added comments

David Mayerich
1 parent b50c840e
Showing 4 changed files with 55 additions and 61 deletions Show diff stats
stim/gl/gl_spider.h
stim/gl/gl_texture.h
stim/grids/image_stack.h
stim/visualization/cylinder.h
@@ -49,7 +49,7 @@ namespace stim
 {
 template<typename T>
-class gl_spider : public virtual gl_texture<T>
+class gl_spider // : public virtual gl_texture<T>
 {
 	//doen't use gl_texture really, just needs the GLuint id.
 	//doesn't even need the texture iD really.
@@ -65,66 +65,70 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			double hit_time;// = 0;
 		#endif
-		//
 		stim::vec3<float> p;  	//vector designating the position of the spider.
-		stim::vec3<float> d;	//vector designating the orientation of the spider
-						//always a unit vector.
-		stim::vec<float> m;	//magnitude of the spider vector.
-						//mag[0] = length.
-						//mag[1] = width.
+		stim::vec3<float> d;	//normalized direction of travel
+		stim::vec<float> m;		//size of the spider in tissue space
+
 		std::vector<stim::vec3<float> > dV;	//A list of all the direction vectors.
-		std::vector<stim::vec3<float> > pV;	//A list of all the position vectors.
+		std::vector<stim::vec3<float> > pV;	//A list of all test positions (relative to p)
 		std::vector<stim::vec3<float> > mV;	//A list of all the size vectors.
-		stim::matrix<float, 4> cT;		//current Transformation matrix
-							//From tissue space to texture space.
-		GLuint texID;
-		stim::vec<float> S;			//Size of a voxel in the volume.
-		stim::vec<float> R;			//Dimensions of the volume.
+		stim::matrix<float, 4> cT;			//current Transformation matrix (tissue)->(texture)
+		GLuint texID;						//OpenGL ID for the texture to be traced
+		stim::vec<float> S;					//Size of a voxel in the volume.
+		stim::vec<float> R;					//Dimensions of the volume.
 		//GL and Cuda variables
-		GLuint dList;				//displaylist ID
-		GLuint fboID;				//framebuffer ID
-		GLuint texbufferID;			//texbuffer ID, only necessary for 
-							//cuda aspect of the calculation.
-		GLuint pfboID;				//buffer object for position tracking.
-		GLuint ptexbufferID;			//texture object for position tracking.
-
-		GLuint mfboID;				//buffer object for magnitude adjustment.
-		GLuint mtexbufferID;			//texture object for magnitude adjustment.
-		GLuint bfboID;				//buffer object for position adjustment.
-		GLuint btexbufferID;			//buffer object for position adjustment.
+		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
+
+		GLuint pfboID;				//framebuffer ID, position templates
+		GLuint ptexbufferID;		//texture ID, position templates
+
+		GLuint mfboID;				//framebuffer ID, radius templates
+		GLuint mtexbufferID;		//texture ID, radius templates
+
+		GLuint bfboID;				//framebuffer ID, cylinder (surrounding fiber)
+		GLuint btexbufferID;		//texture ID, cylinder
 		int numSamples;				//The number of templates in the buffer.
 		int numSamplesPos;
 		int numSamplesMag;
-		float stepsize;// = 5.0;			//Step size.
-//		float stepsize = 3.0;			//Step size.
-		int current_cost;			//variable to store the cost of the current step.
-		
+		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		
 		//Tracing variables.
-		std::stack< stim::vec3<float> > seeds;		//seed positions.
-		std::stack< stim::vec3<float> > seedsvecs;	//seed directions.
-		std::stack< float > 		seedsmags;	//seed magnitudes.
+		std::stack< stim::vec3<float> > seeds;		//seed positions
+		std::stack< stim::vec3<float> > seedsvecs;	//seed directions
+		std::stack< float > 		seedsmags;		//seed magnitudes
-		std::vector< stim::vec3<float> > cL;	//Positions of line currently being traced.
-		std::vector< stim::vec3<float> > cD;	//Direction of line currently being traced.
-		std::vector< stim::vec<float> > cM;	//Magnitude of line currently being traced.
+		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)
+		std::vector< stim::vec<float> > cM;		//radius up to the current point
-		stim::glnetwork<float> nt;		//object for storing the network.
-		stim::glObj<float> sk;
+		stim::glnetwork<float> nt;				//network object holding the currently traced centerlines
+		stim::glObj<float> sk;					//OBJ file storing the network (identical to above)
-		stim::vec<float> rev;			//reverse vector;
-		stim::camera camSel;
-		stim::vec3<float> ps;
-		stim::vec3<float> ups;
-		stim::vec3<float> ds;
+		//consider replacing with two seed points facing opposite directions
+		stim::vec<float> rev;					//reverse vector
-		//static const float t_length = 16.0;
-		float t_length;
+		//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
+
+		float t_length;							//length of the template (in pixels)
 		//cuda texture variables that keep track of the binding.
 		stim::cuda::cuda_texture t_dir;
@@ -148,7 +152,6 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 			setMatrix();			//create the transformation matrix.
 			glCallList(dList);		//move the templates to p, d, m.
 			glFinish();
-//			glFlush();
 			#ifdef TIMING
 				direction_time += gpuStopTimer();
 			#endif
@@ -324,7 +327,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 		///Stored in a display list.
 		///uses the default d vector <0,0,1>
 		void
-		genDirectionVectors(float solidAngle = M_PI/2)
+		genDirectionVectors(float solidAngle = stim::PI/2)
 		{
 			//Set up the vectors necessary for Rectangle creation.
@@ -1318,7 +1321,7 @@ class gl_spider : public virtual gl_texture&lt;T&gt;
 //--------------------------------------------------------------------------//
 		void
-		MonteCarloDirectionVectors(int nSamples, float solidAngle = 2*M_PI)
+		MonteCarloDirectionVectors(int nSamples, float solidAngle = stim::TAU)
 		{
 //			float PHI[2];//, Z[2];//, range;
 //			PHI[0] = asin(solidAngle/2);
@@ -68,10 +68,10 @@ class gl_texture : public virtual image_stack&lt;T&gt;
 		///@param string path to the directory with the image files.
 		///Creates an instance of the gl_texture object with a path to the data.
-		gl_texture(std::string file_path)
+		gl_texture(std::string file_mask)
 		{
-			path = file_path;
-			image_stack<T>::load_images(path.append("/*.jpg"));
+			//path = file_mask;
+			image_stack<T>::load_images(file_mask);
 			setTextureType();
 		}
@@ -32,12 +32,6 @@ public:
 		stim::filename file_path(file_mask);
-		//if the file path is relative, update it with the current working directory
-//		if(file_path.is_relative()){
-//			stim::filename wd = stim::filename::cwd();
-//			file_path = wd.get_relative(file_mask);
-//		}
-
 		//get the list of files
 		std::vector<stim::filename> file_list = file_path.get_list();
@@ -46,11 +40,10 @@ public:
 			std::cout<<"STIM ERROR (image_stack): No matching files for loading a stack."<<std::endl;
 			exit(1);
 		}
-		for(int i = 0; i < file_list.size(); i++)
-			std::cout << file_list[i].str() << std::endl;
+		//for(int i = 0; i < file_list.size(); i++)
+		//	std::cout << file_list[i].str() << std::endl;
 		//load the first image and set all of the image_stack properties
-//		std::cout<<"File to Load: "<<file_list[0].str()<<std::endl;
 		stim::image<T> I(file_list[0].str());
 		//set the image resolution and number of channels
@@ -64,8 +57,6 @@ public:
 		//load and copy each image into the grid
 		for(unsigned int i = 0; i<R[3]; i++){
-
-//			std::cout<<"File to Load: "<<file_list[i].str()<<std::endl;
 			//load the image
 			stim::image<T> I(file_list[i].str());
@@ -331,7 +331,7 @@ class cylinder
 			}
 //			std::cout << e[idx].U.len() << " " << mags[idx][0] << std::endl;
 //			std::cout << v2 << std::endl;
-			return(v2);
+			return(v1);
 //			return (mags[idx][0] + (mags[idx+1][0]-mags[idx][0])*rat);
 	//	(
 		}