void mitk::MorphologicalOperations::FillHoles(mitk::Image::Pointer &image)
{
MITK_INFO << "Start FillHole...";
int timeSteps = static_cast<int>(image->GetTimeSteps());
if (timeSteps > 1)
{
mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New();
timeSelector->SetInput(image);
for (int t = 0; t < timeSteps; ++t)
{
MITK_INFO << " Processing time step " << t;
timeSelector->SetTimeNr(t);
timeSelector->Update();
mitk::Image::Pointer img3D = timeSelector->GetOutput();
img3D->DisconnectPipeline();
AccessByItk_1(img3D, itkFillHoles, img3D);
mitk::ImageReadAccessor accessor(img3D);
image->SetVolume(accessor.GetData(), t);
}
}
else
{
AccessByItk_1(image, itkFillHoles, image);
}
MITK_INFO << "Finished FillHole";
}
void mitk::CompareImageDataFilter::GenerateData()
{
// check inputs
const mitk::Image* input1 = this->GetInput(0);
const mitk::Image* input2 = this->GetInput(1);
// Generally this filter is part of the mitk::Image::Equal() method and only checks the equality of the image data
// so no further image type comparison is performed!
// CAVE: If the images differ in a parameter other then the image data, the filter may fail!!
// check what number of components the inputs have
if(input1->GetPixelType().GetNumberOfComponents() == 1 &&
input2->GetPixelType().GetNumberOfComponents() == 1)
{
AccessByItk_1( input1, EstimateValueDifference, input2);
}
else if(input1->GetPixelType().GetNumberOfComponents() > 1 &&
input2->GetPixelType().GetNumberOfComponents() > 1 )
{
this->ResetCompareResultsToInitial();
MultiComponentImageDataComparisonFilter::Pointer mcComparator = MultiComponentImageDataComparisonFilter::New();
mcComparator->SetTestImage(input1);
mcComparator->SetValidImage(input2);
mcComparator->SetCompareFilterResult( &m_CompareDetails);
mcComparator->Update();
m_CompareResult = mcComparator->GetResult();
}
}
void mitk::ImageWriter::WriteByITK(mitk::Image* image, const std::string& fileName)
{
// Pictures and picture series like .png are written via a different mechanism then volume images.
// So, they are still multiplexed and thus not support vector images.
if (fileName.find(".png") != std::string::npos || fileName.find(".tif") != std::string::npos || fileName.find(".jpg") != std::string::npos)
{
AccessByItk_1( image, _mitkItkPictureWrite, fileName );
return;
}
// Implementation of writer using itkImageIO directly. This skips the use
// of templated itkImageFileWriter, which saves the multiplexing on MITK side.
unsigned int dimension = image->GetDimension();
unsigned int* dimensions = image->GetDimensions();
mitk::PixelType pixelType = image->GetPixelType();
mitk::Vector3D spacing = image->GetGeometry()->GetSpacing();
mitk::Point3D origin = image->GetGeometry()->GetOrigin();
itk::ImageIOBase::Pointer imageIO = itk::ImageIOFactory::CreateImageIO( fileName.c_str(),
itk::ImageIOFactory::WriteMode );
if(imageIO.IsNull())
{
itkExceptionMacro(<< "Error: Could not create itkImageIO via factory for file " << fileName);
}
void QmitkVirtualSurgery::ManualErodeVesselClicked()
{
if(selectedImage.IsNull())
{
QMessageBox::warning ( NULL,
tr("erode vessel not possible"),
tr("Sorry, you must select a image.\n\n"
"The possibility to not load an image."),
QMessageBox::Ok, QMessageBox::NoButton, QMessageBox::NoButton );
return;
}
mitk::DataTreeNode* node = selectedImage->Get();
if ( node )
{
mitk::BaseData* data = node->GetData();
if (data)
{
mitk::Image* image = dynamic_cast<mitk::Image*>( data );
if (image)
{
std::cout << "Erode process begin..." << std::endl;
AccessByItk_1(image, ErodeVessel,image->GetGeometry());
std::cout << "segment process end..." << std::endl;
}
}
}
}
void SegMainWindow::sltThresholding()
{
AccessByItk_1(m_FirstImage, OtsuSegmentation, this);
if (m_ResultImage.IsNotNull())
{
m_ResultNode->SetProperty("volumerendering", mitk::BoolProperty::New(false));
vtkMarchingCubes* surfaceCreator = vtkMarchingCubes::New();
surfaceCreator->SetInputData(m_ResultImage->GetVtkImageData());
surfaceCreator->SetValue(0, 1);
surfaceCreator->Update();
mitk::Surface::Pointer surface = mitk::Surface::New();
surface->SetVtkPolyData(surfaceCreator->GetOutput()); //VTK6_TODO
mitk::DataNode::Pointer surfaceNode = mitk::DataNode::New();
surfaceNode->SetData(surface);
m_DataStorage->Add(surfaceNode);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
surfaceCreator->Delete();
}
//mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
mitk::DataNode::Pointer RTDoseReader::
LoadRTDose(const char* filename)
{
DcmFileFormat fileformat;
OFCondition outp = fileformat.loadFile(filename, EXS_Unknown);
if(outp.bad())
{
MITK_ERROR << "Cant read the file" << std::endl;
}
DcmDataset *dataset = fileformat.getDataset();
std::string name = filename;
itk::FilenamesContainer file;
file.push_back(name);
mitk::DicomSeriesReader* reader = new mitk::DicomSeriesReader;
mitk::DataNode::Pointer originalNode = reader->LoadDicomSeries(file,false);
if(originalNode.IsNull())
{
MITK_ERROR << "Error reading the dcm file" << std::endl;
return 0;
}
mitk::Image::Pointer originalImage
= dynamic_cast<mitk::Image*>(originalNode->GetData());
DRTDoseIOD doseObject;
OFCondition result = doseObject.read(*dataset);
if(result.bad())
{
MITK_ERROR << "Error reading the Dataset" << std::endl;
return 0;
}
OFString gridScaling;
Float32 gridscale;
doseObject.getDoseGridScaling(gridScaling);
gridscale = OFStandard::atof(gridScaling.c_str());
AccessByItk_1(originalImage, MultiplayGridScaling, gridscale);
double prescripeDose = this->GetMaxDoseValue(dataset);
originalNode->SetName("RT Dose");
originalNode->SetFloatProperty(mitk::Constants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str(),prescripeDose);
originalNode->SetFloatProperty(mitk::Constants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), 40);
originalNode->SetBoolProperty(mitk::Constants::DOSE_PROPERTY_NAME.c_str(),true);
return originalNode;
}
void mitk::CLUtil::CountVoxel(mitk::Image::Pointer image, unsigned int & count)
{
AccessByItk_1(image, mitk::CLUtil::itkCountVoxel, count);
}
void mitk::CLUtil::CountVoxel(mitk::Image::Pointer image, std::map<unsigned int, unsigned int> & map)
{
AccessByItk_1(image, mitk::CLUtil::itkCountVoxel, map);
}
void mitk::CLUtil::MergeLabels(mitk::Image::Pointer & img, const std::map<unsigned int, unsigned int> & map)
{
AccessByItk_1(img, mitk::CLUtil::itkMergeLabels, map);
}
void Step6::StartRegionGrowing()
{
AccessByItk_1(m_FirstImage, RegionGrowing, this);
mitk::RenderingManager::GetInstance()->RequestUpdateAll();
}
void mitk::OtsuTool3D::UpdateBinaryPreview(std::vector<int> regionIDs)
{
m_MultiLabelResultNode->SetVisibility(false);
mitk::Image::Pointer multiLabelSegmentation = dynamic_cast<mitk::Image *>(m_MultiLabelResultNode->GetData());
AccessByItk_1(multiLabelSegmentation, CalculatePreview, regionIDs);
}
std::vector<itk::SmartPointer<BaseData> > RTDoseReader::Read()
{
std::vector<itk::SmartPointer<mitk::BaseData> > result;
DICOMTag referencedRTPlan(0x300c, 0x0002);
mitk::IDICOMTagsOfInterest* toiSrv = GetDicomTagsOfInterestService();
if (toiSrv)
{
toiSrv->AddTagOfInterest(referencedRTPlan);
}
std::string location = GetInputLocation();
mitk::DICOMFileReaderSelector::Pointer selector = mitk::DICOMFileReaderSelector::New();
selector->LoadBuiltIn3DConfigs();
selector->SetInputFiles({ location });
mitk::DICOMFileReader::Pointer reader = selector->GetFirstReaderWithMinimumNumberOfOutputImages();
reader->SetAdditionalTagsOfInterest(toiSrv->GetTagsOfInterest());
reader->SetInputFiles({ location });
reader->AnalyzeInputFiles();
reader->LoadImages();
if (reader->GetNumberOfOutputs() == 0){
MITK_ERROR << "Could not determine a DICOM reader for this file" << std::endl;
return result;
}
const mitk::DICOMImageBlockDescriptor& desc = reader->GetOutput(0);
mitk::Image::Pointer originalImage = desc.GetMitkImage();
if (originalImage.IsNull())
{
MITK_ERROR << "Error reading the RTDOSE file in mitk::DicomFileReader" << std::endl;
return result;
}
DcmFileFormat fileformat;
OFCondition outp = fileformat.loadFile(location.c_str(), EXS_Unknown);
if (outp.bad())
{
MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl;
return result;
}
DcmDataset *dataset = fileformat.getDataset();
DRTDoseIOD doseObject;
OFCondition DCMTKresult = doseObject.read(*dataset);
if (DCMTKresult.bad())
{
MITK_ERROR << "Error reading the RTDOSE file in DCMTK" << std::endl;
return result;
}
OFString gridScaling;
Float32 gridscale;
doseObject.getDoseGridScaling(gridScaling);
gridscale = OFStandard::atof(gridScaling.c_str());
AccessByItk_1(originalImage, MultiplyGridScaling, gridscale);
auto statistics = this->scaledDoseImage->GetStatistics();
double maxDose = statistics->GetScalarValueMax();
this->scaledDoseImage->SetPropertyList(originalImage->GetPropertyList());
this->scaledDoseImage->SetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str(), mitk::GenericProperty<double>::New(0.8*maxDose));
result.push_back(this->scaledDoseImage.GetPointer());
return result;
}
mitk::DataNode::Pointer RTDoseReader::LoadRTDose(const char* filename)
{
DICOMTag referencedRTPlan(0x300c, 0x0002);
mitk::IDICOMTagsOfInterest* toiSrv = GetDicomTagsOfInterestService();
if (toiSrv)
{
toiSrv->AddTagOfInterest(referencedRTPlan);
}
mitk::StringList oneFile = { filename };
mitk::DICOMFileReaderSelector::Pointer selector = mitk::DICOMFileReaderSelector::New();
selector->LoadBuiltIn3DConfigs();
selector->SetInputFiles(oneFile);
mitk::DICOMFileReader::Pointer reader = selector->GetFirstReaderWithMinimumNumberOfOutputImages();
reader->SetAdditionalTagsOfInterest(toiSrv->GetTagsOfInterest());
reader->SetInputFiles(oneFile);
reader->AnalyzeInputFiles();
reader->LoadImages();
if (reader->GetNumberOfOutputs() == 0){
MITK_ERROR << "Error reading the dicom file" << std::endl;
return nullptr;
}
const mitk::DICOMImageBlockDescriptor& desc = reader->GetOutput(0);
mitk::Image::Pointer originalImage = desc.GetMitkImage();
if (originalImage.IsNull())
{
MITK_ERROR << "Error reading the dcm file" << std::endl;
return nullptr;
}
DcmFileFormat fileformat;
OFCondition outp = fileformat.loadFile(filename, EXS_Unknown);
if (outp.bad())
{
MITK_ERROR << "Can't read the RTDOSE file" << std::endl;
}
DcmDataset *dataset = fileformat.getDataset();
DRTDoseIOD doseObject;
OFCondition result = doseObject.read(*dataset);
if(result.bad())
{
MITK_ERROR << "Error reading the Dataset" << std::endl;
return nullptr;
}
OFString gridScaling;
Float32 gridscale;
doseObject.getDoseGridScaling(gridScaling);
gridscale = OFStandard::atof(gridScaling.c_str());
AccessByItk_1(originalImage, MultiplyGridScaling, gridscale);
auto statistics = this->scaledDoseImage->GetStatistics();
double maxDose = statistics->GetScalarValueMax();
this->scaledDoseImage->SetPropertyList(originalImage->GetPropertyList());
this->scaledDoseImage->SetProperty(mitk::RTConstants::PRESCRIBED_DOSE_PROPERTY_NAME.c_str(), mitk::GenericProperty<double>::New(0.8*maxDose));
mitk::DataNode::Pointer originalNode = mitk::DataNode::New();
originalNode->SetName("RT Dose");
originalNode->SetData(this->scaledDoseImage);
originalNode->SetFloatProperty(mitk::RTConstants::REFERENCE_DOSE_PROPERTY_NAME.c_str(), 40.0);
return originalNode;
}
int main(int argc, char* argv[])
{
mitkCommandLineParser parser;
parser.setTitle("Dicom Loader");
parser.setCategory("Preprocessing Tools");
parser.setDescription("");
parser.setContributor("MBI");
parser.setArgumentPrefix("--","-");
// Add command line argument names
parser.addArgument("help", "h",mitkCommandLineParser::Bool, "Help:", "Show this help text");
parser.addArgument("input", "i", mitkCommandLineParser::InputDirectory, "Input folder:", "Input folder", us::Any(), false);
parser.addArgument("output", "o", mitkCommandLineParser::OutputFile, "Output file:", "Output file",us::Any(),false);
std::map<std::string, us::Any> parsedArgs = parser.parseArguments(argc, argv);
if (parsedArgs.size()==0)
return EXIT_FAILURE;
// Show a help message
if ( parsedArgs.count("help") || parsedArgs.count("h"))
{
std::cout << parser.helpText();
return EXIT_SUCCESS;
}
std::string inputFile = us::any_cast<std::string>(parsedArgs["input"]);
std::string outFileName = us::any_cast<std::string>(parsedArgs["output"]);
MITK_INFO << "Start Image Loading";
mitk::Image::Pointer image = mitk::IOUtil::Load<mitk::Image>(inputFile);
MITK_INFO << "Loaded Image";
mitk::OtsuSegmentationFilter::Pointer otsuFilter = mitk::OtsuSegmentationFilter::New();
otsuFilter->SetNumberOfThresholds(2);
otsuFilter->SetValleyEmphasis(false);
otsuFilter->SetNumberOfBins(128);
otsuFilter->SetInput(image);
try
{
otsuFilter->Update();
}
catch (...)
{
mitkThrow() << "itkOtsuFilter error (image dimension must be in {2, 3} and image must not be RGB)";
}
MITK_INFO << "Calculated Otsu";
mitk::LabelSetImage::Pointer resultImage = mitk::LabelSetImage::New();
resultImage->InitializeByLabeledImage(otsuFilter->GetOutput());
mitk::Image::Pointer rawMask = resultImage->CreateLabelMask(1);
mitk::Image::Pointer pickedMask;
AccessByItk_1(rawMask, StartRegionGrowing, pickedMask);
mitk::MorphologicalOperations::FillHoles(pickedMask);
mitk::MorphologicalOperations::Closing(pickedMask, 5, mitk::MorphologicalOperations::StructuralElementType::Ball);
mitk::MorphologicalOperations::FillHoles(pickedMask);
mitk::IOUtil::Save(pickedMask, outFileName);
return EXIT_SUCCESS;
}
void mitk::WatershedTool::DoIt()
{
// get image from tool manager
mitk::DataNode::Pointer referenceData = m_ToolManager->GetReferenceData(0);
mitk::Image::Pointer input = dynamic_cast<mitk::Image*>(referenceData->GetData());
if (input.IsNull())
return;
unsigned int timestep = mitk::RenderingManager::GetInstance()->GetTimeNavigationController()->GetTime()->GetPos();
input = Get3DImage(input, timestep);
mitk::Image::Pointer output;
try {
// create and run itk filter pipeline
AccessByItk_1(input.GetPointer(),ITKWatershed,output);
// create a new datanode for output
mitk::DataNode::Pointer dataNode = mitk::DataNode::New();
dataNode->SetData(output);
// set properties of datanode
dataNode->SetProperty("binary", mitk::BoolProperty::New(false));
dataNode->SetProperty("name", mitk::StringProperty::New("Watershed Result"));
mitk::RenderingModeProperty::Pointer renderingMode = mitk::RenderingModeProperty::New();
renderingMode->SetValue( mitk::RenderingModeProperty::LOOKUPTABLE_LEVELWINDOW_COLOR );
dataNode->SetProperty("Image Rendering.Mode", renderingMode);
// since we create a multi label image, define a vtk lookup table
mitk::LookupTable::Pointer lut = mitk::LookupTable::New();
mitk::LookupTableProperty::Pointer prop = mitk::LookupTableProperty::New(lut);
vtkSmartPointer<vtkLookupTable> lookupTable = vtkSmartPointer<vtkLookupTable>::New();
lookupTable->SetHueRange(1.0, 0.0);
lookupTable->SetSaturationRange(1.0, 1.0);
lookupTable->SetValueRange(1.0, 1.0);
lookupTable->SetTableRange(-1.0, 1.0);
lookupTable->Build();
lookupTable->SetTableValue(1,0,0,0);
lut->SetVtkLookupTable(lookupTable);
prop->SetLookupTable(lut);
dataNode->SetProperty("LookupTable",prop);
// make the levelwindow fit to right values
mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New();
mitk::LevelWindow levelwindow;
levelwindow.SetRangeMinMax(0, output->GetStatistics()->GetScalarValueMax());
levWinProp->SetLevelWindow( levelwindow );
dataNode->SetProperty( "levelwindow", levWinProp );
dataNode->SetProperty( "opacity", mitk::FloatProperty::New(0.5));
// set name of data node
std::string name = referenceData->GetName() + "_Watershed";
dataNode->SetName( name );
// look, if there is already a node with this name
mitk::DataStorage::SetOfObjects::ConstPointer children = m_ToolManager->GetDataStorage()->GetDerivations(referenceData);
mitk::DataStorage::SetOfObjects::ConstIterator currentNode = children->Begin();
mitk::DataNode::Pointer removeNode;
while(currentNode != children->End())
{
if(dataNode->GetName().compare(currentNode->Value()->GetName()) == 0)
{
removeNode = currentNode->Value();
}
currentNode++;
}
// remove node with same name
if(removeNode.IsNotNull())
m_ToolManager->GetDataStorage()->Remove(removeNode);
// add output to the data storage
m_ToolManager->GetDataStorage()->Add(dataNode,referenceData);
}
catch(itk::ExceptionObject& e)
{
MITK_ERROR<<"Watershed Filter Error: " << e.GetDescription();
}
RenderingManager::GetInstance()->RequestUpdateAll();
}