segmentation / netmets

Commit 94a07643239456d0039b886f542e3dabeda30be7

Authored by David Mayerich
1 parent 9e6d89eb

removed ANN

Showing 2 changed files with 8 additions and 301 deletions   Show diff stats
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@@ -21,6 +21,9 @@ endif(NOT STIM_INCLUDE_DIRS) @@ -21,6 +21,9 @@ endif(NOT STIM_INCLUDE_DIRS)
21 #find BOOST 21 #find BOOST
22 find_package(Boost REQUIRED) 22 find_package(Boost REQUIRED)
23 23
  24 +#find cuda
  25 +find_package(CUDA REQUIRED)
  26 +
24 #find the GLUT library for visualization 27 #find the GLUT library for visualization
25 find_package(OpenGL REQUIRED) 28 find_package(OpenGL REQUIRED)
26 29
@@ -33,7 +36,7 @@ find_package(Threads) @@ -33,7 +36,7 @@ find_package(Threads)
33 find_package(X11) 36 find_package(X11)
34 37
35 #find the Approximate Nearest Neighbor Library 38 #find the Approximate Nearest Neighbor Library
36 -find_package(ANN REQUIRED) 39 +#find_package(ANN REQUIRED)
37 40
38 #build the executable in the binary directory on MS Visual Studio 41 #build the executable in the binary directory on MS Visual Studio
39 if ( MSVC ) 42 if ( MSVC )
@@ -45,16 +48,16 @@ include_directories( @@ -45,16 +48,16 @@ include_directories(
45 ${OPENGL_INCLUDE_DIRS} 48 ${OPENGL_INCLUDE_DIRS}
46 ${GLUT_INCLUDE_DIR} 49 ${GLUT_INCLUDE_DIR}
47 ${STIM_INCLUDE_DIRS} 50 ${STIM_INCLUDE_DIRS}
48 - ${ANN_INCLUDE_DIR} 51 + #${ANN_INCLUDE_DIR}
49 ${Boost_INCLUDE_DIR} 52 ${Boost_INCLUDE_DIR}
50 ) 53 )
51 54
52 #Assign source files to the appropriate variables 55 #Assign source files to the appropriate variables
53 -file(GLOB SRC_CPP "*.cpp") 56 +file(GLOB SRC_CPP "*.cu")
54 file(GLOB SRC_H "*.h") 57 file(GLOB SRC_H "*.h")
55 58
56 #create an executable file 59 #create an executable file
57 -add_executable(netmets 60 +cuda_add_executable(netmets
58 ${SRC_H} 61 ${SRC_H}
59 ${SRC_CPP} 62 ${SRC_CPP}
60 ) 63 )
@@ -66,7 +69,7 @@ target_link_libraries(netmets @@ -66,7 +69,7 @@ target_link_libraries(netmets
66 ${OPENGL_glu_LIBRARY} 69 ${OPENGL_glu_LIBRARY}
67 ${GLUT_LIBRARIES} 70 ${GLUT_LIBRARIES}
68 ${CMAKE_THREAD_LIBS_INIT} 71 ${CMAKE_THREAD_LIBS_INIT}
69 - ${ANN_LIBRARY} 72 + #${ANN_LIBRARY}
70 ${X11_LIBRARIES} 73 ${X11_LIBRARIES}
71 ) 74 )
72 75
main.cpp deleted
View file @9e6d89e
1 -#include <stdlib.h>  
2 -#include <string>  
3 -#include <fstream>  
4 -#include <algorithm>  
5 -  
6 -//OpenGL includes  
7 -#include <GL/glut.h>  
8 -#include <GL/freeglut.h>  
9 -  
10 -//STIM includes  
11 -#include <stim/visualization/gl_network.h>  
12 -#include <stim/biomodels/network.h>  
13 -#include <stim/visualization/gl_aaboundingbox.h>  
14 -#include <stim/parser/arguments.h>  
15 -#include <stim/visualization/camera.h>  
16 -  
17 -//ANN includes  
18 -#include <ANN/ANN.h>  
19 -  
20 -//BOOST includes  
21 -#include <boost/tuple/tuple.hpp>  
22 -  
23 -//visualization objects  
24 -stim::gl_aaboundingbox<float> bb; //axis-aligned bounding box object  
25 -stim::camera cam; //camera object  
26 -  
27 -unsigned num_nets = 0;  
28 -stim::gl_network<float> GT; //ground truth network  
29 -stim::gl_network<float> T; //test network  
30 -  
31 -//hard-coded parameters  
32 -float resample_rate = 0.5; //sample rate for the network (fraction of sigma used as the maximum sample rate)  
33 -float camera_factor = 1.2; //start point of the camera as a function of X and Y size  
34 -float orbit_factor = 0.01; //degrees per pixel used to orbit the camera  
35 -  
36 -//mouse position tracking  
37 -int mouse_x;  
38 -int mouse_y;  
39 -  
40 -//OpenGL objects  
41 -GLuint cmap_tex = 0; //texture name for the color map  
42 -  
43 -//sets an OpenGL viewport taking up the entire window  
44 -void glut_render_single_projection(){  
45 -  
46 - glMatrixMode(GL_PROJECTION); //load the projection matrix for editing  
47 - glLoadIdentity(); //start with the identity matrix  
48 - int X = glutGet(GLUT_WINDOW_WIDTH); //use the whole screen for rendering  
49 - int Y = glutGet(GLUT_WINDOW_HEIGHT);  
50 - glViewport(0, 0, X, Y); //specify a viewport for the entire window  
