Currently job artifacts in CI/CD pipelines on LRZ GitLab never expire. Starting from Wed 26.1.2022 the default expiration time will be 30 days (GitLab default). Currently existing artifacts in already completed jobs will not be affected by the change. The latest artifacts for all jobs in the latest successful pipelines will be kept. More information: https://gitlab.lrz.de/help/user/admin_area/settings/continuous_integration.html#default-artifacts-expiration

Commit f924ccfd authored by Oliver Zettining's avatar Oliver Zettining Committed by Cristina Precup
Browse files

working dir files backup --jakob

parent b293e0b1
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// 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 Universitt Mnchen
// Boltzmannstr. 3, 85748 Garching b. Mnchen, Germany
//
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
// Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file
// except in compliance with the License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software distributed under the
// License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
// either express or implied. See the License for the specific language governing permissions
// and limitations under the License.
//
// ================================================================================================
#include "itksegmentation.h"
#include "tgt/glmath.h"
#include "tgt/logmanager.h"
#include "modules/itk/core/genericimagerepresentationitk.h"
#include <itkIntTypes.h>
#include <itkGradientMagnitudeImageFilter.h>
#include <itkWatershedImageFilter.h>
#include <itkCastImageFilter.h>
#include <itkConnectedThresholdImageFilter.h>
#include <itkMaskImageFilter.h>
#include "core/datastructures/imagedata.h"
#include "core/datastructures/genericimagerepresentationlocal.h"
// In this class we want to use various ITK segmentation methods.
/**
* Executes the specified segmentation on the data.
* \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 MD_filterBody additional stuff to execute between filter definition and execution
*/
#define PERFORM_ITK_SEGMENTATION(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; \
itk::MA_filterType<InputImageType, OutputImageType>::Pointer filter = itk::MA_filterType<InputImageType, OutputImageType>::New(); \
typedef itk::Image<itk::IdentifierType, MA_dimensionality> LabelImageType; \
typedef itk::MaskImageFilter< OutputImageType, OutputImageType > MaskFilterType;\
MaskFilterType::Pointer maskFilter = MaskFilterType::New();\
MD_filterBody \
filter->SetInput(itkRep->getItkImage()); \
filter->Update(); \
maskFilter->SetInput(itkRep->getItkImage()); \
maskFilter->SetMaskImage(filter->GetOutput());\
itk::CastImageFilter<OutputImageType, OutputImageType>::Pointer caster = itk::CastImageFilter<OutputImageType, OutputImageType>::New(); \
caster->SetInput(maskFilter->GetOutput()); \
caster->Update(); \
\
GenericImageRepresentationItk<MA_baseType, MA_numChannels, MA_dimensionality>::create(id, caster->GetOutput()); \
} \
}
#define DISPATCH_ITK_SEGMENTATION_BRD(MA_WTP, MA_baseType, MA_returnType, MA_dimensionality, MA_filterType, MD_filterBody) \
tgtAssert(MA_WTP._numChannels == 1, "ItkSegmentation only supports single-channel images.") \
PERFORM_ITK_SEGMENTATION(MA_baseType, MA_returnType, 1, MA_dimensionality, MA_filterType, MD_filterBody)
#define DISPATCH_ITK_SEGMENTATION_D(MA_WTP, MA_dimensionality, MA_filterType, MD_filterBody) \
switch (MA_WTP._baseType) { \
case WeaklyTypedPointer::UINT8: \
DISPATCH_ITK_SEGMENTATION_BRD(MA_WTP, uint8_t, uint8_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT8: \
DISPATCH_ITK_SEGMENTATION_BRD(MA_WTP, int8_t, int8_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::UINT16: \
DISPATCH_ITK_SEGMENTATION_BRD(MA_WTP, uint16_t, uint16_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT16: \
DISPATCH_ITK_SEGMENTATION_BRD(MA_WTP, int16_t, int16_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::UINT32: \
DISPATCH_ITK_SEGMENTATION_BRD(MA_WTP, uint32_t, uint32_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::INT32: \
DISPATCH_ITK_SEGMENTATION_BRD(MA_WTP, int32_t, int32_t, MA_dimensionality, MA_filterType, MD_filterBody) \
break; \
case WeaklyTypedPointer::FLOAT: \
DISPATCH_ITK_SEGMENTATION_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 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_SEGMENTATION(MA_localRep, MA_filterType, MD_filterBody) \
do { \
WeaklyTypedPointer wtp = MA_localRep->getWeaklyTypedPointer(); \
switch (MA_localRep->getDimensionality()) { \
case 2: DISPATCH_ITK_SEGMENTATION_D(wtp, 2, MA_filterType, MD_filterBody) break; \
case 3: DISPATCH_ITK_SEGMENTATION_D(wtp, 3, MA_filterType, MD_filterBody) break; \
default: tgtAssert(false, "Unsupported dimensionality!"); break; \
} \
} while (0)
// ================================================================================================
// = Macros defined, let the party begin! =
// ================================================================================================
namespace campvis {
static const GenericOption<std::string> segmentationTypes[1] = {
GenericOption<std::string>("regionGrowing", "Region Growing")
};
const std::string ItkSegmentation::loggerCat_ = "CAMPVis.modules.classification.ItkSegmentation";
ItkSegmentation::ItkSegmentation()
: AbstractProcessor()
, p_sourceImageID("InputVolume", "Input Volume ID", "volume", DataNameProperty::READ)
, p_targetImageID("OutputGradients", "Output Segmented Volume ID", "segmented_volume", DataNameProperty::WRITE)
, p_segmentationType("SegmentationType", "Segmentation Type", segmentationTypes, 1)
, p_seedX("SeedX", "Seed X", 162, 0, 0, 1)
, p_seedY("SeedY", "Seed Y", 169, 0, 0, 1)
, p_seedZ("SeedZ", "Seed Z", 182, 0, 0, 1)
, p_thresMin("ThresMin", "Min Threshold", 70, 0, 255, 1)
, p_thresMax("ThresMax", "Max Threshold", 130, 0, 255, 1)
{
addProperty(p_sourceImageID);
addProperty(p_targetImageID);
addProperty(p_segmentationType, INVALID_RESULT | INVALID_PROPERTIES);
addProperty(p_seedX);
addProperty(p_seedY);
addProperty(p_seedZ);
addProperty(p_thresMin);
addProperty(p_thresMax);
}
ItkSegmentation::~ItkSegmentation() {
}
void ItkSegmentation::updateResult(DataContainer& data) {
ImageRepresentationLocal::ScopedRepresentation input(data, p_sourceImageID.getValue());
if (input != 0 && input->getParent()->getNumChannels() == 1 && (input->getDimensionality() == 2 || input->getDimensionality() == 3)) {
const size_t dim = input->getDimensionality();
p_seedX.setMaxValue(input->getSize().elem[0]);
p_seedY.setMaxValue(input->getSize().elem[1]);
p_seedZ.setMaxValue(input->getSize().elem[2]);
ImageData* id = new ImageData(dim, input->getSize(), 1);
if (p_segmentationType.getOptionValue() == "regionGrowing") {
if (dim == 2) {
#pragma GCC diagnostic ignored "-Warray-bounds"
DISPATCH_ITK_SEGMENTATION(input, ConnectedThresholdImageFilter, \
InputImageType::IndexType index; \
index[0] = p_seedX.getValue(); \
index[1] = p_seedY.getValue(); \
filter->SetLower(p_thresMin.getValue()); \
filter->SetUpper(p_thresMax.getValue()); \
filter->SetReplaceValue(255); \
filter->SetSeed(index); \
);
} else if (dim == 3) {
#pragma GCC diagnostic ignored "-Warray-bounds"
DISPATCH_ITK_SEGMENTATION(input, ConnectedThresholdImageFilter, \
InputImageType::IndexType index; \
index[0] = p_seedX.getValue(); \
index[1] = p_seedY.getValue(); \
index[2] = p_seedZ.getValue(); \
filter->SetLower(p_thresMin.getValue()); \
filter->SetUpper(p_thresMax.getValue()); \
filter->SetReplaceValue(255); \
filter->SetSeed(index); \
);
} else {
tgtAssert(false, "Unsupported dimensionality!");
}
}
data.addData(p_targetImageID.getValue(), id);
}
else {
LDEBUG("No suitable input image found.");
}
validate(INVALID_RESULT);
}
void ItkSegmentation::updateProperties(DataContainer& /*dataContainer*/) {
if (p_segmentationType.getOptionValue() == "regionGrowing") {
p_seedX.setVisible(true);
p_seedY.setVisible(true);
p_seedZ.setVisible(true);
p_thresMin.setVisible(true);
p_thresMax.setVisible(true);
}
validate(AbstractProcessor::INVALID_PROPERTIES);
}
}
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// 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 Universitt Mnchen
// Boltzmannstr. 3, 85748 Garching b. Mnchen, Germany
//
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
// Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file
// except in compliance with the License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software distributed under the
// License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
// either express or implied. See the License for the specific language governing permissions
// and limitations under the License.
//
// ================================================================================================
#ifndef ITKSEGMENTATION_H__
#define ITKSEGMENTATION_H__
#include <string>
#include "core/pipeline/visualizationprocessor.h"
#include "core/properties/datanameproperty.h"
#include "core/properties/genericproperty.h"
#include "core/properties/floatingpointproperty.h"
#include "core/properties/numericproperty.h"
#include "core/properties/optionproperty.h"
#include "modules/preprocessing/tools/abstractimagefilter.h"
namespace campvis {
/**
* Performs watershed image filter on input image using ITK.
*/
class ItkSegmentation : public AbstractProcessor {
public:
/**
* Constructs a new ItkSegmentation Processor
**/
ItkSegmentation();
/**
* Destructor
**/
virtual ~ItkSegmentation();
/// \see AbstractProcessor::getName()
virtual const std::string getName() const { return "ItkSegmentation"; };
/// \see AbstractProcessor::getDescription()
virtual const std::string getDescription() const { return "Performs a segmentation on input image using ITK."; };
/// \see AbstractProcessor::getAuthor()
virtual const std::string getAuthor() const { return "Cristina Precup <cristina.precup@tum.de>"; };
/// \see AbstractProcessor::getProcessorState()
virtual ProcessorState getProcessorState() const { return AbstractProcessor::TESTING; };
DataNameProperty p_sourceImageID; ///< ID for input volume
DataNameProperty p_targetImageID; ///< ID for output gradient volume
GenericOptionProperty<std::string> p_segmentationType; ///< Segmentation type
IntProperty p_seedX;
IntProperty p_seedY;
IntProperty p_seedZ;
IntProperty p_thresMin;
IntProperty p_thresMax;
protected:
/// \see AbstractProcessor::updateResult
virtual void updateResult(DataContainer& dataContainer);
/// \see AbstractProcessor::updateProperties
virtual void updateProperties(DataContainer& dataContainer);
static const std::string loggerCat_;
};
}
#endif // ITKSEGMENTATION_H__
// ================================================================================================
//
// 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 "segmentationdemo.h"
#include "tgt/event/keyevent.h"
#include "core/datastructures/imagedata.h"
#include "core/classification/geometry1dtransferfunction.h"
#include "core/classification/tfgeometry1d.h"
namespace campvis {
SegmentationDemo::SegmentationDemo(DataContainer* dc)
: AutoEvaluationPipeline(dc)
, _lsp()
, _imageReader()
, _ve(&_canvasSize)
, _itkFilter()
, _itkSegmentation()
{
addProcessor(&_lsp);
addProcessor(&_imageReader);
addProcessor(&_ve);
addProcessor(&_itkFilter);
addProcessor(&_itkSegmentation);
addEventListenerToBack(&_ve);
}
SegmentationDemo::~SegmentationDemo() {
}
void SegmentationDemo::init() {
AutoEvaluationPipeline::init();
_ve.p_outputImage.setValue("result");
_renderTargetID.setValue("result");
//_imageReader.setURL(CAMPVIS_SOURCE_DIR "/modules/vis/sampledata/smallHeart.mhd");
//_imageReader.setURL(CAMPVIS_SOURCE_DIR "/../misc/mha_loader_CAMPVis_volumes/prostate_phantom_US/prostate_phantom_fcal_volume_uncompressed.mhd");
_imageReader.setURL(CAMPVIS_SOURCE_DIR "/../misc/mha_loader_CAMPVis_volumes/prostate_phantom_US/prostate_phantom_fcal_volume_uncompressed.mha");
_imageReader.setTargetImageId("reader.output");
_imageReader.setTargetImageIdSharedProperty(&_ve.p_inputVolume);
Geometry1DTransferFunction* dvrTF = new Geometry1DTransferFunction(128, tgt::vec2(0.f, .05f));
dvrTF->addGeometry(TFGeometry1D::createQuad(tgt::vec2(.4f, .5f), tgt::col4(32, 192, 0, 128), tgt::col4(32, 192, 0, 128)));
dvrTF->addGeometry(TFGeometry1D::createQuad(tgt::vec2(.12f, .15f), tgt::col4(85, 0, 0, 128), tgt::col4(255, 0, 0, 128)));
dvrTF->addGeometry(TFGeometry1D::createQuad(tgt::vec2(.19f, .28f), tgt::col4(89, 89, 89, 155), tgt::col4(89, 89, 89, 155)));
dvrTF->addGeometry(TFGeometry1D::createQuad(tgt::vec2(.41f, .51f), tgt::col4(170, 170, 128, 64), tgt::col4(192, 192, 128, 64)));
static_cast<TransferFunctionProperty*>(_ve.getNestedProperty("VolumeRendererProperties::RaycasterProps::TransferFunction"))->replaceTF(dvrTF);
static_cast<FloatProperty*>(_ve.getNestedProperty("VolumeRendererProperties::RaycasterProps::SamplingRate"))->setValue(4.f);
}
void SegmentationDemo::deinit() {
_canvasSize.s_changed.disconnect(this);
AutoEvaluationPipeline::deinit();
}
}
\ No newline at end of file
// ================================================================================================
//
// This file is part of the CAMPVis Software Framework.
//
// 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 Universitt Mnchen
// Boltzmannstr. 3, 85748 Garching b. Mnchen, Germany
//
// For a full list of authors and contributors, please refer to the file "AUTHORS.txt".
//
// Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file
// except in compliance with the License. You may obtain a copy of the License at
//
// http://www.apache.org/licenses/LICENSE-2.0
//
// Unless required by applicable law or agreed to in writing, software distributed under the
// License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
// either express or implied. See the License for the specific language governing permissions
// and limitations under the License.
//
// ================================================================================================
#ifndef SegmentationDemo_H__
#define SegmentationDemo_H__
#include "core/pipeline/autoevaluationpipeline.h"
#include "modules/base/processors/lightsourceprovider.h"
#include "modules/io/processors/genericimagereader.h"
#include "modules/vis/processors/volumeexplorer.h"
#include "modules/itk/processors/itkimagefilter.h"
#include "modules/itk/processors/itksegmentation.h"
namespace campvis {
class SegmentationDemo : public AutoEvaluationPipeline {
public:
/**
* Creates a AutoEvaluationPipeline.
*/
SegmentationDemo(DataContainer* dc);
/**
* Virtual Destructor
**/
virtual ~SegmentationDemo();
/// \see AutoEvaluationPipeline::init()
virtual void init();
/// \see AutoEvaluationPipeline::deinit()
virtual void deinit();
/// \see AbstractPipeline::getName()
virtual const std::string getName() const { return getId(); };
/// \see AbstractPipeline::getId()
static const std::string getId() { return "SegmentationDemo"; };
protected:
LightSourceProvider _lsp;
GenericImageReader _imageReader;
VolumeExplorer _ve;
ItkImageFilter _itkFilter;
ItkSegmentation _itkSegmentation;
};
}
#endif // SegmentationDemo_H__
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment