preparation for paper publication

Author: Joaopmoliveira

applications/medical/CMakeLists.txt

@@ -1,4 +1,5 @@
 add_subdirectory(calibrate_ultrasound)
+add_subdirectory(extract_intersections_ultrasound)
 add_subdirectory(temporal_calibration)
 add_subdirectory(volumetric_reconstruction)
 add_subdirectory(volumetric_path_planing_dicom_capable)

applications/medical/calibrate_ultrasound/main.cpp

@@ -3,6 +3,7 @@
 #include "ceres/ceres.h"
 #include "optimization/WireCalibration.h"
 #include "utils/FileStructures.h"
+#include "utils/DateManipulation.h"
 
 #define STB_IMAGE_IMPLEMENTATION
 #include "CalibratePages.h"
@@ -201,18 +202,22 @@ int main(int argc, char* argv[]) {
 	std::cout << "Final: \n" << transformation_matrix << std::endl;
 	std::cout << "(all units in meters)" << std::endl; 
 
-	auto return_current_time_and_date = [](){
-	    auto now = std::chrono::system_clock::now();
-    	auto in_time_t = std::chrono::system_clock::to_time_t(now);
-
-    	std::stringstream ss;
-    	ss << std::put_time(std::localtime(&in_time_t), "%Y-%m-%d %X");
-   		return ss.str();
-	};
+	std::vector<Eigen::Matrix<double,1,4>> line_parameterization;
+	line_parameterization.resize(number_of_strings);
+	size_t offset = 6; 
+	for(size_t i = 0; i < number_of_strings; ++i, offset += 4){
+		Eigen::Matrix<double,1,4> params_wire_i = Eigen::Matrix<double,1,4>::Zero();
+		std::memcpy(params_wire_i.data(),best_run.initial_guess.data()+offset,4*sizeof(double));
+		std::cout << params_wire_i.transpose() << std::endl;
+		line_parameterization.at(i) = params_wire_i;
+	}
 
 	std::printf("\nRememeber that you always need to\nperform the temporal calibration before attempting the\nspacial calibration! Produced JSON file:\n");
 
-	curan::utilities::UltrasoundCalibrationData calibration{return_current_time_and_date(),transformation_matrix,best_run.summary.final_cost};
+	curan::utilities::UltrasoundCalibrationData calibration{curan::utilities::formated_date<std::chrono::system_clock>(std::chrono::system_clock::now()),
+															transformation_matrix,
+															line_parameterization,
+															best_run.summary.final_cost};
 
 	// write prettified JSON to another file
 	std::ofstream o(CURAN_COPIED_RESOURCE_PATH"/spatial_calibration.json");

applications/medical/extract_intersections_ultrasound/CMakeLists.txt

@@ -0,0 +1,19 @@
+find_package(ITK CONFIG REQUIRED)     
+
+include(${ITK_USE_FILE})
+
+add_executable(Ultrasoundintesection main.cpp 
+MessageProcessing.cpp
+CalibratePages.cpp
+)
+
+target_compile_definitions(Ultrasoundintesection PRIVATE CURAN_COPIED_RESOURCE_PATH="${post_build_resource_path}")
+
+
+target_link_libraries(Ultrasoundintesection PUBLIC
+${ITK_LIBRARIES}
+imageprocessing
+userinterface
+communication
+optimization
+)

