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#include <stdlib.h>
#include <string>
#include <fstream>
#include <algorithm>
// CUDA include
#ifdef __CUDACC__
#include "device_launch_parameters.h"
#include <cuda.h>
#include <cuda_runtime_api.h>
#include "cuda_runtime.h"
#endif
// OPENGL include
#include <GL/glut.h>
#include <GL/freeglut.h>
#include "flow.h"
// STIM include
#include <stim/visualization/gl_aaboundingbox.h>
#include <stim/parser/arguments.h>
#include <stim/visualization/camera.h>
#include <stim/visualization/colormap.h>
#include <stim/cuda/cudatools/error.h>
//********************parameter setting********************
// overall parameters
int vX, vY;
float dx, dy, dz; // x, y and z image scaling(units/pixel)
std::string stackdir = ""; // directory where image stacks will be stored
stim::arglist args; // create an instance of arglist
stim::gl_aaboundingbox<float> bb; // axis-aligned bounding box object
stim::camera cam; // camera object
unsigned num_edge; // number of edges in the network
unsigned num_vertex; // number of vertex in the network
std::vector<unsigned> pendant_vertex; // list of pendant vertex index in GT
std::vector<std::string> menu_option = { "simulation", "build inlet/outlet", "manufacture" };
stim::flow<float> flow; // flow object
float move_pace; // camera moving parameter
float u; // viscosity
float rou; // density
float max_v;
float min_v;
int mods; // special keyboard input
std::vector<unsigned char> color; // velocity color map
std::vector<int> velocity_bar; // velocity bar
// hard-coded parameters
float camera_factor = 1.2f; // start point of the camera as a function of X and Y size
float orbit_factor = 0.01f; // degrees per pixel used to orbit the camera
float zoom_factor = 10.0f; // zooming factor
float border_factor = 20.0f; // border
float radii_factor = 1.0f; // radii changing factor
GLint subdivision = 20; // slices and stacks
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float default_radius = 5.0f; // default radii of network vertex
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float delta = 0.01f; // small discrepancy
float eps = 20.0f; // epsilon threshold
float max_pressure = 0.0f; // maximum pressure that the channel can bear
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float height_threshold = 100.0f; // connection height constraint
float fragment_ratio = 0.0f; // fragment ratio
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// glut event parameters
int mouse_x; // window x-coordinate
int mouse_y; // window y-coordinate
bool LTbutton = false; // true means down while false means up
// simulation parameters
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bool render_direction = false; // flag indicates rendering flow direction for one edge
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bool simulation = false; // flag indicates simulation mode
bool color_bound = false; // flag indicates velocity color map bound
bool to_select_pressure = false; // flag indicates having selected a vertex to modify pressure
unsigned pressure_index; // the index of vertex that is clicked
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unsigned direction_index = -1; // the index of edge that is pointed at
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// build inlet/outlet parameters
bool build_inlet_outlet = false; // flag indicates building inlets and outlets
bool modified_bridge = false; // flag indicates having modified inlet/outlet connection
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bool hilbert_curve = false; // flag indicates enabling hilbert curves constructions
bool change_fragment = false; // flag indicates changing fragment for square wave connections
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// manufacture parameters
bool manufacture = false; // flag indicates manufacture mode
//********************helper function*********************
// get the network basic information
inline void get_background() {
pendant_vertex = flow.get_boundary_vertex();
num_edge = flow.edges();
num_vertex = flow.vertices();
// set the initial radii
flow.init(num_edge, num_vertex); // initialize flow object
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// if no radius information laoded
if (!flow.get_radius(0, 0))
for (unsigned i = 0; i < num_edge; i++)
flow.set_r(i, default_radius);
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}
// convert from window coordinates to world coordinates
inline void window_to_world(GLdouble &x, GLdouble &y, GLdouble &z) {
GLint viewport[4];
GLdouble modelview[16];
GLdouble projection[16];
GLdouble winX, winY;
GLfloat winZ;
glGetIntegerv(GL_VIEWPORT, viewport);
glGetDoublev(GL_MODELVIEW_MATRIX, modelview);
glGetDoublev(GL_PROJECTION_MATRIX, projection);
winX = (GLdouble)mouse_x;
winY = viewport[3] - (GLdouble)mouse_y;
glReadPixels((GLint)winX, (GLint)winY, (GLsizei)1, (GLsizei)1, GL_DEPTH_COMPONENT, GL_FLOAT, &winZ);
gluUnProject(winX, winY, winZ, modelview, projection, viewport, &x, &y, &z);
}
//********************simulation function**********************
// initialize flow object
void flow_initialize() {
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flow.set = true;
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stim::vec3<float> center = bb.center();
for (unsigned i = 0; i < pendant_vertex.size(); i++) {
if (flow.get_vertex(pendant_vertex[i])[0] <= center[0])
flow.P[pendant_vertex[i]] = max_pressure - i * delta; // should set minor discrepancy
else
flow.P[pendant_vertex[i]] = (i + 1) * delta; // algorithm treat 0 as no initial pressure
}
}
// find the stable flow state
void flow_stable_state() {
flow.solve_flow(u);
flow.get_color_map(max_v, min_v, color, pendant_vertex);
color_bound = true;
velocity_bar.resize(num_edge);
for (unsigned i = 0; i < num_edge; i++)
velocity_bar[i] = i;
std::sort(velocity_bar.begin(), velocity_bar.end(), [&](int x, int y) {return abs(flow.v[x]) < abs(flow.v[y]); });
}
//********************glut function********************
// dynamically set menu
// @param num: number of current menu options
// @param range: range of option to be set from menu_option list
void glut_set_menu(int num, int range) {
// remove last time menu options
for (int i = 1; i < num + 1; i++)
glutRemoveMenuItem(1);
// set new menu options
std::string menu_name;
for (int i = 1; i < range + 1; i++) {
menu_name = menu_option[i - 1];
glutAddMenuEntry(menu_name.c_str(), i);
}
}
// set up the squash transform to whole screen
void glut_projection() {
glMatrixMode(GL_PROJECTION); // load the projection matrix for editing
glLoadIdentity(); // start with the identity matrix
vX = glutGet(GLUT_WINDOW_WIDTH); // use the whole screen for rendering
vY = glutGet(GLUT_WINDOW_HEIGHT);
glViewport(0, 0, vX, vY); // specify a viewport for the entire window
float aspect = (float)vX / (float)vY; // calculate the aspect ratio
gluPerspective(60, aspect, 0.1, 1000000); // set up a perspective projection
}
// translate camera to origin
void glut_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
gluLookAt(eye[0], eye[1], eye[2], focus[0], focus[1], focus[2], up[0], up[1], up[2]); // set up the OpenGL camera
}
// glut render function
void glut_render() {
glEnable(GL_DEPTH_TEST);
glClear(GL_COLOR_BUFFER_BIT | GL_DEPTH_BUFFER_BIT);
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glClearColor(1.0f, 1.0f, 1.0f, 1.0f);
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glut_projection();
glut_modelview();
if (!simulation && !build_inlet_outlet || manufacture) {
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glColor3f(0.0f, 0.0f, 0.0f);
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flow.glCylinder0();
}
else {
flow.bounding_box();
flow.glSolidSphere(max_pressure, subdivision);
flow.mark_vertex();
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//flow.glSolidCone(subdivision);
flow.glSolidCylinder(direction_index, color, subdivision);
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flow.glSolidCuboid();
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if (render_direction)
flow.glSolidCone(direction_index, subdivision);
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}
if (build_inlet_outlet) {
flow.line_bridge();
}
if (manufacture) {
flow.glSolidCuboid();
flow.tube_bridge(subdivision);
}
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// render bars
// bring up a pressure bar on left
if (to_select_pressure) {
glMatrixMode(GL_PROJECTION); // set up the 2d viewport for mode text printing
glPushMatrix();
glLoadIdentity();
vX = glutGet(GLUT_WINDOW_WIDTH); // get the current window width
vY = glutGet(GLUT_WINDOW_HEIGHT); // get the current window height
glViewport(0, 0, vX, vY); // locate to left bottom corner
gluOrtho2D(0, vX, 0, vY); // define othogonal aspect
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
glLoadIdentity();
glLineWidth(border_factor);
glBegin(GL_LINES);
glColor3f(0.0, 0.0, 1.0); // blue to red
glVertex2f(border_factor, border_factor);
glColor3f(1.0, 0.0, 0.0);
glVertex2f(border_factor, (vY - 2.0f * border_factor));
glEnd();
glFlush();
// pressure bar text
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glColor3f(0.0f, 0.0f, 0.0f);
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glRasterPos2f(0.0f, vY - border_factor);
std::stringstream ss_p;
ss_p << "Pressure Bar";
glutBitmapString(GLUT_BITMAP_HELVETICA_18, (const unsigned char*)(ss_p.str().c_str()));
// pressure range text
float step = vY - 3.0f * border_factor;
step /= 10;
for (unsigned i = 0; i < 11; i++) {
glRasterPos2f((border_factor * 1.5f), (border_factor + i * step));
std::stringstream ss_n;
ss_n << (float)i * max_pressure / 10;
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glutBitmapString(GLUT_BITMAP_HELVETICA_18, (const unsigned char*)(ss_n.str().c_str()));
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}
glPopMatrix();
glMatrixMode(GL_PROJECTION);
glPopMatrix();
}
// bring up a velocity bar on left
if (simulation && !to_select_pressure) {
glMatrixMode(GL_PROJECTION); // set up the 2d viewport for mode text printing
glPushMatrix();
glLoadIdentity();
vX = glutGet(GLUT_WINDOW_WIDTH); // get the current window width
vY = glutGet(GLUT_WINDOW_HEIGHT); // get the current window height
glViewport(0, 0, vX, vY); // locate to left bottom corner
gluOrtho2D(0, vX, 0, vY); // define othogonal aspect
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
glLoadIdentity();
float step = (vY - 3 * border_factor);
step /= num_edge;
for (unsigned i = 0; i < num_edge; i++) {
glLineWidth(border_factor);
glBegin(GL_LINES);
glColor3f((float)color[velocity_bar[i] * 3 + 0] / 255, (float)color[velocity_bar[i] * 3 + 1] / 255, (float)color[velocity_bar[i] * 3 + 2] / 255);
glVertex2f(border_factor, border_factor + i * step);
glVertex2f(border_factor, border_factor + (i + 1) * step);
glEnd();
}
glFlush();
// pressure bar text
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glColor3f(0.0f, 0.0f, 0.0f);
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glRasterPos2f(0.0f, vY - border_factor);
std::stringstream ss_p;
ss_p << "Velocity range";
glutBitmapString(GLUT_BITMAP_HELVETICA_18, (const unsigned char*)(ss_p.str().c_str()));
// pressure range text
step = vY - 3 * border_factor;
step /= 10;
for (unsigned i = 0; i < 11; i++) {
glRasterPos2f(border_factor * 1.5f, border_factor + i * step);
std::stringstream ss_n;
ss_n << min_v + i * (max_v - min_v) / 10;
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glutBitmapString(GLUT_BITMAP_HELVETICA_18, (const unsigned char*)(ss_n.str().c_str()));
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}
glPopMatrix();
glMatrixMode(GL_PROJECTION);
glPopMatrix();
}
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// bring up a ratio bar on the left
if (change_fragment) {
glMatrixMode(GL_PROJECTION); // set up the 2d viewport for mode text printing
glPushMatrix();
glLoadIdentity();
vX = glutGet(GLUT_WINDOW_WIDTH); // get the current window width
vY = glutGet(GLUT_WINDOW_HEIGHT); // get the current window height
glViewport(0, 0, vX, vY); // locate to left bottom corner
gluOrtho2D(0, vX, 0, vY); // define othogonal aspect
glMatrixMode(GL_MODELVIEW);
glPushMatrix();
glLoadIdentity();
glLineWidth(border_factor);
glBegin(GL_LINES);
glColor3f(0.0, 0.0, 1.0); // blue to red
glVertex2f(border_factor, border_factor);
glColor3f(1.0, 0.0, 0.0);
glVertex2f(border_factor, (vY - 2.0f * border_factor));
glEnd();
glFlush();
// pressure bar text
glColor3f(0.0f, 0.0f, 0.0f);
glRasterPos2f(0.0f, vY - border_factor);
std::stringstream ss_p;
ss_p << "Ratio bar";
glutBitmapString(GLUT_BITMAP_HELVETICA_18, (const unsigned char*)(ss_p.str().c_str()));
// pressure range text
float step = vY - 3.0f * border_factor;
step /= 10;
for (unsigned i = 0; i < 11; i++) {
glRasterPos2f((border_factor * 1.5f), (border_factor + i * step));
std::stringstream ss_n;
ss_n << (float)i * 1.0f / 10;
glutBitmapString(GLUT_BITMAP_HELVETICA_18, (const unsigned char*)(ss_n.str().c_str()));
}
glPopMatrix();
glMatrixMode(GL_PROJECTION);
glPopMatrix();
}
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glutSwapBuffers();
}
// register glut menu options
void glut_menu(int value) {
int num = glutGet(GLUT_MENU_NUM_ITEMS);
if (value == 1) {
simulation = true;
build_inlet_outlet = false;
manufacture = false;
modified_bridge = false;
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if (!flow.set)
flow_initialize();
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flow_stable_state(); // main function of solving the linear system
flow.print_flow();
glut_set_menu(num, 2);
}
if (value == 2) {
simulation = false;
build_inlet_outlet = true;
manufacture = false;
if (!modified_bridge) {
flow.set_main_feeder();
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flow.build_synthetic_connection(u, default_radius);
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}
glut_set_menu(num, 3);
}
if (value == 3) {
simulation = false;
build_inlet_outlet = false;
manufacture = true;
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flow.check_synthetic_connection(u, default_radius);
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}
glutPostRedisplay();
}
// defines camera motion based on mouse dragging
void glut_motion(int x, int y) {
mods = glutGetModifiers();
if (LTbutton && mods == 0) {
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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// defines passive mouse motion function
void glut_passive_motion(int x, int y) {
mouse_x = x;
mouse_y = y;
// check whether the mouse point near to an edge
GLdouble posX, posY, posZ;
window_to_world(posX, posY, posZ); // get the world coordinates
if (simulation || build_inlet_outlet) {
bool flag = flow.epsilon_edge((float)posX, (float)posY, (float)posZ, eps, direction_index);
if (flag)
render_direction = true;
else {
if (render_direction) // if the direction is displaying currently, do a short delay
Sleep(1000);
render_direction = false;
direction_index = -1;
}
}
glutPostRedisplay(); // re-draw the visualization
}
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// get click window coordinates
void glut_mouse(int button, int state, int x, int y) {
mouse_x = x;
mouse_y = y;
if (button == GLUT_LEFT_BUTTON && state == GLUT_DOWN)
LTbutton = true;
else if (button == GLUT_LEFT_BUTTON && state == GLUT_UP)
LTbutton = false;
if (button == GLUT_LEFT_BUTTON && state == GLUT_DOWN && simulation && !to_select_pressure) {
GLdouble posX, posY, posZ;
window_to_world(posX, posY, posZ); // get the world coordinates
bool flag = flow.epsilon_vertex((float)posX, (float)posY, (float)posZ, eps, pressure_index);
if (flag) {
std::vector<unsigned>::iterator it = std::find(pendant_vertex.begin(), pendant_vertex.end(), pressure_index);
if (it != pendant_vertex.end()) // if it is dangle vertex
to_select_pressure = true;
}
}
else if (button == GLUT_LEFT_BUTTON && state == GLUT_DOWN && simulation && to_select_pressure) {
if (y > 2 * border_factor || y < vY - border_factor) { // within the pressure bar range
to_select_pressure = false;
float tmp_pressure = (float)(vY - y - border_factor) / ((float)vY - border_factor) * max_pressure;
flow.set_pressure(pressure_index, tmp_pressure);
flow_stable_state(); // main function of solving the linear system
flow.print_flow();
}
}
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else if (button == GLUT_LEFT_BUTTON && state == GLUT_DOWN && modified_bridge && change_fragment) {
if (y > 2 * border_factor || y < vY - border_factor) { // within the ratio bar range
fragment_ratio = (float)(vY - y - border_factor) / ((float)vY - border_factor) * 1.0f;
flow.modify_synthetic_connection(u, rou, hilbert_curve, height_threshold, fragment_ratio, default_radius);
change_fragment = false;
}
}
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}
// define camera move based on mouse wheel move
void glut_wheel(int wheel, int direction, int x, int y) {
mouse_x = x;
mouse_y = y;
GLdouble posX, posY, posZ;
window_to_world(posX, posY, posZ); // get the world coordinates
if (!to_select_pressure) {
bool flag = flow.epsilon_vertex((float)posX, (float)posY, (float)posZ, eps, pressure_index);
if (flag && simulation) {
float tmp_r;
if (direction > 0) { // increase radii
tmp_r = flow.get_radius(pressure_index);
tmp_r += radii_factor;
}
else {
tmp_r = flow.get_radius(pressure_index);
tmp_r -= radii_factor;
if (tmp_r <= 0)
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tmp_r = default_radius;
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}
flow.set_radius(pressure_index, tmp_r);
flow_stable_state();
flow.print_flow();
}
else {
if (direction > 0) // if it is button 3(up), move closer
move_pace = zoom_factor;
else // if it is button 4(down), leave farther
move_pace = -zoom_factor;
cam.Push(move_pace);
}
}
glutPostRedisplay();
}
// define keyboard inputs
void glut_keyboard(unsigned char key, int x, int y) {
// register different keyboard operation
switch (key) {
// zooming
case 'w': // if keyboard 'w' is pressed, then move closer
move_pace = zoom_factor;
cam.Push(move_pace);
break;
case 's': // if keyboard 's' is pressed, then leave farther
move_pace = -zoom_factor;
cam.Push(move_pace);
break;
// output image stack
case 'm':
if (manufacture) {
#ifdef __CUDACC__
flow.make_image_stack(dx, dy, dz, stackdir);
#else
std::cout << "You need to have a gpu to make image stack, sorry." << std::endl;
#endif
}
else if (build_inlet_outlet && !modified_bridge) {
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modified_bridge = true;
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if (hilbert_curve)
flow.modify_synthetic_connection(u, rou, hilbert_curve, height_threshold);
else
change_fragment = true;
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}
break;
}
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glutPostRedisplay();
}
// glut initialization
void glut_initialize() {
int myargc = 1;
char* myargv[1];
myargv[0] = strdup("generate_network_network");
glutInit(&myargc, myargv);
glutInitDisplayMode(GLUT_DEPTH | GLUT_DOUBLE | GLUT_RGBA);
glutInitWindowPosition(100, 100); // set the initial window position
glutInitWindowSize(1000, 1000);
glutCreateWindow("3D flow simulation");
glutDisplayFunc(glut_render);
glutMouseFunc(glut_mouse);
glutMotionFunc(glut_motion);
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glutPassiveMotionFunc(glut_passive_motion);
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glutMouseWheelFunc(glut_wheel);
glutKeyboardFunc(glut_keyboard);
glutCreateMenu(glut_menu); // create a menu object
glut_set_menu(0, 1);
glutAttachMenu(GLUT_RIGHT_BUTTON); // register right mouse to open menu option
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]);
}
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// 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 synthetic microvascular model generator for microfluidics tool!|" << std::endl;
std::cout << "|Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston |" << std::endl;
std::cout << "|Developers: Jiaming Guo, David Mayerich |" << std::endl;
std::cout << "|Source: https://git.stim.ee.uh.edu/Jack/flow3.git |" << std::endl;
std::cout << " =======================================================================================" << std::endl << std::endl;
std::cout << args.str();
}
// main function: parse arguments and initialize GLUT
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int main(int argc, char* argv[]) {
// add arguments
args.add("help", "prints the help");
args.add("network", "load network from .obj or .swc file");
args.add("maxpress", "maximum allowed pressure in g / units / s^2, default 2 is for blood when units = um", "2", "real value > 0");
args.add("viscosity", "set the viscosity of the fluid (in g / units / s), default .00001 is for blood when units = um", ".00001", "real value > 0");
args.add("rou", "set the desity of the fluid (in g / units^3), default 1.06*10^-12 is for blood when units = um", ".00000000000106", "real value > 0");
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args.add("hilbert", "activate hilbert curves connections", "0", "value 1 for enablement");
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args.add("stackres", "spacing between pixel samples in each dimension(in units/pixel)", "1 1 1", "real value > 0");
args.add("stackdir", "set the directory of the output image stack", "", "any existing directory (ex. /home/name/network)");
args.parse(argc, argv); // parse the command line
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if (args["help"].is_set()) {
advertise();
std::exit(1);
}
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// load network
if (args["network"].is_set()) { // load network from user
std::vector<std::string> tmp = stim::parser::split(args["network"].as_string(), '.');
if ("obj" == tmp[1])
flow.load_obj(args["network"].as_string());
else if ("swc" == tmp[1])
flow.load_swc(args["network"].as_string());
else {
std::cout << "Invalid file type" << std::endl;
std::exit(1);
}
}
get_background();
// blood pressure in capillaries range from 15 - 35 torr
// 1 torr = 133.3 Pa
max_pressure = args["maxpress"].as_float();
// normal blood viscosity range from 4 - 15 mPa·s(cP)
// 1 Pa·s = 1 g / mm / s
u = args["viscosity"].as_float(); // g / units / s
// normally the blood density in capillaries: 1060 kg/m^3 = 1.06*10^-12 g/um^3
rou = args["rou"].as_float();
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// check whether to enable hilbert curves or not
hilbert_curve = args["hilbert"].as_int();
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// get the vexel and image stack size
dx = args["stackres"].as_float(0);
dy = args["stackres"].as_float(1);
dz = args["stackres"].as_float(2);
// get the save directory of image stack
if (args["stackdir"].is_set())
stackdir = args["stackdir"].as_string();
// glut main loop
bb = flow.boundingbox();
glut_initialize();
glutMainLoop();
}
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