Commit 47a68024 authored by Christian Schulte zu Berge's avatar Christian Schulte zu Berge
Browse files

Started on fixing various issues in ITK module

parent 72597c1d
......@@ -5,8 +5,8 @@
// If not explicitly stated otherwise: Copyright (C) 2012-2013, all rights reserved,
// Christian Schulte zu Berge <christian.szb@in.tum.de>
// Chair for Computer Aided Medical Procedures
// Technische Universität München
// Boltzmannstr. 3, 85748 Garching b. München, Germany
// Technische Universitt Mnchen
// Boltzmannstr. 3, 85748 Garching b. Mnchen, Germany
//
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
......@@ -97,20 +97,25 @@ namespace campvis {
// what source could be. Thank god, there exists macro magic to create the 56
// different templated conversion codes.
#define CONVERT_ITK_TO_GENERIC_LOCAL(basetype, numchannels, dimensionality) \
if (const GenericImageRepresentationItk<basetype, 1, 3>* tester = dynamic_cast< const GenericImageRepresentationItk<basetype, 1, 3>* >(source)) { \
typedef GenericImageRepresentationItk<basetype, 1, 3>::ItkImageType ImageType; \
typedef ImageType::PixelType PixelType; \
const PixelType* pixelData = tester->getItkImage()->GetBufferPointer(); \
if (const GenericImageRepresentationItk<basetype, numchannels, dimensionality>* tester = dynamic_cast< const GenericImageRepresentationItk<basetype, numchannels, dimensionality>* >(source)) { \
typedef typename GenericImageRepresentationItk<basetype, numchannels, dimensionality>::ItkImageType ItkImageType; \
typedef typename ItkImageType::PixelType ItkElementType; \
typedef typename GenericImageRepresentationItk<basetype, numchannels, dimensionality>::ElementType ElementType; \
const ItkElementType* pixelData = tester->getItkImage()->GetBufferPointer(); \
\
ImageType::RegionType region; \
ItkImageType::RegionType region; \
region = tester->getItkImage()->GetBufferedRegion(); \
\
ImageType::SizeType s = region.GetSize(); \
tgt::svec3 size(s[0], s[1], s[2]); \
ItkImageType::SizeType s = region.GetSize(); \
tgt::svec3 size(s[0], 1, 1); \
if (dimensionality >= 2) \
size.y = s[1]; \
if (dimensionality == 3) \
size.z = s[2]; \
\
PixelType* pixelDataCopy = new PixelType[tgt::hmul(size)]; \
memcpy(pixelDataCopy, pixelData, tgt::hmul(size) * TypeTraits<basetype, 1>::elementSize); \
return GenericImageRepresentationLocal<PixelType, 1>::create(const_cast<ImageData*>(source->getParent()), pixelDataCopy); \
ElementType* pixelDataCopy = new ElementType[tgt::hmul(size)]; \
memcpy(pixelDataCopy, pixelData, tgt::hmul(size) * TypeTraits<basetype, numchannels>::elementSize); \
return GenericImageRepresentationLocal<basetype, numchannels>::create(const_cast<ImageData*>(source->getParent()), pixelDataCopy); \
}
#define DISPATCH_ITK_TO_GENERIC_LOCAL_CONVERSION_ND(numchannels, dimensionality) \
......
......@@ -30,6 +30,7 @@
#include "core/tools/typetraits.h"
#include "core/tools/weaklytypedpointer.h"
#include "modules/itk/core/itktypetraits.h"
#include <../voreen-4.3/voreen-snapshot/ext/boost/include/boost/mpl/aux_/na_fwd.hpp>
#include <itkImage.h>
#include <itkImportImageFilter.h>
......@@ -270,20 +271,20 @@ namespace campvis {
return 0;
}
if (const GenericImageRepresentationLocal<BASETYPE, NUMCHANNELS>* tester = dynamic_cast< const GenericImageRepresentationLocal<BASETYPE, 1>* >(source)) {
typename itk::ImportImageFilter<BASETYPE, DIMENSIONALITY>::Pointer importer = itk::ImportImageFilter<BASETYPE, DIMENSIONALITY>::New();
if (const GenericImageRepresentationLocal<BASETYPE, NUMCHANNELS>* tester = dynamic_cast< const GenericImageRepresentationLocal<BASETYPE, NUMCHANNELS>* >(source)) {
typename itk::ImportImageFilter<ItkElementType, DIMENSIONALITY>::Pointer importer = itk::ImportImageFilter<ItkElementType, DIMENSIONALITY>::New();
typename itk::Image<BASETYPE, DIMENSIONALITY>::SizeType size;
typename ItkImageType::SizeType size;
size[0] = tester->getSize().x;
if (source->getDimensionality() >= 2)
if (DIMENSIONALITY >= 2)
size[1] = tester->getSize().y;
if (source->getDimensionality() >= 3)
if (DIMENSIONALITY >= 3)
size[2] = tester->getSize().z;
typename itk::Image<BASETYPE, DIMENSIONALITY>::IndexType start;
typename ItkImageType::IndexType start;
start.Fill(0);
typename itk::Image<BASETYPE, DIMENSIONALITY>::RegionType region;
typename ItkImageType::RegionType region;
region.SetSize(size);
region.SetIndex(start);
importer->SetRegion(region);
......@@ -291,8 +292,8 @@ namespace campvis {
importer->SetSpacing(tester->getParent()->getMappingInformation().getVoxelSize().elem);
importer->SetOrigin(tester->getParent()->getMappingInformation().getOffset().elem);
typedef typename itk::Image<BASETYPE, DIMENSIONALITY>::PixelType PixelType;
const PixelType* pixelData = tester->getImageData();
typedef typename ItkImageType::PixelType PixelType;
const PixelType* pixelData = reinterpret_cast<const PixelType*>(tester->getImageData());
importer->SetImportPointer(const_cast<PixelType*>(pixelData), tester->getNumElements(), false);
importer->Update();
......
......@@ -29,7 +29,7 @@
#include "tgt/tgt_math.h"
#include "tgt/vector.h"
#include <itkCovariantVector.h>
#include <itkVector.h>
#include "core/tools/typetraits.h"
......@@ -60,19 +60,19 @@ namespace {
template<typename BASETYPE>
struct ItkTypeTraitsHelperOfBasetypePerChannel<BASETYPE, 2> {
typedef itk::CovariantVector< BASETYPE, 2 > ItkElementType;
typedef itk::Vector< BASETYPE, 2 > ItkElementType;
};
template<typename BASETYPE>
struct ItkTypeTraitsHelperOfBasetypePerChannel<BASETYPE, 3> {
typedef itk::CovariantVector< BASETYPE, 3 > ItkElementType;
typedef itk::Vector< BASETYPE, 3 > ItkElementType;
};
template<typename BASETYPE>
struct ItkTypeTraitsHelperOfBasetypePerChannel<BASETYPE, 4> {
typedef itk::CovariantVector< BASETYPE, 4 > ItkElementType;
typedef itk::Vector< BASETYPE, 4 > ItkElementType;
};
......
......@@ -22,6 +22,10 @@
//
// ================================================================================================
// disable known false-positive warning in ITK code when using GCC:
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Warray-bounds"
#include "itkimagefilter.h"
#include "tgt/glmath.h"
......@@ -40,6 +44,9 @@
#include "core/datastructures/imagedata.h"
#include "core/datastructures/genericimagerepresentationlocal.h"
#pragma GCC diagnostic pop
// In this class we want to use various ITK filters. Each filter needs the same ITK boilerplate
// code to be written before and after calling the filter. Futhermore, we need to distinguish
// between the different input base types, since ITK doesn't know runtime type inference.
......@@ -59,8 +66,8 @@
{ \
GenericImageRepresentationItk<MA_baseType, MA_numChannels, MA_dimensionality>::ScopedRepresentation itkRep(data, p_sourceImageID.getValue()); \
if (itkRep != 0) { \
typedef GenericImageRepresentationItk<MA_baseType, MA_numChannels, MA_dimensionality>::ItkImageType InputImageType; \
typedef GenericImageRepresentationItk<MA_returnType, MA_numChannels, MA_dimensionality>::ItkImageType OutputImageType; \
typedef typename GenericImageRepresentationItk<MA_baseType, MA_numChannels, MA_dimensionality>::ItkImageType InputImageType; \
typedef typename GenericImageRepresentationItk<MA_returnType, MA_numChannels, MA_dimensionality>::ItkImageType OutputImageType; \
itk::MA_filterType<InputImageType, OutputImageType>::Pointer filter = itk::MA_filterType<InputImageType, OutputImageType>::New(); \
\
MD_filterBody \
......@@ -71,12 +78,10 @@
} \
}
// Multi-channel images not supported by most ITK processors...
#define DISPATCH_ITK_FILTER_BRD(MA_WTP, MA_baseType, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
switch (MA_WTP._numChannels) { \
case 1 : PERFORM_ITK_FILTER_SPECIFIC(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
case 2 : PERFORM_ITK_FILTER_SPECIFIC(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
case 3 : PERFORM_ITK_FILTER_SPECIFIC(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
case 4 : PERFORM_ITK_FILTER_SPECIFIC(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
}
#define DISPATCH_ITK_FILTER_RD(MA_WTP, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
......@@ -218,6 +223,9 @@ namespace campvis {
if (input != 0 && input->getParent()->getNumChannels() == 1) {
ImageData* id = new ImageData(input->getDimensionality(), input->getSize(), 1);
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Warray-bounds"
if (p_filterMode.getOptionValue() == "median") {
DISPATCH_ITK_FILTER(input, MedianImageFilter, \
InputImageType::SizeType indexRadius; \
......@@ -251,6 +259,9 @@ namespace campvis {
else if (p_filterMode.getOptionValue() == "laplacianSharpening") {
DISPATCH_ITK_FILTER(input, LaplacianSharpeningImageFilter, /* nothing here */);
}
#pragma GCC diagnostic pop
data.addData(p_targetImageID.getValue(), id);
}
else {
......
......@@ -22,6 +22,11 @@
//
// ================================================================================================
// disable known false-positive warning in ITK code when using GCC:
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Warray-bounds"
#include "itkimagefilterkernel.h"
#include "tgt/glmath.h"
......@@ -37,6 +42,8 @@
#include "core/datastructures/imagedata.h"
#include "core/datastructures/genericimagerepresentationlocal.h"
#pragma GCC diagnostic pop
// In this class we want to use various ITK filters. Each filter needs the same ITK boilerplate
// code to be written before and after calling the filter. Futhermore, we need to distinguish
// between the different input base types, since ITK doesn't know runtime type inference.
......@@ -73,12 +80,10 @@
} \
}
// Multi-channel images not supported by most ITK processors...
#define DISPATCH_ITK_FILTER_BRD(MA_WTP, MA_baseType, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
switch (MA_WTP._numChannels) { \
case 1 : PERFORM_ITK_FILTER_KERNEL(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
case 2 : PERFORM_ITK_FILTER_KERNEL(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
case 3 : PERFORM_ITK_FILTER_KERNEL(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
case 4 : PERFORM_ITK_FILTER_KERNEL(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody) break; \
}
#define DISPATCH_ITK_FILTER_RD(MA_WTP, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
......@@ -207,6 +212,10 @@ namespace campvis {
if (input != 0 && input->getParent()->getNumChannels() == 1) {
ImageData* id = new ImageData(input->getDimensionality(), input->getSize(), 1);
// disable known false-positive warning in ITK code when using GCC:
#pragma GCC diagnostic push
#pragma GCC diagnostic ignored "-Warray-bounds"
if (p_filterMode.getOptionValue() == "opening") {
DISPATCH_ITK_FILTER(input, BinaryMorphologicalOpeningImageFilter, /* nothing here */);
}
......@@ -214,6 +223,8 @@ namespace campvis {
DISPATCH_ITK_FILTER(input, BinaryMorphologicalClosingImageFilter, /* nothing here */);
}
#pragma GCC diagnostic pop
data.addData(p_targetImageID.getValue(), id);
}
else {
......
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