segmentation / ivote3

  #ifndef STIM_CUDA_VOTE3_H
  #define STIM_CUDA_VOTE3_H
  
  #include <iostream>
  #include <cuda.h>
  #include <stim/cuda/cudatools.h>
  #include <stim/cuda/sharedmem.cuh>
  #include <stim/cuda/cudatools/error.h>

  #include "cpyToshare.cuh"

  
  		// this kernel calculates the vote value by adding up the gradient magnitudes of every voter that this pixel is located in their voting area
  		template<typename T>

  		__global__ void vote3(T* gpu_vote, T* gpu_grad, T cos_phi, int rx, int ry, int rz, int x, int y, int z){

  			extern __shared__ float s[];

  			//calculate x,y,z coordinates for this thread
  			int xi = blockIdx.x * blockDim.x + threadIdx.x;
  			//find the grid size along y
  			int grid_y = y / blockDim.y;
  			int blockidx_y = blockIdx.y % grid_y;
  			int yi = blockidx_y * blockDim.y + threadIdx.y;
  			int zi = blockIdx.y / grid_y;
  			int i = zi * x * y + yi * x + xi;			
  			
  			if(xi>=x || yi>=y || zi>=z) return;
  			

  			//find the starting points and the size of the window, which will be copied to the 2D-shared memory
  			int bxs = blockIdx.x * blockDim.x - rx;
  			int bys = blockidx_y * blockDim.y - ry;
  			int xwidth = 2 * rx + blockDim.x;
  			int ywidth = 2 * ry + blockDim.y;
  			//calculate the starting point of shared memory for storing the magnitude.
  			unsigned int b_s = 3 * xwidth * ywidth;
  			//compute the coordinations of this pixel in the 2D-shared memory.
  			int sx_rx = threadIdx.x + rx;
  			int sy_ry = threadIdx.y + ry;
  

  			// define a local variable to sum the votes from the voters
  			float sum = 0;
  			
  			int rx_sq = rx * rx;
  			int ry_sq = ry * ry;
  			int rz_sq = rz * rz;
  
  			for (int z_v = -rz; z_v<=rz; z_v++){

  				int zi_v = zi + z_v;
  				if ((zi_v) >=0 && (zi_v) <z){
  					//call the function to copy one slide of the gradient from global to the 2D-shared memory.					
  					__syncthreads();
  					cpyG2S2D3ch<float>(s, gpu_grad, bxs, bys, zi + z_v, 3*xwidth, ywidth, threadIdx, blockDim, x, y);
  					__syncthreads();
  					mag_share2D<float>(s, b_s, xwidth, ywidth, threadIdx, blockDim);
  					__syncthreads();
  					float z_sq = z_v * z_v;	
  					float d_z_sq = z_sq/rz_sq;
  
  					for(int y_v = -ry; y_v <= ry; y_v++){

  						int yi_v = (yi + y_v) ;

  						//compute the position of the current voter in the shared memory along the y axis.
  						unsigned int sIdx_y1d = (sy_ry + y_v)* xwidth;
  
  						float y_sq = y_v * y_v;
  						float yz_sq = z_sq + y_sq;
  						float d_yz_sq = y_sq/ry_sq + d_z_sq;
  						for(int x_v = -rx; x_v <= rx; x_v++){
  
  							//check if the current voter is inside of the data-set
  							int xi_v = (xi + x_v) ;
  							if (yi_v >=0 && yi_v < y && xi_v >=0 && xi_v < x){
  
  								//compute the position of the current voter in the 2D-shared memory along the x axis.
  								unsigned int sIdx_x = (sx_rx + x_v);
  								//find the 1D index of this voter in the 2D-shared memory.
  								unsigned int s_Idx = (sIdx_y1d  + sIdx_x);
  								unsigned int s_Idx3 = s_Idx * 3;
  								
  								//save the gradient values for the current voter to the local variables and compute the gradient magnitude.					
  								float g_v_x = s[s_Idx3];
  								float g_v_y = s[s_Idx3 + 1];
  								float g_v_z = s[s_Idx3 + 2];																						
  								float mag_v = s[b_s + s_Idx]; //sqrt( g_v_x * g_v_x + g_v_y * g_v_y + g_v_z * g_v_z);										
  						
  								//calculate the distance between the pixel and the current voter.
  								float x_sq = x_v * x_v;									
  								float d_pv = sqrt(x_sq + yz_sq);

  								// calculate the angle between the pixel and the current voter.
  								float cos_diff = (g_v_x * (-x_v) + g_v_y * (-y_v) + g_v_z * (-z_v))/(d_pv * mag_v);

  								// check if the current voter is located in the voting area of this pixel.
  								if ((((x_sq)/rx_sq + d_yz_sq)<= 1) && (cos_diff >= cos_phi)){

  									sum += mag_v;	
  								}

  							}

  						}	
  					}

  				}
  			}
  						
  			gpu_vote[i] = sum;			
  		}
  
  		template<typename T>

  		void gpu_vote3(T* gpu_vote, T* gpu_grad, T cos_phi, unsigned int r[], unsigned int x, unsigned int y, unsigned int z){

  			unsigned int max_threads = stim::maxThreadsPerBlock();
  			dim3 threads(sqrt (max_threads),sqrt (max_threads));
  			dim3 blocks(x / threads.x + 1, (y / threads.y + 1) * z);

  			unsigned int shared_bytes = (threads.x + 2*r[0])*(threads.y + 2*r[1])*4*sizeof(T);			

  			//call the kernel to do the voting

  			vote3 <T> <<< blocks, threads, shared_bytes >>>(gpu_vote, gpu_grad, cos_phi, r[0], r[1], r[2], x , y, z);

  
  		}
  
  
  		template<typename T>

  		void cpu_vote3(T* cpu_vote, T* cpu_grad, T cos_phi, unsigned int r[], unsigned int x, unsigned int y, unsigned int z){

  
  			//calculate the number of bytes in the array
  			unsigned int bytes = x * y * z * sizeof(T);
  
  			
  			//allocate space on the GPU for the Vote Image
  			T* gpu_vote;
  			cudaMalloc(&gpu_vote, bytes);		
  
  			//allocate space on the GPU for the input Gradient image
  			T* gpu_grad;
  			cudaMalloc(&gpu_grad, bytes*3);
  			

  			//copy the Gradient data to the GPU
  			cudaMemcpy(gpu_grad, cpu_grad, bytes*3, cudaMemcpyHostToDevice);
  			

  			//call the GPU version of the vote calculation function

  			gpu_vote3<T>(gpu_vote, gpu_grad, cos_phi, r, x , y, z);

  							
  			//copy the Vote Data back to the CPU
  			cudaMemcpy(cpu_vote, gpu_vote, bytes, cudaMemcpyDeviceToHost) ;
  
  			//free allocated memory
  			cudaFree(gpu_vote);
  			cudaFree(gpu_grad);

  		}
  
  
  #endif