/*=========================================================================
Program: vv http://www.creatis.insa-lyon.fr/rio/vv
- Authors belong to:
+ Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
#include "itkBinaryMorphologicalOpeningImageFilter.h"
#include "itkBinaryBallStructuringElement.h"
#include "itkCastImageFilter.h"
+#include "itkConstantPadImageFilter.h"
//--------------------------------------------------------------------
template <class TInputImageType>
this->SetNumberOfRequiredInputs(1);
SetBackgroundValue(0); // Must be zero
SetForegroundValue(1);
+ SetPrimaryOpeningRadius(0);
// Step 1: Threshold + CC + sort (Find low density areas)
SetUpperThreshold(-300);
SetRadius2(r);
SetMaximumNumberOfLabels2(2);
SetNumberOfNewLabels2(1);
-
+
// Step 5: Only keep label corresponding (Keep patient's labels)
SetFirstKeep(1);
SetLastKeep(1);
-
+
// Step 4: OpenClose (option)
FinalOpenCloseOff();
AutoCropOn();
//--------------------------------------------------------------------
template <class TInputImageType>
-void
+void
clitk::ExtractPatientFilter<TInputImageType>::
-SetInput(const TInputImageType * image)
+SetInput(const TInputImageType * image)
{
this->SetNthInput(0, const_cast<TInputImageType *>(image));
}
//--------------------------------------------------------------------
template <class TInputImageType>
-void
+void
clitk::ExtractPatientFilter<TInputImageType>::
-GenerateOutputInformation() {
+GenerateOutputInformation() {
clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK
// Get input pointers
static const unsigned int Dim = InputImageType::ImageDimension;
//input = dynamic_cast<const TInputImageType*>(itk::ProcessObject::GetInput(0));
-
+
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- // Step 1:
+ // Step 1:
StartNewStep("Find low densities areas");
- typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> BinarizeFilterType;
+
+ // Pad images with air to prevent patient touching the image border
+ typedef itk::ConstantPadImageFilter<InputImageType, InputImageType> PadFilterType;
+ typename PadFilterType::Pointer padFilter = PadFilterType::New();
+ padFilter->SetInput(input);
+ padFilter->SetConstant(GetUpperThreshold() - 1);
+ typename InputImageType::SizeType bounds;
+ for (unsigned i = 0; i < Dim - 1; ++i)
+ bounds[i] = 1;
+ bounds[Dim - 1] = 0;
+ padFilter->SetPadLowerBound(bounds);
+ padFilter->SetPadUpperBound(bounds);
+ padFilter->Update();
+
+ typedef itk::BinaryThresholdImageFilter<InputImageType, InternalImageType> BinarizeFilterType;
typename BinarizeFilterType::Pointer binarizeFilter=BinarizeFilterType::New();
- binarizeFilter->SetInput(input);
+ binarizeFilter->SetInput(padFilter->GetOutput());
if (m_UseLowerThreshold) binarizeFilter->SetLowerThreshold(GetLowerThreshold());
binarizeFilter->SetUpperThreshold(GetUpperThreshold());
binarizeFilter ->SetInsideValue(this->GetForegroundValue());
binarizeFilter ->SetOutsideValue(this->GetBackgroundValue());
+ padFilter->GetOutput()->ReleaseData();
+ working_image = binarizeFilter->GetOutput();
+
+ typedef itk::BinaryBallStructuringElement<InternalPixelType,Dim> KernelType;
+ unsigned int radius = this->GetPrimaryOpeningRadius();
+ if (radius > 0)
+ {
+ if (this->GetVerboseOptionFlag()) std::cout << ("Opening after threshold; R = ") << radius << std::endl;
+ KernelType kernel;
+ kernel.SetRadius(radius);
+
+ typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType , KernelType> OpenFilterType2;
+ typename OpenFilterType2::Pointer openFilter2 = OpenFilterType2::New();
+ openFilter2->SetInput(working_image);
+ openFilter2->SetBackgroundValue(0);
+ openFilter2->SetForegroundValue(1);
+ openFilter2->SetKernel(kernel);
+ openFilter2->Update();
+ working_image->ReleaseData();
+ working_image = openFilter2->GetOutput();
+ }
+ if (this->GetVerboseOptionFlag()) std::cout << ("Labelling") << std::endl;
// Connected component labeling
typedef itk::ConnectedComponentImageFilter<InternalImageType, InternalImageType> ConnectFilterType;
typename ConnectFilterType::Pointer connectFilter=ConnectFilterType::New();
- connectFilter->SetInput(binarizeFilter->GetOutput());
+ connectFilter->SetInput(working_image);
connectFilter->SetBackgroundValue(this->GetBackgroundValue());
connectFilter->SetFullyConnected(false);
-
+ connectFilter->Update();
+ working_image->ReleaseData();
+ working_image = connectFilter->GetOutput();
+
+ if (this->GetVerboseOptionFlag()) std::cout << ("RelabelComponentImageFilter") << std::endl;
// Sort labels according to size
typedef itk::RelabelComponentImageFilter<InternalImageType, InternalImageType> RelabelFilterType;
typename RelabelFilterType::Pointer relabelFilter=RelabelFilterType::New();
relabelFilter->InPlaceOn();
relabelFilter->SetInput(connectFilter->GetOutput());
relabelFilter->Update();
+ working_image->ReleaseData();
working_image = relabelFilter->GetOutput();
-
+
// End
StopCurrentStep<InternalImageType>(working_image);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- // [Optional]
+ // [Optional]
if (GetDecomposeAndReconstructDuringFirstStep()) {
StartNewStep("First Decompose & Reconstruct step");
typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
f->SetFullyConnected(true);
f->SetNumberOfNewLabels(GetNumberOfNewLabels1());
f->Update();
+ working_image->ReleaseData();
working_image = f->GetOutput();
StopCurrentStep<InternalImageType>(working_image);
}
-
+
//--------------------------------------------------------------------
//--------------------------------------------------------------------
+ if (this->GetVerboseOptionFlag()) std::cout << ("Remove the air (largest area)") << std::endl;
StartNewStep("Remove the air (largest area)");
- typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> iBinarizeFilterType;
+ typedef itk::BinaryThresholdImageFilter<InternalImageType, InternalImageType> iBinarizeFilterType;
typename iBinarizeFilterType::Pointer binarizeFilter2 = iBinarizeFilterType::New();
binarizeFilter2->SetInput(working_image);
binarizeFilter2->SetLowerThreshold(GetFirstKeep());
binarizeFilter2->SetUpperThreshold(GetLastKeep());
binarizeFilter2 ->SetInsideValue(0);
binarizeFilter2 ->SetOutsideValue(1);
- // binarizeFilter2 ->Update(); // NEEDED ?
+ binarizeFilter2 ->Update();
+ working_image->ReleaseData();
+ working_image = binarizeFilter2->GetOutput();
typename ConnectFilterType::Pointer connectFilter2 = ConnectFilterType::New();
- connectFilter2->SetInput(binarizeFilter2->GetOutput());
+ connectFilter2->SetInput(working_image);
connectFilter2->SetBackgroundValue(this->GetBackgroundValue());
connectFilter2->SetFullyConnected(false);
+ connectFilter2->Update();
+ working_image->ReleaseData();
+ working_image = connectFilter2->GetOutput();
typename RelabelFilterType::Pointer relabelFilter2 = RelabelFilterType::New();
- relabelFilter2->SetInput(connectFilter2->GetOutput());
+ relabelFilter2->SetInput(working_image);
relabelFilter2->Update();
+ working_image->ReleaseData();
working_image = relabelFilter2->GetOutput();
-
+
// Keep main label
working_image = KeepLabels<InternalImageType>
- (working_image, GetBackgroundValue(), GetForegroundValue(), 1, 1, true);
+ (working_image, GetBackgroundValue(), GetForegroundValue(), 1, 1, true);
StopCurrentStep<InternalImageType>(working_image);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- // [Optional]
+ // [Optional]
if (GetDecomposeAndReconstructDuringSecondStep()) {
StartNewStep("Second Decompose & Reconstruct step");
typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> FilterType;
f->SetFullyConnected(true);
f->SetNumberOfNewLabels(GetNumberOfNewLabels2());
f->Update();
+ working_image->ReleaseData();
working_image = f->GetOutput();
StopCurrentStep<InternalImageType>(working_image);
}
if (GetFinalOpenClose()) {
StartNewStep("Final OpenClose");
// Open
- typedef itk::BinaryBallStructuringElement<InternalPixelType,Dim> KernelType;
KernelType structuringElement;
structuringElement.SetRadius(1);
structuringElement.CreateStructuringElement();
openFilter->SetInput(working_image);
openFilter->SetBackgroundValue(this->GetBackgroundValue());
openFilter->SetForegroundValue(this->GetForegroundValue());
- openFilter->SetKernel(structuringElement);
+ openFilter->SetKernel(structuringElement);
// Close
typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType , KernelType> CloseFilterType;
typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
closeFilter->SetForegroundValue(this->GetForegroundValue());
// closeFilter->SetBackgroundValue(SetBackgroundValue());
closeFilter->SetKernel(structuringElement);
- closeFilter->Update();
+ closeFilter->Update();
+ working_image->ReleaseData();
working_image = closeFilter->GetOutput();
StopCurrentStep<InternalImageType>(working_image);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- // Final Cast
+ // Final Cast
typedef itk::CastImageFilter<InternalImageType, MaskImageType> CastImageFilterType;
typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
caster->SetInput(working_image);
caster->Update();
+ working_image->ReleaseData();
output = caster->GetOutput();
//--------------------------------------------------------------------
typename CropFilterType::Pointer cropFilter = CropFilterType::New();
cropFilter->SetInput(output);
cropFilter->SetBackgroundValue(GetBackgroundValue());
- cropFilter->Update();
+ cropFilter->Update();
+ output->ReleaseData();
output = cropFilter->GetOutput();
StopCurrentStep<MaskImageType>(output);
}
+ else
+ {
+ // Remove Padding region
+ typedef itk::CropImageFilter<MaskImageType, MaskImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(output);
+ cropFilter->SetLowerBoundaryCropSize(bounds);
+ cropFilter->SetUpperBoundaryCropSize(bounds);
+ cropFilter->Update();
+ output->ReleaseData();
+ output = cropFilter->GetOutput();
+ }
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
template <class TInputImageType>
-void
+void
clitk::ExtractPatientFilter<TInputImageType>::
GenerateData() {
// Final Graft
this->GraftOutput(output);
// Store image filename into AFDB
- GetAFDB()->SetImageFilename("Patient", this->GetOutputPatientFilename());
+ GetAFDB()->SetImageFilename("Patient", this->GetOutputPatientFilename());
WriteAFDB();
}
//--------------------------------------------------------------------
-
+
#endif //#define CLITKBOOLEANOPERATORLABELIMAGEFILTER_TXX
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff