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stim/gl/gl_spider.h 56.5 KB
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   #ifndef STIM_GL_SPIDER_H
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  #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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  		int last_fiber;						//variable that tracks the last fiber hit during tracing. -1 if no fiber was hit.
  
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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;
4166e973   Pavel Govyadinov   Added debug tags ...
888
  		#ifdef DEBUG
47fe6300   Pavel Govyadinov   fixed an accident...
889
  			iter = 0;
4166e973   Pavel Govyadinov   Added debug tags ...
890
891
892
893
  			iter_pos = 0;
  			iter_dir = 0;
  			iter_siz = 0;
  		#endif
385d2447   Pavel Govyadinov   Checkpoint: Conve...
894
  		}
ac430567   Pavel Govyadinov   comments comments...
895
896
897
898
899
900
901
  
  		///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...
902
  		(stim::vec3<float> pos, stim::vec3<float> dir, float mag, int samples = 1089, int samplesPos = 441, int samplesMag = 144)
ac430567   Pavel Govyadinov   comments comments...
903
904
905
  		{
  			p = pos;
  			d = dir;
7f297fc6   Pavel Govyadinov   added more detail...
906
  			m = mag;
7d3162a2   Pavel Govyadinov   fixed majority of...
907
908
  			S = vec3<float>(1.0,1.0,1.0);
  			R = vec3<float>(1.0,1.0,1.0);
ac430567   Pavel Govyadinov   comments comments...
909
  			numSamples = samples;
035d798f   Pavel Govyadinov   modified the spid...
910
911
  			numSamplesPos = samplesPos;
  			numSamplesMag = samplesMag;
4166e973   Pavel Govyadinov   Added debug tags ...
912
  		#ifdef DEBUG
47fe6300   Pavel Govyadinov   fixed an accident...
913
  			iter = 0;
4166e973   Pavel Govyadinov   Added debug tags ...
914
915
916
917
  			iter_pos = 0;
  			iter_dir = 0;
  			iter_siz = 0;
  		#endif
ac430567   Pavel Govyadinov   comments comments...
918
919
  		}
  
8303b04d   Pavel Govyadinov   fixed the bug and...
920
  		///destructor deletes all the texture and buffer objects.
8e56a0a7   Pavel Govyadinov   Added the propose...
921
922
923
924
  		~gl_spider
  		(void)
  		{
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
925
926
927
928
929
930
  			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...
931
932
  			glDeleteTextures(1, &length_texID);
  			glDeleteBuffers(1, &length_buffID);     
7f297fc6   Pavel Govyadinov   added more detail...
933
934
  			glDeleteTextures(1, &cylinder_texID);
  			glDeleteBuffers(1, &cylinder_buffID);
8e56a0a7   Pavel Govyadinov   Added the propose...
935
936
  		}
  
ac430567   Pavel Govyadinov   comments comments...
937
  		///@param GLuint id, texture that is going to be sampled.
385d2447   Pavel Govyadinov   Checkpoint: Conve...
938
  		///Attached the spider to the texture with the given GLuint ID.
8e56a0a7   Pavel Govyadinov   Added the propose...
939
  		///Samples in the default d acting as the init method.
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
940
  		///Also acts an init.	
a9b45efe   Pavel Govyadinov   changes to spider
941
  		void
2a18be6d   Pavel Govyadinov   New comments and ...
942
  		attachSpider(GLuint id)
a9b45efe   Pavel Govyadinov   changes to spider
943
  		{
98eecaa9   David Mayerich   VS and win32 updates
944
945
946
947
948
949
950
951
952
  #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...
953
954
  #ifdef DEBUG
  			iter = 0;
4166e973   Pavel Govyadinov   Added debug tags ...
955
956
957
  			iter_pos = 0;
  			iter_dir = 0;
  			iter_siz = 0;
47fe6300   Pavel Govyadinov   fixed an accident...
958
  #endif
97508a2e   Pavel Govyadinov   Added mehtods for...
959
  			stepsize = 3.0;
7f297fc6   Pavel Govyadinov   added more detail...
960
  			n_pixels = 16.0;
98eecaa9   David Mayerich   VS and win32 updates
961
  
