segmentation / ivote3

  #include <iostream>

  #include <string>

  #include <fstream>

  #include <cuda_runtime.h>
  #include <stim/math/vector.h>
  #include <stim/parser/arguments.h>
  #include <stim/parser/filename.h>

  #include <stim/visualization/colormap.h>

  #include <stim/image/image.h>

  #include <stim/math/constants.h>

  stim::arglist args;
  int iter;
  unsigned int rmax;
  unsigned int nlmax;
  float t;
  float sigma;
  float phi;
  size_t x, y, z;

  void ivote3(float* img, float std[], float phi, float d_phi, unsigned int r[], int iter, float t, unsigned int conn[],
  	size_t x, size_t y, size_t z);
  void lmax(float* center, float* vote, float t1, unsigned int conn[], size_t x, size_t y, size_t z);
  
  void invert_data(float* cpuI, size_t x, size_t y, size_t z) {
  	size_t idx;
  	for (size_t ix = 0; ix < x; ix++) {
  		for (size_t iy = 0; iy < y; iy++) {
  			for (size_t iz = 0; iz < z; iz++) {
  				idx = iz * x * y + iy * x + ix;
  				cpuI[idx] = 255 - cpuI[idx];

  			}
  		}
  	}

  }
  

  void advertise() {
  	std::cout << std::endl << std::endl;
  	std::cout << "=========================================================================" << std::endl;
  	std::cout << "Thank you for using the ivote3 segmentation tool!" << std::endl;
  	std::cout << "Scalable Tissue Imaging and Modeling (STIM) Lab, University of Houston" << std::endl;
  	std::cout << "Developers: Laila Saadatifard and David Mayerich" << std::endl;
  	std::cout << "Source: https://git.stim.ee.uh.edu/segmentation/ivote3" << std::endl;
  	std::cout << "=========================================================================" << std::endl << std::endl;

  }

  void init_args(int argc, char* argv[]) {

  #ifdef _WIN32
  	args.set_ansi(false);
  #endif
  
  	//add arduments
  	args.add("help", "prints this help");
  	args.add("x", "size of the dataset along X axis", "positive value");
  	args.add("y", "size of the dataset along Y axis", "positive value");
  	args.add("z", "size of the dataset along Z axis", "positive value");

  	args.add("t", "threshold value for the final result", "0", "positive valu");

  	args.add("invert", "to invert the input data set", "string");

  	args.add("rmax", "maximum possible radius of the cells in the input image", "10", "[positive value]");
  	args.add("phi", "starting angle for the vote region (in degrees)", "25.0", "0 <= phi < 180");
  	args.add("iter", "number of iterations for voting", "8", "i > 0");

  	args.add("sigma", "the gaussian blur standard deviation", "3", "s >=0 (s = 0, no blurring)");

  	args.add("conn", "the number of connected neighbors for calculating the local maxima", "5", "[positive value]");

  	//parse the command line arguments.
  	args.parse(argc, argv);
  
  	//display the help text if requested

  	if (args["help"].is_set()) {
  		advertise();
  		std::cout << std::endl << "usage: ivote input_image output_list --option [A B C ...]" << std::endl;
  		std::cout << std::endl << std::endl
  			<< "examples: ivote blue.bmp list.txt " << std::endl;
  
  		std::cout << std::endl << std::endl;
  		std::cout << args.str() << std::endl;

  		exit(1);
  	}
  
  	//if the input and output files aren't specified, throw an error and exit

  	if (args.nargs() < 3) {
  		std::cout << "ERROR: three files must be specified for segmentation, enter ivote --help for options." << std::endl << std::endl;

  		exit(1);
  	}
  

  	//set the x, y, z.
  	x = (size_t)args["x"].as_int();
  	y = (size_t)args["y"].as_int();
  	z = (size_t)args["z"].as_int();
  	iter = args["iter"].as_int();
  	rmax = (unsigned int)args["rmax"].as_int();
  	nlmax = (unsigned int)args["conn"].as_int();
  	t = args["t"].as_float();
  	sigma = args["sigma"].as_float();
  	phi = (float)args["phi"].as_float() * (float)stim::PI / 180;

  }

  int main(int argc, char** argv) {

  	cudaDeviceProp prop;
  	int count;
  	cudaGetDeviceCount(&count);

  	for (int i = 0; i<count; i++) {

  		cudaGetDeviceProperties(&prop, i);
  		printf("current device ID: %d\n", i);
  		printf("device name: %s\n", prop.name);
  		printf("total global mem: %lu\n", prop.totalGlobalMem);
  		printf("shared memory per block: %lu\n", prop.sharedMemPerBlock);
  	}

  	init_args(argc, argv);

  	unsigned int r[3] = { rmax , rmax, rmax };
  
  	float sigma3[3] = { sigma, sigma, sigma };
  	unsigned int conn[3] = { nlmax, nlmax, nlmax };
  	float d_phi = phi / (iter);
  
  	size_t bytes = x*y*z * sizeof(float);

  	//allocate space on the cpu for the input data

  	float* cpuI = (float*)malloc(bytes);

  	//load the input file into the cpuI

  	std::ifstream nissl(args.arg(0), std::ios::in | std::ios::binary);

  	nissl.read((char*)cpuI, bytes);
  	nissl.close();

  	if (args["invert"].is_set())

  		invert_data(cpuI, x, y, z);

  	//write a new file from the cpuI.

  	std::ofstream original("0-inv-128.vol", std::ofstream::out | std::ofstream::binary);

  	original.write((char*)cpuI, bytes);
  	original.close();

  	ivote3(cpuI, sigma3, phi, d_phi, r, iter, t, conn, x, y, z);			// call the ivote function

  
  	std::ofstream fvote("00-vote8_aabb.vol", std::ofstream::out | std::ofstream::binary);

  	fvote.write((char*)cpuI, bytes);
  	fvote.close();

  	//allocate space on the cpu for the output result
  	float* cpu_out = (float*)malloc(bytes * 3);
  

  	//write the output file.

  	//for (int t0=0; t0<=5000; t0+=100){
  	//	float t1 = t0;

  	int t0 = t;
  	lmax(cpu_out, cpuI, t, conn, x, y, z);

  	std::ofstream fo(args.arg(1), std::ofstream::out | std::ofstream::binary);
  	fo.write((char*)cpu_out, bytes);
  	fo.close();
  

  	// creat a file for saving the list centers

  
  	std::ofstream list(args.arg(2));
  	// set the number of detected cells to zero.
  	int nod = 0;
  	if (list.is_open()) {
  
  		for (int iz = 0; iz<z; iz++) {
  			for (int iy = 0; iy<y; iy++) {
  				for (int ix = 0; ix<x; ix++) {
  
  					int idx = iz * x * y + iy * x + ix;
  					if (cpu_out[idx]>0) {
  						nod++;
  						list << ix << " " << iy << " " << iz << " " << cpu_out[idx] << '\n';
  

  					}
  				}

  			}

  		}
  

  		list.close();
  	}
  

  	//}

  	cudaDeviceReset();

  }