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stim/gl/gl_spider.h 56.5 KB
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  #ifndef STIM_GL_SPIDER_H
  #define STIM_GL_SPIDER_H
  
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  //#include <GL/glew.h>
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  #include <GL/glut.h>
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  #include <cuda.h>
  #include <cuda_gl_interop.h>
  #include <cudaGL.h>
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  #include <math.h>
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  #include <stim/gl/gl_texture.h>
  #include <stim/visualization/camera.h>
  #include <stim/gl/error.h>
  #include <stim/math/vector.h>
  #include <stim/math/vec3.h>
  #include <stim/math/rect.h>
  #include <stim/math/matrix.h>
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  #include <stim/math/constants.h>
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  #include <stim/cuda/spider_cost.cuh>
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  #include <stim/cuda/cudatools/glbind.h>
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  #include <stim/cuda/arraymath.cuh>
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  #include <stim/cuda/cuda_texture.cuh>
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  #include <stim/cuda/cudatools.h>
  #include <stim/cuda/ivote.cuh>
  #include <stim/visualization/glObj.h>
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  #include <vector>
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  #include <stack>
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  #include <stim/cuda/branch_detection.cuh>
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  #include "../../../volume-spider/glnetwork.h"
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  #include <stim/visualization/cylinder.h>
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  #include <stim/cuda/testKernel.cuh>
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  #include <iostream>
  #include <fstream>
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  #ifdef TIMING
  	#include <ctime>
  	#include <cstdio>	
  #endif
  
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  #ifdef TESTING
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  	#include <cstdio>
  	#include <ctime>
  #endif
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  namespace stim
  {
  
  template<typename T>
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  class gl_spider // : public virtual gl_texture<T>
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  {
  	//doen't use gl_texture really, just needs the GLuint id.
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  	//doesn't even need the texture iD really.
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  	private:
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  		#ifdef TIMING
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  			double branch_time;// = 0;
  			double direction_time;// = 0;
  			double position_time;// = 0;
  			double size_time;// = 0;
  			double cost_time;// = 0;
  			double network_time;// = 0;
  			double hit_time;// = 0;
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  		#endif
  
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  		stim::vec3<float> p;  	//vector designating the position of the spider.
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  		stim::vec3<float> d;	//normalized direction of travel
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  		float m;			//size of the spider in tissue space.
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  		std::vector<stim::vec3<float> > dV;	//A list of all the direction vectors.
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  		std::vector<stim::vec3<float> > pV;	//A list of all test positions (relative to p)
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  		std::vector<float> mV;	//A list of all the size vectors.
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  		std::vector<float> lV;	//A list of all the size vectors.
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  		stim::matrix<float, 4> cT;			//current Transformation matrix (tissue)->(texture)
  		GLuint texID;						//OpenGL ID for the texture to be traced
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  		stim::vec3<float> S;					//Size of a voxel in the volume.
  		stim::vec3<float> R;					//Dimensions of the volume.
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  		//GL and Cuda variables
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  		GLuint dList;				//ID of the starting display lists (series of 4)
  									//dList + 0 = direction template rectangles
  									//dList + 1 = position template rectangles
  									//dList + 2 = size template rectangles
  									//dList + 3 = branch detection cylinder around the fiber
  
  		GLuint fboID;				//framebuffer ID for direction templates
  		GLuint texbufferID;			//texture ID for direction templates
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  		GLuint direction_buffID;				//framebuffer ID, position templates
  		GLuint direction_texID;		//texture ID, position templates
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  		GLuint position_buffID;				//framebuffer ID, position templates
  		GLuint position_texID;		//texture ID, position templates
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  		GLuint radius_buffID;				//framebuffer ID, radius templates
  		GLuint radius_texID;		//texture ID, radius templates
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  		GLuint length_buffID;				//framebuffer ID, radius templates
  		GLuint length_texID;		//texture ID, radius templates
  
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  		GLuint cylinder_buffID;				//framebuffer ID, cylinder (surrounding fiber)
  		GLuint cylinder_texID;		//texture ID, cylinder
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  		int numSamples;				//The number of templates in the buffer.
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  		int numSamplesPos;
  		int numSamplesMag;
  
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  		float length;				//this will be a function of the radius
  		float stepsize;				//this will be a function of the length
  
  		int current_cost;			//variable to store the cost of the current step		
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  		//Tracing variables.
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  		std::stack< stim::vec3<float> > seeds;		//seed positions
  		std::stack< stim::vec3<float> > seedsvecs;	//seed directions
  		std::stack< float > 		seedsmags;		//seed magnitudes
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  		std::vector< stim::vec3<float> > cL;	//centerline up to the current point
  		std::vector< stim::vec3<float> > cD;	//directions up to the current point (debugging)
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  		std::vector< float > cM;		//radius up to the current point
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  		std::vector< float > cLen;		//radius up to the current point
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  		stim::glnetwork<float> nt;				//network object holding the currently traced centerlines
  		stim::glObj<float> sk;					//OBJ file storing the network (identical to above)
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  		//consider replacing with two seed points facing opposite directions
  		stim::vec<float> rev;					//reverse vector
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  		//selection mode - detecting fiber intersections
  		stim::camera camSel;					//camera for selection mode (detecting collisions)
  		stim::vec3<float> ps;					//position for the selection camera
  		stim::vec3<float> ups;					//up direction for the selection camera
  		stim::vec3<float> ds;					//direction for the selection camera
  
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  		float n_pixels;							//length of the template (in pixels)
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  		//cuda texture variables that keep track of the binding.
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  		stim::cuda::cuda_texture t_dir;				//cuda_texture object used as an interface between OpenGL and cuda for direction vectors.
  		stim::cuda::cuda_texture t_pos;				//cuda_texture object used as an interface between OpenGL and cuda for position vectors.
  		stim::cuda::cuda_texture t_mag;				//cuda_texture object used as an interface between OpenGL and cuda for size vectors.
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  		stim::cuda::cuda_texture t_len;				//cuda_texture object used as an interface between OpenGL and cuda for size vectors.
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  		#ifdef DEBUG
  			stringstream name;
  			int iter;
  			int iter_pos;
  			int iter_dir;
  			int iter_siz;
  		#endif
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  //--------------------------------------------------------------------------//
  //-------------------------------PRIVATE METHODS----------------------------//
  //--------------------------------------------------------------------------//
  
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  		/// Method for finding the best scale for the spider.
  		/// changes the x, y, z size of the spider to minimize the cost
  		/// function. 
  		void
  		findOptimalDirection()
  		{
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  			#ifdef TIMING
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  				gpuStartTimer();	//Timer for profiling
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  			#endif
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  			setMatrix();			//create the transformation matrix.
  			glCallList(dList);		//move the templates to p, d, m.
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  			glFinish();			//flush the pipeline
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  			#ifdef TIMING
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  				direction_time += gpuStopTimer();	//profiling
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  			#endif
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  			int best = getCost(t_dir.getTexture(), t_dir.getAuxArray() ,numSamples);		//find min cost.
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  			#ifdef DEBUG
  				name.str("");
  				name << "Final_Cost_Direction_fiber_"<< iter << "_" << iter_dir << ".bmp";	
  				test(t_dir.getTexture(), n_pixels*2.0, numSamples*n_pixels, name.str());
  				iter_dir++;
  			#endif
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  			stim::vec<float> next(		///calculate the next vector.
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  			dV[best][0]*S[0]*R[0],
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  			dV[best][1]*S[1]*R[1],
  			dV[best][2]*S[2]*R[2],
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  			0);
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  			next = (cT*next).norm();	///transform the next vector into Tissue space.
  			setPosition(	p[0]+next[0]*m/stepsize,
  					p[1]+next[1]*m/stepsize,
  					p[2]+next[2]*m/stepsize);	
  			setDirection(next[0], next[1], next[2]);		//move forward and change direction.
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  		}
  
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  		/// Method for finding the best d (direction) for the spider.
  		/// Not sure if necessary since the next p (position) for the spider
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  		/// will be at d * m.
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  		void
  		findOptimalPosition()
  		{
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  			#ifdef TIMING
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  				gpuStartTimer();	//timer for profiling
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  			#endif
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  			setMatrix();			//create the transformation matrix.
  			glCallList(dList+1);		//move the templates to p, d, m.
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  			glFinish();			//flush the pipeline
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  //			glFlush();
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  			#ifdef TIMING
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  				position_time += gpuStopTimer();		///timer for profiling
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  			#endif
  
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  			int best = getCost(t_pos.getTexture(), t_pos.getAuxArray(), numSamplesPos);		//find min cost.
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  			#ifdef DEBUG
  				name.str("");
  				name << "Final_Cost_Position_" << iter << "_" << iter_pos << ".bmp";	
  				test(t_pos.getTexture(), n_pixels*2.0, numSamplesPos*n_pixels, name.str());
  				iter_pos++;
  			#endif
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  			stim::vec<float> next(		//find next position.
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   				pV[best][0],
  				pV[best][1],
  				pV[best][2],
  				1);
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  			next = cT*next;			//transform the next position vector into tissue space.
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  			setPosition(
  					next[0]*S[0]*R[0],
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  					next[1]*S[1]*R[1],
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  					next[2]*S[2]*R[2]
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  				   );			//adjust position.
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  		}
  	
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  		/// Method for finding the best scale for the spider.
  		/// changes the x, y, z size of the spider to minimize the cost
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  		/// function. 
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  		void
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  		findOptimalRadius()
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  		{
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  			#ifdef TIMING
  				gpuStartTimer();
  			#endif
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  			setMatrix();			//create the transformation.
  			glCallList(dList+2);		//move the templates to p, d, m.
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  			glFinish();			//flush the drawing pipeline.
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  			#ifdef TIMING
  				size_time += gpuStopTimer();
  			#endif
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  			int best = getCost(t_mag.getTexture(), t_mag.getAuxArray(), numSamplesMag);		//get best cost.
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  			#ifdef DEBUG
  				name.str("");
  				name << "Final_Cost_Size_" << iter << "_" <<  iter_siz << ".bmp";	
  				test(t_mag.getTexture(), n_pixels*2.0, numSamplesMag*n_pixels, name.str());
  				iter_siz++;
  			#endif
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  			setMagnitude(m*mV[best]);	//adjust the magnitude.
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  		}
  
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  		/// Method for finding the best length for the spider.
  		/// changes the x, y, z size of the spider to minimize the cost
  		/// function. 
  		void
  		findOptimalLength()
  		{
  			#ifdef TIMING
  				gpuStartTimer();
  			#endif
  			setMatrix();			//create the transformation.
  			glCallList(dList+3);		//move the templates to p, d, m.
  			glFinish();			//flush the drawing pipeline.
  			#ifdef TIMING
  				size_time += gpuStopTimer();
  			#endif
  			int best = getCost(t_len.getTexture(), t_len.getAuxArray(), numSamplesMag);		//get best cost.
  			#ifdef DEBUG
  //				name.str("");
  //				name << "Final_Cost_Size_" << iter << "_" <<  iter_siz << ".bmp";	
  //				test(t_mag.getTexture(), n_pixels*2.0, numSamplesMag*n_pixels, name.str());
  //				iter_siz++;
  			#endif
  			setLength(mV[best]);	//adjust the magnitude.
  		}
  
