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::TumorInvasionClassification::DescriptionToLogFile(mitk::DataCollection *collection, std::string outputFile)
{
std::ofstream fileStream;
fileStream.open(outputFile.c_str(),std::ios_base::app);
fileStream << "Configuration:" << std::endl;
for (size_t patient = 0; patient < collection->Size(); ++patient)
{
DataCollection* dataPatient = dynamic_cast<DataCollection*>(collection->GetData(patient).GetPointer());
fileStream << "Name : " << dataPatient->GetName() << " with time steps:" << std::endl;
for (size_t timeStep = 0; timeStep < dataPatient->Size(); ++timeStep)
{
fileStream << dataPatient->IndexToName(timeStep)<< "-" << std::endl;
DataCollection* dataTS = dynamic_cast<DataCollection*>(dataPatient->GetData(timeStep).GetPointer());
for (size_t ts = 0; ts < dataTS->Size(); ++ts)
fileStream << dataTS->IndexToName(ts)<< "-" << std::endl;
}
}
}
bool mitk::DiffusionCollectionWriter::ExportCollectionToFolder(DataCollection *dataCollection, std::string xmlFile, std::vector<std::string> filter)
{
// Quick and Dirty: Assumes three level DataCollection
QDir fileName = QFileInfo(xmlFile.c_str()).absoluteDir();
std::string outputFolder = fileName.path().toStdString() + QDir::separator().toLatin1();
QDir baseFolder(outputFolder.c_str());
baseFolder.mkpath(outputFolder.c_str());
std::ofstream xmlFileStream;
xmlFileStream.open (xmlFile.c_str());
xmlFileStream << "<!-- MITK - DataCollection - File Version 1.0 --> \n";
xmlFileStream << "<" << COLLECTION << " " << NAME << "=\"" << dataCollection->GetName() << "\" >\n";
unsigned int subColId = 0;
unsigned int dataId = 0;
QDir dir(QString::fromStdString(outputFolder));
for (size_t i = 0 ; i < dataCollection->Size(); ++i)
{
// Write Subcollection tag
xmlFileStream << " <" << SUBCOLLECTION << " " << NAME << "=\"" << dataCollection->IndexToName(i) << "\" " << FILEPATH << "=\"" << dataCollection->GetDataFilePath(i) << "\" id=\"Col" << subColId << "\" >\n";
// Create Sub-Folder
dir.mkpath(QString::fromStdString(dataCollection->IndexToName(i)));
// Herein create data folders
DataCollection* subCollections = dynamic_cast<DataCollection*> (dataCollection->GetData(i).GetPointer());
if (subCollections == nullptr)
{
MITK_ERROR<< "mitk::DiffusionCollectionWriter::SaveCollectionToFolder: Container is illformed. Aborting";
return false;
}
for (size_t d = 0; d < subCollections->Size(); d++ )
{
// Create Sub Paths
QString subPath = QString::fromStdString(dataCollection->IndexToName(i))+"/"+QString::fromStdString(subCollections->IndexToName(d));
dir.mkpath(subPath);
xmlFileStream << " <" << DATA << " " << NAME << "=\"" << subCollections->IndexToName(d) << "\" " << FILEPATH << "=\"" << subCollections->GetDataFilePath(d) << "\" id=\"Data" << dataId << "\" >\n";
DataCollection* itemCollections = dynamic_cast<DataCollection*> (subCollections->GetData(d).GetPointer());
if (itemCollections == nullptr)
{
MITK_ERROR<< "mitk::DiffusionCollectionWriter::SaveCollectionToFolder: Container is illformed. Aborting";
return false;
}
for (size_t s = 0; s < itemCollections->Size(); s++)
{
if (filter.size() > 0)
{
bool isSelected = false;
for (size_t f = 0; f < filter.size(); f++)
{
if (filter.at(f) == itemCollections->IndexToName(s) )
{
isSelected = true;
break;
}
}
if (isSelected == false)
continue;
}
Image* image = dynamic_cast<Image*> (itemCollections->GetData(s).GetPointer());
QString fileName = dir.path() + dir.separator() + subPath + dir.separator() + QString::fromStdString(dataCollection->IndexToName(i)) + "_" + QString::fromStdString(subCollections->IndexToName(d)) + "_" + QString::fromStdString(itemCollections->IndexToName(s));
try
{
if (itemCollections->IndexToName(s) == "DTI" || itemCollections->IndexToName(s) == "DTIFWE")
{
fileName += ".dti";
IOUtil::Save(image,fileName.toStdString());
}
else if (itemCollections->IndexToName(s) == "FIB")
{
fileName += ".fib";
FiberBundle* fib = dynamic_cast<FiberBundle*> (itemCollections->GetData(s).GetPointer());
IOUtil::Save(fib, fileName.toStdString());
}
else if (itemCollections->IndexToName(s) == "DWI")
{
fileName += ".dwi";
IOUtil::Save(image,fileName.toStdString());
}
else
{
fileName += ".nrrd";
Image::Pointer image = itemCollections->GetMitkImage(s).GetPointer();
IOUtil::Save(image,fileName.toStdString());
}
}
catch( const std::exception& e)
{
MITK_ERROR << "Caught exception: " << e.what();
}
std::string relativeFilename = baseFolder.relativeFilePath(fileName).toStdString();
xmlFileStream << " <" << ITEM << " " << NAME << "=\"" <<itemCollections->IndexToName(s) << "\" " << FILEPATH << "=\"" << "\" " << LINK << "=\"" << relativeFilename << "\" />\n";
}
xmlFileStream << " </" << DATA << ">\n";
dataId++;
}
xmlFileStream << " </" << SUBCOLLECTION << ">\n";
subColId++;
}
xmlFileStream << "</" << COLLECTION << ">\n";
xmlFileStream.flush();
xmlFileStream.close();
return true;
}