c0e09133   Pavel Govyadinov   STABLE: made temp...
962
  			srand(100);	
a9b45efe   Pavel Govyadinov   changes to spider
963
  			texID = id;
7f297fc6   Pavel Govyadinov   added more detail...
964
  			GenerateFBO(n_pixels*2, numSamples*n_pixels, direction_texID, direction_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
965
  			CHECK_OPENGL_ERROR
7f297fc6   Pavel Govyadinov   added more detail...
966
  			GenerateFBO(n_pixels*2, numSamplesPos*n_pixels, position_texID, position_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
967
  			CHECK_OPENGL_ERROR
7f297fc6   Pavel Govyadinov   added more detail...
968
  			GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, radius_texID, radius_buffID); 
97508a2e   Pavel Govyadinov   Added mehtods for...
969
970
  			CHECK_OPENGL_ERROR
  			GenerateFBO(n_pixels*2, numSamplesMag*n_pixels, length_texID, length_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
971
  			CHECK_OPENGL_ERROR
7f297fc6   Pavel Govyadinov   added more detail...
972
  			GenerateFBO(16, 216, cylinder_texID, cylinder_buffID); 
c0e09133   Pavel Govyadinov   STABLE: made temp...
973
  			CHECK_OPENGL_ERROR
09049866   Pavel Govyadinov   fixed a drawing b...
974
  			t_dir.MapCudaTexture(direction_texID, GL_TEXTURE_2D);
c37611a6   Pavel Govyadinov   removed the time ...
975
  			t_dir.Alloc(numSamples);
7f297fc6   Pavel Govyadinov   added more detail...
976
  			t_pos.MapCudaTexture(position_texID, GL_TEXTURE_2D);
c37611a6   Pavel Govyadinov   removed the time ...
977
  			t_pos.Alloc(numSamplesPos);
7f297fc6   Pavel Govyadinov   added more detail...
978
  			t_mag.MapCudaTexture(radius_texID, GL_TEXTURE_2D);
c37611a6   Pavel Govyadinov   removed the time ...
979
  			t_mag.Alloc(numSamplesMag);
8303b04d   Pavel Govyadinov   fixed the bug and...
980
981
  			t_len.MapCudaTexture(length_texID, GL_TEXTURE_2D);
  			t_len.Alloc(numSamplesMag);
5eeaf941   Pavel Govyadinov   changer to the ba...
982
  			setMatrix();
8303b04d   Pavel Govyadinov   fixed the bug and...
983
  			dList = glGenLists(4);
db3c28c9   Pavel Govyadinov   Implemented glDis...
984
  			glListBase(dList);
7f297fc6   Pavel Govyadinov   added more detail...
985
  			Bind(direction_texID, direction_buffID, numSamples, n_pixels);
b50c840e   David Mayerich   eliminated ANN fr...
986
  				genDirectionVectors(5*stim::PI/4);
3f15dade   Pavel Govyadinov   changed the plane...
987
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
988
  			Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
4166e973   Pavel Govyadinov   Added debug tags ...
989
  				genPositionVectors(0.2);
3f15dade   Pavel Govyadinov   changed the plane...
990
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
991
  			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
035d798f   Pavel Govyadinov   modified the spid...
992
  				genMagnitudeVectors();
3f15dade   Pavel Govyadinov   changed the plane...
993
  			Unbind();
97508a2e   Pavel Govyadinov   Added mehtods for...
994
995
996
  			Bind(length_texID, length_buffID, numSamplesMag, n_pixels);
  				genLengthVectors();
  			Unbind();
a39577bf   Pavel Govyadinov   Changes to the sp...
997
  		}
5f81932b   David Mayerich   restored Pavel's ...
998
  		
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
999
1000
1001
  //--------------------------------------------------------------------------//
  //-----------------------------ACCESS METHODS-------------------------------//
  //--------------------------------------------------------------------------//
8e56a0a7   Pavel Govyadinov   Added the propose...
1002
  		///Returns the p vector.
7d3162a2   Pavel Govyadinov   fixed majority of...
1003
  		vec3<float>
a39577bf   Pavel Govyadinov   Changes to the sp...
1004
  		getPosition()
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1005
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1006
  			return p;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1007
1008
  		}
  	
8e56a0a7   Pavel Govyadinov   Added the propose...
1009
  		///Returns the d vector.
7d3162a2   Pavel Govyadinov   fixed majority of...
1010
  		vec3<float>
a39577bf   Pavel Govyadinov   Changes to the sp...
1011
  		getDirection()
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1012
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1013
  			return d;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1014
1015
  		}
  
8e56a0a7   Pavel Govyadinov   Added the propose...
1016
  		///Returns the m vector.
09049866   Pavel Govyadinov   fixed a drawing b...
1017
  		float	
a39577bf   Pavel Govyadinov   Changes to the sp...
1018
  		getMagnitude()
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1019
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1020
  			return m;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1021
1022
  		}
  	
ac430567   Pavel Govyadinov   comments comments...
1023
  		///@param stim::vec<float> pos, the new p.
8e56a0a7   Pavel Govyadinov   Added the propose...
1024
  		///Sets the p vector to input vector pos.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1025
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1026
  		setPosition(stim::vec3<float> pos)
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1027
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1028
  			p = pos;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1029
  		}
385d2447   Pavel Govyadinov   Checkpoint: Conve...
1030
  
ac430567   Pavel Govyadinov   comments comments...
1031
1032
1033
  		///@param float x x-coordinate.
  		///@param float y y-coordinate.
  		///@param float z z-coordinate.
8e56a0a7   Pavel Govyadinov   Added the propose...
1034
  		///Sets the p vector to the input float coordinates x,y,z.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1035
1036
1037
  		void
  		setPosition(float x, float y, float z)
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1038
1039
1040
  			p[0] = x;
  			p[1] = y;
  			p[2] = z;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1041
  		}
887a3e49   Pavel Govyadinov   fixed some order ...
1042
  		
ac430567   Pavel Govyadinov   comments comments...
1043
  		///@param stim::vec<float> dir, the new d.
8e56a0a7   Pavel Govyadinov   Added the propose...
1044
  		///Sets the d vector to input vector dir.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1045
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1046
  		setDirection(stim::vec3<float> dir)
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1047
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1048
  			d = dir;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1049
1050
  		}
  		
ac430567   Pavel Govyadinov   comments comments...
1051
1052
1053
  		///@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...
1054
  		///Sets the d vector to the input float coordinates x,y,z.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1055
1056
1057
  		void
  		setDirection(float x, float y, float z)
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1058
1059
1060
  			d[0] = x;
  			d[1] = y;
  			d[2] = z;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1061
  		}
385d2447   Pavel Govyadinov   Checkpoint: Conve...
1062
  			
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1063
  		
ac430567   Pavel Govyadinov   comments comments...
1064
  		///@param float mag, size of the sampled region.
97508a2e   Pavel Govyadinov   Added mehtods for...
1065
  		///Sets the m value to the input mag for both templates.
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1066
  		void
5f81932b   David Mayerich   restored Pavel's ...
1067
  		setMagnitude(float mag)
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1068
  		{
7f297fc6   Pavel Govyadinov   added more detail...
1069
  			m = mag;
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1070
  		}
97508a2e   Pavel Govyadinov   Added mehtods for...
1071
1072
1073
1074
1075
1076
1077
1078
  
