void mitk::PickingTool::OnPointAdded()
{
if (m_WorkingData != this->GetWorkingData())
{
DataStorage *dataStorage = this->GetDataStorage();
if (dataStorage->Exists(m_PointSetNode))
{
dataStorage->Remove(m_PointSetNode);
dataStorage->Add(m_PointSetNode, this->GetWorkingData());
}
if (dataStorage->Exists(m_ResultNode))
{
dataStorage->Remove(m_ResultNode);
dataStorage->Add(m_ResultNode, this->GetWorkingData());
}
m_WorkingData = this->GetWorkingData();
}
// Perform region growing/picking
int timeStep =
mitk::BaseRenderer::GetInstance(mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1"))->GetTimeStep();
mitk::PointSet::PointType seedPoint = m_PointSet->GetPointSet(timeStep)->GetPoints()->Begin().Value();
// as we want to pick a region from our segmentation image use the working data from ToolManager
mitk::Image::Pointer orgImage = dynamic_cast<mitk::Image *>(m_ToolManager->GetWorkingData(0)->GetData());
if (orgImage.IsNotNull())
{
if (orgImage->GetDimension() == 4)
{ // there may be 4D segmentation data even though we currently don't support that
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(orgImage);
timeSelector->SetTimeNr(timeStep);
timeSelector->UpdateLargestPossibleRegion();
mitk::Image *timedImage = timeSelector->GetOutput();
AccessByItk_2(timedImage, StartRegionGrowing, timedImage->GetGeometry(), seedPoint);
}
else if (orgImage->GetDimension() == 3)
{
AccessByItk_2(orgImage, StartRegionGrowing, orgImage->GetGeometry(), seedPoint);
}
this->m_PointSet->Clear();
}
}
void mitk::GeometryClipImageFilter::GenerateData()
{
Image::ConstPointer input = this->GetInput();
Image::Pointer output = this->GetOutput();
if((output->IsInitialized()==false) || (m_ClippingGeometry.IsNull()))
return;
const Geometry2D * clippingGeometryOfCurrentTimeStep = NULL;
if(m_TimeSlicedClippingGeometry.IsNull())
{
clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_ClippingGeometry.GetPointer());
}
else
{
clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_TimeSlicedClippingGeometry->GetGeometry3D(0));
}
if(clippingGeometryOfCurrentTimeStep == NULL)
return;
m_InputTimeSelector->SetInput(input);
m_OutputTimeSelector->SetInput(this->GetOutput());
mitk::Image::RegionType outputRegion = output->GetRequestedRegion();
const mitk::TimeSlicedGeometry *outputTimeGeometry = output->GetTimeSlicedGeometry();
const mitk::TimeSlicedGeometry *inputTimeGeometry = input->GetTimeSlicedGeometry();
ScalarType timeInMS;
int timestep=0;
int tstart=outputRegion.GetIndex(3);
int tmax=tstart+outputRegion.GetSize(3);
int t;
for(t=tstart;t<tmax;++t)
{
timeInMS = outputTimeGeometry->TimeStepToMS( t );
timestep = inputTimeGeometry->MSToTimeStep( timeInMS );
m_InputTimeSelector->SetTimeNr(timestep);
m_InputTimeSelector->UpdateLargestPossibleRegion();
m_OutputTimeSelector->SetTimeNr(t);
m_OutputTimeSelector->UpdateLargestPossibleRegion();
if(m_TimeSlicedClippingGeometry.IsNotNull())
{
timestep = m_TimeSlicedClippingGeometry->MSToTimeStep( timeInMS );
if(m_TimeSlicedClippingGeometry->IsValidTime(timestep) == false)
continue;
clippingGeometryOfCurrentTimeStep = dynamic_cast<const Geometry2D*>(m_TimeSlicedClippingGeometry->GetGeometry3D(timestep));
}
AccessByItk_2(m_InputTimeSelector->GetOutput(),_InternalComputeClippedImage,this,clippingGeometryOfCurrentTimeStep);
}
m_TimeOfHeaderInitialization.Modified();
}
mitk::GIFFirstOrderStatistics::FeatureListType mitk::GIFFirstOrderStatistics::CalculateFeatures(const Image::Pointer & image, const Image::Pointer &mask)
{
FeatureListType featureList;
AccessByItk_2(image, CalculateFirstOrderStatistics, mask, featureList);
return featureList;
}
mitk::Image::Pointer mitk::LabelSetImageConverter::ConvertLabelSetImageToImage(const mitk::LabelSetImage::ConstPointer input)
{
unsigned int numberOfLayers = input->GetNumberOfLayers();
if (numberOfLayers == 0)
{
mitkThrow() << "Tried to convert LabelSetImage without layers";
}
mitk::Image::Pointer output;
AccessByItk_2(input->GetLayerImage(0), VectorOfMitkImagesToMitkVectorImage, output, input);
return output;
}
void mitk::ImageStatisticsHolder::ComputeImageStatistics(int t, unsigned int component)
{
// timestep valid?
if (!m_Image->IsValidTimeStep(t)) return;
// image modified?
if (this->m_Image->GetMTime() > m_LastRecomputeTimeStamp.GetMTime())
this->ResetImageStatistics();
Expand(t+1);
// do we have valid information already?
if( m_ScalarMin[t] != itk::NumericTraits<ScalarType>::max() ||
m_Scalar2ndMin[t] != itk::NumericTraits<ScalarType>::max() ) return; // Values already calculated before...
// used to avoid statistics calculation on qball images. property will be replaced as soons as bug 17928 is merged and the diffusion image refactoring is complete.
mitk::BoolProperty* isqball = dynamic_cast< mitk::BoolProperty* >( m_Image->GetProperty( "IsQballImage" ).GetPointer() );
const mitk::PixelType pType = m_Image->GetPixelType(0);
if(pType.GetNumberOfComponents() == 1 && (pType.GetPixelType() != itk::ImageIOBase::UNKNOWNPIXELTYPE) && (pType.GetPixelType() != itk::ImageIOBase::VECTOR) )
{
// recompute
mitk::ImageTimeSelector::Pointer timeSelector = this->GetTimeSelector();
if(timeSelector.IsNotNull())
{
timeSelector->SetTimeNr(t);
timeSelector->UpdateLargestPossibleRegion();
const mitk::Image* image = timeSelector->GetOutput();
AccessByItk_2( image, _ComputeExtremaInItkImage, this, t );
}
}
else if (pType.GetPixelType() == itk::ImageIOBase::VECTOR && (!isqball || !isqball->GetValue())) // we have a vector image
{
// recompute
mitk::ImageTimeSelector::Pointer timeSelector = this->GetTimeSelector();
if(timeSelector.IsNotNull())
{
timeSelector->SetTimeNr(t);
timeSelector->UpdateLargestPossibleRegion();
const mitk::Image* image = timeSelector->GetOutput();
AccessVectorPixelTypeByItk_n( image, _ComputeExtremaInItkVectorImage, (this, t, component) );
}
}
else
{
m_ScalarMin[t] = 0;
m_ScalarMax[t] = 255;
m_Scalar2ndMin[t] = 0;
m_Scalar2ndMax[t] = 255;
}
}
void mitk::PlaneCutFilter::GenerateData()
{
if (!this->m_Plane)
{
return;
}
InputImageType *input = const_cast<InputImageType*>(this->GetInput());
if (!input)
{
return;
}
//Allocate output.
OutputImageType *output = this->GetOutput();
output->Initialize(input);
output->SetImportVolume(input->GetData());
//Do the intersection.
AccessByItk_2(output, _computeIntersection, this->m_Plane, input->GetGeometry());
}
void mitk::ImageStatisticsHolder::ComputeImageStatistics(int t)
{
// timestep valid?
if (!m_Image->IsValidTimeStep(t)) return;
// image modified?
if (this->m_Image->GetMTime() > m_LastRecomputeTimeStamp.GetMTime())
this->ResetImageStatistics();
Expand(t+1);
// do we have valid information already?
if( m_ScalarMin[t] != itk::NumericTraits<ScalarType>::max() ||
m_Scalar2ndMin[t] != itk::NumericTraits<ScalarType>::max() ) return; // Values already calculated before...
const mitk::PixelType pType = m_Image->GetPixelType(0);
if(pType.GetNumberOfComponents() == 1 && (pType.GetPixelType() != itk::ImageIOBase::UNKNOWNPIXELTYPE) && (pType.GetPixelType() != itk::ImageIOBase::VECTOR) )
{
// recompute
mitk::ImageTimeSelector::Pointer timeSelector = this->GetTimeSelector();
if(timeSelector.IsNotNull())
{
timeSelector->SetTimeNr(t);
timeSelector->UpdateLargestPossibleRegion();
const mitk::Image* image = timeSelector->GetOutput();
AccessByItk_2( image, _ComputeExtremaInItkImage, this, t );
}
}
else
{
m_ScalarMin[t] = 0;
m_ScalarMax[t] = 255;
m_Scalar2ndMin[t] = 0;
m_Scalar2ndMax[t] = 255;
}
}
void mitk::RegionGrow3DTool::RunSegmentation()
{
//safety if no pointSet or pointSet empty
mitk::PointSet::Pointer seedPointSet = dynamic_cast<mitk::PointSet*> (m_PointSetNode->GetData());
if (seedPointSet.IsNull())
{
return;
}
if (!(seedPointSet->GetSize() > 0))
{
return;
}
mitk::PointSet::PointType seedPoint = seedPointSet->GetPointSet()->GetPoints()->Begin().Value();
mitk::Image::Pointer image = dynamic_cast<mitk::Image*> (m_NodeToProceed->GetData());
if (image.IsNotNull())
{
m_LowerThreshold = static_cast<int> (m_RoiMin);
m_UpperThreshold = static_cast<int> (m_RoiMax);
AccessByItk_2(image, StartRegionGrowing, image->GetGeometry(), seedPoint);
}
}
void mitk::CLUtil::CountVoxel(mitk::Image::Pointer image, unsigned int label, unsigned int & count)
{
AccessByItk_2(image, mitk::CLUtil::itkCountVoxel, label, count);
}
void mitk::CLUtil::InsertLabel(mitk::Image::Pointer & image, mitk::Image::Pointer & maskImage, unsigned int label)
{
AccessByItk_2(image, mitk::CLUtil::itkInsertLabel, maskImage, label);
}
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
// required params
parser.addArgument("image", "i", mitkCommandLineParser::InputImage, "Input Image", "Path to the input VTK polydata", us::Any(), false);
parser.addArgument("output", "o", mitkCommandLineParser::OutputFile, "Output text file", "Target file. The output statistic is appended to this file.", us::Any(), false);
parser.addArgument("gaussian","g",mitkCommandLineParser::String, "Gaussian Filtering of the input images", "Gaussian Filter. Followed by the used variances seperated by ';' ",us::Any());
parser.addArgument("difference-of-gaussian","dog",mitkCommandLineParser::String, "Difference of Gaussian Filtering of the input images", "Difference of Gaussian Filter. Followed by the used variances seperated by ';' ",us::Any());
parser.addArgument("laplace-of-gauss","log",mitkCommandLineParser::String, "Laplacian of Gaussian Filtering", "Laplacian of Gaussian Filter. Followed by the used variances seperated by ';' ",us::Any());
parser.addArgument("hessian-of-gauss","hog",mitkCommandLineParser::String, "Hessian of Gaussian Filtering", "Hessian of Gaussian Filter. Followed by the used variances seperated by ';' ",us::Any());
parser.addArgument("local-histogram", "lh", mitkCommandLineParser::String, "Local Histograms", "Calculate the local histogram based feature. Specify Offset and Delta, for exampel -3;0.6 ", us::Any());
// Miniapp Infos
parser.setCategory("Classification Tools");
parser.setTitle("Global Image Feature calculator");
parser.setDescription("Calculates different global statistics for a given segmentation / image combination");
parser.setContributor("MBI");
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
{
return EXIT_FAILURE;
}
if ( parsedArgs.count("help") || parsedArgs.count("h"))
{
return EXIT_SUCCESS;
}
bool useCooc = parsedArgs.count("cooccurence");
mitk::Image::Pointer image = mitk::IOUtil::LoadImage(parsedArgs["image"].ToString());
std::string filename=parsedArgs["output"].ToString();
////////////////////////////////////////////////////////////////
// CAlculate Gaussian Features
////////////////////////////////////////////////////////////////
MITK_INFO << "Check for Local Histogram...";
if (parsedArgs.count("local-histogram"))
{
std::vector<mitk::Image::Pointer> outs;
auto ranges = splitDouble(parsedArgs["local-histogram"].ToString(), ';');
if (ranges.size() < 2)
{
MITK_INFO << "Missing Delta and Offset for Local Histogram";
}
else
{
AccessByItk_3(image, LocalHistograms, outs, ranges[0], ranges[1]);
for (int i = 0; i < outs.size(); ++i)
{
std::string name = filename + "-lh" + us::any_value_to_string<int>(i)+".nii.gz";
mitk::IOUtil::SaveImage(outs[i], name);
}
}
}
////////////////////////////////////////////////////////////////
// CAlculate Gaussian Features
////////////////////////////////////////////////////////////////
MITK_INFO << "Check for Gaussian...";
if (parsedArgs.count("gaussian"))
{
MITK_INFO << "Calculate Gaussian... " << parsedArgs["gaussian"].ToString();
auto ranges = splitDouble(parsedArgs["gaussian"].ToString(),';');
for (int i = 0; i < ranges.size(); ++i)
{
mitk::Image::Pointer output;
AccessByItk_2(image, GaussianFilter, ranges[i], output);
std::string name = filename + "-gaussian-" + us::any_value_to_string(ranges[i])+".nii.gz";
mitk::IOUtil::SaveImage(output, name);
}
}
////////////////////////////////////////////////////////////////
// CAlculate Difference of Gaussian Features
////////////////////////////////////////////////////////////////
MITK_INFO << "Check for DoG...";
if (parsedArgs.count("difference-of-gaussian"))
{
MITK_INFO << "Calculate Difference of Gaussian... " << parsedArgs["difference-of-gaussian"].ToString();
auto ranges = splitDouble(parsedArgs["difference-of-gaussian"].ToString(),';');
for (int i = 0; i < ranges.size(); ++i)
{
mitk::Image::Pointer output;
AccessByItk_2(image, DifferenceOfGaussFilter, ranges[i], output);
std::string name = filename + "-dog-" + us::any_value_to_string(ranges[i])+".nii.gz";
mitk::IOUtil::SaveImage(output, name);
}
}
MITK_INFO << "Check for LoG...";
////////////////////////////////////////////////////////////////
// CAlculate Laplacian Of Gauss Features
////////////////////////////////////////////////////////////////
if (parsedArgs.count("laplace-of-gauss"))
{
MITK_INFO << "Calculate LoG... " << parsedArgs["laplace-of-gauss"].ToString();
auto ranges = splitDouble(parsedArgs["laplace-of-gauss"].ToString(),';');
for (int i = 0; i < ranges.size(); ++i)
{
mitk::Image::Pointer output;
AccessByItk_2(image, LaplacianOfGaussianFilter, ranges[i], output);
std::string name = filename + "-log-" + us::any_value_to_string(ranges[i])+".nii.gz";
mitk::IOUtil::SaveImage(output, name);
}
}
MITK_INFO << "Check for HoG...";
////////////////////////////////////////////////////////////////
// CAlculate Hessian Of Gauss Features
////////////////////////////////////////////////////////////////
if (parsedArgs.count("hessian-of-gauss"))
{
MITK_INFO << "Calculate HoG... " << parsedArgs["hessian-of-gauss"].ToString();
auto ranges = splitDouble(parsedArgs["hessian-of-gauss"].ToString(),';');
for (int i = 0; i < ranges.size(); ++i)
{
std::vector<mitk::Image::Pointer> outs;
outs.push_back(mitk::Image::New());
outs.push_back(mitk::Image::New());
outs.push_back(mitk::Image::New());
AccessByItk_2(image, HessianOfGaussianFilter, ranges[i], outs);
std::string name = filename + "-hog0-" + us::any_value_to_string(ranges[i])+".nii.gz";
mitk::IOUtil::SaveImage(outs[0], name);
name = filename + "-hog1-" + us::any_value_to_string(ranges[i])+".nii.gz";
mitk::IOUtil::SaveImage(outs[1], name);
name = filename + "-hog2-" + us::any_value_to_string(ranges[i])+".nii.gz";
mitk::IOUtil::SaveImage(outs[2], name);
}
}
return 0;
}
static void TestOverlay(mitk::Image::Pointer original,
mitk::Image::Pointer truth,
const double lower,
const double upper)
{
mitk::Image::Pointer overlayImage;
const double th[] = {lower, upper};
typedef itk::Image<unsigned int, 3> ImageType;
ImageType::Pointer itkOverlayImage = ImageType::New();
AccessByItk_2(original, InternalThreshold, overlayImage, th);
/*
AccessFixedDimensionByItk_2( original, InternalThreshold2,
3, itkOverlayImage,
th );
overlayImage = mitk::ImportItkImage( itkOverlayImage );
*/
// mitk::IOUtil::Save(truth, "/tmp/truth_TestOverlay.nii");
try
{
// mitk::Image::Pointer temp = overlayImage;
mitk::IOUtil::Save(overlayImage, "/tmp/overlayImage_TestOverlay.nrrd");
}
catch (const itk::ExceptionObject &e)
{
MITK_ERROR << "Save image: exception : " << e.what();
}
typedef itk::Image<unsigned int, 3> InputImageType;
InputImageType::Pointer overlayItk;
try
{
mitk::CastToItkImage(overlayImage, overlayItk);
}
catch (const mitk::Exception &e)
{
MITK_ERROR << "(CAST) Catched exception while creating accessor " << e.what();
// MITK_TEST_FAILED_MSG("Exception for ouverlay image");
}
/*
typedef itk::ImageFileWriter< InputImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName("/tmp/overlayITK_TestOverlay.nii");
writer->SetInput(overlayItk);
writer->Update();
*/
InputImageType::Pointer truthItk;
mitk::CastToItkImage(truth, truthItk);
bool difference = false;
/*
try
{
typedef unsigned int TPixel;
itk::ImageRegionConstIteratorWithIndex< InputImageType > iter( truthItk, truthItk->GetLargestPossibleRegion()
);
iter.GoToBegin();
mitk::ImagePixelReadAccessor< TPixel, 3 > readAccessor( overlayImage, overlayImage->GetVolumeData(0),
mitk::ImageAccessorBase::ExceptionIfLocked );
while( !iter.IsAtEnd() )
{
TPixel ref = iter.Get();
TPixel val = readAccessor.GetPixelByIndex( iter.GetIndex() );
difference |= ( ref != val );
//if( difference )
//{
std::cout << iter.GetIndex() << ":" << ref << " ? " << val << "\n";
//}
++iter;
}
}
catch( const mitk::Exception &e)
{
MITK_ERROR << "Catched exception while creating accessor "<< e.what();
//MITK_TEST_FAILED_MSG("Exception for ouverlay image");
}
*/
/*
typedef itk::Testing::ComparisonImageFilter
<InputImageType, InputImageType> ComparisonImageFilterType;
ComparisonImageFilterType::Pointer comp =
ComparisonImageFilterType::New();
comp->SetValidInput(truthItk);
comp->SetTestInput(overlayItk);
try
{
comp->Update();
}
catch( const itk::ExceptionObject& e)
{
MITK_ERROR << "ITK Exception: " << e.what();
}
*/
typedef unsigned int TPixel;
itk::ImageRegionConstIteratorWithIndex<InputImageType> iter(truthItk, truthItk->GetLargestPossibleRegion());
itk::ImageRegionConstIteratorWithIndex<InputImageType> iter2(overlayItk, overlayItk->GetLargestPossibleRegion());
iter.GoToBegin();
unsigned int counter = 0;
while (!iter.IsAtEnd() && !iter2.IsAtEnd())
{
TPixel ref = iter.Get();
TPixel val = iter2.Get();
if (ref != val)
{
counter++;
// std::cout << iter.GetIndex() << ":" << ref << " ? " << val << "\n";
}
++iter;
++iter2;
}
std::cout << "Differs in " << counter << "voxels" << std::endl;
MITK_TEST_CONDITION_REQUIRED(
// comp->GetNumberOfPixelsWithDifferences() == 0,
counter == 0,
"Comparing overlay with ground truth")
}
void QmitkAdaptiveRegionGrowingToolGUI::RunSegmentation()
{
if (m_InputImageNode.IsNull())
{
QMessageBox::information( NULL, "Adaptive Region Growing functionality", "Please specify the image in Datamanager!");