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  		///finds all the branches in the a given fiber.
  		///using LoG method.
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  		void
  		branchDetection2(int n = 8, int l_template = 8, int l_square = 8)
  		{
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  			#ifdef TIMING
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  				gpuStartTimer();		///timer for performance analysis
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  			#endif
  
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  			if(cL.size() < 4){}		///if the size of the fiber is less then 4 we do nothing.
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  			else{
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  			setMatrix(1);			///finds the current transformation matrix
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  			DrawLongCylinder(n, l_template, l_square);	///Draw the cylinder.
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  			stim::cylinder<float> cyl(cL, cM);
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  			std::vector< stim::vec<float> > result = find_branch(cylinder_texID, GL_TEXTURE_2D, n*l_square, (cL.size()-1)*l_template);		///find all the centers in cuda
  			stim::vec3<float> size(S[0]*R[0], S[1]*R[1], S[2]*R[2]);			///the borders of the texture.
  			float pval;									//pvalue associated with the points on the cylinder.
  			if(!result.empty())								///if we have any points
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  			{
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  				for(int i = 0; i < result.size(); i++)					///for each point
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  				{
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  					int id = result[i][2];
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  					if(fmod(result[i][2], id) != 0 && id != 0)			///if the remainer is odd
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  					{
  						
  						pval = ((cyl.getl(id+1)-cyl.getl(id))*
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  							(fmod(result[i][2], id))+cyl.getl(id))/cyl.getl(cL.size()-1);		///calculate pvalue
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  					}
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  					else if(id == 0)									///if the point is on the edge
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  					{
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  						pval = (cyl.getl(id+1)*result[i][2])/cyl.getl(cL.size()-1);			
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  					}
  					else
  					{
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  						pval = (cyl.getl(id)/cyl.getl(cL.size()-1));					///if the point is somewhere on the surface of the cylinder other than the edge
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  					}
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  					stim::vec3<float> v = cyl.surf(pval, result[i][0]);					///find the coordinates of the point at pval on the surface in tissue space.
  					stim::vec3<float> di = cyl.p(pval);							///find the coord of v in tissue space projected on the centerline.
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  					float rad = cyl.r(pval)/2;								///find the radius at the pvalue's location
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  					if(
  					 !(v[0] > size[0] || v[1] > size[1]
  					 || v[2] > size[2] || v[0] < 0
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  					 || v[1] < 0 || v[2] < 0))								///if the v point is INSIDE the volume
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  					{
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  						setSeed(v);									///add a seedpoint's position.
  						setSeedVec((v-di).norm());							///add a seedpoints direction
  						setSeedMag(rad);								///add the starting radius.
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  					}
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  				}
  			}
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  			}
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  			#ifdef TIMING
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  				branch_time += gpuStopTimer();									///timer for performance.
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  			#endif
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  		}
  
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  		float uniformRandom()
  		{
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  			return (  (float)(rand()))/(  (float)(RAND_MAX));							///generates a random number between 0 and 1 using the uniform distribution.
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  		}
  
  		float normalRandom()
  		{
  			float u1 = uniformRandom();
  			float u2 = uniformRandom();
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  			return cos(2.0*atan(1.0)*u2)*sqrt(-1.0*log(u1));							///generate a random number using the normal distribution between 0 and 1.
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  		}
  
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  		stim::vec3<float> uniformRandVector()
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  		{
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  			stim::vec3<float> r(uniformRandom(), uniformRandom(), 1.0);						///generate a random vector using the uniform distribution between 0 and 1.
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  			return r;
  		}
  
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  		stim::vec3<float> normalRandVector()
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  		{
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  			stim::vec3<float> r(normalRandom(), normalRandom(), 1.0);						///generate a random vector using the normal distribution between 0 and 1.
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  			return r;
  		}
  
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  //--------------------------------------------------------------------------//
  //---------------------TEMPLATE CREATION METHODS----------------------------//
  //--------------------------------------------------------------------------//
  
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  		///@param solidAngle, the size of the arc to sample.
  		///Method for populating the vector arrays with sampled vectors.
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  		///Objects created are rectangles the with the created directions.
  		///All points are sampled from a texture.
  		///Stored in a display list.
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  		///uses the default d vector <0,0,1>
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  		void
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  		genDirectionVectors(float solidAngle = stim::PI/2)
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  		{
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  			//Set up the vectors necessary for Rectangle creation.
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  			stim::vec3<float> Y(1.0,0.0,0.0);		//orthogonal vec.
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  			stim::vec3<float> pos(0.0,0.0,0.0);		//center point of a rectangle
  			float mag = 1.0;				//size of the generated rectangle.
  			stim::vec3<float> dir(0.0, 0.0, 1.0);		//normal of the rectangle
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  			float PHI[2], Z[2], range;			
  			PHI[0] = solidAngle/2;				///Project the solid angle into spherical coordinates
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  			PHI[1] = asin(0);
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  			Z[0] = cos(PHI[0]);				///Project the z into spherical coordinates
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  			Z[1] = cos(PHI[1]);
  			
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  			range = Z[0] - Z[1];				///The range the possible values can be.
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  			float z, theta, phi;
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  			glNewList(dList, GL_COMPILE); 			///create a display list of all the direction templates.
  			for(int i = 0; i < numSamples; i++)		///for each sample
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  			{
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  				z = uniformRandom()*range + Z[1];	///generate a z coordinate
  				theta = uniformRandom()*stim::TAU;	///generate a theta coordinate
  				phi = acos(z);				///generate a phi from the z.
  				stim::vec3<float> sph(1, theta, phi);	///combine into a vector in spherical coordinates.
  				stim::vec3<float> cart = sph.sph2cart();///convert to cartesian.	
  				dV.push_back(cart);			///save the generated vector for further use.
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  				#ifdef DEBUG
  //					std::cout << cart << std::endl;
  				#endif
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  				if(cos(Y.dot(cart)) < 0.087)		///make sure that the Y is not parallel to the new vector.
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  				{
  						Y[0] = 0.0; Y[1] = 1.0;
  				}else{
  					Y[0] = 1.0; Y[1] = 0.0;
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  				}
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                                  hor = stim::rect<float>(mag,		///generate a rectangle with the new vectro as a normal.
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  					 pos, cart,
                         			((Y.cross(cart)).cross(cart)).norm());
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  				#ifdef DEBUG
  			//		std::cout << hor.n() << std::endl;
  				#endif
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         				ver = stim::rect<float>(mag,		///generate another rectangle that's perpendicular the first but parallel to the cart vector.
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  					 pos, cart,
                         			hor.n());
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  				UpdateBuffer(0.0, 0.0+i*n_pixels);	///Put the necessary points into the diplaylist.
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  			}
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  			glEndList();					///finilize the display list.
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  		}
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  		///@param float delta, How much the rectangles vary in position.
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  		///Method for populating the buffer with the sampled texture.
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  		///Objects created are rectangles the with the created positions.
  		///All points are sampled from a texture.
  		///Stored in a display list.
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  		///uses the default vector <0,0,0>
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  		void
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  		genPositionVectors(float delta = 0.4)
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  		{
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  			//Set up the vectors necessary for Rectangle creation.
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  			stim::vec3<float> Y(1.0,0.0,0.0);		//orthogonal vec.
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  			stim::vec3<float> pos(0.0,0.0,0.0);		//center point of a rectangle
  			float mag = 1.0;				///size of each rectangle
  			stim::vec3<float> dir(0.0, 0.0, 1.0);		///normal of the rectangle plane.
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  			//Set up the variable necessary for vector creation.
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  			glNewList(dList+1, GL_COMPILE);			///generate a new display list.
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  			pV.push_back(pos);
  			hor = stim::rect<float>(mag,                    ///generate a rec     tangle with the new vector as a normal.  
                  	        pos, dir,
  	                       	((Y.cross(d)).cross(d))
  	                        .norm());
                          ver = stim::rect<float>(mag,                    ///generate anoth     er rectangle that's perpendicular the first but parallel to the cart vector.
          	                pos, dir,
  	                        hor.n()); 
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  									///The first vector is always in the center.
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                          UpdateBuffer(0.0, 0.0+0*n_pixels);
  			for(int i = 1; i < numSamplesPos; i++)		///for the number of position samples
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  			{
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  				stim::vec3<float> temp = uniformRandVector();	///generate a random point on a plane.
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  				temp[0] = temp[0]*delta;
  				temp[1] = temp[1]*2*stim::PI;
  				
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  				temp[2] = 0.0;
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  				temp = temp.cyl2cart();
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  				pV.push_back(temp);				///save the point for further use.
                  		hor = stim::rect<float>(mag,			///generate a rectangle with the new vector as a normal.
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  					 temp, dir,
                        			((Y.cross(d)).cross(d))
  					.norm());
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                  		ver = stim::rect<float>(mag,			///generate another rectangle that's perpendicular the first but parallel to the cart vector.
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  					 temp, dir,
                          		hor.n());
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  				UpdateBuffer(0.0, 0.0+i*n_pixels);		///sample the necessary points and put them into a display list.
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  			}
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  			glEndList();					///finilize the display list.
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  			#ifdef DEBUG
  				for(int i = 0; i < numSamplesPos; i++)
  					std::cout << pV[i] << std::endl;
  			#endif
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  		}
  
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  		///@param float delta, How much the rectangles are allowed to expand.
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  		///Method for populating the buffer with the sampled texture.
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  		///Objects created are rectangles the with the created sizes.
  		///All points are sampled from a texture.
  		///Stored in a display list.
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  		///uses the default m <1,1,0>
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  		void
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  		genMagnitudeVectors(float delta = 0.70)
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  		{
  			
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  			//Set up the vectors necessary for Rectangle creation.
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  			stim::vec3<float> Y(1.0, 0.0, 0.0);		//orthogonal vec.
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  			stim::vec3<float> pos(0.0, 0.0, 0.0);		//center of the future rect.
  			float mag = 1.0;				///size of the rectangle
  			stim::vec3<float> dir(0.0, 0.0, 1.0);		///normal of the rectangle plane.
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  			//Set up the variable necessary for vector creation.
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  			float min 	= 1.0-delta;			///smallest size
  			float max 	= 1.0+delta;			///largers size.
  			float step	= (max-min)/(numSamplesMag-1);	///the size variation from one rect to the next.
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  			float factor;
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  			glNewList(dList+2, GL_COMPILE);
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  			for(int i = 0; i < numSamplesMag; i++){		///for the number of position samples
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  				//Create linear index
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  				factor = (min+step*i)*mag;		///scaling factor
  				mV.push_back(factor);			///save the size factor for further use.
  				hor = stim::rect<float>(factor,		///generate a rectangle with the new vector as a normal.
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  					 pos, dir, 
         	       				((Y.cross(d)).cross(d))
  					.norm());
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                 			ver = stim::rect<float>(factor,		///generate another rectangle that's perpendicular the first but parallel to the cart vector.
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  					 pos, dir,
                         			hor.n());
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  				UpdateBuffer(0.0, 0.0+i*n_pixels);	///sample the necessary points and put them into a display list.
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  			CHECK_OPENGL_ERROR
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  			}
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  			glEndList();					///finilize the displaylist.
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  		}
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  		///@param float delta, How much the rectangles are allowed to expand.
  		///Method for populating the buffer with the sampled texture.
  		///Objects created are rectangles the with the created sizes.
  		///All points are sampled from a texture.
  		///Stored in a display list.
  		///uses the default m <1,1,0>
  		void
  		genLengthVectors(float delta = 0.70)
  		{
  			
