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>
#define pi	3.14159

//#define M_PI	3.14159
//#include <stim/math/circle.h>
//#include <stim/math/vec3.h>
//#include <stim/math/plane.h>
//#include <stim/math/vector.h>
//#include <stim/visualization/aabb3.h>



/*void test_3(float* gpu_out, float* gpu_grad, float rmax, float phi, int n, int x, int y, int z);

int main(){
	
	int  n=20;
	float rmax;
	float phi_deg;
	float phi;
	rmax=4;
	phi_deg = 15;
	phi = phi_deg * pi/180;
	int x,y,z;
	x=y=z=1;
	unsigned int size = x*y*z*sizeof (float);
	float* cpu_grad = (float*) malloc(3*size);
	float* gpu_grad;
	cudaMalloc(&gpu_grad, 3*size);
	cpu_grad[0]=1;
	cpu_grad[1]=0;
	cpu_grad[2]=-0.5;
	cudaMemcpy(gpu_grad, cpu_grad, 3*size, cudaMemcpyHostToDevice);
	float* cpu_out = (float*) malloc(3*size*(n+1));
	float* gpu_out;
	cudaMalloc(&gpu_out, 3*size*(n+1));
	test_3(gpu_out, gpu_grad, rmax, phi, n, x, y, z);
	cudaMemcpy(cpu_out, gpu_out, 3*size*(n+1), cudaMemcpyDeviceToHost);
	std::ofstream list("circle_check_cuda1.txt");
	if (list.is_open()){
		for (int j=0; j<=n; ++j)
			list << cpu_out[3*j] << '\t' << cpu_out[3*j +1] << '\t' << cpu_out[3*j + 2] << '\n';
	}
	list.close();
	*/
/*
	int main(){


		stim::vec3<float> g(-44,-3.4,-0.005);   // form a vec3 variable for the gradient vector
			stim::vec3<float> g_sph = g.cart2sph();			//convert cartesian coordinate to spherical for the gradient vector
			int n =36;										//set the number of points to find the boundaries of the conical voting area
			int xi = 105;
			int yi = 17;
			int zi = 23;
			float xc = 12 * cos(g_sph[1]) * sin(g_sph[2]);			//calculate the center point of the surface of the voting area for the voter
			float yc = 10 * sin(g_sph[1]) * sin(g_sph[2]) ;
			float zc = 10 * cos(g_sph[2]) ;
			float r = sqrt(xc*xc + yc*yc + zc*zc);
			xc+=xi;
			yc+=yi;
			zc+=zi;
			stim::vec3<float> center(xc,yc,zc);
			
			float d = 2 * r * tan(25*pi/180 );		//find the diameter of the conical voting area
			stim::vec3<float> norm = g.norm();			//compute the normalize gradient vector
			float step = 360.0/(float) n;
			stim::circle<float>  cir(center, d, norm);
			stim::aabb3<int> bb(xi,yi,zi);
			bb.insert(xc,yc,zc);
			for(float j = 0; j <360.0; j += step){
				stim::vec3<float> out = cir.p(j);
				bb.insert(out[0], out[1], out[2]);
			}

			bb.trim_low(0,0,0);
			bb.trim_high(128-1, 128-1, 128-1);

			std::cout<< bb.low[0] << '\t' << bb.low[1] << '\t' << bb.low[2] << '\n';
			std::cout<< bb.high[0] << '\t' << bb.high[1] << '\t' << bb.high[2] << '\n';
			std::cin >> n;
*/
		/*int  n=10;
		stim::circle<float>  cir;
		float* c0= (float*) malloc(3*sizeof(float));
		c0[0] =-4;
		c0[1]=0;
		c0[2] = 3;
		stim::vec3<float> c(c0[0],c0[1],c0[2]);
		float len = c.len();
		stim::vec3<float> norm(c0[0]/len,c0[1]/len,c0[2]/len);
		std::cout<< len << '\n';
		std::cout<< norm << '\n';
		cir.center(c);
		cir.normal(norm);
		cir.scale(2);
		stim::vec3<float> out = cir.p(45);
		std::vector<stim::vec3<float>> out2 = cir.getPoints(n);
	
		std::cout<< out << '\n';
		std::cout <<out[0] << '\t' << out[1] << '\t' << out[2] <<'\n';
		std::cout<< c << '\n';
	
		for (std::vector<stim::vec3<float>>::const_iterator i = out2.begin(); i != out2.end(); ++i)
		std::cout << *i << '\n';
		std::ofstream list("circle_check.txt");
		if (list.is_open()){
			for (std::vector<stim::vec3<float>>::const_iterator j = out2.begin(); j != out2.end(); ++j)
				list << *j << '\n';
		}
		list.close();
		std::cin >> n;

}
*/


void ivote3(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 lmax(float* center, float* vote, float t1, 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", "1");
	//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] = { 12, 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-v1/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);
	ivote3(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.
	//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("shared2D-v8/" + OutName.str(), std::ofstream::out | std::ofstream::binary);
			std::ofstream fo( OutName.str()+std::to_string(t0)+".vol", 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(OutName.str()+std::to_string(t0)+".obj");
		// 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 << "v" << "\t" << ix << "\t" << iy << "\t"<< iz << "\t" << cpu_out[idx] << '\n' ;
					
							}
						}
					}
				}
				list << "p" << "\t";
				for (unsigned int i_nod =1 ; i_nod <=nod; i_nod++){
					list << i_nod << "\t";
				}

		list.close();
		}


	//}
		cudaDeviceReset();       
	
}