======================================================================-====*/
// clitk
+#include "clitkCropLikeImageFilter.h"
#include "clitkSegmentationUtils.h"
#include "clitkExtractSliceFilter.h"
+#include "clitkResampleImageWithOptionsFilter.h"
+
+// itk
+#include <itkJoinSeriesImageFilter.h>
//--------------------------------------------------------------------
template <class ImageType>
clitk::SliceBySliceRelativePositionFilter<ImageType>::
SliceBySliceRelativePositionFilter():
- clitk::FilterBase(),
- itk::ImageToImageFilter<ImageType, ImageType>()
+ clitk::AddRelativePositionConstraintToLabelImageFilter<ImageType>()
{
- this->SetNumberOfRequiredInputs(2);
SetDirection(2);
- SetObjectBackgroundValue(0);
- SetFuzzyThreshold(0.6);
- SetOrientationType(RelPosFilterType::LeftTo);
- SetIntermediateSpacing(10);
- ResampleBeforeRelativePositionFilterOff();
+ UniqueConnectedComponentBySliceFlagOff();
+ SetIgnoreEmptySliceObjectFlag(false);
+ UseTheLargestObjectCCLFlagOff();
+ this->VerboseStepFlagOff();
+ this->WriteStepFlagOff();
+ this->SetCombineWithOrFlag(false);
+ ObjectCCLSelectionFlagOff();
+ SetObjectCCLSelectionDimension(0);
+ SetObjectCCLSelectionDirection(1);
+ ObjectCCLSelectionIgnoreSingleCCLFlagOff();
}
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::SliceBySliceRelativePositionFilter<ImageType>::
-GenerateOutputInformation()
-{
- ImagePointer input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
- ImagePointer outputImage = this->GetOutput(0);
- outputImage->SetRegions(input->GetLargestPossibleRegion());
+PrintOptions(std::ostream & os)
+{
+ os << "Slice direction = " << this->GetDirection() << std::endl
+ << "BG value = " << this->GetBackgroundValue() << std::endl;
+ for(int i=0; i<this->GetNumberOfAngles(); i++) {
+ os << "Orientation = " << this->GetOrientationTypeString()[i] << std::endl;
+ os << "Angles = " << clitk::rad2deg(this->GetAngle1InRad(i))
+ << " " << clitk::rad2deg(this->GetAngle2InRad(i)) << std::endl;
+ }
+ os << "InverseOrientationFlag = " << this->GetInverseOrientationFlag() << std::endl
+ << "SpacingFlag = " << this->GetIntermediateSpacingFlag() << std::endl
+ << "Spacing = " << this->GetIntermediateSpacing() << std::endl
+ << "FuzzyThreshold = " << this->GetFuzzyThreshold() << std::endl
+ << "UniqueConnectedComponentBySliceFlag = " << this->GetUniqueConnectedComponentBySliceFlag() << std::endl
+ << "AutoCropFlag = " << this->GetAutoCropFlag() << std::endl
+ << "RemoveObjectFlag= " << this->GetRemoveObjectFlag() << std::endl
+ << "CombineWithOrFlag = " << this->GetCombineWithOrFlag() << std::endl
+ << "UseTheLargestObjectCCLFlag = " << this->GetUseTheLargestObjectCCLFlag() << std::endl
+ << "ObjectCCLSelectionFlag = " << this->GetObjectCCLSelectionFlag() << std::endl
+ << "ObjectCCLSelectionDimension = " << this->GetObjectCCLSelectionDimension() << std::endl
+ << "ObjectCCLSelectionIgnoreSingleCCLFlag = " << this->GetObjectCCLSelectionIgnoreSingleCCLFlag() << std::endl
+ << "IgnoreEmptySliceObjectFlag = " << this->GetIgnoreEmptySliceObjectFlag() << std::endl;
}
//--------------------------------------------------------------------
}
//--------------------------------------------------------------------
-
+
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::SliceBySliceRelativePositionFilter<ImageType>::
-GenerateData()
+GenerateOutputInformation()
{
+ if (this->GetVerboseOptionFlag()) {
+ PrintOptions();
+ }
+
// Get input pointer
input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
object = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
//--------------------------------------------------------------------
// Resample object to the same spacing than input
if (!clitk::HaveSameSpacing<ImageType, ImageType>(object, input)) {
- StartNewStep("Resample object to the same spacing than input");
+ this->StartNewStep("Resample object to the same spacing than input");
m_working_object = clitk::ResampleImageSpacing<ImageType>(object, input->GetSpacing());
- StopCurrentStep<ImageType>(m_working_object);
+ this->template StopCurrentStep<ImageType>(m_working_object);
}
else {
- DD("no resampling");
m_working_object = object;
}
//--------------------------------------------------------------------
// Pad object to the same size than input
