7c1b82bc
Jiaming Guo
test for 00_GT.swc
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#include <stdlib.h>
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db598823
David Mayerich
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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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//OpenGL objects
GLuint cmap_tex = 0; //texture name for the color map
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float delta;
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Jiaming Guo
test for 00_GT.swc
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float sigma = 3; //default sigma
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float radius = 0.7; //equals to radius
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int adjoint_fac = 0;
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int light_fac = 0;
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int difference_fac = 0;
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test for 00_GT.swc
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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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stim::vec3<float> p1 = cam.getLookAt() + cam.getUp() * 100000;
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stim::vec3<float> p2 = cam.getPosition();
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// light
GLfloat global_ambient[] = { 0.5, 0.5, 0.5, 1.0 };
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GLfloat ambient[] = { 0.0, 0.0, 0.0, 1.0 };
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GLfloat diffuse1[] = { 1.0, 1.0, 1.0, 1.0 };
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GLfloat diffuse2[] = { 0.4, 0.4, 0.4, 1.0 };
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GLfloat specular[] = { 1.0, 1.0, 1.0, 1.0 };
GLfloat position1[] = { p1[0], p1[1], p1[2], 1.0 }; // upper right light source
GLfloat position2[] = { p2[0], p2[1], p2[2], 1.0 }; // lower left light source
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glClearColor(0.0, 0.0, 0.0, 1.0);
glShadeModel(GL_SMOOTH);
glLightModelfv(GL_LIGHT_MODEL_AMBIENT, global_ambient);
glLightfv(GL_LIGHT0, GL_AMBIENT, ambient);
glLightfv(GL_LIGHT0, GL_DIFFUSE, diffuse1);
glLightfv(GL_LIGHT0, GL_SPECULAR, specular);
glLightfv(GL_LIGHT0, GL_POSITION, position1);
glLightfv(GL_LIGHT1, GL_AMBIENT, ambient);
glLightfv(GL_LIGHT1, GL_DIFFUSE, diffuse2);
glLightfv(GL_LIGHT1, GL_SPECULAR, specular);
glLightfv(GL_LIGHT1, GL_POSITION, position2);
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//no mapping, just comparing
if (ind == 0) {
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Jiaming Guo
test for 00_GT.swc
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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)
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normalization
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glDisable(GL_DEPTH_TEST);
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test for 00_GT.swc
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}
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if (num_nets == 2) { //if two networks are loaded
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glEnable(GL_TEXTURE_1D); //enable texture mapping
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if (light_fac == 0)
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glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE); //texture map will be used as the network color
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glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_MODULATE);
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glBindTexture(GL_TEXTURE_1D, cmap_tex); //bind the Brewer texture map
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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
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GT.glCylinder(sigma, radius); //render the GT network
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//GT.glCenterline();
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if (adjoint_fac == 1) {
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glDisable(GL_TEXTURE_1D); //disable texture in order to render in other color
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glEnable(GL_BLEND); //enable color blend
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); //set blend function
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glDisable(GL_DEPTH_TEST); //should disable depth to render transparancy
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glColor4f(0.0f, 0.3f, 0.0f, 0.2f);
T.glAdjointCylinder(sigma, radius);
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//T.glAdjointCenterline();
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glDisable(GL_BLEND);
glEnable(GL_DEPTH_TEST);
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glEnable(GL_TEXTURE_1D);
glColor4f(1.0f, 1.0f, 1.0f, 1.0f);
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}
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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
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//T.glCenterline();
if (adjoint_fac == 1) {
glDisable(GL_TEXTURE_1D); //temporarily disable texture
glEnable(GL_BLEND); //enable color blend
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); //set blend function
glDisable(GL_DEPTH_TEST); //should disable depth
glColor4f(0.0f, 0.3f, 0.0f, 0.2f);
GT.glAdjointCylinder(sigma, radius);
//GT.glAdjointCenterline();
glDisable(GL_BLEND);
glEnable(GL_DEPTH_TEST);
glEnable(GL_TEXTURE_1D); //re-enable texture
glColor4f(1.0f, 1.0f, 1.0f, 1.0f);
}
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sigma = radius; // set sigma equal to radius
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glDisable(GL_TEXTURE_1D);
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test for 00_GT.swc
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}
}
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Jiaming Guo
test for 00_GT.swc
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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_TEXTURE_1D); //enable texture mapping
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if (light_fac == 0)
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glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_REPLACE); //texture map will be used as the network color
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else
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glTexEnvf(GL_TEXTURE_ENV, GL_TEXTURE_ENV_MODE, GL_MODULATE);//map light to texture
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glBindTexture(GL_TEXTURE_1D, cmap_tex); //bind the Brewer texture map
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normalization
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glEnable(GL_DEPTH_TEST); //enable depth
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some tests
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glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); //clear the screen
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normalization
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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
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some tests
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_GT.glCylinder(sigma, radius); //render the GT network
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//_GT.glCenterline();
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if (adjoint_fac == 1) {
glDisable(GL_TEXTURE_1D); //temporarily disable texture
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glEnable(GL_BLEND); //enable color blend
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); //set blend function
glDisable(GL_DEPTH_TEST); //should disable depth
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glColor4f(0.0f, 0.3f, 0.0f, 0.2f);
_T.glAdjointCylinder(sigma, radius);
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//_T.glAdjointCenterline();
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glDisable(GL_BLEND);
glEnable(GL_DEPTH_TEST);
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glEnable(GL_TEXTURE_1D); //re-enable texture
glColor4f(1.0f, 1.0f, 1.0f, 1.0f);
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}
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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
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//_T.glCenterline();
if (adjoint_fac == 1) {
glDisable(GL_TEXTURE_1D); //temporarily disable texture
glEnable(GL_BLEND); //enable color blend
glBlendFunc(GL_SRC_ALPHA, GL_ONE_MINUS_SRC_ALPHA); //set blend function
glDisable(GL_DEPTH_TEST); //should disable depth
glColor4f(0.0f, 0.3f, 0.0f, 0.2f);
_GT.glAdjointCylinder(sigma, radius);
//_GT.glAdjointCenterline();
glDisable(GL_BLEND);
glEnable(GL_DEPTH_TEST);
glEnable(GL_TEXTURE_1D); //re-enable texture
glColor4f(1.0f, 1.0f, 1.0f, 1.0f);
}
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sigma = radius; //set sigma equal to radius
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glDisable(GL_TEXTURE_1D);
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}
else {
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glEnable(GL_COLOR_MATERIAL);
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glEnable(GL_DEPTH_TEST); //enable depth
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glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT); //clear the screen
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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
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if (difference_fac == 0)
_GT.glRandColorCylinder(0, _gt_t, colormap, sigma, radius);
//_GT.glRandColorCenterline(0, _gt_t, colormap);
else
_GT.glDifferenceCylinder(0, _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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if (difference_fac == 0)
_T.glRandColorCylinder(1, _t_gt, colormap, sigma, radius);
//_T.glRandColorCenterline(1, _t_gt, colormap);
else
_T.glDifferenceCylinder(1, _t_gt, colormap, sigma, radius);
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Jiaming Guo
add light
|
301
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add 00_GT.swc,now...
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sigma = radius; //set sigma equal to radius
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}
}
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db598823
David Mayerich
fixed GCC errors ...
|
305
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}
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c62540c7
Jiaming Guo
normalization
|
306
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glDisable(GL_DEPTH_TEST);
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e1700dd0
Jiaming Guo
fixed bugs when i...
