ep.patch
weihs (Tobias Weihs)
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	weihs
	Nov 18 2016, 3:01 PM

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ep.patch
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	diff --git a/CMakeLists.txt b/CMakeLists.txt
	index 194301a..1d45a7a 100644
	--- a/CMakeLists.txt
	+++ b/CMakeLists.txt
	@@ -770,6 +770,7 @@ if(WIN32)
	mitkFunctionCheckCompilerFlags("/wd4231" MITK_CXX_FLAGS) # warning C4231: nonstandard extension used : 'extern' before template explicit instantiation
	# the following line should be removed after fixing bug 17637
	mitkFunctionCheckCompilerFlags("/wd4316" MITK_CXX_FLAGS) # warning C4316: object alignment on heap
	+ mitkFunctionCheckCompilerFlags("/wd4180" MITK_CXX_FLAGS) # warning C4316: pragma
	endif()

	if(NOT MSVC_VERSION)
	diff --git a/Modules/AlgorithmsExt/CMakeLists.txt b/Modules/AlgorithmsExt/CMakeLists.txt
	index 9b10f5c..bfc0e5c 100644
	--- a/Modules/AlgorithmsExt/CMakeLists.txt
	+++ b/Modules/AlgorithmsExt/CMakeLists.txt
	@@ -1,7 +1,7 @@
	mitk_create_module(DEPENDS MitkDataTypesExt MitkLegacyGL
	PACKAGE_DEPENDS
	PUBLIC ITK\|ITKThresholding
	- PRIVATE ANN
	+ PUBLIC ANN
	WARNINGS_AS_ERRORS
	)

	diff --git a/Modules/AlgorithmsExt/include/itkIntelligentBinaryClosingFilter.txx b/Modules/AlgorithmsExt/include/itkIntelligentBinaryClosingFilter.txx
	index cd64340..b1d26f3 100644
	--- a/Modules/AlgorithmsExt/include/itkIntelligentBinaryClosingFilter.txx
	+++ b/Modules/AlgorithmsExt/include/itkIntelligentBinaryClosingFilter.txx
	@@ -50,11 +50,12 @@ void IntelligentBinaryClosingFilter<TInputImage, TOutputImage>::GenerateData()

	// set up structuring element for closing
	StructuringElementType seClosing;
	- unsigned long radius[ImageDimension];
	+ StructuringElementType::RadiusType radius;
	const typename InputImageType::SpacingType spacing = input->GetSpacing();
	for (unsigned int d=0; d<ImageDimension; d++)
	{ // closing works in voxel coordinates, so use spacing (and add 0.5 for correct rounding - cast just truncates)
	- radius[d] = (unsigned long)(m_ClosingRadius / spacing[d] + 0.5);
	+ radius[d] = (StructuringElementType::RadiusType::SizeValueType)(
	+ m_ClosingRadius / spacing[d] + 0.5);
	}
	MITK_INFO << " Closing kernel size = [" << radius[0] << ", " << radius[1] << ", " << radius[2] << "]" << std::endl;
	seClosing.SetRadius( radius );
	@@ -79,7 +80,7 @@ void IntelligentBinaryClosingFilter<TInputImage, TOutputImage>::GenerateData()

	// set up structuring element for border voxel detection
	StructuringElementType seBorder;
	- for (auto & radiu : radius) { radiu = 1; }
	+ for (unsigned int d=0; d<ImageDimension; d++) { radius[d] = 1; }
	seBorder.SetRadius( radius );
	seBorder.CreateStructuringElement();

	diff --git a/Modules/AlgorithmsExt/include/mitkBoundingObjectCutter.txx b/Modules/AlgorithmsExt/include/mitkBoundingObjectCutter.txx
	index 39208f2..de8ca85 100644
	--- a/Modules/AlgorithmsExt/include/mitkBoundingObjectCutter.txx
	+++ b/Modules/AlgorithmsExt/include/mitkBoundingObjectCutter.txx
	@@ -54,13 +54,19 @@ void CutImageWithOutputTypeSelect

	// first convert the index
	typename ItkRegionType::IndexType::IndexValueType tmpIndex[3];
	- itk2vtk(cutter->m_InputRequestedRegion.GetIndex(), tmpIndex);
	+ tmpIndex[0] = cutter->m_InputRequestedRegion.GetIndex()[0];
	+ tmpIndex[1] = cutter->m_InputRequestedRegion.GetIndex()[1];
	+ tmpIndex[2] = cutter->m_InputRequestedRegion.GetIndex()[2];
	+ // itk2vtk(cutter->m_InputRequestedRegion.GetIndex(), tmpIndex);
	typename ItkRegionType::IndexType index;
	index.SetIndex(tmpIndex);

