Commit f7af6ea1 authored by Christian Schulte zu Berge's avatar Christian Schulte zu Berge
Browse files

introducing ItkImageFilterKernel (for opening and closing filter), yet untested

parent 545df53f
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// If not explicitly stated otherwise: Copyright (C) 2012, all rights reserved,
// Christian Schulte zu Berge <christian.szb@in.tum.de>
// Chair for Computer Aided Medical Procedures
// 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".
//
// The licensing of this softare is not yet resolved. Until then, redistribution in source or
// binary forms outside the CAMP chair is not permitted, unless explicitly stated in legal form.
// However, the names of the original authors and the above copyright notice must retain in its
// original state in any case.
//
// Legal disclaimer provided by the BSD license:
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
// AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
//
// ================================================================================================
#include "itkimagefilterkernel.h"
#include "tgt/glmath.h"
#include "tgt/logmanager.h"
#include "modules/itk/core/genericimagerepresentationitk.h"
#include <itkBinaryBallStructuringElement.h>
#include <itkBinaryMorphologicalClosingImageFilter.h>
#include <itkBinaryMorphologicalOpeningImageFilter.h>
#include "tbb/tbb.h"
#include "core/datastructures/imagedata.h"
#include "core/datastructures/genericimagerepresentationlocal.h"
// 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.
// Hence, we define various handy macros that will assemble the necessary C++ code for using the
// corresponding ITK filters within this processor. Good luck!
/**
* Executes the specified filter on the data specified filter.
* \param MA_baseType base type of input image
* \param MA_returnType base type of ouput image
* \param MA_numChannels number of channels of input image
* \param MA_dimensionality dimensionality of images
* \param MA_filterType type name if the ITK filter to use (within itk:: namespace)
* \param MD_filterBody additional stuff to execute between filter definition and execution
*/
#define PERFORM_ITK_FILTER_KERNEL(MA_baseType, MA_returnType, MA_numChannels, MA_dimensionality, MA_filterType, MD_filterBody) \
{ \
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 itk::BinaryBallStructuringElement<MA_baseType, MA_dimensionality> StructuringElementType; \
\
StructuringElementType structuringElement; structuringElement.SetRadius(p_kernelSize.getValue()); \
structuringElement.CreateStructuringElement(); \
itk::MA_filterType<InputImageType, OutputImageType, StructuringElementType>::Pointer filter = itk::MA_filterType<InputImageType, OutputImageType, StructuringElementType>::New(); \
\
MD_filterBody \
\
filter->SetKernel(structuringElement); \
filter->SetInput(itkRep->getItkImage()); \
filter->Update(); \
GenericImageRepresentationItk<MA_returnType, MA_numChannels, MA_dimensionality>::create(id, filter->GetOutput()); \
} \
}
#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) \
switch (MA_WTP._baseType) { \
case WeaklyTypedPointer::UINT8: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, uint8_t, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT8: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, int8_t, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::UINT16: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, uint16_t, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT16: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, int16_t, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::UINT32: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, uint32_t, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT32: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, int32_t, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::FLOAT: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, float, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
default: \
tgtAssert(false, "Should not reach this - wrong base type in WeaklyTypedPointer!"); \
} \
#define DISPATCH_ITK_FILTER_D(MA_WTP, MA_dimensionality, MA_filterType, MD_filterBody) \
switch (MA_WTP._baseType) { \
case WeaklyTypedPointer::UINT8: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, uint8_t, uint8_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT8: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, int8_t, int8_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::UINT16: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, uint16_t, uint16_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT16: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, int16_t, int16_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::UINT32: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, uint32_t, uint32_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT32: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, int32_t, int32_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::FLOAT: \
DISPATCH_ITK_FILTER_BRD(MA_WTP, float, float, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
default: \
tgtAssert(false, "Should not reach this - wrong base type in WeaklyTypedPointer!"); \
} \
/**
* Dispatches the execution for the ITK filter \a MA_filterType with the output base type
* of \a MA_returnType for the image \a MA_localRep.
* \param MA_localRep local representation of the image to apply the filter to
* \param MA_returnType base type of ouput image
* \param MA_filterType type name if the ITK filter to use (within itk:: namespace)
* \param MD_filterBody additional stuff to execute between filter definition and execution
*/
#define DISPATCH_ITK_FILTER_WITH_EXTRA_RETURN_TYPE(MA_localRep, MA_returnType, MA_filterType, MD_filterBody) \
do { \
WeaklyTypedPointer wtp = MA_localRep->getWeaklyTypedPointer(); \
switch (MA_localRep->getDimensionality()) { \
case 1: DISPATCH_ITK_FILTER_RD(wtp, MA_returnType, 1, MA_filterType, MD_filterBody) break; \
case 2: DISPATCH_ITK_FILTER_RD(wtp, MA_returnType, 2, MA_filterType, MD_filterBody) break; \
case 3: DISPATCH_ITK_FILTER_RD(wtp, MA_returnType, 3, MA_filterType, MD_filterBody) break; \
} \
} while (0)
/**
* Dispatches the execution for the ITK filter \a MA_filterType for the image \a MA_localRep.
* \param MA_localRep local representation of the image to apply the filter to
* \param MA_filterType type name if the ITK filter to use (within itk:: namespace)
* \param MD_filterBody additional stuff to execute between filter definition and execution
*/
#define DISPATCH_ITK_FILTER(MA_localRep, MA_filterType, MD_filterBody) \
do { \
WeaklyTypedPointer wtp = MA_localRep->getWeaklyTypedPointer(); \
switch (MA_localRep->getDimensionality()) { \
case 1: DISPATCH_ITK_FILTER_D(wtp, 1, MA_filterType, MD_filterBody) break; \
case 2: DISPATCH_ITK_FILTER_D(wtp, 2, MA_filterType, MD_filterBody) break; \
case 3: DISPATCH_ITK_FILTER_D(wtp, 3, MA_filterType, MD_filterBody) break; \
} \
} while (0)
// ================================================================================================
// = Macros defined, let the party begin! =
// ================================================================================================
namespace campvis {
static const GenericOption<std::string> filterModes[2] = {
GenericOption<std::string>("opening", "Opening"),
GenericOption<std::string>("closing", "Closing")
};
const std::string ItkImageFilterKernel::loggerCat_ = "CAMPVis.modules.classification.ItkImageFilterKernel";
ItkImageFilterKernel::ItkImageFilterKernel()
: AbstractProcessor()
, p_sourceImageID("InputVolume", "Input Volume ID", "volume", DataNameProperty::READ)
, p_targetImageID("OutputGradients", "Output Gradient Volume ID", "gradients", DataNameProperty::WRITE)
, p_filterMode("FilterMode", "Filter Mode", filterModes, 2, AbstractProcessor::INVALID_RESULT | AbstractProcessor::INVALID_PROPERTIES)
, p_kernelSize("KernelSize", "Kernel Size", 3, 3, 15)
{
addProperty(&p_sourceImageID);
addProperty(&p_targetImageID);
addProperty(&p_filterMode);
addProperty(&p_kernelSize);
}
ItkImageFilterKernel::~ItkImageFilterKernel() {
}
void ItkImageFilterKernel::process(DataContainer& data) {
ImageRepresentationLocal::ScopedRepresentation input(data, p_sourceImageID.getValue());
if (input != 0 && input->getParent()->getNumChannels() == 1) {
ImageData* id = new ImageData(input->getDimensionality(), input->getSize(), 1);
if (p_filterMode.getOptionValue() == "opening") {
DISPATCH_ITK_FILTER(input, BinaryMorphologicalOpeningImageFilter, /* nothing here */);
}
else if (p_filterMode.getOptionValue() == "closing") {
DISPATCH_ITK_FILTER(input, BinaryMorphologicalClosingImageFilter, /* nothing here */);
}
data.addData(p_targetImageID.getValue(), id);
p_targetImageID.issueWrite();
}
else {
LDEBUG("No suitable input image found.");
}
validate(INVALID_RESULT);
}
void ItkImageFilterKernel::updateProperties() {
}
}
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// If not explicitly stated otherwise: Copyright (C) 2012, 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
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
// The licensing of this softare is not yet resolved. Until then, redistribution in source or
// binary forms outside the CAMP chair is not permitted, unless explicitly stated in legal form.
// However, the names of the original authors and the above copyright notice must retain in its
// original state in any case.
//
// Legal disclaimer provided by the BSD license:
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR
// IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY
// AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR
// CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
// CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
// SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
// POSSIBILITY OF SUCH DAMAGE.
//
// ================================================================================================
#ifndef ITKIMAGEFILTERKERNEL_H__
#define ITKIMAGEFILTERKERNEL_H__
#include <string>
#include "core/pipeline/visualizationprocessor.h"
#include "core/properties/datanameproperty.h"
#include "core/properties/genericproperty.h"
#include "core/properties/numericproperty.h"
#include "core/properties/optionproperty.h"
#include "modules/preprocessing/tools/abstractimagefilter.h"
namespace campvis {
/**
* Performs different filter operations on images.
*/
class ItkImageFilterKernel : public AbstractProcessor {
public:
/**
* Constructs a new ItkImageFilterKernel Processor
**/
ItkImageFilterKernel();
/**
* Destructor
**/
virtual ~ItkImageFilterKernel();
/// \see AbstractProcessor::getName()
virtual const std::string getName() const { return "ItkImageFilterKernel"; };
/// \see AbstractProcessor::getDescription()
virtual const std::string getDescription() const { return "Creates the gradient volume for the given intensity volume."; };
virtual void process(DataContainer& data);
DataNameProperty p_sourceImageID; ///< ID for input volume
DataNameProperty p_targetImageID; ///< ID for output gradient volume
GenericOptionProperty<std::string> p_filterMode; ///< Filter mode
IntProperty p_kernelSize;
protected:
/// \see AbstractProcessor::updateProperties
virtual void updateProperties();
static const std::string loggerCat_;
};
}
#endif // ITKIMAGEFILTERKERNEL_H__
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