PrintOptions();
}
+ // if (this->GetFuzzyMapOnlyFlag()) this->ComputeFuzzyMapFlagOn();
+
// Get input pointer
input = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(0));
object = dynamic_cast<ImageType*>(itk::ProcessObject::GetInput(1));
+ m_working_object = object;
+ m_working_input = input;
//--------------------------------------------------------------------
// Resample object to the same spacing than input
m_working_object = clitk::ResampleImageSpacing<ImageType>(object, input->GetSpacing());
this->template StopCurrentStep<ImageType>(m_working_object);
}
- else {
- m_working_object = object;
- }
//--------------------------------------------------------------------
- // Pad object to the same size than input
+ // Resize image according to common area (except in Z)
if (!clitk::HaveSameSizeAndSpacing<ImageType, ImageType>(m_working_object, input)) {
+ this->StartNewStep("Resize images (union in XY and like input in Z)");
+
+ /* OLD STUFF
this->StartNewStep("Pad object to the same size than input");
m_working_object = clitk::ResizeImageLike<ImageType>(m_working_object,
- input,
- this->GetObjectBackgroundValue());
+ input,
+ this->GetObjectBackgroundValue());
this->template StopCurrentStep<ImageType>(m_working_object);
+ */
+
+ // Compute union of bounding boxes in X and Y
+ static const unsigned int dim = ImageType::ImageDimension;
+ typedef itk::BoundingBox<unsigned long, dim> BBType;
+ typename BBType::Pointer bb1 = BBType::New();
+ ComputeBBFromImageRegion<ImageType>(m_working_object, m_working_object->GetLargestPossibleRegion(), bb1);
+ typename BBType::Pointer bb2 = BBType::New();
+ ComputeBBFromImageRegion<ImageType>(input, input->GetLargestPossibleRegion(), bb2);
+ typename BBType::Pointer bbo = BBType::New();
+ ComputeBBUnion<dim>(bbo, bb1, bb2);
+
+ //We set Z BB like input
+ typename ImageType::PointType maxs = bbo->GetMaximum();
+ typename ImageType::PointType mins = bbo->GetMinimum();
+ maxs[2] = bb2->GetMaximum()[2];
+ mins[2] = bb2->GetMinimum()[2];
+ bbo->SetMaximum(maxs);
+ bbo->SetMinimum(mins);
+
+ // Crop
+ m_working_input = clitk::ResizeImageLike<ImageType>(input, bbo, this->GetBackgroundValue());
+ m_working_object = clitk::ResizeImageLike<ImageType>(m_working_object,
+ m_working_input,
+ this->GetObjectBackgroundValue());
+ this->template StopCurrentStep<ImageType>(m_working_input);
}
- else {
- }
-
- /*
+
+ //--------------------------------------------------------------------
+ /* Steps :
- extract vector of slices in input, in object
- slice by slice rel position
- joint result
- post process
*/
-
//--------------------------------------------------------------------
// Extract input slices
this->StartNewStep("Extract input slices");
typedef clitk::ExtractSliceFilter<ImageType> ExtractSliceFilterType;
typename ExtractSliceFilterType::Pointer extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(input);
+ extractSliceFilter->SetInput(m_working_input);
extractSliceFilter->SetDirection(GetDirection());
extractSliceFilter->Update();
typedef typename ExtractSliceFilterType::SliceType SliceType;
// Extract object slices
this->StartNewStep("Extract object slices");
extractSliceFilter = ExtractSliceFilterType::New();
- extractSliceFilter->SetInput(m_working_object);//object);
+ extractSliceFilter->SetInput(m_working_object);
extractSliceFilter->SetDirection(GetDirection());
extractSliceFilter->Update();
std::vector<typename SliceType::Pointer> mObjectSlices;
int nb=0;
mObjectSlices[i] = LabelizeAndCountNumberOfObjects<SliceType>(mObjectSlices[i], 0, true, 1, nb);
- // If no object and empty slices :
+ // If no object and empty slices and if we need the full fuzzy map, create a dummy one.
if ((nb==0) && (this->GetFuzzyMapOnlyFlag())) {
typename FloatSliceType::Pointer one = FloatSliceType::New();
one->CopyInformation(mObjectSlices[0]);
one->Allocate();
one->FillBuffer(2.0);
mFuzzyMapSlices[i] = one;
- }
+ } // End nb==0 && GetComputeFuzzyMapFlag
else {
if ((!GetIgnoreEmptySliceObjectFlag()) || (nb!=0)) {
-
+
// Select or not a single CCL ?
if (GetUseTheLargestObjectCCLFlag()) {
mObjectSlices[i] = KeepLabels<SliceType>(mObjectSlices[i], 0, 1, 1, 1, true);
relPosFilter->VerboseStepFlagOff();
relPosFilter->WriteStepFlagOff();
+ // relPosFilter->VerboseMemoryFlagOn();
+ relPosFilter->SetCurrentStepBaseId(this->GetCurrentStepId()+"-"+toString(i));
+
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());
// should we stop after fuzzy map ?
relPosFilter->SetFuzzyMapOnlyFlag(this->GetFuzzyMapOnlyFlag());
+ // relPosFilter->SetComputeFuzzyMapFlag(this->GetComputeFuzzyMapFlag());
// Go !
relPosFilter->Update();
mFuzzyMapSlices[i] = relPosFilter->GetFuzzyMap();
// writeImage<FloatSliceType>(mFuzzyMapSlices[i], "slice_"+toString(i)+".mha");
}
- else {
+
+ // Set input slices
+ if (!this->GetFuzzyMapOnlyFlag()) {
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()) {
ComputeCentroids
}
*/
- }
- }
+
+ } // End nb!=0 || GetComputeFuzzyMapFlagOFF
+
+ } // end for i mInputSlices
+
+ // Join the slices
+ m_working_input = clitk::JoinSlices<ImageType>(mInputSlices, m_working_input, GetDirection());
+ this->template StopCurrentStep<ImageType>(m_working_input);
// Join the fuzzy map if needed
if (this->GetFuzzyMapOnlyFlag()) {
- this->m_FuzzyMap = clitk::JoinSlices<FloatImageType>(mFuzzyMapSlices, input, GetDirection());
+ this->m_FuzzyMap = clitk::JoinSlices<FloatImageType>(mFuzzyMapSlices, m_working_input, GetDirection());
this->template StopCurrentStep<FloatImageType>(this->m_FuzzyMap);
- return;
+ if (this->GetFuzzyMapOnlyFlag()) return;
}
- // 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()) {
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff