fix minor errors for loading and rendering networks from swc files

Jiaming Guo
1 parent 484e01e8
Showing 1 changed file with 182 additions and 56 deletions Show diff stats
main.cu
-#include <stdlib.h>
+#ifndef GL_MULTISAMPLE
+#define GL_MULTISAMPLE  0x809D
+#endif
+
+#include <stdlib.h>
 #include <string>
 #include <fstream>
-#include <algorithm>
+#include <algorithm> 
 //OpenGL includes
 #include <GL/glut.h>
@@ -19,12 +23,6 @@
 #include <cuda.h>
 #endif
-//ANN includes
-//#include <ANN/ANN.h>
-
-//chrono includes
-//#include <chrono>
-
 //BOOST includes
 #include <boost/tuple/tuple.hpp>
@@ -32,15 +30,20 @@
 stim::gl_aaboundingbox<float> bb;			//axis-aligned bounding box object
 stim::camera cam;					//camera object
+// number of networks
 unsigned num_nets = 0;
+
+// networks
 stim::gl_network<float> GT;			//ground truth network
 stim::gl_network<float> T;			//test network
 stim::gl_network<float> _GT;		//splitted GT
 stim::gl_network<float> _T;			//splitted T
+// indicator
 unsigned ind = 0;						//indicator of mapping
 unsigned swc_ind = 0;					//indicator of rendering swc file as networks
+// relationships
 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
@@ -57,6 +60,10 @@ bool RButtonDown = false;
 int mouse_x;
 int mouse_y;
+// mouse wheel move
+float des = 0.0f;
+
+// render modes
 bool compareMode = true;			// default mode is compare mode
 bool mappingMode = false;
@@ -117,6 +124,7 @@ void glut_render_modelview(){
 	stim::vec3<float> focus = cam.getLookAt();		//get the camera focal point
 	stim::vec3<float> up = cam.getUp();				//get the camera "up" orientation
+	eye[2] += des;									//get camera closer to target by factor des
 	gluLookAt(eye[0], eye[1], eye[2], focus[0], focus[1], focus[2], up[0], up[1], up[2]);	//set up the OpenGL camera
 }
@@ -125,9 +133,10 @@ void glut_render(void) {
 	//no mapping, just comparing
 	if (ind == 0) {	
-		//working with obj files
+		//-----working with obj files-----
 		if (swc_ind == 0) {
 			if (num_nets == 1) {										//if a single network is loaded
+				glEnable(GL_DEPTH_TEST);								//enable depth
 				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
@@ -135,7 +144,7 @@ void glut_render(void) {
 			}
 			if (num_nets == 2) {										//if two networks are loaded	
-
+				glEnable(GL_DEPTH_TEST);								//enable depth
 				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
@@ -144,16 +153,17 @@ 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.glCylinder();							//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.glCylinder();								//render the T network
 			}
 		}
-		//working with swc files
+		//-----working with swc files-----
 		else {
 			if (num_nets == 1) {										//if a single network is loaded
+				glEnable(GL_DEPTH_TEST);								//enable depth
 				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
@@ -161,7 +171,7 @@ void glut_render(void) {
 			}
 			if (num_nets == 2) {										//if two networks are loaded	
-
+				glEnable(GL_DEPTH_TEST);								//enable depth
 				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
@@ -179,9 +189,9 @@ void glut_render(void) {
 		}
 	}
-	//do mapping
+	//do comparing and mapping
 	else {	
-		//working with obj files
+		//-----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
@@ -189,6 +199,48 @@ void glut_render(void) {
 			}
 			if (num_nets == 2) {											//if two networks are loaded
 				if (compareMode) {
+					glEnable(GL_DEPTH_TEST);								//enable depth
+					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.glCylinder();							//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.glCylinder();							//render the T network
+
+				}
+				else {
+					glEnable(GL_DEPTH_TEST);								//enable depth
+					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.glRandColorCylinder1(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.glRandColorCylinder2(dlist2, _t_gt, colormap);
+				}
+			}
+		}
+		//-----working with swc files-----
+		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
+				//in compare mode
+				if (compareMode) {
+					glEnable(GL_DEPTH_TEST);								//enable depth
 					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
@@ -204,37 +256,38 @@ void glut_render(void) {
 					_T.glCenterline();							//render the T network
 				}
+				//in mapping mode
 				else {
-					glEnable(GL_DEPTH_TEST);
+					glEnable(GL_DEPTH_TEST);								//enable depth
 					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);
+					_GT.glRandColorCylinder1_swc(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);
+					_T.glRandColorCylinder2_swc(dlist2, _t_gt, colormap);
 				}
 			}
 		}
 	}
-	if (num_nets == 2) {
+	if (num_nets == 2) {											// works only with two networks
 		std::ostringstream ss;
 		if (mappingMode)											// if it is in mapping mode
 			ss << "Mapping Mode";
 		else
-			ss << "Compare Mode";								// default mode is compare mode
+			ss << "Compare Mode";									// default mode is compare mode
 		glDisable(GL_TEXTURE_1D);
-		glMatrixMode(GL_PROJECTION);										//Set up the 2d viewport for mode text printing
+		glMatrixMode(GL_PROJECTION);										// set up the 2d viewport for mode text printing
 		glPushMatrix();
 		glLoadIdentity();
-		int X = glutGet(GLUT_WINDOW_WIDTH);
-		int Y = glutGet(GLUT_WINDOW_HEIGHT);
+		int X = glutGet(GLUT_WINDOW_WIDTH);									// get the current window width
+		int Y = glutGet(GLUT_WINDOW_HEIGHT);								// get the current window height
 		glViewport(0, 0, X / 2, Y);											// locate to left bottom corner
 		gluOrtho2D(0, X, 0, Y);												// define othogonal aspect
 		glColor3f(0.0, 1.0, 0.0);											// using green to show mode
@@ -243,7 +296,7 @@ void glut_render(void) {
 		glPushMatrix();
 		glLoadIdentity();
-		glRasterPos2f(0, 5);											//print text in the bottom left corner
+		glRasterPos2f(0, 5);												//print text in the left bottom corner
 		glutBitmapString(GLUT_BITMAP_TIMES_ROMAN_24, (const unsigned char*)(ss.str().c_str()));
 		glPopMatrix();
@@ -270,6 +323,22 @@ void glut_motion(int x, int y){
 	}
 }
+// sets the menu options
+void glut_menu(int value) {
+	if (value == 1) {								// menu 1 represents comparing mode
+		compareMode = true;
+		mappingMode = false;
+	}
+	if (value == 2) {								// menu 2 represents mapping mode
+		compareMode = false;
+		mappingMode = true;
+	}
+	if (value == 3) {
+		exit(0);
+	}
+	glutPostRedisplay();
+}
+
 // sets the mouse position when clicked
 void glut_mouse(int button, int state, int x, int y){
@@ -319,8 +388,23 @@ void glut_mouse(int button, int state, int x, int y){
 		}
 }
+// define camera move based on mouse wheel move(actually we can combine this with glut_mouse)
+void glut_wheel(int wheel, int direction, int x, int y) {
+	float cam_move_fac;								// camera move unit length
+	stim::vec3<float> eye = cam.getPosition();		// get the camera position (eye point)
+	stim::vec3<float> focus = cam.getLookAt();		// get the camera focal point
+	cam_move_fac = fabs(focus[2] - eye[2]) / 50;	// divided by 50
+	
+	if (direction > 0)								// if it is button 3(up)
+		des -= cam_move_fac;
+	else											// if it is button 4(down)
+		des += cam_move_fac;
+	glutPostRedisplay();
+}
+
+// define keyboard inputs
 void glut_keyboard(unsigned char key, int x, int y){
-	if(key == 'm')											// press m to change mode
+	if(key == 'm')											// if keyboard 'm' is pressed
 	{
 		if(compareMode && !mappingMode){					// if it is in compare mode
 			compareMode = false;
@@ -331,6 +415,9 @@ void glut_keyboard(unsigned char key, int x, int y){
 			mappingMode = false;
 		}
 	}
+	if (key == 27) {										// if keyboard "ESC" is pressed
+		exit(0);											// exit
+	}
 	glutPostRedisplay();
 }
@@ -370,18 +457,27 @@ void glut_initialize(){
 	myargv [0]=strdup ("netmets");
 	glutInit(&myargc, myargv);									//pass bogus arguments to glutInit()
-	glutInitDisplayMode(GLUT_DEPTH | GLUT_DOUBLE | GLUT_RGBA);	//generate a color buffer, depth buffer, and enable double buffering
+	glutSetOption(GLUT_MULTISAMPLE, 8);
+	glutInitDisplayMode(GLUT_DEPTH | GLUT_DOUBLE | GLUT_RGBA | GLUT_MULTISAMPLE);	//generate a color buffer, depth buffer, and enable double buffering
 	glutInitWindowPosition(100,100);							//set the initial window position
 	glutInitWindowSize(320, 320);								//set the initial window size
 	glutCreateWindow("NetMets - STIM Lab, UH");					//set the dialog box title
-
+	glEnable(GL_MULTISAMPLE);
 	// register callback functions
 	glutDisplayFunc(glut_render);			//function executed for rendering - renders networks
 	glutMouseFunc(glut_mouse);				//executed on a mouse click - sets starting mouse positions for rotations
 	glutMotionFunc(glut_motion);			//executed when the mouse is moved while a button is pressed
-	if(ind == 1)							//only in mapping mode, keyboard will be used
-		glutKeyboardFunc(glut_keyboard);
+	if (ind == 1) {							//only in mapping mode, keyboard will be used
+		glutKeyboardFunc(glut_keyboard);	//register keyboard callback
+		glutCreateMenu(glut_menu);			//register menu option callback
+		glutAddMenuEntry("Comparing Mode", 1);//register menu 1 as comparing mode
+		glutAddMenuEntry("Mapping Mode", 2);  //register menu 2 as mapping mode
+		glutAddMenuEntry("Exit", 3);		  //register menu 3 as exiting
+		glutAttachMenu(GLUT_RIGHT_BUTTON);	//register right mouse to open menu option
+	}						
+	if (swc_ind == 1)						//only in rendering swc files, mouse wheel will be used
+		glutMouseWheelFunc(glut_wheel);		
 	texture_initialize();									//set up texture mapping (create texture maps, enable features)
@@ -393,6 +489,7 @@ void glut_initialize(){
 }
 #ifdef __CUDACC__
+// set specific device to work on
 void setdevice(int &device){
 	int count;
 	cudaGetDeviceCount(&count);				// numbers of device that are available
@@ -403,7 +500,7 @@ void setdevice(int &amp;device){
 }
 #else
 void setdevice(int &device){
-	device = -1;
+	device = -1;							// set to default -1
 }
 #endif
@@ -421,18 +518,22 @@ void compare(float sigma, int device){
 	std::cout << "FPR: " << FNR << std::endl;
 }
+//split and map two networks and fill the networks' R with metric information
 void map(float sigma, int device, float threshold){
+	// compare and split two networks
 	_GT.split(GT, T, sigma, device, threshold);
 	_T.split(T, GT, sigma, device, threshold);
+	// mapping two new splitted networks and get their edge relation
 	_GT.mapping(_T, _gt_t, device, threshold);
 	_T.mapping(_GT, _t_gt, device, threshold);
+	// generate random color set based on the number of edges in GT
 	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
 	for(int i = 0; i < 3 * num; i++)
-		colormap[i] = rand()/(float)RAND_MAX;
+		colormap[i] = rand()/(float)RAND_MAX;			// set to [0, 1]
 	//calculate the metrics
 	float FPR = _GT.average(0);						//calculate the metrics
@@ -442,6 +543,30 @@ void map(float sigma, int device, float threshold){
 	std::cout << "FPR: " << FNR << std::endl;
 }
+void map_swc(float sigma, int device, float threshold) {
+
+	// compare two networks
+	_GT = GT.compare(T, sigma, device);						//compare the ground truth to the test case - store errors in _GT
+	_T = T.compare(_GT, sigma, device);						//compare the test case to the ground truth - store errors in _T
+
+	// mapping two networks and get their edge relation
+	_GT.mapping(_T, _gt_t, device, threshold);
+	_T.mapping(_GT, _t_gt, device, threshold);
+
+	// generate random color set based on the number of edges in GT
+	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
+	for (int i = 0; i < 3 * num; i++)
+		colormap[i] = rand() / (float)RAND_MAX;			// set to [0, 1]
+
+	//calculate the metrics
+	float FPR = _GT.average(0);						//calculate the metrics
+	float FNR = _T.average(0);
+
+	std::cout << "FNR: " << FPR << std::endl;		//print false alarms and misses
+	std::cout << "FPR: " << FNR << std::endl;
+}
+
 // writes features of the networks i.e average segment length, tortuosity, branching index, contraction, fractal dimension, number of end and branch points to a csv file
 // Pranathi wrote this - saves network features to a CSV file
 void features(std::string filename){
@@ -480,7 +605,7 @@ void advertise(){
 	std::cout<<"========================================================================="<<std::endl<<std::endl;
 	std::cout<<"usage: netmets file1 file2 --sigma 3"<<std::endl;
-	std::cout<<"            compare two files with a tolerance of 3 (units defined by the network)"<<std::endl<<std::endl;
+	std::cout<<"            compare two .obj files with a tolerance of 3 (units defined by the network)"<<std::endl<<std::endl;
 	std::cout<<"       netmets file1 --gui"<<std::endl;
 	std::cout<<"            load a file and display it using OpenGL"<<std::endl<<std::endl;
 	std::cout<<"       netmets file1 file2 --device 0"<<std::endl;
@@ -500,7 +625,6 @@ 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
@@ -510,15 +634,26 @@ int main(int argc, char* argv[])
 		exit(1);											//exit
 	}
-	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
+	if (args.nargs() >= 1) {			// if at least one network file is specified
+		num_nets = 1;					// set the number of networks to one
+		std::vector<std::string> tmp = stim::parser::split(args.arg(0), '.');	// split the filename at '.'
+		if ("swc" == tmp[1]) {			// loading swc file
+			GT.load_swc(args.arg(0));	// load the specified file as the ground truth
+			swc_ind = 1;				// set the indicator of swc file to 1
+		}			
+		else if ("obj" == tmp[1])		// loading obj file
+			GT.load_obj(args.arg(0));	// load the specified file as the ground truth
+		else {
+			std::cout << "Invalid loading file" << std::endl;
+			exit(1);
+		}	
+	}
+
+	if (args.nargs() == 2) {								//if two files are specified, they will be displayed in neighboring viewports and compared
+		if (1 == swc_ind) {									//loading swc files
 			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??
+																//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
@@ -526,21 +661,15 @@ int main(int argc, char* argv[])
 			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);
+				float threshold = args["mapping"].as_float();
+				map_swc(sigma, device, threshold);
+				//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
 		}
-	}
-	
-	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
+		else {
 			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
@@ -554,15 +683,12 @@ int main(int argc, char* argv[])
 				map(sigma, device, threshold);
 			}
 			else
-				compare(sigma, device);										//run the comparison algorithm
+				compare(sigma, device);							//run the comparison algorithm
 		}
 	}
 	//if a GUI is requested, display the network using OpenGL
 	if(args["gui"].is_set()){
-		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