if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(m_working_object, input)) {
- StartNewStep("Pad object to the same size than input");
- m_working_object = clitk::EnlargeImageLike<ImageType>(m_working_object,
- input,
- GetObjectBackgroundValue());
- StopCurrentStep<ImageType>(m_working_object);
+ this->StartNewStep("Pad object to the same size than input");
+ m_working_object = clitk::ResizeImageLike<ImageType>(m_working_object,
+ input,
+ this->GetObjectBackgroundValue());
+ this->template StopCurrentStep<ImageType>(m_working_object);
}
else {
- DD("no pad");
}
/*
//--------------------------------------------------------------------
// Extract input slices
- StartNewStep("Extract input slices");
+ this->StartNewStep("Extract input slices");
typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
typename ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
extractSliceFilter->SetInput(input);
typedef typename ExtractSliceFilterType::SliceType SliceType;
std::vector<typename SliceType::Pointer> mInputSlices;
extractSliceFilter->GetOutputSlices(mInputSlices);
- StopCurrentStep<SliceType>(mInputSlices[0]);
+ this->template StopCurrentStep<SliceType>(mInputSlices[0]);
//--------------------------------------------------------------------
// Extract object slices
- StartNewStep("Extract object slices");
+ this->StartNewStep("Extract object slices");
extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(object);
+ extractSliceFilter->SetInput(m_working_object);//object);
extractSliceFilter->SetDirection(GetDirection());
extractSliceFilter->Update();
std::vector<typename SliceType::Pointer> mObjectSlices;
extractSliceFilter->GetOutputSlices(mObjectSlices);
- StopCurrentStep<SliceType>(mObjectSlices[0]);
+ this->template StopCurrentStep<SliceType>(mObjectSlices[0]);
+
+ //--------------------------------------------------------------------
+ // Prepare fuzzy slices (if needed)
+ std::vector<typename FloatSliceType::Pointer> mFuzzyMapSlices;
+ mFuzzyMapSlices.resize(mInputSlices.size());
//--------------------------------------------------------------------
// Perform slice by slice relative position
- StartNewStep("Perform slice by slice relative position");
+ this->StartNewStep("Perform slice by slice relative position");
for(unsigned int i=0; i<mInputSlices.size(); i++) {
- // DD(i);
- // DD(mInputSlices[i]->GetOrigin());
- // writeImage<SliceType>(mInputSlices[i], "inp"+clitk::toString(i)+".mhd");
-
- // Select main CC in each object slice : this should be the main bronchus
- mObjectSlices[i] = Labelize<SliceType>(mObjectSlices[i], 0, true, 1);
- mObjectSlices[i] = KeepLabels<SliceType>(mObjectSlices[i], 0, 1, 1, 1, true);
-
- // Relative position
- typedef clitk::AddRelativePositionConstraintToLabelImageFilter<SliceType> RelPosFilterType;
- typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
- relPosFilter->VerboseStepOff();
- relPosFilter->WriteStepOff();
- relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId());
- relPosFilter->SetInput(mInputSlices[i]);
- relPosFilter->SetInputObject(mObjectSlices[i]);
- relPosFilter->SetOrientationType(this->GetOrientationType());
- relPosFilter->SetIntermediateSpacing(this->GetIntermediateSpacing());
- relPosFilter->SetResampleBeforeRelativePositionFilter(this->GetResampleBeforeRelativePositionFilter());
- relPosFilter->SetFuzzyThreshold(this->GetFuzzyThreshold());
- relPosFilter->AutoCropOff(); // important ! because we join the slices after this loop
- relPosFilter->Update();
- // writeImage<SliceType>(relPosFilter->GetOutput(), "inp-after"+clitk::toString(i)+".mhd");
- mInputSlices[i] = relPosFilter->GetOutput();
+
+ // Count the number of CCL (allow to ignore empty slice)
+ int nb=0;
+ mObjectSlices[i] = LabelizeAndCountNumberOfObjects<SliceType>(mObjectSlices[i], 0, true, 1, nb);
+
+ // If no object and empty slices :
+ if ((nb==0) && (this->GetFuzzyMapOnlyFlag())) {
+ typename FloatSliceType::Pointer one = FloatSliceType::New();
+ one->CopyInformation(mObjectSlices[0]);
+ one->SetRegions(mObjectSlices[0]->GetLargestPossibleRegion());
+ one->Allocate();
+ one->FillBuffer(2.0);
+ mFuzzyMapSlices[i] = one;
+ }
+ else {
+ if ((!GetIgnoreEmptySliceObjectFlag()) || (nb!=0)) {
+
+ // Select or not a single CCL ?
+ if (GetUseTheLargestObjectCCLFlag()) {
+ mObjectSlices[i] = KeepLabels<SliceType>(mObjectSlices[i], 0, 1, 1, 1, true);
+ }
+
+ // Select a single according to a position if more than one CCL
+ if (GetObjectCCLSelectionFlag()) {
+ // if several CCL, choose the most extrema according a direction,
+ // if not -> should we consider this slice ?
+ if (nb<2) {
+ if (GetObjectCCLSelectionIgnoreSingleCCLFlag()) {
+ mObjectSlices[i] = SetBackground<SliceType, SliceType>(mObjectSlices[i], mObjectSlices[i],
+ 1, this->GetBackgroundValue(),
+ true);
+ }
+ }
+ int dim = GetObjectCCLSelectionDimension();
+ int direction = GetObjectCCLSelectionDirection();
+ std::vector<typename SliceType::PointType> centroids;
+ ComputeCentroids<SliceType>(mObjectSlices[i], this->GetBackgroundValue(), centroids);
+ uint index=1;
+ for(uint j=1; j<centroids.size(); j++) {
+ if (direction == 1) {
+ if (centroids[j][dim] > centroids[index][dim]) index = j;
+ }
+ else {
+ if (centroids[j][dim] < centroids[index][dim]) index = j;
+ }
+ }
+ for(uint v=1; v<centroids.size(); v++) {
+ if (v != index) {
+ mObjectSlices[i] = SetBackground<SliceType, SliceType>(mObjectSlices[i], mObjectSlices[i],
+ (char)v, this->GetBackgroundValue(),
+ true);
+ }
+ }
+ } // end GetbjectCCLSelectionFlag = true
+
+ // Relative position
+ typedef clitk::AddRelativePositionConstraintToLabelImageFilter<SliceType> RelPosFilterType;
+ typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
+
+ relPosFilter->VerboseStepFlagOff();
+ relPosFilter->WriteStepFlagOff();
+ relPosFilter->SetBackgroundValue(this->GetBackgroundValue());
+ relPosFilter->SetInput(mInputSlices[i]);
+ relPosFilter->SetInputObject(mObjectSlices[i]);
+ relPosFilter->SetRemoveObjectFlag(this->GetRemoveObjectFlag());
+ // This flag (InverseOrientation) *must* be set before
+ // AddOrientation because AddOrientation can change it.
+ relPosFilter->SetInverseOrientationFlag(this->GetInverseOrientationFlag());
+ for(int j=0; j<this->GetNumberOfAngles(); j++) {
+ // relPosFilter->AddOrientationTypeString(this->GetOrientationTypeString(j));
+ relPosFilter->AddAnglesInRad(this->GetAngle1InRad(j), this->GetAngle2InRad(j));
+ // DD(this->GetOrientationTypeString(j));
+ }
+ // DD(this->GetInverseOrientationFlag());
+ //relPosFilter->SetOrientationType(this->GetOrientationType());
+ relPosFilter->SetIntermediateSpacing(this->GetIntermediateSpacing());
+ relPosFilter->SetIntermediateSpacingFlag(this->GetIntermediateSpacingFlag());
+ relPosFilter->SetFuzzyThreshold(this->GetFuzzyThreshold());
+ relPosFilter->AutoCropFlagOff(); // important ! because we join the slices after this loop
+ relPosFilter->SetCombineWithOrFlag(this->GetCombineWithOrFlag());
+
+ // should we stop after fuzzy map ?
+ relPosFilter->SetFuzzyMapOnlyFlag(this->GetFuzzyMapOnlyFlag());
+
+ // Go !
+ relPosFilter->Update();
+
+ // If we stop after the fuzzy map, store the fuzzy slices
+ if (this->GetFuzzyMapOnlyFlag()) {
+ mFuzzyMapSlices[i] = relPosFilter->GetFuzzyMap();
+ // writeImage<FloatSliceType>(mFuzzyMapSlices[i], "slice_"+toString(i)+".mha");
+ }
+ else {
+ mInputSlices[i] = relPosFilter->GetOutput();
+ // Select main CC if needed
+ if (GetUniqueConnectedComponentBySliceFlag()) {
+ mInputSlices[i] = Labelize<SliceType>(mInputSlices[i], 0, true, 1);
+ mInputSlices[i] = KeepLabels<SliceType>(mInputSlices[i], 0, 1, 1, 1, true);
+ }
+
+ }
+
+ }
+ /*
+ // Select unique CC according to the most in a given direction
+ if (GetUniqueConnectedComponentBySliceAccordingToADirection()) {
+ int nb;
+ mInputSlices[i] = LabelizeAndCountNumberOfObjects<SliceType>(mInputSlices[i], 0, true, 1, nb);
+ std::vector<typename ImageType::PointType> & centroids;
+ ComputeCentroids
+ }
+ */
+ }
}
- DD(this->GetIntermediateSpacing());
- DD(this->GetResampleBeforeRelativePositionFilter());
- DD("End slice");
-
- typedef itk::JoinSeriesImageFilter<SliceType, ImageType> JoinSeriesFilterType;
- typename JoinSeriesFilterType::Pointer joinFilter = JoinSeriesFilterType::New();
- joinFilter->SetOrigin(input->GetOrigin()[GetDirection()]);
- joinFilter->SetSpacing(input->GetSpacing()[GetDirection()]);
- for(unsigned int i=0; i<mInputSlices.size(); i++) {
- // DD(mInputSlices[i]->GetLargestPossibleRegion().GetIndex());
-// DD(mInputSlices[i]->GetLargestPossibleRegion().GetSize());
-// DD(mInputSlices[i]->GetRequestedRegion().GetIndex());
-// DD(mInputSlices[i]->GetRequestedRegion().GetSize());
- joinFilter->PushBackInput(mInputSlices[i]);
- //SetInput(i, mInputSlices[i]);
+
+ // Join the fuzzy map if needed
+ if (this->GetFuzzyMapOnlyFlag()) {
+ this->m_FuzzyMap = clitk::JoinSlices<FloatImageType>(mFuzzyMapSlices, input, GetDirection());
+ this->template StopCurrentStep<FloatImageType>(this->m_FuzzyMap);
+ return;
}
- DD("before update");
- joinFilter->Update();
- DD("after update");
- m_working_input = joinFilter->GetOutput();
-
- // Update the origin
- DD(input->GetSpacing());
- DD(input->GetOrigin());
- DD(mInputSlices[0]->GetSpacing());
- DD(mInputSlices[0]->GetOrigin());
- DD(m_working_input->GetSpacing());
- DD(m_working_input->GetOrigin());
- // typename ImageType::PointType origin = m_working_input->GetOrigin();
-// origin[GetDirection()] = input->GetOrigin()[GetDirection()];
-// m_working_input->SetOrigin(origin);
-// DD(m_working_input->GetOrigin());
- StopCurrentStep<ImageType>(m_working_input);
+ // Join the slices
+ m_working_input = clitk::JoinSlices<ImageType>(mInputSlices, input, GetDirection());
+ this->template StopCurrentStep<ImageType>(m_working_input);
+
+ //--------------------------------------------------------------------
+ // Step 7: autocrop
+ if (this->GetAutoCropFlag()) {
+ this->StartNewStep("Final AutoCrop");
+ typedef clitk::AutoCropFilter<ImageType> CropFilterType;
+ typename CropFilterType::Pointer cropFilter = CropFilterType::New();
+ cropFilter->SetInput(m_working_input);
+ cropFilter->ReleaseDataFlagOff();
+ cropFilter->Update();
+ m_working_input = cropFilter->GetOutput();
+ this->template StopCurrentStep<ImageType>(m_working_input);
+ }
+
+ // Update output info
+ this->GetOutput(0)->SetRegions(m_working_input->GetLargestPossibleRegion());
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class ImageType>
+void
+clitk::SliceBySliceRelativePositionFilter<ImageType>::
+GenerateData()
+{
+ // Get input pointer
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// Final Step -> set output
- this->SetNthOutput(0, m_working_input);
+ //this->SetNthOutput(0, m_working_input);
+ if (this->GetFuzzyMapOnlyFlag()) return; // no output in this case
+ this->GraftOutput(m_working_input);
return;
}
//--------------------------------------------------------------------
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff