void mitk::BinaryThresholdULTool::CreateNewSegmentationFromThreshold(DataNode* node)
{
if (node)
{
Image::Pointer feedBackImage = dynamic_cast<Image*>( m_ThresholdFeedbackNode->GetData() );
if (feedBackImage.IsNotNull())
{
// create a new image of the same dimensions and smallest possible pixel type
DataNode::Pointer emptySegmentation = GetTargetSegmentationNode();
if (emptySegmentation)
{
// actually perform a thresholding and ask for an organ type
for (unsigned int timeStep = 0; timeStep < feedBackImage->GetTimeSteps(); ++timeStep)
{
try
{
ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
timeSelector->SetInput( feedBackImage );
timeSelector->SetTimeNr( timeStep );
timeSelector->UpdateLargestPossibleRegion();
Image::Pointer feedBackImage3D = timeSelector->GetOutput();
if (feedBackImage3D->GetDimension() == 2)
{
AccessFixedDimensionByItk_2( feedBackImage3D, ITKSetVolume, 2, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
}
else
{
AccessFixedDimensionByItk_2( feedBackImage3D, ITKSetVolume, 3, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
}
}
catch(...)
{
Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation.");
}
}
//since we are maybe working on a smaller image, pad it to the size of the original image
if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer())
{
mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New();
padFilter->SetInput(0, dynamic_cast<mitk::Image*> (emptySegmentation->GetData()));
padFilter->SetInput(1, dynamic_cast<mitk::Image*> (m_OriginalImageNode->GetData()));
padFilter->SetBinaryFilter(true);
padFilter->SetUpperThreshold(1);
padFilter->SetLowerThreshold(1);
padFilter->Update();
emptySegmentation->SetData(padFilter->GetOutput());
}
m_ToolManager->SetWorkingData( emptySegmentation );
m_ToolManager->GetWorkingData(0)->Modified();
}
}
}
}
void job_test()
{
typedef itk::Image<int,3> Image;
typedef itk::ImageFileReader<Image> Reader;
// Read in the image (when debugging in VC++, it may be necessary to set the working directory to "$(TargetDir)").
std::cout << "Loading input image...\n";
Reader::Pointer reader = Reader::New();
reader->SetFileName("../resources/test.bmp");
reader->Update();
Image::Pointer image = reader->GetOutput();
// Create a DICOM volume (obviously not a proper one, as the image being read in is actually a greyscale one).
DICOMVolume_Ptr volume(new DICOMVolume(image));
// Set the segmentation options.
itk::Size<3> size = image->GetLargestPossibleRegion().GetSize();
WindowSettings windowSettings(40, 400); // dummy window settings
CTSegmentationOptions options(30, CTSegmentationOptions::INPUTTYPE_HOUNSFIELD, size, 10, windowSettings);
// Build the IPF.
std::cout << "Building IPF...\n";
typedef CTIPFBuilder::IPF_Ptr IPF_Ptr;
IPF_Ptr ipf;
Job_Ptr job(new CTIPFBuilder(volume, options, ipf));
Job::execute_in_thread(job);
while(!job->is_finished());
// Output the mosaic images for each of the partition forest layers.
std::cout << "Outputting mosaic images...\n";
for(int i=0; i<=ipf->highest_layer(); ++i)
{
output_mosaic_image(ipf, i, size[0], size[1]);
}
}
//#################### HELPER FUNCTIONS ####################
itk::Image<unsigned char,2>::Pointer make_mosaic_image(const boost::shared_ptr<const PartitionForest<CTImageLeafLayer,CTImageBranchLayer> >& ipf, int layerIndex,
int width, int height)
{
typedef itk::Image<unsigned char,2> Image;
typedef PartitionForest<CTImageLeafLayer,CTImageBranchLayer> IPF;
Image::Pointer image = ITKImageUtil::make_image<unsigned char>(width, height);
Image::IndexType index;
int n = 0;
for(index[1]=0; index[1]<height; ++index[1])
for(index[0]=0; index[0]<width; ++index[0])
{
unsigned char mosaicValue;
if(layerIndex > 0)
{
PFNodeID ancestor = ipf->ancestor_of(PFNodeID(0, n), layerIndex);
mosaicValue = static_cast<unsigned char>(ipf->branch_properties(ancestor).mean_grey_value());
}
else mosaicValue = ipf->leaf_properties(n).grey_value();
image->SetPixel(index, mosaicValue);
++n;
}
return image;
}
bool CalculateSegmentationVolume::ReadyToRun()
{
Image::Pointer image;
GetPointerParameter("Input", image);
return image.IsNotNull() && GetGroupNode();
}
void mitk::SegTool2D::WriteBackSegmentationResult(std::vector<mitk::SegTool2D::SliceInformation> sliceList, bool writeSliceToVolume)
{
std::vector<mitk::Surface::Pointer> contourList;
contourList.reserve(sliceList.size());
ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
Image* image = dynamic_cast<Image*>(workingNode->GetData());
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput( image );
timeSelector->SetTimeNr( 0 );
timeSelector->SetChannelNr( 0 );
timeSelector->Update();
Image::Pointer dimRefImg = timeSelector->GetOutput();
for (unsigned int i = 0; i < sliceList.size(); ++i)
{
SliceInformation currentSliceInfo = sliceList.at(i);
if(writeSliceToVolume)
this->WriteSliceToVolume(currentSliceInfo);
if (m_SurfaceInterpolationEnabled && dimRefImg->GetDimension() == 3)
{
currentSliceInfo.slice->DisconnectPipeline();
contourExtractor->SetInput(currentSliceInfo.slice);
contourExtractor->Update();
mitk::Surface::Pointer contour = contourExtractor->GetOutput();
contour->DisconnectPipeline();
contourList.push_back(contour);
}
}
mitk::SurfaceInterpolationController::GetInstance()->AddNewContours(contourList);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
bool CalculateSegmentationVolume::ThreadedUpdateFunction()
{
// get image
Image::Pointer image;
GetPointerParameter("Input", image);
AccessFixedDimensionByItk(image.GetPointer(),
ItkImageProcessing,
3); // some magic to call the correctly templated function (we only do 3D images here!)
