Jiaming Guo · Jiaming Guo
Showing 6 changed files Show diff stats
stim/grids/image_stack.h
stim/math/matrix.h
stim/visualization/camera.h
stim/visualization/colormap.h
stim/visualization/gl_network.h
stim/visualization/obj.h
@@ -38,6 +38,20 @@ public:
 		return R[1] * R[2] * R[3];						//return the number of spatial samples
 	}
+	// get the number of pixels in each dimension
+	size_t nc() {
+		return R[0];
+	}
+	size_t nx() {
+		return R[1];
+	}
+	size_t ny() {
+		return R[2];
+	}
+	size_t nz() {
+		return R[3];
+	}
+
 	/// Returns the number of color channels
 	size_t channels(){
 		return R[0];
@@ -187,6 +201,10 @@ public:
 		for (unsigned i = 0; i < R[0] * R[1] * R[2]; i++)
 			ptr[i + k * R[0] * R[1] * R[2]] = Ptr[i];
 	}
+	void copy(T* Ptr) {
+		ptr = Ptr;
+	}
+
 	void read(std::string file, unsigned int X, unsigned int Y, unsigned int Z, unsigned int C = 1, unsigned int header = 0){
 		read(file, stim::vec<unsigned long>(C, X, Y, Z), header);
@@ -408,7 +408,7 @@ public:
 	//save the data as a CSV file
 	void csv(std::string filename) const {
-		ofstream basisfile(filename.c_str());
+		std::ofstream basisfile(filename.c_str());
 		basisfile << csv();
 		basisfile.close();
 	}
@@ -436,7 +436,7 @@ public:
 	}
 	void raw(std::string filename) {
-		ofstream out(filename, std::ios::binary);
+		std::ofstream out(filename, std::ios::binary);
 		if (out) {
 			out.write((char*)data(), rows() * cols() * sizeof(T));
 			out.close();
@@ -72,7 +72,6 @@ public:
 			delta = focus;
 		focus -= delta;
-		std::cout << focus << std::endl;
 		Dolly(d*delta);
 	}
@@ -33,6 +33,30 @@ static float  BREWERCP[BREWER_CTRL_PTS*4] = {0.192157f, 0.211765f, 0.584314f, 1.
                                       0.843137f, 0.188235f, 0.152941f, 1.0f,
                                       0.647059f, 0.0f, 0.14902f, 1.0f};
+//static float  BREWERCP[BREWER_CTRL_PTS * 4] = { 0.192157f, 0.584314f, 0.211765f, 1.0f,
+//										0.270588f, 0.705882f, 0.458824f, 1.0f,
+//										0.454902f, 0.819608f, 0.678431f, 1.0f,
+//										0.670588f, 0.913725f, 0.85098f, 1.0f,
+//										0.878431f, 0.972549f, 0.952941f, 1.0f,
+//										1.0f, 0.74902f, 1.0f, 1.0f,
+//										0.996078f, 0.878431f, 0.564706f, 1.0f,
+//										0.992157f, 0.682353f, 0.380392f, 1.0f,
+//										0.956863f, 0.427451f, 0.262745f, 1.0f,
+//										0.843137f, 0.188235f, 0.152941f, 1.0f,
+//										0.647059f, 0.0f, 0.14902f, 1.0f };
+
+//static float  BREWERCP[BREWER_CTRL_PTS * 4] = { 0.0f, 0.407843f, 0.215686f, 1.0f,
+//										0.101960f, 0.596078f, 0.313725f, 1.0f,
+//										0.4f, 0.741176f, 0.388235f, 1.0f,
+//										0.650980f, 0.850980f, 0.415686f, 1.0f,
+//										0.850980f, 0.937254f, 0.545098f, 1.0f,
+//										1.0f, 1.0f, 0.749019f, 1.0f,
+//										0.996078f, 0.878431f, 0.545098f, 1.0f,
+//										0.992156f, 0.682352f, 0.380392f, 1.0f,
+//										0.956862f, 0.427450f, 0.262745f, 1.0f,
+//										0.843137f, 0.188235f, 0.152941f, 1.0f,
+//										0.647058f, 0.0f, 0.149019f, 1.0f };
+
 #ifdef __CUDACC__
 texture<float4, cudaTextureType1D> cudaTexBrewer;
@@ -167,9 +167,9 @@ public:
 					stim::circle<T> C1 = E[e].circ(p - 1);
 					stim::circle<T> C2 = E[e].circ(p);
 					r1 = E[e].r(p - 1);
-					r2 = E[e].r(p);
-					C1.set_R(2 * r1);								// re-scale the circle to the same
-					C2.set_R(2 * r2);
+					r2 = E[e].r(p);	
+					C1.set_R(r1);									// re-scale the circle to the same
+					C2.set_R(r2);
 					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);
 					glBegin(GL_QUAD_STRIP);
@@ -191,7 +191,7 @@ public:
 						break;
 					}
 				}
-				renderBall(V[n][0], V[n][1], V[n][2], 2 * r1, 20);
+				renderBall(V[n][0], V[n][1], V[n][2], r1, 20);
 			}
 			glEndList();						// end the display list
 		}
@@ -694,6 +694,10 @@ public:
 		return V.size();
 	}
+	unsigned int numVT() {
+		return VT.size();
+	}
+
 	/// Retrieve the vertex stored in index i
 	/// @param vi is the desired vertex index
 	stim::vec<T> getV(unsigned int vi){