return;
}
mitk::DataNode::Pointer node = m_RegionGrow3DTool->GetPointSetNode();
if (node.IsNull())
{
QMessageBox::information( NULL, "Adaptive Region Growing functionality", "Please insert a seed point inside the image.\n\nFirst press the \"Define Seed Point\" button,\nthen click left mouse button inside the image.");
return;
}
//safety if no pointSet or pointSet empty
mitk::PointSet::Pointer seedPointSet = dynamic_cast<mitk::PointSet*> (node->GetData());
if (seedPointSet.IsNull())
{
m_Controls.m_pbRunSegmentation->setEnabled(true);
QMessageBox::information( NULL, "Adaptive Region Growing functionality", "The seed point is empty! Please choose a new seed point.");
return;
}
int timeStep = mitk::BaseRenderer::GetInstance( mitk::BaseRenderer::GetRenderWindowByName("stdmulti.widget1") )->GetTimeStep();
if (!(seedPointSet->GetSize(timeStep)))
{
m_Controls.m_pbRunSegmentation->setEnabled(true);
QMessageBox::information( NULL, "Adaptive Region Growing functionality", "The seed point is empty! Please choose a new seed point.");
return;
}
QApplication::setOverrideCursor( QCursor(Qt::WaitCursor) );
mitk::PointSet::PointType seedPoint = seedPointSet->GetPointSet(timeStep)->GetPoints()->Begin().Value();
mitk::Image::Pointer orgImage = dynamic_cast<mitk::Image*> (m_InputImageNode->GetData());
if (orgImage.IsNotNull())
{
if (orgImage->GetDimension() == 4)
{
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(orgImage);
timeSelector->SetTimeNr( timeStep );
timeSelector->UpdateLargestPossibleRegion();
mitk::Image* timedImage = timeSelector->GetOutput();
AccessByItk_2( timedImage , StartRegionGrowing, timedImage->GetGeometry(), seedPoint);
}
else if (orgImage->GetDimension() == 3)
{
//QApplication::setOverrideCursor(QCursor(Qt::WaitCursor)); //set the cursor to waiting
AccessByItk_2(orgImage, StartRegionGrowing, orgImage->GetGeometry(), seedPoint);
//QApplication::restoreOverrideCursor();//reset cursor
}
else
{
QApplication::restoreOverrideCursor();//reset cursor
QMessageBox::information( NULL, "Adaptive Region Growing functionality", "Only images of dimension 3 or 4 can be processed!");
return;
}
}
EnableControls(true); // Segmentation ran successfully, so enable all controls.
node->SetVisibility(true);
QApplication::restoreOverrideCursor();//reset cursor
}
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
// required params
parser.addArgument("planar", "p", mitkCommandLineParser::Directory, "Input Polydata", "Path to the input VTK polydata", us::Any(), false, false, false, mitkCommandLineParser::Input);
parser.addArgument("image", "i", mitkCommandLineParser::Directory, "Input Image", "Image which defines the dimensions of the Segmentation", us::Any(), false, false, false, mitkCommandLineParser::Output);
parser.addArgument("output", "o", mitkCommandLineParser::File, "Output file", "Output file. ", us::Any(), false, false, false, mitkCommandLineParser::Input);
// Miniapp Infos
parser.setCategory("Classification Tools");
parser.setTitle("Planar Data to Nrrd Segmentation");
parser.setDescription("Creates a Nrrd segmentation based on a 2d-vtk polydata.");
parser.setContributor("MBI");
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
{
return EXIT_FAILURE;
}
if ( parsedArgs.count("help") || parsedArgs.count("h"))
{
return EXIT_SUCCESS;
}
try
{
mitk::BaseData::Pointer data = mitk::IOUtil::Load(parsedArgs["planar"].ToString())[0];
mitk::PlanarFigure::Pointer planar = dynamic_cast<mitk::PlanarFigure*>(data.GetPointer());
mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(parsedArgs["image"].ToString());
mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New();
pfMaskGen->SetPlanarFigure(planar);
pfMaskGen->SetTimeStep(0);
pfMaskGen->SetInputImage(image.GetPointer());
mitk::Image::Pointer mask = pfMaskGen->GetMask();
unsigned int axis = pfMaskGen->GetPlanarFigureAxis();
unsigned int slice = pfMaskGen->GetPlanarFigureSlice();
//itk::Image<unsigned short, 3>::IndexType index;
mitk::Image::Pointer fullMask;
MaskParameter param;
param.slice = slice;
param.axis = axis;
param.mask = mask;
AccessByItk_2(image, CreateNewMask, param, fullMask);
std::string saveAs = parsedArgs["output"].ToString();
MITK_INFO << "Save as: " << saveAs;
mitk::IOUtil::Save(pfMaskGen->GetMask(), saveAs);
mitk::IOUtil::Save(fullMask, saveAs);
return 0;
}
catch (...)
