Merge branch 'JACK' into 'master'

make it render better for both swc and obj files add a new function in circle class in order to get a close circle See merge request !25

Merge branch 'JACK' into 'master'
make it render better for both swc and obj files add a new function in circle class in order to get a close circle See merge request !25
David Mayerich
2 parents ff4ee63d 30b20d4f
Showing 3 changed files with 60 additions and 129 deletions Show diff stats
stim/biomodels/network.h
stim/math/circle.h
stim/visualization/gl_network.h
@@ -144,7 +144,7 @@ protected:
 	std::vector<edge> E;       //list of edges
 	std::vector<vertex> V;	   //list of vertices.
-	std::vector<int> NT;	   //stores a list of neuronal type for each point in the centerline (will set value only when centerline is built from swc file)
+	//std::vector<int> NT;	   //stores a list of neuronal type for each point in the centerline (will set value only when centerline is built from swc file)
 public:
@@ -396,11 +396,11 @@ public:
 		S.load(filename);									// load the node information
 		S.create_tree();									// link those node according to their linking relationships as a tree
-		NT.push_back(S.node[0].type);						// set the neuronal_type value to the first vertex in the network
+		//NT.push_back(S.node[0].type);						// set the neuronal_type value to the first vertex in the network
 		std::vector<unsigned> id2vert;						// this list stores the SWC vertex ID associated with each network vertex
 		unsigned i[2];										// temporary, IDs associated with the first and last points
 		for (unsigned int l = 1; l < S.numL(); l++) {		// for every node starts from second one
-			NT.push_back(S.node[l].type);
+			//NT.push_back(S.node[l].type);
 			stim::centerline<T> c3(2);						// every fiber contains two vertices
 			int p_idx = S.node[l].parent_idx - 1;			// get the parent node loop idx of current node
 			c3[0] = S.node[p_idx].point;					// store the begin vertex
@@ -479,7 +479,7 @@ public:
 	stim::network<T> resample(T spacing){
 		stim::network<T> n;								//create a new network that will be an exact copy, with resampled fibers
 		n.V = V;									//copy all vertices
-		n.NT = NT;										//copy all the neuronal type information
+		//n.NT = NT;										//copy all the neuronal type information
 		n.E.resize(edges());								//allocate space for the edge list
 		//copy all fibers, resampling them in the process
@@ -820,7 +820,7 @@ public:
 				V[V.size() - 1].e[0].push_back((unsigned)E.size() - 1);									// push second half edge to the outgoing of new vertex
 				for(unsigned i = 0; i < V[tmp.v[1]].e[1].size(); i++)									// find the incoming edge of original ending vertex
 					if(V[tmp.v[1]].e[1][i] == e)
-						V[tmp.v[1]].e[1][i] = (unsigned)V.size() - 1;
+						V[tmp.v[1]].e[1][i] = (unsigned)E.size() - 1;									// set to new edge
 			}
 		}
 	}
@@ -193,9 +193,20 @@ public:
 			result[i] = p(i * dt);							//calculate a point on the edge of the circle
 		return result;
 	}	
-	
-	
+	///returns a vector with the points on the initialized circle
+	///connecting the points results in a circle
+	///@param n: integer for the number of points representing the circle
+	///the only difference between points and glpoints is that the first point appears twice in the returning lists
+	std::vector< stim::vec3<T> > glpoints(unsigned n) {
+		std::vector< stim::vec3<T> > result(n + 1);
+		float dt = stim::TAU / n;
+		for (unsigned i = 0; i < n; i++)
+			result[i] = p(i * dt);
+		result[n] = p(0);									//close the circle!
+		return result;
+	}
+	
 	std::string str() const
 	{
 		std::stringstream ss;
@@ -87,7 +87,7 @@ public:
 	/// 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() {
+	/*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
@@ -163,7 +163,7 @@ public:
 			glEndList();						//end the display list
 		}
 		glCallList(dlist);					// render the display list
-	}
+	}*/
 	///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
@@ -188,7 +188,7 @@ public:
 	///render the network cylinder as a series of tubes
 	///colors are based on metric values 
-	void glCylinder() {
+	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
@@ -196,12 +196,12 @@ public:
 				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(10);									// scale the circle to the same
-					C2.set_R(10);
-					std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-					std::vector< stim::vec3<T> >Cp2 = C2.points(20);
+					C1.set_R(3*sigma);								// scale the circle to the same
+					C2.set_R(3*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
+					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));
@@ -209,6 +209,18 @@ public:
 					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], 3*sigma, 20);
+			}
 			glEndList();						//end the display list
 		}
 		glCallList(dlist);						//render the display list
@@ -218,53 +230,7 @@ public:
 	///@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
-	void glRandColorCylinder1(GLuint &dlist1, std::vector<unsigned> map, std::vector<T> colormap) {
-		if (!glIsList(dlist1)) {								// if dlist1 isn't a display list, create it
-			dlist1 = glGenLists(1);								// generate a display list
-			glNewList(dlist1, GL_COMPILE);						// start a new display list
-			for (unsigned e = 0; e < E.size(); e++) {			// for each edge in the network
-				if (map[e] != unsigned(-1)) {
-					glColor3f(colormap[e * 3 + 0], colormap[e * 3 + 1], colormap[e * 3 + 2]);
-					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(10);							// scale the circle to the same
-						C2.set_R(10);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
-						renderCylinder(Cp1, Cp2);
-					}
-				}
-				else {
-					glColor3f(1.0f, 1.0f, 1.0f);					// white color for the un-mapping edges
-					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(10);								// scale the circle to the same
-						C2.set_R(10);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
-						renderCylinder(Cp1, Cp2);
-					}
-				}
-			}
-			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) {					// if it is the joint vertex
-					glColor3f(0.3, 0.3, 0.3);		// gray color 
-					renderBall(V[v][0], V[v][1], V[v][2], 20, 20);
-				}
-				else {								// if it is the terminal vertex
-					glColor3f(0.6, 0.6, 0.6);		// more white gray
-					renderBall(V[v][0], V[v][1], V[v][2], 20, 20);
-				}
-			}
-			glEndList();
-		}
-		glCallList(dlist1);
-	}
-
-	void glRandColorCylinder1_swc(GLuint &dlist1, std::vector<unsigned> map, std::vector<T> colormap) {
+	void glRandColorCylinder1(GLuint &dlist1, std::vector<unsigned> map, std::vector<T> colormap, float sigma) {
 		if (!glIsList(dlist1)) {								// if dlist1 isn't a display list, create it
 			dlist1 = glGenLists(1);								// generate a display list
 			glNewList(dlist1, GL_COMPILE);						// start a new display list
@@ -274,10 +240,10 @@ public:
 					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(0.5);							// scale the circle to the same
-						C2.set_R(0.5);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
+						C1.set_R(3*sigma);							// scale the circle to the same
+						C2.set_R(3*sigma);
+						std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
+						std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
 						renderCylinder(Cp1, Cp2);
 					}
 				}
@@ -286,10 +252,10 @@ public:
 					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(0.5);								// scale the circle to the same
-						C2.set_R(0.5);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
+						C1.set_R(3*sigma);								// scale the circle to the same
+						C2.set_R(3*sigma);
+						std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
+						std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
 						renderCylinder(Cp1, Cp2);
 					}
 				}
@@ -298,11 +264,11 @@ public:
 				size_t num_edge = V[v].e[0].size() + V[v].e[1].size();
 				if (num_edge > 1) {					// if it is the joint vertex
 					glColor3f(0.3, 0.3, 0.3);		// gray color 
-					renderBall(V[v][0], V[v][1], V[v][2], 1, 20);
+					renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
 				}
 				else {								// if it is the terminal vertex
 					glColor3f(0.6, 0.6, 0.6);		// more white gray
-					renderBall(V[v][0], V[v][1], V[v][2], 1, 20);
+					renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
 				}
 			}
 			glEndList();
@@ -314,53 +280,7 @@ public:
 	///@param dlist2 is the display list
 	///@param map is the mapping relationship between two networks
 	///@param colormap is the random generated color set for render
-	void glRandColorCylinder2(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++) {				// for each edge in the network
-				if (map[e] != unsigned(-1)) {
-					glColor3f(colormap[map[e] * 3 + 0], colormap[map[e] * 3 + 1], colormap[map[e] * 3 + 2]);
-					for (unsigned p = 0; p < E[e].size() - 1; p++) {// for each point on that edge
-						stim::circle<T> C1 = E[e].circ(p);
-						stim::circle<T> C2 = E[e].circ(p + 1);
-						C1.set_R(10);								// scale the circle to the same
-						C2.set_R(10);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
-						renderCylinder(Cp1, Cp2);
-					}
-				}
-				else {
-					glColor3f(1.0f, 1.0f, 1.0f);					// white color for the un-mapping edges
-					for (unsigned p = 0; p < E[e].size() - 1; p++) {// for each point on that edge
-						stim::circle<T> C1 = E[e].circ(p);
-						stim::circle<T> C2 = E[e].circ(p + 1);
-						C1.set_R(10);								// scale the circle to the same
-						C2.set_R(10);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
-						renderCylinder(Cp1, Cp2);
-					}
-				}
-			}
-			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) {					// if it is the joint vertex
-					glColor3f(0.3, 0.3, 0.3);		// gray color 
-					renderBall(V[v][0], V[v][1], V[v][2], 20, 20);
-				}
-				else {								// if it is the terminal vertex
-					glColor3f(0.6, 0.6, 0.6);		// more white gray
-					renderBall(V[v][0], V[v][1], V[v][2], 20, 20);
-				}
-			}
-			glEndList();
-		}
-		glCallList(dlist2);
-	}
-
-	void glRandColorCylinder2_swc(GLuint &dlist2, std::vector<unsigned> map, std::vector<T> colormap) {
+	void glRandColorCylinder2(GLuint &dlist2, std::vector<unsigned> map, std::vector<T> colormap, float sigma) {
 		if (!glIsList(dlist2)) {
 			dlist2 = glGenLists(1);
 			glNewList(dlist2, GL_COMPILE);
@@ -370,10 +290,10 @@ public:
 					for (unsigned p = 0; p < E[e].size() - 1; p++) {// for each point on that edge
 						stim::circle<T> C1 = E[e].circ(p);
 						stim::circle<T> C2 = E[e].circ(p + 1);
-						C1.set_R(0.5);								// scale the circle to the same
-						C2.set_R(0.5);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
+						C1.set_R(3*sigma);								// scale the circle to the same
+						C2.set_R(3*sigma);
+						std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
+						std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
 						renderCylinder(Cp1, Cp2);
 					}
 				}
@@ -382,10 +302,10 @@ public:
 					for (unsigned p = 0; p < E[e].size() - 1; p++) {// for each point on that edge
 						stim::circle<T> C1 = E[e].circ(p);
 						stim::circle<T> C2 = E[e].circ(p + 1);
-						C1.set_R(0.5);								// scale the circle to the same
-						C2.set_R(0.5);
-						std::vector< stim::vec3<T> >Cp1 = C1.points(20);
-						std::vector< stim::vec3<T> >Cp2 = C2.points(20);
+						C1.set_R(3*sigma);								// scale the circle to the same
+						C2.set_R(3*sigma);
+						std::vector< stim::vec3<T> >Cp1 = C1.glpoints(20);
+						std::vector< stim::vec3<T> >Cp2 = C2.glpoints(20);
 						renderCylinder(Cp1, Cp2);
 					}
 				}
@@ -394,11 +314,11 @@ public:
 				size_t num_edge = V[v].e[0].size() + V[v].e[1].size();
 				if (num_edge > 1) {					// if it is the joint vertex
 					glColor3f(0.3, 0.3, 0.3);		// gray color 
-					renderBall(V[v][0], V[v][1], V[v][2], 1, 20);
+					renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
 				}
 				else {								// if it is the terminal vertex
 					glColor3f(0.6, 0.6, 0.6);		// more white gray
-					renderBall(V[v][0], V[v][1], V[v][2], 1, 20);
+					renderBall(V[v][0], V[v][1], V[v][2], 6*sigma, 20);
 				}
 			}
 			glEndList();