// consider single voxel volume
Vector3D spacing = image->GetSlicedGeometry()->GetSpacing(); // spacing in mm
float volumeML = (ScalarType)m_Volume * spacing[0] * spacing[1] * spacing[2] / 1000.0; // convert to ml
DataNode *groupNode = GetGroupNode();
if (groupNode)
{
groupNode->SetProperty("volume", FloatProperty::New(volumeML));
groupNode->SetProperty("centerOfMass", Vector3DProperty::New(m_CenterOfMass));
groupNode->SetProperty("boundingBoxMinimum", Vector3DProperty::New(m_MinIndexOfBoundingBox));
groupNode->SetProperty("boundingBoxMaximum", Vector3DProperty::New(m_MaxIndexOfBoundingBox));
groupNode->SetProperty("showVolume", BoolProperty::New(true));
}
return true;
}
/*
* What is the input requested region that is required to produce the output
* requested region? By default, the largest possible region is always
* required but this is overridden in many subclasses. For instance, for an
* image processing filter where an output pixel is a simple function of an
* input pixel, the input requested region will be set to the output
* requested region. For an image processing filter where an output pixel is
* a function of the pixels in a neighborhood of an input pixel, then the
* input requested region will need to be larger than the output requested
* region (to avoid introducing artificial boundary conditions). This
* function should never request an input region that is outside the the
* input largest possible region (i.e. implementations of this method should
* crop the input requested region at the boundaries of the input largest
* possible region).
*/
void mitk::ExtractImageFilter::GenerateInputRequestedRegion()
{
Superclass::GenerateInputRequestedRegion();
ImageToImageFilter::InputImagePointer input = const_cast< ImageToImageFilter::InputImageType* > ( this->GetInput() );
Image::Pointer output = this->GetOutput();
if (input->GetDimension() == 2)
{
input->SetRequestedRegionToLargestPossibleRegion();
return;
}
Image::RegionType requestedRegion;
requestedRegion = output->GetRequestedRegion();
requestedRegion.SetIndex(0, 0);
requestedRegion.SetIndex(1, 0);
requestedRegion.SetIndex(2, 0);
requestedRegion.SetSize(0, input->GetDimension(0));
requestedRegion.SetSize(1, input->GetDimension(1));
requestedRegion.SetSize(2, input->GetDimension(2));
requestedRegion.SetIndex( m_SliceDimension, m_SliceIndex ); // only one slice needed
requestedRegion.SetSize( m_SliceDimension, 1 );
input->SetRequestedRegion( &requestedRegion );
}
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();
}
static IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, itk::PolyLineParametricPath<3>::Pointer path)
{
IntensityProfile::Pointer intensityProfile = IntensityProfile::New();
itk::PolyLineParametricPath<3>::InputType input = path->StartOfInput();
BaseGeometry* imageGeometry = image->GetGeometry();
const PixelType pixelType = image->GetPixelType();
IntensityProfile::MeasurementVectorType measurementVector;
itk::PolyLineParametricPath<3>::OffsetType offset;
Point3D worldPoint;
itk::Index<3> index;
do
{
imageGeometry->IndexToWorld(path->Evaluate(input), worldPoint);
imageGeometry->WorldToIndex(worldPoint, index);
mitkPixelTypeMultiplex3(ReadPixel, pixelType, image, index, measurementVector.GetDataPointer());
intensityProfile->PushBack(measurementVector);
offset = path->IncrementInput(input);
} while ((offset[0] | offset[1] | offset[2]) != 0);
return intensityProfile;
}
ImageBinary::Pointer label2mask(Image::Pointer label, unsigned int element)
{
ImageBinary::Pointer mask = ImageBinary::New();
Image::RegionType region = label->GetLargestPossibleRegion();
mask->SetRegions(region);
mask->Allocate();
mask->FillBuffer(0);
ConstIterator iterator_label(label, label->GetLargestPossibleRegion());
IteratorBinary iterator_mask(mask, mask->GetLargestPossibleRegion());
try
{
while(!iterator_label.IsAtEnd())
{
if(iterator_label.Get() == element && element || iterator_label.Get() != 0 && !element)
iterator_mask.Set(1);
++iterator_label; ++iterator_mask;
}
}
catch(itk::ExceptionObject & err)
{
std::cerr<<"Exception caught, outside bounds using iterators"<<std::endl;
std::cerr<<err<<std::endl;
}
return mask;
}
void mitk::SegTool2D::UpdateSurfaceInterpolation(const Image *slice,
const Image *workingImage,
const PlaneGeometry *plane,
bool detectIntersection)
{
if (!m_SurfaceInterpolationEnabled)
return;
ImageToContourFilter::Pointer contourExtractor = ImageToContourFilter::New();
mitk::Surface::Pointer contour;
if (detectIntersection)
{
// Test whether there is something to extract or whether the slice just contains intersections of others
mitk::Image::Pointer slice2 = slice->Clone();
mitk::MorphologicalOperations::Erode(slice2, 2, mitk::MorphologicalOperations::Ball);
contourExtractor->SetInput(slice2);
contourExtractor->Update();
contour = contourExtractor->GetOutput();
if (contour->GetVtkPolyData()->GetNumberOfPoints() == 0)
{
// Remove contour!
mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
contourInfo.contourNormal = plane->GetNormal();
contourInfo.contourPoint = plane->GetOrigin();
mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo);
return;
}
}
contourExtractor->SetInput(slice);
contourExtractor->Update();
contour = contourExtractor->GetOutput();
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(workingImage);
timeSelector->SetTimeNr(0);
timeSelector->SetChannelNr(0);
timeSelector->Update();
Image::Pointer dimRefImg = timeSelector->GetOutput();
if (contour->GetVtkPolyData()->GetNumberOfPoints() != 0 && dimRefImg->GetDimension() == 3)
{
mitk::SurfaceInterpolationController::GetInstance()->AddNewContour(contour);
contour->DisconnectPipeline();
}
else
{
// Remove contour!
mitk::SurfaceInterpolationController::ContourPositionInformation contourInfo;
contourInfo.contourNormal = plane->GetNormal();
contourInfo.contourPoint = plane->GetOrigin();
mitk::SurfaceInterpolationController::GetInstance()->RemoveContour(contourInfo);
}
}
void mitk::BinaryThresholdULTool::CreateNewSegmentationFromThreshold(DataNode* node, const std::string& organName, const Color& color)
{
if (node)
{
Image::Pointer image = dynamic_cast<Image*>( m_NodeForThresholding->GetData() );
if (image.IsNotNull())
{
// create a new image of the same dimensions and smallest possible pixel type
DataNode::Pointer emptySegmentation = Tool::CreateEmptySegmentationNode( image, organName, color );
if (emptySegmentation)
{
// actually perform a thresholding and ask for an organ type
for (unsigned int timeStep = 0; timeStep < image->GetTimeSteps(); ++timeStep)
{
try
{
ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
timeSelector->SetInput( image );
timeSelector->SetTimeNr( timeStep );
timeSelector->UpdateLargestPossibleRegion();
Image::Pointer image3D = timeSelector->GetOutput();
AccessFixedDimensionByItk_2( image3D, ITKThresholding, 3, dynamic_cast<Image*>(emptySegmentation->GetData()), timeStep );
}
catch(...)
{
Tool::ErrorMessage("Error accessing single time steps of the original image. Cannot create segmentation.");
}
}
//since we are maybe working on a smaller image, pad it to the size of the original image
if (m_OriginalImageNode.GetPointer() != m_NodeForThresholding.GetPointer())
{
mitk::PadImageFilter::Pointer padFilter = mitk::PadImageFilter::New();
padFilter->SetInput(0, dynamic_cast<mitk::Image*> (emptySegmentation->GetData()));
padFilter->SetInput(1, dynamic_cast<mitk::Image*> (m_OriginalImageNode->GetData()));
padFilter->SetBinaryFilter(true);
padFilter->SetUpperThreshold(1);
padFilter->SetLowerThreshold(1);
padFilter->Update();
emptySegmentation->SetData(padFilter->GetOutput());
}
if (DataStorage* ds = m_ToolManager->GetDataStorage())
{
ds->Add( emptySegmentation, m_OriginalImageNode );
}
m_ToolManager->SetWorkingData( emptySegmentation );
}
}
}
}
bool SegmentationSink::ReadyToRun()
{
Image::Pointer image;
GetPointerParameter("Input", image);
DataNode::Pointer groupNode;
GetPointerParameter("Group node", groupNode);
return image.IsNotNull() && groupNode.IsNotNull();
}
mitk::Image::Pointer mitk::CompressedImageContainer::GetImage()
{
if (m_ByteBuffers.empty())
return nullptr;
// uncompress image data, create an Image
Image::Pointer image = Image::New();
unsigned int dims[20]; // more than 20 dimensions and bang
for (unsigned int dim = 0; dim < m_ImageDimension; ++dim)
dims[dim] = m_ImageDimensions[dim];
image->Initialize(*m_PixelType, m_ImageDimension, dims); // this IS needed, right ?? But it does allocate memory ->
// does create one big lump of memory (also in windows)
unsigned int timeStep(0);
for (auto iter = m_ByteBuffers.begin(); iter != m_ByteBuffers.end(); ++iter, ++timeStep)
{
ImageReadAccessor imgAcc(image, image->GetVolumeData(timeStep));
