-void rtsNetwork::calcGraph()
-{
-	//make sure that all graph information is cleared
-	EdgeList.clear();
-	NodeList.clear();
-
-	//find the maximum extents of the fiber network
-	int numFibers = network.size();
-	int f;
-	float Max = 0;
-	float temp;
-	for(f=0; f<numFibers; f++)
-	{
-		temp = max(network[f].front().x,
-			   max(network[f].front().y,
-			   max(network[f].front().z,
-			   max(network[f].back().x,
-			   max(network[f].back().y, 
-			   network[f].back().z)))));
-		if(temp > Max) Max = temp;
-	}
-
-	//place each point ID inside the octree
-	unsigned int id = 0;
-	Octree<unsigned int> tree(OCTREE_SIZE);
-	tree.setEmptyValue(UINT_MAX);
-	unsigned int v0, v1;
-
-
-	for(f=0; f<numFibers; f++)
-	{
-		//get the appropriate id from the tree
-		NodeType v0pos, v1pos;
-		v0pos.p = network[f].front();
-		v1pos.p = network[f].back();
-		v0pos.valid = 1;
-		v1pos.valid = 1;
-		v0 = tree(v0pos.p.x, v0pos.p.y, v0pos.p.z);
-		v1 = tree(v1pos.p.x, v1pos.p.y, v1pos.p.z);
-
-		//if the id doesn't exist, add it
-		if(v0 == UINT_MAX)
-		{
-			v0 = id;								//set the id of the current vertex
-			tree(v0pos.p.x, v0pos.p.y, v0pos.p.z) = id;	//add the id to the octree
-			NodeList.push_back(v0pos);	//add the node position to the node list
-
-			id++;									//increment the id
-		}
-		if(v1 == UINT_MAX)
-		{
-			v1 = id;								//set the id of the current vertex
-			tree(v1pos.p.x, v1pos.p.y, v1pos.p.z) = id;	//add the id to the octree
-			NodeList.push_back(v1pos);	//add the node position to the node list
-
-			id++;									//increment the id
-		}
-
-		//add the current edge to the edge list
-		EdgeType e;
-		e.v0 = v0;
-		e.v1 = v1;
-		e.valid = 1;
-		e.length = calcFiberLength(f);
-		EdgeList.push_back(e);
-		//add this edge to each point's edge list
-		NodeList[e.v0].edges.push_back(EdgeList.size() - 1);
-		NodeList[e.v1].edges.push_back(EdgeList.size() - 1);
-
-		//cout<<"Edge: "<<v0<<"--->"<<v1<<"  "<<"w = "<<e.w<<endl;
-	}
-
-	/*Computes a connectivity matrix based on the edge list and vertices in Attributes*/
-
-	/*
-	//create the matrix and zero it out
-	Array2D<unsigned int> matrix(NodeList.size(), NodeList.size());
-	unsigned int numNodes = NodeList.size();
-	int x, y;
-	for(x=0; x<numNodes; x++)
-		for(y=0; y<numNodes; y++)
-			matrix(x, y) = 0;
-
-	//iterate through each edge, assigning values to the connectivity matrix
-	vector<EdgeType>::iterator e;
-	for(e = EdgeList.begin(); e!= EdgeList.end(); e++)
-	{
-		matrix((*e).v0, (*e).v1) = 1;
-		matrix((*e).v1, (*e).v0) = 1;
-	}
-
-	ConnectivityMatrix = matrix;
-	*/
-}
-
-vector<BranchType> rtsNetwork::getFiberAngles(unsigned int fiber)
-{
-	vector<BranchType> result;
-
-	int b;
-	vector3D<float> currentTrajectory;
-	vector3D<float> branchTrajectory;
-	unsigned int f;
-
-	unsigned int node = EdgeList[fiber].v0;
-
-	int numBranches = NodeList[node].edges.size();	
-	currentTrajectory = calcTrajectory(network[fiber], 0).Normalize();
-	//currentTrajectory.print();
-	for(b=0; b<numBranches; b++)
-	{
-		f = NodeList[node].edges[b];
-		if(f != fiber && EdgeList[f].valid)
-		{
-			if(EdgeList[f].v0 == node)
-				branchTrajectory = calcTrajectory(network[f], 0).Normalize();
-			else
-				branchTrajectory = calcTrajectory(network[f], 1).Normalize();
-			//branchTrajectory.print();
-			BranchType newBranch;
-			newBranch.angle = acos((branchTrajectory*(-1))*currentTrajectory)*(180.0/3.14159);
-			newBranch.branch_id = f;
-			result.push_back(newBranch);
-		}
-		
-	}
-
-	node = EdgeList[fiber].v1;
-
-	numBranches = NodeList[node].edges.size();	
-	currentTrajectory = calcTrajectory(network[fiber], 1).Normalize();
-	//currentTrajectory.print();
-	for(b=0; b<numBranches; b++)
-	{
-		f = NodeList[node].edges[b];
-		if(f != fiber && EdgeList[f].valid)
-		{
-			if(EdgeList[f].v0 == node)
-				branchTrajectory = calcTrajectory(network[f], 0).Normalize();
-			else
-				branchTrajectory = calcTrajectory(network[f], 1).Normalize();
-			//branchTrajectory.print();
-			BranchType newBranch;
-			newBranch.angle = acos((branchTrajectory*(-1))*currentTrajectory)*(180.0/3.14159);
-			newBranch.branch_id = f;
-			result.push_back(newBranch);
-		}
-		
-	}
-	
-	//mark the fiber as traversed
-	EdgeList[fiber].valid = false;
-
-	return result;
-}
-//public
-void rtsNetwork::CalculateAttributes()
-{
-	Attributes.TotalFiberLength = calcTotalLength();
-	Attributes.NumFibers = network.size();
-	
-	Attributes.NumPoints = 0;
-	Attributes.TotalVolume = 0;
-	Attributes.NumDisconnectedFibers = 0;
-	Attributes.NumBoundaryFibers = 0;
-	int numFibers = network.size();
-	for(int f=0; f<numFibers; f++)
-	{
-		Attributes.NumPoints += network[f].size();
-		Attributes.TotalVolume += EdgeList[f].volume;
-		if(NodeList[EdgeList[f].v0].edges.size() == 1 ||
-			NodeList[EdgeList[f].v1].edges.size() ==1)
-			if(isBoundaryNode(EdgeList[f].v0) || isBoundaryNode(EdgeList[f].v1))
-				Attributes.NumBoundaryFibers++;
-			else
-				Attributes.NumDisconnectedFibers++;
-
-	}
-
-	Attributes.NumBifurcations = 0;
-	int numNodes = NodeList.size();
-	for(int n=0; n<numNodes; n++)
-		if(NodeList[n].edges.size() >= 2)
-			Attributes.NumBifurcations++;
-
-
-}
-
-
-
-
-
-rtsOBJ rtsNetwork::Repair(float max_distance, float cos_angle)
-{
-	/*This function repairs the network by serching a solid angle around each endpoint
-	for a suitable candidate endpoint to connect to.*/
-
-	cout<<"repairing...."<<endl;
-
-	rtsOBJ preview;
-
-	//create the complete and incomplete connectable lists
-	list<ConnectableType> complete;
-	list<ConnectableType> incomplete;
-
-	cout<<"Finding Valence-1 Fibers..."<<endl;
-	//go through each fiber, adding ones with valence-1 endpoints to <incomplete>
-	int numFibers = network.size();
-	int f;
-	unsigned int v0;
-	unsigned int v1;
-	int numVerts, v;
-	for(f=0; f<numFibers; f++)
-	{
-		ConnectableType c;
-		v0 = EdgeList[f].v0;
-		v1 = EdgeList[f].v1;
-		//test valence and boundary
-		if(NodeList[v0].edges.size() == 1 && !isBoundaryNode(v0))
-		{
-			c.front = false;
-		}
-		else c.front = true;
-
-		if(NodeList[v1].edges.size() == 1 && !isBoundaryNode(v1))
-		{
-			c.back = false;
-		}
-		else c.back = true;
-
-		if(c.front == false || c.back == false)
-		{
-			c.fiber = network[f];
-			c.id = f;
-			incomplete.push_back(c);
-			numVerts = c.fiber.size();
-			//preview.objBegin(OBJ_LINE_STRIP);
-			//for(v=0; v<numVerts; v++)
-			//	preview.objVertex3f(c.fiber[v].x, c.fiber[v].y, c.fiber[v].z);
-			//preview.objEnd();
-		}
-		else
-		{
-			c.fiber = network[f];
-			c.id = f;
-			complete.push_back(c);
-		}
-		
-	}
-	cout<<"Valence-1 Fibers: "<<incomplete.size()<<endl;
-
-	//find all of the possible connections
-	list<ConnectableType>::iterator i;
-	list<ConnectableType>::iterator j;
-	list<ConnectableType>::iterator temp;
-	FilamentType newFiber;
-	bool endpoint0, endpoint1;
-	
-	int iIndex, jIndex;
-
-	iIndex = 0;
-	for(i=incomplete.begin(); i!=incomplete.end(); i++)
-	{
-		jIndex = iIndex;
-		j = i;
-		while(j != incomplete.end() && i != incomplete.end())
-		{
-			if(i!=j)
-			{
-				if(isConnectable((*i), (*j), endpoint0, endpoint1, max_distance, cos_angle))
-				{
-					ConnectableType newConnectable;
-					newConnectable.fiber = combineFibers((*i).fiber, endpoint0, (*j).fiber, endpoint1);
-					//determine the new connectivity
-					if(endpoint0 == 0)
-						newConnectable.front = (*i).back;
-					else
-						newConnectable.front = (*i).front;
-
-					if(endpoint1 == 0)
-						newConnectable.back = (*j).back;
-					else
-						newConnectable.back = (*j).front;
-
-					//remove the previous connectables
-					temp = i;
-					i++;
-					iIndex++;
-					incomplete.erase(temp);
-					temp = j;
-					//this is just in case the fibers are next to each otehr
-					if(j == i)
-					{
-						i++;
-						iIndex++;
-						j = i;
-						jIndex = iIndex;
-					}
-					else
-					{
-						j = i;
-						jIndex = iIndex;
-					}
-					incomplete.erase(temp);
-					//insert the new connectable in the proper list
-					if(newConnectable.front == 0 || newConnectable.back == 0)
-						incomplete.push_back(newConnectable);
-					else
-						complete.push_back(newConnectable);
-					
-					
-
-					//numVerts = newConnectable.fiber.size();
-					//preview.objBegin(OBJ_LINE_STRIP);
-					//for(v=0; v<numVerts; v++)
-					//	preview.objVertex3f(newConnectable.fiber[v].x, newConnectable.fiber[v].y, newConnectable.fiber[v].z);
-					//preview.objEnd();
-				}
-				else
-				{
-					j++;
-					jIndex++;
-				}
-				
-			}
-			else
-			{
-				j++;
-				jIndex++;
-			}
-			//cout<<"i: "<<iIndex<<"j: "<<jIndex<<endl;
-			//cout<<"size of incomplete: "<<incomplete.size()<<endl;
-		}
-		iIndex++;
-	}
-
-	//reconstruct the fiber list
-	vector<FilamentType> newNetwork;
-	for(i=incomplete.begin(); i!=incomplete.end(); i++)
-		newNetwork.push_back((*i).fiber);
-	for(i=complete.begin(); i!=complete.end(); i++)
-		newNetwork.push_back((*i).fiber);
-
-	network = newNetwork;
-	calcGraph();
-
-	
-	//build the model to return
-	preview = CreateModel();
-	
-	return preview;
-
-}
-void rtsNetwork::printFiberStats(unsigned int fiber)
-{
-	/*
-	cout<<"-----------------------------------------------------"<<endl;
-	cout<<"Fiber nodes:"<<endl;
-	int numVerts = network[fiber].size();
-	for(int v=0; v<numVerts; v++)
-	{
-		cout<<network[fiber][v].x<<","<<network[fiber][v].y<<","<<network[fiber][v].z<<endl;
-	}
-	*/
-	cout<<"------------------------------------------------------"<<endl;
-	cout<<"Selected node: "<<fiber<<endl;
-
-
-	int b;
-	vector3D<float> currentTrajectory;
-	vector3D<float> branchTrajectory;
-	unsigned int f;
-
-	//get the list of angles
-	vector<BranchType> angles = getFiberAngles(fiber);
-
-	unsigned int node = EdgeList[fiber].v0;
-	int numBranches = NodeList[node].edges.size()-1;	
-	cout<<"V0 Valence: "<<getConnections(node).size()<<endl; 
-
-	for(b=0; b<numBranches; b++)
-	{
-		cout<<"     ["<<angles[b].branch_id<<"] "<<angles[b].angle<<(char)248<<endl;
-	}
-
-
-	node = EdgeList[fiber].v1;	
-	cout<<"V1 Valence: "<<getConnections(node).size()<<endl;
-	numBranches = angles.size();
-	for(; b<numBranches; b++)
-	{
-		cout<<"     ["<<angles[b].branch_id<<"] "<<angles[b].angle<<(char)248<<endl;
-	}
-
-	reset();
-
-	cout<<"End Points: ["<<NodeList[EdgeList[fiber].v0].p.x<<","
-						<<NodeList[EdgeList[fiber].v0].p.y<<","
-						<<NodeList[EdgeList[fiber].v0].p.z<<"]"
-						<<"["<<NodeList[EdgeList[fiber].v1].p.x<<","
-						<<NodeList[EdgeList[fiber].v1].p.y<<","
-						<<NodeList[EdgeList[fiber].v1].p.z<<"]"<<endl;
-	cout<<"Fiber Length: "<<calcFiberLength(fiber)<<"um"<<endl;
-	cout<<"Average Radius: "<<EdgeList[fiber].avg_radius<<"um"<<endl;
-	cout<<"Min Radius: "<<EdgeList[fiber].min_radius<<"um"<<endl;
-	cout<<"Max Radius: "<<EdgeList[fiber].max_radius<<"um"<<endl;
-	cout<<"Fiber Volume: "<<EdgeList[fiber].volume<<"um^3"<<endl;
-	cout<<"Maximum Bend: "<<calcFiberBend(fiber)<<endl;
-	cout<<"------------------------------------------------------"<<endl;
-
-	int numVertices = network[fiber].size();
-	//for(int v=0; v<numVertices; v++)
-	//	cout<<network[fiber][v].x<<","<<network[fiber][v].y<<","<<network[fiber][v].z<<endl;
-
-
-}
-void rtsNetwork::Clean(float degenerate_length = 5, float barb_length = 30)
-{
-	int changes;
-	do
-	{
-		changes = 0;
-		int degen = cleanDegenerateEdges(degenerate_length);
-		cout<<"Degen: "<<degen<<endl;
-		changes += degen;
-		
-		int barbs = cleanBarbs(barb_length);
-		cout<<"Barbs: "<<barbs<<endl;
-		changes += barbs;
-		
-		int redundant = cleanRedundantEdges();
-		cout<<"Redundant: "<<redundant<<endl;
-		changes += redundant;
-
-	}while(changes != 0);
-
-
-}
-void rtsNetwork::ReMesh(float resample_length)
-{
-	//Resample the skeleton at the given frequency
-	NetworkType newNetwork;
-
-	int numFibers = network.size();
-	int f;
-	int numVerts, v;
-	FilamentType newFiber;
-	vector3D<float> distanceVector;
-	point3D<float> prevPoint;
-	for(f=0; f<numFibers; f++)
-	{
-		newFiber.clear();
-		numVerts = network[f].size();
-		newFiber.push_back(network[f][0]);
-		prevPoint = network[f][0];
-		for(v=1; v<numVerts-1; v++)
-		{
-			distanceVector = toTissue(network[f][v]) - toTissue(prevPoint);
-			if(distanceVector.Length() >= resample_length)
-			{
-				newFiber.push_back(network[f][v]);
-				prevPoint = network[f][v];
-			}
-		}
-		
-		//deal with the last vertex
-		//newFiber.push_back(network[f][v]);
-		
-		distanceVector = toTissue(network[f][v]) - toTissue(prevPoint);
-		if(distanceVector.Length() >= resample_length || newFiber.size() == 1)
-		{
-			newFiber.push_back(network[f][v]);
-		}
-		else
-		{
-			//change the last point
-			newFiber[newFiber.size() - 1] = network[f][v];
-		}
-		
-		
-		//cout<<"old: "<<network[f].size()<<endl;
-		//cout<<"new: "<<newFiber.size()<<endl;
-		newNetwork.push_back(newFiber);
-	}
-
-	//replace the network
-	//cout<<"old network: "<<network.size()<<endl;
-	//cout<<"new network: "<<newNetwork.size()<<endl;
-	network = newNetwork;
-	calcGraph();
-
-}
-void rtsNetwork::SaveAngles(const char *filename)
-{
-	ofstream outfile;
-	outfile.open(filename);
-
-	int errors = 0;
-
-	//get the list of angles for each fiber
-	unsigned int f;
-	int numFibers = EdgeList.size();
-	for(f=0; f<numFibers; f++)
-	{
-		vector<BranchType> angles = getFiberAngles(f);
-		for(int a=0; a<angles.size(); a++)
-		{
-			outfile<<angles[a].angle<<endl;
-
-			//print out errors
-			if(angles[a].angle >179 && angles[a].angle < 181)
-			{
-				//cout<<"ERROR"<<endl;
-				//printFiberStats(f);
-				errors++;
-			}
-			if(angles[a].angle >90 && angles[a].angle < 90.01)
-			{
-				//cout<<"ERROR"<<endl;
-				//printFiberStats(f);
-				errors++;
-			}
-			if(angles[a].angle < 0)
-			{
-				//cout<<"ERROR"<<endl;
-				//printFiberStats(f);
-				errors++;
-			}
-		}
-	}
-
-	cout<<"ERRORS: "<<errors<<endl;
-
-	outfile.close();
-
-	reset();
-
-}
-void rtsNetwork::SaveBends(const char *filename)
-{
-	ofstream outfile;
-	outfile.open(filename);
-
-	int numFibers = EdgeList.size();
-	for(int f = 0; f<numFibers; f++)
-		if(network[f].size() >2)
-			outfile<<calcFiberBend(f)<<endl;
-
-	outfile.close();
-
-}
-
-void rtsNetwork::SaveLengths(const char *filename)
-{
-	ofstream outfile;
-	outfile.open(filename);
-
-	int numFibers = EdgeList.size();
-	for(int f = 0; f<numFibers; f++)
-		if(network[f].size() >2)
-			outfile<<calcFiberLength(f)<<endl;
-
-	outfile.close();
-}
-
-void rtsNetwork::SaveMathematicaGraph(const char* filename)
-{
-	ofstream outfile;
-	outfile.open(filename);
-
-	outfile<<"<< Combinatorica`"<<endl;
-	outfile<<"<< GraphUtilities`"<<endl;
-	outfile<<"e = {";
-
-	int numEdges = EdgeList.size();
-	int e;
-
-	for(e=0; e<numEdges-1; e++)
-	{
-		outfile<<""<<EdgeList[e].v0+1<<"->"<<EdgeList[e].v1+1<<",";
-	}
-	outfile<<""<<EdgeList[e].v0+1<<"->"<<EdgeList[e].v1+1<<"};";
-
-	//assign weights
-	outfile<<endl<<"w = {";
-	for(e=0; e<numEdges-1; e++)
-	{
-		outfile<<calcFiberLength(e)<<", ";
-	}
-	outfile<<calcFiberLength(e)<<"};";
-
-	int numVertices = NodeList.size();
-	int v;
-	outfile<<endl<<"v = {";
-	for(v=0; v<numVertices-1; v++)
-	{
-		//outfile<<"{{"<<NodeList[v].p.x<<","<<NodeList[v].p.y<<"}}, ";
-		outfile<<"{"<<NodeList[v].p.x<<","<<NodeList[v].p.y<<","<<NodeList[v].p.z<<"}, ";
-	}
-	//outfile<<"{{"<<NodeList[v].p.x<<","<<NodeList[v].p.y<<"}}};";
-	outfile<<"{"<<NodeList[v].p.x<<","<<NodeList[v].p.y<<","<<NodeList[v].p.z<<"}};";
-
-
-	outfile.close();
-}
-
-void rtsNetwork::SaveMathematicaNodeDistances(const char* filename)
-{
-	ofstream outfile;
-	outfile.open(filename);
-
-	//for each node, save the distance between all other nodes
-	int numNodes = NodeList.size();
-	int i, j;
-	vector3D<float> distance;
-	outfile<<"d = {";
-	for(i=0; i<numNodes-1; i++)
-	{
-		outfile<<"{";
-		for(j=0; j<numNodes-1; j++)
-		{
-			distance = toTissue(NodeList[i].p) - toTissue(NodeList[j].p);
-			outfile<<distance.Length()<<",";
-		}
-		distance = toTissue(NodeList[i].p) - toTissue(NodeList[j].p);
-		outfile<<distance.Length()<<"},";
-	}
-	outfile<<"{";
-	for(j=0; j<numNodes-1; j++)
-	{
-		distance = toTissue(NodeList[i].p) - toTissue(NodeList[j].p);
-		outfile<<distance.Length()<<",";
-	}
-	distance = toTissue(NodeList[i].p) - toTissue(NodeList[j].p);
-	outfile<<distance.Length()<<"}};";
-
-	outfile.close();
-		
-
-}
-void rtsNetwork::RemoveTerminalComponents()
-{
-	int removed;
-	do{
-		removed = EdgeList.size();
-		//removes fibers that are shorter than the specified length
-		NetworkType newNetwork;
-
-		unsigned int numEdges, e;
-		numEdges = EdgeList.size();
-		unsigned int numVertices, v;
-
-		for(e=0; e<numEdges; e++)
-		{
-			//if the fiber is not an end fiber (one vertex has valence 1)
-			if(getConnections(EdgeList[e].v0).size() != 1 && getConnections(EdgeList[e].v1).size() != 1)
-			{
-					newNetwork.push_back(network[e]);
-					removed--;
-				
-			}
-
-		}
-
-		network.clear();
-		network = newNetwork;
-
-		Clean();
-		calcGraph();
-	}while(removed != 0);
-
-}
-
-void rtsNetwork::RemoveBoundaryComponents()
-{
-	int removed;
-	do{
-		removed = EdgeList.size();
-		//removes fibers that are shorter than the specified length
-		NetworkType newNetwork;
-
-		unsigned int numEdges, e;
-		numEdges = EdgeList.size();
-		unsigned int numVertices, v;
-
-		for(e=0; e<numEdges; e++)
-		{
-			//if the fiber is not an end fiber (one vertex has valence 1)
-			if(getConnections(EdgeList[e].v0).size() != 1 && getConnections(EdgeList[e].v1).size() != 1)
-			{
-					newNetwork.push_back(network[e]);
-					removed--;
-				
-			}
-			//if the fiber is an end fiber
-			else if(!isBoundaryNode(EdgeList[e].v0) && !isBoundaryNode(EdgeList[e].v1))
-			{
-				newNetwork.push_back(network[e]);
-				removed--;
-			}
-
-
-		}
-
-		network.clear();
-		network = newNetwork;
-
-		Clean();
-		calcGraph();
-	}while(removed != 0);
-
-}
-void rtsNetwork::GetRadiusFromVolume(const char *filename, unsigned int threshold, unsigned int range = 2)
-{
-	//load the volume image
-	VOLType::Pointer volume = LoadVOL(filename);
-	VOLType::SpacingType spacing;
-	// Note: measurement units (e.g., mm, inches, etc.) are defined by the application.
-	spacing[0] = 0.86; // spacing along X
-	spacing[1] = 1.0; // spacing along Y
-	spacing[2] = 1.4; // spacing along Z
-	volume->SetSpacing(spacing);
-	SaveSlice(volume, 20, "original.bmp");
-	//volume->ReleaseDataFlagOn();
-
-/*
-	cout<<"Expanding Image..."<<endl;
-	typedef itk::ExpandImageFilter<VOLType, VOLType> ResizeFilterType;
-	ResizeFilterType::Pointer resizeFilter = ResizeFilterType::New();
-	resizeFilter->SetExpandFactors(resample);
-	resizeFilter->SetInput(volume);
-	resizeFilter->Update();
-	VOLType::Pointer resizedImage = resizeFilter->GetOutput();
-	SaveSlice(resizedImage, 20, "resized.bmp");
-	cout<<"done."<<endl;
-*/	
-
-	typedef itk::DiscreteGaussianImageFilter<VOLType, FloatType> BlurFilterType;
-	BlurFilterType::Pointer blurFilter = BlurFilterType::New();
-	blurFilter->SetUseImageSpacingOn();
-	float variance[3] = {0.61, 1.5, 0.61};
-	blurFilter->SetVariance(variance);
-	blurFilter->SetMaximumKernelWidth(8);
-	blurFilter->SetInput(volume);
-	try
-	{
-		blurFilter->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-	FloatType::Pointer blurredImage = blurFilter->GetOutput();
-
-	typedef itk::CastImageFilter<FloatType, VOLType> CastingFilterType;
-	CastingFilterType::Pointer castFilter = CastingFilterType::New();
-	castFilter->SetInput(blurredImage);
-	castFilter->Update();
-	VOLType::Pointer resizedImage = castFilter->GetOutput();
-
-	SaveSlice(resizedImage, 20, "resized.bmp");
-
-
-	//threshold the input image
-	cout<<"Thresholding Volume..."<<endl;
-	typedef itk::BinaryThresholdImageFilter<VOLType, VOLType> ThresholdFilterType;
-	ThresholdFilterType::Pointer thresholdFilter = ThresholdFilterType::New();
-	thresholdFilter->SetInsideValue(255);
-	thresholdFilter->SetOutsideValue(0);
-	thresholdFilter->SetLowerThreshold(threshold);
-	thresholdFilter->SetUpperThreshold(255);
-	thresholdFilter->SetInput(resizedImage);
-	try
-	{
-		thresholdFilter->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-	VOLType::Pointer thresholdImage = thresholdFilter->GetOutput();
-	//volume->ReleaseData();
-	//thresholdFilter->ReleaseDataFlagOn();
-
-	SaveSlice(thresholdImage, 20, "threshold.bmp");
-
-	cout<<"done."<<endl;
-
-	
-	cout<<"Computing Distance Field..."<<endl;
-	//create the distance transform filter
-	typedef itk::DanielssonDistanceMapImageFilter<VOLType, FloatType> DistanceFilterType;
-	DistanceFilterType::Pointer distanceFilter = DistanceFilterType::New();
-	distanceFilter->SetInput(thresholdImage);
-	distanceFilter->UseImageSpacingOn();
-
-	try
-	{
-		distanceFilter->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-	//SaveSlice(distanceFilter->GetOutput(), 20, "distance.bmp");
-	FloatType::Pointer distanceMap = distanceFilter->GetOutput();
-	//SaveFloatRAW(distanceMap, "distanceMap.raw");
-	cout<<"done."<<endl;
-
-	cout<<"Computing Radii..."<<endl;
-
-	
-
-	//create a neighborhood iterator
-	typedef itk::ConstNeighborhoodIterator<FloatType> NeighborhoodIteratorType;
-	NeighborhoodIteratorType::RadiusType radius;
-	radius.Fill(range);
-	NeighborhoodIteratorType i(radius, distanceMap, distanceMap->GetBufferedRegion());
-	vector<NeighborhoodIteratorType::OffsetType> OffsetVector;
-	OffsetVector.resize((range*2+1)*(range*2+1)*(range*2+1));
-	int x, y, z, j;
-	j=0;
-	for(x=-range; x<=range; x++)
-		for(y=-range; y<=range; y++)
-			for(z=-range; z<=range; z++)
-			{
-				OffsetVector[j][0]=x;
-				OffsetVector[j][1]=y;
-				OffsetVector[j][2]=z;
-				//cout<<"offset: "<<OffsetVector[j]<<endl;
-				j++;
-			}
-
-
-	int numFibers = network.size();
-	int f, numVertices, v;
-	point3D<float> position;
-	float total_radius, near_radius, total_volume, max_radius, min_radius;
-	FloatType::IndexType pixelIndex;
-	float prev_radius;
-	point3D<float> p0, p1;
-	float height;
-	for(f=0; f<numFibers; f++)
-	{
-		total_radius = 0;
-		total_volume = 0;
-		max_radius = 0;
-		min_radius = 999;
-		numVertices = network[f].size();
-		for(v=0; v<numVertices; v++)
-		{
-			position = network[f][v];
-			//pixelIndex[0] = position.x*resample;
-			//pixelIndex[1] = position.y*resample;
-			//pixelIndex[2] = position.z*resample;
-			pixelIndex[0] = position.x;
-			pixelIndex[1] = position.y;
-			pixelIndex[2] = position.z;
-			i.SetLocation(pixelIndex);
-			near_radius = 0;
-			for(j=0; j<OffsetVector.size(); j++)
-			{
-				near_radius = max(near_radius, (float)i.GetPixel(OffsetVector[j]));
-				//cout<<(float)i.GetPixel(OffsetVector[j])<<endl;
-				//cout<<"j = "<<j<<"   "<<i.GetPixel(OffsetVector[j])<<endl;
-			}
-			//cout<<"v = "<<v<<"   "<<near_radius<<endl;
-			if(near_radius > max_radius)
-				max_radius = near_radius;
-			if(near_radius < min_radius)
-				min_radius = near_radius;
-			total_radius += near_radius;
-			if(v>0)
-			{
-				//compute the volume of the segment
-				p0 = toTissue(network[f][v-1]);
-				p1 = toTissue(network[f][v]);
-				height = (p1 - p0).Length();
-				total_volume += ((3.14159*height)/3.0)*(prev_radius * prev_radius + near_radius*near_radius + prev_radius*near_radius);
-
-			}
-			prev_radius = near_radius;
-		}
-		EdgeList[f].avg_radius = total_radius/numVertices;
-		EdgeList[f].min_radius = min_radius;
-		EdgeList[f].max_radius = max_radius;
-		EdgeList[f].volume = total_volume;
-	}
-
-	cout<<"done."<<endl;
-
-}
-void rtsNetwork::GetRadiusFromDistanceMap(const char *filename, int range = 2)
-{
-	//load the volume image
-	FloatType::Pointer distanceMap = LoadRAWFloat(filename, 256, 256, 256);
-
-	//create a neighborhood iterator
-	typedef itk::ConstNeighborhoodIterator<FloatType> NeighborhoodIteratorType;
-	NeighborhoodIteratorType::RadiusType radius;
-	radius.Fill(range);
-	NeighborhoodIteratorType i(radius, distanceMap, distanceMap->GetRequestedRegion());
-	vector<NeighborhoodIteratorType::OffsetType> OffsetVector;
-	OffsetVector.resize((range*2+1)*(range*2+1)*(range*2+1));
-	int x, y, z, j;
-	j=0;
-	for(x=-range; x<=range; x++)
-		for(y=-range; y<=range; y++)
-			for(z=-range; z<=range; z++)
-			{
-				OffsetVector[j][0]=x;
-				OffsetVector[j][1]=y;
-				OffsetVector[j][2]=z;
-				//cout<<"offset: "<<OffsetVector[j]<<endl;
-				j++;
-			}
-
-	
-
-	cout<<"Computing Radii..."<<endl;
-	int numFibers = network.size();
-	int f, numVertices, v;
-	point3D<float> position;
-	float total_radius, max_radius;
-	FloatType::IndexType pixelIndex;
-	for(f=0; f<numFibers; f++)
-	{
-		total_radius = 0;
-		numVertices = network[f].size();
-		for(v=0; v<numVertices; v++)
-		{
-			position = network[f][v];
-			pixelIndex[0] = position.x;
-			pixelIndex[1] = position.y;
-			pixelIndex[2] = position.z;
-			i.SetLocation(pixelIndex);
-			max_radius = 0;
-			for(j=0; j<OffsetVector.size(); j++)
-			{
-				max_radius = max(max_radius, (float)i.GetPixel(OffsetVector[j]));
-				//cout<<"j = "<<j<<"   "<<i.GetPixel(OffsetVector[j])<<endl;
-			}
-
-			total_radius += max_radius;
-		}
-		EdgeList[f].avg_radius = total_radius/numVertices;
-	}
-
-	cout<<"done."<<endl;
-
-}
-
-point3D<float> rtsNetwork::GetFiberRadius(unsigned int fiber)
-{
-	point3D<float> result;
-	result.x = EdgeList[fiber].min_radius;
-	result.y = EdgeList[fiber].max_radius;
-	result.z = EdgeList[fiber].avg_radius;
-	return result;
-}
\ No newline at end of file
diff --git a/legacy/rtsOctree.h b/legacy/rtsOctree.h
deleted file mode 100755
index fb60cf4..0000000
--- a/legacy/rtsOctree.h
+++ /dev/null
@@ -1,70 +0,0 @@
-#ifndef RTSOCTREE_H
-#define RTSOCTREE_H
-
-#include "rtspoint3D.h"
-
-template <class T>
-struct octree_node
-{
-	unsigned int center;
-	T data;
-	octree_node* ppp;
-	octree_node* ppn;
-	octree_node* pnp;
-	octree_node* pnn;
-	octree_node* npp;
-	octree_node* npn;
-	octree_node* nnp;
-	octree_node* nnn;
-	octree_node();
-}
-
-template <class T>
-octree_node::octree_node()
-{
-	ppp = NULL;
-	ppn = NULL;
-	pnp = NULL;
-	pnn = NULL;
-	npp = NULL;
-	npn = NULL;
-	nnp = NULL;
-	nnn = NULL;
-}
-
-
-template <class T>
-class rtsOctree
-{
-public:
-	unsigned int num_leaves;
-	point3D<unsigned int> center;
-	octree_node* root;
-	rtsOctree(unsigned int sizex, unsigned int sizey, unsigned int sizez);
-	void Insert(unsigned int x, unsigned int y, unsigned int z, T value);
-
-};
-
-template <class T>
-rtsOctree<T>::rtsOctree(unsigned int sizex, unsigned int sizey, unsigned int sizez)
-{
-	center.x = sizex/2;
-	center.y = sizey/2;
-	center.z = sizez/2;
-	root = new octree_node();
-	num_leaves = 1;
-}
-
-template <class T>
-void rtsOctree<T>::Insert(unsigned int x, unsigned int y, unsigned int z, T value)
-{
-	point3D<unsigned int> current;
-	point3D<unsigned int> destination(x, y, z);
-	while(!(current == destination))
-	{
-		
-
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsParser.h b/legacy/rtsParser.h
deleted file mode 100755
index 650c0dd..0000000
--- a/legacy/rtsParser.h
+++ /dev/null
@@ -1,279 +0,0 @@
-#include<vector>
-#include<fstream>
-
-using namespace std;
-
-//define the parameter data types
-#define RTS_ERROR			0
-#define RTS_OK				1
-
-
-#define RTS_STRING			2
-#define RTS_DOUBLE			3
-
-struct parameter
-{
-	//name of the specified parameter
-	char* name;
-	int ID;
-	char* char_value;
-	double double_value;
-	int type;
-	bool set;
-};
-
-class rtsParser
-{
-private:
-	vector<parameter> parameters;
-	vector<parameter>::iterator p_SearchParams(char* name);
-	bool p_SetParameter(char* name, char* value);
-	bool p_SetParameter(char* name, double value);
-
-public:
-	void AddParameter(char* name, int ID, int type);
-	void AddParameter(char* name, int type);
-	void OutputParameters();
-	void Load(const char* filename);
-	int GetDoubleParameter(char* name, double& result);
-	int GetStringParameter(char* name, char*& result);
-};
-
-vector<parameter>::iterator rtsParser::p_SearchParams(char *name)
-{
-	//search the parameters vector for a name matching the input parameter
-
-	vector<parameter>::iterator iter;
-	
-	//run through the vector
-	for(iter = parameters.begin(); iter != parameters.end(); iter++)
-	{
-		//if the name matches the parameter name, return the iterator
-		if(strcmp((*iter).name, name) == 0)
-			return iter;
-	}
-	
-	return parameters.end();
-}
-
-bool rtsParser::p_SetParameter(char *name, char *value)
-{
-	//sets the character value of a parameter
-
-	//first, find the parameter
-	vector<parameter>::iterator iter;
-	for(iter = parameters.begin(); iter != parameters.end(); iter++)
-	{
-		//if the parameter is found
-		if(strcmp((*iter).name, name) == 0)
-		{
-			//if the parameter type is wrong, return false
-			if((*iter).type != RTS_STRING)
-				return false;
-			//otherwise, set the parameter value
-			(*iter).char_value = value;
-			(*iter).set = true;
-			return true;
-		}
-	}
-	//if the parameter was not found, return false
-	return false;
-}
-
-bool rtsParser::p_SetParameter(char *name, double value)
-{
-	//sets the character value of a parameter
-
-	//first, find the parameter
-	vector<parameter>::iterator iter;
-	for(iter = parameters.begin(); iter != parameters.end(); iter++)
-	{
-		//if the parameter is found
-		if(strcmp((*iter).name, name) == 0)
-		{
-			//if the parameter type is wrong, return false
-			if((*iter).type != RTS_DOUBLE)
-				return false;
-			//otherwise, set the parameter value
-			(*iter).double_value = value;
-			(*iter).set = true;
-			return true;
-		}
-	}
-	//if the parameter was not found, return false
-	return false;
-}
-
-void rtsParser::Load(const char* filename)
-{
-	//loads a parameter file and fills the list with the parameter values
-
-	//create an input stream and load the file
-	ifstream infile;
-	infile.open(filename);
-
-	//create temporary variables to store values
-	char param_name[1000];
-	vector<parameter>::iterator iter;
-
-	//for each line in the parameter file
-	while(!infile.eof())
-	{
-		//get the parameter name token
-		infile.get(param_name, 100, ' ');
-		//find the proper parameter in the parameter list
-		iter = p_SearchParams(param_name);
-
-		//test to make sure the parameter was found
-		if(iter == parameters.end())
-		{
-			cout<<"Error, could not find parameter: "<<param_name<<endl;
-			exit(1);
-		}
-
-		//cout<<"infile.get:  "<<param_name<<endl;
-
-		//get the equal sign
-		char equals;
-		infile>>equals;
-
-		//cout<<"infile>>equals: "<<equals<<endl;
-		
-
-		//create space for the string
-		char* temp_value_string= new char[500];
-		infile.get(temp_value_string, 500);
-
-		//cout<<"temp_value_string: "<<temp_value_string<<endl;
-
-		if((*iter).type == RTS_STRING)
-		{
-			//remove the quotation marks
-			temp_value_string = strchr(temp_value_string, '"');
-			if(temp_value_string != NULL)
-			{
-				temp_value_string++;
-				char* end = strrchr(temp_value_string, '"');
-				*end = 0;
-				
-				//set the parameter
-				(*iter).char_value = temp_value_string;
-				(*iter).set = true;
-			}
-			else
-			{
-				cout<<"Error, no quotes in parameter value: "<<(*iter).name<<endl;
-			}
-		}
-		else if((*iter).type == RTS_DOUBLE)
-		{
-			(*iter).double_value = atof(temp_value_string);
-			(*iter).set = true;
-		}
-		
-
-		
-
-		//get the final line character
-		//char temp[2];
-		//infile.get(temp, 2);
-		//skip to the next line
-		infile.getline(param_name, 1000);
-		//}
-
-	}
-
-}
-
-int rtsParser::GetDoubleParameter(char* name, double& result)
-{
-	//find the appropriate parameter
-	vector<parameter>::iterator iter = p_SearchParams(name);
-	
-	//check for errors
-	if(iter == parameters.end())
-	{
-		cout<<"Error finding parameter: "<<name<<endl;
-		return RTS_ERROR;
-	}
-	else if((*iter).type != RTS_DOUBLE)
-	{
-		cout<<"Invalid data type for parameter: "<<name<<endl;
-		return RTS_ERROR;
-	}
-	else if(!(*iter).set)
-	{
-		cout<<"Parameter not set during load: "<<name<<endl;
-		return RTS_ERROR;
-	}
-
-	//return the appropriate value as a reference parameter
-	result = (*iter).double_value;
-	return RTS_OK;
-}
-
-int rtsParser::GetStringParameter(char* name, char*& result)
-{
-	//find the appropriate parameter
-	vector<parameter>::iterator iter = p_SearchParams(name);
-	
-	//check for errors
-	if(iter == parameters.end())
-	{
-		cout<<"Error finding parameter: "<<name<<endl;
-		return RTS_ERROR;
-	}
-	else if((*iter).type != RTS_STRING)
-	{
-		cout<<"Invalid data type for parameter: "<<name<<endl;
-		return RTS_ERROR;
-	}
-	else if(!(*iter).set)
-	{
-		cout<<"Parameter not set during load: "<<name<<endl;
-		return RTS_ERROR;
-	}
-
-	//return the appropriate value as a reference parameter
-	result = (*iter).char_value;
-	return RTS_OK;
-}
-
-void rtsParser::AddParameter(char *name, int ID, int type)
-{
-	//this function adds an expected parameter to the parser
-
-	//create a new parameter and store the user-defined variables
-	parameter new_param;
-	new_param.name = name;
-	new_param.ID = ID;
-	new_param.type = type;
-	new_param.set = false;
-
-	//add the parameter to the parameter list
-	parameters.push_back(new_param);
-}
-
-void rtsParser::AddParameter(char* name, int type)
-{
-	AddParameter(name, 0, type);
-}
-
-void rtsParser::OutputParameters()
-{
-	vector<parameter>::iterator iter;
-	for(iter = parameters.begin(); iter!= parameters.end(); iter++)
-	{
-		//test to see if the parameter was set by the file
-		if((*iter).set)
-		{
-			cout<<"name: "<<(*iter).name;
-			
-			if((*iter).type == RTS_DOUBLE)
-				cout<<"  value: "<<(*iter).double_value<<endl;
-			else
-				cout<<"  value: "<<(*iter).char_value<<endl;
-		}
-	}
-}
-
diff --git a/legacy/rtsPoint3d.h b/legacy/rtsPoint3d.h
deleted file mode 100755
index 1d29c69..0000000
--- a/legacy/rtsPoint3d.h
+++ /dev/null
@@ -1,141 +0,0 @@
-#ifndef RTSPOINT3D_H
-#define RTSPOINT3D_H
-#include "rtsVector3d.h"
-
-///This class is used to store information about a 3D point.  It is designed to work with the class vector3D<T> for linear algebra operations.
-
-template <class T> class point3D
-{
-	//friend class vector3D<T>;
-public:
-	//data values
-	T x;
-	T y;
-	T z;
-
-	point3D();									///<Constructor initializes the point at the origin (0,0,0).
-	point3D(T new_x, T new_y, T new_z);			///<Constructor initializes the point to the position specified by (new_x, new_y, new_z).
-
-	//operators
-	bool operator==(point3D<T> param);			///<Overloaded boolean operator.  Returns true if the two oparands are at the same position.
-	bool operator!=(point3D<T> param);			///<Overloaded boolean operator for !=
-	point3D<T> operator+(vector3D<T> param);	///<Overloaded arithmetic oparator.  Returns the sum of the current point and a given vector.
-	point3D<T> operator-(vector3D<T> param);	///<Overloaded arithmetic operator.  Returns the sum of the current point and the negative of a given vector.
-	vector3D<T> operator-(point3D<T> param);	///<Overloaded arithmetic operator.  Returns the vector representing the space between two points.
-
-	//casting operators
-	template <class U> operator point3D<U>();  ///<Overloaded casting operator.  Allows casting between points of different types.
-
-	//output
-	friend ostream& operator<<(ostream& os, const point3D<T> &rhs)
-	{
-		os<<"("<<rhs.x<<","<<rhs.y<<","<<rhs.z<<")";
-		return os;
-	}
-
-	/*point3D<T> & operator=(const point3D<T> & rhs)
-	{
-		if(this != &rhs)
-		{
-			x = rhs.x;
-			y = rhs.y;
-			z = rhs.z;
-		}
-		return *this;
-	}*/
-	
-	void print();
-};
-
-template <class T>
-template <class U>
-point3D<T>::operator point3D<U>()
-{
-	point3D<U> cast_result(x, y, z);
-	return cast_result;
-}
-
-template <class T> point3D<T>::point3D()
-{
-	x=0;
-	y=0;
-	z=0;
-}
-
-template <class T> point3D<T>::point3D(T new_x, T new_y, T new_z)
-{
-	x=new_x;
-	y=new_y;
-	z=new_z;
-}
-
-template <class T>
-point3D<T> point3D<T>::operator -(vector3D<T> param)
-{
-	point3D<T> result;			//create the result
-	
-	result.x = x-param.x;		//perform the computation
-	result.y = y-param.y;
-	result.z = z-param.z;
-
-	return result;
-}
-
-template <class T>
-vector3D<T> point3D<T>::operator -(point3D<T> param)
-{
-	vector3D<T> result;
-	result.x = x - param.x;
-	result.y = y - param.y;
-	result.z = z - param.z;
-	
-	return result;
-}
-
-template <class T>
-point3D<T> point3D<T>::operator+(vector3D<T> param)
-{
-	point3D<T> result;			//create the result
-	
-	result.x = x+param.x;		//perform the computation
-	result.y = y+param.y;
-	result.z = z+param.z;
-
-	return result;
-}
-
-template <class T>
-bool point3D<T>::operator ==(point3D<T> param)
-{
-	if(x == param.x && y == param.y && z == param.z)
-		return true;
-	else
-		return false;
-}
-
-template <class T>
-bool point3D<T>::operator !=(point3D<T> param)
-{
-	if(x != param.x || y != param.y || z != param.z)
-		return true;
-	else
-		return false;
-}
-
-
-
-template <class T>
-void point3D<T>::print()
-{
-	cout<<"("<<x<<","<<y<<","<<z<<")"<<endl;
-}
-
-/*template <class T>
-ostream& point3D<T>::operator<<(ostream& os, point3D<T> &rhs)
-{
-	os<<"("<<x<<","<<y<<","<<z<<")";
-	return os;
-}
-*/
-
-#endif
diff --git a/legacy/rtsProgressBar.cpp b/legacy/rtsProgressBar.cpp
deleted file mode 100755
index dbb2cde..0000000
--- a/legacy/rtsProgressBar.cpp
+++ /dev/null
@@ -1,28 +0,0 @@
-#include <iostream>
-#include <sstream>
-using namespace std;
-
-void rtsProgressBar(int percent)
-{
-	stringstream bar;
-	static int x = 0;
-	string slash[4];
-	slash[0] = "\\";
-	slash[1] = "-";
-	slash[2] = "/";
-	slash[3] = "|";
-	bar<<"[";
-	for(int i=0; i<40; i++)
-	{
-		if(percent > (float)i/(float)40 *100)
-			bar << "*";
-		else
-			bar << " ";
-	}
-	bar<<"]";
-	cout << "\r"; // carriage return back to beginning of line
-	cout << bar.str() << " " << slash[x] << " " << percent << " %"; // print the bars and percentage
-	x++; // increment to make the slash appear to rotate
-	if(x == 4)
-	x = 0; // reset slash animation
-}
\ No newline at end of file
diff --git a/legacy/rtsQuaternion.h b/legacy/rtsQuaternion.h
deleted file mode 100755
index bef1331..0000000
--- a/legacy/rtsQuaternion.h
+++ /dev/null
@@ -1,144 +0,0 @@
-#include "rtsMatrix4x4.h"
-
-#ifndef RTS_QUATERNION_H
-#define RTS_QUATERNION_H
-
-template<typename T>
-class rtsQuaternion
-{
-public:
-	T w;
-	T x;
-	T y;
-	T z;
-
-	void normalize();
-	void CreateRotation(T theta, T axis_x, T axis_y, T axis_z);
-	rtsQuaternion<T> operator*(rtsQuaternion<T> &rhs);
-	matrix4x4<T> toMatrix();
-	
-
-	rtsQuaternion();
-	rtsQuaternion(T w, T x, T y, T z);
-
-};
-
-template<typename T>
-void rtsQuaternion<T>::normalize()
-{
-	double length=sqrt(w*w + x*x + y*y + z*z);
-	w=w/length;
-	x=x/length;
-	y=y/length;
-	z=z/length;
-}
-
-template<typename T>
-void rtsQuaternion<T>::CreateRotation(T theta, T axis_x, T axis_y, T axis_z)
-{
-	//assign the given Euler rotation to this quaternion
-	w = cos(theta/2.0);
-	x = axis_x*sin(theta/2.0);
-	y = axis_y*sin(theta/2.0);
-	z = axis_z*sin(theta/2.0);
-
-
-}
-
-template<typename T>
-rtsQuaternion<T> rtsQuaternion<T>::operator *(rtsQuaternion<T> &param)
-{
-	float A, B, C, D, E, F, G, H;
-
-
-	A = (w + x)*(param.w + param.x);
-	B = (z - y)*(param.y - param.z);
-	C = (w - x)*(param.y + param.z); 
-	D = (y + z)*(param.w - param.x);
-	E = (x + z)*(param.x + param.y);
-	F = (x - z)*(param.x - param.y);
-	G = (w + y)*(param.w - param.z);
-	H = (w - y)*(param.w + param.z);
-
-	rtsQuaternion<T> result;
-	result.w = B + (-E - F + G + H) /2;
-	result.x = A - (E + F + G + H)/2; 
-	result.y = C + (E - F + G - H)/2; 
-	result.z = D + (E - F - G + H)/2;
-
-	return result;
-}
-
-template<typename T>
-matrix4x4<T> rtsQuaternion<T>::toMatrix()
-{
-	matrix4x4<T> result;
-
-
-    double wx, wy, wz, xx, yy, yz, xy, xz, zz, x2, y2, z2;
-
-
-    // calculate coefficients
-    x2 = x + x; y2 = y + y;
-    z2 = z + z;
-    xx = x * x2; xy = x * y2; xz = x * z2;
-    yy = y * y2; yz = y * z2; zz = z * z2;
-    wx = w * x2; wy = w * y2; wz = w * z2;
-
-	result(0, 0) = 1.0 - (yy + zz);
-	result(0, 1) = xy - wz;
-    //m[0][0] = 1.0 - (yy + zz); m[1][0] = xy - wz;
-
-	result(0, 2) = xz + wy;
-	result(0, 3) = 0.0;
-    //m[2][0] = xz + wy; m[3][0] = 0.0;
-
-	result(1, 0) = xy + wz;
-	result(1, 1) = 1.0 - (xx + zz);
-    //m[0][1] = xy + wz; m[1][1] = 1.0 - (xx + zz);
-
-	result(1, 2) = yz - wx;
-	result(1, 3) = 0.0;
-    //m[2][1] = yz - wx; m[3][1] = 0.0;
-
-	result(2, 0) = xz - wy;
-	result(2, 1) = yz + wx;
-    //m[0][2] = xz - wy; m[1][2] = yz + wx;
-
-	result(2, 2) = 1.0 - (xx + yy);
-	result(3, 2) = 0.0;
-    //m[2][2] = 1.0 - (xx + yy); m[3][2] = 0.0;
-
-	result(3, 0) = 0.0;
-	result(3, 1) = 0.0;
-	result(3, 2) = 0.0;
-	result(3, 3) = 1.0;
-    //m[0][3] = 0; m[1][3] = 0;
-    //m[2][3] = 0; m[3][3] = 1;
-	/*
-	double* orientationmatrix=(double*)m;
-	char c;
-
-
-	double* result=new double[16];
-	double* array=(double*)m;
-	for(int i=0; i<16; i++)
-		result[i]=array[i];
-	*/
-
-	return result;
-}
-
-template<typename T>
-rtsQuaternion<T>::rtsQuaternion()
-{
-	w=0.0; x=0.0; y=0.0; z=0.0;
-}
-
-template<typename T>
-rtsQuaternion<T>::rtsQuaternion(T c, T i, T j, T k)
-{
-	w=c;  x=i;  y=j;  z=k;
-}
-
-#endif
diff --git a/legacy/rtsSkeleton.h b/legacy/rtsSkeleton.h
deleted file mode 100755
index b85d884..0000000
--- a/legacy/rtsSkeleton.h
+++ /dev/null
@@ -1,107 +0,0 @@
-#include <vector>
-using namespace std;
-
-#include "rtsPoint3d.h"
-#include "rts_itkVolume.h"
-typedef vector<point3D<double>> filament;
-
-#define BACKGROUND_NODE	0
-#define SKELETON_NODE	255
-#define ENDPOINT_NODE	128
-#define VISITED_NODE	64
-
-class rtsSkeleton
-{
-	rts_itkVolume<unsigned char> implicit_skeleton;
-	vector<filament> explicit_filaments;
-	vector<point3D<unsigned int>> explicit_endpoints;
-
-	void ComputeEndPoints();
-
-public:
-	void ConstructExplicitSkeleton();
-	void SmoothExplicitSkeleton(int iterations);
-	void SaveExplicitSkeleton(const char* filename);
-}
-
-void rtsSkeleton::ComputeEndPoints()
-{
-	/*This function finds all of the filament end points in the implicit skeleton.
-	The end points are stored in the explicit_endpoints vector.
-	An end point is defined as a node with (n == 1) or (n > 2) connected components.
-	*/
-
-	unsigned int max_x = implicit_skeleton.DimX();
-	unsigned int max_y = implicit_skeleton.DimY();
-	unsigned int max_z = implicit_skeleton.DimZ();
-	unsigned int conn;
-
-	indextype x, y, z;
-	for(x=0; x<max_x; x++)		//go through each voxel in the data set
-		for(y=0; y<max_y; y++)
-			for(z=0; z<max_z; z++)
-			{
-				if(implicit_skeleton.GetPixel(x, y, z) == SKELETON_NODE)	//if the voxel is part of the skeleton
-				{
-					conn = Neighbors26(&implicit_skeleton, x, y, z, 1);	//test the number of connected components
-					if(conn == 1 || conn > 2)	//if the number of connected components meets the
-												//criteria, store the node in the explicit_endpoints vector.
-					{
-						explicit_endpoints.push_back(point3D<unsigned int>(x, y, z));
-					}
-				}
-
-			}
-
-	//tag the endpoints in the implicit function
-	vector<point3D<unsigned int>>::iterator i;
-	for(i=explicit_endpoints.begin(); i!=explicit_endpoints.end(); i++)
-		implicit_skeleton.xyz(i->x, i->y, i->z) = ENDPOINT_NODE;
-
-			//cout<<"Number of end points:  "<<explicit_endpoints.size()<<endl;
-}
-
-void rtsSkeleton::ConstructExplicitSkeleton()
-{
-	/*The implicit skeleton is constructed as follows:
-	1)  Label all branch nodes.
-	2)  For each branch, find the number of fibers connected to that branch.
-		a)  Create each fiber as a seperate structure and store them in a queue.
-		b)  Iteratively track each fiber.
-	*/
-	ComputeEndPoints();	//compute the endpoints for the explicit skeleton and
-						//label them in the implicit skeleton
-	
-	//iterate through each end point
-	vector<point3D<unsigned int>>::iterator i;
-	rtsFunction3D<unsigned char> local;
-	unsigned int x, y, z;
-	for(i = explicit_endpoints.begin(); i != explicit_endpoints.end(); i++)
-	{
-		//cout<<"Tracing Filament..."<<endl;
-		//i->print();
-		local = getLocalRegion(i->x, i->y, i->z);
-		local(1, 1, 1) = 0;
-		//local.toConsole();
-		for(x=0; x<3; x++)
-			for(y=0; y<3; y++)
-				for(z=0; z<3; z++)
-					if(local.xyz(x, y, z) > VISITED_NODE)
-					{
-						//cout<<(int)local.xyz(x, y, z)<<endl;
-						//cout<<(int)implicit_skeleton.xyz(i->x - 1 + x,
-						//							  i->y - 1 + y,
-						//							  i->z - 1 + z)<<endl;
-						TraceFilament((*i), point3D<unsigned int>(i->x - 1 + x,
-																  i->y - 1 + y,
-																  i->z - 1 + z));
-					}
-		//since we have tracked all filaments attached to an endpoint
-		//set the endpoint as visited
-		implicit_skeleton.xyz(i->x, i->y, i->z) = VISITED_NODE;
-	}
-
-	//cout<<"Tracing complete"<<endl;
-
-
-}
\ No newline at end of file
diff --git a/legacy/rtsSkeletonizer.h b/legacy/rtsSkeletonizer.h
deleted file mode 100755
index 80b4231..0000000
--- a/legacy/rtsSkeletonizer.h
+++ /dev/null
@@ -1,680 +0,0 @@
-#ifndef RTSSKELETONIZER_H
-#define RTSSKELETONIZER_H
-
-#include "rts_itkVolume.h"
-#include "objJedi.h"
-#include <vector>
-#include <queue>
-
-using namespace std;
-
-typedef vector<point3D<double>> filament;
-typedef unsigned int indextype;
-
-#define BACKGROUND_NODE	0
-#define SKELETON_NODE	255
-#define ENDPOINT_NODE	128
-#define VISITED_NODE	64
-
-class rtsSkeletonizer
-{
-private:
-	rts_itkVolume<unsigned char> implicit_skeleton;
-	/*Key:
-	0 - background node
-	255 - skeleton node
-	128 - endpoint node
-	*/
-
-	vector<filament> explicit_filaments;
-	vector<point3D<unsigned int>> explicit_endpoints;
-
-
-
-public:
-	rtsSkeletonizer(rts_itkVolume<unsigned char> input);
-	unsigned int BackgroundComponents6(rts_itkVolume<unsigned char>* function,
-									   indextype x, 
-									   indextype y, 
-									   indextype z, 
-									   unsigned char threshold);
-	unsigned int rtsSkeletonizer::Peel(unsigned char isovalue);
-	int Neighbors26(rts_itkVolume<unsigned char>* function, 
-					indextype x, 
-					indextype y, 
-					indextype z, 
-					unsigned char isovalue);
-	vector<point3D<unsigned int>> FloodFill6(rts_itkVolume<unsigned char>* function, indextype x, indextype y, indextype z, unsigned char target_value);
-	void FloodFill26(rts_itkVolume<unsigned char>* function, int x, int y, int z, unsigned char target_value);
-	unsigned int Neighbors6(rts_itkVolume<unsigned char>* function, indextype x, indextype y, indextype z, unsigned char threshold);
-	rts_itkVolume<unsigned char> getImplicitResult(){return implicit_skeleton;}
-	unsigned int NumConnectedComponents(indextype x, indextype y, indextype z, unsigned char threshold);
-
-	void ComputeEndPoints();	//find all of the filament end points
-	void TraceFilament(point3D<unsigned int> p0, point3D<unsigned int> p1);
-	rts_itkVolume<unsigned char> getLocalRegion(unsigned int x, unsigned int y, unsigned int z);
-
-	void ConstructExplicitSkeleton();
-	void SmoothExplicitSkeleton(int iterations);
-	void SaveExplicitSkeleton(const char* filename);
-
-
-};
-
-void rtsSkeletonizer::SmoothExplicitSkeleton(int iterations)
-{
-	/*This function smooths the vessels by repeatedly taking the dual of the skeleton.
-	Branch points and end points are constrained to their initial positions.
-	*/
-
-	vector<filament>::iterator f;
-	int num_verts, end_vert;
-	int v;
-	point3D<double> new_vert;
-
-	for(int i = 0; i<iterations; i++)
-	{
-		for(f=explicit_filaments.begin(); f!=explicit_filaments.end(); f++)
-		{
-			filament new_filament;
-			
-			//find the number of vertices in the filament
-			num_verts = f->size();
-			end_vert = num_verts - 1;
-
-			//take care of the first vertex
-			new_filament.push_back((*f)[0]);
-
-			for(v=1; v<end_vert; v++)
-			{
-				//find the position of the next vertex (midpoint between the last and current vertices)
-				new_vert = (*f)[v-1] + ((*f)[v] - (*f)[v-1])*0.5;
-				new_filament.push_back(new_vert);			
-			}
-
-			//take care of the last vertex
-			new_filament.push_back((*f)[end_vert]);
-
-			//delete the old filament and add the new one
-			(*f) = new_filament;
-		}
-	}
-		
-}
-
-void rtsSkeletonizer::SaveExplicitSkeleton(const char* filename)
-{
-	/*Save the filament file as an OBJ*/
-	//create the OBJ object
-	rtsOBJ output;
-
-	unsigned int num_filaments = explicit_filaments.size();
-	//cout<<"Number of filaments:  "<<num_filaments<<endl;
-	vector<filament>::iterator i;
-	filament::iterator f;
-	for(i=explicit_filaments.begin(); i!=explicit_filaments.end(); i++)
-	{
-		output.objBegin(OBJ_LINE_STRIP);
-		//cout<<"start filament"<<endl;
-		for(f=i->begin(); f!=i->end(); f++)
-		{
-			output.objVertex3f((*f).x, (*f).y, (*f).z);
-			//f->print();
-		}
-		//cout<<"end filament"<<endl<<endl;
-		output.objEnd();
-	}
-
-	output.SaveFile(filename);
-		
-}
-
-rts_itkVolume<unsigned char> rtsSkeletonizer::getLocalRegion(unsigned int x, unsigned int y, unsigned int z)
-{
-	rts_itkVolume<unsigned char> local(3, 3, 3);
-	point3D<indextype> corner;
-	indextype u, v, w;
-	corner = point3D<indextype>(x-1, y-1, z-1);
-	for(u=0; u<3; u++)
-		for(v=0; v<3; v++)
-			for(w=0; w<3; w++)
-				local.SetPixel(u, v, w, implicit_skeleton.GetPixel(corner.x + u, corner.y + v, corner.z + w));
-	return local;
-}
-
-
-void rtsSkeletonizer::TraceFilament(point3D<unsigned int> p0, point3D<unsigned int> p1)
-{
-	//create the new filament and start it with the two given points
-	filament result;
-	result.push_back(p0);
-	result.push_back(p1);
-
-	//if(p0 == point3D<unsigned int>(156, 433, 254))
-	//	cout<<"Stop here"<<endl;
-
-	//if p1 is an endpoint, go ahead and end the filament right away
-	if(implicit_skeleton.GetPixel(p1.x, p1.y, p1.z) == ENDPOINT_NODE)
-	{
-		explicit_filaments.push_back(result);
-		return;
-	}
-
-	rts_itkVolume<unsigned char> local;
-	point3D<unsigned int> current = p1;
-	point3D<unsigned int> next;
-	point3D<unsigned int> possible_end;
-	int x, y, z;
-	int c;		//possible connections
-
-	while(1)	//continue tracing until the next endpoint
-	{
-		c=0;
-		local = getLocalRegion(current.x, current.y, current.z);
-		//cout<<"Local Region at ("<<current.x<<","<<current.y<<","<<current.z<<")"<<endl;
-		//local.toConsole();
-		local.SetPixel(1, 1, 1, 0);
-		for(x=0; x<3; x++)
-			for(y=0; y<3; y++)
-				for(z=0; z<3; z++)
-				{
-					//if the node is a skeleton node, store it as the next point
-					if(local(x, y, z) == SKELETON_NODE)
-					{
-						c++;
-						next = current - vector3D<unsigned int>(1, 1, 1) + vector3D<unsigned int>(x, y, z);
-					}
-					//if it is an endpoint node, check for a termination
-					if(local(x, y, z) == ENDPOINT_NODE)
-					{
-						//if we are not backtracking to the start node
-						possible_end = current - vector3D<unsigned int>(1, 1, 1) + vector3D<unsigned int>(x, y, z);
-						if(possible_end != p0 || result.size() > 2)
-						{
-							//terminate the fiber
-							result.push_back(current - vector3D<unsigned int>(1, 1, 1) + vector3D<unsigned int>(x, y, z));
-							explicit_filaments.push_back(result);
-							implicit_skeleton.SetPixel(current.x, current.y, current.z, VISITED_NODE);
-							return;
-						}
-					}
-				}
-		//return when there is nowhere to go
-		if(c == 0)
-			return;
-		//now we have the next node in the filament, go ahead and label the current
-		//one as traversed
-		implicit_skeleton.SetPixel(current.x, current.y, current.z, VISITED_NODE);
-		//now insert it into the fiber and move to the next node
-		result.push_back(next);
-		if(current == next)
-		{
-			//cout<<"I've been waiting for you Obi-Wan"<<endl;
-			local = getLocalRegion(current.x, current.y, current.z);
-			//cout<<"Local Region at ("<<current.x<<","<<current.y<<","<<current.z<<")"<<endl;
-			//local.toConsole();
-
-			//cout<<"Number of neighbors: "<<Neighbors26(&implicit_skeleton, current.x, current.y, current.z, 1);
-		}
-		current = next;
-	}
-	
-	
-}
-
-void rtsSkeletonizer::ConstructExplicitSkeleton()
-{
-	/*The implicit skeleton is constructed as follows:
-	1)  Label all branch nodes.
-	2)  For each branch, find the number of fibers connected to that branch.
-		a)  Create each fiber as a seperate structure and store them in a queue.
-		b)  Iteratively track each fiber.
-	*/
-	ComputeEndPoints();	//compute the endpoints for the explicit skeleton and
-						//label them in the implicit skeleton
-	
-	//iterate through each end point
-	vector<point3D<unsigned int>>::iterator i;
-	rts_itkVolume<unsigned char> local;
-	unsigned int x, y, z;
-	for(i = explicit_endpoints.begin(); i != explicit_endpoints.end(); i++)
-	{
-		//cout<<"Tracing Filament..."<<endl;
-		//i->print();
-		local = getLocalRegion(i->x, i->y, i->z);
-		local.SetPixel(1, 1, 1, 0);
-		//local.toConsole();
-		for(x=0; x<3; x++)
-			for(y=0; y<3; y++)
-				for(z=0; z<3; z++)
-					if(local.GetPixel(x, y, z) > VISITED_NODE)
-					{
-						//cout<<(int)local.xyz(x, y, z)<<endl;
-						//cout<<(int)implicit_skeleton.xyz(i->x - 1 + x,
-						//							  i->y - 1 + y,
-						//							  i->z - 1 + z)<<endl;
-						TraceFilament((*i), point3D<unsigned int>(i->x - 1 + x,
-																  i->y - 1 + y,
-																  i->z - 1 + z));
-					}
-		//since we have tracked all filaments attached to an endpoint
-		//set the endpoint as visited
-		implicit_skeleton.SetPixel(i->x, i->y, i->z, VISITED_NODE);
-	}
-
-	//cout<<"Tracing complete"<<endl;
-
-
-}
-
-
-rtsSkeletonizer::rtsSkeletonizer(rts_itkVolume<unsigned char> input)
-{
-	implicit_skeleton = input;
-}
-
-void rtsSkeletonizer::ComputeEndPoints()
-{
-	/*This function finds all of the filament end points in the implicit skeleton.
-	The end points are stored in the explicit_endpoints vector.
-	An end point is defined as a node with (n == 1) or (n > 2) connected components.
-	*/
-
-	unsigned int max_x = implicit_skeleton.DimX();
-	unsigned int max_y = implicit_skeleton.DimY();
-	unsigned int max_z = implicit_skeleton.DimZ();
-	unsigned int conn;
-
-	indextype x, y, z;
-	for(x=0; x<max_x; x++)		//go through each voxel in the data set
-		for(y=0; y<max_y; y++)
-			for(z=0; z<max_z; z++)
-			{
-				if(implicit_skeleton(x, y, z) == SKELETON_NODE)	//if the voxel is part of the skeleton
-				{
-					conn = Neighbors26(&implicit_skeleton, x, y, z, 1);	//test the number of connected components
-					if(conn == 1 || conn > 2)	//if the number of connected components meets the
-												//criteria, store the node in the explicit_endpoints vector.
-					{
-						explicit_endpoints.push_back(point3D<unsigned int>(x, y, z));
-					}
-				}
-
-			}
-
-	//tag the endpoints in the implicit function
-	vector<point3D<unsigned int>>::iterator i;
-	for(i=explicit_endpoints.begin(); i!=explicit_endpoints.end(); i++)
-		implicit_skeleton.SetPixel(i->x, i->y, i->z, ENDPOINT_NODE);
-
-			//cout<<"Number of end points:  "<<explicit_endpoints.size()<<endl;
-}
-
-
-
-unsigned int rtsSkeletonizer::NumConnectedComponents(indextype x, indextype y, indextype z, unsigned char threshold)
-{
-	unsigned int result = 0;
-
-	rts_itkVolume<unsigned char> local(3, 3, 3);
-	
-
-	local = getLocalRegion(x, y, z);
-//	local.toConsole();
-	local.SetPixel(1, 1, 1, 0);
-//	local.toConsole();
-
-	indextype xi, yi, zi;
-	//iterate through each voxel
-	for(xi=0; xi<3; xi++)
-		for(yi=0; yi<3; yi++)
-			for(zi=0; zi<3; zi++)
-				if(local(xi, yi, zi) >= threshold)
-				{
-					FloodFill6(&local, xi, yi, zi, 0);
-					result++;
-				}
-	/*
-	if(result == 1 || result > 2)
-	{
-		cout<<result<<endl;
-		local = getLocalRegion(x, y, z);
-		local.toConsole();
-	}
-	*/
-	return result;
-
-
-}
-
-unsigned int rtsSkeletonizer::BackgroundComponents6(rts_itkVolume<unsigned char>* function, 
-													   indextype x, 
-													   indextype y, 
-													   indextype z, 
-													   unsigned char threshold)
-{
-	/**
-	This function computes the number of 6-connected background components in the local region of (x, y, z).
-	This computation is performed by testing all 6 possible voxels that can connect to the specified node.  If
-	a background node is found, the entire background component associated with that node is filled and the counter
-	is incremented by 1.  The value n specifies the connectivity domain for the flood fill.
-	The definition of background components is that specified by He, Kischell, Rioult and Holmes.
-	**/
-
-	//see if there is at least one BG component
-	if(Neighbors6(function, x, y, z, threshold) == 6)
-		return 0;
-
-	
-	//retrieve the local region of the function
-	rts_itkVolume<unsigned char> local(3, 3, 3);
-	point3D<indextype> corner(x-1, y-1, z-1);
-	indextype u, v, w;
-	for(u=0; u<3; u++)
-		for(v=0; v<3; v++)
-			for(w=0; w<3; w++)
-				local.SetPixel(u, v, w, function->GetPixel(corner.x + u, corner.y + v, corner.z + w));
-
-	//threshold the background to find inside/outside points
-	local.Binary(threshold, 1);
-	//fill points that are not in the connectivity domain
-	/*if(n == 18)
-	{
-		local(0, 0, 0) = 1;
-		local(0, 0, 2) = 1;
-		local(0, 2, 0) = 1;
-		local(0, 2, 2) = 1;
-		local(2, 0, 0) = 1;
-		local(2, 0, 2) = 1;
-		local(2, 2, 0) = 1;
-		local(2, 2, 2) = 1;
-	}*/
-	//local.toConsole();
-
-	//search all 6 possible connected points.  If a background node is found, fill the component
-	unsigned int components = 0;
-	if(local(0, 1, 1) == 0)
-	{
-		components++;
-		FloodFill6(&local, 0, 1, 1, 1);
-	}
-	if(local(2, 1, 1) == 0)
-	{
-		components++;
-		FloodFill6(&local, 2, 1, 1, 1);
-	}
-	if(local(1, 0, 1) == 0)
-	{
-		components++;
-		FloodFill6(&local, 1, 0, 1, 1);
-	}
-	if(local(1, 2, 1) == 0)
-	{
-		components++;
-		FloodFill6(&local, 1, 2, 1, 1);
-	}
-	if(local(1, 1, 0) == 0)
-	{
-		components++;
-		FloodFill6(&local, 1, 1, 0, 1);
-	}
-	if(local(1, 1, 2) == 0)
-	{
-		components++;
-		FloodFill6(&local, 1, 1, 2, 1);
-	}
-
-	return components;
-}
-
-unsigned int rtsSkeletonizer::Neighbors6(rts_itkVolume<unsigned char>* function, indextype x, indextype y, indextype z, unsigned char threshold)
-{
-
-	unsigned int neighbors = 0;
-	if(function->GetPixel(x+1, y, z) >= threshold)
-		neighbors++;
-	if(function->GetPixel(x-1, y, z) >= threshold)
-		neighbors++;
-	if(function->GetPixel(x, y+1, z) >= threshold)
-		neighbors++;
-	if(function->GetPixel(x, y-1, z) >= threshold)
-		neighbors++;
-	if(function->GetPixel(x, y, z+1) >= threshold)
-		neighbors++;
-	if(function->GetPixel(x, y, z-1) >= threshold)
-		neighbors++;
-
-	return neighbors;
-}
-
-int rtsSkeletonizer::Neighbors26(rts_itkVolume<unsigned char>* function,
-									indextype x, 
-									indextype y, 
-									indextype z, 
-									unsigned char isovalue)
-{
-	int neighbors = 0;
-	int u,v,w;
-
-	for(u=-1; u<=1; u++)
-		for(v=-1; v<=1; v++)
-			for(w=-1; w<=1; w++)
-				if(function->GetPixel(x+u, y+v, z+w) >= isovalue)
-					neighbors++;
-	if(function->GetPixel(x, y, z) > isovalue)
-		neighbors--;
-
-	return neighbors;
-}
-
-unsigned int rtsSkeletonizer::Peel(unsigned char isovalue)
-{
-	/**
-	Removes one layer of pixels from the specified isosurface.
-	**/
-
-	unsigned int res_x = implicit_skeleton.DimX();
-	unsigned int res_y = implicit_skeleton.DimY();
-	unsigned int res_z = implicit_skeleton.DimZ();
-	vector<point3D<indextype>> border_nodes;	//get the border nodes for the image
-	indextype x, y, z;
-	int condition;
-	for(x=0; x<res_x; x++)
-	for(y=0; y<res_y; y++)
-	for(z=0; z<res_z; z++)
-		//find the border nodes
-		if(implicit_skeleton(x, y, z) >= isovalue && BackgroundComponents6(&implicit_skeleton, x, y, z, isovalue) == 1 && Neighbors26(&implicit_skeleton, x, y, z, isovalue) != 1)
-		{
-			condition = 0;
-			//now find the border pairs.  A border point must meet two of the following conditions to be a border pair.
-			//south border: s(p) is background
-			if(implicit_skeleton(x, y-1, z) < isovalue)
-				condition++;
-			//north border: n(p) is background, s(p) and s(s(p)) are foreground
-			if(implicit_skeleton(x, y+1, z) < isovalue && implicit_skeleton(x, y-1, z) >= isovalue && implicit_skeleton(x, y-2, z) >= isovalue)
-				condition++;
-			//west border: w(p) is background
-			if(implicit_skeleton(x-1, y, z) < isovalue)
-				condition++;
-			//east border: e(p) is background, w(p) and w(w(p)) are foreground
-			if(implicit_skeleton(x+1, y, z) < isovalue && implicit_skeleton(x-1, y, z) >= isovalue && implicit_skeleton(x-2, y, z) >= isovalue)
-				condition++;
-			//up border: u(p) is background
-			if(implicit_skeleton(x, y, z-1) < isovalue)
-				condition++;
-			//down border: d(p) is background, u(p) and u(u(p)) are foreground
-			if(implicit_skeleton(x, y, z+1) < isovalue && implicit_skeleton(x, y, z-1) >= isovalue && implicit_skeleton(x, y, z-2) >= isovalue)
-				condition++;
-			
-			if(condition > 1)
-				border_nodes.push_back(point3D<indextype>(x, y, z));
-		}
-	//cout<<"Number of border nodes: "<<border_nodes.size()<<endl;
-
-	//determine if each edge node can be removed without changing the topology of the model
-	//declare some initial variables
-	rts_itkVolume<unsigned char> local(3, 3, 3);	//store the region local to the current voxel
-	int nodes_before, nodes_after;		//number of neighboring nodes before and after the filling operation
-	point3D<indextype> fill_start;
-	vector<point3D<indextype>>::iterator i;
-
-	/*
-	Here we determine if a point can be removed by looking at the number of foreground connected
-	components in the local region.  If there is more than one connected component
-	*/
-	unsigned int removed = 0;
-	for(i=border_nodes.begin(); i<border_nodes.end(); i++)
-	{
-		//get the local region around the current point
-		for(x=-1; x<=1; x++)
-			for(y=-1; y<=1; y++)
-				for(z=-1; z<=1; z++)
-					local.SetPixel(x+1, y+1, z+1, implicit_skeleton((*i).x + x, (*i).y + y, (*i).z + z));
-
-		local.SetPixel(1, 1, 1, 0);				//remove the center voxel
-		local.Binary(isovalue, 1);
-		nodes_before = Neighbors26(&local, 1, 1, 1, 1);
-
-
-		//find an interior voxel to fill
-		for(x=0; x<3; x++)
-			for(y=0; y<3; y++)
-				for(z=0; z<3; z++)
-					if(local(x, y, z) > 0)
-						fill_start = point3D<indextype>(x, y, z);
-
-		//fill the local region
-		FloodFill26(&local, fill_start.x, fill_start.y, fill_start.z, 2);
-		//get the number of filled neighbors
-		nodes_after = Neighbors26(&local, 1, 1, 1, 2);
-		if(nodes_after == nodes_before)
-		{
-			implicit_skeleton.SetPixel((*i).x, (*i).y, (*i).z, 0);
-			removed++;
-		}
-
-	}
-	return removed;
-}
-
-vector<point3D<unsigned int>> rtsSkeletonizer::FloodFill6(rts_itkVolume<unsigned char>* function, indextype x, indextype y, indextype z, unsigned char target_value)
-{
-	//create a vector containing all of the filled nodes
-	vector<point3D<unsigned int>> result;
-
-	unsigned char old_value = function->GetPixel(x, y, z);					//find the old value (the value being flood-filled)
-	if(target_value == old_value)				//if the target value is the same as the old value, nothing to do
-		return result;
-
-	queue<point3D<indextype>> Q;				//create a queue for neighboring points
-	point3D<indextype> current(x, y, z);		//start with the current point
-	function->SetPixel(current.x, current.y, current.z, target_value);
-	point3D<indextype> next;
-	Q.push(current);
-	indextype u, v, w;
-
-
-	while(!Q.empty())							//continue until the queue is empty
-	{
-		current = Q.front();					//get the first element from the queue
-		Q.pop();							
-		
-		if(current.x != function->DimY() - 1)
-			if(function->GetPixel(current.x + 1, current.y, current.z) == old_value)
-			{
-				function->SetPixel(current.x + 1, current.y, current.z, target_value);
-				result.push_back(point3D<unsigned int>(current.x + 1, current.y, current.z));
-				Q.push(point3D<indextype>(current.x + 1, current.y, current.z));
-			}
-		if(current.x != 0)
-			if(function->GetPixel(current.x - 1, current.y, current.z) == old_value)
-			{
-				function->SetPixel(current.x - 1, current.y, current.z, target_value);
-				result.push_back(point3D<unsigned int>(current.x - 1, current.y, current.z));
-				Q.push(point3D<indextype>(current.x - 1, current.y, current.z));
-			}
-		if(current.y != function->DimY() - 1)
-			if(function->GetPixel(current.x, current.y +1, current.z) == old_value)
-			{
-				function->SetPixel(current.x, current.y+1, current.z, target_value);
-				result.push_back(point3D<unsigned int>(current.x, current.y+1, current.z));
-				Q.push(point3D<indextype>(current.x, current.y+1, current.z));
-			}
-		if(current.y != 0)
-			if(function->GetPixel(current.x, current.y-1, current.z) == old_value)
-			{
-				function->SetPixel(current.x, current.y-1, current.z, target_value);
-				result.push_back(point3D<unsigned int>(current.x, current.y-1, current.z));
-				Q.push(point3D<indextype>(current.x, current.y-1, current.z));
-			}
-		if(current.z != function->DimZ() - 1)
-			if(function->GetPixel(current.x, current.y, current.z+1) == old_value)
-			{
-				function->SetPixel(current.x, current.y, current.z+1, target_value);
-				result.push_back(point3D<unsigned int>(current.x, current.y, current.z+1));
-				Q.push(point3D<indextype>(current.x, current.y, current.z+1));
-			}
-		if(current.z != 0)
-			if(function->GetPixel(current.x, current.y, current.z-1) == old_value)
-			{
-				function->SetPixel(current.x, current.y, current.z-1, target_value);
-				result.push_back(point3D<unsigned int>(current.x, current.y, current.z-1));
-				Q.push(point3D<indextype>(current.x, current.y, current.z-1));
-			}
-
-	}
-
-	return result;
-
-}
-
-void rtsSkeletonizer::FloodFill26(rts_itkVolume<unsigned char>* function, int x, int y, int z, unsigned char target_value)
-{
-	unsigned char old_value = function->GetPixel(x, y, z);
-	if(target_value == old_value)
-		return;
-
-	queue<point3D<indextype>> Q;
-	point3D<indextype> current(x, y, z);
-	point3D<indextype> next;
-	Q.push(current);
-	indextype u, v, w;
-	while(!Q.empty())
-	{
-		current = Q.front();
-		if(function->GetPixel(current.x, current.y, current.z) == old_value)
-			function->SetPixel(current.x, current.y, current.z, target_value);
-		Q.pop();
-
-		unsigned int res_x = function->DimX();
-		unsigned int res_y = function->DimY();
-		unsigned int res_z = function->DimZ();
-		for(u=-1; u<=1; u++)
-		for(v=-1; v<=1; v++)
-		for(w=-1; w<=1; w++)
-		{
-			next.x = current.x + u;
-			next.y = current.y + v;
-			next.z = current.z + w;
-
-			if(next.x >= 0 && next.x < res_x &&
-				next.y >= 0 && next.y < res_y &&
-				next.z >= 0 && next.z < res_z &&
-				function->GetPixel(next.x, next.y, next.z) == old_value)
-				{
-					function->SetPixel(next.x, next.y, next.z, target_value);
-					Q.push(next);
-				}
-		}
-	}
-
-				
-}
-
-
-
-
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsSourceCode.h b/legacy/rtsSourceCode.h
deleted file mode 100755
index 0ff6c25..0000000
--- a/legacy/rtsSourceCode.h
+++ /dev/null
@@ -1,65 +0,0 @@
-#ifndef RTSSOURCECODE_H
-#define RTSSOURCECODE_H
-
-#include <string>
-#include <fstream>
-#include <vector>
-#include <iostream>
-
-using namespace std;
-
-///This class defines generic source code that can be loaded from text files.  It is primarily used by the rts_glShaderProgram class for GLSL programming.
-
-class rtsSourceCode
-{
-public:
-	vector<string> source;			//the actual source code
-	void clear()					///<Clears any current source code from the class.
-	{
-		source.clear();
-	}
-	void LoadSource(const char* filename)	///<Loads source code from a specified file.
-	{
-		ifstream infile;		//create an input file
-		infile.open(filename);	//load the specified file
-	
-		if(!infile.is_open())	//if the file is not open, exit
-		{
-			return;
-		}
-		source.clear();			//remove any previous code
-
-		while(!infile.eof())
-		{
-			string current_line;		
-			getline(infile, current_line);
-			current_line += '\n';
-			source.push_back(current_line);
-		}
-	}
-	rtsSourceCode(const char* filename)	///<Constructor creates the class and loads source code from the specified file.
-	{
-		LoadSource(filename);
-	}
-	rtsSourceCode(){}						///<Constructor creates a blank class.
-	rtsSourceCode& operator+=(const rtsSourceCode& rhs)
-	{
-		int lines = rhs.source.size();
-		for(int l=0; l<lines; l++)
-			source.push_back(rhs.source[l]);
-		return *this;
-	}
-	rtsSourceCode& operator+=(const string& rhs)
-	{
-		source.push_back(rhs);
-		return *this;
-	}
-	void ConsoleOut()						///<Sends the source code to the standard output.
-	{
-		unsigned int lines = source.size();
-		for(unsigned int l = 0; l<lines; l++)
-			cout<<l<<":  "<<source[l];
-	}
-};
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsUtilities.cpp b/legacy/rtsUtilities.cpp
deleted file mode 100755
index 2fcb480..0000000
--- a/legacy/rtsUtilities.cpp
+++ /dev/null
@@ -1,173 +0,0 @@
-#include "rtsUtilities.h"
-
-char* rtsInt_to_String(int num, int min_chars)
-{
-	//returns a null-terminated string representing the passed parameter
-	
-	//find out if the number is negative
-	bool negative = false;
-	if(num < 0)
-	{
-		negative = true;
-		num *= -1;
-	}
-
-	//first, count the number of digits that will be in the string
-	int num_digits = 0;
-	int dividend = 1;
-	while((num/dividend) != 0)
-	{
-		dividend*=10;
-		num_digits++;
-	}
-
-
-	//calculate the number of characters required by number
-
-	int num_chars = 0;
-
-	if(negative)
-		num_chars = num_digits+1;
-	else
-		num_chars = num_digits;
-	
-	//allocate memory for the string (add 1 for the NULL character)
-	char* result;	
-	int total_chars = 0;
-	if(num_chars > min_chars)
-		total_chars = num_chars;
-	else
-		total_chars = min_chars;
-	result =  new char[total_chars + 1];
-	//initialize the string to 0's
-	for(int i=0; i<total_chars; i++)
-		result[i] = '0';
-
-	//calculate the starting point for the character string
-	int start_char = total_chars - num_digits;
-	if(negative)
-		result[0] = '-';
-
-	//finally, calculate each character and assign it to the string
-	dividend = pow(10.0, num_digits-1);	//calculate the character from biggest to smallest
-	unsigned char digit = 0;
-	int i;
-	for(i=0; i < num_digits; i++)
-	{
-		digit = num/dividend;
-		num -= digit*dividend;
-		dividend /= 10;
-		result[start_char + i] = '0' + digit;
-	}
-
-	result[start_char + i] = NULL;
-
-	return result;
-}
-
-char** rtsGetFileList(const char* mask, unsigned int start, unsigned int end)
-{
-	//retrieves a list of names based on the supplied mask "?" is a number and the passed integers
-
-	//first, find the length of the string
-	int length = strlen(mask);
-	int num_length = 0;
-	int start_index = -1;
-	//get the number of number characters in the mask by counting "?"
-	for(int i=0; i<length; i++)
-	{
-		if(mask[i] == '?')
-		{
-			if(start_index == -1)
-				start_index = i;
-
-			num_length++;
-		}
-	}
-
-	//allocate space for a list of filenames
-	char** result = new char*[end - start + 1];
-
-	//now, for each string name
-	for(int i=0; i<(end - start) + 1; i++)
-	{
-		//create a new slot for a filename
-		char* filename = new char[length+1];
-		//find the string version of the current number
-		char* number = rtsInt_to_String(start+i, num_length);
-		//now, for each character in the filename
-		for(int j=0; j<length; j++)
-		{
-			//if we are at the mask, output the number
-			if(j >= start_index && (j < start_index + num_length))
-			{
-				filename[j] = number[j - start_index];
-			}
-			//otherwise output the mask value
-			else
-				filename[j] = mask[j];
-		}
-		filename[length] = 0;
-		result[i] = filename;
-	}
-	return result;
-}
-
-
-unsigned char* rtsCalculateDifferenceImage(int length, unsigned char* a, unsigned char* b)
-{
-	//calculates the difference between two images and returns the absolute value
-	unsigned char* result = new unsigned char[length];
-	for(int i=0; i<length; i++)
-		result[i] = (unsigned char)(abs((int)a[i]-(int)b[i]));
-	return result;
-}
-
-unsigned int rtsSumPixels(int length, unsigned char* pixels)
-{
-	//calculates the sum of all pixels in the array
-	unsigned int result = 0;
-	for(int i=0; i<length; i++)
-		result+=(unsigned int)pixels[i];
-
-	return result;
-}
-
-unsigned char* rts2DGaussian(int width, int height, double std_dev)
-{
-	//this function creates a 2D gaussian with a mean at the center of the image
-	//and a standard deviation as specified
-	unsigned char* gaussian = new unsigned char[width*height];
-	double high_value = (1.0/(2.0*RTS_PI*std_dev*std_dev))*exp(0.0);
-	for(int x = 0; x<width; x++)
-		for(int y=0; y<height; y++)
-		{
-			double exponent = exp(-((x-width/2.0)*(x-width/2.0) + (y-height/2.0)*(y-height/2.0))/(2.0*std_dev*std_dev));
-			gaussian[y*width+x] = (255.0/high_value)*(1.0/(2.0*RTS_PI*std_dev*std_dev))*exponent;
-		}
-	return gaussian;
-}
-
-unsigned char* rtsInvertImage(int width, int height, unsigned char* pixels)
-{
-	//this function inverts an image
-	unsigned char* result = new unsigned char[width*height];
-	for(int x = 0; x<width; x++)
-		for(int y=0; y<height; y++)
-		{
-			result[y*width+x] = 255 - pixels[y*width+x];
-		}
-	return result;
-}
-
-unsigned char* rtsMultiplyImages(int width, int height, unsigned char* pixels_a, unsigned char* pixels_b)
-{
-	//this function multiplies one image by another
-	unsigned char* result = new unsigned char[width*height];
-	for(int x = 0; x<width; x++)
-		for(int y=0; y<height; y++)
-		{
-			result[y*width+x] = (unsigned char)255*((pixels_a[y*width+x]/255.0) * (pixels_b[y*width+x]/255.0));
-		}
-	return result;
-}
\ No newline at end of file
diff --git a/legacy/rtsUtilities.h b/legacy/rtsUtilities.h
deleted file mode 100755
index 3b5ee1d..0000000
--- a/legacy/rtsUtilities.h
+++ /dev/null
@@ -1,20 +0,0 @@
-#ifndef RTS_UTILITIES_H
-#define RTS_UTILITIES_H
-
-//#include<stdlib.h>
-#include <math.h>
-#include <iostream>
-#include <string.h>
-#include "rtsMath.h"
-
-using namespace std;
-
-char* rtsInt_to_String(int num, int min_chars);
-char** rtsGetFileList(const char* mask, unsigned int start, unsigned int end);
-unsigned char* rtsCalculateDifferenceImage(int length, unsigned char* a, unsigned char* b);
-unsigned int rtsSumPixels(int length, unsigned char* pixels);
-unsigned char* rts2DGaussian(int width, int height, double std_dev);
-unsigned char* rtsInvertImage(int width, int height, unsigned char* pixels);
-unsigned char* rtsMultiplyImages(int width, int height, unsigned char* pixels_a, unsigned char* pixels_b);
-
-#endif
\ No newline at end of file
diff --git a/legacy/rtsVector3d.h b/legacy/rtsVector3d.h
deleted file mode 100755
index 38ff66d..0000000
--- a/legacy/rtsVector3d.h
+++ /dev/null
@@ -1,164 +0,0 @@
-///This class is used to store information for a 3D vector.
-#include <iostream>
-#include <math.h>
-using namespace std;
-
-#ifndef RTSVECTOR3D_H
-#define RTSVECTOR3D_H
-
-
-template <class T> class vector3D
-{
-	//friend class point3D<T>;
-public:
-	//data values
-	T x;
-	T y;
-	T z;
-
-	vector3D();								///<Constructor.  The resulting vector is initialized to (0,0,0)
-	vector3D(T new_x, T new_y, T new_z);	///<Constructor.  Initialize the resulting vector to the value specified by (new_x, new_y, new_z)
-
-	//operators
-	vector3D<T> operator+(vector3D<T> param);	///<Used for vector arithmetic.  Allows two vectors with similar types to be added.
-	vector3D<T> operator-(vector3D<T> param);	///<Used for vector arithmetic.  Allows two vectors with similar types to be subtracted.
-	T operator*(vector3D<T> param);				///<Used for vector arithmetic.  Computes the inner product of two vectors of the same type.
-	vector3D<T> operator*(T param);				///<Used for vector arithmetic.  Multiplies a vector by a scalar value of type T.
-	vector3D<T> X(vector3D<T> param);			///<Compute the cross product between two vectors
-	
-	friend vector3D<T> operator*(const T lhs, vector3D<T> rhs){return rhs*lhs;}	///<Allows vectors to be multiplied by scalars in either order
-
-	//methods
-	vector3D<T> Times(vector3D<T> param);			///<Performs piecewise multiplication between two vectors [ex. (x1*x2, y1*y2, z1*z2)].
-	vector3D<T> Normalize();						///<Returns the normalized version of the vector.
-	T Length();										///<Returns the length of the vector.
-
-	//casting operators
-	template <class U> operator vector3D<U>();		///<Casting operator allows explicit casting between vector types.
-	//output
-	friend ostream& operator<<(ostream& os, const vector3D<T> &rhs)
-	{
-		os<<"("<<rhs.x<<","<<rhs.y<<","<<rhs.z<<")";
-		return os;
-	}
-	void print();
-};
-
-template <class T>
-template <class U>
-vector3D<T>::operator vector3D<U>()
-{
-	vector3D<U> cast_result(x, y, z);
-	return cast_result;
-}
-
-template <class T> vector3D<T>::vector3D()
-{
-	x=0;
-	y=0;
-	z=0;
-}
-
-template <class T> vector3D<T>::vector3D(T new_x, T new_y, T new_z)
-{
-	x=new_x;
-	y=new_y;
-	z=new_z;
-}
-
-template <class T>
-vector3D<T> vector3D<T>::operator -(vector3D<T> param)
-{
-	vector3D<T> result;			//create the result
-	
-	result.x = x-param.x;		//perform the computation
-	result.y = y-param.y;
-	result.z = z-param.z;
-
-	return result;
-}
-
-template <class T>
-vector3D<T> vector3D<T>::operator+(vector3D<T> param)
-{
-	vector3D<T> result;			//create the result
-	
-	result.x = x+param.x;		//perform the computation
-	result.y = y+param.y;
-	result.z = z+param.z;
-
-	return result;
-}
-
-template <class T>
-vector3D<T> vector3D<T>::Times(vector3D<T> param)
-{
-	vector3D<T> result;			//create the result
-	
-	result.x = x*param.x;		//perform the computation
-	result.y = y*param.y;
-	result.z = z*param.z;
-
-	return result;
-}
-
-template <class T>
-vector3D<T> vector3D<T>::operator*(T param)
-{
-	vector3D<T> result;			//create the result
-	
-	result.x = x*param;		//perform the computation
-	result.y = y*param;
-	result.z = z*param;
-
-	return result;
-}
-
-template <class T>
-T vector3D<T>::operator *(vector3D<T> param)
-{
-	//This function computes the dot product between two vectors
-	return x*param.x + y*param.y + z*param.z;
-}
-
-template <class T>
-vector3D<T> vector3D<T>::X(vector3D<T> param)
-{
-	vector3D<T> result;
-	result.x=y*param.z - z*param.y;
-	result.y=z*param.x - x*param.z;
-	result.z=x*param.y - y*param.x;
-
-	return result;
-}
-
-template <class T>
-vector3D<T> vector3D<T>::Normalize()
-{
-	T length = Length();
-	if(length ==0.0)
-	{
-		x = y = z = 0;
-	}
-	else
-	{
-		x/= length;
-		y /=length;
-		z /=length;
-	}
-	return *this;
-}
-
-template <class T>
-T vector3D<T>::Length()
-{
-	return sqrt(x*x + y*y + z*z);
-}
-
-template <class T>
-void vector3D<T>::print()
-{
-	cout<<"["<<x<<","<<y<<","<<z<<"]"<<endl;
-}
-
-#endif
diff --git a/legacy/rtsVolume.cpp b/legacy/rtsVolume.cpp
deleted file mode 100755
index a936e56..0000000
--- a/legacy/rtsVolume.cpp
+++ /dev/null
@@ -1,211 +0,0 @@
-#include "rtsVolume.h"
-
-rtsVolume::rtsVolume()
-{
-	m_data = NULL;
-	m_size_x = 0;
-	m_size_y = 0;
-	m_size_z = 0;
-}
-
-rtsVolume::rtsVolume(unsigned int size_x, unsigned int size_y, unsigned int size_z)
-{
-	m_size_x = size_x;
-	m_size_y = size_y;
-	m_size_z = size_z;
-
-	//allocate space for the data
-	m_data = new unsigned char[m_size_x * m_size_y * m_size_z];
-	for(int i=0; i<m_size_x*m_size_y*m_size_z; i++)
-		m_data[i] = 0;
-}
-
-rtsVolume::rtsVolume(const unsigned char* data, unsigned int size_x, unsigned int size_y, unsigned int size_z)
-{
-	//assign variables
-	m_size_x = size_x;
-	m_size_y = size_y;
-	m_size_z = size_z;
-	//allocate data
-	m_data = new unsigned char[m_size_x * m_size_y * m_size_z];
-	//blit data
-	blit3D(data, m_size_x, m_size_y, m_size_z, m_data, 0,0,0,m_size_x, m_size_y, m_size_z);
-
-}
-
-rtsVolume::~rtsVolume()
-{
-	delete m_data;
-}
-
-void rtsVolume::open(const char *filename)
-{
-	if(m_data != NULL)
-		delete m_data;
-	
-
-	ifstream infile(filename, ios::in | ios::binary);
-
-	//load the dimensions of the data set
-	infile.read((char*)&m_size_x, sizeof(int));
-	infile.read((char*)&m_size_y, sizeof(int));
-	infile.read((char*)&m_size_z, sizeof(int));
-
-	m_data = new unsigned char[m_size_x*m_size_y*m_size_z];
-	infile.read((char*)m_data, m_size_x*m_size_y*m_size_z*sizeof(unsigned char));
-
-	//calculate min and maxes
-	infile.close();
-}
-
-void rtsVolume::save(const char *filename)
-{
-	ofstream outfile(filename, ios::out | ios::binary);
-	outfile.write((char*)&m_size_x, sizeof(int));
-	outfile.write((char*)&m_size_y, sizeof(int));
-	outfile.write((char*)&m_size_z, sizeof(int));
-
-	outfile.write((char*)m_data, m_size_x*m_size_y*m_size_z*sizeof(unsigned char));
-	outfile.close();
-}
-
-void rtsVolume::resize_canvas(unsigned int size_x, unsigned int size_y, unsigned int size_z)
-{
-	//allocate memory for the new size
-	unsigned char* temp = m_data;
-	m_data = new unsigned char[size_x * size_y * size_z];
-
-	//copy the data from old (temp) to new (m_data)
-	blit3D(temp, m_size_x, m_size_y, m_size_z, m_data, 0, 0, 0, size_x, size_y, size_z);
-
-	//set the size variables
-	m_size_x = size_x;
-	m_size_y = size_y;
-	m_size_z = size_z;
-
-}
-
-void rtsVolume::blacken_border()
-{
-	//code to put a black border around the volume
-	//create a few volumes for each side of the cube
-	rtsVolume front_back(m_size_x, m_size_y, 1);
-	rtsVolume left_right(1, m_size_y, m_size_z);
-	rtsVolume top_bottom(m_size_x, 1, m_size_z);
-
-	//copy these into the current object
-	this->insert(front_back, 0, 0, 0);
-	this->insert(front_back, 0, 0, m_size_z-1);
-	this->insert(left_right, 0, 0, 0);
-	this->insert(left_right, m_size_x-1, 0, 0);
-	this->insert(top_bottom, 0, 0, 0);
-	this->insert(top_bottom, 0, m_size_y-1, 0);
-
-}
-
-void rtsVolume::invert()
-{
-	//inverts the data stored in the volume
-	unsigned int length = m_size_x*m_size_y*m_size_z;
-	for(int i=0; i<length; i++)
-		m_data[i] = 255 - m_data[i];
-}
-
-void rtsVolume::blacken(unsigned char threshold)
-{
-	unsigned int size = m_size_x*m_size_y*m_size_z;
-	for(unsigned int i=0; i<size; i++)
-		if(m_data[i] <= threshold)
-			m_data[i] = 0;
-}
-
-void rtsVolume::whiten(unsigned char threshold)
-{
-	unsigned int size = m_size_x*m_size_y*m_size_z;
-	for(unsigned int i=0; i<size; i++)
-		if(m_data[i] >= threshold)
-			m_data[i] = 255;
-}
-
-void rtsVolume::blit3D(const unsigned char* source,
-				   unsigned int s_sx, unsigned int s_sy, unsigned int s_sz,
-				   unsigned char* dest,
-				   unsigned int d_px, unsigned int d_py, unsigned int d_pz,
-				   unsigned int d_sx, unsigned int d_sy, unsigned int d_sz)
-{
-	unsigned int ps, pd;		//stores the mapping for the source point to the dest point
-	//find the maximum points that can be blit to (in case source overlaps the edges of dest)
-	unsigned int blit_size_x = min(s_sx, d_sx - d_px);
-	unsigned int blit_size_y = min(s_sy, d_sy - d_py);
-	unsigned int blit_size_z = min(s_sz, d_sz - d_pz);
-
-	unsigned int source_z_offset = s_sx * s_sy;
-	unsigned int dest_z_offset = d_sx * d_sy;
-
-	unsigned int z,y;
-	for(z=0; z<blit_size_z; z++)
-		for(y=0; y<blit_size_y; y++)
-		{
-			ps = z * source_z_offset + y * s_sx;
-			pd = (z + d_pz) * dest_z_offset + (y + d_py) * d_sx + d_px;
-			memcpy((void*)(&dest[pd]), (void*)(&source[ps]), sizeof(unsigned char)*blit_size_x);
-		}
-
-
-
-}
-
-inline unsigned char rtsVolume::operator ()(unsigned int x, unsigned int y, unsigned int z)
-{
-	return m_data[z * m_size_x * m_size_y + y * m_size_x + z];
-}
-
-rtsVolume& rtsVolume::operator=(const rtsVolume& rhs)
-{
-	//check for self-assignment
-	if(this == &rhs)
-		return *this;
-
-	//deallocate memory
-	if(m_data != NULL)
-		delete m_data;
-
-	//copy variables
-	m_size_x = rhs.m_size_x;
-	m_size_y = rhs.m_size_y;
-	m_size_z = rhs.m_size_z;
-
-	//allocate and copy memory
-	m_data = new unsigned char[m_size_x * m_size_y * m_size_z];
-	//copy the data
-	blit3D(rhs.m_data, m_size_x, m_size_y, m_size_z,m_data, 0, 0, 0, m_size_x, m_size_y, m_size_z);
-
-	//return the left hand side
-	return *this;
-}
-
-
-rtsVolume::rtsVolume(const rtsVolume& original)
-{
-	//copy the shallow variables
-	m_size_x = original.m_size_x;
-	m_size_y = original.m_size_y;
-	m_size_z = original.m_size_z;
-
-	//allocate space for the data
-	m_data = new unsigned char[m_size_x * m_size_y * m_size_z];
-	//copy the data
-	blit3D(original.m_data, m_size_x, m_size_y, m_size_z,m_data, 0, 0, 0, m_size_x, m_size_y, m_size_z);
-}
-
-unsigned char* rtsVolume::get_bits()
-{
-	return m_data;
-}
-
-void rtsVolume::insert(rtsVolume source, unsigned int pos_x, unsigned int pos_y, unsigned int pos_z)
-{
-	unsigned char* source_bits = source.get_bits();
-	blit3D(source_bits, source.get_dimx(), source.get_dimy(), source.get_dimz(), 
-		m_data, pos_x, pos_y, pos_z, m_size_x, m_size_y, m_size_z);
-}
\ No newline at end of file
diff --git a/legacy/rtsVolume.h b/legacy/rtsVolume.h
deleted file mode 100755
index ef6d66a..0000000
--- a/legacy/rtsVolume.h
+++ /dev/null
@@ -1,64 +0,0 @@
-#ifndef RTS_VOLUME_H
-#define RTS_VOLUME_H
-
-#include <time.h>
-#include <iostream>
-#include <fstream>
-
-using namespace std;
-
-class rtsVolume
-{
-
-private:
-	unsigned char* m_data;			//pointer to the volume data
-	unsigned int m_size_x;			//variables specifying the size of the volume
-	unsigned int m_size_y;
-	unsigned int m_size_z;
-
-	//static function for copying 3D data from one pointer to another
-	//this function does not test boundaries so can quite easily crash
-	void blit3D(const unsigned char* source,
-				   unsigned int s_sx, unsigned int s_sy, unsigned int s_sz,
-				   unsigned char* dest,
-				   unsigned int d_px, unsigned int d_py, unsigned int d_pz,
-				   unsigned int d_sx, unsigned int d_sy, unsigned int d_sz);
-
-public:
-	rtsVolume();
-	//construct a blank volume of a given size
-	rtsVolume(unsigned int size_x, unsigned int size_y, unsigned int size_z);
-	//construct a volume from specified data
-	rtsVolume(const unsigned char* data, unsigned int size_x, unsigned int size_y, unsigned int size_z);
-	rtsVolume(const rtsVolume &original);	//copy constructor
-	~rtsVolume();
-
-	//overloaded operators
-	rtsVolume& operator=(const rtsVolume& original);
-	inline unsigned char operator()(unsigned int x, unsigned int y, unsigned int z);
-
-	//load and save methods
-	void open(const char* filename);
-	void save(const char* filename);
-	/*Allow resizing of the canvas.  This resizes the volume without
-	resizing the existing data within the volume*/
-	void resize_canvas(unsigned int size_x, unsigned int size_y, unsigned int size_z);
-	void insert(const rtsVolume source, unsigned int pos_x, unsigned int pos_y, unsigned int pos_z);
-	void blacken_border();
-	void invert();
-	void blacken(unsigned char threshold);
-	void whiten(unsigned char threshold);
-
-	//get functions
-	unsigned char* get_bits();
-	unsigned int get_dimx() {return m_size_x;}
-	unsigned int get_dimy() {return m_size_y;}
-	unsigned int get_dimz() {return m_size_z;}
-		
-
-	
-};
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_cudaBrewer.h b/legacy/rts_cudaBrewer.h
deleted file mode 100755
index 885188d..0000000
--- a/legacy/rts_cudaBrewer.h
+++ /dev/null
@@ -1,59 +0,0 @@
-#include "rtsVector3d.h"
-#include "cudaHandleError.h"
-
-#define BREWER_CTRL_PTS 11
-texture<float4, cudaTextureType1D> cudaTexBrewer;
-cudaArray* gpuBrewer;
-
-
-__device__ float4 colorBrewer(float val, float min_range, float max_range, float min_fade = 0.000)
-{
-	float t = (val - min_range)/(max_range - min_range)*((float)(BREWER_CTRL_PTS-2)/BREWER_CTRL_PTS);
-	float shift = 1.0/BREWER_CTRL_PTS;
-	float4 color = tex1D(cudaTexBrewer, t+shift);
-	if(t < min_fade)
-		color.w = (val - min_range)/(max_range - min_range)/min_fade;
-	return color;
-}
-
-
-void rts_cudaInitBrewer()
-{
-	//allocate CPU space
-	float4 cpuColorMap[BREWER_CTRL_PTS];
-
-	//define control points
-	cpuColorMap[0] = make_float4(0.192157f, 0.211765f, 0.584314f, 1.0f);
-	cpuColorMap[1] = make_float4(0.270588f, 0.458824f, 0.705882f, 1.0f);
-	cpuColorMap[2] = make_float4(0.454902f, 0.678431f, 0.819608f, 1.0f);
-	cpuColorMap[3] = make_float4(0.670588f, 0.85098f, 0.913725f, 1.0f);
-	cpuColorMap[4] = make_float4(0.878431f, 0.952941f, 0.972549f, 1.0f);
-	cpuColorMap[5] = make_float4(1.0f, 1.0f, 0.74902f, 1.0f);
-	cpuColorMap[6] = make_float4(0.996078f, 0.878431f, 0.564706f, 1.0f);
-	cpuColorMap[7] = make_float4(0.992157f, 0.682353f, 0.380392f, 1.0f);
-	cpuColorMap[8] = make_float4(0.956863f, 0.427451f, 0.262745f, 1.0f);
-	cpuColorMap[9] = make_float4(0.843137f, 0.188235f, 0.152941f, 1.0f);
-	cpuColorMap[10] = make_float4(0.647059f, 0.0f, 0.14902f, 1.0f);
-
-
-	int width = BREWER_CTRL_PTS;
-	int height = 0;
-
-
-	// allocate array and copy colormap data
-	cudaChannelFormatDesc channelDesc = cudaCreateChannelDesc(32, 32, 32, 32, cudaChannelFormatKindFloat);
-
-	HANDLE_ERROR(cudaMallocArray(&gpuBrewer, &channelDesc, width, height));
-
-	cudaMemcpyToArray(gpuBrewer, 0, 0, cpuColorMap, sizeof(float4)*width, cudaMemcpyHostToDevice);
-
-	// set texture parameters
-    cudaTexBrewer.addressMode[0] = cudaAddressModeClamp;
-	//texBrewer.addressMode[1] = cudaAddressModeClamp;
-    cudaTexBrewer.filterMode = cudaFilterModeLinear;
-    cudaTexBrewer.normalized = true;  // access with normalized texture coordinates
-
-	// Bind the array to the texture
-    HANDLE_ERROR( cudaBindTextureToArray( cudaTexBrewer, gpuBrewer, channelDesc));
-
-}
diff --git a/legacy/rts_cudaCufftShift.h b/legacy/rts_cudaCufftShift.h
deleted file mode 100755
index c42cde4..0000000
--- a/legacy/rts_cudaCufftShift.h
+++ /dev/null
@@ -1,65 +0,0 @@
-#ifndef CUDA_CUFFT_SHIFT_H
-#define CUDA_CUFFT_SHIFT_H
-
-#define BLOCK_SIZE 16
-
-__global__ void devCufftShift(char* gpuSource, int sE, int sX, int sY, int sZ)
-{
-	int ix = blockIdx.x * blockDim.x + threadIdx.x;
-	int blocks_per_slice = sY/blockDim.y + 1;
-	int iy = (blockIdx.y % blocks_per_slice)*blockDim.y + threadIdx.y;
-	int iz = blockIdx.y/blocks_per_slice;
-
-	if(ix >= sX || iy >= sY || iz >= sZ/2)
-		return;
-
-	//array index
-	int i = iz*sX*sY*sE + iy*sX*sE + ix*sE;
-
-	int iSwap = (iz + sZ/2)*sX*sY*sE;
-	
-	if(iy < sY/2)
-		iSwap += (iy + sY/2)*sX*sE;
-	else
-		iSwap += (iy - sY/2)*sX*sE;
-
-	if(ix < sX/2)
-		iSwap += (ix + sX/2)*sE;
-	else
-		iSwap += (ix - sX/2)*sE;
-	//iSwap = (iz + sZ/2)*sX*sY*sE + (iy + sY/2)*sX*sE + (ix + sX/2)*sE;
-
-	char temp;
-	for(int e=0; e<sE; e++)
-	{
-		temp = gpuSource[i + e];
-		gpuSource[i + e] = gpuSource[iSwap + e];
-		gpuSource[iSwap + e] = temp;
-	}
-	
-}
-
-void rts_cudaCufftShift(char* gpuSource, int elementSize, int sX, int sY, int sZ)
-{
-	//This function duplicates the Matlab fftshift function, making it easier to apply certain filters in
-	//the frequency domain.
-
-	//currently only usable for even numbers
-	if(sX%2 != 0 || sY%2 != 0 || sZ%2 != 0)
-	{
-		printf("Error: cudaCufftShift dimensions must be even (for now)\n");
-		exit(1);
-	}
-
-	dim3 block(BLOCK_SIZE, BLOCK_SIZE);
-	dim3 grid(sX/block.x + 1, (sY/block.y + 1)* sZ);
-
-	//call the kernel
-	devCufftShift<<<grid, block>>>(gpuSource, elementSize, sX, sY, sZ);
-
-
-
-}
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glBrewer.glsl b/legacy/rts_glBrewer.glsl
deleted file mode 100755
index e69de29..0000000
--- a/legacy/rts_glBrewer.glsl
+++ /dev/null
diff --git a/legacy/rts_glBrewer.h b/legacy/rts_glBrewer.h
deleted file mode 100755
index 18ca3e4..0000000
--- a/legacy/rts_glBrewer.h
+++ /dev/null
@@ -1,17 +0,0 @@
-#include "rtsPoint3d.h"
-
-void rts_glBrewerPts(point3D<float>* brewerPts)
-{
-	//define control points
-	brewerPts[0] = point3D<float>(0.192157f, 0.211765f, 0.584314f);
-	brewerPts[1] = point3D<float>(0.270588f, 0.458824f, 0.705882f);
-	brewerPts[2] = point3D<float>(0.454902f, 0.678431f, 0.819608f);
-	brewerPts[3] = point3D<float>(0.670588f, 0.85098f, 0.913725f);
-	brewerPts[4] = point3D<float>(0.878431f, 0.952941f, 0.972549f);
-	brewerPts[5] = point3D<float>(1.0f, 1.0f, 0.74902f);
-	brewerPts[6] = point3D<float>(0.996078f, 0.878431f, 0.564706f);
-	brewerPts[7] = point3D<float>(0.992157f, 0.682353f, 0.380392f);
-	brewerPts[8] = point3D<float>(0.956863f, 0.427451f, 0.262745f);
-	brewerPts[9] = point3D<float>(0.843137f, 0.188235f, 0.152941f);
-	brewerPts[10] = point3D<float>(0.647059f, 0.0f, 0.14902f);
-}
\ No newline at end of file
diff --git a/legacy/rts_glFilamentNetwork.cpp b/legacy/rts_glFilamentNetwork.cpp
deleted file mode 100755
index 404260f..0000000
--- a/legacy/rts_glFilamentNetwork.cpp
+++ /dev/null
@@ -1,17 +0,0 @@
-#include "rts_glFilamentNetwork.h"
-
-void rts_glFilamentNetwork::glRender()
-{
-	((rts_glOBJ*)network)->glRender();
-}
-
-void rts_glFilamentNetwork::glRenderSelected()
-{
-	((rts_glOBJ*)network)->glRenderSelected();
-}
-
-int rts_glFilamentNetwork::LoadFIB(const char* filename)
-{
-	((rts_glOBJ*)network)->Invalidate();
-	return fib_load(filename);
-}
\ No newline at end of file
diff --git a/legacy/rts_glFilamentNetwork.h b/legacy/rts_glFilamentNetwork.h
deleted file mode 100755
index 00c9114..0000000
--- a/legacy/rts_glFilamentNetwork.h
+++ /dev/null
@@ -1,26 +0,0 @@
-#ifndef RTS_GLFILAMENTNETWORK_H
-#define RTS_GLFILAMENTNETWORK_H
-
-#include "rtsFilamentNetwork.h"
-#include "rts_glOBJ.h"
-#include <windows.h>
-#include <gl/gl.h>
-#include <gl/glut.h>
-
-class rts_glFilamentNetwork:public rtsFilamentNetwork
-{
-public:
-	rts_glFilamentNetwork(){network = new rts_glOBJ();}
-	void glRender();
-	void glRenderSelected();
-
-	int LoadFIB(const char* filename);		//overload the parent function to reset the display list
-
-	void Pick(unsigned int x, unsigned int y, unsigned int size_x, unsigned int size_y)
-	{
-		((rts_glOBJ*)network)->Pick(x, y, size_x, size_y);
-	}
-};
-		
-				
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glIntegrateTexture.cpp b/legacy/rts_glIntegrateTexture.cpp
deleted file mode 100755
index e69de29..0000000
--- a/legacy/rts_glIntegrateTexture.cpp
+++ /dev/null
diff --git a/legacy/rts_glIntegrateTexture.h b/legacy/rts_glIntegrateTexture.h
deleted file mode 100755
index 2e86d67..0000000
--- a/legacy/rts_glIntegrateTexture.h
+++ /dev/null
@@ -1,172 +0,0 @@
-/*This class performs integration across a series of rectangular
-texture samples.  Basically, this is a downsample using a large box
-filter and can be used to sum the results of multiple calculations
-that are combined in a single texture.*/
-
-#include "rts_glRenderToTexture.h"
-#include "rts_glShaderProgram.h"
-
-#define MEAN		0
-#define SUM			1
-#define MIN			2
-#define MAX			3
-
-
-class rts_glIntegrateTexture
-{
-private:
-	int x_sample_size;
-	int y_sample_size;
-	int x_sample_num;
-	int y_sample_num;
-
-	rts_glShaderProgram x_pass_mean;
-	rts_glShaderProgram y_pass_mean;
-
-	rts_glShaderProgram x_pass_min;
-	rts_glShaderProgram y_pass_min;
-
-	rts_glShaderProgram x_pass_max;
-	rts_glShaderProgram y_pass_max;
-
-	//this is a two-pass downsample
-	rts_glRenderToTexture x_pass;
-	rts_glRenderToTexture y_pass;
-
-	void initialize_shaders();
-	inline void x_pass_enable(int type, rts_glTextureMap texture);
-	inline void x_pass_disable(int type);
-	inline void y_pass_enable(int type);
-	inline void y_pass_disable(int type);
-
-public:
-	//initialize the integrator with the number and size of samples
-	void Init(int x_size, int y_size,
-				int samples_x, int samples_y,
-				rts_glTextureMap test);
-
-	void Integrate(float* result, rts_glTextureMap texture, int type = MEAN);
-	rts_glTextureMap getResultTexture(){return y_pass.GetTexture(0);}
-};
-
-void rts_glIntegrateTexture::initialize_shaders()
-{
-	//load and initialize the integration shaders
-	x_pass_mean.AttachShader(GL_FRAGMENT_SHADER,
-							"x_pass_mean.glsl");
-	x_pass_mean.Compile();
-	x_pass_mean.Link();
-	cout<<"x_pass_mean.glsl"<<endl;
-	x_pass_mean.PrintLog();
-	//x_pass_program.AttachTextureMap("difference_tex",
-	//							test);
-	x_pass_mean.AttachGlobalUniform("templatesize", &x_sample_size);
-
-
-	y_pass_mean.AttachShader(GL_FRAGMENT_SHADER,
-							"y_pass_mean.glsl");
-	y_pass_mean.Compile();
-	y_pass_mean.Link();
-	cout<<"y_pass_mean.glsl"<<endl;
-	y_pass_mean.PrintLog();
-	y_pass_mean.AttachTextureMap("xfunnel_tex",
-								x_pass.GetTexture(0));
-	y_pass_mean.AttachGlobalUniform("templatesize", &x_sample_size);
-
-}
-
-void rts_glIntegrateTexture::x_pass_enable(int type, rts_glTextureMap texture)
-{
-	x_pass_mean.BeginProgram();
-	x_pass_mean.AttachTextureMap("difference_tex",
-								texture);
-	x_pass_mean.UpdateGlobalUniforms();
-}
-
-void rts_glIntegrateTexture::x_pass_disable(int type)
-{
-	x_pass_mean.EndProgram();
-}
-
-void rts_glIntegrateTexture::y_pass_enable(int type)
-{
-	y_pass_mean.BeginProgram();
-	y_pass_mean.UpdateGlobalUniforms();
-}
-
-void rts_glIntegrateTexture::y_pass_disable(int type)
-{
-	y_pass_mean.EndProgram();
-}
-
-
-void rts_glIntegrateTexture::Init(int x_size, int y_size,
-				int samples_x, int samples_y,
-				rts_glTextureMap test)
-{
-	//set provate variables
-	x_sample_size = x_size;
-	y_sample_size = y_size;
-	x_sample_num = samples_x;
-	y_sample_num = samples_y;
-
-	//initialize the integrator texture maps
-	x_pass.Init(x_sample_num, y_sample_num*y_sample_size);
-	x_pass.AddTexture(GL_TEXTURE_RECTANGLE_ARB, GL_RGBA32F_ARB, GL_RGBA, GL_FLOAT);
-	y_pass.Init(x_sample_num, y_sample_num);
-	y_pass.AddTexture(GL_TEXTURE_RECTANGLE_ARB, GL_RGBA32F_ARB, GL_RGBA, GL_FLOAT);
-
-	initialize_shaders();	
-}
-
-void rts_glIntegrateTexture::Integrate(float* result, rts_glTextureMap texture, int type)
-{
-	
-	x_pass.BeginRender(0);
-	glMatrixMode(GL_PROJECTION);
-	glLoadIdentity();
-	x_pass.UseMaxViewport();
-	gluOrtho2D(0.0, 1.0, 0.0, 1.0);
-
-	x_pass_enable(MEAN, texture);
-
-	int total_w = x_sample_size * x_sample_num;
-	int total_h = y_sample_size * y_sample_num;
-
-	//GLint prog;
-	//glGetIntegerv(GL_CURRENT_PROGRAM, &prog);
-	glBegin(GL_QUADS);
-		glTexCoord2f(0.0, 0.0);	glVertex2f(0.0, 0.0);
-		glTexCoord2f(total_w, 0.0); glVertex2f(1.0, 0.0);
-		glTexCoord2f(total_w, total_h); glVertex2f(1.0, 1.0);
-		glTexCoord2f(0.0, total_h);	glVertex2f(0.0, 1.0);
-	glEnd();
-	x_pass_disable(MEAN);
-	glFinish();
-	x_pass.EndRender();
-
-	//funnel along Y
-	y_pass.BeginRender(0);
-	glMatrixMode(GL_PROJECTION);
-	glLoadIdentity();
-	y_pass.UseMaxViewport();
-	gluOrtho2D(0.0, 1.0, 0.0, 1.0);
-	
-	//glColor3f(1.0, 0.0, 0.0);
-	y_pass_enable(type);
-	glBegin(GL_QUADS);
-		glTexCoord2f(0.0, 0.0);	glVertex2f(0.0, 0.0);
-		glTexCoord2f(x_sample_num, 0.0); glVertex2f(1.0, 0.0);
-		glTexCoord2f(x_sample_num, total_h); glVertex2f(1.0, 1.0);
-		glTexCoord2f(0.0, total_h);	glVertex2f(0.0, 1.0);
-	glEnd();
-	int fb;
-	glGetIntegerv(GL_FRAMEBUFFER_BINDING, &fb);
-	y_pass_disable(type);
-	y_pass.EndRender();
-
-	y_pass.GetTexture(0).BeginTexture();
-	glGetTexImage(GL_TEXTURE_RECTANGLE_ARB, 0, GL_RGBA, GL_FLOAT, result);
-	y_pass.GetTexture(0).EndTexture();
-	
-}
\ No newline at end of file
diff --git a/legacy/rts_glOBJ.cpp b/legacy/rts_glOBJ.cpp
deleted file mode 100755
index 88fbd05..0000000
--- a/legacy/rts_glOBJ.cpp
+++ /dev/null
@@ -1,465 +0,0 @@
-#include "rts_glOBJ.h"
-#include "gl\glut.h"
-
-OBJint rts_glOBJ::f_RenderTexCoord(vertex_texture &texcoord)
-{
-	if(texcoord.mask & OBJ_VT_W)
-		glTexCoord3f(texcoord.u, texcoord.v, texcoord.w);
-	else if(texcoord.mask & OBJ_VT_V)
-		glTexCoord2f(texcoord.u, texcoord.v);
-	else
-		glTexCoord1f(texcoord.u);
-	return OBJ_OK;
-}
-
-OBJint rts_glOBJ::f_RenderNormal(vertex_normal &normal)
-{
-	if(normal.mask & OBJ_VN_K)
-		glNormal3f(normal.i, normal.j, normal.k);
-	else
-		return OBJ_ERROR;
-
-	return OBJ_OK;
-
-}
-
-OBJint rts_glOBJ::f_RenderVertex(vertex_position &v)
-{
-	if(v.mask & OBJ_V_W)
-		glVertex4f(v.x, v.y, v.z, v.w);
-	else if(v.mask & OBJ_V_Z)
-		glVertex3f(v.x, v.y, v.z);
-	else if(v.mask & OBJ_V_Y)
-		glVertex2f(v.x, v.y);
-	else
-		//glVertex1f(v.x);
-		return OBJ_ERROR;
-
-	return OBJ_OK;
-}
-
-inline void rts_glOBJ::f_RenderPointList(unsigned int id)
-{
-	glBegin(GL_POINTS);
-	unsigned int num_vertices = primitives[id].p.size();
-	for(unsigned int v = 0; v<num_vertices; v++)
-	{
-		f_RenderVertex(v_list[primitives[id].p[v].v]);
-	}
-	glEnd();
-}
-
-inline void rts_glOBJ::f_RenderLineStrip(unsigned int id)
-{
-	//render each line as a line strip
-	glBegin(GL_LINE_STRIP);
-	unsigned int num_vertices = primitives[id].p.size();
-	for(unsigned int v=0; v<num_vertices; v++)
-	{
-		f_RenderVertex(v_list[primitives[id].p[v].v]);
-	}
-
-	//end rendering
-	glEnd();
-
-}
-
-inline void rts_glOBJ::f_RenderFace(unsigned int id)
-{
-	//start the proper render mode
-	if(primitives[id].p.size() > 4)
-		glBegin(GL_POLYGON);
-	else if(primitives[id].p.size() == 4)
-		glBegin(GL_QUADS);
-	else if(primitives[id].p.size() == 3)
-		glBegin(GL_TRIANGLES);
-	else
-		return;
-
-	//now run through each vertex
-	unsigned int num_vertices = primitives[id].p.size();
-	for(unsigned int v=0; v<num_vertices; v++)
-	{
-		f_RenderVertex(v_list[primitives[id].p[v].v]);
-	}
-
-	//end rendering
-	glEnd();
-
-}
-
-OBJint rts_glOBJ::f_RenderPrimitive(unsigned int i)
-{
-	switch(primitives[i].type)
-	{
-	case OBJ_POINTS:
-		f_RenderPointList(i);
-		break;
-	case OBJ_LINES:
-		f_RenderLineStrip(i);
-		break;
-	case OBJ_FACE:
-		f_RenderFace(i);
-		break;
-	}
-
-	return OBJ_OK;
-
-}
-
-OBJint rts_glOBJ::f_CreateDisplayList()
-{
-	/*This function creates a display list representing the OBJ.
-	*/
-	
-	//create the display list
-	if(glIsList(dl))	//if the list already exists
-		glDeleteLists(dl, 1);
-	//create a new display list
-	dl = glGenLists(1);
-
-	//start the list
-	glNewList(dl, GL_COMPILE);
-
-	//draw the OBJ
-	unsigned int prim = primitives.size();
-	for(unsigned int i=0; i<prim; i++)
-		f_RenderPrimitive(i);
-
-	//finish the list
-	glEndList();
-
-	dl_valid = true;	//the display list is now valid
-
-	return OBJ_OK;
-}
-
-OBJint rts_glOBJ::glRender()
-{
-	//create the display list if necessary
-	if(!dl_valid)
-		f_CreateDisplayList();
-
-	//call the display list
-	glCallList(dl);
-
-	return OBJ_OK;
-}
-
-OBJint rts_glOBJ::glRenderSelected()
-{
-	if(is_selected)
-	{
-		list<unsigned int>::iterator p;
-		for(p = selected_primitives.begin(); p!=selected_primitives.end(); p++)
-			f_RenderPrimitive(*p);
-	}
-	return OBJ_OK;
-}
-
-
-void rts_glOBJ::SelectPrimitive(unsigned int primitive)
-{
-	//adds a primitive to the selection list
-	selected_primitives.push_back(primitive);
-	selected_primitives.unique();
-}
-
-void rts_glOBJ::UnselectPrimitive(unsigned int primitive)
-{
-	selected_primitives.remove(primitive);
-}
-
-void rts_glOBJ::SelectMultipleHits(GLuint* buffer, unsigned int num_hits)
-{
-	GLuint* hit_entry = buffer;
-	GLuint num_names;
-	GLuint nearest_name;
-	GLuint minZ = 0xffffffff;
-	
-	//push the hits into the selection buffer
-	for(int h=0; h<num_hits; h++)
-	{
-		num_names = hit_entry[0];
-		SelectPrimitive(hit_entry[3]);
-	
-		hit_entry = hit_entry + 3 + num_names;
-	}
-
-}
-
-void rts_glOBJ::UnselectMultipleHits(GLuint* buffer, unsigned int num_hits)
-{
-	GLuint* hit_entry = buffer;
-	GLuint num_names;
-	GLuint nearest_name;
-	GLuint minZ = 0xffffffff;
-	
-	//push the hits into the selection buffer
-	for(int h=0; h<num_hits; h++)
-	{
-		num_names = hit_entry[0];
-		UnselectPrimitive(hit_entry[3]);
-	
-		hit_entry = hit_entry + 3 + num_names;
-	}
-
-}
-
-void rts_glOBJ::SelectClosestHit(GLuint* buffer, unsigned int num_hits)
-{
-	GLuint* hit_entry = buffer;
-	GLuint num_names;
-	GLuint nearest_name;
-	GLuint minZ = 0xffffffff;
-	
-	//push the hits into the selection buffer
-	for(int h=0; h<num_hits; h++)
-	{
-		num_names = hit_entry[0];
-		if(hit_entry[1] < minZ)
-		{
-			nearest_name = hit_entry[3];
-			minZ = hit_entry[1];
-		}		
-		hit_entry = hit_entry + 3 + num_names;
-
-	}
-	SelectPrimitive(nearest_name);
-
-}
-
-void rts_glOBJ::UnselectClosestHit(GLuint* buffer, unsigned int num_hits)
-{
-	GLuint* hit_entry = buffer;
-	GLuint num_names;
-	GLuint nearest_name;
-	GLuint minZ = 0xffffffff;
-	
-	//push the hits into the selection buffer
-	for(int h=0; h<num_hits; h++)
-	{
-		num_names = hit_entry[0];
-		if(hit_entry[1] < minZ)
-		{
-			nearest_name = hit_entry[3];
-			minZ = hit_entry[1];
-		}		
-		hit_entry = hit_entry + 3 + num_names;
-
-	}
-	UnselectPrimitive(nearest_name);
-
-}
-
-
-void rts_glOBJ::Pick(unsigned int x, unsigned int y, unsigned int size_x, unsigned int size_y,
-					 unsigned int picktype)
-{
-	//initialize selection buffer properties
-	GLuint selectBuf[BUFSIZE];
-	GLint hits;
-	GLint viewport[4];		//storage space for viewport data
-
-	//get the viewport information
-	glGetIntegerv(GL_VIEWPORT, viewport);
-	
-	//set the selection buffer
-	glSelectBuffer(BUFSIZE, selectBuf);
-
-	//set the render mode to selection
-	glRenderMode(GL_SELECT);
-
-	//we pick the object with the assumption that the active projection
-	//matrix is the one used to display the object in the viewport
-
-	//get the current projection matrix
-	float projection[16];
-	glGetFloatv(GL_PROJECTION_MATRIX, projection);
-
-	//save and reset the current projection matrix
-	glMatrixMode(GL_PROJECTION);
-	glPushMatrix();
-	glLoadIdentity();
-
-	//set the picking matrix using GLU
-	gluPickMatrix(x, viewport[3] - y, size_x, size_y, viewport);
-	//multiply in the saved projection matrix
-	glMultMatrixf(projection);
-
-	//Draw the object with names for each primitive.
-
-	int num_prim = primitives.size();	//get the number of primitives
-	glInitNames();						//set the name stack to zero
-	for(int p = 0; p < num_prim; p++)
-	{
-		glPushName(p);				//push the name on to the stack
-		f_RenderPrimitive(p);			//render the primitive
-		glPopName();
-	}
-
-	glFinish();				//force the rendering to complete	
-
-	hits = glRenderMode(GL_RENDER);		//find the number of hits
-
-	if(hits)					//if there is a hit, select the OBJ and the primitive
-	{
-		is_selected = true;		//select the object
-
-		//if this is a new selection, clear the list
-		if(picktype == RTS_GLOBJ_SINGLE_NEW_SELECTION || 
-		   picktype == RTS_GLOBJ_MULTI_NEW_SELECTION)
-			selected_primitives.clear();
-
-		//if this is adding multiple hits to the selection list
-		if(picktype == RTS_GLOBJ_MULTI_NEW_SELECTION ||
-		   picktype == RTS_GLOBJ_MULTI_ADD_SELECTION)
-			SelectMultipleHits(selectBuf, hits);
-
-		if(picktype == RTS_GLOBJ_SINGLE_NEW_SELECTION ||
-		   picktype == RTS_GLOBJ_SINGLE_ADD_SELECTION)
-			SelectClosestHit(selectBuf, hits);
-
-		if(picktype == RTS_GLOBJ_SINGLE_SUB_SELECTION)
-			UnselectClosestHit(selectBuf, hits);
-
-		if(picktype == RTS_GLOBJ_MULTI_SUB_SELECTION)
-			UnselectMultipleHits(selectBuf, hits);
-		//SelectPrimitive(processHits(selectBuf, hits), picktype);
-		//selected_primitives.clear();
-		
-		//select the primitive
-		//selected_primitives.push_back(processHits(selectBuf, hits));
-	}
-	else
-		is_selected = false;
-
-	//restore the previous projection matrix
-	glMatrixMode(GL_PROJECTION);
-	glPopMatrix();
-
-}
-rts_glOBJ rts_glOBJ::GetSelected()
-{
-	//right now this creates duplicate vertices
-	
-	rts_glOBJ result;
-
-	//for each primitive
-	list<unsigned int>::iterator p;
-	for(p = selected_primitives.begin(); p != selected_primitives.end(); p++)
-	{
-		primitive selected_prim = primitives[(*p)];
-		//create a new primitive
-		primitive new_prim;
-		new_prim.mask = selected_prim.mask;
-		new_prim.type = selected_prim.type;
-
-		//for each vertex in the primitive
-		int num_vertices = selected_prim.p.size();
-		for(int v = 0; v<num_vertices; v++)
-		{
-			vertex new_vert;
-			if(new_prim.mask & OBJ_V)	//if the primitive has a vertex coord
-			{
-				new_vert.v = result.v_list.size();
-				new_prim.p.push_back(new_vert);
-				result.v_list.push_back(v_list[selected_prim.p[v].v]);				
-			}
-		}
-		result.primitives.push_back(new_prim);
-	}
-
-	return result;
-
-
-}
-
-void rts_glOBJ::ExpandSelection()
-{
-	/*
-	//create a list of all selected vertices
-	list<unsigned int> selected_v;
-
-	list<unsigned int>::iterator p;	//selected primitive
-	vector<vertex>::iterator v;		//vertex
-
-	//insert all selected vertex indices into selected_v
-	for(p = selected_primitives.begin(); p!=selected_primitives.end(); p++)
-	{
-		for(v=primitives[(*p)].p.begin(); v!=primitives[(*p)].p.end(); v++)
-		{
-			selected_v.push_back((*v).v);
-		}
-	}
-	selected_v.unique();	//remove redundant entries
-
-	//now find all primitives connected to these vertices
-	int num_primitives = primitives.size();
-	int prim;
-	list<unsigned int>::iterator s_v;
-	for(prim =0; prim<num_primitives; prim++)
-	{
-		for(v=primitives[prim].p.begin(); v!=primitives[prim].p.end(); v++)
-		{
-			for(s_v = selected_v.begin(); s_v!=selected_v.end(); s_v++)
-			{
-				if((*s_v) == (*v).v)
-				{
-					selected_primitives.push_back(prim);
-				}
-			}
-		}
-	}
-		selected_primitives.unique();
-
-	*/
-	
-
-	//create the vertex-primitive list
-	vector<unsigned int>* vertex_to_prim = new vector<unsigned int>[v_list.size()];
-	int num_primitives = primitives.size();
-	int p;
-	int num_vertices, v;
-	int vertex;
-	for(p=0; p<num_primitives; p++)
-	{
-		num_vertices = primitives[p].p.size();
-		for(v = 0; v<num_vertices; v++)
-		{
-			vertex = primitives[p].p[v].v;
-			vertex_to_prim[vertex].push_back(p);
-		}
-	}
-
-	//create the list of selected vertices
-	list<unsigned int> selected_verts;
-	list<unsigned int>::iterator sel;
-	for(sel = selected_primitives.begin(); sel != selected_primitives.end(); sel++)
-	{
-		num_vertices = primitives[(*sel)].p.size();
-		for(v=0; v<num_vertices; v++)
-		{
-			selected_verts.push_back(primitives[(*sel)].p[v].v);
-		}
-	}
-	selected_verts.unique();
-
-	//erase the selected array
-	selected_primitives.clear();
-	list<unsigned int>::iterator s_v;
-	for(s_v = selected_verts.begin(); s_v != selected_verts.end(); s_v++)
-	{
-		num_primitives = vertex_to_prim[(*s_v)].size();
-		for(p=0; p<num_primitives; p++)
-			selected_primitives.push_back(vertex_to_prim[(*s_v)][p]);
-	}
-	cout<<"Before: "<<selected_primitives.size()<<endl;
-
-	selected_primitives.sort();
-	selected_primitives.unique();
-	cout<<"After: "<<selected_primitives.size()<<endl;
-	
-
-
-}
\ No newline at end of file
diff --git a/legacy/rts_glOBJ.h b/legacy/rts_glOBJ.h
deleted file mode 100755
index 1b1125b..0000000
--- a/legacy/rts_glOBJ.h
+++ /dev/null
@@ -1,93 +0,0 @@
-#ifndef RTS_GLOBJ_H
-#define RTS_GLOBJ_H
-
-#include "objJedi.h"
-#include <windows.h>
-#include <gl/gl.h>
-#include <gl/glu.h>
-#include <list>
-
-using namespace std;
-
-#define BUFSIZE 20000
-
-#define OBJ_NOT_SELECTED		0x0000
-#define OBJ_SELECTED			0x0001
-#define OBJ_SELECTED_PRIMITIVES	0x0002
-
-#define RTS_GLOBJ_SINGLE_NEW_SELECTION	0
-#define RTS_GLOBJ_SINGLE_ADD_SELECTION	1
-#define RTS_GLOBJ_SINGLE_SUB_SELECTION  2
-
-#define RTS_GLOBJ_MULTI_NEW_SELECTION	3
-#define RTS_GLOBJ_MULTI_ADD_SELECTION	4
-#define RTS_GLOBJ_MULTI_SUB_SELECTION	5
-
-class rts_glOBJ : public rtsOBJ
-{
-private:
-	int is_selected;			//the object, or part of the object, is selected
-	list<unsigned int> selected_primitives;
-
-	//rendering variables
-	GLint dl;
-	bool dl_valid;				//true if the display list is valid
-	
-	OBJint f_CreateDisplayList();
-
-	void f_RenderPointList(unsigned int pointlist);
-	void f_RenderLineStrip(unsigned int line);
-	void f_RenderFace(unsigned int face);
-
-	OBJint f_RenderTexCoord(vertex_texture &texcoord);
-	OBJint f_RenderNormal(vertex_normal &normal);
-	OBJint f_RenderVertex(vertex_position &v);
-	OBJint f_RenderPrimitive(unsigned int id);
-
-	void SelectMultipleHits(GLuint* buffer, unsigned int num_hits);
-	void SelectClosestHit(GLuint* buffer, unsigned int num_hits);
-	void SelectPrimitive(unsigned int primitive);
-	void UnselectMultipleHits(GLuint* buffer, unsigned int num_hits);
-	void UnselectClosestHit(GLuint* buffer, unsigned int num_hits);
-	void UnselectPrimitive(unsigned int primitive);
-	
-public:
-	//constructors
-	//basic
-	rts_glOBJ()
-	{
-		is_selected = false;
-		dl_valid = false;
-		cout<<selected_primitives.size()<<endl;
-	}
-	//assignment
-	rts_glOBJ& operator=(const rtsOBJ& obj)
-	{
-		CopyOBJ(obj);
-		is_selected = false;
-		dl_valid = false;
-		return *this;
-	}
-	//copy
-	rts_glOBJ(const rtsOBJ& obj)
-	{
-		CopyOBJ(obj);
-		is_selected = false;
-		dl_valid = false;
-		//return *this;
-	}
-
-	OBJint glRender();
-	OBJint glRenderSelected();
-	void Invalidate(){dl_valid = false;}			//invalidate the display list
-
-	//return true of the object is currently selected
-	int selected(){return is_selected;};
-	//unsigned int getSelected(unsigned int i = 0){return selected_primitives[i];}
-	void Pick(unsigned int x, unsigned int y, unsigned int size_x, unsigned int size_y, unsigned int picktype = RTS_GLOBJ_SINGLE_NEW_SELECTION);
-	rts_glOBJ GetSelected();
-	void ExpandSelection();
-	
-};
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glRenderToTexture.cpp b/legacy/rts_glRenderToTexture.cpp
deleted file mode 100755
index 060d732..0000000
--- a/legacy/rts_glRenderToTexture.cpp
+++ /dev/null
@@ -1,86 +0,0 @@
-#include "rts_glRenderToTexture.h"
-
-void rts_glRenderToTexture::Clean()
-{
-	//clean up the fbo
-	glDeleteFramebuffersEXT(1, &fbo);
-	int num_tex = textures.size();
-
-	//clean up all textures associated with the fbo
-	for(int i=0; i<num_tex; i++)
-		textures[i].Clean();
-	textures.clear();
-
-	fbo = 0;
-}
-
-void rts_glRenderToTexture::Init(int w, int h)
-{
-	CHECK_OPENGL_ERROR
-	if(fbo != 0)
-		Clean();
-	CHECK_OPENGL_ERROR
-	glGenFramebuffersEXT(1, &fbo);	//create the framebuffer object
-	CHECK_OPENGL_ERROR
-	width = w;
-	height = h;
-
-}
-
-void rts_glRenderToTexture::AddTexture(GLenum target,
-									   GLint internalformat,
-									   GLenum format,
-									   GLenum datatype,
-									   GLint interpolation)
-{
-
-	//create the new texture
-	rts_glTextureMap new_texture;
-	new_texture.Init(NULL, 
-					 target, 
-					 width, 
-					 height, 
-					 0, 
-					 internalformat, 
-					 format, 
-					 datatype,
-					 interpolation);
-	//push it into the texture vector
-	textures.push_back(new_texture);
-	cout<<"Texture Name: "<<new_texture.name<<endl;
-	
-	//bind it to the frame buffer
-	
-	glBindFramebufferEXT(GL_FRAMEBUFFER, fbo);
-	CHECK_OPENGL_ERROR
-	glFramebufferTexture2DEXT(GL_FRAMEBUFFER,
-							  GL_COLOR_ATTACHMENT0 + textures.size() - 1,
-							  target,
-							  new_texture.name,
-							  0);
-
-	CHECK_OPENGL_ERROR
-	GLenum status = glCheckFramebufferStatusEXT(GL_FRAMEBUFFER);
-	CHECK_OPENGL_ERROR
-	if(status != GL_FRAMEBUFFER_COMPLETE)
-		cout<<"Framebuffer status invalid!"<<endl;
-
-	//restore normal rendering
-	glBindFramebufferEXT(GL_FRAMEBUFFER, 0);
-	
-}
-
-void rts_glRenderToTexture::BeginRender(int texture)
-{
-	
-	//bind the framebuffer
-	glBindFramebufferEXT(GL_FRAMEBUFFER, fbo);
-	glDrawBuffer(GL_COLOR_ATTACHMENT0+texture);
-}
-
-void rts_glRenderToTexture::EndRender()
-{
-	//glFinish();
-	//bind the screen buffer
-	glBindFramebufferEXT(GL_FRAMEBUFFER, 0);
-}
\ No newline at end of file
diff --git a/legacy/rts_glRenderToTexture.h b/legacy/rts_glRenderToTexture.h
deleted file mode 100755
index 366a825..0000000
--- a/legacy/rts_glRenderToTexture.h
+++ /dev/null
@@ -1,45 +0,0 @@
-#ifndef RTS_GLRENDERTOTEXTURE_H
-#define RTS_GLRENDERTOTEXTURE_H
-//#include <gl/gl.h>
-#include <vector>
-#include "rts_glTextureMap.h"
-
-using namespace std;
-
-class rts_glRenderToTexture
-{
-private:
-	bool init;
-
-	GLuint fbo;		//framebuffer object
-	int width;		//width and height of the framebuffer
-	int height;
-	vector<rts_glTextureMap> textures;
-
-public:
-	//constructors
-	rts_glRenderToTexture(){init = false; fbo = 0;}						
-	rts_glRenderToTexture(int width, int height){Init(width, height);}
-
-	void Init(int width, int height);	//initialization
-	void Clean();
-
-	void AddTexture(GLenum target,
-					GLint internalformat = 1, 
-					GLenum format = GL_LUMINANCE, 
-					GLenum datatype = GL_UNSIGNED_BYTE,
-					GLint interpolation = GL_NEAREST);
-	void BeginTexture(int texture){textures[texture].BeginTexture();}
-	void EndTexture(int texture){textures[texture].EndTexture();}
-	rts_glTextureMap GetTexture(int texture){return textures[texture];}
-
-	void BeginRender(int texture);
-	void EndRender();
-
-	int Width(){return width;}
-	int Height(){return height;}
-	void UseMaxViewport(){glViewport(0, 0, width, height);}
-
-};
-
-#endif
diff --git a/legacy/rts_glRenderableDTGrid.cpp b/legacy/rts_glRenderableDTGrid.cpp
deleted file mode 100755
index 1a24fcc..0000000
--- a/legacy/rts_glRenderableDTGrid.cpp
+++ /dev/null
@@ -1,260 +0,0 @@
-#include "rts_glRenderableDTGrid.h"
-
-
-/*ITERATOR INITIALIZATION*/
-void rts_glRenderableDTGrid::init_iter_ppp()
-{
-	m_iterator = begin();
-	m_iter_type = PPP;
-}
-void rts_glRenderableDTGrid::init_iter_nnn()
-{
-	m_iterator = last();
-	m_iter_type = NNN;
-}
-void rts_glRenderableDTGrid::init_iter_ppn()
-{
-	m_iterator = begin();	//put the iterator at the beginning of the data set
-
-	if(m_iterator.grid->acc.size() > 1)	//if there is more than one pcolumn
-	{
-		m_iterator.loc.iv = m_iterator.grid->proj2D.value[1].to_value - 1;
-		m_iterator.loc.z = zCoord[m_iterator.grid->proj2D.value[1].to_coord - 1];
-	}
-	else
-	{
-		m_iterator.loc.iv = value.size() - 1;
-		m_iterator.loc.z = zCoord.back();
-	}
-	m_iter_type = PPN;
-}
-
-void rts_glRenderableDTGrid::init_iter_npp()
-{
-	//set the 1D iterator location
-	m_iterator.Iterator2D.Iterator1D.loc.iv = proj2D.proj1D.value.size()-1;	//start at the last 1D p-column
-	m_iterator.Iterator2D.Iterator1D.loc.ic = proj2D.proj1D.xCoord.size() - 2;
-	m_iterator.Iterator2D.Iterator1D.loc.x = proj2D.proj1D.xCoord[m_iterator.Iterator2D.Iterator1D.loc.ic+1];
-	m_iterator.Iterator2D.Iterator1D.value = proj2D.proj1D.value[m_iterator.Iterator2D.Iterator1D.loc.iv];
-	m_iterator.Iterator2D.Iterator1D.grid = &(proj2D.proj1D);
-
-	//set the 2D iterator location
-	m_iterator.Iterator2D.loc.iv = proj2D.proj1D.value[m_iterator.Iterator2D.Iterator1D.loc.iv].to_value;
-	m_iterator.Iterator2D.loc.ic = proj2D.proj1D.value[m_iterator.Iterator2D.Iterator1D.loc.iv].to_coord;
-	m_iterator.Iterator2D.loc.y = proj2D.yCoord[m_iterator.Iterator2D.loc.ic];
-	m_iterator.Iterator2D.value = proj2D.value[m_iterator.Iterator2D.loc.iv];
-	m_iterator.Iterator2D.grid = &(proj2D);
-
-	//set the 3D iterator location
-	m_iterator.loc.iv = proj2D.value[m_iterator.Iterator2D.loc.iv].to_value;
-	m_iterator.loc.ic = proj2D.value[m_iterator.Iterator2D.loc.iv].to_coord;
-	m_iterator.loc.z = zCoord[m_iterator.loc.ic];
-	m_iterator.value = value[m_iterator.loc.iv];
-	m_iterator.grid = this;
-
-	m_iter_type = NPP;
-}
-
-void rts_glRenderableDTGrid::iter_next_npp()
-{	
-	//if we are at the end of a p-column
-	if(m_iterator.loc.iv == value.size() - 1 ||	//if we are at the end of the last p-column or
-		(m_iterator.Iterator2D.loc.iv != m_iterator.grid->proj2D.value.size() - 1 &&
-		m_iterator.loc.iv == proj2D.value[m_iterator.Iterator2D.loc.iv + 1].to_value - 1)) //we are at the end of a p-column
-	{
-		iter_next_npx(m_iterator.Iterator2D);	//increment the 2D iterator
-		m_iterator.loc.iv = proj2D.value[m_iterator.Iterator2D.loc.iv].to_value;
-		m_iterator.loc.ic = proj2D.value[m_iterator.Iterator2D.loc.iv].to_coord;
-		m_iterator.loc.z = zCoord[m_iterator.loc.ic];
-	}
-	//if we are at the end of a connected component
-	else if(m_iterator.loc.z == zCoord[m_iterator.loc.ic+1])
-	{
-		m_iterator.loc.iv++;
-		m_iterator.loc.ic+=2;
-		m_iterator.loc.z = zCoord[m_iterator.loc.ic];
-	}
-	//else if we are in a p-column
-	else
-	{
-		m_iterator.loc.iv++;
-		m_iterator.loc.z++;
-	}
-	m_iterator.value = value[m_iterator.loc.iv];
-}
-
-void rts_glRenderableDTGrid::iter_next_ppn()
-{
-	//if we are at the beginning of a p-column
-	if(m_iterator.loc.z == zCoord[m_iterator.loc.ic] &&
-		m_iterator.loc.ic == proj2D.value[m_iterator.Iterator2D.loc.iv].to_coord)
-	{
-		m_iterator.Iterator2D.increment();	//move to the next p-column
-		if(m_iterator.Iterator2D.loc.iv >= proj2D.value.size())	//return
-			return;
-		//now update the 3D locator
-		if(m_iterator.Iterator2D.loc.iv == proj2D.value.size() - 1)	//if this is the last p-column
-		{
-			m_iterator.loc.iv = value.size() - 1;
-			m_iterator.loc.ic = zCoord.size() - 2;
-			m_iterator.loc.z = zCoord.back();
-		}
-		else
-		{
-			m_iterator.loc.iv = proj2D.value[m_iterator.Iterator2D.loc.iv+1].to_value - 1;
-			m_iterator.loc.ic = proj2D.value[m_iterator.Iterator2D.loc.iv+1].to_coord - 2;
-			m_iterator.loc.z = zCoord[m_iterator.loc.ic + 1];
-		}
-	}
-	//if we are at the beginning of a connected component
-	else if(m_iterator.loc.z == zCoord[m_iterator.loc.ic])
-	{
-		m_iterator.loc.iv-=1;
-		m_iterator.loc.ic-=2;
-		m_iterator.loc.z = zCoord[m_iterator.loc.ic + 1];
-	}
-	//if we're in the middle of a connected component
-	else
-	{
-		m_iterator.loc.iv--;
-		m_iterator.loc.z--;
-	}
-	m_iterator.value = value[m_iterator.loc.iv];
-}
-
-void rts_glRenderableDTGrid::iter_next_npx(rtsDTGrid2D<IndexPair>::iterator &i2d)
-{
-	//if we are at the end of a p-column
-	if(i2d.loc.iv == i2d.grid->value.size() - 1	||	//if this is the last p-column
-		(i2d.Iterator1D.loc.iv != i2d.grid->proj1D.value.size() - 1 &&	//we are not in the last p-column and
-		i2d.loc.iv == i2d.grid->proj1D.value[i2d.Iterator1D.loc.iv+1].to_value - 1))
-	{
-		//if(i2d.Iterator1D.loc.iv == 0)	//if it is the first p-column
-		//	return;
-		i2d.Iterator1D.decrement();		//decrement the 1D iterator
-		//update the 2D locator
-		i2d.loc.iv = i2d.grid->proj1D.value[i2d.Iterator1D.loc.iv].to_value;
-		i2d.loc.ic = i2d.grid->proj1D.value[i2d.Iterator1D.loc.iv].to_coord;
-		i2d.loc.y = i2d.grid->yCoord[i2d.loc.ic];
-	}
-	//if we are at the end of a connected component
-	else if(i2d.loc.y == i2d.grid->yCoord[i2d.loc.ic+1])
-	{
-		i2d.loc.iv++;
-		i2d.loc.ic+=2;
-		i2d.loc.y = i2d.grid->yCoord[i2d.loc.ic];
-	}
-	else
-	{
-		i2d.loc.iv++;
-		i2d.loc.y++;
-	}
-	//set value
-	i2d.value = i2d.grid->value[i2d.loc.iv];
-}
-	
-
-void rts_glRenderableDTGrid::iter_next()
-{
-	if(m_iter_type == PPP)
-		m_iterator.increment();
-	if(m_iter_type == NNN)
-		m_iterator.decrement();
-	if(m_iter_type == PPN)
-		iter_next_ppn();
-	if(m_iter_type == NPP)
-		iter_next_npp();
-}
-void rts_glRenderableDTGrid::RenderPoints(unsigned int size, float camera_x, float camera_y, float camera_z)
-{
-	/*This function renders a single point to the screen for each voxel in the
-	DT-Grid.
-	*/
-	//determine which directions to iterate
-	if(camera_x > 0)
-	{
-		if(camera_y > 0)
-		{
-			if(camera_z > 0)
-			{
-				//cout<<"+++"<<endl;
-				init_iter_ppp();
-			}
-			else
-			{
-				//cout<<"++-"<<endl;
-				init_iter_ppn();
-			}
-		}
-		else
-		{
-			if(camera_z > 0)
-			{
-				//cout<<"+-+"<<endl;
-				init_iter_ppp();
-			}
-			else
-			{
-				//cout<<"+--"<<endl;
-				init_iter_ppp();
-			}
-		}
-	}
-	else
-	{
-		if(camera_y > 0)
-		{
-			if(camera_z > 0)
-			{
-				//cout<<"-++"<<endl;
-				init_iter_npp();
-			}
-			else
-			{
-				//cout<<"-+-"<<endl;
-				init_iter_nnn();
-			}
-		}
-		else
-		{
-			if(camera_z > 0)
-			{
-				//cout<<"--+"<<endl;
-				init_iter_nnn();
-			}
-			else
-			{
-				//cout<<"---"<<endl;
-				init_iter_nnn();
-			}
-		}
-	}
-
-
-	//init_iter_npp();
-
-
-	glPointSize(3);
-	glDisable(GL_DEPTH_TEST);
-	glEnable(GL_BLEND);
-	glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
-
-
-
-	glBegin(GL_POINTS);					//render voxels as points
-	unsigned int i;
-	unsigned int num_values = value.size();
-	for(i=0; i<num_values; i++)
-	{
-		glColor4f(m_iterator.value.r, m_iterator.value.g, m_iterator.value.b, m_iterator.value.a);
-		glVertex3f(m_iterator.getX()/(float)MaxX(), m_iterator.getY()/(float)MaxY(), m_iterator.getZ()/(float)MaxZ());
-		//cout<<"("<<m_iterator.getX()<<","<<m_iterator.getY()<<","<<m_iterator.getZ()<<"):"<<m_iterator.value<<endl;
-		iter_next();
-	}
-	//cout<<"---------------------------------------"<<endl;
-	i=0;
-	glEnd();
-
-	glDisable(GL_BLEND);
-	glEnable(GL_DEPTH_TEST);
-}
\ No newline at end of file
diff --git a/legacy/rts_glRenderableDTGrid.h b/legacy/rts_glRenderableDTGrid.h
deleted file mode 100755
index dfb1b29..0000000
--- a/legacy/rts_glRenderableDTGrid.h
+++ /dev/null
@@ -1,38 +0,0 @@
-#ifndef RTS_GLRENDERABLEDTGRID_H
-#define RTS_GLRENDERABLEDTGRID_H
-
-#include "gl/glew.h"
-#include "gl/gl.h"
-#include "rtsDTGrid3D.h"
-
-enum IteratorType {PPP, PPN, PNP, PNN, NPP, NPN, NNP, NNN};
-
-struct ValueType
-{
-	float r;
-	float g;
-	float b;
-	float a;
-};
-
-
-class rts_glRenderableDTGrid : public rtsDTGrid3D<ValueType>
-{
-private:
-	IteratorType m_iter_type;
-	rtsDTGrid3D<ValueType>::iterator m_iterator;
-	void init_iter_ppp();
-	void init_iter_ppn();
-	void iter_next_ppn();
-	void init_iter_npp();
-	void iter_next_npp();
-	void init_iter_nnn();
-	void iter_next_npx(rtsDTGrid2D<IndexPair>::iterator &i2d);
-	void iter_next();
-public:
-	void RenderPoints(unsigned int size, float camera_x, float camera_y, float camera_z);
-
-};
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glShaderObject.h b/legacy/rts_glShaderObject.h
deleted file mode 100755
index 85a96c5..0000000
--- a/legacy/rts_glShaderObject.h
+++ /dev/null
@@ -1,115 +0,0 @@
-#ifndef RTS_GLSHADERS
-#define RTS_GLSHADERS
-
-#include <GL/glew.h>
-//#include "windows.h"
-#include <GL/gl.h>
-#include "rtsSourceCode.h"
-
-class rts_glShaderObject
-{
-private:
-	void init()
-	{
-		id = 0;
-		compiled = false;
-		type = GL_FRAGMENT_SHADER;
-	}
-public:
-	bool compiled;
-	GLenum type;
-	rtsSourceCode source;
-	GLuint id;
-	string log;
-
-	rts_glShaderObject(GLenum type, const char* filename)
-	{
-		init();					//initialize the shader
-		SetType(type);	//set the shader type
-		LoadSource(filename);	//load the source code
-	}
-	rts_glShaderObject(GLenum type, rtsSourceCode sourceCode)
-	{
-		init();					//initialize the shader
-		SetType(type);	//set the shader type
-		source = sourceCode;
-	}
-	rts_glShaderObject()
-	{
-		init();
-	}
-	rts_glShaderObject(GLenum type)
-	{
-		init();
-		SetType(type);
-	}
-	void LoadSource(const char* filename)
-	{
-		source = rtsSourceCode(filename);	//get the shader source code
-
-	}
-	void SetType(GLenum type)
-	{
-		if(id != 0)					//if a shader currently exists, delete it
-		{
-			glDeleteShader(id);
-			id = 0;
-		}
-		type = type;
-		id = glCreateShader(type);		//create a shader object
-		if(id == 0)						//if a shader was not created, log an error
-		{
-			log = "Error getting shader ID from OpenGL";
-			return;
-		}
-	}
-	void UploadSource()
-	{
-		//create the structure for the shader source code
-		GLsizei count = source.source.size();
-		GLchar** code_string = new GLchar*[count];
-		GLint* length = new GLint[count];
-		for(int l = 0; l<count; l++)	//for each line of code
-		{
-			length[l] = source.source[l].size();
-			code_string[l] = new GLchar[length[l]];	//copy the string into a new structure
-			source.source[l].copy(code_string[l], (unsigned int)length[l]);
-
-		}
-		glShaderSource(id, count, (const GLchar**)code_string, length);		//attach the shader source
-	}
-	void Compile()
-	{
-		/*
-		This function compiles the shader source code, records any errors to a log, and sets the compiled flag.
-		*/
-		//send the source code to the GPU
-		UploadSource();
-
-		//compile the shader
-		glCompileShader(id);												//compile the shader
-		GLint compile_status;
-		glGetShaderiv(id, GL_COMPILE_STATUS, &compile_status);				//get the compile status
-		if(compile_status != GL_TRUE)	//if there was an error
-		{
-			GLchar buffer[1000];		//create a log buffer
-			GLsizei length;
-			glGetShaderInfoLog(id, 1000, &length, buffer);	//get the log
-			log = buffer;
-			compiled = false;
-		}
-		else
-			compiled = true;
-
-	}
-	void PrintLog()
-	{
-		cout<<log;
-		if(log.size() != 0) cout<<endl;
-	}
-	void Clean(){if(id != 0) glDeleteShader(id);}
-};
-
-
-
-#endif
diff --git a/legacy/rts_glShaderProgram.h b/legacy/rts_glShaderProgram.h
deleted file mode 100755
index a39f375..0000000
--- a/legacy/rts_glShaderProgram.h
+++ /dev/null
@@ -1,295 +0,0 @@
-#ifndef RTS_GLSHADERPROGRAM_H
-#define RTS_GLSHADERPROGRAM_H
-
-/*********************************************************
-//create a shader program
-	rts_glShaderProgram myProgram;
-//initialize
-	myProgram.Init();
-//Attach shaders
-	myProgram.AttachShader(GL_FRAGMENT_SHADER, "filename.glsl");
-//Compile and link
-	myProgram.Compile();
-	myProgram.Link();
-	myProgram.PrintLog();
-//attach uniform variables
-	myProgram.AttachTextureMap("texture", texture);
-	myProgram.AttachGlobalUniform("light_intensity", &intensity);
-
-//use the program
-	myProgram.BeginProgram();
-	//render
-	myProgram.EndProgram();
-**********************************************************/
-
-
-#include "rts_glShaderObject.h"
-#include "rts_glShaderUniform.h"
-#include "rts_glTextureMap.h"
-#include <algorithm>
-
-using namespace std;
-
-class rts_glShaderProgram
-{
-private:
-	void get_uniforms()
-	{
-		GLint num_uniforms;
-		glGetProgramiv(id, GL_ACTIVE_UNIFORMS, &num_uniforms);		//get the number of uniform variables
-		GLint max_name_length;
-		glGetProgramiv(id, GL_ACTIVE_UNIFORM_MAX_LENGTH, &max_name_length);	//get the maximum uniform name length
-		GLchar* name_buffer = new GLchar[max_name_length];			//create a buffer to store the name
-		GLsizei length;						//I'm not using these yet
-		GLint size;
-		GLenum type;						//variable's data type
-		GLint location;						//GPU location of the variable
-		for(int i=0; i<num_uniforms; i++)		//create an rts_glShaderUniform structure for each variable
-		{
-			glGetActiveUniform(id, i, max_name_length, &length, &size, &type, name_buffer);	//get the uniform information
-			location = glGetUniformLocation(id, name_buffer);		//get the GPU location of the variable
-			//create the rts_glShaderUniform structure
-			rts_glShaderUniform current;
-			current.location = location;
-			current.name = name_buffer;
-			current.type = type;
-			current.p_value = NULL;
-
-
-			uniform_list.push_back(current);
-		}
-
-	}
-	int get_index(const char* name)
-	{
-		unsigned int size = uniform_list.size();
-		for(unsigned int i=0; i<size; i++)
-		{
-			if(uniform_list[i].name == name)
-				return i;
-		}
-		return -1;
-	}
-	string log;
-public:
-	GLuint id;
-	bool linked;
-	vector<rts_glShaderObject> shader_list;	//list of opengl shaders
-	vector<rts_glShaderUniform> uniform_list;	//list of active uniform variables
-	vector<rts_glTextureMap> texture_list;		//list of texture maps
-
-	rts_glShaderProgram()
-	{
-		linked = false;
-		id = 0;
-	}
-	void AttachShader(rts_glShaderObject shader)
-	{
-		if(id == 0)
-		{
-			Init();
-		}
-		if(shader.id == 0)	//if the shader is invalid
-		{
-			log = "Shader is invalid";
-			return;
-		}
-
-		//attach the shader to the program
-		glAttachShader(id, shader.id);			//attach the shader to the program in OpenGL
-		CHECK_OPENGL_ERROR
-		shader_list.push_back(shader);			//push the shader onto our list for later access
-	}
-	//type = GL_FRAGMENT_SHADER or GL_VERTEX_SHADER
-	void AttachShader(GLenum type, const char* filename)
-	{
-		rts_glShaderObject shader(type, filename);
-		AttachShader(shader);
-	}
-	void AttachShader(GLenum type, rtsSourceCode source)
-	{
-		rts_glShaderObject shader(type, source);
-		AttachShader(shader);
-	}
-	void PrintLog()
-	{
-		cout<<log;
-
-		if(log.size() != 0) cout<<endl;
-	}
-	void Compile()
-	{
-		if(shader_list.size() == 0)
-		{
-			log = "No shaders to compile";
-			return;
-		}
-
-		vector<rts_glShaderObject>::iterator iter;
-		for(iter = shader_list.begin(); iter != shader_list.end(); iter++)
-		{
-			(*iter).Compile();
-			//(*iter).PrintLog();
-		}
-	}
-	void Link()
-	{
-		glLinkProgram(id);				//link the current shader program
-		GLint link_status;				//test to see if the link went alright
-		glGetProgramiv(id, GL_LINK_STATUS, &link_status);
-		if(link_status != GL_TRUE)
-		{
-			linked = false;
-		}
-		else
-			linked = true;
-
-		GLsizei length;
-		GLchar buffer[1000];
-		glGetProgramInfoLog(id, 1000, &length, buffer);
-		log = buffer;
-
-		get_uniforms();			//create the list of active uniform variables
-	}
-	void BeginProgram()
-	{
-		CHECK_OPENGL_ERROR
-		if(id == 0)				//if the program is invalid, return
-		{
-			log = "Invalid program, cannot use.";
-			return;
-		}
-		if(!linked)
-		{
-			cout<<"Shader Program used without being linked."<<endl;
-			//exit(1);
-		}
-
-		//set up all of the texture maps
-		int num_textures = texture_list.size();
-
-		for(int t=0; t<num_textures; t++)
-		{
-			glActiveTexture(GL_TEXTURE0 + t);
-			CHECK_OPENGL_ERROR
-			//glEnable(texture_list[t].texture_type);
-			//CHECK_OPENGL_ERROR
-			glBindTexture(texture_list[t].texture_type, texture_list[t].name);
-			CHECK_OPENGL_ERROR
-		}
-
-		glUseProgram(id);
-		CHECK_OPENGL_ERROR
-	}
-	void EndProgram()
-	{
-		CHECK_OPENGL_ERROR
-		//return standard functionality
-		int num_textures = texture_list.size();
-
-		//disable all texture units
-		for(int t=0; t<num_textures; t++)
-		{
-			glActiveTexture(GL_TEXTURE0 + t);
-			glDisable(texture_list[t].texture_type);
-			CHECK_OPENGL_ERROR
-		}
-		//make sure that the single default texture unit is active
-		if(num_textures > 0)
-			glActiveTexture(GL_TEXTURE0);
-		CHECK_OPENGL_ERROR
-
-		//return to OpenGL default shading
-		glUseProgram(0);
-		CHECK_OPENGL_ERROR
-	}
-	void PrintUniforms()
-	{
-		cout<<"Shader Uniforms: "<<endl;
-		unsigned int i;
-		for(i=0; i<uniform_list.size(); i++)
-		{
-			cout<<i<<":  "<<uniform_list[i].name<<"          "<<uniform_list[i].location<<endl;
-		}
-	}
-	void AttachGlobalUniform(unsigned int index, void* param)		//attaches a global variable to the indexed uniform parameter
-	{
-		uniform_list[index].p_value = param;
-	}
-	void AttachGlobalUniform(const char* name, void* param)
-	{
-		//find the index of the shader
-		int index = get_index(name);
-		if(index != -1)
-			AttachGlobalUniform(index, param);
-		else
-		{
-			string strError = "Error finding uniform variable: ";
-			strError += name;
-			cout<<strError<<endl;
-		}
-	}
-	void AttachTextureMap(unsigned int index, rts_glTextureMap texture)	//attaches a texture map to the program
-	{
-		//if there is not a texture map assigned to the variable
-		if(uniform_list[index].p_value == NULL)
-		{
-			uniform_list[index].p_value = new unsigned int[1];
-			((unsigned int*)uniform_list[index].p_value)[0] = texture_list.size();		//set the parameter value to the index of the texture
-			texture_list.push_back(texture);						//add the texture to the texture list
-		}
-		//if there is a texture map assigned, replace it
-		else
-		{
-			texture_list[((unsigned int*)(uniform_list[index].p_value))[0]] = texture;
-		}
-
-	}
-	void AttachTextureMap(const char* name, rts_glTextureMap texture)
-	{
-		int index = get_index(name);
-		if(index != -1)		//make sure that the uniform index is valid
-			AttachTextureMap(index, texture);
-		else
-			cout<<"Error finding texture index.  Try linking."<<endl;
-	}
-	void UpdateGlobalUniforms()									//sends updated uniform information to the GPU
-	{
-		CHECK_OPENGL_ERROR
-		BeginProgram();
-		CHECK_OPENGL_ERROR
-		unsigned int num = uniform_list.size();
-		for(unsigned int i=0; i<num; i++)
-			uniform_list[i].submit_to_gpu();
-		EndProgram();
-	}
-	void Init()	//Initialize the shader program
-	{
-		CHECK_OPENGL_ERROR
-		if(id != 0)
-			Clean();
-		id = glCreateProgram();
-		if(id == 0)
-			log = "Error getting program ID from OpenGL";
-		CHECK_OPENGL_ERROR
-	}
-	void Clean()
-	{
-		if(id != 0)
-			glDeleteProgram(id);
-		id = 0;
-
-		//these are allocated outside the object and can just be cleared
-		uniform_list.clear();
-		texture_list.clear();
-
-		//delete each shader from OpenGL
-		int num_shad = shader_list.size();
-		for(int i=0; i<num_shad; i++)
-			shader_list[i].Clean();
-		//clear the list
-		shader_list.clear();
-	}
-};
-
-#endif
diff --git a/legacy/rts_glShaderUniform.h b/legacy/rts_glShaderUniform.h
deleted file mode 100755
index 804da30..0000000
--- a/legacy/rts_glShaderUniform.h
+++ /dev/null
@@ -1,105 +0,0 @@
-#ifndef RTS_GLSHADERUNIFORM_H
-#define RTS_GLSHADERUNIFORM_H
-
-#include "CHECK_OPENGL_ERROR.h"
-#include <GL/glew.h>
-#include <string>
-
-using namespace std;
-
-enum rtsUniformEnum {RTS_FLOAT, RTS_INT, RTS_BOOL, RTS_FLOAT_MATRIX};
-
-///This class stores a single uniform variable for GLSL and is designed to be used by the rts_glShaderProgram class.
-struct rts_glShaderUniform
-{
-public:
-	string name;		//the name of the variable
-	GLint location;		//the location in the program
-	void* p_value;		//pointer to the global data representing the value in main memory
-	GLenum type;		//variable type (float, int, vec2, etc.)
-	//rtsUniformEnum rts_type;	//type of variable in rts format
-	//unsigned int num;		//the number of values required by the variable (1 for float, 2 for vec2, etc.)
-	string log;
-
-	//void convert_type(GLenum gl_type);		//converts the OpenGL data type to something useful for rts
-	void submit_to_gpu()
-	{
-		if(location < 0)
-			return;
-		if(p_value == NULL)
-		{
-			cout<<"Error in uniform address: "<<name<<endl;
-			return;
-		}
-	
-
-		CHECK_OPENGL_ERROR
-		switch(type)
-		{
-		case GL_FLOAT:
-			glUniform1fv(location, 1, (float*)p_value);
-			break;
-		case GL_FLOAT_VEC2:
-			glUniform2fv(location, 1, (float*)p_value);
-			break;
-		case GL_FLOAT_VEC3:
-			glUniform3fv(location, 1, (float*)p_value);
-			break;
-		case GL_FLOAT_VEC4:
-			glUniform4fv(location, 1, (float*)p_value);
-			break;
-		case GL_INT:
-			glUniform1iv(location, 1, (int*)p_value);
-			break;
-		case GL_INT_VEC2:
-			glUniform2iv(location, 1, (int*)p_value);
-			break;
-		case GL_INT_VEC3:
-			glUniform3iv(location, 1, (int*)p_value);
-			break;
-		case GL_INT_VEC4:
-			glUniform4iv(location, 1, (int*)p_value);
-			break;
-		case GL_BOOL:
-			glUniform1iv(location, 1, (int*)p_value);
-			break;
-		case GL_BOOL_VEC2:
-			glUniform2iv(location, 1, (int*)p_value);
-			break;
-		case GL_BOOL_VEC3:
-			glUniform3iv(location, 1, (int*)p_value);
-			break;
-		case GL_BOOL_VEC4:
-			glUniform4iv(location, 1, (int*)p_value);
-			break;
-		case GL_FLOAT_MAT2:
-			glUniformMatrix2fv(location, 1, GL_FALSE, (float*)p_value);
-			break;
-		case GL_FLOAT_MAT3:
-			glUniformMatrix3fv(location, 1, GL_FALSE, (float*)p_value);
-			break;
-		case GL_FLOAT_MAT4:
-			glUniformMatrix4fv(location, 1, GL_FALSE, (float*)p_value);
-			break;
-		case GL_SAMPLER_1D:
-		case GL_SAMPLER_2D:
-		case GL_SAMPLER_3D:
-		case GL_SAMPLER_CUBE:
-		case GL_SAMPLER_1D_SHADOW:
-		case GL_SAMPLER_2D_SHADOW:
-		default:
-			glUniform1iv(location, 1, (int*)p_value);
-			break;
-		}
-		CHECK_OPENGL_ERROR
-	}
-	rts_glShaderUniform()
-	{
-		location = -1;
-		p_value = NULL;
-	}
-};
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glTextureMap.cpp b/legacy/rts_glTextureMap.cpp
deleted file mode 100755
index da5558d..0000000
--- a/legacy/rts_glTextureMap.cpp
+++ /dev/null
@@ -1,233 +0,0 @@
-#include "rts_glTextureMap.h"
-
-#define RTS_UNKNOWN				0
-
-rts_glTextureMap::rts_glTextureMap()
-{
-	name = 0;
-}
-
-void rts_glTextureMap::get_type()
-{
-	if(size.y == 0)
-		texture_type = GL_TEXTURE_1D;
-	else if(size.z == 0)
-		texture_type = GL_TEXTURE_2D;
-	else
-		texture_type = GL_TEXTURE_3D;
-}
-
-void rts_glTextureMap::set_wrapping()
-{
-	CHECK_OPENGL_ERROR
-	switch(texture_type)
-	{
-	case GL_TEXTURE_3D:
-		glTexParameteri(texture_type, GL_TEXTURE_WRAP_R_EXT, GL_REPEAT);
-	case GL_TEXTURE_2D:
-		glTexParameteri(texture_type, GL_TEXTURE_WRAP_T, GL_REPEAT);
-	case GL_TEXTURE_1D:
-		glTexParameteri(texture_type, GL_TEXTURE_WRAP_S, GL_REPEAT);
-		break;
-	case GL_TEXTURE_RECTANGLE_ARB:
-		glTexParameteri(texture_type, GL_TEXTURE_WRAP_T, GL_CLAMP);
-		glTexParameteri(texture_type, GL_TEXTURE_WRAP_S, GL_CLAMP);
-		break;
-
-	default:
-		break;
-	}
-	CHECK_OPENGL_ERROR
-}
-
-void rts_glTextureMap::SetBits(GLvoid* bits)
-{
-	glEnable(texture_type);						//enable the texture map
-	CHECK_OPENGL_ERROR
-	glBindTexture(texture_type, name);
-	CHECK_OPENGL_ERROR
-
-	switch(texture_type)
-	{
-	case GL_TEXTURE_3D:
-		glTexImage3D(texture_type, 0, internal_format, size.x, size.y, size.z, 0, pixel_format, data_type, bits);
-		break;
-	case GL_TEXTURE_2D:
-	case GL_TEXTURE_RECTANGLE_ARB:
-		glTexImage2D(texture_type, 0, internal_format, size.x, size.y, 0, pixel_format, data_type, bits);
-		break;
-	case GL_TEXTURE_1D:
-		glTexImage1D(texture_type, 0, internal_format, size.x, 0, pixel_format, data_type, bits);
-		break;
-	default:
-		//glTexImage2D(texture_type, 0, internal_format, size.x, size.y, 0, pixel_format, data_type, bits);
-		break;
-	}
-	CHECK_OPENGL_ERROR
-}
-
-void* rts_glTextureMap::GetBits(GLenum format, GLenum type)
-{
-	//returns the texture data
-	
-	int components;
-	switch(format)
-	{
-	case GL_RED:
-	case GL_GREEN:
-	case GL_BLUE:
-	case GL_ALPHA:
-	case GL_LUMINANCE:
-		components = 1;
-		break;
-	case GL_LUMINANCE_ALPHA:
-		components = 2;
-		break;
-	case GL_RGB:
-	case GL_BGR:
-		components = 3;
-		break;
-	case GL_RGBA:
-	case GL_BGRA:
-		components = 4;
-		break;
-	}
-
-	int type_size;
-	switch(type)
-	{
-	case GL_UNSIGNED_BYTE:
-	case GL_BYTE:
-		type_size = sizeof(char);
-		break;
-	case GL_UNSIGNED_SHORT:
-	case GL_SHORT:
-		type_size = sizeof(short);
-		break;
-	case GL_UNSIGNED_INT:
-	case GL_INT:
-		type_size = sizeof(int);
-		break;
-	case GL_FLOAT:
-		type_size = sizeof(float);
-		break;
-	}
-
-	//allocate memory for the texture
-	void* result = malloc(components*type_size * size.x * size.y);
-
-	BeginTexture();
-	glGetTexImage(texture_type, 0, format, type, result);
-
-	CHECK_OPENGL_ERROR
-	EndTexture();
-
-
-	return result;
-
-}
-
-void rts_glTextureMap::ResetBits(GLvoid *bits)
-{
-	glEnable(texture_type);						//enable the texture map
-	CHECK_OPENGL_ERROR
-	glBindTexture(texture_type, name);
-	CHECK_OPENGL_ERROR
-
-	switch(texture_type)
-	{
-	case GL_TEXTURE_3D:
-		//glTexImage3D(texture_type, 0, internal_format, size.x, size.y, size.z, 0, pixel_format, data_type, bits);
-		break;
-	case GL_TEXTURE_2D:
-	case GL_TEXTURE_RECTANGLE_ARB:
-		glTexSubImage2D(texture_type, 0, 0, 0, size.x, size.y, pixel_format, data_type, bits);
-		CHECK_OPENGL_ERROR
-		break;
-	case GL_TEXTURE_1D:
-		//glTexImage1D(texture_type, 0, internal_format, size.x, 0, pixel_format, data_type, bits);
-		break;
-	default:
-		//glTexImage2D(texture_type, 0, internal_format, size.x, size.y, 0, pixel_format, data_type, bits);
-		break;
-	}
-	glDisable(texture_type);
-	CHECK_OPENGL_ERROR
-}
-
-void rts_glTextureMap::BeginTexture()
-{
-	glEnable(texture_type);
-	glBindTexture(texture_type, name);
-	CHECK_OPENGL_ERROR
-}
-
-void rts_glTextureMap::EndTexture()
-{
-	glDisable(texture_type);
-	CHECK_OPENGL_ERROR
-}
-
-
-
-void rts_glTextureMap::Init(GLvoid *bits,
-						   GLenum type,
-						   GLsizei width, 
-						   GLsizei height, 
-						   GLsizei depth, 
-						   GLint internalformat, 
-						   GLenum format, 
-						   GLenum datatype,
-						   GLint interpolation)
-{
-	if(name != 0)
-		glDeleteTextures(1, &name);
-	//see if the texture is supported using a proxy
-	CHECK_OPENGL_ERROR
-	//glTexImage2D(GL_PROXY_TEXTURE_2D, 0, internalformat, width, height, 0, format, datatype, NULL);
-	GLint p;
-	CHECK_OPENGL_ERROR
-	//glGetTexLevelParameteriv(GL_PROXY_TEXTURE_2D, 0, GL_TEXTURE_WIDTH, &p);
-	//if(p == 0)
-	//	cout<<"cannot use a texture with these parameters."<<endl;
-	CHECK_OPENGL_ERROR
-	if(datatype == GL_FLOAT)
-	{
-		glPixelStorei(GL_PACK_ALIGNMENT, 4);
-		glPixelStorei(GL_UNPACK_ALIGNMENT, 4);				//I honestly don't know what this does but it fixes problems
-	}
-	else if(datatype == GL_UNSIGNED_BYTE)
-	{
-		glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
-		//glPixelStorei(GL_PACK_ALIGNMENT, 1);
-	}
-	else if(datatype == GL_UNSIGNED_SHORT)
-	{
-		//glPixelStorei(GL_UNPACK_ALIGNMENT, 2);
-		//glPixelStorei(GL_PACK_ALIGNMENT, 2);
-	}
-	CHECK_OPENGL_ERROR
-	glGenTextures(1, &name);							//get the texture name from OpenGL
-	cout<<"OpenGL Name: "<<name<<endl;
-	CHECK_OPENGL_ERROR
-	size = vector3D<GLuint>(width, height, depth);		//assign the texture size
-	//get_type();											//guess the type based on the size
-	texture_type = type;						//set the type of texture
-	glEnable(texture_type);						//enable the texture map
-	CHECK_OPENGL_ERROR
-	glBindTexture(texture_type, name);							//bind the texture for editing
-	CHECK_OPENGL_ERROR
-	set_wrapping();										//set the texture wrapping parameters
-	CHECK_OPENGL_ERROR
-	glTexParameteri(texture_type, GL_TEXTURE_MAG_FILTER, interpolation);		//set filtering
-	CHECK_OPENGL_ERROR
-	glTexParameteri(texture_type, GL_TEXTURE_MIN_FILTER, interpolation);
-	CHECK_OPENGL_ERROR
-	internal_format = internalformat;					//set the number of components per pixel
-	pixel_format = format;								//set the pixel format
-	data_type = datatype;									//set the data type
-	SetBits(bits);										//send the bits to the OpenGL driver
-	glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);	//replace the specified vertex color
-	CHECK_OPENGL_ERROR
-	glDisable(texture_type);
-}
\ No newline at end of file
diff --git a/legacy/rts_glTextureMap.h b/legacy/rts_glTextureMap.h
deleted file mode 100755
index 9ab7736..0000000
--- a/legacy/rts_glTextureMap.h
+++ /dev/null
@@ -1,260 +0,0 @@
-#ifndef RTS_GLTEXTUREMAP_H
-#define RTS_GLTEXTUREMAP_H
-
-#include <GL/glew.h>
-#include "rtsVector3d.h"
-#include "CHECK_OPENGL_ERROR.h"
-#include <stdlib.h>
-
-///This class stores an OpenGL texture map and is used by rts_glShaderProgram.
-class rts_glTextureMap
-{
-private:
-	void get_type()			//guesses the texture type based on the size
-	{
-		if(size.y == 0)
-			texture_type = GL_TEXTURE_1D;
-		else if(size.z == 0)
-			texture_type = GL_TEXTURE_2D;
-		else
-			texture_type = GL_TEXTURE_3D;
-	}
-	void set_wrapping()		//set the texture wrapping based on the dimensions
-	{
-		CHECK_OPENGL_ERROR
-		switch(texture_type)
-		{
-		case GL_TEXTURE_3D:
-			glTexParameteri(texture_type, GL_TEXTURE_WRAP_R_EXT, GL_REPEAT);
-		case GL_TEXTURE_2D:
-			glTexParameteri(texture_type, GL_TEXTURE_WRAP_T, GL_MIRRORED_REPEAT);
-		case GL_TEXTURE_1D:
-			glTexParameteri(texture_type, GL_TEXTURE_WRAP_S, GL_REPEAT);
-			break;
-		case GL_TEXTURE_RECTANGLE_ARB:
-			glTexParameteri(texture_type, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
-			glTexParameteri(texture_type, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
-			break;
-
-		default:
-			break;
-		}
-		CHECK_OPENGL_ERROR
-	}
-	//void set_bits(GLvoid* bits);
-public:
-	vector3D<GLsizei> size;		//vector representing the size of the texture
-	GLuint name;				//texture name assigned by OpenGL
-	GLenum texture_type;				//1D, 2D, 3D
-	GLint internal_format;	//number of components (ex. 4 for RGBA)
-	GLenum pixel_format;		//type of data (RGBA, LUMINANCE)
-	GLenum data_type;			//data type of the bits (float, int, etc.)
-
-	//constructor
-	rts_glTextureMap()
-	{
-		name = 0;
-	}
-
-	void BeginTexture()
-	{
-		glEnable(texture_type);
-		glBindTexture(texture_type, name);
-		CHECK_OPENGL_ERROR
-	}
-	void EndTexture()
-	{
-		glDisable(texture_type);
-		CHECK_OPENGL_ERROR
-	}
-
-	///Creates an OpenGL texture map. This function requires basic information about the texture map as well as a pointer to the bit data describing the texture.
-	void Init(GLvoid *bits,
-			   GLenum type = GL_TEXTURE_2D,
-			   GLsizei width = 256, 
-			   GLsizei height = 256, 
-			   GLsizei depth = 0, 
-			   GLint internalformat = 1, 
-			   GLenum format = GL_LUMINANCE, 
-			   GLenum datatype = GL_UNSIGNED_BYTE,
-			   GLint interpolation = GL_LINEAR)
-	{
-		CHECK_OPENGL_ERROR
-		if(name != 0)
-			glDeleteTextures(1, &name);
-
-
-		CHECK_OPENGL_ERROR
-		if(datatype == GL_FLOAT)
-		{
-			glPixelStorei(GL_PACK_ALIGNMENT, 4);
-			glPixelStorei(GL_UNPACK_ALIGNMENT, 4);				//I honestly don't know what this does but it fixes problems
-		}
-		else if(datatype == GL_UNSIGNED_BYTE)
-		{
-			//glPixelStorei(GL_UNPACK_ALIGNMENT, 1);
-			//glPixelStorei(GL_PACK_ALIGNMENT, 1);
-		}
-		else if(datatype == GL_UNSIGNED_SHORT)
-		{
-			//glPixelStorei(GL_UNPACK_ALIGNMENT, 2);
-			//glPixelStorei(GL_PACK_ALIGNMENT, 2);
-		}
-		CHECK_OPENGL_ERROR
-		glGenTextures(1, &name);							//get the texture name from OpenGL
-		//cout<<"OpenGL Name: "<<name<<endl;
-		CHECK_OPENGL_ERROR
-		size = vector3D<GLuint>(width, height, depth);		//assign the texture size
-		//get_type();											//guess the type based on the size
-		texture_type = type;						//set the type of texture
-		glEnable(texture_type);						//enable the texture map
-		CHECK_OPENGL_ERROR
-		glBindTexture(texture_type, name);							//bind the texture for editing
-		CHECK_OPENGL_ERROR
-		set_wrapping();										//set the texture wrapping parameters
-		CHECK_OPENGL_ERROR
-		glTexParameteri(texture_type, GL_TEXTURE_MAG_FILTER, interpolation);		//set filtering
-		CHECK_OPENGL_ERROR
-		glTexParameteri(texture_type, GL_TEXTURE_MIN_FILTER, interpolation);
-		CHECK_OPENGL_ERROR
-		internal_format = internalformat;					//set the number of components per pixel
-		pixel_format = format;								//set the pixel format
-		data_type = datatype;									//set the data type
-		SetBits(bits);										//send the bits to the OpenGL driver
-		glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);	//replace the specified vertex color
-		CHECK_OPENGL_ERROR
-		glDisable(texture_type);
-
-		glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_EDGE);
-		glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_EDGE);
-		glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_WRAP_R, GL_CLAMP_TO_EDGE);
-	}
-	void Clean()
-	{
-		if(name != 0)
-		{
-			glDeleteTextures(1, &name);
-			CHECK_OPENGL_ERROR
-			name = 0;
-		}
-	}
-	void SetBits(GLvoid *bits)
-	{
-		glEnable(texture_type);						//enable the texture map
-		CHECK_OPENGL_ERROR
-		glBindTexture(texture_type, name);
-		CHECK_OPENGL_ERROR
-
-		switch(texture_type)
-		{
-		case GL_TEXTURE_3D:
-			glTexImage3D(texture_type, 0, internal_format, size.x, size.y, size.z, 0, pixel_format, data_type, bits);
-			CHECK_OPENGL_ERROR
-			break;
-		case GL_TEXTURE_2D:
-		case GL_TEXTURE_RECTANGLE_ARB:
-			glTexImage2D(texture_type, 0, internal_format, size.x, size.y, 0, pixel_format, data_type, bits);
-			CHECK_OPENGL_ERROR
-			break;
-		case GL_TEXTURE_1D:
-			glTexImage1D(texture_type, 0, internal_format, size.x, 0, pixel_format, data_type, bits);
-			CHECK_OPENGL_ERROR
-			break;
-		default:
-			//glTexImage2D(texture_type, 0, internal_format, size.x, size.y, 0, pixel_format, data_type, bits);
-			break;
-		}
-		CHECK_OPENGL_ERROR
-	}
-	void ResetBits(GLvoid *bits)
-	{
-		glEnable(texture_type);						//enable the texture map
-		CHECK_OPENGL_ERROR
-		glBindTexture(texture_type, name);
-		CHECK_OPENGL_ERROR
-
-		switch(texture_type)
-		{
-		case GL_TEXTURE_3D:
-			//glTexImage3D(texture_type, 0, internal_format, size.x, size.y, size.z, 0, pixel_format, data_type, bits);
-			break;
-		case GL_TEXTURE_2D:
-		case GL_TEXTURE_RECTANGLE_ARB:
-			glTexSubImage2D(texture_type, 0, 0, 0, size.x, size.y, pixel_format, data_type, bits);
-			CHECK_OPENGL_ERROR
-			break;
-		case GL_TEXTURE_1D:
-			//glTexImage1D(texture_type, 0, internal_format, size.x, 0, pixel_format, data_type, bits);
-			break;
-		default:
-			//glTexImage2D(texture_type, 0, internal_format, size.x, size.y, 0, pixel_format, data_type, bits);
-			break;
-		}
-		glDisable(texture_type);
-		CHECK_OPENGL_ERROR
-	}
-	void* GetBits(GLenum format, GLenum type)
-	{
-		//returns the texture data
-	
-		int components;
-		switch(format)
-		{
-		case GL_RED:
-		case GL_GREEN:
-		case GL_BLUE:
-		case GL_ALPHA:
-		case GL_LUMINANCE:
-			components = 1;
-			break;
-		case GL_LUMINANCE_ALPHA:
-			components = 2;
-			break;
-		case GL_RGB:
-		case GL_BGR:
-			components = 3;
-			break;
-		case GL_RGBA:
-		case GL_BGRA:
-			components = 4;
-			break;
-		}
-
-		int type_size;
-		switch(type)
-		{
-		case GL_UNSIGNED_BYTE:
-		case GL_BYTE:
-			type_size = sizeof(char);
-			break;
-		case GL_UNSIGNED_SHORT:
-		case GL_SHORT:
-			type_size = sizeof(short);
-			break;
-		case GL_UNSIGNED_INT:
-		case GL_INT:
-			type_size = sizeof(int);
-			break;
-		case GL_FLOAT:
-			type_size = sizeof(float);
-			break;
-		}
-
-		//allocate memory for the texture
-		void* result = malloc(components*type_size * size.x * size.y);
-
-		BeginTexture();
-		glGetTexImage(texture_type, 0, format, type, result);
-
-		CHECK_OPENGL_ERROR
-		EndTexture();
-
-
-		return result;
-
-	}
-};
-
-#define RTS_UNKNOWN				0
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glTrueEyes.h b/legacy/rts_glTrueEyes.h
deleted file mode 100755
index 1a8809e..0000000
--- a/legacy/rts_glTrueEyes.h
+++ /dev/null
@@ -1,304 +0,0 @@
-#include <iostream>
-#include <string>
-
-#include "rtsCamera.h"
-#include "rtsSourceCode.h"
-#include "rts_glShaderProgram.h"
-using namespace std;
-
-#include <gl/glut.h>
-
-class rts_glTrueEyes
-{
-	static int glut_window;
-
-	static rts_glShaderProgram shader;
-	static string source_file;
-	static rtsCamera camera;
-	static int mouse_x;
-	static int mouse_y;
-	static float camera_pos[3];
-	static float volume_size[3];
-	static rts_glTextureMap volume;
-
-	static bool zooming;
-
-	static void DrawCube()
-	{
-		float sx = volume_size[0]/2;
-		float sy = volume_size[1]/2;
-		float sz = volume_size[2]/2;
-		float tx = volume_size[0]/2;
-		float ty = volume_size[1]/2;
-		float tz = volume_size[2]/2;
-
-		glBegin(GL_QUADS);
-			glTexCoord3f(-tx, -ty, -tz);
-			glVertex3f(-sx, -sy, -sz);
-			glTexCoord3f(-tx, ty, -tz);
-			glVertex3f(-sx, sy, -sz);
-			glTexCoord3f(tx, ty, -tz);
-			glVertex3f(sx, sy, -sz);
-			glTexCoord3f(tx, -ty, -tz);
-			glVertex3f(sx, -sy, -sz);
-			
-			glTexCoord3f(-tx, -ty, tz);
-			glVertex3f(-sx, -sy, sz);
-			glTexCoord3f(-tx, ty, tz);
-			glVertex3f(-sx, sy, sz);
-			glTexCoord3f(tx, ty, tz);
-			glVertex3f(sx, sy, sz);
-			glTexCoord3f(tx, -ty, tz);
-			glVertex3f(sx, -sy, sz);
-
-			glTexCoord3f(-tx, -ty, -tz);
-			glVertex3f(-sx, -sy, -sz);
-			glTexCoord3f(-tx, -ty, tz);
-			glVertex3f(-sx, -sy, sz);
-			glTexCoord3f(tx, -ty, tz);
-			glVertex3f(sx, -sy, sz);
-			glTexCoord3f(tx, -ty, -tz);
-			glVertex3f(sx, -sy, -sz);
-
-			glTexCoord3f(-tx, ty, -tz);
-			glVertex3f(-sx, sy, -sz);
-			glTexCoord3f(-tx, ty, tz);
-			glVertex3f(-sx, sy, sz);
-			glTexCoord3f(tx, ty, tz);
-			glVertex3f(sx, sy, sz);
-			glTexCoord3f(tx, ty, -tz);
-			glVertex3f(sx, sy, -sz);
-
-			glTexCoord3f(-tx, -ty, -tz);
-			glVertex3f(-sx, -sy, -sz);
-			glTexCoord3f(-tx, -ty, tz);
-			glVertex3f(-sx, -sy, sz);
-			glTexCoord3f(-tx, ty, tz);
-			glVertex3f(-sx, sy, sz);
-			glTexCoord3f(-tx, ty, -tz);
-			glVertex3f(-sx, sy, -sz);
-
-			glTexCoord3f(tx, -ty, -tz);
-			glVertex3f(sx, -sy, -sz);
-			glTexCoord3f(tx, -ty, tz);
-			glVertex3f(sx, -sy, sz);
-			glTexCoord3f(tx, ty, tz);
-			glVertex3f(sx, sy, sz);
-			glTexCoord3f(tx, ty, -tz);
-			glVertex3f(sx, sy, -sz);
-		glEnd();
-	}
-
-	static void DisplayFunction()
-	{
-
-
-		//set up the viewport and projection
-		glMatrixMode(GL_PROJECTION);
-		glLoadIdentity();
-		glViewport(0, 0, glutGet(GLUT_WINDOW_WIDTH), glutGet(GLUT_WINDOW_HEIGHT));
-		float aspect_ratio = (float)glutGet(GLUT_WINDOW_WIDTH)/(float)glutGet(GLUT_WINDOW_HEIGHT);
-		gluPerspective(camera.getFOV(), aspect_ratio, 0.01, 10);
-
-		//clear the screen
-		glClear(GL_COLOR_BUFFER_BIT);
-		glClear(GL_DEPTH_BUFFER_BIT);	
-		
-
-		//set up the camera
-		glMatrixMode(GL_MODELVIEW);
-		glLoadIdentity();
-		point3D<float> pos = camera.getPosition();
-		vector3D<float> up = camera.getUp();
-		gluLookAt(pos.x, pos.y, pos.z, 0, 0, 0, up.x, up.y, up.z);
-
-		//draw a cube
-		glColor3f(1.0, 0.0, 0.0);
-		shader.UpdateGlobalUniforms();
-		shader.BeginProgram();
-		DrawCube();
-		shader.EndProgram();
-
-		glutSwapBuffers();
-	}
-	static void IdleFunction()
-	{
-		glutPostRedisplay();
-	}
-
-	static void MouseDrag(int x, int y)
-	{
-		int dx = x - mouse_x;
-		int dy = y - mouse_y;
-
-		if(zooming)
-		{
-			camera.Zoom(dy);
-		}
-		else
-		{
-
-			camera.OrbitFocus(-dx*0.01, dy*0.01);
-			point3D<float> pos = camera.getPosition();
-			camera_pos[0] = pos.x;
-			camera_pos[1] = pos.y;
-			camera_pos[2] = pos.z;
-		}
-
-		mouse_x = x;
-		mouse_y = y;
-
-		glutPostRedisplay();
-		
-	}
-
-	static void MouseMove(int x, int y)
-	{
-		mouse_x = x;
-		mouse_y = y;
-
-	}
-	static void KeyPress(unsigned char key, int x, int y)
-	{
-		//reload the shader
-		if(key == 'r' || key == 'R')
-		{
-			UpdateShader();
-
-
-		}
-
-	}
-
-	static void MousePress(int button, int state, int x, int y)
-	{
-		if(state == GLUT_DOWN && button == GLUT_MIDDLE_BUTTON)
-			zooming = true;
-		else
-			zooming = false;
-	}
-	
-	static void UpdateShader()
-	{
-		//load the source code
-		shader.Clean();
-		shader.AttachShader(GL_FRAGMENT_SHADER, source_file.c_str());
-
-		//compile the shader
-		shader.Compile();
-		shader.PrintLog();
-		shader.Link();
-		shader.PrintLog();
-
-		if(!shader.linked)
-		{
-			cout<<"Error linking shader."<<endl;
-			std::puts("Press any key to continue...");
-			std::getchar();
-			UpdateShader();
-		}
-
-
-		shader.PrintUniforms();
-		shader.AttachGlobalUniform("camera", &camera_pos);
-		shader.AttachGlobalUniform("volume_size", &volume_size);
-		shader.AttachTextureMap("volume", volume);
-
-
-	}
-public:
-	void Begin();
-	void SetShader(string filename);
-	void SetVolume(unsigned char* bits, int sx, int sy, int sz, int channels);
-	void SetVolumeSize(float x, float y, float z);
-	void Initialize();
-
-};
-
-//static variables
-rtsCamera rts_glTrueEyes::camera;
-rts_glShaderProgram rts_glTrueEyes::shader;
-int rts_glTrueEyes::glut_window;
-int rts_glTrueEyes::mouse_x;
-int rts_glTrueEyes::mouse_y;
-float rts_glTrueEyes::camera_pos[3];
-float rts_glTrueEyes::volume_size[3];
-string rts_glTrueEyes::source_file;
-rts_glTextureMap rts_glTrueEyes::volume;
-bool rts_glTrueEyes::zooming;
-
-
-void rts_glTrueEyes::Initialize()
-{
-	//initialize OpenGL
-	glutInitDisplayMode(GLUT_RGBA | GLUT_DEPTH | GLUT_DOUBLE);
-
-	//create the GLUT window
-	glut_window = glutCreateWindow("True Eyes");
-
-	//initialize GLEW
-	GLenum err = glewInit();
-	if(err != GLEW_OK)
-		fprintf(stderr, "Error: %s\n", glewGetErrorString(err));
-	if (glewIsSupported("GL_VERSION_2_0"))
-		printf("Ready for OpenGL 2.0\n");
-	else {
-		printf("OpenGL 2.0 not supported\n");
-		//exit(1);
-	}
-
-	//set the function pointers
-	glutDisplayFunc(&rts_glTrueEyes::DisplayFunction);
-	glutIdleFunc(&rts_glTrueEyes::IdleFunction);
-	glutMotionFunc(&rts_glTrueEyes::MouseDrag);
-	glutMouseFunc(&rts_glTrueEyes::MousePress);
-	glutPassiveMotionFunc(&rts_glTrueEyes::MouseMove);
-	glutKeyboardFunc(&rts_glTrueEyes::KeyPress);
-
-	//set rendering parameters
-	glEnable(GL_DEPTH_TEST);
-	glDisable(GL_CULL_FACE);
-
-	//set up the camera
-	camera.setPosition(0, 0, -1.6);
-	camera_pos[0] = 0;
-	camera_pos[1] = 0;
-	camera_pos[2] = -1.6;
-	camera.LookAt(0.0, 0.0, 0.0);
-	camera.setFOV(60);
-
-	zooming = false;
-
-
-}
-void rts_glTrueEyes::Begin()
-{
-	//start rendering
-	glutMainLoop();
-}
-
-void rts_glTrueEyes::SetShader(string filename)
-{
-	source_file = filename;
-	UpdateShader();
-}
-
-void rts_glTrueEyes::SetVolumeSize(float x, float y, float z)
-{
-	float max_edge = max(x, max(y, z));
-	volume_size[0] = x/max_edge;
-	volume_size[1] = y/max_edge;
-	volume_size[2] = z/max_edge;
-}
-
-void rts_glTrueEyes::SetVolume(unsigned char* bits, int sx, int sy, int sz, int channels)
-{
-	if(channels == 1)
-		volume.Init(bits, GL_TEXTURE_3D, sx, sy, sz, 1, GL_LUMINANCE, GL_UNSIGNED_BYTE, GL_NEAREST);
-	else if(channels == 3)
-		volume.Init(bits, GL_TEXTURE_3D, sx, sy, sz, GL_RGB, GL_RGB, GL_UNSIGNED_BYTE, GL_NEAREST);
-	CHECK_OPENGL_ERROR
-
-
-
-}
\ No newline at end of file
diff --git a/legacy/rts_glUtilities.h b/legacy/rts_glUtilities.h
deleted file mode 100755
index e25a412..0000000
--- a/legacy/rts_glUtilities.h
+++ /dev/null
@@ -1,12 +0,0 @@
-#ifndef RTS_GLUTILITIES_H
-#define RTS_GLUTILITIES_H
-
-
-#define CHECK_OPENGL_ERROR \
-{ GLenum error; \
-   while ( (error = glGetError()) != GL_NO_ERROR) { \
-   printf( "OpenGL ERROR: %s\nCHECK POINT: %s (line %d)\n", gluErrorString(error), __FILE__, __LINE__ ); \
-   } \
-} 
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glVolumeViewer.cpp b/legacy/rts_glVolumeViewer.cpp
deleted file mode 100755
index fec298f..0000000
--- a/legacy/rts_glVolumeViewer.cpp
+++ /dev/null
@@ -1,446 +0,0 @@
-#include "rts_glVolumeViewer.h"
-#include "PerformanceData.h"
-
-PerformanceData PD;
-
-
-rts_glVolumeViewer::rts_glVolumeViewer()
-{
-	m_optimize=false;
-	m_min_threshold = 0;
-	m_max_threshold = 255;
-	m_volume_texture = 0;
-	m_p = point3D(0.0, 0.0, 0.0);
-	m_texture_size = vector3D(2,2,1);
-	m_voxel_size = vector3D(1.0, 1.0, 1.0);
-	m_dimensions = vector3D(m_texture_size.x * m_voxel_size.x,
-							m_texture_size.y * m_voxel_size.y,
-							m_texture_size.z * m_voxel_size.z);
-	m_dimensions.normalize();
-	
-
-	//calculate the radii
-	m_inner_radius = 0.5;
-	m_outer_radius = (vector3D(1.0, 1.0, 1.0).length())*0.5;
-
-	//create the plane display list
-	SetNumPlanes(256);
-
-	//visualization parameters
-	m_alpha_scale = 1.0;
-}
-
-
-rts_glVolumeViewer::rts_glVolumeViewer(rtsVolume volume_data, 
-					   point3D position = point3D(0.0, 0.0, 0.0), 
-					   vector3D voxel_size = vector3D(1.0, 1.0, 1.0))
-{
-	m_optimize=false;
-	m_volume_texture = 0;
-	m_p = position;
-	m_min_threshold = 0;
-	m_max_threshold = 255;
-	m_texture_size = vector3D(volume_data.get_dimx(), volume_data.get_dimy(), volume_data.get_dimz());
-	m_voxel_size = vector3D(1.0, 1.0, 1.0);
-	m_dimensions = vector3D(m_texture_size.x * m_voxel_size.x,
-						    m_texture_size.y * m_voxel_size.y,
-							m_texture_size.z * m_voxel_size.z);
-	m_dimensions.normalize();
-
-
-	//store the volume
-	PD.StartTimer(COPY_DATA);
-	m_source = volume_data;
-	PD.EndTimer(COPY_DATA);
-
-	//calculate the radii
-	//m_inner_radius = max(max(m_dimensions.x, m_dimensions.y), m_dimensions.z) * 0.5;
-	//m_outer_radius = (m_dimensions.length())*0.5;
-	m_inner_radius = 0.5;
-	m_outer_radius = vector3D(1.0, 1.0, 1.0).length()*0.5;
-
-	
-
-	SetNumPlanes(256);
-	CHECK_OPENGL_ERROR
-	//enable 3d texture mapping
-	glEnable(GL_TEXTURE_3D);
-	CHECK_OPENGL_ERROR
-
- 
-
-
-	
-	//3D Texture mapping
-	glGenTextures(1, &m_volume_texture);
-	CHECK_OPENGL_ERROR
-	glBindTexture(GL_TEXTURE_3D, m_volume_texture);
-	CHECK_OPENGL_ERROR
-
-	glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_MIN_FILTER, GL_NEAREST);
-	glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_MAG_FILTER, GL_NEAREST);
-	glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_WRAP_S, GL_CLAMP);
-	glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_WRAP_T, GL_CLAMP);
-	glTexParameteri(GL_TEXTURE_3D, GL_TEXTURE_WRAP_R, GL_CLAMP);
-	CHECK_OPENGL_ERROR
-
-	//load the texture data
-	m_load_texture();
-	CHECK_OPENGL_ERROR
-
-	// our texture colors will replace the untextured colors
-	glTexEnvi(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_BLEND);
-    glShadeModel(GL_FLAT);
-	CHECK_OPENGL_ERROR
-
-	glDisable(GL_TEXTURE_3D);
-
-	//visualization parameters
-	m_alpha_scale = 1.0;
-}
-
-//~rts_glVolumeViewer()
-//{
-
-
-//}
-
-
-void rts_glVolumeViewer::RenderBoundingBox()
-{
-
-	
-	//create the transformation for the volume
-	glMatrixMode(GL_MODELVIEW);
-	glPushMatrix();
-	glScalef(m_dimensions.x, m_dimensions.y, m_dimensions.z);
-	glTranslatef(m_p.x, m_p.y, m_p.z);
-	glutWireCube(1.0);
-	glPopMatrix();
-}
-
-void rts_glVolumeViewer::m_draw_plane(point3D p, vector3D n, vector3D up)
-{
-
-	//calculate the u, v vectors representing the plane
-	vector3D v = up.cross(n); v.normalize();
-	vector3D u = n.cross(v);  u.normalize();
-
-	//compute the points that make up the plane
-	point3D p0 = p - v*m_outer_radius - u*m_outer_radius;
-	point3D p1 = p - v*m_outer_radius + u*m_outer_radius;
-	point3D p2 = p + v*m_outer_radius + u*m_outer_radius;
-	point3D p3 = p + v*m_outer_radius - u*m_outer_radius;
-	//compute texture coordinates
-	point3D t0 = point3D(0.5, 0.5, 0.5) + (p0 - m_p);
-	point3D t1 = point3D(0.5, 0.5, 0.5) + (p1 - m_p);
-	point3D t2 = point3D(0.5, 0.5, 0.5) + (p2 - m_p);
-	point3D t3 = point3D(0.5, 0.5, 0.5) + (p3 - m_p);
-
-	//enable texture mapping
-	//glEnable(GL_TEXTURE_3D);
-	glBindTexture(GL_TEXTURE_3D, m_volume_texture);
-
-	//enable blending
-	glDisable(GL_DEPTH_TEST);
-	glEnable(GL_BLEND);
-	glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
-
-	glColor4f(1.0, 1.0, 1.0, 1.0);
-	glBegin(GL_QUADS);
-		glTexCoord3f(t0.x, t0.y, t0.z);
-		glVertex3f(p0.x, p0.y, p0.z);
-		glTexCoord3f(t1.x, t1.y, t1.z);
-		glVertex3f(p1.x, p1.y, p1.z);
-		glTexCoord3f(t2.x, t2.y, t2.z);
-		glVertex3f(p2.x, p2.y, p2.z);
-		glTexCoord3f(t3.x, t3.y, t3.z);
-		glVertex3f(p3.x, p3.y, p3.z);
-	glEnd();
-
-	glDisable(GL_TEXTURE_3D);
-	glDisable(GL_BLEND);
-
-	
-}
-void rts_glVolumeViewer::RenderCameraSlice(point3D eye_point, vector3D camera_up, float slice_number)
-{
-	/*Renders a slice of the volume at the specified value (0 = closest
-	to the camera while 1 = furthest from the camera).  The slice is oriented towards
-	the camera position*/
-
-	/*//get the vector from the volume to the eye point
-	vector3D to_camera = eye_point - m_p;
-	//normalize in order to compute the plane normal
-	to_camera.normalize();
-	
-	//draw the camera-oriented plane
-	m_draw_plane(m_p, to_camera, camera_up);*/
-
-	glMatrixMode(GL_MODELVIEW);
-	glPushMatrix();
-
-	//calculate the new basis functions
-	vector3D to_camera = (eye_point - m_p);  to_camera.normalize();
-	vector3D side = camera_up.cross(to_camera);  side.normalize();
-	camera_up = to_camera.cross(side);  camera_up.normalize();
-	//create the rotation matrix
-	matrix4x4 mat_rotate(side, camera_up, to_camera);
-	float gl_rotate[16];
-	mat_rotate.gl_get_matrix(gl_rotate);
-
-	//perform the geometric transformations
-	glScalef(m_dimensions.x, m_dimensions.y, m_dimensions.z);
-	glTranslatef(m_p.x, m_p.y, m_p.z);
-	glMultMatrixf(gl_rotate);
-	
-
-	//perform the texture transformations
-	glMatrixMode(GL_TEXTURE);
-	glPushMatrix();
-	glLoadIdentity();
-	glScalef(m_source.get_dimx()/m_texture_size.x, 
-			 m_source.get_dimy()/m_texture_size.y, 
-			 m_source.get_dimz()/m_texture_size.z);
-	glTranslatef(0.5, 0.5, 0.5);
-	glMultMatrixf(gl_rotate);
-	
-
-	//enable texture mapping
-	glEnable(GL_TEXTURE_3D);
-	glBindTexture(GL_TEXTURE_3D, m_volume_texture);
-	
-	//enable blending
-	//glDisable(GL_DEPTH_TEST);
-	glEnable(GL_BLEND);
-	glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
-
-	//draw the planes
-	glColor4f(1.0, 1.0, 1.0, 1.0);
-	//PD.StartTimer(RENDER_PLANES);
-	//glCallList(m_dl_planes);
-	glBegin(GL_QUADS);
-		glTexCoord3f(-m_outer_radius, -m_outer_radius, slice_number);
-		glVertex3f(-m_outer_radius, -m_outer_radius, slice_number);
-		glTexCoord3f(-m_outer_radius, m_outer_radius, slice_number);	
-		glVertex3f(-m_outer_radius, m_outer_radius, slice_number);
-		glTexCoord3f(m_outer_radius, m_outer_radius, slice_number);
-		glVertex3f(m_outer_radius, m_outer_radius, slice_number);
-		glTexCoord3f(m_outer_radius, -m_outer_radius, slice_number);
-		glVertex3f(m_outer_radius, -m_outer_radius, slice_number);
-	glEnd();
-	
-	//glFinish();
-	//PD.EndTimer(RENDER_PLANES);
-
-	glMatrixMode(GL_MODELVIEW);
-	glPopMatrix();
-	glMatrixMode(GL_TEXTURE);
-	glPopMatrix();
-
-	glDisable(GL_TEXTURE_3D);
-	glDisable(GL_BLEND);
-
-
-}
-
-void rts_glVolumeViewer::RenderVolume(point3D eye_point, vector3D camera_up)
-{
-	if(m_volume_texture == 0)
-		return;
-
-	glMatrixMode(GL_MODELVIEW);
-	glPushMatrix();
-
-	//calculate the new basis functions
-	vector3D to_camera = (eye_point - m_p);  to_camera.normalize();
-	vector3D side = camera_up.cross(to_camera);  side.normalize();
-	camera_up = to_camera.cross(side);  camera_up.normalize();
-	//create the rotation matrix
-	matrix4x4 mat_rotate(side, camera_up, to_camera);
-	float gl_rotate[16];
-	mat_rotate.gl_get_matrix(gl_rotate);
-
-	//perform the geometric transformations
-	glScalef(m_dimensions.x, m_dimensions.y, m_dimensions.z);
-	glTranslatef(m_p.x, m_p.y, m_p.z);
-	glMultMatrixf(gl_rotate);
-	
-
-	//perform the texture transformations
-	glMatrixMode(GL_TEXTURE);
-	glPushMatrix();
-	glLoadIdentity();
-	glScalef(m_source.get_dimx()/m_texture_size.x, 
-			 m_source.get_dimy()/m_texture_size.y, 
-			 m_source.get_dimz()/m_texture_size.z);
-	glTranslatef(0.5, 0.5, 0.5);
-	glMultMatrixf(gl_rotate);
-	
-
-	//enable texture mapping
-	glEnable(GL_TEXTURE_3D);
-	glBindTexture(GL_TEXTURE_3D, m_volume_texture);
-	
-	//enable blending
-	glDisable(GL_DEPTH_TEST);
-	//glEnable(GL_DEPTH_TEST);
-	glEnable(GL_BLEND);
-	glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA);
-
-	//draw the planes
-	glColor4f(1.0, 1.0, 1.0, m_alpha_scale);
-	PD.StartTimer(RENDER_PLANES);
-	glCallList(m_dl_planes);
-	glFinish();
-	PD.EndTimer(RENDER_PLANES);
-
-	glMatrixMode(GL_MODELVIEW);
-	glPopMatrix();
-	glMatrixMode(GL_TEXTURE);
-	glPopMatrix();
-
-	glDisable(GL_TEXTURE_3D);
-	glDisable(GL_BLEND);
-	glEnable(GL_DEPTH_TEST);
-	
-
-}
-
-void rts_glVolumeViewer::SetNumPlanes(unsigned int planes)
-{
-	//set the number of planes
-	m_num_planes = planes;
-
-	//create the display list
-	m_dl_planes = glGenLists(1);
-	glNewList(m_dl_planes, GL_COMPILE);
-
-	//the display planes run from (-m_outer_radius, m_outer_radius) in each dimension
-	float z_step = 2.0*m_outer_radius/(planes + 1.0);
-	glBegin(GL_QUADS);
-	for(int z=0; z<planes; z++)
-	{
-		glTexCoord3f(-m_outer_radius, -m_outer_radius, -m_outer_radius+z*z_step);
-		glVertex3f(-m_outer_radius, -m_outer_radius, -m_outer_radius+z*z_step);
-		glTexCoord3f(-m_outer_radius, m_outer_radius, -m_outer_radius+z*z_step);
-		glVertex3f(-m_outer_radius, m_outer_radius, -m_outer_radius+z*z_step);
-		glTexCoord3f(m_outer_radius, m_outer_radius, -m_outer_radius+z*z_step);
-		glVertex3f(m_outer_radius, m_outer_radius, -m_outer_radius+z*z_step);
-		glTexCoord3f(m_outer_radius, -m_outer_radius, -m_outer_radius+z*z_step);
-		glVertex3f(m_outer_radius, -m_outer_radius, -m_outer_radius+z*z_step);
-	}
-	glEnd();
-	glEndList();
-}
-
-void rts_glVolumeViewer::SetSize(float x, float y, float z)
-{
-	m_dimensions.x = x;
-	m_dimensions.y = y;
-	m_dimensions.z = z;
-}
-
-void rts_glVolumeViewer::SetVoxelSize(float x, float y, float z)
-{
-	m_voxel_size.x = x;
-	m_voxel_size.y = y;
-	m_voxel_size.z = z;
-	m_dimensions = vector3D(m_voxel_size.x * m_texture_size.x,
-						    m_voxel_size.y * m_texture_size.y,
-							m_voxel_size.z * m_texture_size.z);
-	m_dimensions.normalize();
-}
-
-vector3D rts_glVolumeViewer::GetSize()
-{
-	return m_dimensions;
-}
-
-vector3D rts_glVolumeViewer::GetVoxelSize()
-{
-	return m_voxel_size;
-}
-
-void rts_glVolumeViewer::SetThreshold(unsigned char lower, unsigned char upper)
-{
-	//set the new threshold values
-	m_min_threshold = lower;
-	m_max_threshold = upper;
-
-	//reload the texture map
-	m_load_texture();
-}
-
-void rts_glVolumeViewer::Optimize(bool flag)
-{
-	//TODO Optimization causes a problem with texture sizing
-	/*//if the user changed the setting, reload the texture
-	if(m_optimize != flag)
-	{
-		m_optimize = flag;
-		m_load_texture();
-	}*/
-	cout<<"Optimization has been removed due to bugs"<<endl;
-	
-	
-}
-
-void rts_glVolumeViewer::Invert()
-{
-	//this function inverts the original data set
-	m_source.invert();
-	m_load_texture();
-}
-
-void rts_glVolumeViewer::m_load_texture()
-{
-	//duplicate the source data
-	PD.StartTimer(LOAD_TEXTURE);
-	rtsVolume texture_volume = m_source;
-
-	//place a black border around the volume
-	PD.StartTimer(BLACKEN_BORDERS);
-	texture_volume.blacken_border();
-	PD.EndTimer(BLACKEN_BORDERS);
-
-	if(m_min_threshold > 0)
-		texture_volume.blacken(m_min_threshold);
-	if(m_max_threshold < 255)
-		texture_volume.whiten(m_max_threshold);
-
-	
-
-	//if we are optimizing the texture, make the dimensions a power-of-two
-	if(m_optimize)
-	{
-		PD.StartTimer(RESIZE_DATA);
-		//find the maximum dimension
-		unsigned int max_dimension = max(max(m_source.get_dimx(), m_source.get_dimy()), m_source.get_dimz());
-		
-		unsigned int new_dimension = 2;
-		//calculate the new dimension
-		while(new_dimension < max_dimension)
-			new_dimension *= 2;
-		//resize the texture volume
-		texture_volume.resize_canvas(new_dimension, new_dimension, new_dimension);
-		PD.EndTimer(RESIZE_DATA);
-	}
-
-	//apply the new image to the texture
-	glBindTexture(GL_TEXTURE_3D, m_volume_texture);
-	unsigned int dimx = texture_volume.get_dimx();
-	unsigned int dimy = texture_volume.get_dimy();
-	unsigned int dimz = texture_volume.get_dimz();
-	m_texture_size = vector3D((double)dimx, (double)dimy, (double)dimz);
-	unsigned char* bits = texture_volume.get_bits();
-	glTexImage3D(GL_TEXTURE_3D, 0, GL_ALPHA8, dimx, dimy, dimz, 0, GL_ALPHA, 
-				 GL_UNSIGNED_BYTE, bits);
-
-	PD.EndTimer(LOAD_TEXTURE);
-
-}
-
-
-
-
diff --git a/legacy/rts_glVolumeViewer.h b/legacy/rts_glVolumeViewer.h
deleted file mode 100755
index b40344a..0000000
--- a/legacy/rts_glVolumeViewer.h
+++ /dev/null
@@ -1,67 +0,0 @@
-#ifndef RTS_GLVOLUMEVIEWER_H
-#define RTS_GLVOLUMEVIEWER_H
-
-#include <windows.h>
-#include <gl/glew.h>
-#include <FL/glut.h>
-#include <gl/gl.h>
-//#include <gl/glxext.h>
-#include <gl/glext.h>
-#include <gl/wglext.h>
-//#include <gl/wglext.h>
-#include "rtsMath.h"
-#include "rtsVolume.h"
-#include "rts_glUtilities.h"
-
-class rts_glVolumeViewer
-{
-private:
-
-	rtsVolume m_source;
-	GLuint m_volume_texture;
-	vector3D m_texture_size;			//size of the volume being viewed (in voxels)
-	vector3D m_voxel_size;
-	bool m_optimize;					//optimization flag (use more texture space for faster viz)
-
-	point3D m_p;				//position of the volume (0,0,0) corner in space
-	vector3D m_dimensions;
-
-	double m_alpha_scale;
-	unsigned char m_min_threshold;	//min and max thresholds to be displayed
-	unsigned char m_max_threshold;
-
-	unsigned int m_num_planes;
-
-	GLuint m_dl_planes;			//planes display list
-
-	
-	double m_inner_radius;			//radius of the inscribed sphere
-	double m_outer_radius;		//radius of the circumscribed sphere
-	
-	void m_draw_plane(point3D p, vector3D n, vector3D u);	//draws a camera-oriented plane at point with normal n
-	void m_load_texture();
-
-
-public:
-	rts_glVolumeViewer();
-	//rts_glVolumeViewer(rtsVolume volume_data, point3D position);
-	rts_glVolumeViewer(rtsVolume volume_data, 
-					   point3D position, 
-					   vector3D voxel_size);
-	void SetSize(float x, float y, float z);
-	void SetVoxelSize(float x, float y, float z);
-	vector3D GetSize();
-	vector3D GetVoxelSize();
-	void RenderBoundingBox();
-	void RenderCameraSlice(point3D eye_point, vector3D camera_up, float slice_number = 0.0);
-	void RenderVolume(point3D eye_point, vector3D camera_up);
-	void SetAlphaScale(double scale){m_alpha_scale = scale;}
-	void SetNumPlanes(unsigned int planes);
-	void SetThreshold(unsigned char lower, unsigned char upper);
-	void Optimize(bool flag);
-	void Invert();
-};
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_glutRenderWindow.h b/legacy/rts_glutRenderWindow.h
deleted file mode 100755
index aa97a19..0000000
--- a/legacy/rts_glutRenderWindow.h
+++ /dev/null
@@ -1,155 +0,0 @@
-#include <GL/glew.h>
-#include <GL/glut.h>
-#include "rtsQuaternion.h"
-#include "rtsCamera.h"
-
-float d_angle = 0.05;
-
-rtsCamera rts_glut_camera;
-unsigned int mouse_x;
-unsigned int mouse_y;
-int mouse_button;
-
-
-//user display function pointer
-void (*UserDisplay)(void);
-
-
-
-/*void KeyboardFunction(unsigned char key, int x, int y)
-{
-	if(key == 27)
-		exit(0);
-
-}*/
-
-/*void SpecialKeys(int key, int x, int y)
-{
-	rtsQuaternion<float> new_rotation;
-
-	if(key == GLUT_KEY_UP)
-		rts_glut_camera.OrbitFocus(0, d_angle);
-	if(key == GLUT_KEY_DOWN)
-		rts_glut_camera.OrbitFocus(0, -d_angle);
-	if(key == GLUT_KEY_LEFT)
-		rts_glut_camera.OrbitFocus(d_angle, 0.0);
-	if(key == GLUT_KEY_RIGHT)
-		rts_glut_camera.OrbitFocus(-d_angle, 0.0);
-}*/
-
-void MouseDrag(int x, int y)
-{
-	int dx = x - mouse_x;
-	int dy = y - mouse_y;
-
-	if(mouse_button == GLUT_LEFT_BUTTON)
-		rts_glut_camera.OrbitFocus(-dx*0.01, dy*0.01);
-	else if(mouse_button == GLUT_MIDDLE_BUTTON)
-		rts_glut_camera.Zoom(dy*rts_glut_camera.getFOV()/60.0);
-
-	mouse_x = x;
-	mouse_y = y;
-
-}
-
-void MouseMove(int x, int y)
-{
-	mouse_x = x;
-	mouse_y = y;
-}
-
-void MouseClick(int button, int state, int x, int y)
-{
-	if(state == GLUT_DOWN)
-		mouse_button = button;
-
-
-}
-
-void IdleFunction()
-{
-	glutPostRedisplay();
-}
-
-void RenderCamera()
-{
-	//set viewport
-	glMatrixMode(GL_PROJECTION);
-	glLoadIdentity();
-	glViewport(0, 0, glutGet(GLUT_WINDOW_WIDTH), glutGet(GLUT_WINDOW_HEIGHT));
-
-	//compute the aspect ratio
-	float aspect_ratio = (float)glutGet(GLUT_WINDOW_WIDTH)/(float)glutGet(GLUT_WINDOW_HEIGHT);
-	gluPerspective(rts_glut_camera.getFOV(), aspect_ratio, 0.01, 10.0);
-
-	//render the camera
-	glMatrixMode(GL_MODELVIEW);
-	glLoadIdentity();
-
-	point3D<float> camera_position = rts_glut_camera.getPosition();
-	vector3D<float> camera_up = rts_glut_camera.getUp();
-	gluLookAt(camera_position.x,
-			  camera_position.y,
-			  camera_position.z,
-			  0.0, 0.0, 0.0,
-			  camera_up.x,
-			  camera_up.y,
-			  camera_up.z);
-}
-
-void rts_glutInitialize(const char* WindowName, int width = 1024, int height = 768)
-{
-	char *myargv [1];
-	int myargc=1;
-	myargv [0]=strdup ("AppName");
-	glutInit(&myargc, myargv);
-
-	glutInitDisplayMode(GLUT_DOUBLE | GLUT_RGBA | GLUT_DEPTH);
-	glutInitWindowSize(width, height);
-	glutInitWindowPosition(200,0);
-	glutCreateWindow(WindowName);
-
-	//initialize GLEW
-	GLenum err = glewInit();
-	if(err != GLEW_OK)
-		fprintf(stderr, "Error: %s\n", glewGetErrorString(err));
-	if (!glewIsSupported("GL_VERSION_2_0"))
-	{
-		printf("OpenGL 2.0 not supported\n");
-		//exit(1);
-	}
-	glEnable(GL_DEPTH_TEST);
-
-	glClearColor(1.0, 1.0, 1.0, 0.0);
-
-	rts_glut_camera.setPosition(0.0, 0.0, -1.0);
-	rts_glut_camera.setFOV(60);
-	rts_glut_camera.LookAt(0.0, 0.0, 0.0, 0.0, 1.0, 0.0);
-}
-
-void DisplayFunction()
-{
-	RenderCamera();
-	UserDisplay();
-	glutSwapBuffers();
-}
-
-void rts_glutStart(void (*display_func)(void))
-{
-	//glutSpecialFunc(SpecialKeys);
-	//glutKeyboardFunc(KeyboardFunction);
-	glutDisplayFunc(DisplayFunction);
-	glutMotionFunc(MouseDrag);
-	glutMouseFunc(MouseClick);
-	glutPassiveMotionFunc(MouseMove);
-	UserDisplay = display_func;
-	glutIdleFunc(IdleFunction);
-
-
-
-	//glutReshapeFunc(ReshapeFunction);
-	//glutMouseFunc(MouseFunction);
-	//glutMotionFunc(MotionFunction);
-	glutMainLoop();
-
-}
diff --git a/legacy/rts_itkFunctions.h b/legacy/rts_itkFunctions.h
deleted file mode 100755
index b95669a..0000000
--- a/legacy/rts_itkFunctions.h
+++ /dev/null
@@ -1,168 +0,0 @@
-#include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkRAWImageIO.h"
-#include "itkImageRegionIteratorWithIndex.h"
-
-typedef itk::Image<unsigned char, 3> VOLType;
-
-VOLType::Pointer rts_itkNewVOL(int x, int y, int z)
-{
-	//Create a new image and allocate the desired amount of space
-	//typedef itk::Image<T, 3> ImageType;
-	VOLType::Pointer result = VOLType::New();
-	VOLType::RegionType region;
-	VOLType::SizeType size = {x, y, z};
-	region.SetSize(size);
-	VOLType::IndexType index = {0, 0, 0};
-	region.SetIndex(index);
-	result->SetRegions(region);
-	result->Allocate();
-
-	return result;
-
-}
-
-VOLType::Pointer rts_itkLoadVOL(const char* filename, unsigned int max_slices = 512)
-{
-	//first load the header information
-	ifstream infile(filename, ios::in | ios::binary);	//create the files stream
-	if(!infile)
-		return VOLType::New();
-
-	unsigned int size_x, size_y, size_z;				//create variables to store the size of the data set
-	//load the dimensions of the data set
-	infile.read((char*)&size_x, sizeof(int));			//load the file header
-	infile.read((char*)&size_y, sizeof(int));
-	infile.read((char*)&size_z, sizeof(int));
-
-	//close the file
-	infile.close();
-
-
-	VOLType::Pointer volume;
-
-
-	//create the reader
-	typedef itk::ImageFileReader<VOLType> ReaderType;
-	typedef itk::RawImageIO<unsigned char, 3> RawType;
-
-	ReaderType::Pointer reader = ReaderType::New();
-	RawType::Pointer rawIO = RawType::New();
-
-	
-
-	reader->SetImageIO(rawIO);
-	reader->SetFileName(filename);
-
-	//set the raw IO parameters
-	rawIO->SetFileTypeToBinary();
-	
-
-	//set the format of the RAW file
-	rawIO->SetHeaderSize(12);
-	rawIO->SetDimensions(0, size_x);
-	rawIO->SetDimensions(1, size_y);
-
-	if(size_z < max_slices)
-		rawIO->SetDimensions(2, size_z);
-	else
-		rawIO->SetDimensions(2, max_slices);
-
-	//read the file
-	try
-	{
-		reader->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-	
-	volume = reader->GetOutput();
-
-	return volume;
-}
-VOLType::Pointer rts_itkLoadRAW(const char* filename, unsigned int size_x, unsigned int size_y, unsigned int size_z)
-{
-	//first load the header information
-	ifstream infile(filename, ios::in | ios::binary);	//create the files stream
-	if(!infile)
-		return VOLType::New();
-
-	
-
-	//close the file
-	infile.close();
-
-
-	VOLType::Pointer volume;
-
-
-	//create the reader
-	typedef itk::ImageFileReader<VOLType> ReaderType;
-	typedef itk::RawImageIO<unsigned char, 3> RawType;
-
-	ReaderType::Pointer reader = ReaderType::New();
-	RawType::Pointer rawIO = RawType::New();
-
-	
-
-	reader->SetImageIO(rawIO);
-	reader->SetFileName(filename);
-
-	//set the raw IO parameters
-	rawIO->SetFileTypeToBinary();
-	
-
-	//set the format of the RAW file
-	rawIO->SetHeaderSize(0);
-	rawIO->SetDimensions(0, size_x);
-	rawIO->SetDimensions(1, size_y);
-	rawIO->SetDimensions(2, size_z);
-
-
-	//read the file
-	try
-	{
-		reader->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-	
-	volume = reader->GetOutput();
-
-	return volume;
-}
-void rts_itkSaveVOL(VOLType::Pointer itk_image, const char* filename)
-{
-	typedef itk::ImageRegionIteratorWithIndex<VOLType> IteratorType;
-	IteratorType i(itk_image, itk_image->GetLargestPossibleRegion());
-
-	//create variables for size and position
-	VOLType::IndexType index;
-	VOLType::SizeType size;
-	//get the volume size
-	size = itk_image->GetLargestPossibleRegion().GetSize();
-	unsigned char* buffer = new unsigned char[size[0]*size[1]*size[2]];
-
-	for(i.GoToBegin(); !i.IsAtEnd(); ++i)
-	{
-		index = i.GetIndex();
-		buffer[index[0] + size[0] * (index[1] + index[2] * size[1])] = i.Get();
-	}
-
-
-	ofstream outfile(filename, ios::out | ios::binary);	//create the binary file stream
-
-	//write the volume size to the file
-	outfile.write((char*)&size[0], sizeof(int));
-	outfile.write((char*)&size[1], sizeof(int));
-	outfile.write((char*)&size[2], sizeof(int));
-
-	outfile.write((char*)buffer, sizeof(char)*size[0]*size[1]*size[2]);
-	outfile.close();
-}
\ No newline at end of file
diff --git a/legacy/rts_itkImage.h b/legacy/rts_itkImage.h
deleted file mode 100755
index 7e8747d..0000000
--- a/legacy/rts_itkImage.h
+++ /dev/null
@@ -1,334 +0,0 @@
-#ifndef _RTS_ITK_IMAGE_H
-#define _RTS_ITK_IMAGE_H
-
-#include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
-#include "itkCastImageFilter.h"
-#include "itkRescaleIntensityImageFilter.h"
-#include "rtsDTGrid2D.h"
-
-#include <string>
-
-using namespace std;
-
-
-
-template<typename T>
-class rts_itkImage
-{
-public:
-	typedef itk::Image<T> ITKImageType;
-	typedef typename ITKImageType::Pointer ITKPointerType;
-	ITKPointerType image_source;
-
-public:
-	rts_itkImage();
-	rts_itkImage(int res_x, int res_y);
-	void Allocate(int res_x, int res_y);
-	void LoadImage(string filename);
-	void LoadRAW(int header_size, int res_x, int res_y, string filename);
-	void SaveImage(string filename);
-	void SaveRAW(string filename);
-	void CastAndSaveImage(string filename);
-	void RescaleImage(T min, T max);
-	void InsertDTGrid(rtsDTGrid2D<T>* grid, bool debug = 0);
-	T* GetPointer();
-	rts_itkImage<T> SubImage(int px, int py, int sx, int sy);
-
-	void SetPixel(int x, int y, T value);
-	T GetPixel(int x, int y);
-
-	//element-wise operators
-	rts_itkImage<T> operator+(T rhs);
-
-	int DimX(){return image_source->GetLargestPossibleRegion().GetSize()[0];}
-	int DimY(){return image_source->GetLargestPossibleRegion().GetSize()[1];}
-
-
-};
-
-template <class T>
-rts_itkImage<T> rts_itkImage<T>::operator+(T rhs)
-{
-	rts_itkImage<T> result(DimX(), DimY());
-
-	int x, y;
-	for(x=0; x<DimX(); x++)
-		for(y=0; y<DimY(); y++)
-			result.SetPixel(x, y, GetPixel(x, y) + rhs);
-
-	return result;
-}
-
-template <typename T>
-void rts_itkImage<T>::SetPixel(int x, int y, T value)
-{
-	ITKImageType::IndexType index;
-	index[0] = x;
-	index[1] = y;
-	image_source->SetPixel(index, value);
-}
-
-template <typename T>
-T rts_itkImage<T>::GetPixel(int x, int y)
-{
-	ITKImageType::IndexType index;
-	index[0] = x;
-	index[1] = y;
-	return image_source->GetPixel(index);
-}
-
-template <class T>
-rts_itkImage<T>::rts_itkImage()
-{
-	if(image_source.IsNotNull())
-		image_source = NULL;
-	image_source = ITKImageType::New();
-}
-
-template <class T>
-rts_itkImage<T>::rts_itkImage(int res_x, int res_y)
-{
-	Allocate(res_x, res_y);		
-}
-
-template<typename T>
-void rts_itkImage<T>::Allocate(int res_x, int res_y)
-{
-	if(image_source.IsNotNull())
-	{
-		image_source = NULL;
-	}
-
-	image_source = ITKImageType::New();
-
-	ITKImageType::RegionType region;
-	ITKImageType::SizeType size;
-	size[0] = res_x;
-	size[1] = res_y;
-
-	region.SetSize(size);
-	image_source->SetRegions(region);
-	
-	try
-	{
-		image_source->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-}
-
-
-template <typename T>
-rts_itkImage<T> rts_itkImage<T>::SubImage(int px, int py, int sx, int sy)
-{
-	/*This function returns the sub-volume specified by a corner point and size*/
-
-	//first make sure that the sub-volume is contained within the image
-	if(px < 0) {sx += px; px = 0;}
-	if(py < 0) {sy += py; py = 0;}
-	if(px >= DimX()) px = DimX() - 1;
-	if(py >= DimY()) py = DimY() - 1;
-	if(px + sx > DimX()) sx = DimX() - px - 1;
-	if(py + sy > DimY()) sy = DimY() - py - 1;
-
-	cout<<px<<","<<py<<","<<sx<<","<<sy<<endl;
-
-	//create the resulting volume
-	rts_itkImage<T> destination(sx, sy);
-
-	//get an iterator for the destination volume
-	itk::ImageRegionIterator<ITKImageType> d(destination.image_source, destination.image_source->GetLargestPossibleRegion());
-
-	//get an iterator for the source region
-	ITKImageType::RegionType region;
-	ITKImageType::IndexType index;
-	ITKImageType::SizeType size;
-	index[0] = px; index[1] = py;
-	size[0] = sx; size[1] = sy;
-	region.SetIndex(index);
-	region.SetSize(size);
-	itk::ImageRegionIterator<ITKImageType> s(image_source, region);
-
-	//copy the data from source region to destination volume
-	for(s.GoToBegin(), d.GoToBegin();
-		!s.IsAtEnd();
-		s++, d++)
-		d.Set(s.Get());
-
-	return destination;
-
-}
-
-template<typename T>
-T* rts_itkImage<T>::GetPointer()
-{
-	return image_source->GetBufferPointer();
-}
-
-template<typename T>
-void rts_itkImage<T>::LoadImage(string filename)
-{
-	typedef itk::ImageFileReader<ITKImageType> ReaderType;
-	ReaderType::Pointer reader = ReaderType::New();
-	reader->SetFileName(filename.c_str());
-	image_source = reader->GetOutput();
-
-	try
-	{
-		reader->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-		
-}
-
-template <typename T>
-void rts_itkImage<T>::LoadRAW(int header_size, int size_x,
-							   int size_y, string filename)
-{
-	Allocate(size_x, size_y);
-
-
-	ifstream infile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!infile)
-		return;
-	//first read the header
-	char* header = new char[header_size];
-	infile.read((char*)header, header_size);
-
-	//now read the actual data
-	infile.read((char*)image_source->GetBufferPointer(), DimX()*DimY()*sizeof(T));
-	
-	infile.close();
-}
-
-template<typename T>
-void rts_itkImage<T>::SaveImage(string filename)
-{
-	typedef itk::ImageFileWriter<ITKImageType> WriterType;
-	WriterType::Pointer writer = WriterType::New();
-	writer->SetFileName(filename.c_str());
-	writer->SetInput(image_source);
-
-	try
-	{
-		writer->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-	
-}
-
-template <typename T>
-void rts_itkImage<T>::SaveRAW(string filename)
-{
-	ofstream outfile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!outfile)
-		return;
-
-	outfile.write((char*)image_source->GetBufferPointer(), DimX()*DimY()*sizeof(T));
-	outfile.close();
-}
-
-template<typename T>
-void rts_itkImage<T>::CastAndSaveImage(string filename)
-{
-	//create the destination image
-	typedef itk::Image<unsigned char> DestinationType;
-	DestinationType::Pointer dest_image = DestinationType::New();
-
-	//create the casting filter
-	typedef itk::CastImageFilter<ITKImageType, DestinationType> CastFilterType;
-	CastFilterType::Pointer castFilter = CastFilterType::New();
-	castFilter->SetInput(image_source);
-
-
-	//cast the current image
-	dest_image = castFilter->GetOutput();
-
-	//save the result
-	typedef itk::ImageFileWriter<DestinationType> WriterType;
-	WriterType::Pointer writer = WriterType::New();
-	writer->SetFileName(filename.c_str());
-	writer->SetInput(dest_image);
-
-	try
-	{
-		writer->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}	
-}
-
-template<typename T>
-void rts_itkImage<T>::RescaleImage(T min_v, T max_v)
-{
-	typedef itk::RescaleIntensityImageFilter<ITKImageType, ITKImageType> RescaleFilter;
-	RescaleFilter::Pointer rescaleFilter = RescaleFilter::New();
-	rescaleFilter->SetInput(image_source);
-	rescaleFilter->SetOutputMinimum(min_v);
-	rescaleFilter->SetOutputMaximum(max_v);
-	image_source = rescaleFilter->GetOutput();
-	rescaleFilter->Update();
-}
-
-template<typename T>
-void rts_itkImage<T>::InsertDTGrid(rtsDTGrid2D<T>* grid, bool debug = false)
-{
-	//find the extents of the DT Grid
-	int min_x, min_y, max_x, max_y;
-	grid->getBounds(min_x, min_y, max_x, max_y);
-
-	//allocate the appropriate amount of space
-	ITKImageType::RegionType region;
-	ITKImageType::SizeType size;
-	size[0] = (max_x - min_x) + 1;
-	size[1] = (max_y - min_y) + 1;
-	region.SetSize(size);
-	image_source->SetRegions(region);
-
-	try
-	{
-		image_source->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-	//fill the image with the background color
-	image_source->FillBuffer(grid->background);
-
-	//copy values from the DT Grid to the image
-	ITKImageType::IndexType index;		//create an image index
-	rtsDTGrid2D<T>::iterator i;			//create an iterator
-
-	for(i = grid->begin(); i!= grid->after(); i++)
-	{
-		index[0] = i.X1() - min_x;
-		index[1] = i.X2() - min_y;
-		image_source->SetPixel(index, i.Value());
-
-		//cout<<index[0]<<","<<index[1]<<": "<<i.Value()<<endl;
-		
-	}
-
-
-
-
-}
-
-
-
-#endif
diff --git a/legacy/rts_itkVolume.h b/legacy/rts_itkVolume.h
deleted file mode 100755
index acd4636..0000000
--- a/legacy/rts_itkVolume.h
+++ /dev/null
@@ -1,781 +0,0 @@
-#ifndef RTS_ITKVOLUME_H
-#define RTS_ITKVOLUME_H
-
-#include <WTypes.h>
-#include "itkImage.h"
-#include "itkImageFileReader.h"
-#include "itkImageFileWriter.h"
-#include "itkRawImageIO.h"
-#include "itkImageRegionIterator.h"
-#include <string>
-#include "rtsFilename.h"
-#include "rtsDTGrid3D.h"
-using namespace std;
-
-#include "itkRescaleIntensityImageFilter.h"
-
-#include "rts_itkImage.h"
-
-void rtsProgressBar(int percent);
-
-template <class T> class rts_itkVolume
-{
-public:
-	typedef int uint;
-	typedef itk::Image<T, 3> ITKVolumeType;	
-	typedef typename ITKVolumeType::Pointer PointerType;
-	typedef itk::Image<T, 2> ITKSliceType;
-	
-	//typedef itk::Image<typename T, 3> ITKVolumeType;
-private:
-	//pointer to the data
-	PointerType imageData;
-
-	char* UnicodeToANSI(wchar_t* unicodestr)
-	{
-		int a = wcslen(unicodestr)+1;
-		char *ansistr = new char[a];
-		::WideCharToMultiByte(CP_ACP, 
-								0, 
-								unicodestr, 
-								-1, 
-								ansistr, 
-								a, 
-								NULL, 
-								NULL);
-		return ansistr;
-
-	}
-
-	BSTR ANSIToUnicode(const char* ansistr)
-	{
-		/*On a side note:  This BSTR crap isn't the way to go.
-		Try to use wchar_t (Unicode) where possible.  Already changed it in
-		the above function because it was causing a bug.*/
-
-		int a = strlen(ansistr);
-		BSTR unicodestr = SysAllocStringLen(NULL, a);
-		::MultiByteToWideChar(CP_ACP, 0, ansistr, a, unicodestr, a);
-		return unicodestr;
-	}
-
-public:
-	//construct an implicit function with a size of 1
-	rts_itkVolume();			///<Create an empty implicit function
-	//construct an implicit function of the specified resolution
-	rts_itkVolume(uint res_x, uint res_y, uint res_z);	///<Create an implicit function with the specified resolution
-	void Init(uint res_x, uint res_y, uint res_z);
-	void SetSpacing(float voxel_x, float voxel_y, float voxel_z);
-	void Clear();
-
-	
-	//loading/saving data to disk
-	void LoadRAW(uint header_size, uint data_x, uint data_y, uint data_z, string filename);	///<Loads RAW data from a file with the specified header size and data size.
-	void SaveRAW(string filename);							///<Save the data as RAW data to disk.
-	void LoadVOL(string filename);							///<Load a VOL file from disk.
-	void SaveVOL(string filename);							///<Save a VOL file to disk.
-	void LoadRAV(string filename);							///<Load a VOL file from disk.
-	void SaveRAV(string filename);							///<Save a VOL file to disk.
-	void LoadStack(string directory, string filename_mask, int max_files = -1);
-	void LoadSlice(string filename, int slice);
-
-	void InsertSlice(uint z_position, typename ITKSliceType::Pointer slice);
-
-	
-	//data access methods
-	T operator ()(uint x, uint y, uint z);
-	PointerType GetITKPointer(){return imageData;}
-	T* GetBits(){return imageData->GetBufferPointer();}
-	T GetMin();
-	T GetMax();
-
-	void SetITKPointer(PointerType pointer){imageData = pointer;}
-	uint DimX(){return imageData->GetLargestPossibleRegion().GetSize()[0];}
-	uint DimY(){return imageData->GetLargestPossibleRegion().GetSize()[1];}
-	uint DimZ(){return imageData->GetLargestPossibleRegion().GetSize()[2];}
-
-	float VoxelSizeX(){return imageData->GetSpacing()[0];}
-	float VoxelSizeY(){return imageData->GetSpacing()[1];}
-	float VoxelSizeZ(){return imageData->GetSpacing()[2];}
-	void SetPixel(uint x, uint y, uint z, T value);
-	void SetSlice(rts_itkImage<T> image, int slice);
-	T GetPixel(uint x, uint y, uint z);
-	rts_itkImage<T> GetSlice(int slice);
-	rts_itkVolume<T> SubVolume(uint px, uint py, uint pz, uint sx, uint sy, uint sz);
-
-	//mathematica operations
-	T operator=(T rhs);
-	rts_itkVolume<T> operator-(T rhs);
-	rts_itkVolume<T> operator+(T rhs);
-	rts_itkVolume<T> operator-(rts_itkVolume<T> rhs);
-
-	void Print(ostream &os);
-
-	//simple data processing
-	void Rescale(T new_min, T new_max);
-	void Binary(T threshold, T true_value);		///<Turns the image into a binary image based on a threshold value T.  All values below T are set to 0, all values above are set to true_value.
-
-	void InsertDTGrid(rtsDTGrid3D<T>* grid, bool debug = false);
-};
-
-template <class T>
-rts_itkVolume<T> rts_itkVolume<T>::SubVolume(uint px, uint py, uint pz, uint sx, uint sy, uint sz)
-{
-	/*This function returns the sub-volume specified by a corner point and size*/
-
-	//first make sure that the sub-volume is contained within the image
-	if(px < 0) {sx += px; px = 0;}
-	if(py < 0) {sy += py; py = 0;}
-	if(pz < 0) {sz += pz; pz = 0;}
-	if(px >= DimX()) px = DimX() - 1;
-	if(py >= DimY()) py = DimY() - 1;
-	if(pz >= DimZ()) pz = DimZ() - 1;
-	if(px + sx > DimX()) sx = DimX() - px - 1;
-	if(py + sy > DimY()) sy = DimY() - py - 1;
-	if(pz + sz > DimZ()) sz = DimZ() - pz - 1;
-
-	//cout<<px<<","<<py<<","<<pz<<","<<sx<<","<<sy<<","<<sz<<endl;
-
-	//create the resulting volume
-	rts_itkVolume destination(sx, sy, sz);
-
-	//get an iterator for the destination volume
-	itk::ImageRegionIterator<ITKVolumeType> d(destination.imageData, destination.imageData->GetLargestPossibleRegion());
-
-	//get an iterator for the source region
-	ITKVolumeType::RegionType region;
-	ITKVolumeType::IndexType index;
-	ITKVolumeType::SizeType size;
-	index[0] = px; index[1] = py; index[2] = pz;
-	size[0] = sx; size[1] = sy; size[2] = sz;
-	region.SetIndex(index);
-	region.SetSize(size);
-	itk::ImageRegionIterator<ITKVolumeType> s(imageData, region);
-
-	//copy the data from source region to destination volume
-	for(s.GoToBegin(), d.GoToBegin();
-		!s.IsAtEnd();
-		s++, d++)
-		d.Set(s.Get());
-
-	return destination;
-
-}
-
-template <class T>
-T rts_itkVolume<T>::operator=(T rhs)
-{
-	/*itk::ImageRegionIterator<ITKVolumeType> i(imageData, imageData->GetLargestPossibleRegion());
-	
-	for(i.GoToBegin(); !i.IsAtEnd(); i++)
-		i.Set(rhs);
-*/
-	imageData->FillBuffer(rhs);
-	return rhs;
-}
-template <class T>
-rts_itkVolume<T> rts_itkVolume<T>::operator-(T rhs)
-{
-	rts_itkVolume<T> result(DimX(), DimY(), DimZ());
-
-	itk::ImageRegionIterator<ITKVolumeType> w(result.imageData, result.imageData->GetLargestPossibleRegion());
-	itk::ImageRegionIterator<ITKVolumeType> r(imageData, imageData->GetLargestPossibleRegion());
-
-	for(r.GoToBegin(), w.GoToBegin(); !r.IsAtEnd(); r++, w++)
-		w.Set(r.Get() - rhs);
-
-	return result;
-}
-
-template <class T>
-rts_itkVolume<T> rts_itkVolume<T>::operator+(T rhs)
-{
-	rts_itkVolume<T> result(DimX(), DimY(), DimZ());
-
-	itk::ImageRegionIterator<ITKVolumeType> w(result.imageData, result.imageData->GetLargestPossibleRegion());
-	itk::ImageRegionIterator<ITKVolumeType> r(imageData, imageData->GetLargestPossibleRegion());
-
-	for(r.GoToBegin(), w.GoToBegin(); !r.IsAtEnd(); r++, w++)
-		w.Set(r.Get() + rhs);
-
-	return result;
-}
-
-template <class T>
-rts_itkVolume<T> rts_itkVolume<T>::operator-(rts_itkVolume<T> rhs)
-{
-	rts_itkVolume<T> result(DimX(), DimY(), DimZ());
-
-	itk::ImageRegionIterator<ITKVolumeType> w(result.imageData, result.imageData->GetLargestPossibleRegion());
-	itk::ImageRegionIterator<ITKVolumeType> r(rhs.imageData, rhs.imageData->GetLargestPossibleRegion());
-	itk::ImageRegionIterator<ITKVolumeType> l(imageData, imageData->GetLargestPossibleRegion());
-
-	for(r.GoToBegin(), l.GoToBegin(), w.GoToBegin(); 
-		!r.IsAtEnd(); 
-		r++, l++, w++)
-		w.Set(l.Get() - r.Get());
-
-	return result;
-}
-
-template <class T>
-void rts_itkVolume<T>::Print(ostream &os)
-{
-	ITKVolumeType::SizeType size;
-	size = imageData->GetLargestPossibleRegion().GetSize();
-
-	int x, y, z;
-	for(z=0; z<size[2]; z++)
-	{
-		os<<"z = "<<z<<":"<<endl;
-		for(y=0; y<size[1]; y++)
-		{
-			for(x=0; x<size[0]; x++)
-				os<<GetPixel(x, y, z)<<" ";
-			os<<endl;
-		}
-	}
-}
-
-template <class T>
-rts_itkVolume<T>::rts_itkVolume()
-{
-	imageData = ITKVolumeType::New();
-}
-
-template <class T>
-rts_itkVolume<T>::rts_itkVolume(uint res_x, uint res_y, uint res_z)
-{
-	imageData = ITKVolumeType::New();
-
-	itk::Image<T, 3>::RegionType region;
-	itk::Image<T, 3>::SizeType size;
-	size[0] = res_x;
-	size[1] = res_y;
-	size[2] = res_z;
-
-	region.SetSize(size);
-	imageData->SetRegions(region);
-	
-	try
-	{
-		imageData->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-		
-}
-
-template <class T>
-void rts_itkVolume<T>::Init(uint res_x, uint res_y, uint res_z)
-{
-	itk::Image<T, 3>::RegionType region;
-	itk::Image<T, 3>::SizeType size;
-	size[0] = res_x;
-	size[1] = res_y;
-	size[2] = res_z;
-
-	region.SetSize(size);
-	imageData->SetRegions(region);
-
-	
-	try
-	{
-		imageData->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-}
-
-template <class T>
-void rts_itkVolume<T>::SetSpacing(float voxel_x, float voxel_y, float voxel_z)
-{
-	float spacing[3];
-	spacing[0] = voxel_x; spacing[1]= voxel_y; spacing[2] = voxel_z;
-	imageData->SetSpacing(spacing);
-}
-
-
-template <class T>
-inline T rts_itkVolume<T>::GetPixel(uint x, uint y, uint z)
-{
-	T result;
-	if(x < 0 || x >= DimX() || y < 0 || y >= DimY() || z < 0 || z >= DimZ())
-	{
-		memset(&result, 0, sizeof(T));
-		return result;
-	}
-
-	itk::Image<T, 3>::IndexType index;
-	index[0] = x; index[1] = y; index[2] = z;
-	return imageData->GetPixel(index);
-}
-
-template <class T>
-inline T rts_itkVolume<T>::GetMin()
-{
-	int ix, iy, iz;
-	T currentMin = GetPixel(0, 0, 0);
-	T n;
-	for(ix=0; ix<DimX(); ix++)
-		for(iy=0; iy<DimY(); iy++)
-			for(iz=0; iz<DimZ(); iz++)
-			{
-				n = GetPixel(ix, iy, iz);
-				if(n < currentMin)
-					currentMin = n;
-			}
-	return currentMin;
-}
-
-template <class T>
-inline T rts_itkVolume<T>::GetMax()
-{
-	int ix, iy, iz;
-	T currentMax = GetPixel(0, 0, 0);
-	T n;
-	for(ix=0; ix<DimX(); ix++)
-		for(iy=0; iy<DimY(); iy++)
-			for(iz=0; iz<DimZ(); iz++)
-			{
-				n = GetPixel(ix, iy, iz);
-				if(n > currentMax)
-					currentMax = n;
-			}
-	return currentMax;
-}
-
-template <class T>
-inline T rts_itkVolume<T>::operator ()(uint x, uint y, uint z)
-{
-	return GetPixel(x, y, z);
-}
-
-
-
-template <class T>
-void rts_itkVolume<T>::LoadRAW(uint header_size, uint size_x,
-							   uint size_y, uint size_z, string filename)
-{
-	ITKVolumeType::RegionType region;
-	ITKVolumeType::SizeType size;
-	size[0] = size_x;
-	size[1] = size_y;
-	size[2] = size_z;
-	region.SetSize(size);
-	imageData->SetRegions(region);
-
-	try
-	{
-		imageData->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-	
-	//cout<<imageData<<endl;
-
-	ifstream infile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!infile)
-		return;
-	//first read the header
-	char* header = new char[header_size];
-	infile.read((char*)header, header_size);
-
-	//now read the actual data
-	infile.read((char*)imageData->GetBufferPointer(), DimX()*DimY()*DimZ()*sizeof(T));
-	
-	infile.close();
-}
-
-template <class T>
-void rts_itkVolume<T>::LoadRAV(string filename)
-{
-	
-	//open the file
-	ifstream infile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!infile)
-		return;
-
-	//first read the header
-	int dimx, dimy, dimz, bytesize;
-	infile.read((char*)&dimx, sizeof(int));
-	infile.read((char*)&dimy, sizeof(int));
-	infile.read((char*)&dimz, sizeof(int));
-	infile.read((char*)&bytesize, sizeof(int));
-
-	//allocate space for the image
-	ITKVolumeType::RegionType region;
-	ITKVolumeType::SizeType size;
-	size[0] = dimx;
-	size[1] = dimy;
-	size[2] = dimz;
-	region.SetSize(size);
-	imageData->SetRegions(region);
-	try
-	{
-		imageData->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-	
-
-	//now read the actual data
-	infile.read((char*)imageData->GetBufferPointer(), DimX()*DimY()*DimZ()*sizeof(T));
-	
-	infile.close();	
-}
-
-template <class T>
-void rts_itkVolume<T>::LoadVOL(string filename)
-{
-	
-	//open the file
-	ifstream infile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!infile)
-		return;
-
-	//first read the header
-	int dimx, dimy, dimz, bytesize;
-	infile.read((char*)&dimx, sizeof(int));
-	infile.read((char*)&dimy, sizeof(int));
-	infile.read((char*)&dimz, sizeof(int));
-
-	//allocate space for the image
-	ITKVolumeType::RegionType region;
-	ITKVolumeType::SizeType size;
-	size[0] = dimx;
-	size[1] = dimy;
-	size[2] = dimz;
-	region.SetSize(size);
-	imageData->SetRegions(region);
-	try
-	{
-		imageData->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-	
-
-	//now read the actual data
-	infile.read((char*)imageData->GetBufferPointer(), DimX()*DimY()*DimZ()*sizeof(T));
-	
-	infile.close();	
-}
-
-template <class T>
-void rts_itkVolume<T>::LoadStack(string directory, string filename_mask, int max_files = -1)
-{
-	/*Load a list of file names based on the user-specified mask*/
-	//create the complete mask
-	if(directory[directory.size() - 1] != '/')
-		directory += '/';
-
-	string full_mask = directory;	
-	full_mask += filename_mask;
-	
-	//create a temporary vector to store the file names
-	vector<rtsFilename> fileList;
-	//create a handle for the search
-	HANDLE search_handle;
-	WIN32_FIND_DATA found_data;
-
-	//start the search
-	BSTR unicodestr = ANSIToUnicode(full_mask.c_str());
-	search_handle = FindFirstFile(unicodestr, &found_data);
-	::SysFreeString(unicodestr);
-
-	//if there are no files, return
-	if(search_handle == INVALID_HANDLE_VALUE)
-		return;
-
-	string new_file;
-	char* ansistr = UnicodeToANSI(found_data.cFileName);
-	//char* ansistr = (char*)found_data.cFileName;
-	//save the first filename
-	new_file = directory;
-	new_file += ansistr;
-	fileList.push_back(new_file);
-	delete[] ansistr;
-		
-	//now loop through the rest of the files
-	while(FindNextFile(search_handle, &found_data))
-	{
-		char* ansistr = UnicodeToANSI(found_data.cFileName);
-		new_file = directory;
-		new_file += ansistr;
-		//cout<<new_file<<endl;
-		fileList.push_back(new_file);
-		delete[] ansistr;
-	}
-
-
-
-	/*Load the first file in order to get volume information*/
-	typedef itk::ImageFileReader<ITKSliceType> ReaderType;
-	ReaderType::Pointer reader = ReaderType::New();
-	reader->SetFileName(fileList[0].getString());
-	ITKSliceType::Pointer image = reader->GetOutput();
-	
-	try
-	{
-		reader->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-	/*Insert each image into the volume*/
-	int i;
-	cout<<"Files found: "<<fileList.size()<<endl;
-	if(max_files == -1)
-		max_files = fileList.size();
-	else
-		max_files = min<int>(fileList.size(), max_files);
-	cout<<"Loading: "<<max_files<<endl;
-	//set the max number of files based on user input and number of files found
-
-	/*Set up the volume based on information from the first file*/
-	ITKSliceType::SizeType size = image->GetLargestPossibleRegion().GetSize();	//get the slice size
-	ITKVolumeType::SizeType volSize;	//compute the volume size
-	volSize[0] = size[0];
-	volSize[1] = size[1];
-	volSize[2] = max_files;
-
-	imageData = ITKVolumeType::New();	//create the volume
-	ITKVolumeType::RegionType region;
-	region.SetSize(volSize);
-	imageData->SetRegions(region);
-	imageData->Allocate();				//allocate space
-
-
-
-	for(i=0; i<max_files; i++)
-	{
-		reader = ReaderType::New();
-		reader->SetFileName(fileList[i].getString());
-		ITKSliceType::Pointer slice = reader->GetOutput();
-		reader->Update();
-		InsertSlice(i, slice);
-		//cout<<i+1<<"/"<<fileList.size()<<endl;
-		rtsProgressBar((float)(i+1)/(float)max_files*100);
-	}	
-}
-
-template <class T>
-void rts_itkVolume<T>::LoadSlice(string filename, int slice)
-{
-	//load the specified image
-	typedef itk::ImageFileReader<ITKSliceType> ReaderType;
-	ReaderType::Pointer reader = ReaderType::New();
-	reader->SetFileName(filename.c_str());
-	ITKSliceType::Pointer image = reader->GetOutput();
-	
-	try
-	{
-		reader->Update();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-	//insert the slice into the volume
-	InsertSlice(slice, image);
-
-}
-
-template <class T>
-rts_itkImage<T> rts_itkVolume<T>::GetSlice(int slice)
-{
-	//create a new image
-	rts_itkImage<T> outSlice(DimX(), DimY());
-
-	int x, y;
-	for(x=0; x<DimX(); x++)
-		for(y=0; y<DimY(); y++)
-		{
-			outSlice.SetPixel(x, y, GetPixel(x, y, slice));
-		}
-
-	return outSlice;
-}
-
-template <class T>
-void rts_itkVolume<T>::SetSlice(rts_itkImage<T> image, int slice)
-{
-	int x, y;
-	for(x=0; x<DimX(); x++)
-		for(y=0; y<DimY(); y++)
-		{
-			SetPixel(x, y, slice, image.GetPixel(x, y));
-		}
-}
-
-template <class T>
-void rts_itkVolume<T>::SaveRAV(string filename)
-{
-	ofstream outfile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!outfile)
-		return;
-
-	int dimx = DimX();
-	int dimy = DimY();
-	int dimz = DimZ();
-	int bytesize = sizeof(T);
-
-	outfile.write((char*)&dimx, sizeof(int));
-	outfile.write((char*)&dimy, sizeof(int));
-	outfile.write((char*)&dimz, sizeof(int));
-	outfile.write((char*)&bytesize, sizeof(int));
-
-	outfile.write((char*)imageData->GetBufferPointer(), DimX()*DimY()*DimZ()*sizeof(T));
-	outfile.close();
-	
-}
-
-template <class T>
-void rts_itkVolume<T>::SaveVOL(string filename)
-{
-	ofstream outfile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!outfile)
-		return;
-
-	int dimx = DimX();
-	int dimy = DimY();
-	int dimz = DimZ();
-
-	outfile.write((char*)&dimx, sizeof(int));
-	outfile.write((char*)&dimy, sizeof(int));
-	outfile.write((char*)&dimz, sizeof(int));
-
-	outfile.write((char*)imageData->GetBufferPointer(), DimX()*DimY()*DimZ()*sizeof(T));
-	outfile.close();
-	
-}
-
-template <class T>
-void rts_itkVolume<T>::InsertSlice(uint z_position, typename ITKSliceType::Pointer slice)
-{
-	itk::Image<T>::SizeType size = slice->GetLargestPossibleRegion().GetSize();
-	itk::Image<T>::IndexType index;
-	int x, y;
-	for(x=0; x<size[0]; x++)
-		for(y=0; y<size[1]; y++)
-		{
-			index[0] = x; index[1] = y;
-			SetPixel(x, y, z_position, slice->GetPixel(index));
-		}
-
-
-
-}
-
-template <class T>
-void rts_itkVolume<T>::SaveRAW(string filename)
-{
-	ofstream outfile(filename.c_str(), ios::out | ios::binary);	//create the files stream
-	if(!outfile)
-		return;
-
-	outfile.write((char*)imageData->GetBufferPointer(), DimX()*DimY()*DimZ()*sizeof(T));
-	outfile.close();
-}
-
-template <class T>
-void rts_itkVolume<T>::SetPixel(uint x, uint y, uint z, T value)
-{
-	ITKVolumeType::IndexType index;
-	index[0] = x;
-	index[1] = y;
-	index[2] = z;
-	imageData->SetPixel(index, value);
-}
-
-template <class T>
-void rts_itkVolume<T>::Rescale(T new_min, T new_max)
-{
-	typedef itk::RescaleIntensityImageFilter<ITKVolumeType, ITKVolumeType> RescaleFilterType;
-	RescaleFilterType::Pointer rescaleFilter = RescaleFilterType::New();
-	rescaleFilter->SetOutputMinimum(new_min);
-	rescaleFilter->SetOutputMaximum(new_max);
-	rescaleFilter->SetInput(imageData);
-	rescaleFilter->Update();
-
-	imageData = rescaleFilter->GetOutput();
-}
-
-template <class T>
-void rts_itkVolume<T>::Binary(T threshold, T true_value)
-{
-	/**
-	This function converts an implicit function into a binary or characteristic function describing the solid represented by the level
-	set at isovalue "threshold".  All values below threshold are set to zero while all values above threshold are set to the specified
-	"true_value".  In order to use this function, the data type T must be able to be set to 0.
-	**/
-	int max_index = DimX() * DimY() * DimZ();	//find the size of the data array
-	int i;
-	T* ptrBits = imageData->GetBufferPointer();
-	for(i=0; i<max_index; i++)
-		if(ptrBits[i] >= threshold)
-			ptrBits[i] = true_value;
-		else
-			ptrBits[i] = 0;
-}
-
-
-template<typename T>
-void rts_itkVolume<T>::InsertDTGrid(rtsDTGrid3D<T>* grid, bool debug = false)
-{
-	//find the extents of the DT Grid
-	int min_x, min_y, min_z, max_x, max_y, max_z;
-	grid->getBounds(min_x, min_y, min_z, max_x, max_y, max_z);
-
-	//allocate the appropriate amount of space
-	ITKVolumeType::RegionType region;
-	ITKVolumeType::SizeType size;
-	size[0] = (max_x - min_x) + 1;
-	size[1] = (max_y - min_y) + 1;
-	size[2] = (max_z - min_z) + 1;
-	region.SetSize(size);
-	imageData->SetRegions(region);
-
-	try
-	{
-		imageData->Allocate();
-	}
-	catch(itk::ExceptionObject & exp)
-	{
-		std::cout<<exp<<std::endl;
-	}
-
-	//fill the image with the background color
-	imageData->FillBuffer(grid->background);
-
-	//copy values from the DT Grid to the image
-	ITKVolumeType::IndexType index;		//create an image index
-	rtsDTGrid3D<T>::iterator i;			//create an iterator
-
-	for(i = grid->begin(); i!= grid->after(); i++)
-	{
-		index[0] = i.X1() - min_x;
-		index[1] = i.X2() - min_y;
-		index[2] = i.X3() - min_z;
-		imageData->SetPixel(index, i.Value());
-
-		//cout<<index[0]<<","<<index[1]<<": "<<i.Value()<<endl;
-		
-	}
-}
-#endif
\ No newline at end of file
diff --git a/legacy/rts_old_Camera.cpp b/legacy/rts_old_Camera.cpp
deleted file mode 100755
index 421ae00..0000000
--- a/legacy/rts_old_Camera.cpp
+++ /dev/null
@@ -1,382 +0,0 @@
-#include "rtsCameraController.h"
-#include <math.h>
-rtsCamera::rtsCamera()
-{
-	position = point3D<float>(0, 0, 0);
-	view_vector = vector3D<float>(0, 0, -1);
-	up_vector = vector3D<float>(0, 1, 0);
-	lookat_point = point3D<float>(0, 0, -1);
-
-	pers_view_angle = 60;
-	ortho_width = 1.0;
-	ortho_height = 1.0;
-
-	near_plane = 1;
-	far_plane = 100;
-}
-
-rtsCamera::LookAt(
-
-/*
-rtsCamera::rtsCamera(rtsCameraState initial_state)
-{
-	m_camera_state = initial_state;
-
-	//make sure that the view and lookat vectors are orthogonal
-	vector3D<float> lookat = m_camera_state.lookat - m_camera_state.position;
-	vector3D<float> up = m_camera_state.up;
-	vector3D<float> side = lookat.X(up);
-	up = side.X(lookat);
-	up.Normalize();
-	m_camera_state.up = up;
-}
-
-rtsCameraState rtsCamera::getState()
-{
-	return m_camera_state;
-}
-
-
-
-
-void rtsCamera::setState(rtsCameraState camera_state)
-{
-	m_camera_state = camera_state;
-	
-	//re-orthogonalize the vectors
-	vector3D<float> view = m_camera_state.lookat - m_camera_state.position;
-	vector3D<float> side = view.X(m_camera_state.up);
-	m_camera_state.up = side.X(view);
-	m_camera_state.up.Normalize();
-}
-
-void rtsCamera::LookAt(point3D<float> point)
-{
-	//looks at a point
-
-	//find the new view vector
-	vector3D<float> view = point - m_camera_state.position;
-
-	//normalize the view vector
-	view.Normalize();
-
-	//prepare a new side vector and up vector
-	vector3D<float> side;
-	vector3D<float> up;
-
-	//get the up vector
-	//if the new viewvector is at 0 or 180 degrees to the up vector
-	float cos_angle = view*m_camera_state.up;
-	if(cos_angle == 1.0f || cos_angle == -1.0f)
-	{
-		//re-calculate the up vector
-		up = m_camera_state.up.X(m_camera_state.lookat - m_camera_state.position);
-	}
-	else
-	{
-		//otherwise, just get the current up vector
-		up = m_camera_state.up;
-	}
-	
-
-	//correct the up vector based on the new view vector
-	side = up.X(view);
-	up = view.X(side);
-	up.Normalize();
-
-	//change the camera state
-	m_camera_state.up = up;
-	m_camera_state.lookat = point;
-}
-
-void rtsCamera::Position(point3D<float> p)
-{
-	m_camera_state.position = p;
-}
-
-void rtsCamera::Up(vector3D<float> up)
-{
-	m_camera_state.up = up;
-}
-
-void rtsCamera::DollyPosition(point3D<float> p)
-{
-	vector3D<float> adjustment = p-m_camera_state.position;
-	m_camera_state.position = p;
-	m_camera_state.lookat = m_camera_state.lookat + adjustment;
-}
-
-point3D<float> rtsCamera::getLookAtPoint()
-{
-	return m_camera_state.lookat;
-}
-
-
-
-void rtsCamera::Pan(double x, double y)
-{
-	//first calculate the lookat and side vectors
-	vector3D<float> lookatvector=m_camera_state.lookat - m_camera_state.position;
-	vector3D<float> sidevector = lookatvector.X(m_camera_state.up);
-	sidevector.Normalize();
-
-	m_camera_state.position=m_camera_state.position+sidevector*x;
-	m_camera_state.lookat=m_camera_state.lookat+sidevector*x;
-
-	vector3D<float> upvector = lookatvector.X(sidevector);
-	upvector.Normalize();
-	m_camera_state.position=m_camera_state.position+upvector*y;
-	m_camera_state.lookat=m_camera_state.lookat+upvector*y;
-}
-
-void rtsCamera::RotateUpDown(double degrees)
-{
-	//first calculate the lookat and side vectors
-	vector3D<float> lookatvector=m_camera_state.lookat-m_camera_state.position;
-	vector3D<float> sidevector = lookatvector.X(m_camera_state.up);
-	m_camera_state.up=sidevector.X(lookatvector);
-	m_camera_state.up.Normalize();
-	sidevector.Normalize();
-
-	//translate the look-at point to the origin (and the camera with it)
-	point3D<float> origin = point3D<float>(0.0, 0.0, 0.0);
-	vector3D<float> translateCamera = origin-m_camera_state.lookat;
-
-	point3D<float> translatedCamera=m_camera_state.position+translateCamera;
-
-	//the next step is to rotate the side vector so that it lines up with the z axis
-	double a=sidevector.x;
-	double b=sidevector.y;
-	double c=sidevector.z;
-
-	double d=sqrt(b*b + c*c);
-
-	//error correction for when we are already looking down the z-axis
-	if(d==0)
-		return;
-
-	vector3D<float> XZplane = vector3D<float>(translatedCamera.x, 
-								(translatedCamera.y*c/d - translatedCamera.z*b/d), 
-								(translatedCamera.y*b/d + translatedCamera.z*c/d));
-
-	vector3D<float> Zaxis = vector3D<float>(XZplane.x*d - XZplane.z*a,
-								XZplane.y,
-								XZplane.x*a + XZplane.z*d);
-
-	vector3D<float> rotated = vector3D<float>(Zaxis.x*cos(TORADIANS(degrees)) - Zaxis.y*sin(TORADIANS(degrees)),
-								Zaxis.x*sin(TORADIANS(degrees)) + Zaxis.y*cos(TORADIANS(degrees)),
-								Zaxis.z);
-
-	vector3D<float> XZout = vector3D<float>( rotated.x*(d/(a*a + d*d)) + rotated.z*(a/(a*a + d*d)),
-								rotated.y,
-								rotated.x*(-a/(a*a+d*d)) + rotated.z*(d/(a*a + d*d)));
-
-	vector3D<float> result = vector3D<float>( XZout.x,
-								XZout.y*(c*d/(b*b + c*c)) + XZout.z*(b*d/(b*b + c*c)),
-								XZout.y*(-b*d/(b*b + c*c)) + XZout.z*(c*d/(b*b + c*c)));
-
-	result=result-translateCamera;
-
-	m_camera_state.position.x=result.x;
-	m_camera_state.position.y=result.y;
-	m_camera_state.position.z=result.z;
-
-}
-
-void rtsCamera::Yaw(double degrees)
-{
-	//basically, we have to rotate the look-at point around the up vector
-	//first, translate the look-at point so that the camera is at the origin
-	point3D<float> origin(0.0, 0.0, 0.0);
-	point3D<float> temp_lookat = m_camera_state.lookat - (m_camera_state.position - origin);
-	
-	//create a rotation matrix to rotate the lookat point around the up vector
-	float x=m_camera_state.up.x;
-	float y=m_camera_state.up.y;
-	float z=m_camera_state.up.z;
-	float c=cos(TORADIANS(-degrees));
-	float s=sin(TORADIANS(-degrees));
-	float t=1.0 - cos(TORADIANS(-degrees));
-	float m00 = t*x*x + c;
-	float m01 = t*x*y + s*z;
-	float m02 = t*x*z - s*y;
-	float m03 = 0;
-	float m10 = t*x*y - s*z;
-	float m11 = t*y*y + c;
-	float m12 = t*y*z + s*x;
-	float m13 = 0;
-	float m20 = t*x*z + s*y;
-	float m21 = t*y*z - s*x;
-	float m22 = t*z*z + c;
-	float m23 = 0;
-	float m30 = 0;
-	float m31 = 0;
-	float m32 = 0;
-	float m33 = 1;
-	matrix4x4<float> rotation(m00, m01, m02, m03,
-					   m10, m11, m12, m13,
-					   m20, m21, m22, m23,
-					   m30, m31, m32, m33);
-	point3D<float> result = rotation*temp_lookat + (m_camera_state.position - origin);
-	m_camera_state.lookat = result;
-}
-
-void rtsCamera::Pitch(double degrees)
-{
-	//basically, we have to rotate the look-at point and up vector around the side vector
-	//first, translate the look-at point so that the camera is at the origin
-	point3D<float> origin(0.0, 0.0, 0.0);
-	
-	//find all three necessary vectors
-	vector3D<float> temp_lookat = m_camera_state.lookat - m_camera_state.position;
-	double lookat_length = temp_lookat.Length();
-	vector3D<float> temp_up = m_camera_state.up;
-	vector3D<float> temp_side = temp_lookat.X(temp_up);
-	temp_lookat.Normalize();
-	temp_up.Normalize();
-	temp_side.Normalize();
-
-
-	//create a rotation matrix to rotate around the side vector
-	float x=temp_side.x;
-	float y=temp_side.y;
-	float z=temp_side.z;
-	float c=cos(TORADIANS(degrees));
-	float s=sin(TORADIANS(degrees));
-	float t=1.0 - cos(TORADIANS(degrees));
-	float m00 = t*x*x + c;
-	float m01 = t*x*y + s*z;
-	float m02 = t*x*z - s*y;
-	float m03 = 0;
-	float m10 = t*x*y - s*z;
-	float m11 = t*y*y + c;
-	float m12 = t*y*z + s*x;
-	float m13 = 0;
-	float m20 = t*x*z + s*y;
-	float m21 = t*y*z - s*x;
-	float m22 = t*z*z + c;
-	float m23 = 0;
-	float m30 = 0;
-	float m31 = 0;
-	float m32 = 0;
-	float m33 = 1;
-	matrix4x4<float> rotation(m00, m01, m02, m03,
-					   m10, m11, m12, m13,
-					   m20, m21, m22, m23,
-					   m30, m31, m32, m33);
-	
-	//rotate the up and look-at vectors around the side vector
-	vector3D<float> result_lookat = rotation*temp_lookat;
-	vector3D<float> result_up = rotation*temp_up;
-	result_lookat.Normalize();
-	result_up.Normalize();
-
-	m_camera_state.lookat = m_camera_state.position + result_lookat * lookat_length;
-	m_camera_state.up = result_up;
-}
-	
-
-void rtsCamera::RotateLeftRight(double degrees)
-//this function rotates the camera around the up vector (which always points along hte positive
-//Y world axis).
-{
-	//translate the look-at point to the origin (and the camera with it)
-	point3D<float> origin = point3D<float>(0.0, 0.0, 0.0);
-	vector3D<float> translateCamera = origin-m_camera_state.lookat;
-
-	point3D<float> translatedCamera=m_camera_state.position+translateCamera;
-
-
-	//perform the rotation around the look-at point
-	//using the y-axis as the rotation axis
-	point3D<float> newcamera;
-	newcamera.x=translatedCamera.x*cos(TORADIANS(degrees)) - translatedCamera.z*sin(TORADIANS(degrees));
-	newcamera.z=translatedCamera.x*sin(TORADIANS(degrees)) + translatedCamera.z*cos(TORADIANS(degrees));
-	newcamera.y=translatedCamera.y;
-
-	vector3D<float> newup;
-	newup.x=m_camera_state.up.x*cos(TORADIANS(degrees)) - m_camera_state.up.z*sin(TORADIANS(degrees));
-	newup.z=m_camera_state.up.x*sin(TORADIANS(degrees)) + m_camera_state.up.z*cos(TORADIANS(degrees));
-	newup.y=m_camera_state.up.y;
-
-	//translate the lookat point back to it's original position (along with the camera)
-	newcamera=newcamera-translateCamera;
-
-    m_camera_state.position.x=newcamera.x;
-	m_camera_state.position.y=newcamera.y;
-	m_camera_state.position.z=newcamera.z;
-
-	m_camera_state.up.x=newup.x;
-	m_camera_state.up.y=newup.y;
-	m_camera_state.up.z=newup.z;
-	m_camera_state.up.Normalize();
-
-}
-
-void rtsCamera::Forward(double distance)
-{
-	//calculate the lookat vector (direction of travel)
-	vector3D<float> old_lookat=m_camera_state.lookat-m_camera_state.position;
-	old_lookat.Normalize();
-
-	//calculate the new position of the camera
-	point3D<float> new_position = m_camera_state.position+old_lookat*distance;
-	//now calculate the new lookat vector
-	vector3D<float> new_lookat=m_camera_state.lookat-new_position;
-	//find the length of the new lookat vector
-
-	//move the camera to the new position
-	m_camera_state.position = new_position;
-}
-
-void rtsCamera::ScaleForward(double factor, double min, double max)
-{
-	//This function moves the camera forward, scaling the magnitude
-	//of the motion by the length of the view vector.  Basically, the closer
-	//the camera is to the lookat point, the slower the camera moves.
-
-	//calculate the lookat vector (direction of travel)
-	vector3D<float> lookatvector=m_camera_state.lookat-m_camera_state.position;
-	//find the length of the view vector
-	double length = lookatvector.Length();
-	//normalize
-	lookatvector.Normalize();
-
-	//prevent motion if the bounds would be passed
-	double new_distance = length - (factor*length);
-	if(new_distance < min || new_distance > max)
-		factor = 0;
-	//move the camera
-	m_camera_state.position=m_camera_state.position+lookatvector*factor*length;
-	lookatvector=m_camera_state.lookat-m_camera_state.position;
-	
-}
-
-void rtsCamera::DollyLeftRight(double distance)
-{
-	//calculate the side vector vector (direction of travel)
-	vector3D<float> lookatvector=m_camera_state.lookat-m_camera_state.position;
-	vector3D<float> side = lookatvector.X(m_camera_state.up);
-	side.Normalize();	
-
-	m_camera_state.position=m_camera_state.position+side*distance;
-	m_camera_state.lookat = m_camera_state.lookat + side*distance;
-	//lookatvector=m_camera_state.lookat-m_camera_state.position;
-}
-
-void rtsCamera::DollyUpDown(double distance)
-{
-	//move along the up vector
-	m_camera_state.up.Normalize();	
-
-	m_camera_state.position=m_camera_state.position+m_camera_state.up*distance;
-	m_camera_state.lookat = m_camera_state.lookat + m_camera_state.up*distance;
-	//lookatvector=m_camera_state.lookat-m_camera_state.position;
-}
-
-void rtsCamera::Zoom(double angle)
-{
-	m_camera_state.pers_view_angle += angle;
-}
-
-*/
\ No newline at end of file
diff --git a/legacy/rts_old_Camera.h b/legacy/rts_old_Camera.h
deleted file mode 100755
index 4b542e8..0000000
--- a/legacy/rts_old_Camera.h
+++ /dev/null
@@ -1,77 +0,0 @@
-#include "rtsLinearAlgebra.h"
-
-#ifndef _RTSMATH_H
-#define _RTSMATH_H
-
-#define	CAMERA_UP		-1
-#define CAMERA_DOWN		 1
-#define CAMERA_LEFT		-1
-#define CAMERA_RIGHT	 1
-
-struct rtsCameraState
-{
-	point3D<float> position;
-	point3D<float> lookat;
-	vector3D<float> up;
-	float pers_view_angle;
-	float ortho_width;
-	float ortho_height;
-	float near_plane;
-	float far_plane;
-};
-
-class rtsCamera
-{
-	//members
-	point3D<float> position;
-	vector3D<float> view_vector;
-	vector3D<float> up_vector;
-	point3D<float> lookat_point;
-	float pers_view_angle;
-	float ortho_width;
-	float ortho_height;
-	float near_plane;
-	float far_plane;
-
-public:
-
-
-	//constructors
-	rtsCamera();
-	~rtsCamera(){};
-	
-	//methods
-	void LookAt(point3D<float> pos, point3D<float> lookat, vector3D<float> up);
-	/*
-	void RotateUpDown(double degrees);		
-	void RotateLeftRight(double degrees);	
-	void Pan(double x, double y);
-	void Yaw(double degrees);
-	void Pitch(double degrees);
-	void Forward(double distance);
-	void ScaleForward(double factor, double min = 0, double max = 999999);
-	void DollyLeftRight(double distance);
-	void DollyUpDown(double distance);
-	void Zoom(double angle);
-	void LookAt(point3D<float> point);
-	void Position(point3D<float> point);
-	void Up(vector3D<float> up);
-	void DollyPosition(point3D<float> point);		//moves the camera but keeps the current orientation
-	*/
-
-	//get methods
-	rtsCameraState getState();
-	vector3D<float> getView(){return view_vector;}
-	vector3D<float> getUp(){return up_vector;}
-	point3D<float> getPosition(){return position;}
-	point3D<float> getLookAt(){return lookat_point;}
-	double getViewAngle(){return pers_view_angle;}
-	double getNearPlane(){return near_plane;}
-	double getFarPlane(){return far_plane;}
-	double getOrthoWidth(){return ortho_width;}
-	double getOrthoHeight(){return ortho_height;}
-
-	
-};
-
-#endif
\ No newline at end of file
diff --git a/legacy/rts_vtkFunctions.h b/legacy/rts_vtkFunctions.h
deleted file mode 100755
index 00d0572..0000000
--- a/legacy/rts_vtkFunctions.h
+++ /dev/null
@@ -1,55 +0,0 @@
-#include "vtkImageData.h"
-#include "rtsVolume.h"
-#include "rtsImplicit3D.h"
-
-/*vtkImageData* rtsVolume2vtkImageData(rtsVolume* inputVolume, int data_type)
-{
-	vtkImageData* outputImageData = vtkImageData::New();
-	outputImageData->SetScalarType(data_type);
-	outputImageData->SetDimensions(inputVolume->get_dimx(), inputVolume->get_dimy(), inputVolume->get_dimz());
-	unsigned char* scalar_pointer = (unsigned char*)outputImageData->GetScalarPointer();
-	unsigned char* volume_pointer = inputVolume->get_bits();
-	unsigned int vol_size = inputVolume->get_dimx()*inputVolume->get_dimy()*inputVolume->get_dimz();
-	for(int i=0; i<vol_size; i++)
-	{
-		scalar_pointer[i] = volume_pointer[i];
-	}
-
-	return outputImageData;
-}*/
-
-template <class T>
-vtkImageData* rtsImplicit3D2vtkImageData(rtsImplicit3D<T>* in_function, int data_type)
-{
-	//create the vtkImageData class for storing a uniform grid
-	vtkImageData* outputImageData = vtkImageData::New();
-	//set the data type of the scalar field
-	outputImageData->SetScalarType(data_type);
-	//set the dimensions of the image data based on the function resolution
-	outputImageData->SetDimensions(in_function->DimX(), in_function->DimY(), in_function->DimZ());
-	//get a pointer to the scalar field data and the function data
-	unsigned char* scalar_pointer = (unsigned char*)outputImageData->GetScalarPointer();
-	unsigned char* volume_pointer = (unsigned char*)in_function->GetBits();
-	unsigned int vol_size;
-	switch(data_type)
-	{
-	case VTK_UNSIGNED_CHAR:
-		vol_size = sizeof(char)*in_function->DimX()*in_function->DimY()*in_function->DimZ();
-		break;
-	case VTK_DOUBLE:
-		vol_size = sizeof(double)*in_function->DimX()*in_function->DimY()*in_function->DimZ();
-		break;
-	default:
-		exit(1);
-	}
-
-	memcpy(scalar_pointer, volume_pointer, vol_size);
-	
-	//for(int i=0; i<vol_size; i++)
-	//{
-	//	scalar_pointer[i] = volume_pointer[i];
-	//}
-
-
-	return outputImageData;
-}
\ No newline at end of file
diff --git a/legacy/rts_winFileDialog.cpp b/legacy/rts_winFileDialog.cpp
deleted file mode 100755
index c01f934..0000000
--- a/legacy/rts_winFileDialog.cpp
+++ /dev/null
@@ -1,80 +0,0 @@
-/*Make sure to not use Unicode characters.  Using the Unicode character set does some
-strange stuff unless you change the character pointers to LPWSTR and LPWCHAR
-*/
-
-#include <iostream>
-using namespace std;
-
-
-#pragma comment( lib, "comctl32" )
-
-#include <windows.h>
-#include <commctrl.h>
-#include <commdlg.h>
-#include <rts_winFileDialog.h>
-
-bool rtsOpenFileDialog( char *filename, int filenameSize, const char *filetypes="All Files (*.*)\0*.*;")
-{
-	OPENFILENAME *ofn = (OPENFILENAME*)GlobalAlloc(GMEM_FIXED,sizeof(OPENFILENAME));
-	ZeroMemory(ofn, sizeof(OPENFILENAME));
-	ofn->lStructSize = sizeof(OPENFILENAME);
-	ofn->hwndOwner = NULL;
-	ofn->lpstrFile = filename;
-	cout<<ofn->lpstrFile<<endl;
-	ofn->nMaxFile = filenameSize;
-	ofn->lpstrFilter = filetypes ? filetypes : "All Files (*.*)\0*.*;";
-	ofn->nFilterIndex = 0;
-	ofn->lpstrFileTitle = NULL;
-	ofn->nMaxFileTitle = 0;
-	ofn->lpstrInitialDir = NULL;
-	ofn->Flags = OFN_ENABLESIZING | OFN_PATHMUSTEXIST | OFN_FILEMUSTEXIST
-|OFN_EXPLORER | OFN_HIDEREADONLY;
-
-	//allow multiple files to be loaded if the user says so
-	//if(multi) ofn->Flags = ofn->Flags | OFN_ALLOWMULTISELECT;
-
-	BOOL success = GetOpenFileNameA(ofn);
-	//DWORD myfoo = CommDlgExtendedError();
-	GlobalFree(ofn);
-	return success;
-}
-
-bool rtsSaveFileDialog( char *filename, int filenameSize, const char *filetypes="All Files (*.*)\0*.*;" )
-{
-	OPENFILENAME *ofn = (OPENFILENAME*)GlobalAlloc(GMEM_FIXED,sizeof(OPENFILENAME));
-	ZeroMemory(ofn, sizeof(OPENFILENAME));
-	ofn->lStructSize = sizeof(OPENFILENAME);
-	ofn->hwndOwner = NULL;
-	ofn->lpstrFile = filename;
-	ofn->nMaxFile = filenameSize;
-	ofn->lpstrFilter = filetypes ? filetypes : "All Files (*.*)\0*.*;";
-	ofn->nFilterIndex = 0;
-	ofn->lpstrFileTitle = NULL;
-	ofn->nMaxFileTitle = 0;
-	ofn->lpstrInitialDir = NULL;
-	ofn->Flags = OFN_ENABLESIZING | OFN_PATHMUSTEXIST | OFN_FILEMUSTEXIST
-|OFN_EXPLORER | OFN_HIDEREADONLY;
-	BOOL success = GetSaveFileNameA(ofn);
-	//DWORD myfoo = CommDlgExtendedError();
-	GlobalFree(ofn);
-	return success;
-}
-
-bool rts_winBrowseFolderDialog(char* title, char* foldername)
-{
-	BROWSEINFO* bi = (BROWSEINFO*)GlobalAlloc(GMEM_FIXED,sizeof(BROWSEINFO));
-	ZeroMemory(bi, sizeof(BROWSEINFO));
-	char directory[MAX_PATH] = "";
-
-	bi->pszDisplayName = directory;
-	bi->lpszTitle = title;
-	bi->pidlRoot = NULL;
-	bi->lpfn = NULL;
-	bi->ulFlags = 0;
-	PIDLIST_ABSOLUTE pID = SHBrowseForFolder(bi);
-
-	SHGetPathFromIDList(pID, foldername);
-
-	return true;
-
-}
\ No newline at end of file
diff --git a/legacy/rts_winFileDialog.h b/legacy/rts_winFileDialog.h
deleted file mode 100755
index 0e4f5db..0000000
--- a/legacy/rts_winFileDialog.h
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
-1) Make sure to not use Unicode characters.  Using the Unicode character set does some
-strange stuff involving LPWSTR and LPWCHAR.
-2) Make sure an empty string is passed:
-	char filename[255] = "";
-	rtsOpenFileDialog(filename, 255);
-*/
-
-#pragma comment( lib, "comctl32" )
-
-#include <windows.h>
-#include <commctrl.h>
-#include <commdlg.h>
-#include <Shlobj.h>
-
-bool rtsOpenFileDialog( char *filename, int filenameSize, const char *filetypes);
-bool rtsSaveFileDialog( char *filename, int filenameSize, const char *filetypes);
-bool rts_winBrowseFolderDialog( char* title, char* foldername);
diff --git a/legacy/rts_winFiles.h b/legacy/rts_winFiles.h
deleted file mode 100755
index 9fabeaa..0000000
--- a/legacy/rts_winFiles.h
+++ /dev/null
@@ -1,41 +0,0 @@
-#include "rtsFilename.h"
-
-#include <windows.h>
-#include <vector>
-
-
-vector<rtsFilename> rts_winGetFileList(const char* mask)
-{
-	/*This function returns a list of file names based on the mask passed by
-	the user.  The value returned is the number of rtsFilename elements in the
-	file_list parameter.*/
-	
-	//create a temporary vector to store the file names
-	vector<rtsFilename> result;
-	//create a handle for the search
-	HANDLE search_handle;
-	WIN32_FIND_DATA found_data;
-
-	//start the search
-	search_handle = FindFirstFile((LPCSTR)mask, &found_data);
-
-	//loop through the rest of the data
-	rtsFilename new_file;
-	if(search_handle != INVALID_HANDLE_VALUE)
-	{
-		//save the first filename
-		new_file = found_data.cFileName;
-		result.push_back(new_file);
-		
-		//now loop through the rest of the files
-		while(FindNextFile(search_handle, &found_data))
-		{
-			new_file = found_data.cFileName;
-			result.push_back(new_file);
-		}
-	}
-
-	return result;
-}
-
-
diff --git a/legacy/rtsf_LoadTexture.h b/legacy/rtsf_LoadTexture.h
deleted file mode 100755
index 24bc0fc..0000000
--- a/legacy/rtsf_LoadTexture.h
+++ /dev/null
@@ -1,77 +0,0 @@
-#include "cimg/cimg.h"
-#include "rtsFunction3D.h"
-#include "rtspoint3D.h"
-
-using namespace cimg_library;
-
-typedef point3D<unsigned char> RGB;
-
-rtsFunction3D<RGB> rtsf_LoadTexture(const char* filename)
-{
-
-	CImg<unsigned char> image(filename);
-
-	unsigned int max_x = image.dimx();
-	unsigned int max_y = image.dimy();
-	unsigned int max_z = image.dimz();
-
-	rtsFunction3D<RGB> bits(max_x, max_y, max_z);
-
-	unsigned int x, y, z;
-	for(x = 0; x<max_x; x++)
-		for(y = 0; y<max_y; y++)
-			for(z = 0; z<max_z; z++)
-			{
-				bits.xyz(x, max_y - y, z).x = image(x, y, z, 0);
-				bits.xyz(x, max_y - y, z).y = image(x, y, z, 1);
-				bits.xyz(x, max_y - y, z).z = image(x, y, z, 2);
-			}
-	
-
-	return bits;
-
-}
-
-rtsFunction3D<unsigned char> rtsf_LoadGrayTexture(const char* filename)
-{
-
-	CImg<unsigned char> image(filename);
-
-	//CImgDisplay main_disp(image);
-	//while(true);
-
-	unsigned int dim_x = image.dimx();
-	unsigned int dim_y = image.dimy();
-	unsigned int dim_z = image.dimz();
-
-	rtsFunction3D<unsigned char> bits(dim_x, dim_y, dim_z);
-	
-
-	float r, g, b;
-	float greyscale;
-	float max_length = sqrt(3.0f);
-
-	unsigned int x, y, z;
-	for(x = 0; x<dim_x; x++)
-		for(y = 0; y<dim_y; y++)
-			for(z = 0; z<dim_z; z++)
-			{
-				if(image.dimv() == 3)
-				{
-					r = image(x, y, z, 0)/255.0f;
-					g = image(x, y, z, 1)/255.0f;
-					b = image(x, y, z, 2)/255.0f;
-					greyscale = 0.3*r + 0.59*g + 0.11*b;
-				}
-				else
-					greyscale = image(x, y, z, 0)/255.0f;
-
-
-
-				bits.xyz(x, dim_y - y - 1, z) = greyscale * 255;
-			}
-	
-
-	return bits;
-
-}
\ No newline at end of file
diff --git a/legacy/temp_rtsBoundingVolumes.h b/legacy/temp_rtsBoundingVolumes.h
deleted file mode 100755
index 4ac35fe..0000000
--- a/legacy/temp_rtsBoundingVolumes.h
+++ /dev/null
@@ -1,144 +0,0 @@
-#ifndef RTS_BOUNDING_VOLUMES
-#define RTS_BOUNDING_VOLUMES
-
-#include "rtsLinearAlgebra.h"
-#include <math.h>
-
-template <class T>
-class rtsAABB
-{
-public:
-	point3D<T> minimum;
-	point3D<T> maximum;
-
-	//overloaded operators
-	rtsAABB<T> operator+(rtsAABB<T> param);
-	rtsAABB<unsigned int> getGridAlignedAABB();
-	inline bool isIn(T x, T y, T z);
-};
-
-template <class T>
-class rtsBoundingSphere
-{
-public:
-	point3D<T> center;
-	T radius;
-
-	inline bool isIn(T x, T y, T z);
-};
-
-template <class T>
-class rtsTGC
-{
-public:
-	point3D<T> posA;
-	point3D<T> posB;
-	vector3D<T> normA;
-	vector3D<T> normB;
-	T radA;
-	T radB;
-
-	rtsAABB<T> BoundAABB();
-};
-
-template <class T>
-rtsAABB<T> rtsAABB<T>::operator+(rtsAABB<T> param)
-{
-/*	This function creates an AABB by finding the minimum bound
-	of two other AABBs.
-*/
-
-	rtsAABB<T> result;
-	
-	result.minimum.x = min(minimum.x, param.minimum.x);
-	result.minimum.y = min(minimum.y, param.minimum.y);
-	result.minimum.z = min(minimum.z, param.minimum.z);
-
-	result.maximum.x = max(maximum.x, param.maximum.x);
-	result.maximum.y = max(maximum.y, param.maximum.y);
-	result.maximum.z = max(maximum.z, param.maximum.z);
-	return result;
-}
-
-template <class T>
-inline bool rtsAABB<T>::isIn(T x, T y, T z)
-{
-	if(x >= minimum.x && x <= maximum.x &&
-		y >= minimum.y && y <= maximum.y &&
-		z >= minimum.z && z <= maximum.z)
-		return true;
-	else
-		return false;
-}
-
-template <class T>
-inline bool rtsBoundingSphere<T>::isIn(T x, T y, T z)
-{
-	vector3D<T> to_point = center - point3D<T>(x, y, z);
-	T length_squared = to_point*to_point;
-	if(length_squared < radius*radius)
-		return true;
-	else
-		return false;
-}
-
-template <class T>
-rtsAABB<unsigned int> rtsAABB<T>::getGridAlignedAABB()
-{
-/*	This function returns a version of the current AABB that is snapped
-	to a grid (ie the floor of the position and the ceiling of the size).
-*/
-	rtsAABB<unsigned int> result;
-	result.minimum.x = floor(minimum.x);
-	result.minimum.y = floor(minimum.y);
-	result.minimum.z = floor(minimum.z);
-	result.maximum.x = ceil(maximum.x);
-	result.maximum.y = ceil(maximum.y);
-	result.maximum.z = ceil(maximum.z);
-	return result;
-}
-
-template <class T>
-rtsAABB<T> rtsTGC<T>::BoundAABB()
-{
-/*	This function returns an axis-aligned bounding box
-	that is the minimum bound for the given truncated-generalized cone.
-*/
-	//create a vector representing each axis
-	vector3D<double> x(1.0, 0.0, 0.0);
-	vector3D<double> y(0.0, 1.0, 0.0);
-	vector3D<double> z(0.0, 0.0, 1.0);
-
-	//store the extents
-	point3D<T> a_extents(radA*(1.0 - fabs(normA*x)),
-					  radA*(1.0 - fabs(normA*y)),
-					  radA*(1.0 - fabs(normA*z)));
-	point3D<T> b_extents(radB*(1.0 - fabs(normB*x)),
-					  radB*(1.0 - fabs(normB*y)),
-					  radB*(1.0 - fabs(normB*z)));
-
-	//create the AABB
-	rtsAABB<T> result;
-
-	//calculate the bounding box information
-	//calculate bounding box position as the minima of all extents and positions
-	result.minimum.x = min(posA.x - a_extents.x, posB.x - b_extents.x);
-	result.minimum.y = min(posA.y - a_extents.y, posB.y - b_extents.y);
-	result.minimum.z = min(posA.z - a_extents.z, posB.z - b_extents.z);
-
-	//now find the size of the block
-	result.maximum.x = max(posA.x + a_extents.x, posB.x + b_extents.x);
-	result.maximum.y = max(posA.y + a_extents.y, posB.y + b_extents.y);
-	result.maximum.z = max(posA.z + a_extents.z, posB.z + b_extents.z);
-	
-	return result;
-}
-
-
-
-
-
-
-
-
-#endif
\ No newline at end of file
diff --git a/legacy/temp_rtsSignedDistance.h b/legacy/temp_rtsSignedDistance.h
deleted file mode 100755
index ea17d37..0000000
--- a/legacy/temp_rtsSignedDistance.h
+++ /dev/null
@@ -1,321 +0,0 @@
-#include "rtsImplicit3D.h"
-#include <iostream>
-using namespace std;
-
-#define DIST_MAX			255
-#define DIST_UNSIGNED		0
-#define DIST_SIGNED			1
-
-float ComputeSurfaceDistance(point3D<float> p0, point3D<float> p1, float val0, float val1, float s)
-{
-	/*This function computes the distance from p0 to the surface, given two points p0 and p1
-	on either side of the surface (with values v0 and v1 respectively).  surface specifies
-	the value at the surface.
-	*/
-
-	//compute the normalized position of the surface between p0 and p1
-	float s_norm_pos = (s - val0) / (val1 - val0);
-	//compute the actual position of the surface
-	point3D<float> s_pos = p0 + s_norm_pos * (p1 - p0);
-	//compute the distance from p0 to the surface
-	float result = (s_pos - p0).Length();
-	//cout<<"distance: "<<result<<endl;
-	return result;
-}
-
-void CreateBoundaryConditions(rtsImplicit3D<unsigned char>* function, float threshold,
-							  rtsImplicit3D<float>* &result, rtsImplicit3D<bool>* &mask)
-{
-	/*This function creates an initial signed distance function from a threshold image.
-	All voxels adjacent to the surface specified by the threshold are initialized with a
-	distance value.  Low values are inside, high values are outside.
-	*/
-	//current and neighboring voxel flags (false = inside, true = outside)
-	bool c, x_p, x_n, y_p, y_n, z_p, z_n;
-	float d_xp, d_xn, d_yp, d_yn, d_zp, d_zn;
-	float in_out = 1;
-
-	//boundary condition function and the mask
-	result = new rtsImplicit3D<float>(function->DimX(), function->DimY(), function->DimZ());
-	//get the parameterization
-	point3D<float> min_domain= function->getMinDomain();
-	point3D<float> max_domain = function->getMaxDomain();
-	result->Parameterize(min_domain.x, max_domain.x, min_domain.y, max_domain.y, min_domain.z, max_domain.z);
-	(*result) = DIST_MAX;
-	//create a mask
-	mask = new rtsImplicit3D<bool>(function->DimX(), function->DimY(), function->DimZ());
-	(*mask) = false;
-
-	cout<<"done making boundary condition function"<<endl;
-	//for each voxel
-	vector3D<int> size(function->DimX(), function->DimY(), function->DimZ());	//get the function size
-	int x, y, z;
-	for(x=0; x<size.x; x++)
-		for(y=0; y<size.y; y++)
-			for(z=0; z<size.z; z++)
-			{
-				//reset flags
-				c=x_p=x_n=y_p=y_n=z_p=z_n=true;
-				in_out = 1.0;
-				//look at the current voxel
-				if((*function)(x, y, z) < threshold)
-					c=false;
-				else c=true;
-				//look at each neighboring voxel
-				if(x-1 < 0) x_n = c;	//X
-				else if((*function)(x-1, y, z) < threshold) x_n = false;
-				if(x+1 >= size.x) x_p = c;
-				else if((*function)(x+1, y, z) < threshold) x_p = false;
-				if(y-1 < 0) y_n = c;	//Y
-				else if((*function)(x, y-1, z) < threshold) y_n = false;
-				if(y+1 >= size.y) y_p = c;
-				else if((*function)(x, y+1, z) < threshold) y_p = false;
-				if(z-1 < 0) z_n = c;	//Z
-				else if((*function)(x, y, z-1) < threshold) z_n = false;
-				if(z+1 >= size.z) z_p = c;
-				else if((*function)(x, y, z+1) < threshold) z_p = false;
-
-				//set the distance from the isosurface
-				if(c == false)
-					in_out = -1.0;
-				if(x_n != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-										 ComputeSurfaceDistance((*function).getParameter(x, y, z), 
-													  (*function).getParameter(x-1, y, z),
-													  (*function)(x, y, z),
-													  (*function)(x-1, y, z),
-													  threshold) * in_out);
-				if(x_p != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											ComputeSurfaceDistance((*function).getParameter(x, y, z), 
-													  (*function).getParameter(x+1, y, z),
-													  (*function)(x, y, z),
-													  (*function)(x+1, y, z),
-													  threshold) * in_out);
-				if(y_n != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											ComputeSurfaceDistance((*function).getParameter(x, y, z), 
-													  (*function).getParameter(x, y-1, z),
-													  (*function)(x, y, z),
-													  (*function)(x, y-1, z),
-													  threshold) * in_out);
-				if(y_p != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											ComputeSurfaceDistance((*function).getParameter(x, y, z), 
-													  (*function).getParameter(x, y+1, z),
-													  (*function)(x, y, z),
-													  (*function)(x, y+1, z),
-													  threshold) * in_out);
-				if(z_n != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											ComputeSurfaceDistance((*function).getParameter(x, y, z-1), 
-													  (*function).getParameter(x, y, z),
-													  (*function)(x, y, z),
-													  (*function)(x, y, z-1),
-													  threshold) * in_out);
-				if(z_p != c)
-					(*result)(x, y, z) = min((*result)(x,y,z),
-											ComputeSurfaceDistance((*function).getParameter(x, y, z), 
-													  (*function).getParameter(x, y, z+1),
-													  (*function)(x, y, z),
-													  (*function)(x, y, z+1),
-													  threshold) * in_out);
-
-				//set the mask to 1 if the voxel is on an edge node
-				if(x_n != c || x_p != c || y_n != c || y_p != c || z_n != c || z_p != c)
-					(*mask)(x, y, z) = true;
-			}
-				
-
-	//if a line between the two voxels crosses the surface
-		//find the distance between the voxel center and the surface
-
-
-			cout<<"done computing boundary conditions"<<endl;
-}
-
-double ManhattanDistance(rtsImplicit3D<float>* function,
-						 point3D<indextype> point,
-						 vector3D<float> voxelsize,
-						 int type = DIST_UNSIGNED)
-{
-	/*This function updates the manhattan distance from a surface using the manhattan
-	distance of its neighboring points.
-	*/
-	indextype x, y, z;
-	x=point.x; y=point.y, z=point.z;
-	int sign = 1;
-	float result = DIST_MAX;
-	float near_value;				//the value of the neighbor being considered
-	float possible_value;			
-	if(x!=0)
-	{ 
-		near_value = (*function)(x-1, y, z);
-		if(type == DIST_UNSIGNED)
-			result = min(result, near_value + voxelsize.x);
-		else if(type == DIST_SIGNED)
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + voxelsize.x);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-
-	}
-	if(x!=function->DimX()-1)
-	{
-		near_value = (*function)(x+1, y, z);
-		if(type == DIST_UNSIGNED)
-			result = min(result, near_value + voxelsize.x);
-		else if(type == DIST_SIGNED)
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + voxelsize.x);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(y!=0)
-	{
-		near_value = (*function)(x, y-1, z);
-		if(type == DIST_UNSIGNED)
-			result = min(result, near_value + voxelsize.y);
-		else if(type == DIST_SIGNED)
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + voxelsize.y);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(y!=function->DimY()-1)
-	{
-		near_value = (*function)(x, y+1, z);
-		if(type == DIST_UNSIGNED)
-			result = min(result, near_value + voxelsize.y);
-		else if(type == DIST_SIGNED)
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + voxelsize.y);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(z!=0)
-	{
-		near_value = (*function)(x, y, z-1);
-		if(type == DIST_UNSIGNED)
-			result = min(result, near_value + voxelsize.z);
-		else if(type == DIST_SIGNED)
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + voxelsize.z);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	if(z!=function->DimZ()-1)
-	{
-		near_value = (*function)(x, y, z+1);
-		if(type == DIST_UNSIGNED)
-			result = min(result, near_value + voxelsize.z);
-		else if(type == DIST_SIGNED)
-		{
-			if(near_value<0) sign = -1; else sign = 1;	//determine if the value is inside or outside
-			possible_value = sign*(fabs(near_value) + voxelsize.z);
-			if(fabs(possible_value) < fabs(result))
-				result = possible_value;
-		}
-	}
-	return result;
-
-}
-void Eikonal_Manhattan(rtsImplicit3D<float>* &function, 
-					   rtsImplicit3D<bool>* mask, 
-					   int type = DIST_UNSIGNED)
-{
-	/*This function estimates the Eikonal equation based on the manhattan distance.  The
-	function constantly increases values outwards from the boundary conditions.
-	*/
-
-	//compute the distance between two voxels
-	vector3D<float> voxel_size;
-	voxel_size.x = fabs(function->getParameter(0, 0, 0).x - function->getParameter(1, 0, 0).x);
-	voxel_size.y = fabs(function->getParameter(0, 0, 0).y - function->getParameter(0, 1, 0).y);
-	voxel_size.z = fabs(function->getParameter(0, 0, 0).z - function->getParameter(0, 0, 1).z);
-	
-	//use fast sweeping to compute the manhattan distance
-	//0:X  0:Y  0:Z
-	cout<<"first iteration..."<<endl;
-	int x,y,z;
-	for(x=0; x<function->DimX(); x++)
-		for(y=0; y<function->DimY(); y++)
-			for(z=0; z<function->DimZ(); z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-	cout<<"second iteration..."<<endl;
-	//0:X 0:Y Z:0
-	for(x=0; x<function->DimX(); x++)
-		for(y=0; y<function->DimY(); y++)
-			for(z=function->DimZ()-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-	cout<<"third iteration..."<<endl;
-	//0:X Y:0 0:Z
-	for(x=0; x<function->DimX(); x++)
-		for(y=function->DimY()-1; y>=0; y--)
-			for(z=0; z<function->DimZ(); z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-	cout<<"fourth iteration..."<<endl;
-	//0:X Y:0 Z:0
-	for(x=0; x<function->DimX(); x++)
-		for(y=function->DimY()-1; y>=0; y--)
-			for(z=function->DimZ()-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-	cout<<"fifth iteration..."<<endl;
-	//X:0 0:Y 0:Z
-	for(x=function->DimX()-1; x>=0; x--)
-		for(y=0; y<function->DimY(); y++)
-			for(z=0; z<function->DimZ(); z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-	cout<<"sixth iteration..."<<endl;
-	//X:0 0:Y Z:0
-	for(x=function->DimX()-1; x>=0; x--)
-		for(y=0; y<function->DimY(); y++)
-			for(z=function->DimZ()-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-	cout<<"seventh iteration..."<<endl;
-	//X:0 Y:0 0:Z
-	for(x=function->DimX()-1; x>=0; x--)
-		for(y=function->DimY()-1; y>=0; y--)
-			for(z=0; z<function->DimZ(); z++)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-	cout<<"eighth iteration..."<<endl;
-	//X:0 Y:0 Z:0
-	for(x=function->DimX()-1; x>=0; x--)
-		for(y=function->DimY()-1; y>=0; y--)
-			for(z=function->DimZ()-1; z>=0; z--)
-				//if the current point is not a boundary value
-				if(!(*mask)(x, y, z))
-					(*function)(x,y,z) = ManhattanDistance(function, point3D<indextype>(x, y, z), voxel_size, type);
-	cout<<"done."<<endl;
-}
diff --git a/legacy/temp_rts_glFilamentNetwork.cpp b/legacy/temp_rts_glFilamentNetwork.cpp
deleted file mode 100755
index bb34632..0000000
--- a/legacy/temp_rts_glFilamentNetwork.cpp
+++ /dev/null
@@ -1,403 +0,0 @@
-#include "temp_rts_glFilamentNetwork.h"
-
-void rts_glFilamentNetwork::RenderEdges()
-{
-	//for each edge
-	vector<netEdge*>::iterator i;
-	int a, b;
-	point3D<double> v_a, v_b;
-	glBegin(GL_LINES);						//start rendering lines
-	for(i=m_edge_list.begin(); i!=m_edge_list.end(); i++)
-	{
-		v_a = (*i)->vertex_a->position;			//get the positions of the two vertex edges
-		v_b = (*i)->vertex_b->position;
-		glVertex3f(v_a.x, v_a.y, v_a.z);	//draw the vertices
-		glVertex3f(v_b.x, v_b.y, v_b.z);
-	}
-	glEnd();	//finish drawing
-}
-
-void rts_glFilamentNetwork::RenderBranches()
-{
-	//for each vertex
-	vector<netVertex*>::iterator i;
-	point3D<double> v;
-	glBegin(GL_POINTS);
-	for(i=m_vertex_list.begin(); i!=m_vertex_list.end(); i++)
-	{
-		if((*i)->v_neighbors.size() > 2)
-		{
-			v = (*i)->position;
-			glVertex3f(v.x, v.y, v.z);
-		}
-	}
-	glEnd();
-}
-
-void rts_glFilamentNetwork::RenderFilaments()
-{
-	vector<netFilament*>::iterator i;
-	int num_edges;
-	point3D<double> v_a, v_b;
-	int e;
-	glBegin(GL_LINES);
-	for(i=m_filament_list.begin(); i!=m_filament_list.end(); i++)	//for each filament
-	{
-		num_edges = (*i)->edges.size();
-		for(e=0; e<num_edges; e++)
-		{
-			v_a = (*i)->edges[e]->vertex_a->position;
-			v_b = (*i)->edges[e]->vertex_b->position;
-			glVertex3f(v_a.x, v_a.y, v_a.z);
-			glVertex3f(v_b.x, v_b.y, v_b.z);
-		}
-	}
-	glEnd();
-}
-
-void rts_glFilamentNetwork::RenderSelectedFilaments()
-{
-	vector<unsigned int>::iterator f;
-	int num_edges;
-	point3D<double> v_a, v_b;
-	int e;
-	glBegin(GL_LINES);
-	for(f=m_selected_list.begin(); f!=m_selected_list.end(); f++)
-	{
-		num_edges = m_filament_list[(*f)]->edges.size();
-		for(e=0; e<num_edges; e++)
-		{
-			v_a = m_filament_list[(*f)]->edges[e]->vertex_a->position;
-			v_b = m_filament_list[(*f)]->edges[e]->vertex_b->position;
-			glVertex3f(v_a.x, v_a.y, v_a.z);
-			glVertex3f(v_b.x, v_b.y, v_b.z);
-		}
-	}
-	glEnd();
-}
-
-void rts_glFilamentNetwork::RenderOrientationColor(double x, double y, double z, double r, double g, double b)
-{
-	vector<netFilament*>::iterator i;
-	int num_edges;
-	point3D<double> v_a, v_b;
-
-	//orientation variables
-	vector3D<double> orientation;
-	double cos_a;
-	vector3D<double> A(x, y, z);
-	A.Normalize();
-
-	int e;
-	glBegin(GL_LINES);
-	for(i=m_filament_list.begin(); i!=m_filament_list.end(); i++)	//for each filament
-	{
-		//set the color of the filament based on orientation
-		v_a = (*i)->vertex_a->position;
-		v_b = (*i)->vertex_b->position;
-		
-
-		num_edges = (*i)->edges.size();
-		for(e=0; e<num_edges; e++)
-		{
-			v_a = (*i)->edges[e]->vertex_a->position;
-			v_b = (*i)->edges[e]->vertex_b->position;
-
-			//determine color
-			orientation = (v_a - v_b).Normalize();
-			cos_a = fabs(orientation*A);
-			glColor3f(r*cos_a, g*cos_a, b*cos_a);
-
-			glVertex3f(v_a.x, v_a.y, v_a.z);
-			glVertex3f(v_b.x, v_b.y, v_b.z);
-		}
-	}
-	glEnd();
-}
-
-void rts_glFilamentNetwork::RenderEdgeDistanceColor(float r, float g, float b, float cutoff)
-{
-	vector<netEdge*>::iterator e;
-	glBegin(GL_LINES);
-	point3D<double> p;
-	double d;
-	double exp = 3;
-	for(e=m_edge_list.begin(); e!=m_edge_list.end(); e++)
-	{
-		d = (*e)->distance;
-		if(d<cutoff)
-		{
-			if(d<0.0) d=0.0;
-			if(d>1.0) d=1.0;
-
-			glColor3f(pow((1.0-d),exp)*r, pow((1.0-d),exp)*g, pow((1.0-d),exp)*b);
-			p = (*e)->vertex_a->position;
-			glVertex3f(p.x, p.y, p.z);
-			p = (*e)->vertex_b->position;
-			glVertex3f(p.x, p.y, p.z);
-		}
-	}
-	glEnd();
-}
-
-void rts_glFilamentNetwork::RenderFilamentDistanceColor(float r, float g, float b, float cutoff)
-{
-	vector<netFilament*>::iterator f;
-	unsigned int e;
-	unsigned int num_edges;
-	double d;
-	point3D<double> v;
-	double exp = 3.0;
-	for(f = m_filament_list.begin(); f!=m_filament_list.end(); f++)
-	{
-		d = (*f)->distance;
-		if(d<cutoff)
-		{
-			if(d>1.0) d=1.0;
-			if(d<0.0) d=0.0;
-			//cout<<"d: "<<d<<endl;
-			num_edges = (*f)->edges.size();
-			glColor3f(pow((1.0-d), exp)*r, pow((1.0-d), exp)*g, pow((1.0-d), exp)*b);
-			glBegin(GL_LINES);
-			for(e=0; e<num_edges; e++)
-			{
-				v = (*f)->edges[e]->vertex_a->position;
-				glVertex3f(v.x, v.y, v.z);
-				v = (*f)->edges[e]->vertex_b->position;
-				glVertex3f(v.x, v.y, v.z);
-			}
-			glEnd();
-		}
-	}
-		
-}
-
-
-void rts_glFilamentNetwork::RenderRadiusColor(float min_r, float min_g, float min_b,
-								   float max_r, float max_g, float max_b,
-								   float min_radius, float max_radius)
-{
-	/*Render each segment with a color based on the radius of the filament
-	*/
-
-	vector<netFilament*>::iterator i;
-	int e;
-	int num_edges;
-	point3D<double> v;
-	vector3D<float> color_min(min_r, min_g, min_b);
-	vector3D<float> color_max(max_r, max_g, max_b);
-	max_radius /= m_data_scale;
-	min_radius /= m_data_scale;
-	float diff = max_radius - min_radius;
-	float p;						//parameter value (position between min and max radii)
-	vector3D<float> color_p;
-
-	for(i=m_filament_list.begin(); i!=m_filament_list.end(); i++)
-	{
-		glBegin(GL_LINES);
-		num_edges = (*i)->edges.size();
-		for(e=0; e<num_edges; e++)
-		{
-			//determine the color
-			p = ((*i)->edges[e]->vertex_a->radius - min_radius)/diff;
-			//cout<<"p: "<<p<<endl;
-			color_p = (1.0 - p)*color_min + (p)*color_max;
-			glColor3f(color_p.x, color_p.y, color_p.z);
-			//determine the vertex position
-			v = (*i)->edges[e]->vertex_a->position;
-			glVertex3f(v.x, v.y, v.z);
-			//determine the second color
-			p = ((*i)->edges[e]->vertex_b->radius - min_radius)/diff;
-			color_p = (1.0 - p)*color_min + (p)*color_max;
-			glColor3f(color_p.x, color_p.y, color_p.z);
-			//determine the vertex position
-			v = (*i)->edges[e]->vertex_b->position;
-			glVertex3f(v.x, v.y, v.z);
-		}
-		glEnd();
-	}
-}
-
-void rts_glFilamentNetwork::RenderEdgeBoundingBoxes()
-{
-	glMatrixMode(GL_MODELVIEW);	//switch to the modelview matrix and store it
-
-	vector<netEdge*>::iterator e;
-	point3D<double> center;
-	vector3D<double> size;
-	for(e=m_edge_list.begin(); e!=m_edge_list.end(); e++)
-	{
-		glPushMatrix();
-		size = (*e)->bounding_box.maximum - (*e)->bounding_box.minimum;
-		center = (*e)->bounding_box.minimum + 0.5*(size);
-		glTranslatef(center.x, center.y, center.z);
-		glScalef(size.x,
-				size.y,
-				size.z);
-		glutWireCube(1.0);
-		glPopMatrix();
-	}
-
-}
-
-void rts_glFilamentNetwork::RenderFilamentBoundingBoxes()
-{
-	glMatrixMode(GL_MODELVIEW);	//switch to the modelview matrix and store it
-
-	vector<netFilament*>::iterator f;
-	point3D<double> center;
-	vector3D<double> size;
-	for(f=m_filament_list.begin(); f!=m_filament_list.end(); f++)
-	{
-		glPushMatrix();
-		size = (*f)->bounding_box.maximum - (*f)->bounding_box.minimum;
-		center = (*f)->bounding_box.minimum + 0.5*size;
-		glTranslatef(center.x, center.y, center.z);
-		glScalef(size.x,
-				size.y,
-				size.z);
-		glutWireCube(1.0);
-		glPopMatrix();
-	}
-}
-
-void rts_glFilamentNetwork::RenderCellSpheres()
-{
-	glMatrixMode(GL_MODELVIEW);
-
-	vector<netCell*>::iterator c;
-	for(c=m_cell_list.begin(); c!=m_cell_list.end(); c++)
-	{
-		glPushMatrix();
-		glTranslatef((*c)->position.x, (*c)->position.y, (*c)->position.z);
-		glutSolidSphere((*c)->radius, 10, 10);
-		glPopMatrix();
-	}
-}
-void rts_glFilamentNetwork::RenderSelectedCells()
-{
-	glMatrixMode(GL_MODELVIEW);
-
-	vector<unsigned int>::iterator f;
-	vector<netCell*>::iterator c;
-	for(f = m_selected_list.begin(); f!=m_selected_list.end(); f++)
-	{
-		for(c=m_filament_list[(*f)]->cells.begin(); c!=m_filament_list[(*f)]->cells.end(); c++)
-		{
-			glPushMatrix();
-			glTranslatef((*c)->position.x, (*c)->position.y, (*c)->position.z);
-			glutSolidSphere((*c)->radius, 10, 10);
-			glPopMatrix();
-		}
-	}
-}
-
-void rts_glFilamentNetwork::p_ProcessPickHits(GLuint num_hits, GLuint* buffer, 
-											  unsigned int start_filament, bool append, int max)
-{
-	//cout<<"hits "<<start_filament<<" to "<<start_filament+63<<": "<<num_hits<<endl;
-	/*This structure is kinda complicated.  Extract the selected filaments here and put the indices
-	into the selection vector.
-	*/
-	//cout<<"selected filaments:"<<endl;
-	if(num_hits > max)
-		num_hits = max;
-	unsigned int h, n;
-	unsigned int num_names;
-	unsigned int name;
-	GLuint* ptr = buffer;			//index into buffer array
-	for(h=0; h<num_hits; h++)	//for each hit
-	{
-		num_names = *ptr;	//get the number of names in the hit
-		ptr+=3;				//skip to the names
-		for(n=0; n<num_names; n++)	//this should really only execute once (since we don't push names)
-		{
-			name = start_filament + (*ptr);
-			if(append)	//if we are appending
-			{
-				if(!p_IsSelected(name))
-					m_selected_list.push_back(name);
-			}
-			else
-				m_selected_list.push_back(name);
-			//cout<<start_filament+(*ptr)<<endl;
-			ptr++;
-		}
-	}
-
-
-
-}
-		
-void rts_glFilamentNetwork::PickFilaments(int x_center, int y_center, int width, int height, bool append, int max)
-{
-	if(!append)
-		m_selected_list.clear();			//first empty the selected list to start a new selection
-	//set up the selection buffer
-	GLuint selection_buffer[1000];
-	GLuint hits;
-
-	glSelectBuffer(1000, selection_buffer);
-	glRenderMode(GL_SELECT);				//change to selection mode
-	glInitNames();			//start naming objects
-	glPushName(0);
-
-	//set up projection matrix
-	//note that the pick matrix has to be multiplied in first, so we have to store the projection
-	//matrix and multiply it in afterwards
-	glMatrixMode(GL_PROJECTION);
-	GLfloat projection_matrix[16];
-	glGetFloatv(GL_PROJECTION_MATRIX, projection_matrix);	//get the current projection matrix
-	glPushMatrix();					//store the projection matrix
-	glLoadIdentity();				//start from scratch
-	GLint viewport[4];
-	glGetIntegerv(GL_VIEWPORT, viewport);	//set up the pick matrix
-	gluPickMatrix((GLdouble)x_center, (GLdouble)(viewport[3]-y_center), width, height, viewport);
-	glMultMatrixf(projection_matrix);
-
-
-	//run through each filament
-	int num_filaments = m_filament_list.size();
-	int num_edges, e, f;
-	point3D<double> v_a, v_b;
-	int name = 0;
-	unsigned int total_hits = 0;
-	for(f=0; f<num_filaments; f++)		//for each filament
-	{
-		glLoadName(name);		//push a name for the filament
-		glBegin(GL_LINES);	//begin drawing the filament
-		num_edges = m_filament_list[f]->edges.size();
-		for(e = 0; e<num_edges; e++)
-		{
-			//draw each edge
-			v_a = m_filament_list[f]->edges[e]->vertex_a->position;
-			v_b = m_filament_list[f]->edges[e]->vertex_b->position;
-			glVertex3f(v_a.x, v_a.y, v_a.z);
-			glVertex3f(v_b.x, v_b.y, v_b.z);
-		}
-		glEnd();
-		name++;				//increment the name
-		//We have to make sure that the name count doesn't exceed 64
-		if(name == 64)		//if the name hits 64, check for and store hits, then reset the name
-		{
-			hits = glRenderMode(GL_RENDER);
-			p_ProcessPickHits(hits, selection_buffer, f-63, append, max - total_hits);	//process the hits (store selected fibers)
-			total_hits += hits;
-			if(total_hits >= max)		//if we've reached the max, return
-			{
-				glPopMatrix();
-				return;
-			}
-			name = 0;		//reset the selection queue
-			glRenderMode(GL_SELECT);				//change to selection mode
-			glInitNames();			//start naming objects
-			glPushName(0);			//insert the first name
-		}
-	}
-	glFlush();		//finish rendering
-	hits = glRenderMode(GL_RENDER);	//switch back to normal mode, get the number of hits
-	p_ProcessPickHits(hits, selection_buffer, f/64, append, max - total_hits);	//get any left-over hits
-	total_hits += hits;
-
-	glPopMatrix();
-}
diff --git a/legacy/temp_rts_glFilamentNetwork.h b/legacy/temp_rts_glFilamentNetwork.h
deleted file mode 100755
index 3d360d9..0000000
--- a/legacy/temp_rts_glFilamentNetwork.h
+++ /dev/null
@@ -1,37 +0,0 @@
-#ifndef RTS_GLFILAMENTNETWORK_H
-#define RTS_GLFILAMENTNETWORK_H
-
-#include "temp_rtsFilamentNetwork.h"
-#include <windows.h>
-#include <gl/gl.h>
-#include <gl/glut.h>
-
-class rts_glFilamentNetwork:public rtsFilamentNetwork
-{
-private:
-	void p_ProcessPickHits(GLuint num_hits, GLuint* buffer, unsigned int start_filament, 
-							bool append = false, int max = 1);
-public:
-	
-	void RenderEdges();
-	void RenderBranches();
-	void RenderFilaments();
-	void RenderOrientationColor(double x, double y, double z, double r, double g, double b);
-	void RenderSelectedFilaments();
-	void RenderRadiusColor(float min_r, float min_g, float min_b,
-								   float max_r, float max_g, float max_b,
-								   float min_radius, float max_radius);
-	void RenderEdgeDistanceColor(float r, float g, float b, float cutoff);
-	void RenderFilamentDistanceColor(float r, float g, float b, float cutoff);
-	void RenderEdgeBoundingBoxes();
-	void RenderFilamentBoundingBoxes();
-	void RenderCellSpheres();
-	void RenderSelectedCells();
-
-	//pick filaments based on the current projection
-	void PickFilaments(int x_center, int y_center, int width, int height, bool append = false, int max = 1);
-	
-};
-		
-				
-#endif
\ No newline at end of file
diff --git a/validate/CMakeLists.txt b/validate/CMakeLists.txt
deleted file mode 100755
index 2d54c3d..0000000
--- a/validate/CMakeLists.txt
+++ /dev/null
@@ -1,52 +0,0 @@
-#Specify the version being used aswell as the language
-cmake_minimum_required(VERSION 2.8)
-#Name your project here
-project(rts-validate)
-
-#set the module directory
-set(CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH} "${CMAKE_SOURCE_DIR}")
-
-#set up CUDA
-find_package(CUDA)
-
-#find OpenGL
-find_package(OpenGL REQUIRED)
-
-#find GLUT
-set(GLUT_ROOT_PATH $ENV{GLUT_ROOT_PATH})
-find_package(GLUT REQUIRED)
-
-#find GLEW
-find_package(GLEW REQUIRED)
-
-#ask the user for the RTS location
-set(RTS_ROOT_PATH $ENV{RTS_ROOT_PATH})
-find_package(RTS REQUIRED)
-
-#set the include directories
-include_directories(
-	${CMAKE_CURRENT_BINARY_DIR}
-	${OPENGL_INCLUDE_DIR}
-	${GLEW_INCLUDE_PATH}
-	${GLUT_INCLUDE_DIR}
-	${RTS_INCLUDE_DIR}
-)
-
-#enable warnings
-if(CMAKE_COMPILER_IS_GNUCC OR CMAKE_COMPILER_IS_GNUCXX)
-	add_definitions(-Wall)
-endif()
-
-#Assign source files to the appropriate variables
-file(GLOB SRC_CPP "*.cpp")
-file(GLOB SRC_H "*.h")
-file(GLOB SRC_CU "*.cu")
-
-#create an executable
-cuda_add_executable(rts-validate ${SRC_CPP} ${SRC_H} ${UI_H} ${SRC_CU})
-
-#set the link libraries
-target_link_libraries(rts-validate ${OPENGL_gl_LIBRARY} ${OPENGL_glu_LIBRARY} ${GLEW_LIBRARY} ${CUDA_cufft_LIBRARY} ${GLUT_glut_LIBRARY})
-
-
-
diff --git a/validate/FindRTS.cmake b/validate/FindRTS.cmake
deleted file mode 100755
index fbfcc44..0000000
--- a/validate/FindRTS.cmake
+++ /dev/null
@@ -1,14 +0,0 @@
-# Tries to find the RTS include directory
-
-  FIND_PATH( RTS_INCLUDE_DIR NAMES rts_glShaderProgram.h
-    PATHS
-	${CMAKE_CURRENT_SOURCE_DIR}/rts
-	${RTS_ROOT_PATH}
-)
- 
-IF (RTS_FOUND)    
-  #The following deprecated settings are for backwards compatibility with CMake1.4
-  SET (RTS_INCLUDE_PATH ${RTS_INCLUDE_DIR})
-ENDIF(RTS_FOUND)
-
-FIND_PACKAGE_HANDLE_STANDARD_ARGS(RTS REQUIRED_VARS TRUE RTS_INCLUDE_DIR)
diff --git a/validate/compare.h b/validate/compare.h
deleted file mode 100644
index 3d4f4e6..0000000
--- a/validate/compare.h
+++ /dev/null
@@ -1,27 +0,0 @@
-#ifndef RTS_VALIDATE_COMPARE_H
-#define RTS_VALIDATE_COMPARE_H
-
-#define N		5000
-#define epsilon	0.00001
-
-#include <complex>
-#include <iostream>
-#include <stdlib.h>
-#include "rts/complex.h"
-
-template <typename T>
-static void compare(std::complex<T> a, rts::complex<T> b, std::string testName)
-{
-	T diffx = std::abs(a.real() - b.r);
-	T diffy = std::abs(a.imag() - b.i);
-
-	if(diffx > epsilon || diffy > epsilon)
-	{
-		std::cout<<"Failed "<<testName<<std::endl;
-		std::cout<<a<<"------"<<b.toStr()<<std::endl;
-		exit(1);
-	}
-
-}
-
-#endif
diff --git a/validate/main.cpp b/validate/main.cpp
deleted file mode 100644
index 3471197..0000000
--- a/validate/main.cpp
+++ /dev/null
@@ -1,19 +0,0 @@
-void cpuValidateComplex();
-void gpuValidateComplex();
-void cpuValidateBessel();
-void cpuValidateLegendre();
-
-int main()
-{
-	//validate the complex number class
-	//cpuValidateComplex();
-	//gpuValidateComplex();
-
-	//validate Bessel functions
-	cpuValidateBessel();
-
-	//validate the Legendre polynomials
-	cpuValidateLegendre();
-
-	return 0;
-}
diff --git a/validate/validate-bessel.cpp b/validate/validate-bessel.cpp
deleted file mode 100644
index 6d0f9a5..0000000
--- a/validate/validate-bessel.cpp
+++ /dev/null
@@ -1,76 +0,0 @@
-#include <complex>
-#include <iostream>
-#include <stdio.h>
-#include <string.h>
-#include "rts/complex.h"
-#include "rts/sbessel.h"
-
-#include "compare.h"
-
-typedef float precision;
-
-//typedef std::complex<double> ptype;
-typedef rts::complex<precision> ptype;
-
-void cpuValidateBessel()
-{
-
-	//order
-	precision v = 5;
-	precision vm;
-
-	//parameter
-	precision max_z = 5;
-	int nz = 20;
-	precision dz = max_z / nz;
-
-	//bessel function results (first and second kind)
-	int S = sizeof(ptype) * (v + 1);
-
-	ptype* jv = (ptype*)malloc(S);
-	ptype* yv = (ptype*)malloc(S);
-	ptype* hv = (ptype*)malloc(S);
-
-
-    std::cout<<"---------j_v(x)-------------"<<std::endl;
-	rts::complex<precision> z;
-	for(int iz = 0; iz < nz; iz++)
-	{
-		z = iz * dz;
-
-		rts::sbesselj<precision>(v, z, jv);
-
-		std::cout<<z.toStr()<<", "<<jv[0].toStr()<<", "<<jv[1].toStr()<<", "<<jv[2].toStr()<<std::endl;
-
-	}
-
-	std::cout<<"---------y_v(x)-------------"<<std::endl;
-	for(int iz = 0; iz < nz; iz++)
-	{
-		z = iz * dz;
-
-		rts::sbessely<precision>(v, z, yv);
-
-		std::cout<<z.toStr()<<", "<<yv[0].toStr()<<", "<<yv[1].toStr()<<", "<<yv[2].toStr()<<std::endl;
-
-	}
-
-	std::cout<<"---------h(1)_v(x)-------------"<<std::endl;
-	for(int iz = 0; iz < nz; iz++)
-	{
-		z = iz * dz;
-
-		rts::sbesselh1<precision>(v, z, hv);
-
-		std::cout<<z.toStr()<<", "<<hv[0].toStr()<<", "<<hv[1].toStr()<<", "<<hv[2].toStr()<<std::endl;
-
-	}
-
-
-
-
-
-
-
-
-}
diff --git a/validate/validate-complex.cpp b/validate/validate-complex.cpp
deleted file mode 100644
index e7b2e96..0000000
--- a/validate/validate-complex.cpp
+++ /dev/null
@@ -1,140 +0,0 @@
-#include <complex>
-#include <iostream>
-#include "rts/complex.h"
-
-#include "compare.h"
-
-#define N		5
-#define epsilon	0.000001
-
-template <typename T>
-void validateOperators()
-{
-    int precision = sizeof(T) * 8;
-    std::stringstream ss;
-    ss<<" ("<<precision<<"-bit)";
-    std::string bitString = ss.str();
-    //validate complex binary functions
-	T x0, x1, y0, y1;
-    for(int i = 0; i<N; i++)
-	{
-		//generate a random complex number
-		x0 = (double)rand()/(double)RAND_MAX * 2 - 1;
-		y0 = (double)rand()/(double)RAND_MAX * 2 - 1;
-		x1 = (double)rand()/(double)RAND_MAX * 2 - 1;
-		y1 = (double)rand()/(double)RAND_MAX * 2 - 1;
-
-		//create an STD and RTS instance of the complex class
-		std::complex<T> stdComplex0(x0, y0);
-		rts::complex<T> rtsComplex0(x0, y0);
-
-		std::complex<T> stdComplex1(x1, y1);
-		rts::complex<T> rtsComplex1(x1, y1);
-
-		std::complex<T> stdResult;
-		rts::complex<T> rtsResult;
-
-		//test addition
-		stdResult = stdComplex0 + stdComplex1;
-		rtsResult = rtsComplex0 + rtsComplex1;
-		compare(stdResult, rtsResult, std::string("Binary Addition") + bitString);
-		//test addition with real value
-		stdResult = stdComplex1.real() + stdComplex0;
-		rtsResult = rtsComplex1.r + rtsComplex0;
-		compare(stdResult, rtsResult, std::string("Addition with Real Value") + bitString);
-
-		//test subtraction
-		stdResult = stdComplex0 - stdComplex1;
-		rtsResult = rtsComplex0 - rtsComplex1;
-		compare(stdResult, rtsResult, std::string("Binary Subtraction") + bitString);
-		//test subtraction with real value
-		stdResult = stdComplex1.real() - stdComplex0;
-		rtsResult = rtsComplex1.r - rtsComplex0;
-		compare(stdResult, rtsResult, std::string("Subtraction with Real Value") + bitString);
-
-		//test multiplication
-		stdResult = stdComplex0 * stdComplex1;
-		rtsResult = rtsComplex0 * rtsComplex1;
-		compare(stdResult, rtsResult, std::string("Binary Multiplication") + bitString);
-		//test multiplication with real value
-		stdResult = stdComplex1.real() * stdComplex0;
-		rtsResult = rtsComplex1.r * rtsComplex0;
-		compare(stdResult, rtsResult, std::string("Multiplication with Real Value") + bitString);
-
-		//test division
-		stdResult = stdComplex0 / stdComplex1;
-		rtsResult = rtsComplex0 / rtsComplex1;
-		compare(stdResult, rtsResult, std::string("Binary Division") + bitString);
-		//test division with real value
-		stdResult = stdComplex1.real() / stdComplex0;
-		rtsResult = rtsComplex1.r / rtsComplex0;
-		compare(stdResult, rtsResult, std::string("Division with Real Value") + bitString);
-
-		//test abs()
-		stdResult = abs(stdComplex0);
-		rtsResult = abs(rtsComplex0);
-		compare(stdResult, rtsResult, std::string("abs()") + bitString);
-
-		//test log()
-		stdResult = log(stdComplex0);
-		rtsResult = log(rtsComplex0);
-		compare(stdResult, rtsResult, std::string("log()") + bitString);
-
-		//test exp()
-		stdResult = exp(stdComplex0);
-		rtsResult = exp(rtsComplex0);
-		compare(stdResult, rtsResult, std::string("exp()") + bitString);
-
-		//test pow()
-		stdResult = pow(stdComplex0, (T)2.0);
-		rtsResult = pow(rtsComplex0, (T)2.0);
-		compare(stdResult, rtsResult, std::string("pow()") + bitString);
-
-		//test sqrt()
-		stdResult = sqrt(stdComplex0);
-		rtsResult = rts::sqrt(rtsComplex0);
-		compare(stdResult, rtsResult, std::string("sqrt()") + bitString);
-
-		//trigonometric functions
-		stdResult = sin(stdComplex0);
-		rtsResult = rts::sin(rtsComplex0);
-		compare(stdResult, rtsResult, std::string("sin()") + bitString);
-
-		//trigonometric functions
-		stdResult = cos(stdComplex0);
-		rtsResult = rts::cos(rtsComplex0);
-		compare(stdResult, rtsResult, std::string("cos()") + bitString);
-
-		//ASSIGNMENT OPERATORS
-
-		//     +=
-		stdResult = stdComplex0;
-		stdResult += stdComplex1;
-		rtsResult = rtsComplex0;
-		rtsResult += rtsComplex1;
-		compare(stdResult, rtsResult, std::string("operator +=") + bitString);
-
-		//     *=
-		stdResult = stdComplex0;
-		stdResult *= stdComplex1;
-		rtsResult = rtsComplex0;
-		rtsResult *= rtsComplex1;
-		compare(stdResult, rtsResult, std::string("operator *=") + bitString);
-
-		//     /=
-		stdResult = stdComplex0;
-		stdResult /= stdComplex1;
-		rtsResult = rtsComplex0;
-		rtsResult /= rtsComplex1;
-		compare(stdResult, rtsResult, std::string("operator /=") + bitString);
-
-	}
-}
-
-void cpuValidateComplex()
-{
-    //validate both floating point and double precision
-    validateOperators<float>();
-    validateOperators<double>();
-
-}
diff --git a/validate/validate-complex.cu b/validate/validate-complex.cu
deleted file mode 100644
index 9e21509..0000000
--- a/validate/validate-complex.cu
+++ /dev/null
@@ -1,172 +0,0 @@
-#include <complex>
-#include <iostream>
-#include "rts/complex.h"
-
-#include "compare.h"
-
-
-template<typename T>
-__global__ void add(rts::complex<T> a, rts::complex<T> b, rts::complex<T>* c)
-{
-	*c = a + b;
-}
-
-template<typename T>
-__global__ void multiply(rts::complex<T> a, rts::complex<T> b, rts::complex<T>* c)
-{
-	*c = a * b;
-}
-
-template<typename T>
-__global__ void multiply(rts::complex<T> a, T b, rts::complex<T>* c)
-{
-	*c = a * b;
-}
-
-template<typename T>
-__global__ void divide(rts::complex<T> a, rts::complex<T> b, rts::complex<T>* c)
-{
-	*c = a / b;
-}
-
-template<typename T>
-__global__ void log(rts::complex<T> a, rts::complex<T>* c)
-{
-	*c = rts::log(a);
-}
-
-template<typename T>
-__global__ void sqrt(rts::complex<T> a, rts::complex<T>* c)
-{
-	*c = rts::sqrt(a);
-}
-
-template<typename T>
-__global__ void exp(rts::complex<T> a, rts::complex<T>* c)
-{
-	*c = rts::exp(a);
-}
-
-template<typename T>
-__global__ void pow(rts::complex<T> a, rts::complex<T>* c)
-{
-	*c = rts::pow(a, (T)2.0);
-}
-
-template<typename T>
-__global__ void sin(rts::complex<T> a, rts::complex<T>* c)
-{
-	*c = rts::sin(a);
-}
-
-template<typename T>
-__global__ void cos(rts::complex<T> a, rts::complex<T>* c)
-{
-	*c = rts::cos(a);
-}
-
-template <typename T>
-void gpuValidateOperators()
-{
-    int precision = sizeof(T) * 8;
-    std::stringstream ss;
-    ss<<" ("<<precision<<"-bit)";
-    std::string bitString = ss.str();
-
-    rts::complex<T>* gpuResult;
-    cudaMalloc((void**)&gpuResult, sizeof(rts::complex<T>));
-
-    //validate complex binary functions
-	T x0, x1, y0, y1;
-	for(int i = 0; i<N; i++)
-	{
-		//generate a random complex number
-		x0 = (double)rand()/(double)RAND_MAX * 2 - 1;
-		y0 = (double)rand()/(double)RAND_MAX * 2 - 1;
-		x1 = (double)rand()/(double)RAND_MAX * 2 - 1;
-		y1 = (double)rand()/(double)RAND_MAX * 2 - 1;
-
-		//create an STD and RTS instance of the complex class
-		std::complex<T> stdComplex0(x0, y0);
-		rts::complex<T> rtsComplex0(x0, y0);
-
-		std::complex<T> stdComplex1(x1, y1);
-		rts::complex<T> rtsComplex1(x1, y1);
-
-		std::complex<T> stdResult;
-		rts::complex<T> rtsResult;
-
-
-		//test addition
-		stdResult = stdComplex0 + stdComplex1;
-		add<<<1, 1>>>(rtsComplex0, rtsComplex1, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("Binary Addition") + bitString);
-		//std::cout<<stdResult<<"------"<<rtsResult.toStr()<<std::endl;
-
-		//test multiplication
-		stdResult = stdComplex0 * stdComplex1;
-		multiply<<<1, 1>>>(rtsComplex0, rtsComplex1, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("Binary Multiplication") + bitString);
-
-		//test multiplication with constant
-		stdResult = stdComplex0 * stdComplex1.real();
-		multiply<<<1, 1>>>(rtsComplex0, rtsComplex1.r, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("Multiplication with Real Value") + bitString);
-
-		//test division
-		stdResult = stdComplex0 / stdComplex1;
-		divide<<<1, 1>>>(rtsComplex0, rtsComplex1, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("Binary Division") + bitString);
-
-		//test log()
-		stdResult = log(stdComplex0);
-		log<<<1, 1>>>(rtsComplex0, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("log()") + bitString);
-
-		//test exp()
-		stdResult = exp(stdComplex0);
-		exp<<<1, 1>>>(rtsComplex0, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("exp()") + bitString);
-
-		//test pow()
-		stdResult = pow(stdComplex0, 2);
-		pow<<<1, 1>>>(rtsComplex0, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("pow()") + bitString);
-
-		//test sqrt()
-		stdResult = sqrt(stdComplex0);
-		sqrt<<<1, 1>>>(rtsComplex0, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("sqrt()") + bitString);
-
-		//trigonometric functions
-		stdResult = sin(stdComplex0);
-		sin<<<1, 1>>>(rtsComplex0, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("sin()") + bitString);
-
-		//trigonometric functions
-		stdResult = cos(stdComplex0);
-		cos<<<1, 1>>>(rtsComplex0, gpuResult);
-		cudaMemcpy(&rtsResult, gpuResult, sizeof(rts::complex<T>), cudaMemcpyDeviceToHost);
-		compare(stdResult, rtsResult, std::string("cos()") + bitString);
-
-
-	}
-	cudaFree(gpuResult);
-
-}
-
-void gpuValidateComplex()
-{
-
-	gpuValidateOperators<float>();
-	//gpuValidateOperators<double>();
-}
diff --git a/validate/validate-legendre.cpp b/validate/validate-legendre.cpp
deleted file mode 100644
index 3ef7ea7..0000000
--- a/validate/validate-legendre.cpp
+++ /dev/null
@@ -1,43 +0,0 @@
-#include <complex>
-#include <iostream>
-#include <stdio.h>
-#include <string.h>
-#include "rts/legendre.h"
-
-#include "compare.h"
-
-typedef float precision;
-int l = 0;
-
-
-void cpuValidateLegendre()
-{
-
-	//order
-	precision v = 5;
-	precision vm;
-
-	//parameter
-	precision max_z = 2;
-	int nz = 20;
-	precision dz = max_z / nz;
-
-	//bessel function results (first and second kind)
-	int S = sizeof(precision) * (v + 1);
-
-	precision* P = (precision*)malloc(S);
-
-
-    std::cout<<"---------j_v(x)-------------"<<std::endl;
-	precision z;
-	for(int iz = 0; iz < nz; iz++)
-	{
-		z = iz * dz - 1.0;
-
-		rts::legendre<precision>(v, z, P);
-
-		std::cout<<z<<", "<<P[0]<<", "<<P[1]<<", "<<P[2]<<", "<<P[3]<<std::endl;
-
-	}
-
-}
--
libgit2 0.21.4