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#ifndef STIM_GL_NETWORK
#define STIM_GL_NETWORK
#include <stim/biomodels/network.h>
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#include <stim/visualization/aaboundingbox.h>
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namespace stim{
template <typename T>
class gl_network : public stim::network<T>{
protected:
using stim::network<T>::E;
using stim::network<T>::V;
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GLuint dlist;
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public:
/// Default constructor
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gl_network() : stim::network<T>(){
dlist = 0;
}
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/// Constructor creates a gl_network from a stim::network
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gl_network(stim::network<T> N) : stim::network<T>(N){
dlist = 0;
}
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/// Fills the parameters with the minimum and maximum spatial positions in the network,
/// specifying a bounding box for the network geometry
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aaboundingbox<T> boundingbox(){
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aaboundingbox<T> bb; //create a bounding box
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//loop through every edge
for(unsigned e = 0; e < E.size(); e++){
//loop through every point
for(unsigned p = 0; p < E[e].size(); p++)
bb.expand(E[e][p]); //expand the bounding box to include the point
}
return bb; //return the bounding box
}
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///render cylinder based on points from the top/bottom hat
///@param C1 set of points from one of the hat
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void renderCylinder(std::vector< stim::vec3<T> > C1, std::vector< stim::vec3<T> > C2, stim::vec3<T> P1, stim::vec3<T> P2) {
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glBegin(GL_QUAD_STRIP);
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for (unsigned i = 0; i < C1.size(); i++) { // for every point on the circle
stim::vec3<T> n1 = C1[i] - P1; // set normal vector for every vertex on the quads
stim::vec3<T> n2 = C2[i] - P2;
n1 = n1.norm();
n2 = n2.norm();
glNormal3f(n1[0], n1[1], n1[2]);
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glVertex3f(C1[i][0], C1[i][1], C1[i][2]);
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glNormal3f(n2[0], n2[1], n2[2]);
glVertex3f(C2[i][0], C2[i][1], C2[i][2]);
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}
glEnd();
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}
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///render the vertex as sphere based on glut build-in function
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///@param x, y, z are the three coordinates of the center point
///@param radius is the radius of the sphere
///@param subdivisions is the slice/stride along/around z-axis
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void renderBall(T x, T y, T z, T radius, int subdivisions) {
glPushMatrix();
glTranslatef(x, y, z);
glutSolidSphere(radius, subdivisions, subdivisions);
glPopMatrix();
}
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///render the vertex as sphere based on transformation
///@param x, y, z are the three coordinates of the center point
///@param radius is the radius of the sphere
///@param slice is the number of subdivisions around the z-axis
///@param stack is the number of subdivisions along the z-axis
void renderBall(T x, T y, T z, T radius, T slice, T stack) {
T step_z = stim::PI / slice; // step angle along z-axis
T step_xy = 2 * stim::PI / stack; // step angle in xy-plane
T xx[4], yy[4], zz[4]; // store coordinates
T angle_z = 0.0; // start angle
T angle_xy = 0.0;
glBegin(GL_QUADS);
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for (unsigned i = 0; i < slice; i++) { // around the z-axis
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angle_z = i * step_z; // step step_z each time
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for (unsigned j = 0; j < stack; j++) { // along the z-axis
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angle_xy = j * step_xy; // step step_xy each time, draw floor by floor
xx[0] = radius * std::sin(angle_z) * std::cos(angle_xy); // four vertices
yy[0] = radius * std::sin(angle_z) * std::sin(angle_xy);
zz[0] = radius * std::cos(angle_z);
xx[1] = radius * std::sin(angle_z + step_z) * std::cos(angle_xy);
yy[1] = radius * std::sin(angle_z + step_z) * std::sin(angle_xy);
zz[1] = radius * std::cos(angle_z + step_z);
xx[2] = radius * std::sin(angle_z + step_z) * std::cos(angle_xy + step_xy);
yy[2] = radius * std::sin(angle_z + step_z) * std::sin(angle_xy + step_xy);
zz[2] = radius * std::cos(angle_z + step_z);
xx[3] = radius * std::sin(angle_z) * std::cos(angle_xy + step_xy);
yy[3] = radius * std::sin(angle_z) * std::sin(angle_xy + step_xy);
zz[3] = radius * std::cos(angle_z);
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for (unsigned k = 0; k < 4; k++) {
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glVertex3f(x + xx[k], y + yy[k], z + zz[k]); // draw the floor plane
}
}
}
glEnd();
}
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/// Render the network centerline as a series of line strips.
