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();
}
/*
* 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::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());
}
void mitk::OverwriteSliceImageFilter::GenerateData()
{
//
// this is the place to implement the major part of undo functionality (bug #491)
// here we have to create undo/do operations
//
// WHO is the operation actor? This object may not be destroyed ever (design of undo stack)!
// -> some singleton method of this filter?
//
// neccessary additional objects:
// - something that executes the operations
// - the operation class (must hold a binary diff or something)
// - observer commands to know when the image is deleted (no further action then, perhaps even remove the operations from the undo stack)
//
Image::ConstPointer input = ImageToImageFilter::GetInput(0);
Image::ConstPointer input3D = input;
Image::ConstPointer slice = m_SliceImage;
if ( input.IsNull() || slice.IsNull() ) return;
switch (m_SliceDimension)
{
default:
case 2:
m_Dimension0 = 0;
m_Dimension1 = 1;
break;
case 1:
m_Dimension0 = 0;
m_Dimension1 = 2;
break;
case 0:
m_Dimension0 = 1;
m_Dimension1 = 2;
break;
}
if ( slice->GetDimension() < 2 || input->GetDimension() > 4 ||
slice->GetDimension(0) != input->GetDimension(m_Dimension0) ||
slice->GetDimension(1) != input->GetDimension(m_Dimension1) ||
m_SliceIndex >= input->GetDimension(m_SliceDimension)
)
{
itkExceptionMacro("Slice and image dimensions differ or slice index is too large. Sorry, cannot work like this.");
return;
}
if ( input->GetDimension() == 4 )
{
ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
timeSelector->SetInput( input );
timeSelector->SetTimeNr( m_TimeStep );
timeSelector->UpdateLargestPossibleRegion();
input3D = timeSelector->GetOutput();
}
if ( m_SliceDifferenceImage.IsNull() ||
m_SliceDifferenceImage->GetDimension(0) != m_SliceImage->GetDimension(0) ||
m_SliceDifferenceImage->GetDimension(1) != m_SliceImage->GetDimension(1) )
{
m_SliceDifferenceImage = mitk::Image::New();
mitk::PixelType pixelType( mitk::MakeScalarPixelType<short signed int>() );
m_SliceDifferenceImage->Initialize( pixelType, 2, m_SliceImage->GetDimensions() );
}
//MITK_INFO << "Overwriting slice " << m_SliceIndex << " in dimension " << m_SliceDimension << " at time step " << m_TimeStep << std::endl;
// this will do a long long if/else to find out both pixel types
AccessFixedDimensionByItk( input3D, ItkImageSwitch, 3 );
SegmentationInterpolationController* interpolator = SegmentationInterpolationController::InterpolatorForImage( input );
if (interpolator)
{
interpolator->BlockModified(true);
interpolator->SetChangedSlice( m_SliceDifferenceImage, m_SliceDimension, m_SliceIndex, m_TimeStep );
}
if ( m_CreateUndoInformation )
{
// create do/undo operations (we don't execute the doOp here, because it has already been executed during calculation of the diff image
ApplyDiffImageOperation* doOp = new ApplyDiffImageOperation( OpTEST, const_cast<Image*>(input.GetPointer()), m_SliceDifferenceImage, m_TimeStep, m_SliceDimension, m_SliceIndex );
ApplyDiffImageOperation* undoOp = new ApplyDiffImageOperation( OpTEST, const_cast<Image*>(input.GetPointer()), m_SliceDifferenceImage, m_TimeStep, m_SliceDimension, m_SliceIndex );
undoOp->SetFactor( -1.0 );
OperationEvent* undoStackItem = new OperationEvent( DiffImageApplier::GetInstanceForUndo(), doOp, undoOp, this->EventDescription(m_SliceDimension, m_SliceIndex, m_TimeStep) );
UndoController::GetCurrentUndoModel()->SetOperationEvent( undoStackItem );
}
// this image is modified (good to know for the renderer)
input->Modified();
if (interpolator)
{
interpolator->BlockModified(false);
}
}
void mitk::ExtractImageFilter::GenerateData()
{
Image::ConstPointer input = ImageToImageFilter::GetInput(0);
if ( (input->GetDimension() > 4) || (input->GetDimension() < 2) )
{
MITK_ERROR << "mitk::ExtractImageFilter:GenerateData works only with 3D and 3D+t images, sorry." << std::endl;
itkExceptionMacro("mitk::ExtractImageFilter works only with 3D and 3D+t images, sorry.");
return;
}
else if (input->GetDimension() == 4)
{
ImageTimeSelector::Pointer timeSelector = ImageTimeSelector::New();
timeSelector->SetInput( input );
timeSelector->SetTimeNr( m_TimeStep );
timeSelector->UpdateLargestPossibleRegion();
input = timeSelector->GetOutput();
}
else if (input->GetDimension() == 2)
{
Image::Pointer resultImage = ImageToImageFilter::GetOutput();
resultImage = const_cast<Image*>(input.GetPointer());
ImageToImageFilter::SetNthOutput( 0, resultImage );
return;
}
if ( m_SliceDimension >= input->GetDimension() )
{
MITK_ERROR << "mitk::ExtractImageFilter:GenerateData 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;
}
AccessFixedDimensionByItk( input, ItkImageProcessing, 3 );
// set a nice geometry for display and point transformations
Geometry3D* inputImageGeometry = ImageToImageFilter::GetInput(0)->GetGeometry();
if (!inputImageGeometry)
{
MITK_ERROR << "In ExtractImageFilter::ItkImageProcessing: Input image has no geometry!" << std::endl;
return;
}
PlaneGeometry::PlaneOrientation orientation = PlaneGeometry::Axial;
switch ( m_SliceDimension )
{
default:
case 2:
orientation = PlaneGeometry::Axial;
break;
case 1:
orientation = PlaneGeometry::Frontal;
break;
case 0:
orientation = PlaneGeometry::Sagittal;
break;
}
PlaneGeometry::Pointer planeGeometry = PlaneGeometry::New();
planeGeometry->InitializeStandardPlane( inputImageGeometry, orientation, (ScalarType)m_SliceIndex, true, false );
Image::Pointer resultImage = ImageToImageFilter::GetOutput();
planeGeometry->ChangeImageGeometryConsideringOriginOffset(true);
resultImage->SetGeometry( planeGeometry );
}
