WIP: remove qt3support

.gitignore

@@ -10,6 +10,8 @@
 # Precompiled Headers
 *.gch
 *.pch
+*.ipch
+*.bin
 
 # Compiled Dynamic libraries
 *.so

.vscode/.cmaketools.json

@@ -0,0 +1,5 @@
+{
+  "variant": null,
+  "activeEnvironments": [],
+  "codeModel": null
+}

.vscode/c_cpp_properties.json

@@ -0,0 +1,16 @@
+{
+    "configurations": [
+        {
+            "name": "null",
+            "includePath": [],
+            "defines": [],
+            "browse": {
+                "path": [],
+                "limitSymbolsToIncludedHeaders": true,
+                "databaseFilename": ""
+            },
+            "intelliSenseMode": "msvc-x64"
+        }
+    ],
+    "version": 4
+}

CMake/ThirdPartyEigen.cmake

@@ -5,14 +5,14 @@
 # - preprocessor definitions needed by package
 #
 
-#SET(EigenRootDir "" CACHE PATH "Directory containing Eigen/Cholesky")
-#SET(EIGEN_INCLUDE_DIR ${EigenRootDir})
-
 MACRO(USE_EIGEN)
-	find_package (Eigen3 3.3 REQUIRED NO_MODULE)
-
-	#INCLUDE_DIRECTORIES( ${EIGEN_INCLUDE_DIR} )
-	LIST( APPEND MY_EXTERNAL_LINK_LIBRARIES Eigen3::Eigen )
+	FIND_PACKAGE (Eigen3 3.3 REQUIRED QUIET NO_MODULE)
+	IF (Eigen3_FOUND)
+		LIST( APPEND MY_EXTERNAL_LINK_LIBRARIES Eigen3::Eigen )
+	ELSE()
+		FIND_PATH(EIGEN_INCLUDE_DIR NAMES Eigen/Dense Eigen/Dense PATHS /usr/local/include/eigen3)
+		INCLUDE_DIRECTORIES( ${EIGEN_INCLUDE_DIR} )
+	ENDIF()
 ENDMACRO()
 
 # tell Eigen to use MKL BLAS, LAPACK and Intel VML (for vector operations)

Core/ImageWriter.cpp

@@ -13,7 +13,7 @@
 #include "VtkGlue/itkImageToVTKImageFilter.h"
 
 #include "Data/Logger.h"
-#include "Data/SliceHandlerItkWrapper.h"
+#include "Data/SlicesHandlerITKInterface.h"
 #include "Data/Transform.h"
 
 #include <itkCastImageFilter.h>
@@ -30,7 +30,7 @@
 using namespace iseg;
 
 template<typename T>
-bool ImageWriter::writeVolume(const std::string& filename, const std::vector<T*>& all_slices, bool active_slices, const SliceHandlerInterface* handler)
+bool ImageWriter::writeVolume(const std::string& filename, const std::vector<T*>& all_slices, bool active_slices, const SlicesHandlerInterface* handler)
 {
 	unsigned dims[3] = {handler->width(), handler->height(), handler->num_slices()};
 	auto image = wrapToITK(all_slices, dims, handler->start_slice(), handler->end_slice(), handler->spacing(), handler->transform());

Core/ImageWriter.h

@@ -19,7 +19,7 @@
 
 namespace iseg {
 
-class SliceHandlerInterface;
+class SlicesHandlerInterface;
 
 /** \brief Image writer based on ITK image writer factory
 	*/
@@ -29,16 +29,16 @@ class ImageWriter
 	ImageWriter(bool binary = true) : m_Binary(binary) {}
 
 	template<typename T>
-	bool writeVolume(const std::string& filename, const std::vector<T*>& all_slices, bool active_slices, const SliceHandlerInterface* handler);
+	bool writeVolume(const std::string& filename, const std::vector<T*>& all_slices, bool active_slices, const SlicesHandlerInterface* handler);
 
 private:
 	bool m_Binary;
 };
 
 iSegCore_TEMPLATE template ISEG_CORE_API bool ImageWriter::writeVolume<float>(
-	const std::string& filename, const std::vector<float*>& all_slices, bool active_slices, const SliceHandlerInterface* handler);
+	const std::string& filename, const std::vector<float*>& all_slices, bool active_slices, const SlicesHandlerInterface* handler);
 
 iSegCore_TEMPLATE template ISEG_CORE_API bool ImageWriter::writeVolume<tissues_size_t>(
-	const std::string& filename, const std::vector<tissues_size_t*>& all_slices, bool active_slices, const SliceHandlerInterface* handler);
+	const std::string& filename, const std::vector<tissues_size_t*>& all_slices, bool active_slices, const SlicesHandlerInterface* handler);
 
 } // namespace iseg

Core/Morpho.h

@@ -11,7 +11,7 @@
 #pragma once
 
 #include "Data/ItkUtils.h"
-#include "Data/SliceHandlerItkWrapper.h"
+#include "Data/SlicesHandlerITKInterface.h"
 
 #include <itkBinaryDilateImageFilter.h>
 #include <itkBinaryErodeImageFilter.h>
@@ -133,13 +133,13 @@ typename TOutputImage::Pointer
 
