Refactor test2

Core/CMakeLists.txt

@@ -98,11 +98,7 @@ include_directories(strain PUBLIC
 )
 
 if(BUILD_TEST)
-  add_executable (tests ${CMAKE_CURRENT_SOURCE_DIR}/tests.cpp )
-  #TARGET_LINK_LIBRARIES (tests cilDVC Eigen3::Eigen)
-  target_link_libraries (tests cildvc_static)
-  include_directories(tests PUBLIC
-  	${CMAKE_CURRENT_SOURCE_DIR} )
+  add_subdirectory(tests)
 endif()
 
 # BKB: commenting out next 2 lines for make of Core to work

Core/tests/CMakeLists.txt

@@ -0,0 +1,20 @@
+add_executable (tests ${CMAKE_CURRENT_SOURCE_DIR}/tests.cpp )
+target_link_libraries (tests cildvc_static)
+include_directories(tests PUBLIC ${CMAKE_SOURCE_DIR}/Core )
+
+add_executable(test1 test_DataCloud.cpp)
+target_link_libraries (test1 cildvc_static)
+include_directories(test1 PUBLIC ${CMAKE_SOURCE_DIR}/Core )
+
+
+install(TARGETS tests test1
+RUNTIME  DESTINATION "${INSTALL_BIN_DIR}" COMPONENT bin
+)
+
+
+message (WARNING "Adding test test1")
+
+add_test(NAME DATACLOUD_test
+           COMMAND test1 datacloud_input.txt
+           WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR})
+

Core/tests/datacloud_input.txt

@@ -0,0 +1,53 @@
+###############################################################################
+#																	
+#
+#		example dvc process control file		
+#
+#
+###############################################################################
+
+# all lines beginning with a # character are ignored
+# some parameters are conditionally required, depending on the setting of other parameters
+# for example, if subvol_thresh is off, the threshold description parameters are not required
+
+### file names
+reference_filename	reference.npy	### reference tomography image volume   
+correlate_filename	correlate.npy	### correlation tomography image volume 
+
+point_cloud_filename	grid_input.roi	### file of search point locations
+output_filename	42kpoints_out	### base name for output files
+
+### description of the image data files, all must be the same size and structure
+
+vol_bit_depth		8			### 8 or 16
+vol_hdr_lngth		96			### fixed-length header size, may be zero
+vol_wide		20			### width in pixels of each slice
+vol_high		30			### height in pixels of each slice
+vol_tall		40			### number of slices in the stack
+
+### parameters defining the subvolumes that will be created at each search point
+
+subvol_geom		sphere			### cube, sphere
+subvol_size		10			### side length or diameter, in voxels
+subvol_npts		8000			### number of points to distribute within the subvol
+
+subvol_thresh		off			### on or off, evaluate subvolumes based on threshold
+#   gray_thresh_min	27			### lower limit of a gray threshold range if subvol_thresh is on
+#   gray_thresh_max	127			### upper limit of a gray threshold range if subvol_thresh is on
+#   min_vol_fract	0.2			### only search if subvol fraction is greater than
+
+### required parameters defining the basic the search process
+
+disp_max		3			### in voxels, used for range checking and global search limits
+num_srch_dof		6			### 3, 6, or 12
+obj_function		znssd			### sad, ssd, zssd, nssd, znssd 
+interp_type		tricubic		### trilinear, tricubic
+
+### optional parameters tuning and refining the search process
+
+rigid_trans		3.0 4.0 0.0		### rigid body offset of target volume, in voxels
+basin_radius		0.0			### coarse-search resolution, in voxels, 0.0 = none
+subvol_aspect		1.0 1.0 1.0		### subvolume aspect ratio
+
+num_points_to_process 10
+

Core/tests/grid_input.roi

@@ -0,0 +1,10 @@
+1	543.814	391.457	630.000
+2	527.698	419.369	630.000
+3	511.583	447.282	630.000
+4	571.821	407.627	630.000
+5	555.706	435.540	630.000
+6	539.590	463.452	630.000
+7	615.944	395.884	630.000
+8	599.829	423.797	630.000
+9	583.713	451.710	630.000
+10	567.598	479.622	630.000

Core/tests/test_DataCloud.cpp

@@ -0,0 +1,167 @@
+#include "dvc.h"
+
+/******************************************************************************/
+void echo_vect_upto(std::vector<double> vect, unsigned int n)
+{
+	std::cout << std::setprecision(6) << std::fixed;
+
+	for (unsigned int i = 0; i<vect.size(); i++)
+		if (i<n) std::cout << vect[i] << "\t";
+
+}
+
+/******************************************************************************/
+int main(int argc, char *argv[])
+{
+	int nProcessors = omp_get_num_procs();
+
+	int OMP_NUM_THREADS = omp_get_max_threads();
+
+	if (omp_get_max_threads() > nProcessors || !OMP_NUM_THREADS)
+	{
+		omp_set_num_threads(nProcessors);
+	}
+
+#pragma omp parallel
+	{
+		if (omp_get_thread_num() == 0)
+		{
+			cout << "Running with threads = " << omp_get_num_threads() << endl;
+		}
+	}
+
+	InputRead in;
+
+	std::string help("help");
+	std::string example("example");
+	std::string manual("manual");
+
+	bool first_point = true;
+
+	// command entered with no arguments
+	if (argc == 1)
+	{
+		std::cout << endl;
+		std::cout << "Options:" << endl;
+		std::cout << "dvc dvc_in\t\t// execute dvc code with dvc_in controlling the run" << endl;
+		std::cout << "dvc help\t\t// provide additional detail about running the dvc code" << endl;
+		std::cout << "dvc example\t\t// print dvc_in_example with brief keyword descriptions" << endl;
+		std::cout << "dvc manual\t\t// print dvc_manual with more detailed information" << endl;
+		std::cout << endl;
+		return 1;
+	}
+
+	// trap help on the command line
+	if (argv[1] == help)
+	{
+		std::cout << endl;
+		std::cout << "Program execution is controlled by a key_word based input file." << endl;
+		std::cout << "Please refer to an example input file for content and format." << endl;
+		std::cout << "To run the code type dvc followed by the name of the input file." << endl;
+		std::cout << "The input file is evaluated and, if all is good, the run starts." << endl;
+		std::cout << "Common problems are incorrect file paths, missing keywords, and invalid parameters." << endl;
+		std::cout << "A message is sent to the console window if an input file problem is encountered." << endl;
+		std::cout << "Progrm execution can be lengthy, on the order of hours for large point clouds." << endl;
+		std::cout << "Results are written to output_filename.disp during execution." << endl;
+		std::cout << "Information about the run is written to output_filename.stat during execution." << endl;
+		std::cout << "Both files are simple text, and can be opened and viewed at any time." << endl;
+		std::cout << endl;
+		return 0;
+	}
+
+	// trap example on the command line
+	if (argv[1] == example)
+	{
+		std::cout << "\ndvc_in_example printed in the current working directory" << endl << endl;
+		std::ofstream dvc_inp("dvc_in_example");
+		in.print_input_example(dvc_inp, "fio_name");
+		in.print_input_example(dvc_inp, "vox_data");
+		in.print_input_example(dvc_inp, "sub_vols");
+		in.print_input_example(dvc_inp, "opt_mthd");
+		in.print_input_example(dvc_inp, "opt_tune");
+		dvc_inp.seekp(0, dvc_inp.beg);
+		dvc_inp.close();
+		return 0;
+	}
+
+	// trap manual on the command line
+	if (argv[1] == manual)
+	{
+		std::cout << "\ndvc_manual printed in the current working directory" << endl << endl;
+		std::ofstream dvc_man("dvc_manual");
+		in.print_manual_intro(dvc_man);
+		in.print_manual_section(dvc_man, "fio_name");
+		in.print_manual_section(dvc_man, "vox_data");
+		in.print_manual_section(dvc_man, "sub_vols");
+		in.print_manual_section(dvc_man, "opt_mthd");
+		in.print_manual_section(dvc_man, "opt_tune");
+		in.print_manual_output(dvc_man);
+		dvc_man.seekp(0, dvc_man.beg);
+		dvc_man.close();
+		return 0;
+	}
+
+	// check to see if the command line argument is an accessible file
+
+	std::string fname(argv[1]);
+	if (!in.input_file_accessible(fname)) return -1;
+
+	// instantiate storage for run control parameters within Utility
+
+	RunControl run;
+
+	// parse and check the input file
+
+	if (!in.input_file_read(&run)) return -2;
+
+	// instantiate a DataCloud
+	// organize_cloud can be lengthy, does (# points)*(# points) sorting
+
+	DataCloud data;
+
+	if (!in.read_point_cloud(&run, data.points, data.labels)) return -3;
+
+	data.organize_cloud(&run);
+
+	std::cout << "Checking results " << std::endl;
+
+	std::vector<std::vector<int>> solution = {};
+	std::vector<int> row = {
+		0, 1, 3, 4, 2, 7, 5, 6, 8, 9,
+		1, 0, 2, 4, 3, 5, 8, 9, 7, 6,
+		2, 1, 5, 4, 0, 9, 3, 8, 7, 6,
+		3, 4, 0, 7, 1, 8, 6, 5, 9, 2,
+		4, 5, 3, 8, 1, 9, 2, 0, 7, 6,
+		5, 4, 2, 9, 8, 1, 3, 0, 7, 6,
+		6, 7, 3, 8, 4, 0, 1, 9, 5, 2,
+		7, 6, 8, 3, 4, 9, 0, 5, 1, 2,
+		8, 9, 7, 4, 5, 3, 6, 1, 2, 0,
+		9, 8, 5, 4, 7, 2, 3, 1, 0, 6 };
+	for (int i = 0; i < 10; i++) {
+		std::vector<int> drow = {};
+		for (int j = 0; j < 10; j++) {
+			drow.push_back(row[i * 10 + j]);
+		}
+	}
+
+	std::ifstream infile("grid_input.roi.sorted");
+	int a, b, c, d, e, f, g, h, l, m;
+	int result = 0, j = 0;
+	while (infile >> a >> b >> c >> d >> e >> f >> g >> h >> l >> m)
+	{
+		std::vector<int> riga = { a,b,c,d,e,f,g,h,l,m};
+		for (int i = 0; i < 10; i++) {
+			//std::cout << "Checking results " << row[i + j* 10] << " " << riga[i] << std::endl;
+			if (row[i + j * 10] != riga[i]) {
+				result++;
+			}
+
+		}
+		j++;
+	}
+
+	std::cout << "Final result is " << result << std::endl;
+
+	return result;
+}
+/******************************************************************************/