start new network class

Jiabing Li
1 parent db331d8a
Showing 4 changed files with 53 additions and 11 deletions Show diff stats
python/network_dpy.py
stim/iVote/ivote2.cuh
stim/iVote/ivote2/local_max.cuh
stim/image/image.h
+# -*- coding: utf-8 -*-
+"""
+Created on Sat Jan 19 2018
+
+@author: Jiabing
+"""
+
+import struct
+import numpy as np
+import scipy as sp
+import networkx as nx
+import matplotlib.pyplot as plt
+import math
+
+class Point:
+       def __init__(self, x, y, z, radius):
+           self.x = x
+           self.y = y
+           self.z = z
+           self.r = radius
+                      
+            
+class Fiber:
+       def __init__(self, fiber_idx,point_idx):     
+           self.fidx = fiber_idx
+           self.pidx = point_idx
+           
+           
+
+class Node:
+        def __init__(self, point_idx, fidx):
+            self.pidx= point_idx
+            self.fidx = fidx
+            
+            
+#class NWT:
+    
+#class network(point, Fiber, Node):
 \ No newline at end of file
@@ -152,13 +152,17 @@ namespace stim {
 	template<typename T>
-	void cpu_ivote2(T* cpuI, unsigned int rmax, size_t x, size_t y, bool invert = false, T t = 0, int iter = 8, T phi = 15.0f * (float)stim::PI / 180, int conn = 8, bool debug = false) {
+	void cpu_ivote2(T* cpuI, unsigned int rmax, size_t x, size_t y, float &gpu_time, bool invert = false, T t = 0, int iter = 8, T phi = 15.0f * (float)stim::PI / 180, int conn = 8, bool debug = false) {
 		size_t bytes = x*y * sizeof(T);
 		T* gpuI;						//allocate space on the gpu to save the input image
+
+		gpuTimer_start();
 		HANDLE_ERROR(cudaMalloc(&gpuI, bytes));
 		HANDLE_ERROR(cudaMemcpy(gpuI, cpuI, bytes, cudaMemcpyHostToDevice));		//copy the image to the gpu
 		stim::gpu_ivote2<T>(gpuI, rmax, x, y, invert, t, iter, phi, conn, debug);				//call the gpu version of the ivote
 		HANDLE_ERROR(cudaMemcpy(cpuI, gpuI, bytes, cudaMemcpyDeviceToHost));		//copy the output to the cpu
+
+		gpu_time = gpuTimer_end();
 	}
 }
 #endif
 \ No newline at end of file
@@ -10,7 +10,7 @@ namespace stim{
 		// this kernel calculates the local maximum for finding the cell centers
 		template<typename T>
-		__global__ void cuda_local_max(T* gpuCenters, T* gpuVote, int conn, int x, int y){
+		__global__ void cuda_local_max(T* gpuCenters, T* gpuVote, int conn, int x,  int y){
 			// calculate the 2D coordinates for this current thread.
 			int xi = blockIdx.x * blockDim.x + threadIdx.x;
@@ -20,16 +20,16 @@ namespace stim{
 				return;
 			// convert 2D coordinates to 1D
-			int i = yi * x + xi;
+		    int i = yi * x + xi;
 			gpuCenters[i] = 0;		//initialize the value at this location to zero
 			T val = gpuVote[i];
-			for(int xl = xi - conn; xl < xi + conn; xl++){
-				for(int yl = yi - conn; yl < yi + conn; yl++){
+			for(unsigned int xl = xi - conn; xl < xi + conn; xl++){
+				for(unsigned int yl = yi - conn; yl < yi + conn; yl++){
 					if(xl >= 0 && xl < x && yl >= 0 && yl < y){
-						int il = yl * x + xl;
+						unsigned int il = yl * x + xl;
 						if(gpuVote[il] > val){							
 							return;
 							}
@@ -47,7 +47,7 @@ namespace stim{
 		}
 		template<typename T>
-		void gpu_local_max(T* gpuCenters, T* gpuVote,  unsigned int conn, size_t x, size_t y){
+		void gpu_local_max(T* gpuCenters, T* gpuVote,  unsigned int conn, unsigned int x, unsigned int y){
 			unsigned int max_threads = stim::maxThreadsPerBlock();
 			/*dim3 threads(max_threads, 1);
@@ -275,10 +275,10 @@ public:
 		int channels = cvImage.channels();
 		allocate(cols, rows, channels);			//allocate space for the image
 		size_t img_bytes = bytes();
-		unsigned char* cv_ptr = (unsigned char*)cvImage.data;
-		//if (C() == 1)														//if this is a single-color image, just copy the data
-		//	type_copy<T, T>(cv_ptr, img, size());
-		memcpy(img, cv_ptr, bytes());
+		unsigned char* cv_ptr = (unsigned char*)cvImage.data;		
+		if (C() == 1)														//if this is a single-color image, just copy the data
+			type_copy<unsigned char, T>(cv_ptr, img, size());
+		//memcpy(img, cv_ptr, bytes());
 		if(C() == 3)														//if this is a 3-color image, OpenCV uses BGR interleaving
 			from_opencv(cv_ptr, X(), Y());
 #else