51 - float aspect = (float)X / (float)Y; //calculate the aspect ratio  
52 - gluPerspective(60, aspect, 0.1, 1000000); //set up a perspective projection  
53 -}  
54 -  
55 -//sets an OpenGL viewport taking up the left half of the window  
56 -void glut_render_left_projection(){  
57 -  
58 - glMatrixMode(GL_PROJECTION); //load the projection matrix for editing  
59 - glLoadIdentity(); //start with the identity matrix  
60 - int X = glutGet(GLUT_WINDOW_WIDTH) / 2; //only use half of the screen for the viewport  
61 - int Y = glutGet(GLUT_WINDOW_HEIGHT);  
62 - glViewport(0, 0, X, Y); //specify the viewport on the left  
63 - float aspect = (float)X / (float)Y; //calculate the aspect ratio  
64 - gluPerspective(60, aspect, 0.1, 1000000); //set up a perspective projection  
65 -}  
66 -  
67 -//sets an OpenGL viewport taking up the right half of the window  
68 -void glut_render_right_projection(){  
69 -  
70 - glMatrixMode(GL_PROJECTION); //load the projection matrix for editing  
71 - glLoadIdentity(); //start with the identity matrix  
72 - int X = glutGet(GLUT_WINDOW_WIDTH) / 2; //only use half of the screen for the viewport  
73 - int Y = glutGet(GLUT_WINDOW_HEIGHT);  
74 - glViewport(X, 0, X, Y); //specify the viewport on the right  
75 - float aspect = (float)X / (float)Y; //calculate the aspect ratio  
76 - gluPerspective(60, aspect, 0.1, 1000000); //set up a perspective projection  
77 -}  
78 -  
79 -void glut_render_modelview(){  
80 -  
81 - glMatrixMode(GL_MODELVIEW); //load the modelview matrix for editing  
82 - glLoadIdentity(); //start with the identity matrix  
83 - stim::vec3<float> eye = cam.getPosition(); //get the camera position (eye point)  
84 - stim::vec3<float> focus = cam.getLookAt(); //get the camera focal point  
85 - stim::vec3<float> up = cam.getUp(); //get the camera "up" orientation  
86 -  
87 - gluLookAt(eye[0], eye[1], eye[2], focus[0], focus[1], focus[2], up[0], up[1], up[2]); //set up the OpenGL camera  
88 -}  
89 -  
90 -//draws the network(s)  
91 -void glut_render(void) {  
92 -  
93 - if(num_nets == 1){ //if a single network is loaded  
94 - glut_render_single_projection(); //fill the entire viewport  
95 - glut_render_modelview(); //set up the modelview matrix with camera details  
96 - glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); //clear the screen  
97 - GT.glCenterline(GT.nmags() - 1); //render the GT network (the only one loaded)  
98 - }  
99 -  
100 - if(num_nets == 2){ //if two networks are loaded  
101 -  
102 - glut_render_left_projection(); //set up a projection for the left half of the window  
103 - glut_render_modelview(); //set up the modelview matrix using camera details  
104 - glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); //clear the screen  
105 -  
106 - glEnable(GL_TEXTURE_1D); //enable texture mapping  
107 - glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE); //texture map will be used as the network color  
108 - glBindTexture(GL_TEXTURE_1D, cmap_tex); //bind the Brewer texture map  
109 -  
110 - GT.glCenterline(GT.nmags() - 1); //render the GT network  
111 -  
112 - glut_render_right_projection(); //set up a projection for the right half of the window  
113 - glut_render_modelview(); //set up the modelview matrix using camera details  
114 - T.glCenterline(T.nmags() - 1); //render the T network  
115 -  
116 - }  
117 -  
118 - glutSwapBuffers();  
119 -}  
120 -  
121 -// defines camera motion based on mouse dragging  
122 -void glut_motion(int x, int y){  
123 -  
124 -  
125 - float theta = orbit_factor * (mouse_x - x); //determine the number of degrees along the x-axis to rotate  
126 - float phi = orbit_factor * (y - mouse_y); //number of degrees along the y-axis to rotate  
127 -  
128 - cam.OrbitFocus(theta, phi); //rotate the camera around the focal point  
129 -  
130 - mouse_x = x; //update the mouse position  
131 - mouse_y = y;  
132 -  
133 - glutPostRedisplay(); //re-draw the visualization  
134 -}  
135 -  