{
return EXIT_FAILURE;
}
}
int main(int argc, char* argv[])
{
// Commented : Updated to a common interface, include, if possible, mask is type unsigned short, uses Quantification, Comments
// Name follows standard scheme with Class Name::Feature Name
// Commented 2: Updated to use automatic inclusion of list of parameters if required.
mitk::GIFImageDescriptionFeatures::Pointer ipCalculator = mitk::GIFImageDescriptionFeatures::New(); // Commented 2, Tested
mitk::GIFFirstOrderStatistics::Pointer firstOrderCalculator = mitk::GIFFirstOrderStatistics::New(); //Commented 2
mitk::GIFFirstOrderHistogramStatistics::Pointer firstOrderHistoCalculator = mitk::GIFFirstOrderHistogramStatistics::New(); // Commented 2, Tested
mitk::GIFFirstOrderNumericStatistics::Pointer firstOrderNumericCalculator = mitk::GIFFirstOrderNumericStatistics::New(); // Commented 2, Tested
mitk::GIFVolumetricStatistics::Pointer volCalculator = mitk::GIFVolumetricStatistics::New(); // Commented 2, Tested
mitk::GIFVolumetricDensityStatistics::Pointer voldenCalculator = mitk::GIFVolumetricDensityStatistics::New(); // Commented 2, Tested
mitk::GIFCooccurenceMatrix::Pointer coocCalculator = mitk::GIFCooccurenceMatrix::New(); // Commented 2, Will not be tested
mitk::GIFCooccurenceMatrix2::Pointer cooc2Calculator = mitk::GIFCooccurenceMatrix2::New(); //Commented 2
mitk::GIFNeighbouringGreyLevelDependenceFeature::Pointer ngldCalculator = mitk::GIFNeighbouringGreyLevelDependenceFeature::New(); //Commented 2, Tested
mitk::GIFGreyLevelRunLength::Pointer rlCalculator = mitk::GIFGreyLevelRunLength::New(); // Commented 2
mitk::GIFGreyLevelSizeZone::Pointer glszCalculator = mitk::GIFGreyLevelSizeZone::New(); // Commented 2, Tested
mitk::GIFGreyLevelDistanceZone::Pointer gldzCalculator = mitk::GIFGreyLevelDistanceZone::New(); //Commented 2, Tested
mitk::GIFLocalIntensity::Pointer lociCalculator = mitk::GIFLocalIntensity::New(); //Commented 2, Tested
mitk::GIFIntensityVolumeHistogramFeatures::Pointer ivohCalculator = mitk::GIFIntensityVolumeHistogramFeatures::New(); // Commented 2
mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::Pointer ngtdCalculator = mitk::GIFNeighbourhoodGreyToneDifferenceFeatures::New(); //Commented 2, Tested
mitk::GIFCurvatureStatistic::Pointer curvCalculator = mitk::GIFCurvatureStatistic::New(); //Commented 2, Tested
std::vector<mitk::AbstractGlobalImageFeature::Pointer> features;
features.push_back(volCalculator.GetPointer());
features.push_back(voldenCalculator.GetPointer());
features.push_back(curvCalculator.GetPointer());
features.push_back(firstOrderCalculator.GetPointer());
features.push_back(firstOrderNumericCalculator.GetPointer());
features.push_back(firstOrderHistoCalculator.GetPointer());
features.push_back(ivohCalculator.GetPointer());
features.push_back(lociCalculator.GetPointer());
features.push_back(coocCalculator.GetPointer());
features.push_back(cooc2Calculator.GetPointer());
features.push_back(ngldCalculator.GetPointer());
features.push_back(rlCalculator.GetPointer());
features.push_back(glszCalculator.GetPointer());
features.push_back(gldzCalculator.GetPointer());
features.push_back(ipCalculator.GetPointer());
features.push_back(ngtdCalculator.GetPointer());
mitkCommandLineParser parser;
parser.setArgumentPrefix("--", "-");
mitk::cl::GlobalImageFeaturesParameter param;
param.AddParameter(parser);
parser.addArgument("--","-", mitkCommandLineParser::String, "---", "---", us::Any(),true);
for (auto cFeature : features)
{
cFeature->AddArguments(parser);
}
parser.addArgument("--", "-", mitkCommandLineParser::String, "---", "---", us::Any(), true);
parser.addArgument("description","d",mitkCommandLineParser::String,"Text","Description that is added to the output",us::Any());
parser.addArgument("direction", "dir", mitkCommandLineParser::String, "Int", "Allows to specify the direction for Cooc and RL. 0: All directions, 1: Only single direction (Test purpose), 2,3,4... Without dimension 0,1,2... ", us::Any());
parser.addArgument("slice-wise", "slice", mitkCommandLineParser::String, "Int", "Allows to specify if the image is processed slice-wise (number giving direction) ", us::Any());
parser.addArgument("output-mode", "omode", mitkCommandLineParser::Int, "Int", "Defines if the results of an image / slice are written in a single row (0 , default) or column (1).");
// Miniapp Infos
parser.setCategory("Classification Tools");
parser.setTitle("Global Image Feature calculator");
parser.setDescription("Calculates different global statistics for a given segmentation / image combination");
parser.setContributor("MBI");
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
param.ParseParameter(parsedArgs);
if (parsedArgs.size()==0)
{
return EXIT_FAILURE;
}
if ( parsedArgs.count("help") || parsedArgs.count("h"))
{
return EXIT_SUCCESS;
}
//bool savePNGofSlices = true;
//std::string folderForPNGOfSlices = "E:\\tmp\\bonekamp\\fig\\";
std::string version = "Version: 1.22";
MITK_INFO << version;
std::ofstream log;
if (param.useLogfile)
{
log.open(param.logfilePath, std::ios::app);
log << std::endl;
log << version;
log << "Image: " << param.imagePath;
log << "Mask: " << param.maskPath;
}
if (param.useDecimalPoint)
{
std::cout.imbue(std::locale(std::cout.getloc(), new punct_facet<char>(param.decimalPoint)));
}
mitk::Image::Pointer image;
mitk::Image::Pointer mask;
mitk::Image::Pointer tmpImage = mitk::IOUtil::Load<mitk::Image>(param.imagePath);
mitk::Image::Pointer tmpMask = mitk::IOUtil::Load<mitk::Image>(param.maskPath);
image = tmpImage;
mask = tmpMask;
mitk::Image::Pointer morphMask = mask;
if (param.useMorphMask)
{
morphMask = mitk::IOUtil::Load<mitk::Image>(param.morphPath);
}
log << " Check for Dimensions -";
if ((image->GetDimension() != mask->GetDimension()))
{
MITK_INFO << "Dimension of image does not match. ";
MITK_INFO << "Correct one image, may affect the result";
if (image->GetDimension() == 2)
{
mitk::Convert2Dto3DImageFilter::Pointer multiFilter2 = mitk::Convert2Dto3DImageFilter::New();
multiFilter2->SetInput(tmpImage);
multiFilter2->Update();
image = multiFilter2->GetOutput();
}
if (mask->GetDimension() == 2)
{
mitk::Convert2Dto3DImageFilter::Pointer multiFilter3 = mitk::Convert2Dto3DImageFilter::New();
multiFilter3->SetInput(tmpMask);
multiFilter3->Update();
mask = multiFilter3->GetOutput();
}
}
int writeDirection = 0;
if (parsedArgs.count("output-mode"))
{
writeDirection = us::any_cast<int>(parsedArgs["output-mode"]);
}
log << " Check for Resolution -";
if (param.resampleToFixIsotropic)
{
mitk::Image::Pointer newImage = mitk::Image::New();
AccessByItk_2(image, ResampleImage, param.resampleResolution, newImage);
image = newImage;
}
if ( ! mitk::Equal(mask->GetGeometry(0)->GetOrigin(), image->GetGeometry(0)->GetOrigin()))
{
MITK_INFO << "Not equal Origins";
if (param.ensureSameSpace)
{
MITK_INFO << "Warning!";
MITK_INFO << "The origin of the input image and the mask do not match. They are";
MITK_INFO << "now corrected. Please check to make sure that the images still match";
image->GetGeometry(0)->SetOrigin(mask->GetGeometry(0)->GetOrigin());
} else
{
return -1;
}
}
log << " Resample if required -";
if (param.resampleMask)
{
mitk::Image::Pointer newMaskImage = mitk::Image::New();
AccessByItk_2(mask, ResampleMask, image, newMaskImage);
mask = newMaskImage;
}
log << " Check for Equality -";
if ( ! mitk::Equal(mask->GetGeometry(0)->GetSpacing(), image->GetGeometry(0)->GetSpacing()))
{
MITK_INFO << "Not equal Spacing";
if (param.ensureSameSpace)
{
MITK_INFO << "Warning!";
MITK_INFO << "The spacing of the mask was set to match the spacing of the input image.";
MITK_INFO << "This might cause unintended spacing of the mask image";
image->GetGeometry(0)->SetSpacing(mask->GetGeometry(0)->GetSpacing());
} else
{
MITK_INFO << "The spacing of the mask and the input images is not equal.";
MITK_INFO << "Terminating the programm. You may use the '-fi' option";
return -1;
}
}
int direction = 0;
if (parsedArgs.count("direction"))
{
direction = mitk::cl::splitDouble(parsedArgs["direction"].ToString(), ';')[0];
}
MITK_INFO << "Start creating Mask without NaN";
mitk::Image::Pointer maskNoNaN = mitk::Image::New();
AccessByItk_2(image, CreateNoNaNMask, mask, maskNoNaN);
//CreateNoNaNMask(mask, image, maskNoNaN);
bool sliceWise = false;
int sliceDirection = 0;
unsigned int currentSlice = 0;
bool imageToProcess = true;
std::vector<mitk::Image::Pointer> floatVector;
std::vector<mitk::Image::Pointer> maskVector;
std::vector<mitk::Image::Pointer> maskNoNaNVector;
std::vector<mitk::Image::Pointer> morphMaskVector;
if ((parsedArgs.count("slice-wise")) && image->GetDimension() > 2)
{
MITK_INFO << "Enabled slice-wise";
sliceWise = true;
sliceDirection = mitk::cl::splitDouble(parsedArgs["slice-wise"].ToString(), ';')[0];
MITK_INFO << sliceDirection;
ExtractSlicesFromImages(image, mask, maskNoNaN, morphMask, sliceDirection, floatVector, maskVector, maskNoNaNVector, morphMaskVector);
MITK_INFO << "Slice";
}
log << " Configure features -";
for (auto cFeature : features)
{
if (param.defineGlobalMinimumIntensity)
{
cFeature->SetMinimumIntensity(param.globalMinimumIntensity);
cFeature->SetUseMinimumIntensity(true);
}
if (param.defineGlobalMaximumIntensity)
{
cFeature->SetMaximumIntensity(param.globalMaximumIntensity);
cFeature->SetUseMaximumIntensity(true);
}
if (param.defineGlobalNumberOfBins)
{
cFeature->SetBins(param.globalNumberOfBins);
MITK_INFO << param.globalNumberOfBins;
}
cFeature->SetParameter(parsedArgs);
cFeature->SetDirection(direction);
cFeature->SetEncodeParameters(param.encodeParameter);
}
bool addDescription = parsedArgs.count("description");
mitk::cl::FeatureResultWritter writer(param.outputPath, writeDirection);
if (param.useDecimalPoint)
{
writer.SetDecimalPoint(param.decimalPoint);
}
std::string description = "";
if (addDescription)
{
description = parsedArgs["description"].ToString();
}
mitk::Image::Pointer cImage = image;
mitk::Image::Pointer cMask = mask;
mitk::Image::Pointer cMaskNoNaN = maskNoNaN;
mitk::Image::Pointer cMorphMask = morphMask;
if (param.useHeader)
{
writer.AddColumn("SoftwareVersion");
writer.AddColumn("Patient");
writer.AddColumn("Image");
writer.AddColumn("Segmentation");
}
// Create a QTApplication and a Datastorage
// This is necessary in order to save screenshots of
// each image / slice.
QApplication qtapplication(argc, argv);
QmitkRegisterClasses();
std::vector<mitk::AbstractGlobalImageFeature::FeatureListType> allStats;
log << " Begin Processing -";
while (imageToProcess)
{
if (sliceWise)
{
cImage = floatVector[currentSlice];
cMask = maskVector[currentSlice];
cMaskNoNaN = maskNoNaNVector[currentSlice];
cMorphMask = morphMaskVector[currentSlice];
imageToProcess = (floatVector.size()-1 > (currentSlice)) ? true : false ;
}
else
{
imageToProcess = false;
}
if (param.writePNGScreenshots)
{
SaveSliceOrImageAsPNG(cImage, cMask, param.pngScreenshotsPath, currentSlice);
}
if (param.writeAnalysisImage)
{
mitk::IOUtil::Save(cImage, param.anaylsisImagePath);
}
if (param.writeAnalysisMask)
{
mitk::IOUtil::Save(cMask, param.analysisMaskPath);
}
mitk::AbstractGlobalImageFeature::FeatureListType stats;
for (auto cFeature : features)
{
log << " Calculating " << cFeature->GetFeatureClassName() << " -";
cFeature->SetMorphMask(cMorphMask);
cFeature->CalculateFeaturesUsingParameters(cImage, cMask, cMaskNoNaN, stats);
}
for (std::size_t i = 0; i < stats.size(); ++i)
{
std::cout << stats[i].first << " - " << stats[i].second << std::endl;
}
writer.AddHeader(description, currentSlice, stats, param.useHeader, addDescription);
if (true)
{
writer.AddSubjectInformation(MITK_REVISION);
writer.AddSubjectInformation(param.imageFolder);
writer.AddSubjectInformation(param.imageName);
writer.AddSubjectInformation(param.maskName);
}
writer.AddResult(description, currentSlice, stats, param.useHeader, addDescription);
allStats.push_back(stats);
++currentSlice;
}
log << " Process Slicewise -";
if (sliceWise)
{
mitk::AbstractGlobalImageFeature::FeatureListType statMean, statStd;
for (std::size_t i = 0; i < allStats[0].size(); ++i)
{
auto cElement1 = allStats[0][i];
cElement1.first = "SliceWise Mean " + cElement1.first;
cElement1.second = 0.0;
auto cElement2 = allStats[0][i];
cElement2.first = "SliceWise Var. " + cElement2.first;
cElement2.second = 0.0;
statMean.push_back(cElement1);
statStd.push_back(cElement2);
}
for (auto cStat : allStats)
{
for (std::size_t i = 0; i < cStat.size(); ++i)
{
statMean[i].second += cStat[i].second / (1.0*allStats.size());
}
}
for (auto cStat : allStats)
{
for (std::size_t i = 0; i < cStat.size(); ++i)
{
statStd[i].second += (cStat[i].second - statMean[i].second)*(cStat[i].second - statMean[i].second) / (1.0*allStats.size());
}
}
for (std::size_t i = 0; i < statMean.size(); ++i)
{
std::cout << statMean[i].first << " - " << statMean[i].second << std::endl;
std::cout << statStd[i].first << " - " << statStd[i].second << std::endl;
}
if (true)
{
writer.AddSubjectInformation(MITK_REVISION);
writer.AddSubjectInformation(param.imageFolder);
writer.AddSubjectInformation(param.imageName);
writer.AddSubjectInformation(param.maskName + " - Mean");
}
writer.AddResult(description, currentSlice, statMean, param.useHeader, addDescription);
if (true)
{
writer.AddSubjectInformation(MITK_REVISION);
writer.AddSubjectInformation(param.imageFolder);
writer.AddSubjectInformation(param.imageName);
writer.AddSubjectInformation(param.maskName + " - Var.");
}
writer.AddResult(description, currentSlice, statStd, param.useHeader, addDescription);
}
if (param.useLogfile)
{
log << "Finished calculation" << std::endl;
log.close();
}
return 0;
}