updating ivote3 to get input parameters in the arguments

Laila Saadatifard
1 parent ae4cb7e9
Showing 2 changed files with 82 additions and 204 deletions Show diff stats
cpp/cudafunc.cu
cpp/main.cpp
-/*#include "circle_check.cuh"
-
-void test_3(float* gpu_out, float* gpu_grad, float rmax, float phi, int n, int x, int y, int z){
-gpu_test3(gpu_out, gpu_grad, rmax, phi, n, x, y, z);
-}
-*/
-
 #include "gaussian_blur3.cuh"
 #include "gradient3.cuh"
@@ -14,7 +7,7 @@ gpu_test3(gpu_out, gpu_grad, rmax, phi, n, x, y, z);
 #include "local_max3.cuh"
-void ivote3(float* img, float sigma[], float anisotropy, float phi, float d_phi, unsigned int r[],
+void ivote3(float* img, float sigma[], float phi, float d_phi, unsigned int r[],
 			int iter, float t, unsigned int conn[], unsigned int x, unsigned int y, unsigned int z){
@@ -33,7 +26,7 @@ void ivote3(float* img, float sigma[], float anisotropy, float phi, float d_phi,
 	float* gpu_grad;												//assign memory on the gpu for the gradient along the X, y, z.
 	cudaMalloc(&gpu_grad, bytes*3);
-	gpu_gradient3<float>(gpu_grad, gpuI0, anisotropy, x, y, z);				//call the gradient function from the gpu.
+	gpu_gradient3<float>(gpu_grad, gpuI0, 1, x, y, z);				//call the gradient function from the gpu.
 	cudaFree(gpuI0);
 	float* gpu_vote;
@@ -57,9 +50,9 @@ void ivote3(float* img, float sigma[], float anisotropy, float phi, float d_phi,
 	}
-	cudaFree(gpu_grad);	
+	cudaFree(gpu_grad);
 	cudaMemcpy(img, gpu_vote, bytes, cudaMemcpyDeviceToHost);
-
+	
 	//allocate space on the gpu for the final detected cells.
 	//float* gpu_output;
 	//cudaMalloc(&gpu_output, bytes);
@@ -7,123 +7,19 @@
 #include <stim/parser/filename.h>
 #include <stim/visualization/colormap.h>
 #include <stim/image/image.h>
-#define pi	3.14159
+#include <stim/math/constants.h>
-//#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>
+stim::arglist args;
+int iter;
+unsigned int rmax;
+unsigned int nlmax;
+float t;
+float sigma;
+float phi;
+size_t x, y, z;
-
-/*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[], 
+void ivote3(float* img, float std[], 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);
@@ -138,32 +34,20 @@ void invert_data(float* cpuI, unsigned int x, unsigned int y, unsigned int z){
 		}
 	}
-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;
+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;
-	stim::arglist args;
+}
+void init_args(int argc, char* argv[]) {
 #ifdef _WIN32
 	args.set_ansi(false);
 #endif
@@ -175,101 +59,106 @@ int main(int argc, char** argv){
 	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");
+	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", "5", "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()){				
-		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;
+	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() < 2){
-		std::cout<<"ERROR: two files must be specified for segmentation, enter ivote --help for options."<<std::endl<<std::endl;
+	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);
 	}
-	//get the input image file
-	stim::filename Ifilename(args.arg(0));
+	//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){
-	//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();
+	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);
-	//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 r[3] = { rmax  , rmax, rmax};
+	
+	float sigma3[3] = { sigma, sigma, sigma};
 	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);
+	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(filename, std::ios::in | std::ios::binary);
+	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("shared2D-v1/inv-128.vol", std::ofstream::out | std::ofstream::binary);
+	std::ofstream original("0-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();
+	ivote3(cpuI, sigma3, phi, d_phi, r, iter, t, conn, x, y, z);			// call the ivote function
+		
+	std::ofstream fvote("0-vote8.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("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);
+			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(OutName.str()+std::to_string(t0)+".obj");
+		std::ofstream list(args.arg(2));
 		// set the number of detected cells to zero.
 		int nod = 0;
 		if (list.is_open()){
@@ -281,17 +170,13 @@ int main(int argc, char** argv){
 							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 << ix << " " << iy << " "<< iz << " " << cpu_out[idx] << '\n' ;
 							}
 						}
 					}
 				}
-				list << "p" << "\t";
-				for (unsigned int i_nod =1 ; i_nod <=nod; i_nod++){
-					list << i_nod << "\t";
-				}
-
+				
 		list.close();
 		}