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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CMakeLists.txt
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... ... @@ -21,6 +21,9 @@ endif(NOT STIM_INCLUDE_DIRS)
21 21 #find BOOST
22 22 find_package(Boost REQUIRED)
23 23  
  24 +#find cuda
  25 +find_package(CUDA REQUIRED)
  26 +
24 27 #find the GLUT library for visualization
25 28 find_package(OpenGL REQUIRED)
26 29  
... ... @@ -33,7 +36,7 @@ find_package(Threads)
33 36 find_package(X11)
34 37  
35 38 #find the Approximate Nearest Neighbor Library
36   -find_package(ANN REQUIRED)
  39 +#find_package(ANN REQUIRED)
37 40  
38 41 #build the executable in the binary directory on MS Visual Studio
39 42 if ( MSVC )
... ... @@ -45,16 +48,16 @@ include_directories(
45 48 ${OPENGL_INCLUDE_DIRS}
46 49 ${GLUT_INCLUDE_DIR}
47 50 ${STIM_INCLUDE_DIRS}
48   - ${ANN_INCLUDE_DIR}
  51 + #${ANN_INCLUDE_DIR}
49 52 ${Boost_INCLUDE_DIR}
50 53 )
51 54  
52 55 #Assign source files to the appropriate variables
53   -file(GLOB SRC_CPP "*.cpp")
  56 +file(GLOB SRC_CPP "*.cu")
54 57 file(GLOB SRC_H "*.h")
55 58  
56 59 #create an executable file
57   -add_executable(netmets
  60 +cuda_add_executable(netmets
58 61 ${SRC_H}
59 62 ${SRC_CPP}
60 63 )
... ... @@ -66,7 +69,7 @@ target_link_libraries(netmets
66 69 ${OPENGL_glu_LIBRARY}
67 70 ${GLUT_LIBRARIES}
68 71 ${CMAKE_THREAD_LIBS_INIT}
69   - ${ANN_LIBRARY}
  72 + #${ANN_LIBRARY}
70 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   -}