codebase / stimlib

Commit a2c755c88e2930d26bbb3796639e408c1cac1228

Authored by Jiabing Li
1 parent db331d8a

start new network class

Showing 4 changed files with 53 additions and 11 deletions   Show diff stats
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python/network_dpy.py 0 → 100644
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  1 +# -*- coding: utf-8 -*-
  2 +"""
  3 +Created on Sat Jan 19 2018
  4 +
  5 +@author: Jiabing
  6 +"""
  7 +
  8 +import struct
  9 +import numpy as np
  10 +import scipy as sp
  11 +import networkx as nx
  12 +import matplotlib.pyplot as plt
  13 +import math
  14 +
  15 +class Point:
  16 + def __init__(self, x, y, z, radius):
  17 + self.x = x
  18 + self.y = y
  19 + self.z = z
  20 + self.r = radius
  21 +
  22 +
  23 +class Fiber:
  24 + def __init__(self, fiber_idx,point_idx):
  25 + self.fidx = fiber_idx
  26 + self.pidx = point_idx
  27 +
  28 +
  29 +
  30 +class Node:
  31 + def __init__(self, point_idx, fidx):
  32 + self.pidx= point_idx
  33 + self.fidx = fidx
  34 +
  35 +
  36 +#class NWT:
  37 +
  38 +#class network(point, Fiber, Node):
0 39 \ No newline at end of file
... ...
stim/iVote/ivote2.cuh
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... ... @@ -152,13 +152,17 @@ namespace stim {
152 152  
153 153  
154 154 template<typename T>
155   - 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) {
  155 + 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) {
156 156 size_t bytes = x*y * sizeof(T);
157 157 T* gpuI; //allocate space on the gpu to save the input image
  158 +
  159 + gpuTimer_start();
158 160 HANDLE_ERROR(cudaMalloc(&gpuI, bytes));
159 161 HANDLE_ERROR(cudaMemcpy(gpuI, cpuI, bytes, cudaMemcpyHostToDevice)); //copy the image to the gpu
160 162 stim::gpu_ivote2<T>(gpuI, rmax, x, y, invert, t, iter, phi, conn, debug); //call the gpu version of the ivote
161 163 HANDLE_ERROR(cudaMemcpy(cpuI, gpuI, bytes, cudaMemcpyDeviceToHost)); //copy the output to the cpu
  164 +
  165 + gpu_time = gpuTimer_end();
162 166 }
163 167 }
164 168 #endif
165 169 \ No newline at end of file
... ...
stim/iVote/ivote2/local_max.cuh
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... ... @@ -10,7 +10,7 @@ namespace stim{
10 10  
11 11 // this kernel calculates the local maximum for finding the cell centers
12 12 template<typename T>
13   - __global__ void cuda_local_max(T* gpuCenters, T* gpuVote, int conn, int x, int y){
  13 + __global__ void cuda_local_max(T* gpuCenters, T* gpuVote, int conn, int x, int y){
14 14  
15 15 // calculate the 2D coordinates for this current thread.
16 16 int xi = blockIdx.x * blockDim.x + threadIdx.x;
... ... @@ -20,16 +20,16 @@ namespace stim{
20 20 return;
21 21  
22 22 // convert 2D coordinates to 1D
23   - int i = yi * x + xi;
  23 + int i = yi * x + xi;
24 24  
25 25 gpuCenters[i] = 0; //initialize the value at this location to zero
26 26  
27 27 T val = gpuVote[i];
28 28  
29   - for(int xl = xi - conn; xl < xi + conn; xl++){
30   - for(int yl = yi - conn; yl < yi + conn; yl++){
  29 + for(unsigned int xl = xi - conn; xl < xi + conn; xl++){
  30 + for(unsigned int yl = yi - conn; yl < yi + conn; yl++){
31 31 if(xl >= 0 && xl < x && yl >= 0 && yl < y){
32   - int il = yl * x + xl;
  32 + unsigned int il = yl * x + xl;
33 33 if(gpuVote[il] > val){
34 34 return;
35 35 }
... ... @@ -47,7 +47,7 @@ namespace stim{
47 47 }
48 48  
49 49 template<typename T>
50   - void gpu_local_max(T* gpuCenters, T* gpuVote, unsigned int conn, size_t x, size_t y){
  50 + void gpu_local_max(T* gpuCenters, T* gpuVote, unsigned int conn, unsigned int x, unsigned int y){
51 51  
52 52 unsigned int max_threads = stim::maxThreadsPerBlock();
53 53 /*dim3 threads(max_threads, 1);
... ...
stim/image/image.h
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... ... @@ -275,10 +275,10 @@ public:
275 275 int channels = cvImage.channels();
276 276 allocate(cols, rows, channels); //allocate space for the image
277 277 size_t img_bytes = bytes();
278   - unsigned char* cv_ptr = (unsigned char*)cvImage.data;
279   - //if (C() == 1) //if this is a single-color image, just copy the data
280   - // type_copy<T, T>(cv_ptr, img, size());
281   - memcpy(img, cv_ptr, bytes());
  278 + unsigned char* cv_ptr = (unsigned char*)cvImage.data;
  279 + if (C() == 1) //if this is a single-color image, just copy the data
  280 + type_copy<unsigned char, T>(cv_ptr, img, size());
  281 + //memcpy(img, cv_ptr, bytes());
282 282 if(C() == 3) //if this is a 3-color image, OpenCV uses BGR interleaving
283 283 from_opencv(cv_ptr, X(), Y());
284 284 #else
... ...