  			//Set up the vectors necessary for Rectangle creation.
  			stim::vec3<float> Y(1.0, 0.0, 0.0);		//orthogonal vec.
  			stim::vec3<float> pos(0.0, 0.0, 0.0);		//center of the future rect.
  			float mag = 1.0;				///size of the rectangle
  			stim::vec3<float> dir(0.0, 0.0, 1.0);		///normal of the rectangle plane.
  			stim::vec<float> temp(0.0,0.0,0.0);
  
  			//Set up the variable necessary for vector creation.
  			float min 	= 1.0-delta;			///smallest size
  			float max 	= 1.0+delta;			///largers size.
  			float step	= (max-min)/(numSamplesMag-1);	///the size variation from one rect to the next.
  			float factor;
  			glNewList(dList+3, GL_COMPILE);
  			for(int i = 0; i < numSamplesMag; i++){		///for the number of position samples
  				//Create linear index
  				factor = (min+step*i)*mag;		///scaling factor
  				lV.push_back(factor);			///save the size factor for further use.
  				temp[0] = factor;
  				temp[1] = mag;
  				hor = stim::rect<float>(temp,		///generate a rectangle with the new vector as a normal.
  					 pos, dir, 
         	       				((Y.cross(d)).cross(d))
  					.norm());
                 			ver = stim::rect<float>(temp,		///generate another rectangle that's perpendicular the first but parallel to the cart vector.
  					 pos, dir,
                         			hor.n());
  				UpdateBuffer(0.0, 0.0+i*n_pixels);	///sample the necessary points and put them into a display list.
  			CHECK_OPENGL_ERROR
  			}
  			glEndList();					///finilize the displaylist.
  		}
  
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  		///@param float v_x x-coordinate in buffer-space,
  		///@param float v_y y-coordinate in buffer-space.
  		///Samples the texture space.
   		///places a sample in the provided coordinates of bufferspace.
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  		void
  		UpdateBuffer(float v_x, float v_y)
  		{	
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  			stim::vec3<float>p1; 				///first point.
          	        stim::vec3<float>p2; 				///second point.
  	                stim::vec3<float>p3; 				///third point.
                  	stim::vec3<float>p4;				///fourth point.
  			p1 = hor.p(1,1);				///generate the top right point from the horizontal template.
  			p2 = hor.p(1,0);				///generate the bottom right point from the horizonatal template.
  			p3 = hor.p(0,0);				///generate the bottom left point from the horizontal template.
  			p4 = hor.p(0,1);				///generate the top left point from the horizonatal template.
  			glBegin(GL_QUADS);				///generate the Quad from the 4 points.
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  				glTexCoord3f(
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  					p1[0],
  					p1[1],
  					p1[2]
  					);
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  				glVertex2f(v_x,v_y);
  				glTexCoord3f(
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  					p2[0],
  					p2[1],
  					p2[2]
  					);
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  				glVertex2f(v_x+n_pixels, v_y);
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  				glTexCoord3f(
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  					p3[0],
  					p3[1],
  					p3[2]
  					);
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  				glVertex2f(v_x+n_pixels, v_y+n_pixels);
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  				glTexCoord3f(
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  					p4[0],
  					p4[1],
  					p4[2]
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  					);
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  				glVertex2f(v_x, v_y+n_pixels);
  			 glEnd();					///finish the quad.
  
  			 p1 = ver.p(1,1);				///generate the top right point from the vertical template.
  			 p2 = ver.p(1,0);                               ///generate the bottom right point from the vertical template.
  			 p3 = ver.p(0,0);                               ///generate the bottom left point from the vertical template.
  			 p4 = ver.p(0,1);                               ///generate the top left point from the vertical template.
  		 	 glBegin(GL_QUADS);				///generate the Quad from the 4 points.
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  				glTexCoord3f(
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  					p1[0],
  					p1[1],
  					p1[2]
  					);
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  				glVertex2f(v_x+n_pixels, v_y);
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  				glTexCoord3f(
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  					p2[0],
  					p2[1],
  					p2[2]
  					);
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  				glVertex2f(v_x+2.0*n_pixels, v_y);
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  				glTexCoord3f(
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  					p3[0],
  					p3[1],
  					p3[2]
  					);
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  				glVertex2f(v_x+2.0*n_pixels, v_y+n_pixels);
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  				glTexCoord3f(
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  					p4[0],
  					p4[1],
  					p4[2]
  					);
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  				glVertex2f(v_x+n_pixels, v_y+n_pixels);
  			glEnd(); 					///finish the quad.
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  		}
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  //--------------------------------------------------------------------------//
  //--------------------------------GL METHODS--------------------------------//
  //--------------------------------------------------------------------------//
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  		///@param uint width sets the width of the buffer.
  		///@param uint height sets the height of the buffer.
  		///@param GLuint &textureID gives the texture ID of the texture to be initialized.
  		///@param GLuint &framebufferID gives the buffer ID of the texture to be initialized.
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  		///Function for setting up the 2D buffer that stores the samples.
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  		///Initiates and sets parameters.
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  		void
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  		GenerateFBO(unsigned int width, unsigned int height, GLuint &textureID, GLuint &framebufferID)
  		{
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  			glDeleteFramebuffers(1, &framebufferID);				///clear the framebuffer.
  			glGenFramebuffers(1, &framebufferID);					///generate a clean buffer.
  			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);			///bind the new buffer.
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  //			int numChannels = 1;
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  //			unsigned char* texels = new unsigned char[width * height * numChannels];
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  			glGenTextures(1, &textureID);						///generate a texture that will attach to the buffer.
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  			glBindTexture(GL_TEXTURE_2D, textureID);
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  			//Textures repeat and use linear interpolation, luminance format.
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  			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_S, GL_CLAMP_TO_BORDER);		///Set up the texture to repeat at edges.
  			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_WRAP_T, GL_CLAMP_TO_BORDER);		
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  			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);	///Set up the texture to use Linear interpolation
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  			glTexParameteri(GL_TEXTURE_2D, GL_TEXTURE_MAG_FILTER, GL_LINEAR);
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  			glTexImage2D(GL_TEXTURE_2D, 0, GL_LUMINANCE,				///Create the texture with no data.
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  				 width, height, 0, GL_LUMINANCE, GL_UNSIGNED_BYTE, NULL);   
  //			delete[] texels;
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  			glBindFramebuffer(GL_FRAMEBUFFER, 0); 					///Bind the frontbuffer
  			glBindTexture(GL_TEXTURE_2D, 0);					///Unbind the texture.
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  		}
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  		///IF type == 0
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  		///Method for using the gl manipulation to align templates from
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  		///Template space (-0.5 0.5) to Texture space (0.0, 1.0),
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  		///Based on the p of the spider in real space (arbitrary).
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  		///IF type == 1
  		///Method for using the gl manipulation to set up a matrix 
  		///To transform from tissue space into texture space.
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  		///All transformation happen in glMatrixMode(GL_TEXTURE).
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  		///All transformation happen in glMatrixMode(GL_TEXTURE).
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  		void setMatrix(int type = 0)
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  		{
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  			if(type == 0)
  			{
  				float curTrans[16];			//array to store the matrix values.
  				stim::vec<float> rot = getRotation(d);	//get the rotation parameters for the current direction vector.
  				glMatrixMode(GL_TEXTURE);
  				glLoadIdentity();
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  				//Scale by the voxel size and number of slices.
  				glScalef(1.0/S[0]/R[0], 1.0/S[1]/R[1], 1.0/S[2]/R[2]);
  				//translate to the current position of the spider in the texture.
  				glTranslatef(p[0],
  					     p[1],
  					     p[2]);
  				//rotate to the current direction of the spider.
  				glRotatef(rot[0], rot[1], rot[2], rot[3]);
  				//scale to the magnitude of the spider.
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  				glScalef(m,
  					 m,
  					 m);
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  				//get and store the current transformation matrix for later use.
  				glGetFloatv(GL_TEXTURE_MATRIX, curTrans);
  				cT.set(curTrans);
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  				CHECK_OPENGL_ERROR
  				//revert back to default gl mode.
  				glMatrixMode(GL_MODELVIEW);
  			}
  			else if(type == 1)
  			{
  				glMatrixMode(GL_TEXTURE);
  				glLoadIdentity();
  				glScalef(1.0/S[0]/R[0], 1.0/S[1]/R[1], 1.0/S[2]/R[2]);
  				glMatrixMode(GL_MODELVIEW);
  			}
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  		}
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  		///Method for controling the buffer and texture binding.
  		///Clears the buffer upon binding.
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  		void
  		Bind()
  		{
  			glBindFramebuffer(GL_FRAMEBUFFER, direction_buffID);//set up GL buffer		
  			glFramebufferTexture2D(
  				GL_FRAMEBUFFER,
  				GL_COLOR_ATTACHMENT0,
  				GL_TEXTURE_2D,
  				direction_texID,
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  				0);			///Bind the texture to the 0th color attachement of the framebuffer
  			glBindFramebuffer(GL_FRAMEBUFFER, direction_buffID);	///Bind the buffer again (safety operation).
  			GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};		///Designate the texture to be the drawbuffer of the framebuffer
  			glDrawBuffers(1, DrawBuffers);				///Set the current drawbuffer to the texture.
  			glBindTexture(GL_TEXTURE_2D, direction_texID);		///Bind the Texture
  			glClearColor(1,1,1,1);					///Set clear color to white
  			glClear(GL_COLOR_BUFFER_BIT);				///Clear the texture
  			glMatrixMode(GL_PROJECTION);				
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  			glLoadIdentity();
  			glMatrixMode(GL_MODELVIEW);
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  			glLoadIdentity();					///Load identity matrix into the projection and modelview
  			glViewport(0,0,2.0*n_pixels, numSamples*n_pixels);	///Designate the viewport and orth
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  			gluOrtho2D(0.0,2.0*n_pixels,0.0,numSamples*n_pixels);
  			glEnable(GL_TEXTURE_3D);
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  			glBindTexture(GL_TEXTURE_3D, texID);			///Bind the larger 3D texture.
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  			CHECK_OPENGL_ERROR
  		}
  
  		///Method for controling the buffer and texture binding.
  		///Clears the buffer upon binding.
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  		///@param GLuint &textureID, texture to be bound.
  		///@param GLuint &framebufferID, framebuffer used for storage.
  		///@param int nSamples, number of rectanges to create. 
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  		void
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  		Bind(GLuint &textureID, GLuint &framebufferID, int nSamples, float len = 8.0)
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  		{
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  			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);	///Bind the framebuffer.
  			glFramebufferTexture2D(					///associate it with the texture
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  				GL_FRAMEBUFFER,
  				GL_COLOR_ATTACHMENT0,
  				GL_TEXTURE_2D,
  				textureID,
  				0);
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  			glBindFramebuffer(GL_FRAMEBUFFER, framebufferID);	///Bind the framebuffer.
  			GLenum DrawBuffers[1] = {GL_COLOR_ATTACHMENT0};		///generate the drawbuffer.
  			glDrawBuffers(1, DrawBuffers);				///set the drawbuffer.
  			glBindTexture(GL_TEXTURE_2D, textureID);		///Bind the texture passed.
  			glMatrixMode(GL_PROJECTION);				///clear out the draw matrices
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  			glLoadIdentity();
  			glMatrixMode(GL_MODELVIEW);
  			glLoadIdentity();
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  			glViewport(0,0,2.0*len, nSamples*len);			///set up viewport
  			gluOrtho2D(0.0,2.0*len,0.0,nSamples*len);		///Set up ortho
  			glEnable(GL_TEXTURE_3D);				
  			glBindTexture(GL_TEXTURE_3D, texID);			///bind the main texture (return to original state).
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  			CHECK_OPENGL_ERROR
  		}
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  		///Unbinds all texture resources.
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  		void
  		Unbind()
  		{
  			//Finalize GL_buffer
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  			glBindTexture(GL_TEXTURE_3D, 0);                      ///Bind the front buffer.
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  			CHECK_OPENGL_ERROR
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  			glBindTexture(GL_TEXTURE_2D, 0);                      ///Bind the default GL texture.
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  			CHECK_OPENGL_ERROR
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  			glBindFramebuffer(GL_FRAMEBUFFER, 0);		      ///Bind the defautl framebuffer.
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  			CHECK_OPENGL_ERROR
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  			glDisable(GL_TEXTURE_3D);			      ///Turn off texturing.
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  			CHECK_OPENGL_ERROR
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  		}
  
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  //--------------------------------------------------------------------------//
  //--------------------------------CUDA METHODS------------------------------//
  //--------------------------------------------------------------------------//
  		
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  		///Entry-point into the cuda code for calculating the cost of a given samples array (in texture form)
  		///finds the minimum cost and sets the current_cost to that value.
  		/// and returns the index of the template with the minimal cost. 
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  		int
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  		getCost(cudaTextureObject_t tObj, float* result, int n)
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  		{
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  			#ifdef TIMING
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  				gpuStartTimer();			///Add timing variables
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  			#endif
  			stim::vec<int> cost = 
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  				stim::cuda::get_cost(tObj, result, n, 2*n_pixels, n_pixels);	///call the cuda function with the appropriate texture buffer.
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  			#ifdef TIMING
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  				cost_time += gpuStopTimer();		
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  			#endif
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  			current_cost = cost[1];							///current cost.
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  			return cost[0];
  		}
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  	public:
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  		///ininializes the cuda device and environment.
  		void
  		initCuda()
  		{	
  			stim::cudaSetDevice();
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  		}
  
  		//horizonal rectangle forming the spider.
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  		stim::rect<float> hor;
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  		//vectical rectangle forming the spider.
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  		stim::rect<float> ver;	
  
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  		//Timing variables.
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  //--------------------------------------------------------------------------//
  //-----------------------------CONSTRUCTORS---------------------------------//
  //--------------------------------------------------------------------------//
  
  
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  		///@param int samples, the number of samples this spider is going to use.
  		///Best results if samples is can create a perfect root.
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  		///Default Constructor
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  		gl_spider
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  		(int samples = 1089, int samplespos = 441,int samplesmag = 144)
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  		{
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  			p = stim::vec3<float>(0.0, 0.0, 0.0);
  			d = stim::vec3<float>(0.0, 0.0, 1.0);
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  			m = 1.0;
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  			S = stim::vec3<float>(1.0, 1.0, 1.0);
  			R = stim::vec3<float>(1.0, 1.0, 1.0);
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  			numSamples = samples;
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  			numSamplesPos = samplespos;
  			numSamplesMag = samplesmag;
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  		#ifdef DEBUG
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  			iter = 0;
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  			iter_pos = 0;
  			iter_dir = 0;
  			iter_siz = 0;
  		#endif
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  		}
  
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  		///Position constructor: floats.
  		///@param float pos_x, position x.
  		///@param float pos_y, position y.
  		///@param float pos_z, position z.
  		///@param float dir_x, direction x.
  		///@param float dir_y, direction y.
  		///@param float dir_z, direction z.
  		///@param float mag_x, size of the vector.
  		///@param int 	samples, number of templates this spider is going to use.
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  		gl_spider
  		(float pos_x, float pos_y, float pos_z, float dir_x, float dir_y, float dir_z,
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  			float mag_x, int numsamples = 1089, int numsamplespos = 441, int numsamplesmag =144)
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  		{
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  			p = stim::vec3<float>(pos_x, pos_y, pos_z);
  			d = stim::vec3<float>(dir_x, dir_y, dir_z);
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  			m = mag_x;
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  			S = stim::vec3<float>(1.0,1.0,1.0);
  			R = stim::vec3<float>(1.0,1.0,1.0);
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  			numSamples = numsamples;
  			numSamplesPos = numsamplespos;
  			numSamplesMag = numsamplesmag;
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886
  		#ifdef DEBUG
47fe6300   Pavel Govyadinov   fixed an accident...
887
  			iter = 0;
4166e973   Pavel Govyadinov   Added debug tags ...
888
889
890
891
  			iter_pos = 0;
  			iter_dir = 0;
  			iter_siz = 0;
  		#endif
385d2447   Pavel Govyadinov   Checkpoint: Conve...
892
  		}
ac430567   Pavel Govyadinov   comments comments...
893
894
895
896
897
898
899
  
  		///Position constructor: vecs of floats.
  		///@param stim::vec<float> pos, position.
  		///@param stim::vec<float> dir, direction.
  		///@param float mag, size of the vector.
  		///@param int 	samples, number of templates this spider is going to use.
  		gl_spider
7d3162a2   Pavel Govyadinov   fixed majority of...
900
  		(stim::vec3<float> pos, stim::vec3<float> dir, float mag, int samples = 1089, int samplesPos = 441, int samplesMag = 144)
ac430567   Pavel Govyadinov   comments comments...
901
902
903
  		{
  			p = pos;
  			d = dir;
7f297fc6   Pavel Govyadinov   added more detail...
904
  			m = mag;
7d3162a2   Pavel Govyadinov   fixed majority of...
905
906
  			S = vec3<float>(1.0,1.0,1.0);
  			R = vec3<float>(1.0,1.0,1.0);
ac430567   Pavel Govyadinov   comments comments...
907
  			numSamples = samples;
035d798f   Pavel Govyadinov   modified the spid...
908
909
  			numSamplesPos = samplesPos;
  			numSamplesMag = samplesMag;
4166e973   Pavel Govyadinov   Added debug tags ...
910
  		#ifdef DEBUG
47fe6300   Pavel Govyadinov   fixed an accident...
911
  			iter = 0;
4166e973   Pavel Govyadinov   Added debug tags ...
912
913
914
915
  			iter_pos = 0;
  			iter_dir = 0;
  			iter_siz = 0;
  		#endif
ac430567   Pavel Govyadinov   comments comments...
916
917
  		}
  
8303b04d   Pavel Govyadinov   fixed the bug and...
918
  		///destructor deletes all the texture and buffer objects.
8e56a0a7   Pavel Govyadinov   Added the propose...
919
920
921
922
  		~gl_spider
  		(void)
  		{
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
923
924
925
926
927
928
  			glDeleteTextures(1, &direction_texID);
  			glDeleteBuffers(1, &direction_buffID);
  			glDeleteTextures(1, &position_texID);
  			glDeleteBuffers(1, &position_buffID);
  			glDeleteTextures(1, &radius_texID);
  			glDeleteBuffers(1, &radius_buffID);     
97508a2e   Pavel Govyadinov   Added mehtods for...
929
930
  			glDeleteTextures(1, &length_texID);
  			glDeleteBuffers(1, &length_buffID);     
7f297fc6   Pavel Govyadinov   added more detail...
931
932
  			glDeleteTextures(1, &cylinder_texID);
  			glDeleteBuffers(1, &cylinder_buffID);
8e56a0a7   Pavel Govyadinov   Added the propose...
933
934
  		}
  
ac430567   Pavel Govyadinov   comments comments...
935
  		///@param GLuint id, texture that is going to be sampled.
385d2447   Pavel Govyadinov   Checkpoint: Conve...
936
  		///Attached the spider to the texture with the given GLuint ID.
8e56a0a7   Pavel Govyadinov   Added the propose...
937
  		///Samples in the default d acting as the init method.
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
938
  		///Also acts an init.	
a9b45efe   Pavel Govyadinov   changes to spider
939
  		void
2a18be6d   Pavel Govyadinov   New comments and ...
940
  		attachSpider(GLuint id)
a9b45efe   Pavel Govyadinov   changes to spider
941
  		{
98eecaa9   David Mayerich   VS and win32 updates
942
943
944
945
946
947
948
949
950
  #ifdef TIMING
  			branch_time = 0;
  			direction_time = 0;
  			position_time = 0;
  			size_time = 0;
  			cost_time = 0;
  			network_time = 0;
  			hit_time = 0;
  #endif
47fe6300   Pavel Govyadinov   fixed an accident...
951
952
  #ifdef DEBUG
  			iter = 0;
4166e973   Pavel Govyadinov   Added debug tags ...
953
954
955
  			iter_pos = 0;
  			iter_dir = 0;
  			iter_siz = 0;
47fe6300   Pavel Govyadinov   fixed an accident...
956
  #endif
97508a2e   Pavel Govyadinov   Added mehtods for...
957
  			stepsize = 3.0;
7f297fc6   Pavel Govyadinov   added more detail...
958
  			n_pixels = 16.0;
98eecaa9   David Mayerich   VS and win32 updates
959
  
c0e09133   Pavel Govyadinov   STABLE: made temp...
960
  			srand(100);	
a9b45efe   Pavel Govyadinov   changes to spider
961
  			texID = id;
7f297fc6   Pavel Govyadinov   added more detail...
962
  			GenerateFBO(n_pixels*2, numSamples*n_pixels, direction_texID, direction_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
963
  			CHECK_OPENGL_ERROR
7f297fc6   Pavel Govyadinov   added more detail...
964
  			GenerateFBO(n_pixels*2, numSamplesPos*n_pixels, position_texID, position_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
965
  			CHECK_OPENGL_ERROR
7f297fc6   Pavel Govyadinov   added more detail...
966
  			GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, radius_texID, radius_buffID); 
97508a2e   Pavel Govyadinov   Added mehtods for...
967
968
  			CHECK_OPENGL_ERROR
  			GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, length_texID, length_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
969
  			CHECK_OPENGL_ERROR
7f297fc6   Pavel Govyadinov   added more detail...
970
  			GenerateFBO(16, 216, cylinder_texID, cylinder_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
971
  			CHECK_OPENGL_ERROR
09049866   Pavel Govyadinov   fixed a drawing b...
972
  			t_dir.MapCudaTexture(direction_texID, GL_TEXTURE_2D);
c37611a6   Pavel Govyadinov   removed the time ...
973
  			t_dir.Alloc(numSamples);
7f297fc6   Pavel Govyadinov   added more detail...
974
  			t_pos.MapCudaTexture(position_texID, GL_TEXTURE_2D);
c37611a6   Pavel Govyadinov   removed the time ...
975
  			t_pos.Alloc(numSamplesPos);
7f297fc6   Pavel Govyadinov   added more detail...
976
  			t_mag.MapCudaTexture(radius_texID, GL_TEXTURE_2D);
c37611a6   Pavel Govyadinov   removed the time ...
977
  			t_mag.Alloc(numSamplesMag);
8303b04d   Pavel Govyadinov   fixed the bug and...
978
979
  			t_len.MapCudaTexture(length_texID, GL_TEXTURE_2D);
  			t_len.Alloc(numSamplesMag);
5eeaf941   Pavel Govyadinov   changer to the ba...
980
  			setMatrix();
8303b04d   Pavel Govyadinov   fixed the bug and...
981
  			dList = glGenLists(4);
db3c28c9   Pavel Govyadinov   Implemented glDis...
982
  			glListBase(dList);
7f297fc6   Pavel Govyadinov   added more detail...
983
  			Bind(direction_texID, direction_buffID, numSamples, n_pixels);
b50c840e   David Mayerich   eliminated ANN fr...
984
  				genDirectionVectors(5*stim::PI/4);
3f15dade   Pavel Govyadinov   changed the plane...
985
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
986
  			Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
4166e973   Pavel Govyadinov   Added debug tags ...
987
  				genPositionVectors(0.2);
3f15dade   Pavel Govyadinov   changed the plane...
988
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
989
  			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
035d798f   Pavel Govyadinov   modified the spid...
990
  				genMagnitudeVectors();
3f15dade   Pavel Govyadinov   changed the plane...
991
  			Unbind();
97508a2e   Pavel Govyadinov   Added mehtods for...
992
993
994
  			Bind(length_texID, length_buffID, numSamplesMag, n_pixels);
  				genLengthVectors();
  			Unbind();
a39577bf   Pavel Govyadinov   Changes to the sp...
995
  		}
5f81932b   David Mayerich   restored Pavel's ...
996
  		