136 -// sets the mouse position when clicked  
137 -void glut_mouse(int button, int state, int x, int y){  
138 - mouse_x = x;  
139 - mouse_y = y;  
140 -}  
141 -  
142 -#define BREWER_CTRL_PTS 11 //number of control points in the Brewer map  
143 -void texture_initialize(){  
144 -  
145 - //define the colormap  
146 - static float brewer_map[BREWER_CTRL_PTS][3] = { //generate a Brewer color map (blue to red)  
147 - {0.192157f, 0.211765f, 0.584314f},  
148 - {0.270588f, 0.458824f, 0.705882f},  
149 - {0.454902f, 0.678431f, 0.819608f},  
150 - {0.670588f, 0.85098f, 0.913725f},  
151 - {0.878431f, 0.952941f, 0.972549f},  
152 - {1.0f, 1.0f, 0.74902f},  
153 - {0.996078f, 0.878431f, 0.564706f},  
154 - {0.992157f, 0.682353f, 0.380392f},  
155 - {0.956863f, 0.427451f, 0.262745f},  
156 - {0.843137f, 0.188235f, 0.152941f},  
157 - {0.647059f, 0.0f, 0.14902f}  
158 - };  
159 -  
160 - glGenTextures(1, &cmap_tex); //generate a texture map name  
161 - glBindTexture(GL_TEXTURE_1D, cmap_tex); //bind the texture map  
162 -  
163 - glTexParameteri(GL_TEXTURE_1D, GL_TEXTURE_MAG_FILTER, GL_LINEAR); //enable linear interpolation  
164 - glTexParameteri(GL_TEXTURE_1D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);  
165 - glTexParameteri(GL_TEXTURE_1D, GL_TEXTURE_WRAP_S, GL_CLAMP); //clamp the values at the minimum and maximum  
166 - glTexImage1D(GL_TEXTURE_1D, 0, 3, BREWER_CTRL_PTS, 0, GL_RGB, GL_FLOAT, //upload the texture map to the GPU  
167 - brewer_map);  
168 -}  
169 -  
170 -//Initialize the OpenGL (GLUT) window, including starting resolution, callbacks, texture maps, and camera  
171 -void glut_initialize(){  
172 -  
173 - int myargc = 1; //GLUT requires arguments, so create some bogus ones  
174 - char* myargv[1];  
175 - myargv [0]=strdup ("netmets");  
176 -  
177 - glutInit(&myargc, myargv); //pass bogus arguments to glutInit()  
178 - glutInitDisplayMode(GLUT_DEPTH | GLUT_DOUBLE | GLUT_RGBA); //generate a color buffer, depth buffer, and enable double buffering  
179 - glutInitWindowPosition(100,100); //set the initial window position  
180 - glutInitWindowSize(320,320); //set the initial window size  
181 - glutCreateWindow("NetMets - STIM Lab, UH"); //set the dialog box title  
182 -  
183 -  
184 - // register callback functions  
185 - glutDisplayFunc(glut_render); //function executed for rendering - renders networks  
186 - glutMouseFunc(glut_mouse); //executed on a mouse click - sets starting mouse positions for rotations  
187 - glutMotionFunc(glut_motion); //executed when the mouse is moved while a button is pressed  
188 -  
189 - texture_initialize(); //set up texture mapping (create texture maps, enable features)  
190 -  
191 - stim::vec3<float> c = bb.center(); //get the center of the network bounding box  
192 -  
193 - //place the camera along the z-axis at a distance determined by the network size along x and y  
194 - cam.setPosition(c + stim::vec<float>(0, 0, camera_factor * std::max(bb.size()[0], bb.size()[1])));  
195 - cam.LookAt(c[0], c[1], c[2]); //look at the center of the network  
196 -}  
197 -  
198 -//compare both networks and fill the networks with error information  
199 -void compare(float sigma){  
200 -  
201 - GT = GT.compare(T, sigma); //compare the ground truth to the test case - store errors in GT  
202 - T = T.compare(GT, sigma); //compare the test case to the ground truth - store errors in T  
203 -  
204 - //calculate the metrics  
205 - float FPR = GT.average(1); //calculate the metrics  
206 - float FNR = T.average(1);  
207 -  
208 - std::cout << "FNR: " << FPR << std::endl; //print false alarms and misses  
209 - std::cout << "FPR: " << FNR << std::endl;  
210 -}  
211 -  
212 -// 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  
213 -// Pranathi wrote this - saves network features to a CSV file  
214 -void features(std::string filename){  
215 - double avgL_t, avgL_gt, avgT_t, avgT_gt, avgB_t, avgB_gt, avgC_t, avgC_gt, avgFD_t, avgFD_gt;  
216 - unsigned int e_t, e_gt, b_gt, b_t;  
217 - avgL_gt = GT.Lengths();  
218 - avgT_gt = GT.Tortuosities();  
219 - avgL_t = T.Lengths();  
220 - avgT_t = T.Tortuosities();  
221 - avgB_gt = GT.BranchingIndex();  
222 - avgB_t = T.BranchingIndex();  
223 - avgC_gt = GT.Contractions();  
224 - avgFD_gt = GT.FractalDimensions();  
225 - avgC_t = T.Contractions();  
226 - avgFD_t = T.FractalDimensions();  
227 - e_gt = GT.EndP();  
228 - e_t = T.EndP();  
229 - b_gt = GT.BranchP();  
230 - b_t = T.BranchP();  
231 - std::ofstream myfile;  
232 - myfile.open (filename.c_str());  
233 - myfile << "Length, Tortuosity, Contraction, Fractal Dimension, Branch Points, End points, Branching Index, \n";  
234 - myfile << avgL_gt << "," << avgT_gt << "," << avgC_gt << "," << avgFD_gt << "," << b_gt << "," << e_gt << "," << avgB_gt <<std::endl;  
235 - myfile << avgL_t << "," << avgT_t << "," << avgC_t << "," << avgFD_t << "," << b_t << "," << e_t << "," << avgB_t <<std::endl;  
236 - myfile.close();  
237 -}  
238 -  
239 -// Output an advertisement for the lab, authors, and usage information  
240 -void advertise(){  
241 - std::cout<<std::endl<<std::endl;  
242 - std::cout<<"========================================================================="<<std::endl;  
243 - std::cout<<"Thank you for using the NetMets network comparison tool!"<<std::endl;  
244 - std::cout<<"Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston"<<std::endl;  
245 - std::cout<<"Developers: Pranathi Vemuri, David Mayerich"<<std::endl;  
246 - std::cout<<"Source: https://git.stim.ee.uh.edu/segmentation/netmets"<<std::endl;  
247 - std::cout<<"========================================================================="<<std::endl<<std::endl;  
248 -  
249 - std::cout<<"usage: netmets file1 file2 --sigma 10"<<std::endl;  
250 - std::cout<<" compare two files with a tolerance of 10 (units defined by the network)"<<std::endl;  
251 - std::cout<<" netmets file1 --gui"<<std::endl<<std::endl;  
252 - std::cout<<" load a file and display it using OpenGL"<<std::endl;  
253 -}  
254 -  
255 -int main(int argc, char* argv[])  
256 -{  
257 - stim::arglist args; //create an instance of arglist  
258 -  
259 - //add arguments  
260 - args.add("help", "prints this help");  
261 - args.add("sigma", "force a sigma value to specify the tolerance of the network comparison", "10");  
262 - args.add("gui", "display the network or network comparison using OpenGL");  
263 - args.add("features", "save features to a CSV file, specify file name");  
264 -  
265 - args.parse(argc, argv); //parse the user arguments  
266 -  
267 - if(args["help"].is_set() || args.nargs() == 0){ //test for help  
268 - advertise(); //output the advertisement  
269 - std::cout<<args.str(); //output arguments  
270 - exit(1); //exit  
271 - }  
272 -  
273 - if(args.nargs() >= 1){ //if at least one network file is specified  
274 - num_nets = 1; //set the number of networks to one  
275 - GT.load_obj(args.arg(0)); //load the specified file as the ground truth  
276 - /*GT.to_txt("Graph.txt");*/  
277 - }  
278 -  
279 - if(args.nargs() == 2){ //if two files are specified, they will be displayed in neighboring viewports and compared  
280 - num_nets = 2; //set the number of networks to two  
281 - float sigma = args["sigma"].as_float(); //get the sigma value from the user  
282 - T.load_obj(args.arg(1)); //load the second (test) network  
283 - if(args["features"].is_set()) //if the user wants to save features  
284 - features(args["features"].as_string());  
285 - GT = GT.resample(resample_rate * sigma); //resample both networks based on the sigma value  
286 - T = T.resample(resample_rate * sigma);  
287 - compare(sigma); //run the comparison algorithm  
288 - }  
289 -  
290 - //if a GUI is requested, display the network using OpenGL  
291 - if(args["gui"].is_set()){  
292 - bb = GT.boundingbox(); //generate a bounding volume  
293 - glut_initialize(); //create the GLUT window and set callback functions  
294 - glutMainLoop(); // enter GLUT event processing cycle  
295 - }  
296 -}