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/// glCenterline0 is for only one input
void glCenterline0(){
if (!glIsList(dlist)) { //if dlist isn't a display list, create it
dlist = glGenLists(1); //generate a display list
glNewList(dlist, GL_COMPILE); //start a new display list
for (unsigned e = 0; e < E.size(); e++) { //for each edge in the network
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) { //for each point on that edge
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]); //set the vertex position based on the current point
glTexCoord1f(0); //set white color
}
glEnd();
}
glEndList(); //end the display list
}
glCallList(dlist); // render the display list
}
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///render the network centerline as a series of line strips(when loading at least two networks, otherwise using glCenterline0())
///colors are based on metric values
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void glCenterline(){
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if(!glIsList(dlist)){ //if dlist isn't a display list, create it
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dlist = glGenLists(1); //generate a display list
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glNewList(dlist, GL_COMPILE); //start a new display list
for(unsigned e = 0; e < E.size(); e++){ //for each edge in the network
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//unsigned errormag_id = E[e].nmags() - 1;
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glBegin(GL_LINE_STRIP);
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for(unsigned p = 0; p < E[e].size(); p++){ //for each point on that edge
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]); //set the vertex position based on the current point
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glTexCoord1f(E[e].r(p)); //set the texture coordinate based on the specified magnitude index
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}
glEnd();
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}
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glEndList(); //end the display list
}
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glCallList(dlist); //render the display list
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}
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///render the network cylinder as a series of tubes
///colors are based on metric values
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void glCylinder(float sigma, float radius) {
if (radius != sigma) // if render radius was changed by user, create a new display list
glDeleteLists(dlist, 1);
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if (!glIsList(dlist)) { // if dlist isn't a display list, create it
dlist = glGenLists(1); // generate a display list
glNewList(dlist, GL_COMPILE); // start a new display list
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for (unsigned e = 0; e < E.size(); e++) { // for each edge in the network
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for (unsigned p = 1; p < E[e].size(); p++) { // for each point on that edge
stim::circle<T> C1 = E[e].circ(p - 1);
stim::circle<T> C2 = E[e].circ(p);
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C1.set_R(2*radius); // re-scale the circle to the same
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C2.set_R(2*radius);
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std::vector< stim::vec3<T> > Cp1 = C1.glpoints(20);// get 20 points on the circle plane
std::vector< stim::vec3<T> > Cp2 = C2.glpoints(20);
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glBegin(GL_QUAD_STRIP);
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for (unsigned i = 0; i < Cp1.size(); i++) {
stim::vec3<T> n1 = Cp1[i] - E[e][p - 1]; // set normal vector for every vertex on the quads
stim::vec3<T> n2 = Cp2[i] - E[e][p];
n1 = n1.norm();
n2 = n2.norm();
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glNormal3f(n1[0], n1[1], n1[2]);
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glTexCoord1f(E[e].r(p - 1));
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glVertex3f(Cp1[i][0], Cp1[i][1], Cp1[i][2]);
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glNormal3f(n2[0], n2[1], n2[2]);
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glTexCoord1f(E[e].r(p));
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glVertex3f(Cp2[i][0], Cp2[i][1], Cp2[i][2]);
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}
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glEnd();
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} // set the texture coordinate based on the specified magnitude index
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}
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for (unsigned n = 0; n < V.size(); n++) {
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size_t num = V[n].e[0].size(); // store the number of outgoing edge of that vertex
if (num != 0) { // if it has outgoing edge
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unsigned idx = V[n].e[0][0]; // find the index of first outgoing edge of that vertex
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glTexCoord1f(E[idx].r(0)); // bind the texture as metric of first point on that edge
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}
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unsigned idx = V[n].e[1][0]; // find the index of first incoming edge of that vertex
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glTexCoord1f(E[idx].r(E[idx].size() - 1)); // bind the texture as metric of last point on that edge
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}
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renderBall(V[n][0], V[n][1], V[n][2], 2*radius, 20);
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}
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glEndList(); // end the display list
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}
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glCallList(dlist); // render the display list
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}
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///render a T as a adjoint network of GT in transparancy(darkgreen, overlaid)
void glAdjointCylinder(float sigma, float radius) {
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if (radius != sigma) // if render radius was changed by user, create a new display list
glDeleteLists(dlist+4, 1);
if (!glIsList(dlist+4)) {
glNewList(dlist+4, GL_COMPILE);
for (unsigned e = 0; e < E.size(); e++) { // for each edge in the network
for (unsigned p = 1; p < E[e].size(); p++) { // for each point on that edge
stim::circle<T> C1 = E[e].circ(p - 1);
stim::circle<T> C2 = E[e].circ(p);
C1.set_R(2 * radius); // scale the circle to the same
C2.set_R(2 * radius);
std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
glBegin(GL_QUAD_STRIP);
for (unsigned i = 0; i < Cp1.size(); i++) { // for every point on the circle(+1 means closing the circle)
glVertex3f(Cp1[i][0], Cp1[i][1], Cp1[i][2]);
glVertex3f(Cp2[i][0], Cp2[i][1], Cp2[i][2]);
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}
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glEnd();
} // set the texture coordinate based on the specified magnitude index
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}
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for (unsigned n = 0; n < V.size(); n++) {
size_t num = V[n].e[0].size(); // store the number of outgoing edge of that vertex
if (num != 0) { // if it has outgoing edge
unsigned idx = V[n].e[0][0]; // find the index of first outgoing edge of that vertex
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}
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else {
unsigned idx = V[n].e[1][0]; // find the index of first incoming edge of that vertex
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}
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renderBall(V[n][0], V[n][1], V[n][2], 2 * radius, 20);
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}
glEndList();
}
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glCallList(dlist+4);
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}
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///render the network cylinder as series of tubes
///@param I is a indicator: 0 -> GT, 1 -> T
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///@param map is the mapping relationship between two networks
///@param colormap is the random generated color set for render
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void glRandColorCylinder(int I, std::vector<unsigned> map, std::vector<T> colormap, float sigma, float radius) {
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if (radius != sigma) // if render radius was changed by user, create a new display list
glDeleteLists(dlist+2, 1);
if (!glIsList(dlist+2)) { // if dlist isn't a display list, create it
glNewList(dlist+2, GL_COMPILE); // start a new display list
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for (unsigned e = 0; e < E.size(); e++) { // for each edge in the network
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if (map[e] != unsigned(-1)) {
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if (I == 0) { // if it is to render GT
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glColor3f(colormap[e * 3 + 0], colormap[e * 3 + 1], colormap[e * 3 + 2]);
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}
else { // if it is to render T
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glColor3f(colormap[map[e] * 3 + 0], colormap[map[e] * 3 + 1], colormap[map[e] * 3 + 2]);
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}
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for (unsigned p = 1; p < E[e].size(); p++) {// for each point on that edge
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stim::circle<T> C1 = E[e].circ(p - 1);
stim::circle<T> C2 = E[e].circ(p);
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C1.set_R(2*radius); // re-scale the circle to the same
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C2.set_R(2*radius);
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std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
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renderCylinder(Cp1, Cp2, E[e][p - 1], E[e][p]);
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}
}
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glColor3f(0.2, 0.0, 0.0); // red color for the un-mapping edges
for (unsigned p = 1; p < E[e].size(); p++) {// for each point on that edge
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stim::circle<T> C1 = E[e].circ(p - 1);
stim::circle<T> C2 = E[e].circ(p);
C1.set_R(2*radius); // scale the circle to the same
C2.set_R(2*radius);
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std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
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renderCylinder(Cp1, Cp2, E[e][p - 1], E[e][p]);
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}
}
}
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for (unsigned n = 0; n < V.size(); n++) {
size_t num_edge = V[n].e[0].size() + V[n].e[1].size();
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if (num_edge > 1) { // if it is the joint vertex
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if (V[n].e[0].size() != 0) {
unsigned idx = V[n].e[0][0]; // find the index of first incoming edge of that vertex
stim::circle<T> C = E[idx].circ(0);
stim::vec3<T> normal = C.n();
glNormal3f(normal[0], normal[1], normal[2]);// for every ball, we only have one normal vector
}
else {
unsigned idx = V[n].e[1][0]; // find the index of first incoming edge of that vertex
stim::circle<T> C = E[idx].circ(E[idx].size() - 1);
stim::vec3<T> normal = C.n();
glNormal3f(normal[0], normal[1], normal[2]);// for every ball, we only have one normal vector
}
glColor3f(0.3, 0.3, 0.3); // gray
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renderBall(V[n][0], V[n][1], V[n][2], 3*radius, 20);
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}
else { // if it is the terminal vertex
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if (V[n].e[0].size() != 0) {
unsigned idx = V[n].e[0][0]; // find the index of first incoming edge of that vertex
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}
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}
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glColor3f(0.6, 0.6, 0.6); // more white gray
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renderBall(V[n][0], V[n][1], V[n][2], 3*radius, 20);
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}
}
glEndList();
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}
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glCallList(dlist+2);
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}
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///render the network centerline as a series of line strips in random different color
///@param I is a indicator: 0 -> GT, 1 -> T
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///@param dlist1 is the display list
///@param map is the mapping relationship between two networks
///@param colormap is the random generated color set for render
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void glRandColorCenterline(int I, GLuint &dlist1, std::vector<unsigned> map, std::vector<T> colormap) {
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if (!glIsList(dlist1)) {
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dlist1 = glGenLists(1);
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glNewList(dlist1, GL_COMPILE);
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for (unsigned e = 0; e < E.size(); e++) {
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if (map[e] != unsigned(-1)) { // if it has corresponding edge in another network
if (I == 0) // if it is to render GT
glColor3f(colormap[e * 3 + 0], colormap[e * 3 + 1], colormap[e * 3 + 2]);
else // if it is to render T
glColor3f(colormap[map[e] * 3 + 0], colormap[map[e] * 3 + 1], colormap[map[e] * 3 + 2]);
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glBegin(GL_LINE_STRIP);
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for (unsigned p = 0; p < E[e].size(); p++) {
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glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
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}
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else {
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glColor3f(0.2, 0.0, 0.0); // red color for the un-mapping edges
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glBegin(GL_LINE_STRIP);
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glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
}
}
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glEndList();
}
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glCallList(dlist1);
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//void glRandColorCenterlineGT(GLuint &dlist1, std::vector<unsigned> map, std::vector<T> colormap){
// if(!glIsList(dlist1)){
// dlist1 = glGenLists(1);
// glNewList(dlist1, GL_COMPILE);
// for(unsigned e = 0; e < E.size(); e++){
// if(map[e] != unsigned(-1)){
// glColor3f(colormap[e * 3 + 0], colormap[e * 3 + 1], colormap[e * 3 + 2]);
// glBegin(GL_LINE_STRIP);
// for(unsigned p = 0; p < E[e].size(); p++){
// glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
// }
// glEnd();
// for (unsigned p = 0; p < E[e].size() - 1; p++) {
// renderCylinder(E[e][p][0], E[e][p][1], E[e][p][2], E[e][p + 1][0], E[e][p + 1][1], E[e][p + 1][2], 10, 20);
// }
// }
// else{
// glColor3f(1.0, 1.0, 1.0);
// glBegin(GL_LINE_STRIP);
// for(unsigned p = 0; p < E[e].size(); p++){
// glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
// }
// glEnd();
// }
// }
// for (unsigned v = 0; v < V.size(); v++) {
// size_t num_edge = V[v].e[0].size() + V[v].e[1].size();
// if (num_edge > 1) {
// glColor3f(0.3, 0.3, 0.3); // gray color for vertex
// renderBall(V[v][0], V[v][1], V[v][2], 20, 20);
// }
// }
// glEndList();
// }
// glCallList(dlist1);
//}
//void glRandColorCenterlineT(GLuint &dlist2, std::vector<unsigned> map, std::vector<T> colormap){
// if(!glIsList(dlist2)){
// dlist2 = glGenLists(1);
// glNewList(dlist2, GL_COMPILE);
// for(unsigned e = 0; e < E.size(); e++){
// if(map[e] != unsigned(-1)){
// glColor3f(colormap[map[e] * 3 + 0], colormap[map[e] * 3 + 1], colormap[map[e] * 3 + 2]);
// glBegin(GL_LINE_STRIP);
// for(unsigned p = 0; p < E[e].size(); p++){
// glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
// }
// glEnd();
// for (unsigned p = 0; p < E[e].size() - 1; p++) {
// renderCylinder(E[e][p][0], E[e][p][1], E[e][p][2], E[e][p + 1][0], E[e][p + 1][1], E[e][p + 1][2], 10, 20);
// }
// }
// else{
// glColor3f(1.0, 1.0, 1.0);
// glBegin(GL_LINE_STRIP);
// for(unsigned p = 0; p < E[e].size(); p++){
// glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
// }
// glEnd();
// }
// }
// for (unsigned v = 0; v < V.size(); v++) {
// size_t num_edge = V[v].e[0].size() + V[v].e[1].size();
// if (num_edge > 1) {
// glColor3f(0.3, 0.3, 0.3); // gray color for vertex
// renderBall(V[v][0], V[v][1], V[v][2], 20, 20);
// }
// }
// glEndList();
// }
// glCallList(dlist2);
//}
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//void renderCylinder(T x1, T y1, T z1, T x2, T y2, T z2, T radius, int subdivisions) {
// T dx = x2 - x1;
// T dy = y2 - y1;
// T dz = z2 - z1;
// /// handle the degenerate case with an approximation
// if (dz == 0)
// dz = .00000001;
// T d = sqrt(dx*dx + dy*dy + dz*dz);
// T ax = 57.2957795*acos(dz / d); // 180°/pi
// if (dz < 0.0)
// ax = -ax;
// T rx = -dy*dz;
// T ry = dx*dz;
// glPushMatrix();
// glTranslatef(x1, y1, z1);
// glRotatef(ax, rx, ry, 0.0);
// glutSolidCylinder(radius, d, subdivisions, 1);
// glPopMatrix();
//}
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/// render the network centerline from swc file as a series of strips in different colors based on the neuronal type
/// glCenterline0_swc is for only one input
/*void glCenterline0_swc() {
if (!glIsList(dlist)) { // if dlist isn't a display list, create it
dlist = glGenLists(1); // generate a display list
glNewList(dlist, GL_COMPILE); // start a new display list
for (unsigned e = 0; e < E.size(); e++) {
int type = NT[e]; // get the neuronal type
switch (type) {
case 0:
glColor3f(1.0f, 1.0f, 1.0f); // white for undefined
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
case 1:
glColor3f(1.0f, 0.0f, 0.0f); // red for soma
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
case 2:
glColor3f(1.0f, 0.5f, 0.0f); // orange for axon
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
case 3:
glColor3f(1.0f, 1.0f, 0.0f); // yellow for undefined
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
case 4:
glColor3f(0.0f, 1.0f, 0.0f); // green for undefined
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
case 5:
glColor3f(0.0f, 1.0f, 1.0f); // verdant for undefined
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
case 6:
glColor3f(0.0f, 0.0f, 1.0f); // blue for undefined
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
case 7:
glColor3f(0.5f, 0.0f, 1.0f); // purple for undefined
glBegin(GL_LINE_STRIP);
for (unsigned p = 0; p < E[e].size(); p++) {
glVertex3f(E[e][p][0], E[e][p][1], E[e][p][2]);
}
glEnd();
break;
}
}
glEndList(); //end the display list
}
glCallList(dlist); // render the display list
}*/
///render the network cylinder as a series of tubes
///colors are based on metric values
//void glCylinder(float sigma) {
// if (!glIsList(dlist)) { //if dlist isn't a display list, create it
// dlist = glGenLists(1); //generate a display list
// glNewList(dlist, GL_COMPILE); //start a new display list
// for (unsigned e = 0; e < E.size(); e++) { //for each edge in the network
// for (unsigned p = 1; p < E[e].size() - 1; p++) { // for each point on that edge
// stim::circle<T> C1 = E[e].circ(p - 1);
// stim::circle<T> C2 = E[e].circ(p);
// C1.set_R(2.5*sigma); // scale the circle to the same
// C2.set_R(2.5*sigma);
// std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
// std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
// glBegin(GL_QUAD_STRIP);
// for (unsigned i = 0; i < Cp1.size(); i++) { // for every point on the circle(+1 means closing the circle)
// glVertex3f(Cp1[i][0], Cp1[i][1], Cp1[i][2]);
// glVertex3f(Cp2[i][0], Cp2[i][1], Cp2[i][2]);
// glTexCoord1f(E[e].r(p));
// }
// glEnd();
// } //set the texture coordinate based on the specified magnitude index
// }
// for (unsigned n = 0; n < V.size(); n++) {
// size_t num = V[n].e[0].size(); //store the number of outgoing edge of that vertex
// if (num != 0) { //if it has outgoing edge
// unsigned idx = V[n].e[0][0]; //find the index of first outgoing edge of that vertex
// glTexCoord1f(E[idx].r(0)); //bind the texture as metric of first point on that edge
// }
// else {
// unsigned idx = V[n].e[1][0]; //find the index of first incoming edge of that vertex
// glTexCoord1f(E[idx].r(E[idx].size() - 1)); //bind the texture as metric of last point on that edge
// }
// renderBall(V[n][0], V[n][1], V[n][2], 2.5*sigma, 20);
// }
// glEndList(); //end the display list
// }
// glCallList(dlist); //render the display list
//}
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}; //end stim::gl_network class
}; //end stim namespace
#endif
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