7c1b82bc
Jiaming Guo
test for 00_GT.swc
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#include <stdlib.h>
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#include <string>
#include <fstream>
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#include <algorithm>
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//OpenGL includes
#include <GL/glut.h>
#include <GL/freeglut.h>
//STIM includes
#include <stim/visualization/gl_network.h>
#include <stim/biomodels/network.h>
#include <stim/visualization/gl_aaboundingbox.h>
#include <stim/parser/arguments.h>
#include <stim/visualization/camera.h>
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#ifdef __CUDACC__
//CUDA includes
#include <cuda.h>
#endif
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//BOOST includes
#include <boost/tuple/tuple.hpp>
//visualization objects
stim::gl_aaboundingbox<float> bb; //axis-aligned bounding box object
stim::camera cam; //camera object
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// number of networks
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unsigned num_nets = 0;
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// networks
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stim::gl_network<float> GT; //ground truth network
stim::gl_network<float> T; //test network
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stim::gl_network<float> _GT; //splitted GT
stim::gl_network<float> _T; //splitted T
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// indicator
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unsigned ind = 0; //indicator of mapping
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// relationships
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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
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//hard-coded parameters
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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
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float zoom_factor = 10.0f;
float radius_factor = 0.5f;
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//mouse click
bool LButtonDown = false; // true when left button down
bool RButtonDown = false;
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//mouse position tracking
int mouse_x;
int mouse_y;
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// render modes
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bool compareMode = true; // default mode is compare mode
bool mappingMode = false;
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// random color set
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std::vector<float> colormap;
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// special key indicator
int mods;
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// create display lists
GLuint dlist1;
GLuint dlist2;
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//OpenGL objects
GLuint cmap_tex = 0; //texture name for the color map
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float delta;
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float sigma = 3; //default sigma
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float radius = 3; //equals to radius
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//sets an OpenGL viewport taking up the entire window
void glut_render_single_projection(){
glMatrixMode(GL_PROJECTION); //load the projection matrix for editing
glLoadIdentity(); //start with the identity matrix
int X = glutGet(GLUT_WINDOW_WIDTH); //use the whole screen for rendering
int Y = glutGet(GLUT_WINDOW_HEIGHT);
glViewport(0, 0, X, Y); //specify a viewport for the entire window
float aspect = (float)X / (float)Y; //calculate the aspect ratio
gluPerspective(60, aspect, 0.1, 1000000); //set up a perspective projection
}
//sets an OpenGL viewport taking up the left half of the window
void glut_render_left_projection(){
glMatrixMode(GL_PROJECTION); //load the projection matrix for editing
glLoadIdentity(); //start with the identity matrix
int X = glutGet(GLUT_WINDOW_WIDTH) / 2; //only use half of the screen for the viewport
int Y = glutGet(GLUT_WINDOW_HEIGHT);
glViewport(0, 0, X, Y); //specify the viewport on the left
float aspect = (float)X / (float)Y; //calculate the aspect ratio
gluPerspective(60, aspect, 0.1, 1000000); //set up a perspective projection
}
//sets an OpenGL viewport taking up the right half of the window
void glut_render_right_projection(){
glMatrixMode(GL_PROJECTION); //load the projection matrix for editing
glLoadIdentity(); //start with the identity matrix
int X = glutGet(GLUT_WINDOW_WIDTH) / 2; //only use half of the screen for the viewport
int Y = glutGet(GLUT_WINDOW_HEIGHT);
glViewport(X, 0, X, Y); //specify the viewport on the right
float aspect = (float)X / (float)Y; //calculate the aspect ratio
gluPerspective(60, aspect, 0.1, 1000000); //set up a perspective projection
}
void glut_render_modelview(){
glMatrixMode(GL_MODELVIEW); //load the modelview matrix for editing
glLoadIdentity(); //start with the identity matrix
stim::vec3<float> eye = cam.getPosition(); //get the camera position (eye point)
stim::vec3<float> focus = cam.getLookAt(); //get the camera focal point
stim::vec3<float> up = cam.getUp(); //get the camera "up" orientation
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gluLookAt(eye[0], eye[1], eye[2], focus[0], focus[1], focus[2], up[0], up[1], up[2]); //set up the OpenGL camera
}
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//draws the network(s)
void glut_render(void) {
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//no mapping, just comparing
if (ind == 0) {
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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
GT.glCenterline0(); //render the GT network (the only one loaded)
}
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
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
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GT.glCylinder(sigma, radius); //render the GT network
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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
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T.glCylinder(sigma, radius); //render the T network
sigma = radius; // set sigma equal to radius
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}
}
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//do comparing and mapping
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) {
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glEnable(GL_DEPTH_TEST); //enable depth
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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
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_GT.glCylinder(sigma, radius); //render the GT network
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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
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_T.glCylinder(sigma, radius); //render the T network
sigma = radius; //set sigma equal to radius
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}
else {
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glEnable(GL_DEPTH_TEST); //enable depth
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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
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//_GT.glRandColorCenterlineGT(dlist1, _gt_t, colormap);
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_GT.glRandColorCylinder1(dlist1, _gt_t, colormap, sigma, radius);
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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
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//_T.glRandColorCenterlineT(dlist2, _t_gt, colormap);
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_T.glRandColorCylinder2(dlist2, _t_gt, colormap, sigma, radius);
sigma = radius; //set sigma equal to radius
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}
}
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}
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if (num_nets == 2) { // works only with two networks
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std::ostringstream ss;
if (mappingMode) // if it is in mapping mode
ss << "Mapping Mode";
else
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ss << "Compare Mode"; // default mode is compare mode
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glDisable(GL_TEXTURE_1D);
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glMatrixMode(GL_PROJECTION); // set up the 2d viewport for mode text printing
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glPushMatrix();
glLoadIdentity();
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int X = glutGet(GLUT_WINDOW_WIDTH); // get the current window width
int Y = glutGet(GLUT_WINDOW_HEIGHT); // get the current window height
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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
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
glLoadIdentity();
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glRasterPos2f(0, 5); //print text in the left bottom corner
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glutBitmapString(GLUT_BITMAP_TIMES_ROMAN_24, (const unsigned char*)(ss.str().c_str()));
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glPopMatrix();
glMatrixMode(GL_PROJECTION);
glPopMatrix();
}
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glutSwapBuffers();
}
// defines camera motion based on mouse dragging
void glut_motion(int x, int y){
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if(LButtonDown == true && RButtonDown == false && mods != GLUT_ACTIVE_CTRL){
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float theta = orbit_factor * (mouse_x - x); //determine the number of degrees along the x-axis to rotate
float phi = orbit_factor * (y - mouse_y); //number of degrees along the y-axis to rotate
cam.OrbitFocus(theta, phi); //rotate the camera around the focal point
mouse_x = x; //update the mouse position
mouse_y = y;
glutPostRedisplay(); //re-draw the visualization
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}
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}
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// 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();
}
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// sets the mouse position when clicked
void glut_mouse(int button, int state, int x, int y){
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if(button == GLUT_LEFT_BUTTON && state == GLUT_DOWN){
mouse_x = x;
mouse_y = y;
LButtonDown = true;
}
else if(button == GLUT_RIGHT_BUTTON && state == GLUT_DOWN){
mouse_x = x;
mouse_y = y;
RButtonDown = true;
}
else if(button == GLUT_LEFT_BUTTON && state == GLUT_UP){
mouse_x = x;
mouse_y = y;
LButtonDown = false;
}
else if(button == GLUT_RIGHT_BUTTON && state == GLUT_UP){
mouse_x = x;
mouse_y = y;
RButtonDown = false;
}
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/// implementation of mouse click mapping feedback
mods = glutGetModifiers(); // get modifier keys
if (mods == GLUT_ACTIVE_CTRL) // if the CTRL key is pressed
if (button == GLUT_LEFT_BUTTON && state == GLUT_DOWN) {
std::cout << "( " << x << ", " << y << " )" << std::endl; // if the CTRL key is pressed and LEFT BUTTON is DOWN, print the window coordinates
GLint viewport[4];
GLdouble modelview[16];
GLdouble projection[16];
GLdouble winX, winY, winZ;
GLdouble posX, posY, posZ;
glGetIntegerv(GL_VIEWPORT, viewport);
glGetDoublev(GL_MODELVIEW_MATRIX, modelview);
glGetDoublev(GL_PROJECTION_MATRIX, projection);
winX = (GLdouble)x;
winY = viewport[3] - (GLdouble)y;
glReadPixels((GLint)winX, (GLint)winY, (GLsizei)1, (GLsizei)1, GL_DEPTH_COMPONENT, GL_FLOAT, &winZ); // need frame buffer FBO
gluUnProject(winX, winY, winZ, modelview, projection, viewport, &posX, &posY, &posZ); // not sure why it should add 1 to the winZ
std::cout << "( " << posX << ", " << posY << ", "<< posZ <<" )" << std::endl;
}
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}
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// 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) {
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if (direction > 0) // if it is button 3(up), move closer
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delta = zoom_factor;
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else // if it is button 4(down), leave farther
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delta = -zoom_factor;
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cam.Push(delta);
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glutPostRedisplay();
}
// define keyboard inputs
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void glut_keyboard(unsigned char key, int x, int y){
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// 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);
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}
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glutPostRedisplay();
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}
#define BREWER_CTRL_PTS 11 //number of control points in the Brewer map
void texture_initialize(){
//define the colormap
static float brewer_map[BREWER_CTRL_PTS][3] = { //generate a Brewer color map (blue to red)
{0.192157f, 0.211765f, 0.584314f},
{0.270588f, 0.458824f, 0.705882f},
{0.454902f, 0.678431f, 0.819608f},
{0.670588f, 0.85098f, 0.913725f},
{0.878431f, 0.952941f, 0.972549f},
{1.0f, 1.0f, 0.74902f},
{0.996078f, 0.878431f, 0.564706f},
{0.992157f, 0.682353f, 0.380392f},
{0.956863f, 0.427451f, 0.262745f},
{0.843137f, 0.188235f, 0.152941f},
{0.647059f, 0.0f, 0.14902f}
};
glGenTextures(1, &cmap_tex); //generate a texture map name
glBindTexture(GL_TEXTURE_1D, cmap_tex); //bind the texture map
glTexParameteri(GL_TEXTURE_1D, GL_TEXTURE_MAG_FILTER, GL_LINEAR); //enable linear interpolation
glTexParameteri(GL_TEXTURE_1D, GL_TEXTURE_MIN_FILTER, GL_LINEAR);
glTexParameteri(GL_TEXTURE_1D, GL_TEXTURE_WRAP_S, GL_CLAMP); //clamp the values at the minimum and maximum
glTexImage1D(GL_TEXTURE_1D, 0, 3, BREWER_CTRL_PTS, 0, GL_RGB, GL_FLOAT, //upload the texture map to the GPU
brewer_map);
}
//Initialize the OpenGL (GLUT) window, including starting resolution, callbacks, texture maps, and camera
void glut_initialize(){
int myargc = 1; //GLUT requires arguments, so create some bogus ones
char* myargv[1];
myargv [0]=strdup ("netmets");
glutInit(&myargc, myargv); //pass bogus arguments to glutInit()
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glutSetOption(GLUT_MULTISAMPLE, 8);
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glutInitDisplayMode(GLUT_DEPTH | GLUT_DOUBLE | GLUT_RGBA); //generate a color buffer, depth buffer, and enable double buffering
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glutInitWindowPosition(100,100); //set the initial window position
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glutInitWindowSize(320, 320); //set the initial window size
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glutCreateWindow("NetMets - STIM Lab, UH"); //set the dialog box title
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// 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
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if (ind == 1) { //only in mapping mode, keyboard will be used
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glutCreateMenu(glut_menu); //register menu option callback
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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
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glutMouseWheelFunc(glut_wheel);
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texture_initialize(); //set up texture mapping (create texture maps, enable features)
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stim::vec3<float> c = bb.center(); //get the center of the network bounding box
//place the camera along the z-axis at a distance determined by the network size along x and y
cam.setPosition(c + stim::vec<float>(0, 0, camera_factor * std::max(bb.size()[0], bb.size()[1])));
cam.LookAt(c[0], c[1], c[2]); //look at the center of the network
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}
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#ifdef __CUDACC__
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// set specific device to work on
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void setdevice(int &device){
int count;
cudaGetDeviceCount(&count); // numbers of device that are available
if(count < device + 1){
std::cout<<"No such device available, please set another device"<<std::endl;
exit(1);
}
}
#else
void setdevice(int &device){
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device = -1; // set to default -1
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}
#endif
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//compare both networks and fill the networks with error information
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void compare(float sigma, int device){
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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
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//calculate the metrics
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float FPR = GT.average(); //calculate the metrics
float FNR = T.average();
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std::cout << "FNR: " << FPR << std::endl; //print false alarms and misses
std::cout << "FPR: " << FNR << std::endl;
}
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//split and map two networks and fill the networks' R with metric information
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void map(float sigma, int device, float threshold){
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// compare and split two networks
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_GT.split(GT, T, sigma, device, threshold);
_T.split(T, GT, sigma, device, threshold);
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// mapping two new splitted networks and get their edge relation
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_GT.mapping(_T, _gt_t, device, threshold);
_T.mapping(_GT, _t_gt, device, threshold);
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// generate random color set based on the number of edges in GT
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size_t num = _gt_t.size(); // also create random color for unmapping edge, but won't be used though
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colormap.resize(3 * num); // 3 portions compound RGB
for(int i = 0; i < 3 * num; i++)
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colormap[i] = rand()/(float)RAND_MAX; // set to [0, 1]
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//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;
}
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// 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){
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double avgL_t, avgL_gt, avgT_t, avgT_gt, avgB_t, avgB_gt, avgC_t, avgC_gt, avgFD_t, avgFD_gt;
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unsigned int e_t, e_gt, b_gt, b_t;
avgL_gt = GT.Lengths();
avgT_gt = GT.Tortuosities();
avgL_t = T.Lengths();
avgT_t = T.Tortuosities();
avgB_gt = GT.BranchingIndex();
avgB_t = T.BranchingIndex();
avgC_gt = GT.Contractions();
avgFD_gt = GT.FractalDimensions();
avgC_t = T.Contractions();
avgFD_t = T.FractalDimensions();
e_gt = GT.EndP();
e_t = T.EndP();
b_gt = GT.BranchP();
b_t = T.BranchP();
std::ofstream myfile;
myfile.open (filename.c_str());
myfile << "Length, Tortuosity, Contraction, Fractal Dimension, Branch Points, End points, Branching Index, \n";
myfile << avgL_gt << "," << avgT_gt << "," << avgC_gt << "," << avgFD_gt << "," << b_gt << "," << e_gt << "," << avgB_gt <<std::endl;
myfile << avgL_t << "," << avgT_t << "," << avgC_t << "," << avgFD_t << "," << b_t << "," << e_t << "," << avgB_t <<std::endl;
myfile.close();
}
// Output an advertisement for the lab, authors, and usage information
void advertise(){
std::cout<<std::endl<<std::endl;
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;
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std::cout<<"Developers: Pranathi Vemuri, David Mayerich, Jiaming Guo"<<std::endl;
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std::cout<<"Source: https://git.stim.ee.uh.edu/segmentation/netmets" <<std::endl;
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std::cout<<"========================================================================="<<std::endl<<std::endl;
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std::cout<<"usage: netmets file1 file2 --sigma 3"<<std::endl;
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std::cout<<" compare two .obj files with a tolerance of 3 (units defined by the network)"<<std::endl<<std::endl;
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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;
std::cout<<" compare two files using device 0 (if there isn't a gpu, use cpu)"<<std::endl<<std::endl;
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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;
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}
int main(int argc, char* argv[])
{
stim::arglist args; //create an instance of arglist
//add arguments
args.add("help", "prints this help");
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args.add("sigma", "force a sigma value to specify the tolerance of the network comparison", "3");
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args.add("gui", "display the network or network comparison using OpenGL");
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args.add("device", "choose specific device to run", "0");
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args.add("features", "save features to a CSV file, specify file name");
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args.add("mapping", "mapping input according to similarity");
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args.parse(argc, argv); //parse the user arguments
if(args["help"].is_set() || args.nargs() == 0){ //test for help
advertise(); //output the advertisement
std::cout<<args.str(); //output arguments
exit(1); //exit
}
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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 '.'
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if ("swc" == tmp[1]) // loading swc file
|
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GT.load_swc(args.arg(0)); // load the specified file as the ground truth
|
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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);
}
}
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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;
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std::vector<std::string> tmp = stim::parser::split(args.arg(1), '.'); // split the filename at '.'
if ("swc" == tmp[1]) //loading swc files
|
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T.load_swc(args.arg(1)); //load the second (test) network
|
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else if ("obj" == tmp[1]) //loading obj files
T.load_obj(args.arg(1));
else {
std::cout << "Invalid loading file" << std::endl;
exit(1);
}
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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);
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}
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else
compare(sigma, device); //run the comparison algorithm
|
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}
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//if a GUI is requested, display the network using OpenGL
|
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if(args["gui"].is_set()){
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if (args["mapping"].is_set()) {
ind = 1; //set indicator of mapping to 1(true)
|
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bb = _GT.boundingbox(); //generate a bounding volume
glut_initialize(); //create the GLUT window and set callback functions
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glutMainLoop(); //enter GLUT event processing cycle
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}
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else {
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bb = GT.boundingbox(); //generate a bounding volume
glut_initialize(); //create the GLUT window and set callback functions
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glutMainLoop(); //enter GLUT event processing cycle
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}
}
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}
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