	// then convert the size
	typename ItkRegionType::SizeType::SizeValueType tmpSize[3];
	- itk2vtk(cutter->m_InputRequestedRegion.GetSize(), tmpSize);
	+ tmpSize[0] = cutter->m_InputRequestedRegion.GetSize()[0];
	+ tmpSize[1] = cutter->m_InputRequestedRegion.GetSize()[1];
	+ tmpSize[2] = cutter->m_InputRequestedRegion.GetSize()[2];
	+ // itk2vtk(cutter->m_InputRequestedRegion.GetSize(), tmpSize);
	typename ItkRegionType::SizeType size;
	size.SetSize(tmpSize);

	@@ -166,13 +172,19 @@ void CutImageWithOutputTypeSelect

	// first convert the index
	typename ItkRegionType::IndexType::IndexValueType tmpIndex[3];
	- itk2vtk(cutter->m_InputRequestedRegion.GetIndex(), tmpIndex);
	+ tmpIndex[0] = cutter->m_InputRequestedRegion.GetIndex()[0];
	+ tmpIndex[1] = cutter->m_InputRequestedRegion.GetIndex()[1];
	+ tmpIndex[2] = cutter->m_InputRequestedRegion.GetIndex()[2];
	+ // itk2vtk(cutter->m_InputRequestedRegion.GetIndex(), tmpIndex);
	typename ItkRegionType::IndexType index;
	index.SetIndex(tmpIndex);

	// then convert the size
	typename ItkRegionType::SizeType::SizeValueType tmpSize[3];
	- itk2vtk(cutter->m_InputRequestedRegion.GetSize(), tmpSize);
	+ tmpSize[0] = cutter->m_InputRequestedRegion.GetSize()[0];
	+ tmpSize[1] = cutter->m_InputRequestedRegion.GetSize()[1];
	+ tmpSize[2] = cutter->m_InputRequestedRegion.GetSize()[2];
	+ // itk2vtk(cutter->m_InputRequestedRegion.GetSize(), tmpSize);
	typename ItkRegionType::SizeType size;
	size.SetSize(tmpSize);

	diff --git a/Modules/AlgorithmsExt/src/mitkPadImageFilter.cpp b/Modules/AlgorithmsExt/src/mitkPadImageFilter.cpp
	index 8c1f134..4738234 100644
	--- a/Modules/AlgorithmsExt/src/mitkPadImageFilter.cpp
	+++ b/Modules/AlgorithmsExt/src/mitkPadImageFilter.cpp
	@@ -54,9 +54,11 @@ void mitk::PadImageFilter::GenerateData()
	mitk::BaseGeometry *referenceImageGeometry = referenceImage->GetGeometry();
	mitk::Point3D referenceOrigin = referenceImageGeometry->GetOrigin();

	+ typedef itk::ConstantPadImageFilter<ImageType, ImageType> PadFilterType;
	+
	double outputOrigin[3];
	- unsigned long padLowerBound[3];
	- unsigned long padUpperBound[3];
	+ PadFilterType::SizeValueType padLowerBound[3];
	+ PadFilterType::SizeValueType padUpperBound[3];

	int i;
	for ( i = 0; i < 3; ++i )
	@@ -75,7 +77,7 @@ void mitk::PadImageFilter::GenerateData()
	itkImage->SetOrigin( outputOrigin );