 /** \brief Do morpological operation on target image
 */
-void MorphologicalOperation(iseg::SliceHandlerInterface* handler,
+void MorphologicalOperation(iseg::SlicesHandlerInterface* handler,
 		boost::variant<int, float> radius, eOperation operation, bool true3d)
 {
-	iseg::SliceHandlerItkWrapper itkhandler(handler);
+	iseg::SlicesHandlerITKInterface itkhandler(handler);
 	if (true3d)
 	{
-		using input_type = iseg::SliceHandlerItkWrapper::image_ref_type;
+		using input_type = iseg::SlicesHandlerITKInterface::image_ref_type;
 		using output_type = itk::Image<unsigned char, 3>;
 
 		auto target = itkhandler.GetTarget(true); // get active slices

Core/PolyLines.h

@@ -36,8 +36,6 @@ void PolylinesToEdges(const std::vector<std::vector<Index>>& polylines, std::vec
 template<typename Index, typename Tuple>
 void RemoveDuplicateEdges(std::vector<Tuple>& edges);
 
-template<typename TVec3>
-void WritePolylinesToVtk(std::vector<std::vector<TVec3>>& polylines, const std::string& file_name);
 } // namespace iseg
 
 #include "PolyLines.inl"

Core/PolyLines.inl

@@ -1,7 +1,5 @@
 #pragma once
 
-#include <fstream>
-
 namespace iseg {
 
 namespace detail {
@@ -248,61 +246,4 @@ void RemoveDuplicateEdges(std::vector<Tuple>& edges)
 	std::swap(new_edges, edges);
 }
 
-template<typename TVec3>
-void WritePolylinesToVtk(std::vector<std::vector<TVec3>>& polylines, const std::string& file_name)
-{
-	using bit32 = unsigned int;
-	std::vector<std::vector<bit32>> polylines_idx;
-	std::vector<TVec3> points;
-	bit32 point_count = 0;
-	size_t lines_counts = 0;
-	for (auto pline : polylines)
-	{
-		bool is_closed = (pline.front() == pline.back());
-
-		std::vector<bit32> iline;
-		for (size_t i = 0; i < (is_closed ? pline.size() - 1 : pline.size()); i++)
-		{
-			iline.push_back(point_count++);
-			points.push_back(pline[i]);
-		}
-		if (is_closed)
-		{
-			iline.push_back(iline.front());
-		}
-		polylines_idx.push_back(iline);
-		lines_counts += iline.size();
-	}
-
-	const bit32 num_points = (bit32)points.size();
-	const bit32 num_lines = (bit32)polylines_idx.size();
-
-	std::ofstream ofile;
-	ofile.open(file_name.c_str());
-
-	ofile << "# vtk DataFile Version 3.0\n";
-	ofile << "vtk output\n";
-	ofile << "ASCII\n";
-	ofile << "DATASET POLYDATA\n";
-
-	ofile << "POINTS " << num_points << " float\n";
-	for (bit32 i = 0; i < num_points; i++)
-	{
-		auto p = points[i];
-		ofile << p[0] << " " << p[1] << " " << p[2] << "\n";
-	}
-
-	ofile << "LINES " << num_lines << " " << lines_counts + num_lines << "\n";
-	for (bit32 i = 0; i < num_lines; i++)
-	{
-		auto line = polylines_idx[i];
-		ofile << line.size();
-		for (auto id : line)
-			ofile << " " << id;
-		ofile << "\n";
-	}
-
-	ofile.close();
-}
-
 } // namespace iseg

Core/SmoothTissues.cpp

@@ -12,7 +12,7 @@
 #include "SmoothTissues.h"
 
 #include "../Data/ItkUtils.h"
-#include "../Data/SliceHandlerItkWrapper.h"
+#include "../Data/SlicesHandlerITKInterface.h"
 
 #include <itkDiscreteGaussianImageFilter.h>
 #include <itkSignedMaurerDistanceMapImageFilter.h>
@@ -105,14 +105,14 @@ bool _SmoothTissues(TInput* tissues, const std::vector<bool>& locks, double sigm
 	return ok;
 }
 
-bool SmoothTissues(SliceHandlerInterface* handler, size_t start_slice, size_t end_slice, double sigma, bool smooth3d)
+bool SmoothTissues(SlicesHandlerInterface* handler, size_t start_slice, size_t end_slice, double sigma, bool smooth3d)
 {
-	SliceHandlerItkWrapper itkhandler(handler);
+	SlicesHandlerITKInterface itkhandler(handler);
 	auto locks = handler->tissue_locks();
 
 	if (smooth3d)
 	{
-		using label_image_type = SliceHandlerItkWrapper::tissues_ref_type;
+		using label_image_type = SlicesHandlerITKInterface::tissues_ref_type;
 
 		auto tissues = itkhandler.GetTissues(start_slice, end_slice);
 

Core/SmoothTissues.h

@@ -17,8 +17,8 @@
 
 namespace iseg {
 
-class SliceHandlerInterface;
+class SlicesHandlerInterface;
 