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
997
998
999
  //--------------------------------------------------------------------------//
  //-----------------------------ACCESS METHODS-------------------------------//
  //--------------------------------------------------------------------------//
8e56a0a7   Pavel Govyadinov   Added the propose...
1000
  		///Returns the p vector.
7d3162a2   Pavel Govyadinov   fixed majority of...
1001
  		vec3<float>
a39577bf   Pavel Govyadinov   Changes to the sp...
1002
  		getPosition()
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1003
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1004
  			return p;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1005
1006
  		}
  	
8e56a0a7   Pavel Govyadinov   Added the propose...
1007
  		///Returns the d vector.
7d3162a2   Pavel Govyadinov   fixed majority of...
1008
  		vec3<float>
a39577bf   Pavel Govyadinov   Changes to the sp...
1009
  		getDirection()
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1010
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1011
  			return d;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1012
1013
  		}
  
8e56a0a7   Pavel Govyadinov   Added the propose...
1014
  		///Returns the m vector.
09049866   Pavel Govyadinov   fixed a drawing b...
1015
  		float	
a39577bf   Pavel Govyadinov   Changes to the sp...
1016
  		getMagnitude()
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1017
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1018
  			return m;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1019
1020
  		}
  	
ac430567   Pavel Govyadinov   comments comments...
1021
  		///@param stim::vec<float> pos, the new p.
8e56a0a7   Pavel Govyadinov   Added the propose...
1022
  		///Sets the p vector to input vector pos.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1023
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1024
  		setPosition(stim::vec3<float> pos)
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1025
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1026
  			p = pos;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1027
  		}
385d2447   Pavel Govyadinov   Checkpoint: Conve...
1028
  
ac430567   Pavel Govyadinov   comments comments...
1029
1030
1031
  		///@param float x x-coordinate.
  		///@param float y y-coordinate.
  		///@param float z z-coordinate.
8e56a0a7   Pavel Govyadinov   Added the propose...
1032
  		///Sets the p vector to the input float coordinates x,y,z.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1033
1034
1035
  		void
  		setPosition(float x, float y, float z)
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1036
1037
1038
  			p[0] = x;
  			p[1] = y;
  			p[2] = z;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1039
  		}
887a3e49   Pavel Govyadinov   fixed some order ...
1040
  		
ac430567   Pavel Govyadinov   comments comments...
1041
  		///@param stim::vec<float> dir, the new d.
8e56a0a7   Pavel Govyadinov   Added the propose...
1042
  		///Sets the d vector to input vector dir.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1043
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1044
  		setDirection(stim::vec3<float> dir)
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1045
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1046
  			d = dir;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1047
1048
  		}
  		
ac430567   Pavel Govyadinov   comments comments...
1049
1050
1051
  		///@param stim::vec<float> x x-coordinate.
  		///@param stim::vec<float> y y-coordinate.
  		///@param stim::vec<float> z z-coordinate.
8e56a0a7   Pavel Govyadinov   Added the propose...
1052
  		///Sets the d vector to the input float coordinates x,y,z.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1053
1054
1055
  		void
  		setDirection(float x, float y, float z)
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1056
1057
1058
  			d[0] = x;
  			d[1] = y;
  			d[2] = z;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1059
  		}
385d2447   Pavel Govyadinov   Checkpoint: Conve...
1060
  			
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1061
  		
ac430567   Pavel Govyadinov   comments comments...
1062
  		///@param float mag, size of the sampled region.
97508a2e   Pavel Govyadinov   Added mehtods for...
1063
  		///Sets the m value to the input mag for both templates.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1064
  		void
5f81932b   David Mayerich   restored Pavel's ...
1065
  		setMagnitude(float mag)
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1066
  		{
7f297fc6   Pavel Govyadinov   added more detail...
1067
  			m = mag;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1068
  		}
97508a2e   Pavel Govyadinov   Added mehtods for...
1069
1070
1071
1072
1073
1074
1075
1076
  
  		///@param float len, length of the sampled region.
  		///Sets the length value to the input len for both templates.
  		void
  		setLength(float len)
  		{
  			length = len;
  		}
5f81932b   David Mayerich   restored Pavel's ...
1077
  		
ac430567   Pavel Govyadinov   comments comments...
1078
1079
1080
1081
  		///@param float x, voxel size in the x direction.
  		///@param float y, voxel size in the y direction.
  		///@param float z, voxel size in the z direction.
  		///Sets the voxel sizes in each direction. necessary for non-standard data.
8e56a0a7   Pavel Govyadinov   Added the propose...
1082
1083
1084
1085
1086
1087
1088
1089
  		void
  		setDims(float x, float y, float z)
  		{
  			S[0] = x;
  			S[1] = y;
  			S[2] = z;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1090
1091
1092
  		///@param stim::vec<float> Dims, voxel size.
  		///Sets the voxel sizes in each direction. necessary for non-standard data.
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1093
  		setDims(stim::vec3<float> Dims)
ac430567   Pavel Govyadinov   comments comments...
1094
1095
1096
1097
1098
1099
1100
1101
  		{
  			S = Dims;
  		}
  
  		///@param float x, size of the data in the x direction.
  		///@param float y, size of the data in the y direction.
  		///@param float z, size of the data in the z direction.
  		///Sets the data volume sizes in each direction.
b710b044   Pavel Govyadinov   Added more tempor...
1102
  		void
8e56a0a7   Pavel Govyadinov   Added the propose...
1103
  		setSize(float x, float y, float z)
b710b044   Pavel Govyadinov   Added more tempor...
1104
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1105
1106
1107
  			R[0] = x;
  			R[1] = y;
  			R[2] = z;
b710b044   Pavel Govyadinov   Added more tempor...
1108
  		}
ac430567   Pavel Govyadinov   comments comments...
1109
1110
1111
1112
  
  		///@param stim::vec<float> Dims, size of the volume.
  		///Sets the data volume sizes in each direction.
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1113
  		setSize(stim::vec3<float> Siz)
ac430567   Pavel Govyadinov   comments comments...
1114
1115
1116
  		{
  			S = Siz;
  		}
b710b044   Pavel Govyadinov   Added more tempor...
1117
  		
ac430567   Pavel Govyadinov   comments comments...
1118
1119
1120
1121
  		///@param stim::vec<float> dir, the vector to which we are rotating.
  		///given a vector to align to, finds the required axis and angle for glRotatef.
  		///rotates from 0.0, 0.0, 1.0 to dir.
  		///return is in degrees for use with glRotatef.
5eeaf941   Pavel Govyadinov   changer to the ba...
1122
  		stim::vec<float>
4fa3f483   Pavel Govyadinov   Fixed the memory ...
1123
  		getRotation(stim::vec3<float> dir)
f304d6de   Pavel Govyadinov   added rotation to...
1124
  		{
8303b04d   Pavel Govyadinov   fixed the bug and...
1125
1126
1127
1128
  			stim::vec<float> out(0.0,0.0,0.0,0.0);	///The 4D rotation matrix for GL rotation
  			stim::vec3<float> from(0.0,0.0,1.0); 	///Converting from template always involves 0,0,1 as a starting vector
  			out[0] = acos(dir.dot(from))*180/stim::PI; ///angle of rotation
  			if(out[0] < 1.0){
f304d6de   Pavel Govyadinov   added rotation to...
1129
1130
1131
1132
  				out[0] = 0.0;
  				out[1] = 0.0;
  				out[2] = 0.0;
  				out[3] = 1.0;
8303b04d   Pavel Govyadinov   fixed the bug and...
1133
1134
  			}					///if we rotate less what one degree don't rotate
  			else if(out[0] < -179.0)		///if we rotate more than -179 degrees rotate 180.
f7b84fb2   Pavel Govyadinov   more debug statem...
1135
1136
1137
1138
1139
  			{
  				out[0] = 180.0;
  				out[1] = 1.0;
  				out[2] = 0.0;
  				out[3] = 0.0;
8303b04d   Pavel Govyadinov   fixed the bug and...
1140
  			} else {				///the rotational axis is the cross fromxdir.
4166e973   Pavel Govyadinov   Added debug tags ...
1141
1142
  				stim::vec3<float> temp(0.0, 0.0, 0.0);;
  				temp = (from.cross(dir)).norm();
f304d6de   Pavel Govyadinov   added rotation to...
1143
1144
1145
1146
  				out[1] = temp[0];
  				out[2] = temp[1];
  				out[3] = temp[2];
  			}
97508a2e   Pavel Govyadinov   Added mehtods for...
1147
1148
1149
1150
  			#ifdef DEBUG
  				std::cout << "out is " << out << std::endl;
  				std::cout << "when rotating from " << from << " to " << dir << std::endl;
  			#endif
f304d6de   Pavel Govyadinov   added rotation to...
1151
1152
  			return out;
  		}
84eff8b1   Pavel Govyadinov   Merged only the n...
1153
  
ac430567   Pavel Govyadinov   comments comments...
1154
  		///@param stim::vec<float> pos, the position of the seed to be added.
84eff8b1   Pavel Govyadinov   Merged only the n...
1155
1156
1157
  		///Adds a seed to the seed list.
  		///Assumes that the coordinates passes are in tissue space.
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1158
  		setSeed(stim::vec3<float> pos)
a9b45efe   Pavel Govyadinov   changes to spider
1159
  		{
84eff8b1   Pavel Govyadinov   Merged only the n...
1160
  			seeds.push(pos);
a9b45efe   Pavel Govyadinov   changes to spider
1161
  		}
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1162
  
ac430567   Pavel Govyadinov   comments comments...
1163
1164
  		///@param stim::vec<float> dir, the direction of the seed to be added.
  		///Adds a seed to the seed directions list.
79a9bf3f   Pavel Govyadinov   new implementatio...
1165
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1166
  		setSeedVec(stim::vec3<float> dir)
59781ee3   Pavel Govyadinov   fixed a stask bug...
1167
1168
1169
1170
  		{
  			seedsvecs.push(dir);
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1171
1172
1173
  		///@param float mag, the size of the seed to be added.
  		///Adds a seed to the seed list.
  		///Assumes that the coordinates passes are in tissue space.
59781ee3   Pavel Govyadinov   fixed a stask bug...
1174
1175
  		void
  		setSeedMag(float mag)
79a9bf3f   Pavel Govyadinov   new implementatio...
1176
  		{
59781ee3   Pavel Govyadinov   fixed a stask bug...
1177
  			seedsmags.push(mag);
84eff8b1   Pavel Govyadinov   Merged only the n...
1178
  		}
79a9bf3f   Pavel Govyadinov   new implementatio...
1179
  
59781ee3   Pavel Govyadinov   fixed a stask bug...
1180
  
ac430567   Pavel Govyadinov   comments comments...
1181
1182
1183
  		///@param float x, x-position of the seed to be added.
  		///@param float y, y-position of the seed to be added.
  		///@param float z, z-position of the seed to be added.
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  		///Adds a seed to the seed list.
  		///Assumes that the coordinates passes are in tissue space.
  		void
  		setSeed(float x, float y, float z)
  		{
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  			seeds.push(stim::vec<float>(x, y, z));
  		}
  
ac430567   Pavel Govyadinov   comments comments...
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  		///@param float x, x-direction of the seed to be added.
  		///@param float y, y-direction of the seed to be added.
  		///@param float z, z-direction of the seed to be added.
  		///Adds a seed to the seed directions list.
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  		void
  		setSeedVec(float x, float y, float z)
  		{
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  			seedsvecs.push(stim::vec<float>(x, y, z));
  		}
ac430567   Pavel Govyadinov   comments comments...
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  		///Method to get the top of the seed positions stack.
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1203
  		stim::vec3<float> 
84eff8b1   Pavel Govyadinov   Merged only the n...
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  		getLastSeed()
  		{
7d3162a2   Pavel Govyadinov   fixed majority of...
1206
  			stim::vec3<float> tp = seeds.top();
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  			return tp;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
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  		///Method to get the top of the seed direction stack.
7d3162a2   Pavel Govyadinov   fixed majority of...
1211
  		stim::vec3<float> 
59781ee3   Pavel Govyadinov   fixed a stask bug...
1212
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  		getLastSeedVec()
  		{
7d3162a2   Pavel Govyadinov   fixed majority of...
1214
  			stim::vec3<float> tp = seedsvecs.top();
59781ee3   Pavel Govyadinov   fixed a stask bug...
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  			return tp;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1218
  		///Method to get the top of the seed magnitude stack.
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  		float
  		getLastSeedMag()
  		{
  			float tp = seedsmags.top();
  			return tp;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1226
  		///deletes all data associated with the last seed.
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  		void
  		popSeed()
  		{
  			seeds.pop();
  			seedsvecs.pop();
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1232
  			seedsmags.pop();
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1233
  		}
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  		///returns the seeds position stack.
7d3162a2   Pavel Govyadinov   fixed majority of...
1236
  		std::stack<stim::vec3<float> >
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  		getSeeds()
  		{
  			return seeds;
  		}
  
efe7b7cc   Pavel Govyadinov   Added a detailed ...
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  		///sets the number of direction templates.
  		void
  		setNumberDirectionTemplates(int n)
  		{
  			numSamples = n;
  		}
  
  		///sets the number of position templates.
  		void
  		setNumberPositionTemplates(int n)
  		{
  			numSamplesPos = n;
  		}
  
  		///sets the number of position templates.
  		void
  		setNumberSizeTemplates(int n)
  		{
  			numSamplesMag = n;
  		}
  
  		#ifdef TIMING
  		///Returns the timings at the moment the method is called.
  		///In the following order: Branch, Direction, Position, Size, Cost, Network, Hit_detetion.
  		std::vector<double> 
  		getTimings()
  		{
  			std::vector <double> ret;
  			ret.resize(7);
  			ret[0] = branch_time;
  			ret[1] = direction_time;
  			ret[2] = position_time;
  			ret[3] = size_time;
  			ret[4] = cost_time;
  			ret[5] = network_time;
  			ret[6] = hit_time;
  
  			return ret;
  		}
  		#endif
  
ac430567   Pavel Govyadinov   comments comments...
1283
  		///returns true if all seed stacks are empty, else false.
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  		bool
  		Empty()
  		{
ac430567   Pavel Govyadinov   comments comments...
1287
  			//return (seeds.empty() && seedsvecs.empty() && seedsmags.empty());
1306fd96   Pavel Govyadinov   minor bug fixes i...
1288
  			return (seeds.empty() && seedsvecs.empty());
84eff8b1   Pavel Govyadinov   Merged only the n...
1289
  		}
ac430567   Pavel Govyadinov   comments comments...
1290
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  		///@param std::string file:file with variables to populate the seed stacks.
  		///Adds a seed to the seed list, including the position, direction and magnitude.
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  		///Assumes that the coordinates passes are in tissue space.
  		void
  		setSeeds(std::string file)
  		{
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1297
  			std::ifstream myfile(file.c_str()); 	///open a stream
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  			string line;
  			if(myfile.is_open())
             		{
                     		while (getline(myfile, line))
                     		{
8303b04d   Pavel Govyadinov   fixed the bug and...
1303
                             		float x, y, z, u, v, w, m;	///read the xyz uvw and m coordinates.
ac430567   Pavel Govyadinov   comments comments...
1304
                             		myfile >> x >> y >> z >> u >> v >> w >> m;
8761b649   Pavel Govyadinov   moved a lot of th...
1305
  					setSeed(x, y, z);
ac430567   Pavel Govyadinov   comments comments...
1306
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  					setSeedVec(u, v, w);
  					setSeedMag(m);
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                     		}
                     	myfile.close();
  	          	} else {
          	                  std::cerr<<"failed" << std::endl;
  			}
79a9bf3f   Pavel Govyadinov   new implementatio...
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  		}
  		
ac430567   Pavel Govyadinov   comments comments...
1315
  		///Saves the network to a file.
79a9bf3f   Pavel Govyadinov   new implementatio...
1316
  		void
84eff8b1   Pavel Govyadinov   Merged only the n...
1317
  		saveNetwork(std::string name)
79a9bf3f   Pavel Govyadinov   new implementatio...
1318
  		{
0311ab81   Pavel Govyadinov   fixed some issues...
1319
  /*			stim::glObj<float> sk;
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1320
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1322
  			for(int i = 0; i < nt.sizeE(); i++)
  			{
  				std::vector<stim::vec< float > > cm = nt.getEdgeCenterLineMag(i);
7d3162a2   Pavel Govyadinov   fixed majority of...
1323
                   		std::vector<stim::vec3< float > > ce = nt.getEdgeCenterLine(i);
8761b649   Pavel Govyadinov   moved a lot of th...
1324
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  				sk.Begin(stim::OBJ_LINE);
  				for(int j = 0; j < ce.size(); j++)
  				{
  					sk.TexCoord(cm[j][0]);
  					sk.Vertex(ce[j][0], ce[j][1], ce[j][2]);
  				}
  				sk.End();
  			}	
0311ab81   Pavel Govyadinov   fixed some issues...
1332
  */			sk.save(name);
79a9bf3f   Pavel Govyadinov   new implementatio...
1333
  		}
84eff8b1   Pavel Govyadinov   Merged only the n...
1334
  
8761b649   Pavel Govyadinov   moved a lot of th...
1335
  		///Depreciated, but might be reused later()
ac430567   Pavel Govyadinov   comments comments...
1336
  		///returns a COPY of the entire stim::glObj object.
84eff8b1   Pavel Govyadinov   Merged only the n...
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  		stim::glObj<float>
  		getNetwork()
  		{
0311ab81   Pavel Govyadinov   fixed some issues...
1340
  			return sk;
84eff8b1   Pavel Govyadinov   Merged only the n...
1341
  		}
ac430567   Pavel Govyadinov   comments comments...
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  		///returns a COPY of the entire stim::glnetwork object.
  		stim::glnetwork<T>
  		getGLNetwork()
  		{
  			return nt;
  		}
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  		///Function to get back the framebuffer Object attached to the spider.
  		///For external access.
  		GLuint
  		getFB()
  		{
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1355
  			return cylinder_buffID;
84eff8b1   Pavel Govyadinov   Merged only the n...
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  		}
  
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
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  //--------------------------------------------------------------------------//
  //-----------------------------TEMPORARY METHODS----------------------------//
  //--------------------------------------------------------------------------//
  
  		///temporary Method necessary for visualization and testing.
  		void
  		Update()
  		{
7d3162a2   Pavel Govyadinov   fixed majority of...
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  			vec3<float> Y(1.0,0.0,0.0);
8e56a0a7   Pavel Govyadinov   Added the propose...
1367
  			if(cos(Y.dot(d))< 0.087){
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
1368
  				Y[0] = 0.0; Y[1] = 1.0;}
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  			hor = stim::rect<float>(m, p, d.norm(),
  				((Y.cross(d)).cross(d)).norm());
  			ver = stim::rect<float>(m, p, d.norm(),
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  				 hor.n());
  		}
  
  
c4887649   Pavel Govyadinov   fixed a significa...
1376
  		int
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  		Step()
  		{
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1379
  			#ifdef DEBUG
09049866   Pavel Govyadinov   fixed a drawing b...
1380
  			std::cerr << "Took a step" << std::endl;
4166e973   Pavel Govyadinov   Added debug tags ...
1381
  			#endif
7f297fc6   Pavel Govyadinov   added more detail...
1382
  			Bind(direction_texID, direction_buffID, numSamples, n_pixels);
84eff8b1   Pavel Govyadinov   Merged only the n...
1383
  			CHECK_OPENGL_ERROR
035d798f   Pavel Govyadinov   modified the spid...
1384
  				findOptimalDirection();
3f15dade   Pavel Govyadinov   changed the plane...
1385
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
1386
  			Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
035d798f   Pavel Govyadinov   modified the spid...
1387
  				findOptimalPosition();
3f15dade   Pavel Govyadinov   changed the plane...
1388
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
1389
  			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
97508a2e   Pavel Govyadinov   Added mehtods for...
1390
  				findOptimalRadius();
3f15dade   Pavel Govyadinov   changed the plane...
1391
  			Unbind();
84eff8b1   Pavel Govyadinov   Merged only the n...
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  			CHECK_OPENGL_ERROR
  
59781ee3   Pavel Govyadinov   fixed a stask bug...
1394
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  			return current_cost;
  		}
  
556c4e15   Pavel Govyadinov   Changed the handl...
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1400
  
  		void
  		printTransform()
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1401
  			std::cout << cT << std::endl;
b710b044   Pavel Govyadinov   Added more tempor...
1402
  		}
a9b45efe   Pavel Govyadinov   changes to spider
1403
  
f31bf86d   Pavel Govyadinov   Added skeleton fu...
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  //--------------------------------------------------------------------------//
  //-----------------------------EXPERIMENTAL METHODS-------------------------//
  //--------------------------------------------------------------------------//
  
  		void
34ec8a82   David Mayerich   added comments
1410
  		MonteCarloDirectionVectors(int nSamples, float solidAngle = stim::TAU)
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1411
  		{
0311ab81   Pavel Govyadinov   fixed some issues...
1412
1413
1414
  //			float PHI[2];//, Z[2];//, range;
  //			PHI[0] = asin(solidAngle/2);
  //			PHI[1] = asin(0);
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1415
  			
0311ab81   Pavel Govyadinov   fixed some issues...
1416
1417
  //			Z[0] = cos(PHI[0]);
  //			Z[1] = cos(PHI[1]);
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1418
  			
0311ab81   Pavel Govyadinov   fixed some issues...
1419
  //			range = Z[0] - Z[1];
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1420
  
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1421
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  			std::vector<stim::vec3<float> > vecsUni;
  			for(int i = 0; i < numSamplesPos; i++)
  			{
  				stim::vec3<float> a(uniformRandom()*0.8, uniformRandom()*0.8, 0.0);
  				a[0] = a[0]-0.4;
  				a[1] = a[1]-0.4;
  				vecsUni.push_back(a);
  			}
  
  			stringstream name;
  			for(int i = 0; i < numSamplesPos; i++)
  				name << vecsUni[i].str() << std::endl;
  			
  			std::ofstream outFile;
  			outFile.open("New_Pos_Vectors.txt");
  			outFile << name.str().c_str();
  		}
97508a2e   Pavel Govyadinov   Added mehtods for...
1438
  /*
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1439
  		void
f31bf86d   Pavel Govyadinov   Added skeleton fu...
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  		DrawCylinder()
  		{	 
f31bf86d   Pavel Govyadinov   Added skeleton fu...
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  			 glNewList(dList+3, GL_COMPILE);
  			 float z0 = -0.5; float z1 = 0.5; float r0 = 0.5;
97508a2e   Pavel Govyadinov   Added mehtods for...
1444
        			 float x,y;
84eff8b1   Pavel Govyadinov   Merged only the n...
1445
  			 float xold = 0.5; float yold = 0.0;
ac430567   Pavel Govyadinov   comments comments...
1446
1447
  			 float step = 360.0/numSamples*32;
  			 //float step = 360.0/8.0;
f31bf86d   Pavel Govyadinov   Added skeleton fu...
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  			 glEnable(GL_TEXTURE_3D);
  			 glBindTexture(GL_TEXTURE_3D, texID);
ac430567   Pavel Govyadinov   comments comments...
1450
  			 glBegin(GL_QUAD_STRIP);
84eff8b1   Pavel Govyadinov   Merged only the n...
1451
  			 int j = 0;
f31bf86d   Pavel Govyadinov   Added skeleton fu...
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  			 	for(float i = step; i <= 360.0; i += step)
  			 	{
b50c840e   David Mayerich   eliminated ANN fr...
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  					 x=r0*cos(i*stim::TAU/360.0);
  					 y=r0*sin(i*stim::TAU/360.0);
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1456
  					 glTexCoord3f(x,y,z0); 
ac430567   Pavel Govyadinov   comments comments...
1457
1458
  					 glVertex2f(0.0, j*6.4+6.4);
  //					 glVertex2f(0.0, j*27.0+27.0);
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1459
  					 glTexCoord3f(x,y,z1); 
ac430567   Pavel Govyadinov   comments comments...
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1461
  					 glVertex2f(16.0, j*6.4+6.4);
  //					 glVertex2f(16.0, j*27.0+27.0);
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1462
  					 glTexCoord3f(xold,yold,z1); 
ac430567   Pavel Govyadinov   comments comments...
1463
1464
  					 glVertex2f(16.0, j*6.4); 
  //					 glVertex2f(16.0, j*27.0); 
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1465
  					 glTexCoord3f(xold,yold,z0); 
ac430567   Pavel Govyadinov   comments comments...
1466
1467
  					 glVertex2f(0.0, j*6.4);
  //					 glVertex2f(0.0, j*27.0);
f31bf86d   Pavel Govyadinov   Added skeleton fu...
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  					 xold=x;
  					 yold=y;
  					 j++;
  				}
  		      	 glEnd();  
  			 glEndList();
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1474
  		}
97508a2e   Pavel Govyadinov   Added mehtods for...
1475
  */
8c4f5d84   Pavel Govyadinov   fixed the issue w...
1476
  ///need to return the cylinder.
7f297fc6   Pavel Govyadinov   added more detail...
1477
  ///SOMETHING MIGHT BE GOING ON HERE IN GENERATE BUFFER.
e45b97ce   Pavel Govyadinov   safety commit, I ...
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  		void
  		DrawLongCylinder(int n = 8, int l_template = 8,int l_square = 8)
  		{
  			int cylLen = cL.size()-1;
7f297fc6   Pavel Govyadinov   added more detail...
1482
1483
  			GenerateFBO(n*l_square, cylLen*l_template, cylinder_texID, cylinder_buffID);
  			Bind(cylinder_texID, cylinder_buffID, cylLen, l_template*l_square/2.0);
e45b97ce   Pavel Govyadinov   safety commit, I ...
1484
  			stim::cylinder<float> cyl(cL, cM);
7d3162a2   Pavel Govyadinov   fixed majority of...
1485
  			std::vector<std::vector<stim::vec3<float> > > p = cyl.getPoints(n);
e45b97ce   Pavel Govyadinov   safety commit, I ...
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  			for(int i = 0; i < p.size()-1; i++)	///number of circles
  			{
  				for(int j = 0; j < p[0].size()-1; j++)		///points in the circle
  				{
  					glBegin(GL_QUADS);
  						glTexCoord3f(p[i][j][0], p[i][j][1], p[i][j][2]);
  						glVertex2f(j*l_square,  i*(float)l_template); 
  
  						glTexCoord3f(p[i][j+1][0], p[i][j+1][1], p[i][j+1][2]);
  						glVertex2f(j*l_square+l_square, i*(float)l_template); 
  
  						glTexCoord3f(p[i+1][j+1][0], p[i+1][j+1][1], p[i+1][j+1][2]);
  						glVertex2f(j*l_square+l_square, i*(float)l_template+(float)l_template); 
  
  						glTexCoord3f(p[i+1][j][0], p[i+1][j][1], p[i+1][j][2]);
  						glVertex2f(j*l_square,i*(float)l_template+(float)l_template); 
  					glEnd();
  				}
  			}
  			Unbind();
  		}
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  		///@param min_cost the cost value used for tracing
  		///traces out each seedpoint in the seeds queue to completion in both directions.
  		void
  		trace(int min_cost)
  		{	
7d3162a2   Pavel Govyadinov   fixed majority of...
1514
1515
  			stim::vec3<float> curSeed; 
  			stim::vec3<float> curSeedVec;			
8761b649   Pavel Govyadinov   moved a lot of th...
1516
1517
  			float curSeedMag;
  			while(!Empty())
84eff8b1   Pavel Govyadinov   Merged only the n...
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1520
  			{
  				//clear the currently traced line and start a new one.
  				cL.clear();
ac430567   Pavel Govyadinov   comments comments...
1521
  				cM.clear();
8761b649   Pavel Govyadinov   moved a lot of th...
1522
1523
1524
1525
  				cD.clear();
  				curSeed = seeds.top();
  				curSeedVec = seedsvecs.top();
  				curSeedMag = seedsmags.top();
59781ee3   Pavel Govyadinov   fixed a stask bug...
1526
1527
  				seeds.pop();
  				seedsvecs.pop();
ac430567   Pavel Govyadinov   comments comments...
1528
  				seedsmags.pop();
84eff8b1   Pavel Govyadinov   Merged only the n...
1529
1530
  				setPosition(curSeed);
  				setDirection(curSeedVec);
8761b649   Pavel Govyadinov   moved a lot of th...
1531
  				setMagnitude(curSeedMag);
4166e973   Pavel Govyadinov   Added debug tags ...
1532
1533
1534
1535
1536
1537
1538
1539
1540
  
  				#ifdef DEBUG
  					std::cout << "The new seed " << curSeed << curSeedVec << curSeedMag << std::endl;
  				#endif
  				
  //			Bind(direction_texID, direction_buffID, numSamples, n_pixels);
  //			CHECK_OPENGL_ERROR
  //				findOptimalDirection();
  //			Unbind();
ec9d82e1   Pavel Govyadinov   finished the debu...
1541
1542
  //THIS IS EXPERIMENTAL
  			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
97508a2e   Pavel Govyadinov   Added mehtods for...
1543
  				findOptimalRadius();
ec9d82e1   Pavel Govyadinov   finished the debu...
1544
1545
  			Unbind();
  //THIS IS EXPERIMENTAL
0311ab81   Pavel Govyadinov   fixed some issues...
1546
  
8761b649   Pavel Govyadinov   moved a lot of th...
1547
1548
1549
  //				cL.push_back(curSeed);
  //				cM.push_back(curSeedMag);
  //				cD.push_back(curSeedMag);
0311ab81   Pavel Govyadinov   fixed some issues...
1550
  				traceLine(p, m, min_cost);
84eff8b1   Pavel Govyadinov   Merged only the n...
1551
  			}
84eff8b1   Pavel Govyadinov   Merged only the n...
1552
1553
  		}
  
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1554
  		int
7d3162a2   Pavel Govyadinov   fixed majority of...
1555
  		selectObject(stim::vec3<float> loc, stim::vec3<float> dir, float mag) 
84eff8b1   Pavel Govyadinov   Merged only the n...
1556
1557
  		{
  		//Define the varibles and turn on Selection Mode
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1558
1559
1560
1561
  			
  			#ifdef TIMING
  				gpuStartTimer();
  			#endif
84eff8b1   Pavel Govyadinov   Merged only the n...
1562
  
363243dc   Pavel Govyadinov   More comments
1563
1564
1565
1566
1567
  			GLuint selectBuf[2048];			///size of the selection buffer in bytes.
  			GLint hits;				///hit fibers
  			glSelectBuffer(2048, selectBuf);	///bind the selection mode to the selection buffer.
  			glDisable(GL_CULL_FACE);		///Disable cullFace
  			(void) glRenderMode(GL_SELECT);		///initialize GL select mode.
84eff8b1   Pavel Govyadinov   Merged only the n...
1568
1569
  		//Init Names stack
  
363243dc   Pavel Govyadinov   More comments
1570
1571
  			glInitNames();				///Initialize the naming array.
  			glPushName(1);				///Push a single name to the stack.
84eff8b1   Pavel Govyadinov   Merged only the n...
1572
1573
1574
  