  		///@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 ...
1079
  		
ac430567   Pavel Govyadinov   comments comments...
1080
1081
1082
1083
  		///@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...
1084
1085
1086
1087
1088
1089
1090
1091
  		void
  		setDims(float x, float y, float z)
  		{
  			S[0] = x;
  			S[1] = y;
  			S[2] = z;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1092
1093
1094
  		///@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...
1095
  		setDims(stim::vec3<float> Dims)
ac430567   Pavel Govyadinov   comments comments...
1096
1097
1098
1099
1100
1101
1102
1103
  		{
  			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...
1104
  		void
8e56a0a7   Pavel Govyadinov   Added the propose...
1105
  		setSize(float x, float y, float z)
b710b044   Pavel Govyadinov   Added more tempor...
1106
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1107
1108
1109
  			R[0] = x;
  			R[1] = y;
  			R[2] = z;
b710b044   Pavel Govyadinov   Added more tempor...
1110
  		}
ac430567   Pavel Govyadinov   comments comments...
1111
1112
1113
1114
  
  		///@param stim::vec<float> Dims, size of the volume.
  		///Sets the data volume sizes in each direction.
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1115
  		setSize(stim::vec3<float> Siz)
ac430567   Pavel Govyadinov   comments comments...
1116
1117
1118
  		{
  			S = Siz;
  		}
b710b044   Pavel Govyadinov   Added more tempor...
1119
  		
ac430567   Pavel Govyadinov   comments comments...
1120
1121
1122
1123
  		///@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...
1124
  		stim::vec<float>
4fa3f483   Pavel Govyadinov   Fixed the memory ...
1125
  		getRotation(stim::vec3<float> dir)
f304d6de   Pavel Govyadinov   added rotation to...
1126
  		{
8303b04d   Pavel Govyadinov   fixed the bug and...
1127
1128
1129
1130
  			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...
1131
1132
1133
1134
  				out[0] = 0.0;
  				out[1] = 0.0;
  				out[2] = 0.0;
  				out[3] = 1.0;
8303b04d   Pavel Govyadinov   fixed the bug and...
1135
1136
  			}					///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...
1137
1138
1139
1140
1141
  			{
  				out[0] = 180.0;
  				out[1] = 1.0;
  				out[2] = 0.0;
  				out[3] = 0.0;
8303b04d   Pavel Govyadinov   fixed the bug and...
1142
  			} else {				///the rotational axis is the cross fromxdir.
4166e973   Pavel Govyadinov   Added debug tags ...
1143
1144
  				stim::vec3<float> temp(0.0, 0.0, 0.0);;
  				temp = (from.cross(dir)).norm();
f304d6de   Pavel Govyadinov   added rotation to...
1145
1146
1147
1148
  				out[1] = temp[0];
  				out[2] = temp[1];
  				out[3] = temp[2];
  			}
97508a2e   Pavel Govyadinov   Added mehtods for...
1149
  			#ifdef DEBUG
91e2e1ec   Pavel Govyadinov   went to a better ...
1150
1151
  //				std::cout << "out is " << out << std::endl;
  //				std::cout << "when rotating from " << from << " to " << dir << std::endl;
97508a2e   Pavel Govyadinov   Added mehtods for...
1152
  			#endif
f304d6de   Pavel Govyadinov   added rotation to...
1153
1154
  			return out;
  		}
84eff8b1   Pavel Govyadinov   Merged only the n...
1155
  
ac430567   Pavel Govyadinov   comments comments...
1156
  		///@param stim::vec<float> pos, the position of the seed to be added.
84eff8b1   Pavel Govyadinov   Merged only the n...
1157
1158
1159
  		///Adds a seed to the seed list.
  		///Assumes that the coordinates passes are in tissue space.
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1160
  		setSeed(stim::vec3<float> pos)
a9b45efe   Pavel Govyadinov   changes to spider
1161
  		{
84eff8b1   Pavel Govyadinov   Merged only the n...
1162
  			seeds.push(pos);
a9b45efe   Pavel Govyadinov   changes to spider
1163
  		}
fb0bc2f1   Pavel Govyadinov   added the gl_spid...
1164
  
ac430567   Pavel Govyadinov   comments comments...
1165
1166
  		///@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...
1167
  		void
7d3162a2   Pavel Govyadinov   fixed majority of...
1168
  		setSeedVec(stim::vec3<float> dir)
59781ee3   Pavel Govyadinov   fixed a stask bug...
1169
1170
1171
1172
  		{
  			seedsvecs.push(dir);
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1173
1174
1175
  		///@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...
1176
1177
  		void
  		setSeedMag(float mag)
79a9bf3f   Pavel Govyadinov   new implementatio...
1178
  		{
59781ee3   Pavel Govyadinov   fixed a stask bug...
1179
  			seedsmags.push(mag);
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1180
  		}
79a9bf3f   Pavel Govyadinov   new implementatio...
1181
  
59781ee3   Pavel Govyadinov   fixed a stask bug...
1182
  
ac430567   Pavel Govyadinov   comments comments...
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  		///@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)
  		{
84eff8b1   Pavel Govyadinov   Merged only the n...
1191
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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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1198
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  		void
  		setSeedVec(float x, float y, float z)
  		{
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1201
1202
  			seedsvecs.push(stim::vec<float>(x, y, z));
  		}
ac430567   Pavel Govyadinov   comments comments...
1203
1204
  		