	- typedef itk::ConstantPadImageFilter< ImageType, ImageType > PadFilterType;
	+
	PadFilterType::Pointer padFilter = PadFilterType::New();
	padFilter->SetInput( itkImage );
	padFilter->SetConstant( m_PadConstant );
	diff --git a/Modules/Core/CMakeLists.txt b/Modules/Core/CMakeLists.txt
	index 1fb91eb..97e27a2 100644
	--- a/Modules/Core/CMakeLists.txt
	+++ b/Modules/Core/CMakeLists.txt
	@@ -13,12 +13,12 @@ MITK_CREATE_MODULE(
	PACKAGE_DEPENDS
	PRIVATE tinyxml OpenGL
	# Remove public GDCM and ITKIOGDCM dependency after mitkDicomSeriesReader was removed
	- PUBLIC GDCM ITK\|ITKIOGDCM
	- PUBLIC ITK\|ITKTransform+ITKImageGrid+ITKImageFeature
	+ PUBLIC GDCM
	+ PUBLIC ITK\|ITKTransform+ITKImageGrid+ITKImageFeature+ITKIOImageBase+ITKIOGDCM+ITKIOHDF5+ITKIOLSM+ITKIOMRC+ITKIOBioRad+ITKIOGE+ITKIOStimulate
	# We privately use/link all ITK modules in order to support all IO, Transform, etc.
	# factories from ITK which are registered "automatically" via a factory manager.
	PRIVATE ITK
	- PUBLIC VTK\|vtkFiltersTexture+vtkFiltersParallel+vtkImagingStencil+vtkImagingMath+vtkInteractionStyle+vtkRenderingOpenGL+vtkRenderingVolumeOpenGL+vtkRenderingFreeTypeOpenGL+vtkRenderingLabel+vtkInteractionWidgets+vtkIOGeometry+vtkIOXML
	+ PUBLIC VTK\|vtkFiltersTexture+vtkFiltersParallel+vtkImagingStencil+vtkImagingMath+vtkInteractionStyle+vtkRenderingOpenGL+vtkRenderingVolumeOpenGL+vtkRenderingFreeType+vtkRenderingLabel+vtkInteractionWidgets+vtkIOGeometry+vtkIOXML
	WARNINGS_AS_ERRORS
	SUBPROJECTS MITK-Core
	# Do not automatically create CppMicroServices initialization code.
	diff --git a/Modules/Core/TestingHelper/CMakeLists.txt b/Modules/Core/TestingHelper/CMakeLists.txt
	index a922e7a..1a42316 100644
	--- a/Modules/Core/TestingHelper/CMakeLists.txt
	+++ b/Modules/Core/TestingHelper/CMakeLists.txt
	@@ -2,7 +2,7 @@ mitk_create_module(
	DEPENDS PUBLIC MitkCore
	PACKAGE_DEPENDS
	PUBLIC CppUnit
	- PRIVATE VTK\|vtkTestingRendering tinyxml
	+ PRIVATE VTK\|vtkTestingRendering tinyxml OpenGL
	WARNINGS_AS_ERRORS
	)

	diff --git a/Modules/Core/include/itkImportMitkImageContainer.h b/Modules/Core/include/itkImportMitkImageContainer.h
	index 9a35460..f1b4f35 100644
	--- a/Modules/Core/include/itkImportMitkImageContainer.h
	+++ b/Modules/Core/include/itkImportMitkImageContainer.h
	@@ -95,8 +95,8 @@ private:
	//# include "Templates/itkImportMitkImageContainer+-.h"
	//#endif

	-#if ITK_TEMPLATE_TXX
	+//#if ITK_MANUAL_INSTANTIATION
	# include "itkImportMitkImageContainer.txx"
	-#endif
	+//#endif

	#endif
	diff --git a/Modules/Core/include/mitkBaseRenderer.h b/Modules/Core/include/mitkBaseRenderer.h
	index 679a9c7..dbb6e13 100644
	--- a/Modules/Core/include/mitkBaseRenderer.h
	+++ b/Modules/Core/include/mitkBaseRenderer.h
	@@ -95,9 +95,13 @@ namespace mitk
	static BaseRenderer* GetByName(const std::string& name);
	static vtkRenderWindow* GetRenderWindowByName(const std::string& name);

	+#if defined __GNUC__
	#pragma GCC visibility push(default)
	+#endif
	itkEventMacro( RendererResetEvent, itk::AnyEvent );
	+#if defined __GNUC__
	#pragma GCC visibility pop
	+#endif

	/** Standard class typedefs. */
	mitkClassMacroItkParent(BaseRenderer, itk::Object);
	diff --git a/Modules/Core/include/mitkImageToItk.txx b/Modules/Core/include/mitkImageToItk.txx
	index 77ae640..3c368e2 100644
	--- a/Modules/Core/include/mitkImageToItk.txx
	+++ b/Modules/Core/include/mitkImageToItk.txx
	@@ -155,7 +155,7 @@ template<class TOutputImage>
	else
	{
	itkDebugMacro("do not copyMem ...");
	- typedef itk::ImportMitkImageContainer< unsigned long, InternalPixelType > ImportContainerType;
	+ typedef itk::ImportMitkImageContainer< std::uint64_t, InternalPixelType > ImportContainerType;
	typename ImportContainerType::Pointer import;

	import = ImportContainerType::New();
	diff --git a/Modules/Core/include/mitkReferenceCountWatcher.h b/Modules/Core/include/mitkReferenceCountWatcher.h
	index 52daa6d..3386309 100644
	--- a/Modules/Core/include/mitkReferenceCountWatcher.h
	+++ b/Modules/Core/include/mitkReferenceCountWatcher.h
	@@ -69,9 +69,7 @@ public:
	m_DeleteCommand->SetCallbackFunction(this, &ReferenceCountWatcher::DeleteObserver);
	if(m_Object!=NULL)
	m_ObserverTag = m_Object->AddObserver(itk::DeleteEvent(), m_DeleteCommand);
	- m_ReferenceCountLock.Lock();
	m_ReferenceCount = 0;
	- m_ReferenceCountLock.Unlock();
	}
	//##Documentation
	//## @brief Destructor: remove observer
	diff --git a/Modules/Core/include/mitkRenderingManager.h b/Modules/Core/include/mitkRenderingManager.h
	index d7e6d3e..aee9925 100644
	--- a/Modules/Core/include/mitkRenderingManager.h
	+++ b/Modules/Core/include/mitkRenderingManager.h
	@@ -366,12 +366,16 @@ private:
	vtkRenderWindow* m_FocusedRenderWindow;
	};

	+#if defined __GNUC__
	#pragma GCC visibility push(default)
	+#endif

	itkEventMacro( RenderingManagerEvent, itk::AnyEvent );
	itkEventMacro( RenderingManagerViewsInitializedEvent, RenderingManagerEvent );

	+#if defined __GNUC__
	#pragma GCC visibility pop
	+#endif

	/**
	* Generic RenderingManager implementation for "non-rendering-plattform",
	diff --git a/Modules/Core/include/mitkSliceNavigationController.h b/Modules/Core/include/mitkSliceNavigationController.h
	index b0ce92b..832a589 100644
	--- a/Modules/Core/include/mitkSliceNavigationController.h
	+++ b/Modules/Core/include/mitkSliceNavigationController.h
	@@ -23,9 +23,13 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include "mitkRenderingManager.h"
	#include "mitkTimeGeometry.h"
	#include "mitkMessage.h"
	+#if defined __GNUC__
	#pragma GCC visibility push(default)
	+#endif
	#include <itkEventObject.h>
	+#if defined __GNUC__
	#pragma GCC visibility pop
	+#endif
	#include <itkCommand.h>
	#include <sstream>
	#include "mitkRestorePlanePositionOperation.h"
	@@ -291,9 +295,13 @@ class MITKCORE_EXPORT SliceNavigationController : public BaseController
	itkSetObjectMacro(RenderingManager, RenderingManager);
	mitk::RenderingManager* GetRenderingManager() const;

	- #pragma GCC visibility push(default)
	+#if defined __GNUC__
	+#pragma GCC visibility push(default)
	+#endif
	itkEventMacro( UpdateEvent, itk::AnyEvent );
	- #pragma GCC visibility pop
	+#if defined __GNUC__
	+#pragma GCC visibility pop
	+#endif

	class MITKCORE_EXPORT TimeGeometryEvent : public itk::AnyEvent
	{
	diff --git a/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp b/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp
	index f3c68c4..6db5ba8 100644
	--- a/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp
	+++ b/Modules/Core/src/DataManagement/mitkAbstractTransformGeometry.cpp
	@@ -100,7 +100,7 @@ bool mitk::AbstractTransformGeometry::Project(const mitk::Point3D & atPt3d_mm, c
	assert(this->IsBoundingBoxNull() == false);

	Vector3D vec3d_units;
	- vec3d_units = GetIndexToWorldTransform()->GetInverseMatrix() * vec3d_mm;
	+ //vec3d_units = GetIndexToWorldTransform()->GetInverseMatrix() * vec3d_mm;
	vec3d_units[2] = 0;
	projectedVec3d_mm = GetIndexToWorldTransform()->TransformVector(vec3d_units);

	@@ -115,8 +115,8 @@ bool mitk::AbstractTransformGeometry::Project(const mitk::Point3D & atPt3d_mm, c
	{
	pt3d_units[i] = 0.0;

	- for (j = 0; j < 3; ++j)
	- pt3d_units[i] += GetIndexToWorldTransform()->GetInverseMatrix()[i][j] * temp[j];
	+ //for (j = 0; j < 3; ++j)
	+ // pt3d_units[i] += GetIndexToWorldTransform()->GetInverseMatrix()[i][j] * temp[j];
	}

	return const_cast<BoundingBox*>(this->GetBoundingBox())->IsInside(pt3d_units);
	diff --git a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp
	index 3a159ae..80437d6 100644
	--- a/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp
	+++ b/Modules/Core/src/DataManagement/mitkBaseGeometry.cpp
	@@ -733,10 +733,10 @@ void mitk::BaseGeometry::PrintSelf(std::ostream& os, itk::Indent indent) const
	for (i = 0; i < 3; i++)
	{
	os << indent.GetNextIndent();
	- for (j = 0; j < 3; j++)
	- {
	- os << this->GetIndexToWorldTransform()->GetInverseMatrix()[i][j] << " ";
	- }
	+ //for (j = 0; j < 3; j++)
	+ //{
	+ // os << this->GetIndexToWorldTransform()->GetInverseMatrix()[i][j] << " ";
	+ //}
	os << std::endl;
	}

	diff --git a/Modules/Core/src/DataManagement/mitkImage.cpp b/Modules/Core/src/DataManagement/mitkImage.cpp
	index b2b18b5..84c692b 100644
	--- a/Modules/Core/src/DataManagement/mitkImage.cpp
	+++ b/Modules/Core/src/DataManagement/mitkImage.cpp
	@@ -80,18 +80,11 @@ mitk::Image::Image(const Image &other) : SlicedData(other), m_Dimension(0), m_Di

	mitk::Image::~Image()
	{
	- Clear();
	- m_ReferenceCountLock.Lock();
	+ this->Clear();
	m_ReferenceCount = 3;
	- m_ReferenceCountLock.Unlock();
	- m_ReferenceCountLock.Lock();
	m_ReferenceCount = 0;
	- m_ReferenceCountLock.Unlock();
	- if(m_OffsetTable != nullptr)
	- delete [] m_OffsetTable;
	-
	- if(m_ImageStatistics != nullptr)
	- delete m_ImageStatistics;
	+ delete[] m_OffsetTable;
	+ delete m_ImageStatistics;
	}

	const mitk::PixelType mitk::Image::GetPixelType(int n) const
	diff --git a/Modules/Core/src/DataManagement/mitkImageDataItem.cpp b/Modules/Core/src/DataManagement/mitkImageDataItem.cpp
	index 8e3725f..764ac27 100644
	--- a/Modules/Core/src/DataManagement/mitkImageDataItem.cpp
	+++ b/Modules/Core/src/DataManagement/mitkImageDataItem.cpp
	@@ -67,9 +67,7 @@ mitk::ImageDataItem::ImageDataItem(const ImageDataItem& aParent, const mitk::Ima
	delete [] (unsigned char*) data;
	}
	}
	- m_ReferenceCountLock.Lock();
	m_ReferenceCount = 0;
	- m_ReferenceCountLock.Unlock();
	}

	mitk::ImageDataItem::~ImageDataItem()
	@@ -127,9 +125,7 @@ mitk::ImageDataItem::ImageDataItem(const mitk::ImageDescriptor::Pointer desc, in
	m_ManageMemory = true;
	}

	- m_ReferenceCountLock.Lock();
	m_ReferenceCount = 0;
	- m_ReferenceCountLock.Unlock();

	}

	@@ -162,9 +158,7 @@ mitk::ImageDataItem::ImageDataItem(const mitk::PixelType& type, int timestep,
	m_ManageMemory = true;
	}

	- m_ReferenceCountLock.Lock();
	m_ReferenceCount = 0;
	- m_ReferenceCountLock.Unlock();
	}

	mitk::ImageDataItem::ImageDataItem(const ImageDataItem &other)
	diff --git a/Modules/Core/src/Rendering/vtkMitkThickSlicesFilter.cpp b/Modules/Core/src/Rendering/vtkMitkThickSlicesFilter.cpp
	index b6d7f97..83e0145 100644
	--- a/Modules/Core/src/Rendering/vtkMitkThickSlicesFilter.cpp
	+++ b/Modules/Core/src/Rendering/vtkMitkThickSlicesFilter.cpp
	@@ -25,7 +25,7 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include "vtkStreamingDemandDrivenPipeline.h"

	#include <math.h>
	-#include <vtksys/ios/sstream>
	+#include <sstream>

	vtkStandardNewMacro(vtkMitkThickSlicesFilter);

	@@ -356,7 +356,7 @@ int vtkMitkThickSlicesFilter::RequestData(
	}
	vtkImageData* output = vtkImageData::GetData(outputVector);
	vtkDataArray* outArray = output->GetPointData()->GetScalars();
	- vtksys_ios::ostringstream newname;
	+ std::ostringstream newname;
	newname << (outArray->GetName()?outArray->GetName():"")
	<< "Gradient";
	outArray->SetName(newname.str().c_str());
	diff --git a/Modules/Core/test/mitkGeometry3DTest.cpp b/Modules/Core/test/mitkGeometry3DTest.cpp
	index 286bbcf..ea4c388 100644
	--- a/Modules/Core/test/mitkGeometry3DTest.cpp
	+++ b/Modules/Core/test/mitkGeometry3DTest.cpp
	@@ -17,7 +17,7 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include "mitkGeometry3D.h"

	#include <vnl/vnl_quaternion.h>
	-#include <vnl/vnl_quaternion.txx>
	+#include <vnl/vnl_quaternion.hxx>

	#include "mitkRotationOperation.h"
	#include "mitkInteractionConst.h"
	diff --git a/Modules/Core/test/mitkGeometryDataIOTest.cpp b/Modules/Core/test/mitkGeometryDataIOTest.cpp
	index 1417fb6..f078e83 100644
	--- a/Modules/Core/test/mitkGeometryDataIOTest.cpp
	+++ b/Modules/Core/test/mitkGeometryDataIOTest.cpp
	@@ -219,7 +219,8 @@ public:
	{
	for ( int j = 0; j != 4; ++j )
	{
	- (*vtk_matrix)[i][j] = t + (i + j) / 8.0; // just insignificant values
	+ //(*vtk_matrix)[i][j] = t + (i + j) / 8.0; // just insignificant values
	+ vtk_matrix->SetElement( i, j, t + ( i + j ) / 8.0 );
	}
	}

	diff --git a/Modules/Core/test/mitkPlaneGeometryTest.cpp b/Modules/Core/test/mitkPlaneGeometryTest.cpp
	index e467070..fe72d03 100644
	--- a/Modules/Core/test/mitkPlaneGeometryTest.cpp
	+++ b/Modules/Core/test/mitkPlaneGeometryTest.cpp
	@@ -26,7 +26,7 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include <mitkTestFixture.h>

	#include <vnl/vnl_quaternion.h>
	-#include <vnl/vnl_quaternion.txx>
	+#include <vnl/vnl_quaternion.hxx>

	#include <fstream>
	#include <iomanip>
	diff --git a/Modules/Core/test/mitkSliceNavigationControllerTest.cpp b/Modules/Core/test/mitkSliceNavigationControllerTest.cpp
	index 6541f21..94fb0b4 100644
	--- a/Modules/Core/test/mitkSliceNavigationControllerTest.cpp
	+++ b/Modules/Core/test/mitkSliceNavigationControllerTest.cpp
	@@ -27,7 +27,7 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include "usServiceReference.h"

	#include <vnl/vnl_quaternion.h>
	-#include <vnl/vnl_quaternion.txx>
	+#include <vnl/vnl_quaternion.hxx>

	#include <fstream>

	diff --git a/Modules/Core/test/mitkSlicedGeometry3DTest.cpp b/Modules/Core/test/mitkSlicedGeometry3DTest.cpp
	index 2e43cb9..b9bab67 100644
	--- a/Modules/Core/test/mitkSlicedGeometry3DTest.cpp
	+++ b/Modules/Core/test/mitkSlicedGeometry3DTest.cpp
	@@ -21,7 +21,7 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include "mitkTestingMacros.h"

	#include <vnl/vnl_quaternion.h>
	-#include <vnl/vnl_quaternion.txx>
	+#include <vnl/vnl_quaternion.hxx>

	#include <fstream>

	diff --git a/Modules/Core/test/mitkVectorTest.cpp b/Modules/Core/test/mitkVectorTest.cpp
	index e91de13..fcfe368 100644
	--- a/Modules/Core/test/mitkVectorTest.cpp
	+++ b/Modules/Core/test/mitkVectorTest.cpp
	@@ -17,7 +17,7 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include <mitkTestingMacros.h>
	#include <mitkNumericTypes.h>

	-#include <vnl/vnl_vector_fixed.txx>
	+#include <vnl/vnl_vector_fixed.hxx>

	int mitkVectorTest(int /argc/, char* /argv/[])
	{
	diff --git a/Modules/CppMicroServices/CMakeLists.txt b/Modules/CppMicroServices/CMakeLists.txt
	index 9427072..2ea4019 100644
	--- a/Modules/CppMicroServices/CMakeLists.txt
	+++ b/Modules/CppMicroServices/CMakeLists.txt
	@@ -227,7 +227,7 @@ if(CMAKE_COMPILER_IS_GNUCXX)
	endif()

	if(MSVC)
	- set(US_CXX_FLAGS "/MP /WX /wd4996 /wd4251 /wd4503 ${US_CXX_FLAGS}")
	+ set(US_CXX_FLAGS "/MP /WX /wd4180 /wd4996 /wd4251 /wd4503 ${US_CXX_FLAGS}")
	endif()

	set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${US_CXX_FLAGS}")
	diff --git a/Modules/DICOMReader/src/mitkDICOMITKSeriesGDCMReader.cpp b/Modules/DICOMReader/src/mitkDICOMITKSeriesGDCMReader.cpp
	index 6c56d55..56e2a31 100644
	--- a/Modules/DICOMReader/src/mitkDICOMITKSeriesGDCMReader.cpp
	+++ b/Modules/DICOMReader/src/mitkDICOMITKSeriesGDCMReader.cpp
	@@ -15,7 +15,7 @@ See LICENSE.txt or http://www.mitk.org for details.
	===================================================================*/

	//#define MBILOG_ENABLE_DEBUG
	-#define ENABLE_TIMING
	+//#define ENABLE_TIMING

	#include <itkTimeProbesCollectorBase.h>
	#include <gdcmUIDs.h>
	@@ -598,6 +598,12 @@ void mitk::DICOMITKSeriesGDCMReader::EnsureMandatorySortersArePresent(
	splitter->AddDistinguishingTag( DICOMTag(0x0020, 0x0037), new mitk::DICOMTagBasedSorter::CutDecimalPlaces(decimalPlacesForOrientation) ); // Image Orientation (Patient)
	splitter->AddDistinguishingTag( DICOMTag(0x0018, 0x0050) ); // Slice Thickness
	splitter->AddDistinguishingTag( DICOMTag(0x0028, 0x0008) ); // Number of Frames
	+
	+ splitter->AddDistinguishingTag( DICOMTag(0x0028, 0x0100) ); // Bits Allocated
	+ splitter->AddDistinguishingTag( DICOMTag(0x0028, 0x0103) ); // Pixel Representation
	+ splitter->AddDistinguishingTag( DICOMTag(0x0028, 0x0002) ); // Samples per Pixel
	+ splitter->AddDistinguishingTag( DICOMTag(0x0028, 0x0004) ); // Photometric Interpretation
	+
	this->AddSortingElement( splitter, true ); // true = at front

	if ( m_EquiDistantBlocksSorter.IsNull() )
	diff --git a/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp b/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp
	index bfb36fc..7425668 100644
	--- a/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp
	+++ b/Modules/ImageStatistics/mitkImageStatisticsCalculator.cpp
	@@ -1341,7 +1341,8 @@ namespace mitk
	// Make sure that the voxels of mask and image are correctly "aligned", i.e., voxel boundaries are the same in both images
	PointType imageOrigin = image->GetOrigin();
	PointType maskOrigin = maskImage->GetOrigin();
	- long offset[ImageType::ImageDimension];
	+
	+ ChangeInformationFilterType::OutputImageOffsetType offset;

	typedef itk::ContinuousIndex<double, VImageDimension> ContinousIndexType;
	ContinousIndexType maskOriginContinousIndex, imageOriginContinousIndex;
	@@ -1662,7 +1663,7 @@ namespace mitk
	bool keepDistanceToImageBorders( neccessaryDistanceToImageBorderInMM > 0 );
	if (keepDistanceToImageBorders)
	{
	- long distanceInPixels[VImageDimension];
	+ ImageType::RegionType::SizeType distanceInPixels;
	for(unsigned short dimension = 0; dimension < VImageDimension; ++dimension)
	{
	// To confirm that the whole hotspot is inside the image we have to keep a specific distance to the image-borders, which is as long as
	diff --git a/Modules/LegacyGL/CMakeLists.txt b/Modules/LegacyGL/CMakeLists.txt
	index d46b6d6..6cad39c 100644
	--- a/Modules/LegacyGL/CMakeLists.txt
	+++ b/Modules/LegacyGL/CMakeLists.txt
	@@ -2,6 +2,6 @@

	MITK_CREATE_MODULE(
	DEPENDS MitkCore
	- PACKAGE_DEPENDS
	+ PACKAGE_DEPENDS PUBLIC OpenGL
	DEPRECATED_SINCE 2015_05
	)
	diff --git a/Modules/PlanarFigure/include/mitkPlanarFigureInteractor.h b/Modules/PlanarFigure/include/mitkPlanarFigureInteractor.h
	index d93f72b..22e3e29 100644
	--- a/Modules/PlanarFigure/include/mitkPlanarFigureInteractor.h
	+++ b/Modules/PlanarFigure/include/mitkPlanarFigureInteractor.h
	@@ -24,9 +24,13 @@ See LICENSE.txt or http://www.mitk.org for details.
	#include "mitkNumericTypes.h"
	#include "mitkDataInteractor.h"

	+#if defined __GNUC__
	#pragma GCC visibility push(default)
	+#endif
	#include <itkEventObject.h>
	+#if defined __GNUC__
	#pragma GCC visibility pop
	+#endif

	namespace mitk
	{
	@@ -39,7 +43,9 @@ class BaseRenderer;
	class InteractionPositionEvent;
	class StateMachineAction;

	+#if defined __GNUC__
	#pragma GCC visibility push(default)
	+#endif

	// Define events for PlanarFigure interaction notifications
	itkEventMacro( PlanarFigureEvent, itk::AnyEvent );
	@@ -52,7 +58,9 @@ itkEventMacro( StartHoverPlanarFigureEvent, PlanarFigureEvent );
	itkEventMacro( EndHoverPlanarFigureEvent, PlanarFigureEvent );
	itkEventMacro( ContextMenuPlanarFigureEvent, PlanarFigureEvent );

	+#if defined __GNUC__
	#pragma GCC visibility pop
	+#endif


	/**
	diff --git a/Modules/PlanarFigure/src/DataManagement/mitkPlanarFigure.cpp b/Modules/PlanarFigure/src/DataManagement/mitkPlanarFigure.cpp
	index 77952b1..573f41a 100644
	--- a/Modules/PlanarFigure/src/DataManagement/mitkPlanarFigure.cpp
	+++ b/Modules/PlanarFigure/src/DataManagement/mitkPlanarFigure.cpp
	@@ -729,7 +729,7 @@ void mitk::PlanarFigure::PrintSelf( std::ostream& os, itk::Indent indent ) const
	os << indent << "Current number of control points: " << this->GetNumberOfControlPoints(0) << std::endl;


	- for ( auto timeStep = 0; timeStep < GetTimeSteps(); ++timeStep )
	+ for ( auto timeStep = 0u; timeStep < GetTimeSteps(); ++timeStep )
	{
	os << indent << "Control points for timestep :" << timeStep << std::endl;

	diff --git a/Modules/PlanarFigure/src/DataManagement/mitkPlanarSubdivisionPolygon.cpp b/Modules/PlanarFigure/src/DataManagement/mitkPlanarSubdivisionPolygon.cpp
	index c19bf23..dffb362 100644
	--- a/Modules/PlanarFigure/src/DataManagement/mitkPlanarSubdivisionPolygon.cpp
	+++ b/Modules/PlanarFigure/src/DataManagement/mitkPlanarSubdivisionPolygon.cpp
	@@ -45,7 +45,7 @@ void mitk::PlanarSubdivisionPolygon::GeneratePolyLine()
	ControlPointListType newSubdivisionPoints;
	ControlPointListType subdivisionPoints; // = m_ControlPoints;

	- for ( int controlPoint = 0; controlPoint < GetNumberOfControlPoints( timestep ); ++controlPoint )
	+ for ( auto controlPoint = 0u; controlPoint < GetNumberOfControlPoints( timestep ); ++controlPoint )
	{
	subdivisionPoints.push_back( GetControlPoint( controlPoint, timestep ) );
	}

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