change the name of mathvec.h to vector.h, fixed a bug in colormap.h

David Mayerich
1 parent 41acaf5d
Showing 4 changed files with 5 additions and 146 deletions Show diff stats
stim/cuda/imageproc/gaussian_blur.cuh
stim/envi/binary.h
stim/math/mathvec.h → stim/math/vector.h
stim/visualization/colormap.h
-#ifndef STIM_CUDA_GAUSSIAN_BLUR_H
-#define STIM_CUDA_GAUSSIAN_BLUR_H
-
-#include <iostream>
-#include <cuda.h>
-#include "gaussian_blur.cuh"
-#include <stim/cuda/devices.h>
-
-#define pi	3.14159
-
-// This CUDA kernel applies a Gaussian blur along the x axis
-template<typename T>
-__global__ void gaussian_blur_x(T* out, T* in, T sigma, unsigned int x, unsigned int y){
-
-	//calculate the 1D image index for this thread
-	int i = blockIdx.x * blockDim.x + threadIdx.x;
-
-	//convert this to 2D pixel coordinates
-	int yi = i / x;
-	int xi = i - (yi * x);
-
-	int k_size = sigma * 4;				//calculate the kernel size
-
-	int gx, gy, gi;								//variables to store global coordinates
-	T sum = 0;								//variable stores the integral of the kernel times the image
-	T G;									//stores the value of the gaussian kernel
-
-	out[i] = 0;
-	//for each element of the kernel
-	for(int ki = -k_size; ki <= k_size; ki++){
-
-		//calculate the gaussian value
-		G = 1.0 / (sigma * sqrt(2 * pi)) * exp(-(ki*ki) / (2*sigma*sigma));
-
-		//calculate the global coordinates for this point in the kernel
-		gx = xi + ki;
-		gy = yi;
-
-		//make sure we are inside the bounds of the image
-		if(gx >= 0 && gy >= 0 && gx < x && gy < y){
-			gi = gy * x + gx;
-
-			//perform the integration
-			sum += G * in[gi];
-		}
-	}
-
-	//set the output value to the integral of the function times the kernel
-	out[i] = sum;
-}
-
-// This CUDA kernel applies a Gaussian blur along the y axis.
-template<typename T>
-__global__ void gaussian_blur_y(T* out, T* in, T sigma, unsigned int x, unsigned int y){
-
-	//calculate the 1D image index for this thread
-	int i = blockIdx.x * blockDim.x + threadIdx.x;
-
-	//convert this to 2D pixel coordinates
-	int yi = i / x;
-	int xi = i - (yi * x);
-
-	int k_size = sigma * 4;				//calculate the kernel size
-
-	int gx, gy, gi;								//variables to store global coordinates
-	T sum = 0;								//variable stores the integral of the kernel times the image
-	T G;									//stores the value of the gaussian kernel
-
-	out[i] = 0;
-	//for each element of the kernel
-	for(int ki = -k_size; ki <= k_size; ki++){
-
-		//calculate the gaussian value
-		G = 1.0 / (sigma * sqrt(2 * pi)) * exp(-(ki*ki) / (2*sigma*sigma));
-
-		//calculate the global coordinates for this point in the kernel
-		gx = xi;
-		gy = yi + ki;
-
-		//make sure we are inside the bounds of the image
-		if(gx >= 0 && gy >= 0 && gx < x && gy < y){
-			gi = gy * x + gx;
-
-			//perform the integration
-			sum += G * in[gi];
-		}
-	}
-
-	//set the output value to the integral of the function times the kernel
-	out[i] = sum;
-}
-
-/// Applies a Gaussian blur to a 2D image stored on the GPU
-template<typename T>
-void gpu_gaussian_blur_2d(T* image, T sigma, unsigned int x, unsigned int y){
-
-	//get the number of pixels in the image
-	unsigned int pixels = x * y;
-	unsigned int bytes = sizeof(T) * pixels;
-
-	//allocate temporary space on the GPU
-	T* gpuI1;
-	cudaMalloc(&gpuI1, bytes);
-
-	//get the maximum number of threads per block for the CUDA device
-	int threads = stim::maxThreadsPerBlock();
-
-	//calculate the number of blocks
-	int blocks = pixels / threads + (pixels%threads == 0 ? 0:1);
-
-	//run the kernel for the x dimension
-	gaussian_blur_x <<< blocks, threads >>>(gpuI1, image, sigma, x, y);
-
-	//run the kernel for the y dimension
-	gaussian_blur_y <<< blocks, threads >>>(image, gpuI1, sigma, x, y);
-
-}
-
-/// Applies a Gaussian blur to a 2D image stored on the CPU
-template<typename T>
-void cpu_gaussian_blur_2d(T* image, T sigma, unsigned int x, unsigned int y){
-
-	//get the number of pixels in the image
-	unsigned int pixels = x * y;
-	unsigned int bytes = sizeof(T) * pixels;
-
-	//allocate space on the GPU
-	T* gpuI0;
-	cudaMalloc(&gpuI0, bytes);
-
-	//copy the image data to the GPU
-	cudaMemcpy(gpuI0, image, bytes, cudaMemcpyHostToDevice);
-
-	//run the GPU-based version of the algorithm
-	gpu_gaussian_blur_2d<T>(gpuI0, sigma, x, y);
-
-	//copy the image data from the device
-	cudaMemcpy(image, gpuI0, bytes, cudaMemcpyDeviceToHost);
-}
-
-#endif
@@ -100,7 +100,7 @@ public:
 	/// @param filename is the name of the binary file
 	/// @param r is a STIM vector specifying the size of the binary file along each dimension
 	/// @param h is the length (in bytes) of any header file (default zero)
-	bool open(std::string filename, vec<unsigned int, D> r, unsigned int h = 0){
+	bool open(std::string filename, vec<unsigned int> r, unsigned int h = 0){
 		for(unsigned int i = 0; i < D; i++)		//set the dimensions of the binary file object
 			R[i] = r[i];
@@ -117,7 +117,7 @@ public:
 	/// @param filename is the name of the binary file to be created
 	/// @param r is a STIM vector specifying the size of the file along each dimension
 	/// @offset specifies how many bytes to offset the file (used to leave room for a header)
-	bool create(std::string filename, vec<unsigned int, D> r, unsigned int offset = 0){
+	bool create(std::string filename, vec<unsigned int> r, unsigned int offset = 0){
 		std::ofstream target(filename.c_str(), std::ios::binary);
@@ -287,7 +287,7 @@ static void cpu2cpu(T* cpuSource, unsigned char* cpuDest, unsigned int nVals, T 
 }
 template<class T>
-static void cpu2cpu(T* cpuSource, unsigned char* cpuDest, unsigned int nVals, colormapType cm = cmGrayscale)//, bool positive = false)
+static void cpu2cpu(T* cpuSource, unsigned char* cpuDest, unsigned int nVals, colormapType cm = cmGrayscale)
 {
     //computes the max and min range automatically
@@ -329,13 +329,13 @@ static void cpu2image(T* cpuSource, std::string fileDest, unsigned int x_size, u
 }
 template<typename T>
-static void cpu2image(T* cpuSource, std::string fileDest, unsigned int x_size, unsigned int y_size, colormapType cm = cmGrayscale, bool positive = false)
+static void cpu2image(T* cpuSource, std::string fileDest, unsigned int x_size, unsigned int y_size, colormapType cm = cmGrayscale)
 {
     //allocate a color buffer
 	unsigned char* cpuBuffer = (unsigned char*) malloc(sizeof(unsigned char) * 3 * x_size * y_size);
 	//do the mapping
-	cpu2cpu<T>(cpuSource, cpuBuffer, x_size * y_size, cm, positive);
+	cpu2cpu<T>(cpuSource, cpuBuffer, x_size * y_size, cm);
 	//copy the buffer to an image
 	buffer2image(cpuBuffer, fileDest, x_size, y_size);