  		///Method to get the top of the seed positions stack.
7d3162a2   Pavel Govyadinov   fixed majority of...
1205
  		stim::vec3<float> 
84eff8b1   Pavel Govyadinov   Merged only the n...
1206
1207
  		getLastSeed()
  		{
7d3162a2   Pavel Govyadinov   fixed majority of...
1208
  			stim::vec3<float> tp = seeds.top();
84eff8b1   Pavel Govyadinov   Merged only the n...
1209
1210
1211
  			return tp;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1212
  		///Method to get the top of the seed direction stack.
7d3162a2   Pavel Govyadinov   fixed majority of...
1213
  		stim::vec3<float> 
59781ee3   Pavel Govyadinov   fixed a stask bug...
1214
1215
  		getLastSeedVec()
  		{
7d3162a2   Pavel Govyadinov   fixed majority of...
1216
  			stim::vec3<float> tp = seedsvecs.top();
59781ee3   Pavel Govyadinov   fixed a stask bug...
1217
1218
1219
  			return tp;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1220
  		///Method to get the top of the seed magnitude stack.
59781ee3   Pavel Govyadinov   fixed a stask bug...
1221
1222
1223
1224
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1227
  		float
  		getLastSeedMag()
  		{
  			float tp = seedsmags.top();
  			return tp;
  		}
  
ac430567   Pavel Govyadinov   comments comments...
1228
  		///deletes all data associated with the last seed.
59781ee3   Pavel Govyadinov   fixed a stask bug...
1229
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1232
1233
  		void
  		popSeed()
  		{
  			seeds.pop();
  			seedsvecs.pop();
6707e8f5   Pavel Govyadinov   handled the case ...
1234
  			seedsmags.pop();
59781ee3   Pavel Govyadinov   fixed a stask bug...
1235
  		}
ac430567   Pavel Govyadinov   comments comments...
1236
1237
  		
  		///returns the seeds position stack.
7d3162a2   Pavel Govyadinov   fixed majority of...
1238
  		std::stack<stim::vec3<float> >
84eff8b1   Pavel Govyadinov   Merged only the n...
1239
1240
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1243
  		getSeeds()
  		{
  			return seeds;
  		}
  
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1244
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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...
1285
  		///returns true if all seed stacks are empty, else false.
84eff8b1   Pavel Govyadinov   Merged only the n...
1286
1287
1288
  		bool
  		Empty()
  		{
ac430567   Pavel Govyadinov   comments comments...
1289
  			//return (seeds.empty() && seedsvecs.empty() && seedsmags.empty());
1306fd96   Pavel Govyadinov   minor bug fixes i...
1290
  			return (seeds.empty() && seedsvecs.empty());
84eff8b1   Pavel Govyadinov   Merged only the n...
1291
  		}
ac430567   Pavel Govyadinov   comments comments...
1292
1293
1294
  
  		///@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.
84eff8b1   Pavel Govyadinov   Merged only the n...
1295
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  		///Assumes that the coordinates passes are in tissue space.
  		void
  		setSeeds(std::string file)
  		{
8303b04d   Pavel Govyadinov   fixed the bug and...
1299
  			std::ifstream myfile(file.c_str()); 	///open a stream
84eff8b1   Pavel Govyadinov   Merged only the n...
1300
1301
1302
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  			string line;
  			if(myfile.is_open())
             		{
                     		while (getline(myfile, line))
                     		{
8303b04d   Pavel Govyadinov   fixed the bug and...
1305
                             		float x, y, z, u, v, w, m;	///read the xyz uvw and m coordinates.
ac430567   Pavel Govyadinov   comments comments...
1306
                             		myfile >> x >> y >> z >> u >> v >> w >> m;
8761b649   Pavel Govyadinov   moved a lot of th...
1307
  					setSeed(x, y, z);
ac430567   Pavel Govyadinov   comments comments...
1308
1309
  					setSeedVec(u, v, w);
  					setSeedMag(m);
84eff8b1   Pavel Govyadinov   Merged only the n...
1310
1311
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                     		}
                     	myfile.close();
  	          	} else {
          	                  std::cerr<<"failed" << std::endl;
  			}
79a9bf3f   Pavel Govyadinov   new implementatio...
1315
1316
  		}
  		
ac430567   Pavel Govyadinov   comments comments...
1317
  		///Saves the network to a file.
79a9bf3f   Pavel Govyadinov   new implementatio...
1318
  		void
84eff8b1   Pavel Govyadinov   Merged only the n...
1319
  		saveNetwork(std::string name)
79a9bf3f   Pavel Govyadinov   new implementatio...
1320
  		{
91e2e1ec   Pavel Govyadinov   went to a better ...
1321
  			stim::glObj<float> sk1;
8761b649   Pavel Govyadinov   moved a lot of th...
1322
1323
  			for(int i = 0; i < nt.sizeE(); i++)
  			{
91e2e1ec   Pavel Govyadinov   went to a better ...
1324
  				std::vector<float> cm = nt.getEdgeCenterLineMag(i);
7d3162a2   Pavel Govyadinov   fixed majority of...
1325
                   		std::vector<stim::vec3< float > > ce = nt.getEdgeCenterLine(i);
8761b649   Pavel Govyadinov   moved a lot of th...
1326
1327
1328
  				sk.Begin(stim::OBJ_LINE);
  				for(int j = 0; j < ce.size(); j++)
  				{
91e2e1ec   Pavel Govyadinov   went to a better ...
1329
1330
  					sk1.TexCoord(cm[j]);
  					sk1.Vertex(ce[j][0], ce[j][1], ce[j][2]);
8761b649   Pavel Govyadinov   moved a lot of th...
1331
  				}
91e2e1ec   Pavel Govyadinov   went to a better ...
1332
  				sk1.End();
8761b649   Pavel Govyadinov   moved a lot of th...
1333
  			}	
91e2e1ec   Pavel Govyadinov   went to a better ...
1334
  			sk1.save(name);
79a9bf3f   Pavel Govyadinov   new implementatio...
1335
  		}
84eff8b1   Pavel Govyadinov   Merged only the n...
1336
  
8761b649   Pavel Govyadinov   moved a lot of th...
1337
  		///Depreciated, but might be reused later()
ac430567   Pavel Govyadinov   comments comments...
1338
  		///returns a COPY of the entire stim::glObj object.
84eff8b1   Pavel Govyadinov   Merged only the n...
1339
1340
1341
  		stim::glObj<float>
  		getNetwork()
  		{
0311ab81   Pavel Govyadinov   fixed some issues...
1342
  			return sk;
84eff8b1   Pavel Govyadinov   Merged only the n...
1343
  		}
ac430567   Pavel Govyadinov   comments comments...
1344
1345
1346
1347
1348
1349
1350
  
  		///returns a COPY of the entire stim::glnetwork object.
  		stim::glnetwork<T>
  		getGLNetwork()
  		{
  			return nt;
  		}
84eff8b1   Pavel Govyadinov   Merged only the n...
1351
1352
1353
1354
1355
1356
  		
  		///Function to get back the framebuffer Object attached to the spider.
  		///For external access.
  		GLuint
  		getFB()
  		{
7f297fc6   Pavel Govyadinov   added more detail...
1357
  			return cylinder_buffID;
84eff8b1   Pavel Govyadinov   Merged only the n...
1358
1359
  		}
  
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
1360
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  //--------------------------------------------------------------------------//
  //-----------------------------TEMPORARY METHODS----------------------------//
  //--------------------------------------------------------------------------//
  
  		///temporary Method necessary for visualization and testing.
  		void
  		Update()
  		{
7d3162a2   Pavel Govyadinov   fixed majority of...
1368
  			vec3<float> Y(1.0,0.0,0.0);
8e56a0a7   Pavel Govyadinov   Added the propose...
1369
  			if(cos(Y.dot(d))< 0.087){
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
1370
  				Y[0] = 0.0; Y[1] = 1.0;}
8e56a0a7   Pavel Govyadinov   Added the propose...
1371
1372
1373
  			hor = stim::rect<float>(m, p, d.norm(),
  				((Y.cross(d)).cross(d)).norm());
  			ver = stim::rect<float>(m, p, d.norm(),
266aa74a   Pavel Govyadinov   CHECKPOINT: Minor...
1374
1375
1376
1377
  				 hor.n());
  		}
  
  
c4887649   Pavel Govyadinov   fixed a significa...
1378
  		int
13c2a7d4   Pavel Govyadinov   some changes to t...
1379
1380
  		Step()
  		{
4166e973   Pavel Govyadinov   Added debug tags ...
1381
  			#ifdef DEBUG
09049866   Pavel Govyadinov   fixed a drawing b...
1382
  			std::cerr << "Took a step" << std::endl;
4166e973   Pavel Govyadinov   Added debug tags ...
1383
  			#endif
7f297fc6   Pavel Govyadinov   added more detail...
1384
  			Bind(direction_texID, direction_buffID, numSamples, n_pixels);
84eff8b1   Pavel Govyadinov   Merged only the n...
1385
  			CHECK_OPENGL_ERROR
035d798f   Pavel Govyadinov   modified the spid...
1386
  				findOptimalDirection();
3f15dade   Pavel Govyadinov   changed the plane...
1387
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
1388
  			Bind(position_texID, position_buffID, numSamplesPos, n_pixels);
035d798f   Pavel Govyadinov   modified the spid...
1389
  				findOptimalPosition();
3f15dade   Pavel Govyadinov   changed the plane...
1390
  			Unbind();
7f297fc6   Pavel Govyadinov   added more detail...
1391
  			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
97508a2e   Pavel Govyadinov   Added mehtods for...
1392
  				findOptimalRadius();
3f15dade   Pavel Govyadinov   changed the plane...
1393
  			Unbind();
84eff8b1   Pavel Govyadinov   Merged only the n...
1394
1395
  			CHECK_OPENGL_ERROR
  
59781ee3   Pavel Govyadinov   fixed a stask bug...
1396
1397
1398
  			return current_cost;
  		}
  
556c4e15   Pavel Govyadinov   Changed the handl...
1399
1400
1401
1402
  
  		void
  		printTransform()
  		{
8e56a0a7   Pavel Govyadinov   Added the propose...
1403
  			std::cout << cT << std::endl;
b710b044   Pavel Govyadinov   Added more tempor...
1404
  		}
a9b45efe   Pavel Govyadinov   changes to spider
1405
  
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1406
1407
1408
1409
1410
1411
  
  //--------------------------------------------------------------------------//
  //-----------------------------EXPERIMENTAL METHODS-------------------------//
  //--------------------------------------------------------------------------//
  
  		void
34ec8a82   David Mayerich   added comments
1412
  		MonteCarloDirectionVectors(int nSamples, float solidAngle = stim::TAU)
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1413
  		{
0311ab81   Pavel Govyadinov   fixed some issues...
1414
1415
1416
  //			float PHI[2];//, Z[2];//, range;
  //			PHI[0] = asin(solidAngle/2);
  //			PHI[1] = asin(0);
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1417
  			
0311ab81   Pavel Govyadinov   fixed some issues...
1418
1419
  //			Z[0] = cos(PHI[0]);
  //			Z[1] = cos(PHI[1]);
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1420
  			
0311ab81   Pavel Govyadinov   fixed some issues...
1421
  //			range = Z[0] - Z[1];
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1422
  
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1423
1424
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1439
  			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...
1440
  /*
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1441
  		void
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1442
1443
  		DrawCylinder()
  		{	 
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1444
1445
  			 glNewList(dList+3, GL_COMPILE);
  			 float z0 = -0.5; float z1 = 0.5; float r0 = 0.5;
97508a2e   Pavel Govyadinov   Added mehtods for...
1446
        			 float x,y;
84eff8b1   Pavel Govyadinov   Merged only the n...
1447
  			 float xold = 0.5; float yold = 0.0;
ac430567   Pavel Govyadinov   comments comments...
1448
1449
  			 float step = 360.0/numSamples*32;
  			 //float step = 360.0/8.0;
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1450
1451
  			 glEnable(GL_TEXTURE_3D);
  			 glBindTexture(GL_TEXTURE_3D, texID);
ac430567   Pavel Govyadinov   comments comments...
1452
  			 glBegin(GL_QUAD_STRIP);
84eff8b1   Pavel Govyadinov   Merged only the n...
1453
  			 int j = 0;
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1454
1455
  			 	for(float i = step; i <= 360.0; i += step)
  			 	{
b50c840e   David Mayerich   eliminated ANN fr...
1456
1457
  					 x=r0*cos(i*stim::TAU/360.0);
  					 y=r0*sin(i*stim::TAU/360.0);
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1458
  					 glTexCoord3f(x,y,z0); 
ac430567   Pavel Govyadinov   comments comments...
1459
1460
  					 glVertex2f(0.0, j*6.4+6.4);
  //					 glVertex2f(0.0, j*27.0+27.0);
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1461
  					 glTexCoord3f(x,y,z1); 
ac430567   Pavel Govyadinov   comments comments...
1462
1463
  					 glVertex2f(16.0, j*6.4+6.4);
  //					 glVertex2f(16.0, j*27.0+27.0);
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1464
  					 glTexCoord3f(xold,yold,z1); 
ac430567   Pavel Govyadinov   comments comments...
1465
1466
  					 glVertex2f(16.0, j*6.4); 
  //					 glVertex2f(16.0, j*27.0); 
f31bf86d   Pavel Govyadinov   Added skeleton fu...
1467
  					 glTexCoord3f(xold,yold,z0); 
ac430567   Pavel Govyadinov   comments comments...
1468
1469
  					 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...
1476
  		}
97508a2e   Pavel Govyadinov   Added mehtods for...
1477
  */
8c4f5d84   Pavel Govyadinov   fixed the issue w...
1478
  ///need to return the cylinder.
7f297fc6   Pavel Govyadinov   added more detail...
1479
  ///SOMETHING MIGHT BE GOING ON HERE IN GENERATE BUFFER.
e45b97ce   Pavel Govyadinov   safety commit, I ...
1480
1481
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1483
  		void
  		DrawLongCylinder(int n = 8, int l_template = 8,int l_square = 8)
  		{
  			int cylLen = cL.size()-1;
7f297fc6   Pavel Govyadinov   added more detail...
1484
1485
  			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 ...
1486
  			stim::cylinder<float> cyl(cL, cM);
7d3162a2   Pavel Govyadinov   fixed majority of...
1487
  			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();
  		}
84eff8b1   Pavel Govyadinov   Merged only the n...
1509
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1515
  		
  
  		///@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...
1516
1517
  			stim::vec3<float> curSeed; 
  			stim::vec3<float> curSeedVec;			
8761b649   Pavel Govyadinov   moved a lot of th...
1518
1519
  			float curSeedMag;
  			while(!Empty())
84eff8b1   Pavel Govyadinov   Merged only the n...
1520
1521
  			{
  				//clear the currently traced line and start a new one.
8761b649   Pavel Govyadinov   moved a lot of th...
1522
1523
1524
  				curSeed = seeds.top();
  				curSeedVec = seedsvecs.top();
  				curSeedMag = seedsmags.top();
59781ee3   Pavel Govyadinov   fixed a stask bug...
1525
1526
  				seeds.pop();
  				seedsvecs.pop();
ac430567   Pavel Govyadinov   comments comments...
1527
  				seedsmags.pop();
84eff8b1   Pavel Govyadinov   Merged only the n...
1528
1529
  				setPosition(curSeed);
  				setDirection(curSeedVec);
8761b649   Pavel Govyadinov   moved a lot of th...
1530
  				setMagnitude(curSeedMag);
4166e973   Pavel Govyadinov   Added debug tags ...
1531
1532
1533
1534
1535
1536
1537
1538
1539
  
  				#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...
1540
  //THIS IS EXPERIMENTAL
91e2e1ec   Pavel Govyadinov   went to a better ...
1541
1542
1543
  //			Bind(radius_texID, radius_buffID, numSamplesMag, n_pixels);
  //				findOptimalRadius();
  //			Unbind();
ec9d82e1   Pavel Govyadinov   finished the debu...
1544
  //THIS IS EXPERIMENTAL
0311ab81   Pavel Govyadinov   fixed some issues...
1545
  
8761b649   Pavel Govyadinov   moved a lot of th...
1546
1547
1548
  //				cL.push_back(curSeed);
  //				cM.push_back(curSeedMag);
  //				cD.push_back(curSeedMag);
0311ab81   Pavel Govyadinov   fixed some issues...
1549
  				traceLine(p, m, min_cost);
84eff8b1   Pavel Govyadinov   Merged only the n...
1550
  			}
84eff8b1   Pavel Govyadinov   Merged only the n...
1551
1552
  		}
  
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1553
  		int
7d3162a2   Pavel Govyadinov   fixed majority of...
1554
  		selectObject(stim::vec3<float> loc, stim::vec3<float> dir, float mag) 
84eff8b1   Pavel Govyadinov   Merged only the n...
1555
1556
  		{
  		//Define the varibles and turn on Selection Mode
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1557
1558
1559
1560
  			
  			#ifdef TIMING
  				gpuStartTimer();
  			#endif
84eff8b1   Pavel Govyadinov   Merged only the n...
1561
  
363243dc   Pavel Govyadinov   More comments
1562
1563
1564
1565
1566
  			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...
1567
1568
  		//Init Names stack
  
363243dc   Pavel Govyadinov   More comments
1569
1570
  			glInitNames();				///Initialize the naming array.
  			glPushName(1);				///Push a single name to the stack.
84eff8b1   Pavel Govyadinov   Merged only the n...
1571
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1573
  
  			CHECK_OPENGL_ERROR
  		//What would that vessel see in front of it.
363243dc   Pavel Govyadinov   More comments
1574
1575
  				camSel.setPosition(loc);		///Set the viewing camera
  				camSel.setFocalDistance(mag/stepsize);	///Set how far the fiber looks forward.
6ada8448   Pavel Govyadinov   Reverted to 40db1...
1576
1577
  				camSel.LookAt((loc[0]+dir[0]*mag/stepsize),
  					 (loc[1]+dir[1]*mag/stepsize),
363243dc   Pavel Govyadinov   More comments
1578
1579
  					 (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...
1580
1581
  				ups = camSel.getUp();
  				ds  = camSel.getLookAt();
363243dc   Pavel Govyadinov   More comments
1582
1583
  				glMatrixMode(GL_PROJECTION);		///Push the projection matrix.
  				glPushMatrix();				///Reset the current projection matrix
84eff8b1   Pavel Govyadinov   Merged only the n...
1584
  				glLoadIdentity();
363243dc   Pavel Govyadinov   More comments
1585
  				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...
1586
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  				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
1594
  				///Set the look at distance
91e2e1ec   Pavel Govyadinov   went to a better ...
1595
1596
  //				sk.Render();	///Render the network
  				nt.Render();								
23af8e36   Pavel Govyadinov   modified spider t...
1597
  
84eff8b1   Pavel Govyadinov   Merged only the n...
1598
  				CHECK_OPENGL_ERROR
23af8e36   Pavel Govyadinov   modified spider t...
1599
1600
  
  
91e2e1ec   Pavel Govyadinov   went to a better ...
1601
1602
  //				glLoadName((int) sk.numL());		///Load all the names
  				glLoadName(nt.sizeE());
23af8e36   Pavel Govyadinov   modified spider t...
1603
  
91e2e1ec   Pavel Govyadinov   went to a better ...
1604
1605
  //				sk.RenderLine(cL);			///Render the current line.
  				nt.RenderLine(cL);	
23af8e36   Pavel Govyadinov   modified spider t...
1606
  
84eff8b1   Pavel Govyadinov   Merged only the n...
1607
  //				glPopName();
363243dc   Pavel Govyadinov   More comments
1608
  				glFlush();				///Flush the buffer
84eff8b1   Pavel Govyadinov   Merged only the n...
1609
1610
1611
1612
1613
  
  				glMatrixMode(GL_PROJECTION);
  				glPopMatrix();
  				glMatrixMode(GL_MODELVIEW);
  				CHECK_OPENGL_ERROR
363243dc   Pavel Govyadinov   More comments
1614
  				glPopMatrix();				///clear the vis matrices and pop the matrix
84eff8b1   Pavel Govyadinov   Merged only the n...
1615
  
59781ee3   Pavel Govyadinov   fixed a stask bug...
1616
  		//	glEnable(GL_CULL_FACE);
363243dc   Pavel Govyadinov   More comments
1617
1618
  			hits = glRenderMode(GL_RENDER);			///Check for hits.
  			int found_hits = processHits(hits, selectBuf);	///Process the hits.
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1619
1620
1621
1622
  			#ifdef TIMING
  				hit_time += gpuStopTimer();
  			#endif
  
363243dc   Pavel Govyadinov   More comments
1623
  			return found_hits;				///return whether we hit something or not.
84eff8b1   Pavel Govyadinov   Merged only the n...
1624
1625
1626
1627
  		}
  
  		//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...
1628
  		int
84eff8b1   Pavel Govyadinov   Merged only the n...
1629
1630
  		processHits(GLint hits, GLuint buffer[])
  		{
363243dc   Pavel Govyadinov   More comments
1631
  			GLuint *ptr;		///pointer to the detection buffer
84eff8b1   Pavel Govyadinov   Merged only the n...
1632
  			ptr = (GLuint *) buffer;
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1633
1634
1635
  			ptr++;
  			ptr++; //Skip the minimum depth value.  
  			ptr++; //Skip the maximum depth value.
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1636
1637
  
  			
84eff8b1   Pavel Govyadinov   Merged only the n...
1638
  			if(hits == 0)
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1639
1640
1641
  			{
  				return -1;
  			}
84eff8b1   Pavel Govyadinov   Merged only the n...
1642
  			else
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1643
  			{
035d798f   Pavel Govyadinov   modified the spid...
1644
  //				printf ("%u ", *ptr);
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1645
1646
1647
1648
1649
1650
1651
1652
  				return *ptr;
  			}
  		}
  
  		void
  		clearCurrent()
  		{
  			cL.clear();
ac430567   Pavel Govyadinov   comments comments...
1653
  			cM.clear();
0311ab81   Pavel Govyadinov   fixed some issues...
1654
  		}
5de3a9c2   Pavel Govyadinov   CHECKPOINT: befo...
1655
  	
91e2e1ec   Pavel Govyadinov   went to a better ...
1656
  
23af8e36   Pavel Govyadinov   modified spider t...
1657
  		void
91e2e1ec   Pavel Govyadinov   went to a better ...
1658
  		addToNetwork(std::vector<stim::vec3<float> > L, std::vector<float > M, stim::vec3<float> spos, stim::vec3<float> sdir, float smag)
23af8e36   Pavel Govyadinov   modified spider t...
1659
  		{
6707e8f5   Pavel Govyadinov   handled the case ...
1660
  			//if the fiber is longer than 2 steps (the number it takes to diverge)
91e2e1ec   Pavel Govyadinov   went to a better ...
1661
  			if(L.size() > 3)
6707e8f5   Pavel Govyadinov   handled the case ...
1662
1663
  			{	
  				//if we did not hit a fiber
91e2e1ec   Pavel Govyadinov   went to a better ...
1664
  				if(last_fiber == -1)
23af8e36   Pavel Govyadinov   modified spider t...
1665
  				{
91e2e1ec   Pavel Govyadinov   went to a better ...
1666
1667
1668
1669
  					spos[0] = spos[0]-sdir[0]*smag;
  					spos[1] = spos[1]-sdir[1]*smag;
  					spos[2] = spos[2]-sdir[2]*smag;
  					int h = selectObject(spos, -sdir, smag);
6707e8f5   Pavel Govyadinov   handled the case ...
1670
  					//did we start with a fiber?
11c1b46b   Pavel Govyadinov   minor bug fixes a...
1671
  					if(h != -1 && h < nt.sizeE())
91e2e1ec   Pavel Govyadinov   went to a better ...
1672
  						nt.addEdge(L, M, h, -1);
821409d5   Pavel Govyadinov   added a way to ad...
1673
  					else
91e2e1ec   Pavel Govyadinov   went to a better ...
1674
  						nt.addEdge(L, M, -1, -1);
23af8e36   Pavel Govyadinov   modified spider t...
1675
  				}
6707e8f5   Pavel Govyadinov   handled the case ...
1676
  				//if we hit a fiber?
91e2e1ec   Pavel Govyadinov   went to a better ...
1677
  				else if(last_fiber != -1)
23af8e36   Pavel Govyadinov   modified spider t...
1678
  				{
91e2e1ec   Pavel Govyadinov   went to a better ...
1679
1680
1681
1682
1683
  					nt.addEdge(L, M, -1, last_fiber);
  					spos[0] = spos[0]-sdir[0]*smag;
  					spos[1] = spos[1]-sdir[1]*smag;
  					spos[2] = spos[2]-sdir[2]*smag;
  					int h = selectObject(spos, -sdir, smag);
6707e8f5   Pavel Govyadinov   handled the case ...
1684
  					//did start with a fiber?
11c1b46b   Pavel Govyadinov   minor bug fixes a...
1685
  					if(h != -1 && h < nt.sizeE()){	
ac430567   Pavel Govyadinov   comments comments...
1686
  			//			std::cout << "got here double" << smag.str() << std::endl;
91e2e1ec   Pavel Govyadinov   went to a better ...
1687
1688
1689
1690
1691
1692
  						nt.addEdge(L, M, h, last_fiber);	
  					}
  					else
  					{
  					 nt.addEdge(L, M, -1, -1);
  					}
23af8e36   Pavel Govyadinov   modified spider t...
1693
1694
  				}
  			}		
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1695
  
91e2e1ec   Pavel Govyadinov   went to a better ...
1696
1697
  			#ifdef DEBUG
  				iter++;
efe7b7cc   Pavel Govyadinov   Added a detailed ...
1698
  			#endif
23af8e36   Pavel Govyadinov   modified spider t...
1699
  		}
91e2e1ec   Pavel Govyadinov   went to a better ...
1700
  /*
0311ab81   Pavel Govyadinov   fixed some issues...
1701
  		void
09049866   Pavel Govyadinov   fixed a drawing b...
1702
  		addToNetwork(std::vector<stim::vec3<float> > L, std::vector<float > M)
0311ab81   Pavel Govyadinov   fixed some issues...
1703
1704
1705
1706
1707
1708
  		{
  			if(L.size() > 3)
  			{
  				sk.Begin(stim::OBJ_LINE);
  				for(int i = 0; i < L.size(); i++)
  				{
09049866   Pavel Govyadinov   fixed a drawing b...
1709
  					sk.TexCoord(M[i]);
0311ab81   Pavel Govyadinov   fixed some issues...
1710
1711
1712
  					sk.Vertex(L[i][0], L[i][1], L[i][2]);
  				}
  				sk.End();
23af8e36   Pavel Govyadinov   modified spider t...
1713
  
0311ab81   Pavel Govyadinov   fixed some issues...
1714
  				nt.addEdge(L,M);
4166e973   Pavel Govyadinov   Added debug tags ...
1715
1716
1717
  				#ifdef DEBUG
  					iter++;
  				#endif
0311ab81   Pavel Govyadinov   fixed some issues...
1718
1719
  			}
  		}
91e2e1ec   Pavel Govyadinov   went to a better ...
1720
  */
23af8e36   Pavel Govyadinov   modified spider t...
1721
  
821409d5   Pavel Govyadinov   added a way to ad...
1722
1723
1724
  		void
  		printSizes()
  		{
035d798f   Pavel Govyadinov   modified the spid...
1725
1726
  			std::cout << nt.sizeE() << " edges " << std::endl;
  			std::cout << nt.sizeV() << " nodes " << std::endl;
821409d5   Pavel Govyadinov   added a way to ad...
1727
1728
  		}
  
0311ab81   Pavel Govyadinov   fixed some issues...
1729
  		void
09049866   Pavel Govyadinov   fixed a drawing b...
1730
  		traceLine(stim::vec3<float> pos, float mag, int min_cost)
5de3a9c2