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307
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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
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e1700dd0
Jiaming Guo
fixed bugs when i...
|
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if (light_fac == 1)
glDisable(GL_LIGHTING);
glMatrixMode(GL_PROJECTION); // set up the 2d viewport for mode text printing
glPushMatrix();
glLoadIdentity();
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(0.8, 0.0, 0.0); // using red to show mode
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
glLoadIdentity();
glRasterPos2f(0, 5); //print text in the left bottom corner
glutBitmapString(GLUT_BITMAP_TIMES_ROMAN_24, (const unsigned char*)(ss.str().c_str()));
glPopMatrix();
glMatrixMode(GL_PROJECTION);
glPopMatrix();
glColor3f(1.0, 1.0, 1.0); //clear red color
if (light_fac == 1)
glEnable(GL_LIGHTING);
}
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f85b1b3a
Jiaming Guo
add proper light
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341
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glDisable(GL_COLOR_MATERIAL);
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David Mayerich
fixed GCC errors ...
|
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glutSwapBuffers();
}
// defines camera motion based on mouse dragging
void glut_motion(int x, int y){
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5ac53c9e
Jiaming Guo
add keyboardfunc
|
349
|
if(LButtonDown == true && RButtonDown == false && mods != GLUT_ACTIVE_CTRL){
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db598823
David Mayerich
fixed GCC errors ...
|
350
351
352
353
354
355
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359
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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
|
9627c6e6
Jiaming Guo
add splitting and...
|
360
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}
|
db598823
David Mayerich
fixed GCC errors ...
|
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}
|
f001495e
Jiaming Guo
fix minor errors ...
|
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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();
}
|
db598823
David Mayerich
fixed GCC errors ...
|
379
380
|
// sets the mouse position when clicked
void glut_mouse(int button, int state, int x, int y){
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9627c6e6
Jiaming Guo
add splitting and...
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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;
}
|
5ac53c9e
Jiaming Guo
add keyboardfunc
|
402
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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;
}
|
9627c6e6
Jiaming Guo
add splitting and...
|
426
427
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}
|
f001495e
Jiaming Guo
fix minor errors ...
|
428
429
|
// 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) {
|
b31bfd7d
David Mayerich
added SWC files a...
|
430
|
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
431
|
if (direction > 0) // if it is button 3(up), move closer
|
b31bfd7d
David Mayerich
added SWC files a...
|
432
|
delta = zoom_factor;
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
433
|
else // if it is button 4(down), leave farther
|
7c1b82bc
Jiaming Guo
test for 00_GT.swc
|
434
|
delta = -zoom_factor;
|
b31bfd7d
David Mayerich
added SWC files a...
|
435
436
|
cam.Push(delta);
|
f001495e
Jiaming Guo
fix minor errors ...
|
437
438
439
440
|
glutPostRedisplay();
}
// define keyboard inputs
|
9627c6e6
Jiaming Guo
add splitting and...
|
441
|
void glut_keyboard(unsigned char key, int x, int y){
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
442
443
444
445
446
|
// register different keyboard operation
switch (key) {
// change render mode
|
19ec4731
Jiaming Guo
add light
|
447
448
|
case 'm': // if keyboard 'm' is pressed, then change render mode
if (compareMode && !mappingMode && ind && !adjoint_fac) { // if current mode is comparing mode
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
449
450
451
|
compareMode = false;
mappingMode = true;
}
|
19ec4731
Jiaming Guo
add light
|
452
|
else if (!compareMode && mappingMode && ind && !adjoint_fac) { // if current mode is mapping mode
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
453
454
455
456
457
458
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467
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477
|
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;
|
19ec4731
Jiaming Guo
add light
|
478
|
|
e1700dd0
Jiaming Guo
fixed bugs when i...
|
479
480
481
482
483
484
485
|
// turn on/off the light
case 'l': // if keyboard 'l' is pressed, then change the light
if (!light_fac && !adjoint_fac) {
light_fac = 1;
glEnable(GL_LIGHTING);
glEnable(GL_LIGHT0);
glEnable(GL_LIGHT1);
|
e1700dd0
Jiaming Guo
fixed bugs when i...
|
486
487
488
489
490
491
|
}
else if (light_fac && !adjoint_fac) {
light_fac = 0;
glDisable(GL_LIGHTING);
glDisable(GL_LIGHT0);
glDisable(GL_LIGHT1);
|
e1700dd0
Jiaming Guo
fixed bugs when i...
|
492
493
494
|
}
break;
|
19ec4731
Jiaming Guo
add light
|
495
496
|
// render a transparant T very close to GT in compare mode
case 32: // if keyboard 'SPACE' is pressed, then change the adjoint_fac
|
e1700dd0
Jiaming Guo
fixed bugs when i...
|
497
|
if (!adjoint_fac && compareMode && !light_fac)
|
19ec4731
Jiaming Guo
add light
|
498
|
adjoint_fac = 1;
|
3a4a7f69
Jiaming Guo
add new way to se...
|
499
|
else if (adjoint_fac && compareMode && !light_fac)
|
19ec4731
Jiaming Guo
add light
|
500
|
adjoint_fac = 0;
|
8b30eb84
Jiaming Guo
add SPACE keyboar...
|
501
|
break;
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
502
|
|
3a4a7f69
Jiaming Guo
add new way to se...
|
503
504
505
506
507
508
509
510
|
// render only the difference
case 'h':
if (!difference_fac && mappingMode && !light_fac)
difference_fac = 1;
else if (difference_fac && mappingMode && !light_fac)
difference_fac = 0;
break;
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
511
512
513
|
// close window and exit application
case 27: // if keyboard 'ESC' is pressed, then exit
exit(0);
|
f001495e
Jiaming Guo
fix minor errors ...
|
514
|
}
|
9627c6e6
Jiaming Guo
add splitting and...
|
515
|
glutPostRedisplay();
|
db598823
David Mayerich
fixed GCC errors ...
|
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
533
534
535
536
537
538
539
540
541
542
543
544
545
546
547
548
549
550
551
552
553
|
}
#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()
|
f001495e
Jiaming Guo
fix minor errors ...
|
554
|
glutSetOption(GLUT_MULTISAMPLE, 8);
|
7c1b82bc
Jiaming Guo
test for 00_GT.swc
|
555
|
glutInitDisplayMode(GLUT_DEPTH | GLUT_DOUBLE | GLUT_RGBA); //generate a color buffer, depth buffer, and enable double buffering
|
db598823
David Mayerich
fixed GCC errors ...
|
556
|
glutInitWindowPosition(100,100); //set the initial window position
|
5ac53c9e
Jiaming Guo
add keyboardfunc
|
557
|
glutInitWindowSize(320, 320); //set the initial window size
|
db598823
David Mayerich
fixed GCC errors ...
|
558
|
glutCreateWindow("NetMets - STIM Lab, UH"); //set the dialog box title
|
db598823
David Mayerich
fixed GCC errors ...
|
559
|
|
db598823
David Mayerich
fixed GCC errors ...
|
560
561
562
563
|
// 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
|
f001495e
Jiaming Guo
fix minor errors ...
|
564
|
if (ind == 1) { //only in mapping mode, keyboard will be used
|
f001495e
Jiaming Guo
fix minor errors ...
|
565
|
glutCreateMenu(glut_menu); //register menu option callback
|
4d23da9c
Jiaming Guo
add 00_GT.swc,now...
|
566
567
568
569
570
571
|
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
|
b31bfd7d
David Mayerich
added SWC files a...
|
572
|
glutMouseWheelFunc(glut_wheel);
|
db598823
David Mayerich
fixed GCC errors ...
|
573
|
|
9627c6e6
Jiaming Guo
add splitting and...
|
574
|
texture_initialize(); //set up texture mapping (create texture maps, enable features)
|
db598823
David Mayerich
fixed GCC errors ...
|
575
576
577
578
579
580
|
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
|
db598823
David Mayerich
fixed GCC errors ...
|
581
582
|
}
|
f86a38d3
Jiaming Guo
add device choice...
|
583
|
#ifdef __CUDACC__
|
f001495e
Jiaming Guo
fix minor errors ...
|
584
|
// set specific device to work on
|
f86a38d3
Jiaming Guo
add device choice...
|
585
586
587
588
589
590
591
592
593
594
|
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){
|
f001495e
Jiaming Guo
fix minor errors ...
|
595
|
device = -1; // set to default -1
|
f86a38d3
Jiaming Guo
add device choice...
|
596
597
598
|
}
#endif
|
db598823
David Mayerich
fixed GCC errors ...
|
599
|
//compare both networks and fill the networks with error information
|
f86a38d3
Jiaming Guo
add device choice...
|
600
|
void compare(float sigma, int device){
|
db598823
David Mayerich
fixed GCC errors ...
|
601
|
|
f86a38d3
Jiaming Guo
add device choice...
|
602
603
|
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
|
db598823
David Mayerich
fixed GCC errors ...
|
604
605
|
//calculate the metrics
|
691fa079
David Mayerich
initial pass adap...
|
606
607
|
float FPR = GT.average(); //calculate the metrics
float FNR = T.average();
|
db598823
David Mayerich
fixed GCC errors ...
|
608
609
610
611
612
|
std::cout << "FNR: " << FPR << std::endl; //print false alarms and misses
std::cout << "FPR: " << FNR << std::endl;
}
|
f001495e
Jiaming Guo
fix minor errors ...
|
613
|
//split and map two networks and fill the networks' R with metric information
|
21f03d55
Jiaming Guo
add functions for...
|
614
|
void map(float sigma, int device, float threshold){
|
9627c6e6
Jiaming Guo
add splitting and...
|
615
|
|
f001495e
Jiaming Guo
fix minor errors ...
|
616
|
// compare and split two networks
|
21f03d55
Jiaming Guo
add functions for...
|
617
618
|
_GT.split(GT, T, sigma, device, threshold);
_T.split(T, GT, sigma, device, threshold);
|
9627c6e6
Jiaming Guo
add splitting and...
|
619
|
|
f001495e
Jiaming Guo
fix minor errors ...
|
620
|
// mapping two new splitted networks and get their edge relation
|
21f03d55
Jiaming Guo
add functions for...
|
621
622
|
_GT.mapping(_T, _gt_t, device, threshold);
_T.mapping(_GT, _t_gt, device, threshold);
|
9627c6e6
Jiaming Guo
add splitting and...
|
623
|
|
f001495e
Jiaming Guo
fix minor errors ...
|
624
|
// generate random color set based on the number of edges in GT
|
9627c6e6
Jiaming Guo
add splitting and...
|
625
|
size_t num = _gt_t.size(); // also create random color for unmapping edge, but won't be used though
|
5ac53c9e
Jiaming Guo
add keyboardfunc
|
626
627
|
colormap.resize(3 * num); // 3 portions compound RGB
for(int i = 0; i < 3 * num; i++)
|
f001495e
Jiaming Guo
fix minor errors ...
|
628
|
colormap[i] = rand()/(float)RAND_MAX; // set to [0, 1]
|
9627c6e6
Jiaming Guo
add splitting and...
|
629
630
631
632
633
634
635
636
637
|
//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;
}
|
db598823
David Mayerich
fixed GCC errors ...
|
638
639
640
|
// 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){
|
f86a38d3
Jiaming Guo
add device choice...
|
641
|
double avgL_t, avgL_gt, avgT_t, avgT_gt, avgB_t, avgB_gt, avgC_t, avgC_gt, avgFD_t, avgFD_gt;
|
db598823
David Mayerich
fixed GCC errors ...
|
642
643
644
645
646
647
648
649
650
651
652
653
654
655
656
657
658
659
660
661
662
663
664
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666
667
668
669
670
|
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
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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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