-ISEG_CORE_API bool SmoothTissues(SliceHandlerInterface* handler, size_t start_slice, size_t end_slice, double sigma, bool smooth3d);
+ISEG_CORE_API bool SmoothTissues(SlicesHandlerInterface* handler, size_t start_slice, size_t end_slice, double sigma, bool smooth3d);
 
 } // namespace iseg

Core/VotingReplaceLabel.cpp

@@ -14,13 +14,13 @@
 #include "itkLabelVotingBinaryImageFilter.h"
 
 #include "../Data/ItkUtils.h"
-#include "../Data/SliceHandlerItkWrapper.h"
+#include "../Data/SlicesHandlerITKInterface.h"
 
 #include <itkCastImageFilter.h>
 
 namespace iseg {
 
-size_t VotingReplaceLabel(SliceHandlerInterface* handler,
+size_t VotingReplaceLabel(SlicesHandlerInterface* handler,
 		tissues_size_t foreground,
 		tissues_size_t background,
 		std::array<unsigned int, 3> iradius,
@@ -30,10 +30,10 @@ size_t VotingReplaceLabel(SliceHandlerInterface* handler,
 	using image_type = itk::Image<tissues_size_t, 3>;
 	using voting_filter_type = itk::LabelVotingBinaryImageFilter<image_type, image_type>;
 
-	SliceHandlerItkWrapper itkhandler(handler);
+	SlicesHandlerITKInterface itkhandler(handler);
 	auto tissues = itkhandler.GetTissues(true);
 
-	auto cast = itk::CastImageFilter<SliceHandlerItkWrapper::tissues_ref_type, image_type>::New();
+	auto cast = itk::CastImageFilter<SlicesHandlerITKInterface::tissues_ref_type, image_type>::New();
 	cast->SetInput(tissues);
 	cast->Update();
 	auto input = cast->GetOutput();
@@ -83,7 +83,7 @@ size_t VotingReplaceLabel(SliceHandlerInterface* handler,
 	}
 
 	// paste into output
-	iseg::Paste<image_type, SliceHandlerItkWrapper::tissues_ref_type>(output, tissues);
+	iseg::Paste<image_type, SlicesHandlerITKInterface::tissues_ref_type>(output, tissues);
 
 	return number_remaining;
 }

Core/VotingReplaceLabel.h

@@ -17,9 +17,9 @@
 
 namespace iseg {
 
-class SliceHandlerInterface;
+class SlicesHandlerInterface;
 
-ISEG_CORE_API size_t VotingReplaceLabel(SliceHandlerInterface* handler, tissues_size_t foreground, tissues_size_t background,
+ISEG_CORE_API size_t VotingReplaceLabel(SlicesHandlerInterface* handler, tissues_size_t foreground, tissues_size_t background,
 		std::array<unsigned int, 3> iradius, unsigned int majority_threshold, unsigned int max_iterations);
 
 } // namespace iseg

Core/testsuite/test_ImageIO.cpp

@@ -28,7 +28,7 @@ namespace iseg {
 
 namespace {
 
-class TestHandler : public SliceHandlerInterface
+class TestHandler : public SlicesHandlerInterface
 {
 	unsigned short _dims[3];
 	unsigned short _start;

Data/BrushInteraction.cpp

@@ -5,7 +5,7 @@
 
 namespace iseg {
 
-void BrushInteraction::init(iseg::SliceHandlerInterface* handler)
+void BrushInteraction::init(iseg::SlicesHandlerInterface* handler)
 {
 	if (handler == nullptr)
 		throw std::runtime_error("null slice handler");

Data/BrushInteraction.h

@@ -22,7 +22,7 @@ namespace iseg {
 	class ISEG_DATA_API BrushInteraction
 	{
 	public:
-		BrushInteraction(SliceHandlerInterface* handler,
+		BrushInteraction(SlicesHandlerInterface* handler,
 			const boost::function<void(DataSelection)>& begin,
 			const boost::function<void(EndUndoAction)>& end,
 			const boost::function<void(std::vector<Point>*)>& vpdynchanged) 
@@ -34,7 +34,7 @@ namespace iseg {
 		}
 
 		/// throws std::runtime_error if handler is invalid
-		void init(SliceHandlerInterface* handler);
+		void init(SlicesHandlerInterface* handler);
 
 		void set_radius(float radius) { _radius = radius; }
 		void set_brush_target(bool on) { _brush_target = on; }
@@ -54,7 +54,7 @@ namespace iseg {
 		boost::function<void(EndUndoAction)> end_datachange;
 		boost::function<void(std::vector<Point>*)> vpdyn_changed;
 
-		SliceHandlerInterface* _slice_handler;
+		SlicesHandlerInterface* _slice_handler;
 		std::vector<bool> _cached_tissue_locks;
 		unsigned _width;
 		unsigned _height;

Data/CMakeLists.txt

@@ -19,7 +19,7 @@ SET(SOURCES
 	Color.cpp
 	ItkProgressObserver.cpp
 	LogApi.cpp
-	SliceHandlerItkWrapper.cpp
+	SlicesHandlerITKInterface.cpp
 	Transform.cpp
 )