add functions for rendering networks from swc files

Jiaming Guo
1 parent 68944dbf
Showing 1 changed file with 135 additions and 65 deletions Show diff stats
main.cu
@@ -39,6 +39,7 @@ stim::gl_network&lt;float&gt; _GT;		//splitted GT
 stim::gl_network<float> _T;			//splitted T
 unsigned ind = 0;						//indicator of mapping
+unsigned swc_ind = 0;					//indicator of rendering swc file as networks
 std::vector<unsigned> _gt_t;								// store indices of nearest edge points in _T for _GT
 std::vector<unsigned> _t_gt;								// store indices of nearest edge points in _GT for _T
@@ -122,38 +123,19 @@ void glut_render_modelview(){
 //draws the network(s)
 void glut_render(void) {
-	if (ind == 0) {
-		if (num_nets == 1) {											//if a single network is loaded
-			glut_render_single_projection();						//fill the entire viewport
-			glut_render_modelview();								//set up the modelview matrix with camera details
-			glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
-			GT.glCenterline0();										//render the GT network (the only one loaded)
-		}
-
-		if (num_nets == 2) {											//if two networks are loaded	
-
-			glut_render_left_projection();							//set up a projection for the left half of the window
-			glut_render_modelview();								//set up the modelview matrix using camera details
-			glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
-
-			glEnable(GL_TEXTURE_1D);										//enable texture mapping
-			glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);		//texture map will be used as the network color
-			glBindTexture(GL_TEXTURE_1D, cmap_tex);							//bind the Brewer texture map
+	//no mapping, just comparing
+	if (ind == 0) {	
+		//working with obj files
+		if (swc_ind == 0) {
+			if (num_nets == 1) {										//if a single network is loaded
+				glut_render_single_projection();						//fill the entire viewport
+				glut_render_modelview();								//set up the modelview matrix with camera details
+				glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
+				GT.glCenterline0();										//render the GT network (the only one loaded)
+			}
-			GT.glCenterline();						//render the GT network
+			if (num_nets == 2) {										//if two networks are loaded	
-			glut_render_right_projection();							//set up a projection for the right half of the window
-			glut_render_modelview();								//set up the modelview matrix using camera details
-			T.glCenterline();							//render the T network
-		}
-	}
-	else {
-		if (num_nets == 1) {											//if a single network is loaded
-			std::cout << "You should have at least two networks to do mapping." << std::endl;	//exit program because there isn't enough network
-			exit(1);
-		}
-		if (num_nets == 2) {											//if two networks are loaded
-			if (compareMode) {
 				glut_render_left_projection();							//set up a projection for the left half of the window
 				glut_render_modelview();								//set up the modelview matrix using camera details
 				glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
@@ -162,24 +144,80 @@ void glut_render(void) {
 				glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);		//texture map will be used as the network color
 				glBindTexture(GL_TEXTURE_1D, cmap_tex);							//bind the Brewer texture map
-				_GT.glCenterline();						//render the GT network
+				GT.glCenterline();							//render the GT network
 				glut_render_right_projection();							//set up a projection for the right half of the window
 				glut_render_modelview();								//set up the modelview matrix using camera details
-				_T.glCenterline();							//render the T network
-
+				T.glCenterline();							//render the T network
+			}
+		}
+		//working with swc files
+		else {
+			if (num_nets == 1) {										//if a single network is loaded
+				glut_render_single_projection();						//fill the entire viewport
+				glut_render_modelview();								//set up the modelview matrix with camera details
+				glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
+				GT.glCenterline0_swc();									//render the GT network (the only one loaded)
 			}
-			else {
-				glEnable(GL_DEPTH_TEST);
+
+			if (num_nets == 2) {										//if two networks are loaded	
+
 				glut_render_left_projection();							//set up a projection for the left half of the window
 				glut_render_modelview();								//set up the modelview matrix using camera details
 				glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
-				_GT.glRandColorCenterlineGT(dlist1, _gt_t, colormap);
+				glEnable(GL_TEXTURE_1D);										//enable texture mapping
+				glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);		//texture map will be used as the network color
+				glBindTexture(GL_TEXTURE_1D, cmap_tex);							//bind the Brewer texture map
+
+				GT.glCenterline();							//render the GT network
 				glut_render_right_projection();							//set up a projection for the right half of the window
 				glut_render_modelview();								//set up the modelview matrix using camera details
-				_T.glRandColorCenterlineT(dlist2, _t_gt, colormap);
+				T.glCenterline();							//render the T network
+			}
+		}
+	}
+
+	//do mapping
+	else {	
+		//working with obj files
+		if (swc_ind == 0) {
+			if (num_nets == 1) {											//if a single network is loaded
+				std::cout << "You should have at least two networks to do mapping." << std::endl;	//exit program because there isn't enough network
+				exit(1);
+			}
+			if (num_nets == 2) {											//if two networks are loaded
+				if (compareMode) {
+					glut_render_left_projection();							//set up a projection for the left half of the window
+					glut_render_modelview();								//set up the modelview matrix using camera details
+					glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
+
+					glEnable(GL_TEXTURE_1D);										//enable texture mapping
+					glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE);		//texture map will be used as the network color
+					glBindTexture(GL_TEXTURE_1D, cmap_tex);							//bind the Brewer texture map
+
+					_GT.glCenterline();							//render the GT network
+
+					glut_render_right_projection();							//set up a projection for the right half of the window
+					glut_render_modelview();								//set up the modelview matrix using camera details
+					_T.glCenterline();							//render the T network
+
+				}
+				else {
+					glEnable(GL_DEPTH_TEST);
+					glut_render_left_projection();							//set up a projection for the left half of the window
+					glut_render_modelview();								//set up the modelview matrix using camera details
+					glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
+
+																			//_GT.glRandColorCenterlineGT(dlist1, _gt_t, colormap);
+					_GT.glCylinderGT(dlist1, _gt_t, colormap);
+
+					glut_render_right_projection();							//set up a projection for the right half of the window
+					glut_render_modelview();								//set up the modelview matrix using camera details
+																			//_T.glRandColorCenterlineT(dlist2, _t_gt, colormap);
+					_T.glCylinderT(dlist2, _t_gt, colormap);
+				}
 			}
 		}
 	}
@@ -383,13 +421,13 @@ void compare(float sigma, int device){
 	std::cout << "FPR: " << FNR << std::endl;
 }
-void map(float sigma, int device){
+void map(float sigma, int device, float threshold){
-	_GT.split(GT, T, sigma, device);
-	_T.split(T, GT, sigma, device);
+	_GT.split(GT, T, sigma, device, threshold);
+	_T.split(T, GT, sigma, device, threshold);
-	_GT.mapping(_T, _gt_t, device);
-	_T.mapping(_GT, _t_gt, device);
+	_GT.mapping(_T, _gt_t, device, threshold);
+	_T.mapping(_GT, _t_gt, device, threshold);
 	size_t num = _gt_t.size();							// also create random color for unmapping edge, but won't be used though
 	colormap.resize(3 * num);							// 3 portions compound RGB
@@ -437,7 +475,7 @@ void advertise(){
 	std::cout<<"========================================================================="<<std::endl;
 	std::cout<<"Thank you for using the NetMets network comparison tool!"<<std::endl;
 	std::cout<<"Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston"<<std::endl;
-	std::cout<<"Developers: Pranathi Vemuri, David Mayerich"<<std::endl;
+	std::cout<<"Developers: Pranathi Vemuri, David Mayerich, Jiaming Guo"<<std::endl;
 	std::cout<<"Source: https://git.stim.ee.uh.edu/segmentation/netmets" <<std::endl;
 	std::cout<<"========================================================================="<<std::endl<<std::endl;
@@ -447,6 +485,8 @@ void advertise(){
 	std::cout<<"            load a file and display it using OpenGL"<<std::endl<<std::endl;
 	std::cout<<"       netmets file1 file2 --device 0"<<std::endl;
 	std::cout<<"            compare two files using device 0 (if there isn't a gpu, use cpu)"<<std::endl<<std::endl;
+	std::cout<<"       netmets file1 file2 --mapping value"<<std::endl;
+	std::cout<<"            mapping two files in random colors with a threshold of value"<<std::endl<<std::endl;
 }
 int main(int argc, char* argv[])
@@ -460,6 +500,7 @@ int main(int argc, char* argv[])
 	args.add("device", "choose specific device to run", "0");
 	args.add("features", "save features to a CSV file, specify file name");
 	args.add("mapping", "mapping input according to similarity");
+	args.add("swc", "load swc file instead of obj file");
 	args.parse(argc, argv);					//parse the user arguments
@@ -469,40 +510,69 @@ int main(int argc, char* argv[])
 		exit(1);											//exit
 	}
-	if(args.nargs() >= 1){					//if at least one network file is specified
-		num_nets = 1;						//set the number of networks to one
-		GT.load_obj(args.arg(0));			//load the specified file as the ground truth
-		/*GT.to_txt("Graph.txt");*/
+	if (args["swc"].is_set()) {				// if it is to load a swc file, right now we only load two files(.swc and .obj)
+		if (args.nargs() >= 1) {			// if at least one network file is specified
+			num_nets = 1;					// set the number of networks to one
+			GT.load_swc(args.arg(0));		// load the specified file as the ground truth
+		}
+		if (args.nargs() == 2) {			//if two files are specified, they will be displayed in neighboring viewports and compared
+			int device = args["device"].as_int();				//get the device value from the user
+			num_nets = 2;										//set the number of networks to two
+			//does it need to be resampled??