applications/medical/extract_intersections_ultrasound/CalibratePages.cpp

@@ -0,0 +1,67 @@
+#include "CalibratePages.h"
+
+curan::ui::Page create_main_page(std::shared_ptr<ProcessingMessage>& processing ,curan::ui::IconResources& resources) {
+	using namespace curan::ui;
+
+	auto igtlink_viewer = OpenIGTLinkViewer::make();
+	igtlink_viewer->set_size(SkRect::MakeWH(0,0));
+	auto igtlink_viewer_pointer = igtlink_viewer.get();
+	uint_least8_t dicom_compliant_conversion[256] = {0 ,30 ,33 ,35 ,37 ,39 ,40 ,41 ,43 ,44 ,45 ,46 ,47 ,48 ,48 ,49 ,50 ,51 ,51 ,52 ,53 ,54 ,55 ,55 ,56 ,57 ,57 ,58 ,59 ,60 ,60 ,61 ,62 ,62 ,63 ,64 ,64 ,65 ,65 ,66 ,67 ,67 ,68 ,69 ,69 ,70 ,71 ,71 ,72 ,73 ,73 ,74 ,75 ,76 ,76 ,77 ,77 ,78 ,79 ,80 ,80 ,80 ,81 ,82 ,83 ,83 ,84 ,84 ,85 ,86 ,86 ,87 ,88 ,88 ,89 ,90 ,90 ,91 ,92 ,93 ,93 ,94 ,95 ,95 ,96 ,96 ,97 ,98 ,98 ,99 ,100 ,101 ,101 ,102 ,103 ,103 ,104 ,105 ,106 ,106 ,107 ,108 ,109 ,109 ,110 ,111 ,111 ,112 ,113 ,113 ,114 ,115 ,116 ,116 ,117 ,118 ,119 ,119 ,120 ,121 ,122 ,123 ,123 ,124 ,125 ,126 ,126 ,127 ,128 ,128 ,129 ,130 ,131 ,132 ,132 ,133 ,134 ,135 ,136 ,136 ,137 ,138 ,139 ,140 ,141 ,141 ,142 ,143 ,144 ,145 ,145 ,146 ,147 ,148 ,149 ,150 ,151 ,151 ,152 ,153 ,154 ,155 ,156 ,157 ,158 ,158 ,159 ,160 ,161 ,162 ,163 ,164 ,164 ,166 ,167 ,167 ,169 ,170 ,170 ,171 ,172 ,173 ,174 ,175 ,176 ,176 ,178 ,178 ,180 ,181 ,182 ,183 ,184 ,184 ,186 ,186 ,188 ,188 ,189 ,191 ,191 ,192 ,194 ,194 ,196 ,197 ,197 ,199 ,200 ,201 ,202 ,203 ,204 ,205 ,207 ,207 ,208 ,209 ,210 ,212 ,213 ,214 ,215 ,216 ,217 ,218 ,220 ,221 ,222 ,223 ,224 ,225 ,226 ,228 ,229 ,230 ,231 ,233 ,234 ,235 ,236 ,238 ,239 ,240 ,241 ,242 ,244 ,245 ,246 ,248 ,249 ,250 ,251 ,253 ,254 ,255};
+
+	auto image_display = ImageDisplay::make();
+	auto image_display_pointer = image_display.get();
+	image_display->set_color_filter(SkColorFilters::Table(dicom_compliant_conversion));
+	igtlink_viewer->set_color_filter(SkColorFilters::Table(dicom_compliant_conversion));
+
+	auto displaycontainer = Container::make(Container::ContainerType::LINEAR_CONTAINER,Container::Arrangement::HORIZONTAL);
+	*displaycontainer << std::move(igtlink_viewer) << std::move(image_display);
+	displaycontainer->set_divisions({ 0.0 , 0.5 , 1.0 });
+
+	processing = std::make_shared<ProcessingMessage>(image_display_pointer,igtlink_viewer_pointer);
+	processing->port = 18944;
+
+	auto start_connection_callback = [processing](Button* button, Press press ,ConfigDraw* config) {
+		if (!processing->connection_status.value()) {
+			processing->pool->submit("connection thread",[processing]() { processing->communicate();});
+		}
+		else {
+			processing->attempt_stop();
+			processing->connection_status.set(false);
+		}
+	};
+
+	auto start_connection = Button::make("Connect",resources);
+	start_connection->set_click_color(SK_ColorGRAY)
+						.set_hover_color(SK_ColorDKGRAY)
+						.set_waiting_color(SK_ColorBLACK)
+						.set_size(SkRect::MakeWH(100, 80));
+	start_connection->add_press_call(start_connection_callback);
+	auto start_connection_pointer = start_connection.get();
+
+	auto record_images = Button::make("Record",resources);
+	record_images->set_click_color(SK_ColorGRAY)
+					.set_hover_color(SK_ColorDKGRAY)
+					.set_waiting_color(SkColorSetARGB(0xFF, 0x00, 0xFF, 0xFF))
+					.set_size(SkRect::MakeWH(100, 80));
+	record_images->add_press_call([processing](Button* button, Press press ,ConfigDraw* config){
+		processing->record_images = !processing->record_images;
+		if(processing->record_images)
+			button->set_waiting_color(SkColorSetARGB(0xF0, 0x00, 0xFF, 0xFF));
+		else
+			button->set_waiting_color(SkColorSetARGB(0xFF, 0x00, 0xFF, 0xFF));
+	});
+	
+
+	auto buttoncontainer = Container::make(Container::ContainerType::LINEAR_CONTAINER,Container::Arrangement::HORIZONTAL);
+	*buttoncontainer << std::move(start_connection) << std::move(record_images);
+	buttoncontainer->set_shader_colors({SkColorSetRGB(225, 225, 225), SkColorSetRGB(246, 246, 246)});
+	processing->button = start_connection_pointer;
+
+	start_connection_pointer->set_waiting_color(SK_ColorRED);
+
+	auto widgetcontainer = Container::make(Container::ContainerType::LINEAR_CONTAINER,Container::Arrangement::VERTICAL);
+	*widgetcontainer << std::move(buttoncontainer) << std::move(displaycontainer);
+	widgetcontainer->set_divisions({ 0.0 , 0.1 , 1.0 });
+
+	return Page{std::move(widgetcontainer),SK_ColorBLACK};
+}

applications/medical/extract_intersections_ultrasound/CalibratePages.h

@@ -0,0 +1,9 @@
+#ifndef CURAN_CALIBRATEPAGES_HEADER_FILE_
+#define CURAN_CALIBRATEPAGES_HEADER_FILE_
+
+#include "MessageProcessing.h"
+#include "userinterface/widgets/IconResources.h"
+
+curan::ui::Page create_main_page(std::shared_ptr<ProcessingMessage>& processing,curan::ui::IconResources& resources);
+
+#endif