main.cpp
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#include <iostream>
#include <fstream>
#include <cuda_runtime.h>
#include <stim/math/vector.h>
#include <stim/parser/arguments.h>
#include <stim/parser/filename.h>
#include <stim/grids/image_stack.h>
#include <stim/grids/grid.h>
#include <stim/visualization/colormap.h>
#include <stim/image/image.h>
#define pi 3.14159
void ivote3(float* center, float* img, float std[], float anisotropy, float phi, float d_phi, unsigned int r[], int iter, float t, unsigned int conn[],
unsigned int x, unsigned int y, unsigned int z);
void invert_data(float* cpuI, unsigned int x, unsigned int y, unsigned int z){
for(int ix = 0; ix < x; ix++){
for (int iy = 0; iy < y; iy++){
for (int iz = 0; iz < z; iz++){
int idx = iz * x * y + iy * x + ix;
cpuI[idx] = 255 - cpuI[idx];
}
}
}
}
int main(int argc, char** argv){
cudaDeviceProp prop;
int count;
cudaGetDeviceCount(&count);
//printf("cudadevicecount: %i\n", 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);
}
//output advertisement
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;
stim::arglist args;
#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", "positive valu");
args.add("invert", "to invert the input data set", "string");
args.add("anisotropy", "anisotropy value of the imaging", "positive value");
//parse the command line arguments.
args.parse(argc, argv);
//display the help text if requested
if(args["help"].is_set()){
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() < 2){
std::cout<<"ERROR: two files must be specified for segmentation, enter ivote --help for options."<<std::endl<<std::endl;
exit(1);
}
//get the input image file
stim::filename Ifilename(args.arg(0));
//get the output file name
stim::filename OutName(args.arg(1));
//set the x, y, z.
int x = args["x"].as_int();
int y = args["y"].as_int();
int z = args["z"].as_int();
//set the threshold.
float t = args["t"].as_float();
//set the anisotropy
float anisotropy = args["anisotropy"].as_float();
unsigned int rmax = 10 ;
unsigned int r[3] = { rmax, rmax, rmax};
float std = 5;
float sigma[3] = { std, std, std};
unsigned int nlmax = 5;
unsigned int conn[3] = { nlmax, nlmax, nlmax};
float phi_deg = 25.0;
float phi = phi_deg * pi /180;
int iter = 8;
float d_phi = phi/(iter+2);
std::string filename = Ifilename.str();
unsigned int 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(filename, 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("shared2D-v8/inv-128.vol", std::ofstream::out | std::ofstream::binary);
original.write((char*)cpuI, bytes);
original.close();
//allocate space on the cpu for the output result
float* cpu_out = (float*) malloc(bytes);
// call the ivote function
ivote3(cpu_out, cpuI, sigma, anisotropy, phi, d_phi, r, iter, t, conn, x, y, z);
//write the blurred file from the cpuI.
std::ofstream fblur("shared2D-v8/vote8.vol", std::ofstream::out | std::ofstream::binary);
fblur.write((char*)cpuI, bytes);
fblur.close();
/*
stim::image<float>imgrad3;
imgrad3.set_interleaved3(cpu_out, 128,128,128,3);
std::ofstream fgx("syn/gx-128.vol", std::ofstream::out | std::ofstream::binary);
fgx.write((char*)imgrad3.channel(0).data(), bytes);
fgx.close();
*/
//write the output file.
std::ofstream fo("shared2D-v8/" + OutName.str(), 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("shared2D-v8/center.txt");
if (list.is_open()){
for (int ix=0; ix<x; ix++){
for (int iy=0; iy<y; iy++){
for (int iz=0; iz<z; iz++){
int idx = iz * x * y + iy * x + ix;
if (cpu_out[idx]==1){
list << ix << "\t" << iy << "\t"<< iz << '\n' ;
}
}
}
}
list.close();
}
cudaDeviceReset();
}