Merge branch 'JACK' into 'master'

need some data to test on See merge request !9

Merge branch 'JACK' into 'master'
need some data to test on See merge request !9
David Mayerich
2 parents 5c83f00e 30641100
Showing 5 changed files with 130 additions and 102 deletions Show diff stats
CMakeLists.txt
data/00_GT.swc
data/01_GT.swc
data/01_T.swc
main.cu
@@ -85,3 +85,5 @@ configure_file(data/04_Tb.obj ${CMAKE_CURRENT_BINARY_DIR}/04_Tb.obj @ONLY)
 configure_file(data/1.swc ${CMAKE_CURRENT_BINARY_DIR}/1.swc @ONLY)
 configure_file(data/2.swc ${CMAKE_CURRENT_BINARY_DIR}/2.swc @ONLY)
 configure_file(data/00_GT.swc ${CMAKE_CURRENT_BINARY_DIR}/00_GT.swc @ONLY)
+configure_file(data/01_GT.swc ${CMAKE_CURRENT_BINARY_DIR}/01_GT.swc @ONLY)
+configure_file(data/01_T.swc ${CMAKE_CURRENT_BINARY_DIR}/01_T.swc @ONLY)
+# converted from 00_GT.obj 
+1 1 99 677 0 0.5 -1
+2 1 88 563 0 0.5 1
+3 1 229 510 0 0.5 2
+4 1 181 372 0 0.5 3
+5 1 57 347 0 0.5 4
+6 1 316 596 0 0.5 3
+7 1 344 724 0 0.5 6
+8 1 385 425 0 0.5 3
+9 1 581 361 0 0.5 8
+10 1 574 223 0 0.5 9
+11 1 481 165 0 0.5 10
+12 1 341 199 0 0.5 11
+13 1 757 377 0 0.5 9  
+14 1 818 229 0 0.5 13
+15 1 981 152 0 0.5 14
+16 1 793 508 0 0.5 13
+17 1 941 600 0 0.5 16
+18 1 679 601 0 0.5 16
+19 1 647 738 0 0.5 18
+1 1 0.0 0.0 0.0 0.5 -1
+2 3 10 -12 11 0.5 1
+3 3 42 -80 20 0.5 2
+4 3 95 -55 4 0.5 2
+5 3 4 9 0 0.5 1
+6 3 46 55 -15 0.5 5
+7 2 -20 11 30 0.5 1
+8 4 -6 60 -4 0.5 7
+9 4 -44 99 -8 0.5 8
+1 1 0.0 0.0 0.0 0.5 -1
+2 3 10 -12 11 0.5 1
+3 3 30 -40 10 0.5 2
+4 3 4 9 0 0.5 1
+5 3 46 55 -15 0.5 4
+6 2 -20 11 30 0.5 1
+7 4 -6 60 -4 0.5 6
+8 4 -44 99 -8 0.5 7
+9 4 -55 -10 8 0.5 7
+10 4 -66 -10 8 0.5 9
+11 3 40 -80 20 0.5 3
+12 3 50 -90 30 0.5 11
+13 1 20 20 20 0.5 1
@@ -37,7 +37,6 @@ stim::gl_network&lt;float&gt; _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
@@ -47,7 +46,8 @@ std::vector&lt;unsigned&gt; _t_gt;								// store indices of nearest edge points in _
 float resample_rate = 0.5f;			//sample rate for the network (fraction of sigma used as the maximum sample rate)
 float camera_factor = 1.2f;			//start point of the camera as a function of X and Y size
 float orbit_factor = 0.01f;			//degrees per pixel used to orbit the camera
-float zoom_factor = 10.0;
+float zoom_factor = 10.0f;
+float radius_factor = 0.5f;
 //mouse click
 bool LButtonDown = false;			// true when left button down
@@ -74,7 +74,9 @@ GLuint dlist2;
 //OpenGL objects
 GLuint cmap_tex = 0;				//texture name for the color map
+float delta;
 float sigma = 3;					//default sigma
+float radius = 3;					//equals to radius
 //sets an OpenGL viewport taking up the entire window
 void glut_render_single_projection(){
@@ -146,11 +148,12 @@ 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.glCylinder(sigma);							//render the GT network
+			GT.glCylinder(sigma, radius);							//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(sigma);								//render the T network
+			T.glCylinder(sigma, radius);							//render the T network
+			sigma = radius;											// set sigma equal to radius
 		}
 	}
@@ -171,12 +174,12 @@ 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.glCylinder(sigma);							//render the GT network
+				_GT.glCylinder(sigma, radius);							//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(sigma);							//render the T network
-
+				_T.glCylinder(sigma, radius);							//render the T network
+				sigma = radius;											//set sigma equal to radius
 			}
 			else {
 				glEnable(GL_DEPTH_TEST);								//enable depth
@@ -185,12 +188,13 @@ void glut_render(void) {
 				glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);		//clear the screen
 																		//_GT.glRandColorCenterlineGT(dlist1, _gt_t, colormap);
-				_GT.glRandColorCylinder1(dlist1, _gt_t, colormap, sigma);
+				_GT.glRandColorCylinder1(dlist1, _gt_t, colormap, sigma, radius);
 				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, sigma);
+				_T.glRandColorCylinder2(dlist2, _t_gt, colormap, sigma, radius);
+				sigma = radius;											//set sigma equal to radius
 			}
 		}
 	}
@@ -310,20 +314,10 @@ 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;*/
-	float delta;
-	if (direction > 0)								// if it is button 3(up)
+	if (direction > 0)								// if it is button 3(up), move closer
 		delta = zoom_factor;
-	else											// if it is button 4(down)
+	else											// if it is button 4(down), leave farther
 		delta = -zoom_factor;
 	cam.Push(delta);
@@ -332,19 +326,46 @@ void glut_wheel(int wheel, int direction, int x, int y) {
 // define keyboard inputs
 void glut_keyboard(unsigned char key, int x, int y){
-	if(key == 'm')											// if keyboard 'm' is pressed
-	{
-		if(compareMode && !mappingMode){					// if it is in compare mode
-			compareMode = false;
-			mappingMode = true;
-		}
-		else{												// if it is in mapping mode
-			compareMode = true;
-			mappingMode = false;
-		}
-	}
-	if (key == 27) {										// if keyboard "ESC" is pressed
-		exit(0);											// exit
+	
+	// register different keyboard operation
+	switch (key) {
+		
+		// change render mode
+		case 'm':											// if keyboard 'm' is pressed, then change render mode
+			if (compareMode && !mappingMode && ind) {		// if current mode is comparing mode
+				compareMode = false;
+				mappingMode = true;
+			}
+			else if (!compareMode && mappingMode && ind) {	// if current mode is mapping mode
+				compareMode = true;
+				mappingMode = false;
+			}
+			break;
+
+		// zooming
+		case 'w':						// if keyboard 'w' is pressed, then move closer
+			delta = zoom_factor;
+			cam.Push(delta);
+			break;
+		case 's':						// if keyboard 's' is pressed, then leave farther
+			delta = -zoom_factor;
+			cam.Push(delta);
+			break;
+
+		// resample and re-render the cylinder in different radius
+		case 'd':						// if keyboard 'd' is pressed, then increase radius by radius_factor
+			radius += radius_factor;
+			break;
+		case 'a':						// if keyboard 'a' is pressed, then decrease radius by radius_factor
+			radius -= radius_factor;
+			// get rid of the degenerated case when radius decrease below 0
+			if (radius < 0.001f)
+				radius = 0.2;
+			break;
+
+		// close window and exit application
+		case 27:						// if keyboard 'ESC' is pressed, then exit
+			exit(0);
 	}
 	glutPostRedisplay();
 }
@@ -396,13 +417,13 @@ void glut_initialize(){
 	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);	//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
-	}						
+		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
+	}		
+	glutKeyboardFunc(glut_keyboard);		//register keyboard callback
 	glutMouseWheelFunc(glut_wheel);		
 	texture_initialize();									//set up texture mapping (create texture maps, enable features)
@@ -469,30 +490,6 @@ 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){
@@ -563,10 +560,8 @@ int main(int argc, char* argv[])
 	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
+		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 {
@@ -575,43 +570,32 @@ int main(int argc, char* argv[])
 		}	
 	}
-	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??
-			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()) {
-				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
-		}
+	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
+		sigma = args["sigma"].as_float();					//get the sigma value from the user
+		radius = sigma;
+		std::vector<std::string> tmp = stim::parser::split(args.arg(1), '.');	// split the filename at '.'
+		if ("swc" == tmp[1]) 								//loading swc files
+			T.load_swc(args.arg(1));                        //load the second (test) network
+		else if ("obj" == tmp[1])							//loading obj files
+			T.load_obj(args.arg(1));
 		else {
-			int device = args["device"].as_int();				//get the device value from the user
-			num_nets = 2;										//set the number of networks to two
-			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
+			std::cout << "Invalid loading file" << std::endl;
+			exit(1);
+		}
+		if (args["features"].is_set())						//if the user wants to save features
+			features(args["features"].as_string());
+		//does it need to be resampled??
+		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
 		}
-	}
 	//if a GUI is requested, display the network using OpenGL
 	if(args["gui"].is_set()){