  			CHECK_OPENGL_ERROR
  		//What would that vessel see in front of it.
363243dc   Pavel Govyadinov   More comments
1575
1576
  				camSel.setPosition(loc);		///Set the viewing camera
  				camSel.setFocalDistance(mag/stepsize);	///Set how far the fiber looks forward.
6ada8448   Pavel Govyadinov   Reverted to 40db1...
1577
1578
  				camSel.LookAt((loc[0]+dir[0]*mag/stepsize),
  					 (loc[1]+dir[1]*mag/stepsize),
363243dc   Pavel Govyadinov   More comments
1579
1580
  					 (loc[2]+dir[2]*mag/stepsize)); ///Set the look direction
  				ps  = camSel.getPosition();		///get all the necessary rotation variable for openGL
84eff8b1   Pavel Govyadinov   Merged only the n...
1581
1582
  				ups = camSel.getUp();
  				ds  = camSel.getLookAt();
363243dc   Pavel Govyadinov   More comments
1583
1584
  				glMatrixMode(GL_PROJECTION);		///Push the projection matrix.
  				glPushMatrix();				///Reset the current projection matrix
84eff8b1   Pavel Govyadinov   Merged only the n...
1585
  				glLoadIdentity();
363243dc   Pavel Govyadinov   More comments
1586
  				glOrtho(-mag/stepsize/2.0, mag/stepsize/2.0, -mag/stepsize/2.0, mag/stepsize/2.0, 0.0, mag/stepsize/2.0);			///Finalize the look paramenters
84eff8b1   Pavel Govyadinov   Merged only the n...
1587
1588
1589
1590
1591
1592
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1594
  				glMatrixMode(GL_MODELVIEW);
  				glPushMatrix();
  				glLoadIdentity();
  				
  				CHECK_OPENGL_ERROR
  				gluLookAt(ps[0], ps[1], ps[2],
  					 ds[0], ds[1], ds[2],
  					 ups[0], ups[1], ups[2]);
363243dc   Pavel Govyadinov   More comments
1595
1596
  				///Set the look at distance
  				sk.Render();	///Render the network
0311ab81   Pavel Govyadinov   fixed some issues...
1597
  //				nt.Render();								
23af8e36   Pavel Govyadinov   modified spider t...
1598
  
84eff8b1   Pavel Govyadinov   Merged only the n...
1599
  				CHECK_OPENGL_ERROR
23af8e36   Pavel Govyadinov   modified spider t...
1600
1601
  
  
363243dc   Pavel Govyadinov   More comments
1602
  				glLoadName((int) sk.numL());		///Load all the names
0311ab81   Pavel Govyadinov   fixed some issues...
1603
  //				glLoadName(nt.sizeE());
23af8e36   Pavel Govyadinov   modified spider t...
1604
  
363243dc   Pavel Govyadinov   More comments
1605
  				sk.RenderLine(cL);			///Render the current line.
0311ab81   Pavel Govyadinov   fixed some issues...
1606
  //				nt.RenderLine(cL);	
23af8e36   Pavel Govyadinov   modified spider t...
1607
  
84eff8b1   Pavel Govyadinov   Merged only the n...
1608
  //				glPopName();
363243dc   Pavel Govyadinov   More comments
1609
  				glFlush();				///Flush the buffer
84eff8b1   Pavel Govyadinov   Merged only the n...
1610
1611
1612
1613
1614
  
  				glMatrixMode(GL_PROJECTION);
  				glPopMatrix();
  				glMatrixMode(GL_MODELVIEW);
  				CHECK_OPENGL_ERROR
363243dc   Pavel Govyadinov   More comments
1615
  				glPopMatrix();				///clear the vis matrices and pop the matrix
84eff8b1   Pavel Govyadinov   Merged only the n...
1616
  
59781ee3   Pavel Govyadinov   fixed a stask bug...
1617
  		//	glEnable(GL_CULL_FACE);
363243dc   Pavel Govyadinov   More comments
1618
1619
  			hits = glRenderMode(GL_RENDER);			///Check for hits.
  			int found_hits = processHits(hits, selectBuf);	///Process the hits.
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1620
1621
1622
1623
  			#ifdef TIMING
  				hit_time += gpuStopTimer();
  			#endif
  
363243dc   Pavel Govyadinov   More comments
1624
  			return found_hits;				///return whether we hit something or not.
84eff8b1   Pavel Govyadinov   Merged only the n...
1625
1626
1627
1628
  		}
  
  		//Given a size of the array (hits) and the memory holding it (buffer)
  		//returns whether a hit tool place or not.
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1629
  		int
84eff8b1   Pavel Govyadinov   Merged only the n...
1630
1631
  		processHits(GLint hits, GLuint buffer[])
  		{
363243dc   Pavel Govyadinov   More comments
1632
  			GLuint *ptr;		///pointer to the detection buffer
84eff8b1   Pavel Govyadinov   Merged only the n...
1633
  			ptr = (GLuint *) buffer;
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1634
1635
1636
  			ptr++;
  			ptr++; //Skip the minimum depth value.  
  			ptr++; //Skip the maximum depth value.
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1637
1638
  
  			
84eff8b1   Pavel Govyadinov   Merged only the n...
1639
  			if(hits == 0)
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1640
1641
1642
  			{
  				return -1;
  			}
84eff8b1   Pavel Govyadinov   Merged only the n...
1643
  			else
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1644
  			{
035d798f   Pavel Govyadinov   modified the spid...
1645
  //				printf ("%u ", *ptr);
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1646
1647
1648
1649
1650
1651
1652
1653
  				return *ptr;
  			}
  		}
  
  		void
  		clearCurrent()
  		{
  			cL.clear();
ac430567   Pavel Govyadinov   comments comments...
1654
  			cM.clear();
0311ab81   Pavel Govyadinov   fixed some issues...
1655
  		}
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1656
  	
0311ab81   Pavel Govyadinov   fixed some issues...
1657
  /*
23af8e36   Pavel Govyadinov   modified spider t...
1658
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1659
1660
  		addToNetwork(pair<stim::fiber<float>, int> in, stim::vec3<float> spos, 
  				stim::vec<float> smag, stim::vec3<float> sdir)
23af8e36   Pavel Govyadinov   modified spider t...
1661
  		{
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1662
1663
1664
1665
  			#ifdef TIMING
  				 double s = std::clock();
  			#endif
  			
7d3162a2   Pavel Govyadinov   fixed majority of...
1666
                          std::vector<stim::vec3<float> > ce = in.first.centerline();                
23af8e36   Pavel Govyadinov   modified spider t...
1667
                          std::vector<stim::vec<float> > cm = in.first.centerlinemag();
6707e8f5   Pavel Govyadinov   handled the case ...
1668
  			//if the fiber is longer than 2 steps (the number it takes to diverge)
6b8621f8   Pavel Govyadinov   stable version
1669
  			if(ce.size() > 3)
6707e8f5   Pavel Govyadinov   handled the case ...
1670
1671
  			{	
  				//if we did not hit a fiber
23af8e36   Pavel Govyadinov   modified spider t...
1672
1673
  				if(in.second == -1)
  				{
6707e8f5   Pavel Govyadinov   handled the case ...
1674
1675
1676
  					spos[0] = spos[0]-sdir[0]*smag[0]/2.;
  					spos[1] = spos[1]-sdir[1]*smag[0]/2.;
  					spos[2] = spos[2]-sdir[2]*smag[0]/2.;
821409d5   Pavel Govyadinov   added a way to ad...
1677
  					int h = selectObject(spos, -sdir, smag[0]);
6707e8f5   Pavel Govyadinov   handled the case ...
1678
  					//did we start with a fiber?
11c1b46b   Pavel Govyadinov   minor bug fixes a...
1679
  					if(h != -1 && h < nt.sizeE())
821409d5   Pavel Govyadinov   added a way to ad...
1680
1681
1682
  						nt.addEdge(ce, cm, h, -1);
  					else
  						nt.addEdge(ce, cm, -1, -1);
23af8e36   Pavel Govyadinov   modified spider t...
1683
  				}
6707e8f5   Pavel Govyadinov   handled the case ...
1684
  				//if we hit a fiber?
23af8e36   Pavel Govyadinov   modified spider t...
1685
1686
  				else if(in.second != -1)
  				{
6707e8f5   Pavel Govyadinov   handled the case ...
1687
1688
1689
1690
  					nt.addEdge(ce,cm,-1, in.second);
  					spos[0] = spos[0]-sdir[0]*smag[0]/2.;
  					spos[1] = spos[1]-sdir[1]*smag[0]/2.;
  					spos[2] = spos[2]-sdir[2]*smag[0]/2.;
6707e8f5   Pavel Govyadinov   handled the case ...
1691
1692
  					int h = selectObject(spos, -sdir, smag[0]);
  					//did start with a fiber?
11c1b46b   Pavel Govyadinov   minor bug fixes a...
1693
  					if(h != -1 && h < nt.sizeE()){	
ac430567   Pavel Govyadinov   comments comments...
1694
1695
  			//			std::cout << "got here double" << smag.str() << std::endl;
  						nt.addEdge(ce,cm, h, in.second);	
27194b56   Pavel Govyadinov   major bug fixes, ...
1696
  					} else { nt.addEdge(ce,cm, -1, -1);}
23af8e36   Pavel Govyadinov   modified spider t...
1697
1698
  				}
  			}		
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1699
1700
  
  			#ifdef TIMING
6ada8448   Pavel Govyadinov   Reverted to 40db1...
1701
1702
  				double nt = (std::clock() - s) / (double) CLOCKS_PER_SEC;
  				network_time += nt * 1000.0;
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1703
  			#endif
23af8e36   Pavel Govyadinov   modified spider t...
1704
  		}
0311ab81   Pavel Govyadinov   fixed some issues...
1705
1706
  */
  		void
09049866   Pavel Govyadinov   fixed a drawing b...
1707
  		addToNetwork(std::vector<stim::vec3<float> > L, std::vector<float > M)
0311ab81   Pavel Govyadinov   fixed some issues...
1708
1709
1710
1711
1712
1713
  		{
  			if(L.size() > 3)
  			{
  				sk.Begin(stim::OBJ_LINE);
  				for(int i = 0; i < L.size(); i++)
  				{
09049866   Pavel Govyadinov   fixed a drawing b...
1714
  					sk.TexCoord(M[i]);
0311ab81   Pavel Govyadinov   fixed some issues...
1715
1716
1717
  					sk.Vertex(L[i][0], L[i][1], L[i][2]);
  				}
  				sk.End();
23af8e36   Pavel Govyadinov   modified spider t...
1718
  
0311ab81   Pavel Govyadinov   fixed some issues...
1719
  				nt.addEdge(L,M);
4166e973   Pavel Govyadinov   Added debug tags ...
1720
1721
1722
  				#ifdef DEBUG
  					iter++;
  				#endif
0311ab81   Pavel Govyadinov   fixed some issues...
1723
1724
  			}
  		}
6ada8448   Pavel Govyadinov   Reverted to 40db1...
1725
  
23af8e36   Pavel Govyadinov   modified spider t...
1726
  
821409d5   Pavel Govyadinov   added a way to ad...
1727
1728
1729
  		void
  		printSizes()
  		{
035d798f   Pavel Govyadinov   modified the spid...
1730
1731
  			std::cout << nt.sizeE() << " edges " << std::endl;
  			std::cout << nt.sizeV() << " nodes " << std::endl;
821409d5   Pavel Govyadinov   added a way to ad...
1732
1733
  		}
  
0311ab81   Pavel Govyadinov   fixed some issues...
1734
  		void
09049866   Pavel Govyadinov   fixed a drawing b...
1735
  		traceLine(stim::vec3<float> pos, float mag, int min_cost)
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1736
  		{
821409d5   Pavel Govyadinov   added a way to ad...
1737
  			//starting (seed) position and magnitude.
7d3162a2   Pavel Govyadinov   fixed majority of...
1738