+			float sigma = args["sigma"].as_float();				//get the sigma value from the user
+			T.load_swc(args.arg(1));                            //load the second (test) network
+			if (args["features"].is_set())						//if the user wants to save features
+				features(args["features"].as_string());
+			GT = GT.resample(resample_rate * sigma);			//resample both networks based on the sigma value
+			T = T.resample(resample_rate * sigma);
+			if (args["mapping"].is_set()) {
+				std::cout << "right now networks that are loaded from swc files do not need to be mapped with each other!" << std::endl;
+				exit(1);
+			}
+			else
+				compare(sigma, device);							//run the comparison algorithm
+		}
 	}
-	if(args.nargs() == 2){			//if two files are specified, they will be displayed in neighboring viewports and compared
-		int device = args["device"].as_int();				//get the device value from the user
-		num_nets = 2;										//set the number of networks to two
-		float sigma = args["sigma"].as_float();				//get the sigma value from the user
-		T.load_obj(args.arg(1));                           //load the second (test) network
-		if(args["features"].is_set())						//if the user wants to save features
-			features(args["features"].as_string());
-		GT = GT.resample(resample_rate * sigma);			//resample both networks based on the sigma value
-		T = T.resample(resample_rate * sigma);
-		if(args["mapping"].is_set()){
-			map(sigma, device);
+	else {									//if it is to load a obj file	
+		if (args.nargs() >= 1) {			//if at least one network file is specified
+			num_nets = 1;					//set the number of networks to one
+			GT.load_obj(args.arg(0));		//load the specified file as the ground truth
+			/*GT.to_txt("Graph.txt");*/
+		}
+		if (args.nargs() == 2) {								//if two files are specified, they will be displayed in neighboring viewports and compared
+			int device = args["device"].as_int();				//get the device value from the user
+			num_nets = 2;										//set the number of networks to two
+			float sigma = args["sigma"].as_float();				//get the sigma value from the user
+			T.load_obj(args.arg(1));                            //load the second (test) network
+			if (args["features"].is_set())						//if the user wants to save features
+				features(args["features"].as_string());
+			GT = GT.resample(resample_rate * sigma);			//resample both networks based on the sigma value
+			T = T.resample(resample_rate * sigma);
+			if (args["mapping"].is_set()) {
+				float threshold = args["mapping"].as_float();
+				map(sigma, device, threshold);
+			}
+			else
+				compare(sigma, device);										//run the comparison algorithm
 		}
-		else
-			compare(sigma, device);										//run the comparison algorithm
 	}
 	//if a GUI is requested, display the network using OpenGL
 	if(args["gui"].is_set()){
-		if(args["mapping"].is_set()){
-			ind = 1;
+		if (args["swc"].is_set()) {
+			swc_ind = 1;
+		}
+		if (args["mapping"].is_set()) {
+			ind = 1;								//set indicator of mapping to 1(true)
 			bb = _GT.boundingbox();					//generate a bounding volume		
 			glut_initialize();						//create the GLUT window and set callback functions		
-			glutMainLoop();							// enter GLUT event processing cycle
+			glutMainLoop();							//enter GLUT event processing cycle
 		}
-		else{
+		else {
 			bb = GT.boundingbox();					//generate a bounding volume		
 			glut_initialize();						//create the GLUT window and set callback functions		
-			glutMainLoop();							// enter GLUT event processing cycle
+			glutMainLoop();							//enter GLUT event processing cycle
 		}
 	}
 }