auto *dest((unsigned char *)imgAcc.GetData());
::uLongf destLen(m_OneTimeStepImageSizeInBytes);
::Bytef *source(iter->first);
::uLongf sourceLen(iter->second);
int zlibRetVal = ::uncompress(dest, &destLen, source, sourceLen);
if (itk::Object::GetDebug())
{
if (zlibRetVal == Z_OK)
{
MITK_INFO << "Success, destLen now " << destLen << " bytes" << std::endl;
}
else
{
switch (zlibRetVal)
{
case Z_DATA_ERROR:
MITK_ERROR << "compressed data corrupted" << std::endl;
break;
case Z_MEM_ERROR:
MITK_ERROR << "not enough memory" << std::endl;
break;
case Z_BUF_ERROR:
MITK_ERROR << "output buffer too small" << std::endl;
break;
default:
MITK_ERROR << "other, unspecified error" << std::endl;
break;
}
}
}
}
image->SetGeometry(m_ImageGeometry);
image->Modified();
return image;
}
/*
* Generate the information decribing the output data. The default
* implementation of this method will copy information from the input to the
* output. A filter may override this method if its output will have different
* information than its input. For instance, a filter that shrinks an image will
* need to provide an implementation for this method that changes the spacing of
* the pixels. Such filters should call their superclass' implementation of this
* method prior to changing the information values they need (i.e.
* GenerateOutputInformation() should call
* Superclass::GenerateOutputInformation() prior to changing the information.
*/
void mitk::ExtractImageFilter::GenerateOutputInformation()
{
Image::Pointer output = this->GetOutput();
Image::ConstPointer input = this->GetInput();
if (input.IsNull()) return;
if ( m_SliceDimension >= input->GetDimension() && input->GetDimension() != 2 )
{
MITK_ERROR << "mitk::ExtractImageFilter:GenerateOutputInformation m_SliceDimension == " << m_SliceDimension << " makes no sense with an " << input->GetDimension() << "D image." << std::endl;
itkExceptionMacro("This is not a sensible value for m_SliceDimension.");
return;
}
unsigned int sliceDimension( m_SliceDimension );
if ( input->GetDimension() == 2)
{
sliceDimension = 2;
}
unsigned int tmpDimensions[2];
switch ( sliceDimension )
{
default:
case 2:
// orientation = PlaneGeometry::Axial;
tmpDimensions[0] = input->GetDimension(0);
tmpDimensions[1] = input->GetDimension(1);
break;
case 1:
// orientation = PlaneGeometry::Frontal;
tmpDimensions[0] = input->GetDimension(0);
tmpDimensions[1] = input->GetDimension(2);
break;
case 0:
// orientation = PlaneGeometry::Sagittal;
tmpDimensions[0] = input->GetDimension(1);
tmpDimensions[1] = input->GetDimension(2);
break;
}
output->Initialize(input->GetPixelType(), 2, tmpDimensions, 1 /*input->GetNumberOfChannels()*/);
// initialize the spacing of the output
/*
Vector3D spacing = input->GetSlicedGeometry()->GetSpacing();
if(input->GetDimension()>=2)
spacing[2]=spacing[1];
else
spacing[2] = 1.0;
output->GetSlicedGeometry()->SetSpacing(spacing);
*/
output->SetPropertyList(input->GetPropertyList()->Clone());
}
void mitk::CollectionGrayOpening::PerformGrayOpening(mitk::DataCollection *dataCollection,
std::string name,
std::string suffix)
{
for (size_t patient = 0; patient < dataCollection->Size(); ++patient)
{
DataCollection *dataPatient = dynamic_cast<DataCollection *>(dataCollection->GetData(patient).GetPointer());
if (dataPatient == nullptr)
MITK_ERROR << "PerformGrayOpening - Structure of DataCollection is invalid at patient level. Data inconsistent!";
if (dataPatient->Size() == 0)
MITK_ERROR << "Empty Patient Collective. Probably Fatal.";
for (size_t timeStep = 0; timeStep < dataPatient->Size(); ++timeStep)
{
DataCollection *dataTimeStep = dynamic_cast<DataCollection *>(dataPatient->GetData(timeStep).GetPointer());
if (dataTimeStep == nullptr)
MITK_ERROR
<< "DilateBinaryByName- Structure of DataCollection is invalid at time step level. Data inconsistent!";
// BinaryImage::Pointer itkImage = BinaryImage::New();
ImageType::Pointer itkImage = ImageType::New();
Image::Pointer tmp = dataTimeStep->GetMitkImage(name).GetPointer();
if (tmp.IsNull())
MITK_ERROR << "null";
CastToItkImage(tmp, itkImage);
if (itkImage.IsNull())
MITK_ERROR << "Image " << name << " does not exist. Fatal.";
typedef itk::FlatStructuringElement<3> StructuringElementType;
StructuringElementType::RadiusType elementRadius;
elementRadius.Fill(1);
elementRadius[2] = 0;
StructuringElementType structuringElement = StructuringElementType::Box(elementRadius);
typedef itk::GrayscaleMorphologicalOpeningImageFilter<ImageType, ImageType, StructuringElementType>
DilateImageFilterType;
DilateImageFilterType::Pointer dilateFilter0 = DilateImageFilterType::New();
dilateFilter0->SetInput(itkImage);
dilateFilter0->SetKernel(structuringElement);
dilateFilter0->Update();
DilateImageFilterType::Pointer dilateFilter1 = DilateImageFilterType::New();
dilateFilter1->SetInput(dilateFilter0->GetOutput());
dilateFilter1->SetKernel(structuringElement);
dilateFilter1->Update();
Image::Pointer dil = GrabItkImageMemory(dilateFilter1->GetOutput());
dataTimeStep->AddData(dil.GetPointer(), name + suffix, "");
}
}
}
void mitk::SetRegionTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent)
{
auto *positionEvent = dynamic_cast<mitk::InteractionPositionEvent *>(interactionEvent);
if (!positionEvent)
return;
assert(positionEvent->GetSender()->GetRenderWindow());
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's
// working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
DataNode *workingNode(m_ToolManager->GetWorkingData(0));
if (!workingNode)
return;
auto *image = dynamic_cast<Image *>(workingNode->GetData());
const PlaneGeometry *planeGeometry((positionEvent->GetSender()->GetCurrentWorldPlaneGeometry()));
if (!image || !planeGeometry)
return;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage(positionEvent, image);
if (slice.IsNull())
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return;
}
ContourModel *feedbackContour(FeedbackContourTool::GetFeedbackContour());
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice(
slice, feedbackContour, false, false); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull())
return;
auto *labelImage = dynamic_cast<LabelSetImage *>(image);
int activeColor = 1;
if (labelImage != nullptr)
{
activeColor = labelImage->GetActiveLabel()->GetValue();
}
mitk::ContourModelUtils::FillContourInSlice(
projectedContour, timeStep, slice, image, m_PaintingPixelValue * activeColor);
this->WriteBackSegmentationResult(positionEvent, slice);
}
mitk::Image::Pointer mitk::VolumeDataVtkMapper3D::GetMask()
{
if (this->m_Mask)
{
Image::Pointer mask = Image::New();
mask->Initialize(this->m_Mask);
mask->SetImportVolume(this->m_Mask->GetScalarPointer(), 0, 0, Image::ReferenceMemory);
mask->SetGeometry(this->GetInput()->GetGeometry());
return mask;
}
return 0;
}
bool ShowSegmentationAsSurface::ReadyToRun()
{
try
{
Image::Pointer image;
GetPointerParameter("Input", image);
return image.IsNotNull() && GetGroupNode();
}
catch (std::invalid_argument &)
{
return false;
}
}
void mitk::BinaryThresholdTool::SetupPreviewNode()
{
if (m_NodeForThresholding.IsNotNull())
{
Image::Pointer image = dynamic_cast<Image*>(m_NodeForThresholding->GetData());
Image::Pointer originalImage = dynamic_cast<Image*> (m_OriginalImageNode->GetData());
if (image.IsNotNull())
{
mitk::Image* workingimage = dynamic_cast<mitk::Image*>(m_ToolManager->GetWorkingData(0)->GetData());
if (workingimage)
{
m_ThresholdFeedbackNode->SetData(workingimage->Clone());
//Let's paint the feedback node green...
mitk::LabelSetImage::Pointer previewImage = dynamic_cast<mitk::LabelSetImage*> (m_ThresholdFeedbackNode->GetData());
itk::RGBPixel<float> pixel;
pixel[0] = 0.0f;
pixel[1] = 1.0f;
pixel[2] = 0.0f;
previewImage->GetActiveLabel()->SetColor(pixel);
previewImage->GetActiveLabelSet()->UpdateLookupTable(previewImage->GetActiveLabel()->GetValue());
}
else
m_ThresholdFeedbackNode->SetData(mitk::Image::New());
int layer(50);
m_NodeForThresholding->GetIntProperty("layer", layer);
m_ThresholdFeedbackNode->SetIntProperty("layer", layer + 1);
if (DataStorage* ds = m_ToolManager->GetDataStorage())
{
if (!ds->Exists(m_ThresholdFeedbackNode))
ds->Add(m_ThresholdFeedbackNode, m_OriginalImageNode);
}
if (image.GetPointer() == originalImage.GetPointer())
{
Image::StatisticsHolderPointer statistics = originalImage->GetStatistics();
m_SensibleMinimumThresholdValue = static_cast<double>(statistics->GetScalarValueMin());
m_SensibleMaximumThresholdValue = static_cast<double>(statistics->GetScalarValueMax());
}
if ((originalImage->GetPixelType().GetPixelType() == itk::ImageIOBase::SCALAR)
&& (originalImage->GetPixelType().GetComponentType() == itk::ImageIOBase::FLOAT || originalImage->GetPixelType().GetComponentType() == itk::ImageIOBase::DOUBLE))
m_IsFloatImage = true;
else
m_IsFloatImage = false;
m_CurrentThresholdValue = (m_SensibleMaximumThresholdValue + m_SensibleMinimumThresholdValue) / 2.0;
IntervalBordersChanged.Send(m_SensibleMinimumThresholdValue, m_SensibleMaximumThresholdValue, m_IsFloatImage);
ThresholdingValueChanged.Send(m_CurrentThresholdValue);
}
}
}
mitk::Image::Pointer mitk::SegTool2D::GetAffectedImageSliceAs2DImage(const PlaneGeometry* planeGeometry, const Image* image, unsigned int timeStep)
{
if ( !image || !planeGeometry ) return NULL;
//Make sure that for reslicing and overwriting the same alogrithm is used. We can specify the mode of the vtk reslicer
vtkSmartPointer<mitkVtkImageOverwrite> reslice = vtkSmartPointer<mitkVtkImageOverwrite>::New();
//set to false to extract a slice
reslice->SetOverwriteMode(false);
reslice->Modified();
//use ExtractSliceFilter with our specific vtkImageReslice for overwriting and extracting
mitk::ExtractSliceFilter::Pointer extractor = mitk::ExtractSliceFilter::New(reslice);
extractor->SetInput( image );
extractor->SetTimeStep( timeStep );
extractor->SetWorldGeometry( planeGeometry );
extractor->SetVtkOutputRequest(false);
extractor->SetResliceTransformByGeometry( image->GetTimeGeometry()->GetGeometryForTimeStep( timeStep ) );
extractor->Modified();
extractor->Update();
Image::Pointer slice = extractor->GetOutput();
/*============= BEGIN undo feature block ========================*/
//specify the undo operation with the non edited slice
m_undoOperation = new DiffSliceOperation(const_cast<mitk::Image*>(image), extractor->GetVtkOutput(), slice->GetGeometry(), timeStep, const_cast<mitk::PlaneGeometry*>(planeGeometry));
/*============= END undo feature block ========================*/
return slice;
}
float get_mean(Image::Pointer im)
{
ConstIterator it;
it = ConstIterator(im, im->GetLargestPossibleRegion());
float mean = 0, N=0;
try
{
while(!it.IsAtEnd())
{
if(it.Get()!=0)
{
mean = N/(N+1)*mean + it.Get()/(N+1);
++N;
}
++it;
}
}
catch( itk::ExceptionObject & err)
{
std::cout<<"Error calculating mean, iterator error"<<std::endl;
std::cout<<err<<std::endl;
}
return mean;
}
/**
Close the contour, project it to the image slice and fill it in 2D.
*/
bool mitk::ContourTool::OnMouseReleased( StateMachineAction*, InteractionEvent* interactionEvent )
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
//const PositionEvent* positionEvent = dynamic_cast<const PositionEvent*>(stateEvent->GetEvent());
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() );
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || !planeGeometry ) return false;
const AbstractTransformGeometry* abstractTransformGeometry( dynamic_cast<const AbstractTransformGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || abstractTransformGeometry ) return false;
// 2. Slice is known, now we try to get it as a 2D image and project the contour into index coordinates of this slice
Image::Pointer slice = SegTool2D::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( slice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
ContourModel* feedbackContour = FeedbackContourTool::GetFeedbackContour();
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( slice, feedbackContour, true, false ); // true: actually no idea why this is neccessary, but it works :-(
if (projectedContour.IsNull()) return false;
int timestep = positionEvent->GetSender()->GetTimeStep();
FeedbackContourTool::FillContourInSlice( projectedContour, timestep, slice, m_PaintingPixelValue );
this->WriteBackSegmentationResult(positionEvent, slice);
// 4. Make sure the result is drawn again --> is visible then.
assert( positionEvent->GetSender()->GetRenderWindow() );
return true;
}
Image::Pointer WorkbenchUtils::addPadding(Image::Pointer image, Axis axis, bool append, int numberOfSlices, float paddingPixelValue) {
// AccessByItk is a precompiler macro that sets up the instantiations for all possible template combinations. This will directly
// reflect in the compile time and required memory since functions for all permutations of PixelTypes and Dimensions will be created.
// The amount of parameters is not limited. However, a return is not possible. So we work with an out parameter:
Image::Pointer returnImage = Image::New();
AccessByItk_n(image.GetPointer(), addPaddingItk, (axis, append, numberOfSlices, paddingPixelValue, returnImage));
return returnImage;
}
void mitk::ImageTimeSelector::GenerateInputRequestedRegion()
{
Superclass::GenerateInputRequestedRegion();
ImageToImageFilter::InputImagePointer input =
const_cast< mitk::ImageToImageFilter::InputImageType * > ( this->GetInput() );
Image::Pointer output = this->GetOutput();
Image::RegionType requestedRegion;
requestedRegion = output->GetRequestedRegion();
requestedRegion.SetIndex(3, m_TimeNr);
requestedRegion.SetIndex(4, m_ChannelNr);
requestedRegion.SetSize(3, 1);
requestedRegion.SetSize(4, 1);
input->SetRequestedRegion( & requestedRegion );
}
void mitk::ContourUtils::FillContourInSlice( ContourModel* projectedContour, unsigned int timeStep, Image* sliceImage, int paintingPixelValue )
{
// 1. Use ipSegmentation to draw a filled(!) contour into a new 8 bit 2D image, which will later be copied back to the slice.
// We don't work on the "real" working data, because ipSegmentation would restrict us to 8 bit images
// convert the projected contour into a ipSegmentation format
mitkIpInt4_t* picContour = new mitkIpInt4_t[2 * projectedContour->GetNumberOfVertices(timeStep)];
unsigned int index(0);
ContourModel::VertexIterator iter = projectedContour->Begin(timeStep);
ContourModel::VertexIterator end = projectedContour->End(timeStep);
while( iter != end)
{
picContour[ 2 * index + 0 ] = static_cast<mitkIpInt4_t>( (*iter)->Coordinates[0] + 1.0 ); // +0.5 wahrscheinlich richtiger
picContour[ 2 * index + 1 ] = static_cast<mitkIpInt4_t>( (*iter)->Coordinates[1] + 1.0 );
//MITK_INFO << "mitk 2d [" << (*iter)[0] << ", " << (*iter)[1] << "] pic [" << picContour[ 2*index+0] << ", " << picContour[ 2*index+1] << "]";
iter++;
index++;
}
assert( sliceImage->GetSliceData() );
mitkIpPicDescriptor* originalPicSlice = mitkIpPicNew();
CastToIpPicDescriptor( sliceImage, originalPicSlice);
mitkIpPicDescriptor* picSlice = ipMITKSegmentationNew( originalPicSlice );
ipMITKSegmentationClear( picSlice );
assert( originalPicSlice && picSlice );
// here comes the actual contour filling algorithm (from ipSegmentation/Graphics Gems)
ipMITKSegmentationCombineRegion ( picSlice, picContour, projectedContour->GetNumberOfVertices(timeStep), NULL, IPSEGMENTATION_OR, 1); // set to 1
delete[] picContour;
// 2. Copy the filled contour to the working data slice
// copy all pixels that are non-zero to the original image (not caring for the actual type of the working image). perhaps make the replace value a parameter ( -> general painting tool ).
// make the pic slice an mitk/itk image (as little ipPic code as possible), call a templated method with accessbyitk, iterate over the original and the modified slice
Image::Pointer ipsegmentationModifiedSlice = Image::New();
ipsegmentationModifiedSlice->Initialize( CastToImageDescriptor( picSlice ) );
ipsegmentationModifiedSlice->SetSlice( picSlice->data );
AccessFixedDimensionByItk_2( sliceImage, ItkCopyFilledContourToSlice, 2, ipsegmentationModifiedSlice, paintingPixelValue );
ipsegmentationModifiedSlice = NULL; // free MITK header information
ipMITKSegmentationFree( picSlice ); // free actual memory
}
bool mitk::SetRegionTool::OnMouseReleased( StateMachineAction*, InteractionEvent* interactionEvent )
{
// 1. Hide the feedback contour, find out which slice the user clicked, find out which slice of the toolmanager's working image corresponds to that
FeedbackContourTool::SetFeedbackContourVisible(false);
mitk::InteractionPositionEvent* positionEvent = dynamic_cast<mitk::InteractionPositionEvent*>( interactionEvent );
if (!positionEvent) return false;
assert( positionEvent->GetSender()->GetRenderWindow() );
mitk::RenderingManager::GetInstance()->RequestUpdate(positionEvent->GetSender()->GetRenderWindow());
int timeStep = positionEvent->GetSender()->GetTimeStep();
if (!m_FillContour && !m_StatusFillWholeSlice) return true;
DataNode* workingNode( m_ToolManager->GetWorkingData(0) );
if (!workingNode) return false;
Image* image = dynamic_cast<Image*>(workingNode->GetData());
const AbstractTransformGeometry* abstractTransformGeometry( dynamic_cast<const AbstractTransformGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
const PlaneGeometry* planeGeometry( dynamic_cast<const PlaneGeometry*> (positionEvent->GetSender()->GetCurrentWorldPlaneGeometry() ) );
if ( !image || !planeGeometry || abstractTransformGeometry ) return false;
Image::Pointer slice = FeedbackContourTool::GetAffectedImageSliceAs2DImage( positionEvent, image );
if ( slice.IsNull() )
{
MITK_ERROR << "Unable to extract slice." << std::endl;
return false;
}
ContourModel* feedbackContour( FeedbackContourTool::GetFeedbackContour() );
ContourModel::Pointer projectedContour = FeedbackContourTool::ProjectContourTo2DSlice( slice, feedbackContour, false, false ); // false: don't add 0.5 (done by FillContourInSlice)
// false: don't constrain the contour to the image's inside
if (projectedContour.IsNull()) return false;
FeedbackContourTool::FillContourInSlice( projectedContour, timeStep, slice, m_PaintingPixelValue );
this->WriteBackSegmentationResult(positionEvent, slice);
m_WholeImageContourInWorldCoordinates = NULL;
m_SegmentationContourInWorldCoordinates = NULL;
return true;
}
void WorkbenchUtils::resampleImageItk(itk::Image <PixelType, ImageDimension> *itkImage, Interpolator interpolType,
unsigned int *newDimensions, Image::Pointer outImage) {
typedef itk::Image <PixelType, ImageDimension> ImageType;
// get original image informations
const typename ImageType::RegionType &inputRegion = itkImage->GetLargestPossibleRegion();
const typename ImageType::SizeType &inputDimensions = inputRegion.GetSize();
const typename ImageType::SpacingType &inputSpacing = itkImage->GetSpacing();
// calculate spacing
double outputSpacing[ImageDimension];
itk::Size <ImageDimension> outputSize;
for (unsigned int i = 0; i < ImageDimension; ++i) {
outputSpacing[i] = inputSpacing[i] * (double) inputDimensions[i] / newDimensions[i];
outputSize[i] = newDimensions[i];
}
// transform
typedef itk::IdentityTransform<double, ImageDimension> TransformType;
typename TransformType::Pointer transform = TransformType::New();
transform->SetIdentity();
// interpolator typedefs
typedef double CoordinateType;
typedef itk::LinearInterpolateImageFunction <ImageType, CoordinateType> LinearInterpolatorType;
typedef itk::NearestNeighborInterpolateImageFunction <ImageType, CoordinateType> NearestNeighborInterpolatorType;
typedef itk::GaussianInterpolateImageFunction <ImageType, CoordinateType> GaussianInterpolatorType;
typedef itk::BSplineInterpolateImageFunction <ImageType, CoordinateType> BSplineInterpolatorType;
// set up the filter
typedef itk::ResampleImageFilter <ImageType, ImageType> ResampleFilterType;
typename ResampleFilterType::Pointer resampleFilter = ResampleFilterType::New();
resampleFilter->SetTransform(transform);
resampleFilter->SetOutputOrigin(itkImage->GetOrigin());
resampleFilter->SetOutputSpacing(outputSpacing);
resampleFilter->SetSize(outputSize);
switch (interpolType) {
case Interpolator::LINEAR: // the default;
resampleFilter->SetInterpolator(LinearInterpolatorType::New());
break;
case Interpolator::NEAREST_NEIGHBOR:
resampleFilter->SetInterpolator(NearestNeighborInterpolatorType::New());
break;
case Interpolator::GAUSSIAN:
resampleFilter->SetInterpolator(GaussianInterpolatorType::New());
break;
case Interpolator::BSPLINE:
resampleFilter->SetInterpolator(BSplineInterpolatorType::New());
break;
}
resampleFilter->SetInput(itkImage);
resampleFilter->UpdateLargestPossibleRegion();
// get the results and cast them back to mitk. return via out parameter.
outImage->InitializeByItk(resampleFilter->GetOutput());
CastToMitkImage(resampleFilter->GetOutput(), outImage);
}
Image::Pointer WorkbenchUtils::resampleImage(Image::Pointer image, unsigned int *newDimensions, Interpolator interpolationMethod) {
// AccessByItk is a precompiler macro that sets up the instantiations for all possible template combinations. This will directly
// reflect in the compile time and required memory since functions for all permutations of PixelTypes and Dimensions will be created.
// The amount of parameters is not limited. However, a return is not possible. So we work with an out parameter:
Image::Pointer returnImage = Image::New();
AccessByItk_n(image.GetPointer(), resampleImageItk, (interpolationMethod, newDimensions, returnImage));
return returnImage;
}
void mitk::ImageTimeSelector::GenerateOutputInformation()
{
Image::ConstPointer input = this->GetInput();
Image::Pointer output = this->GetOutput();
itkDebugMacro(<<"GenerateOutputInformation()");
int dim=(input->GetDimension()<3?input->GetDimension():3);
output->Initialize(input->GetPixelType(), dim, input->GetDimensions());
if( (unsigned int) m_TimeNr >= input->GetDimension(3) )
{
m_TimeNr = input->GetDimension(3)-1;
}
// initialize geometry
output->SetGeometry(dynamic_cast<Geometry3D*>(input->GetSlicedGeometry(m_TimeNr)->Clone().GetPointer()));
output->SetPropertyList(input->GetPropertyList()->Clone());
}