SetObjectCCLSelectionDimension(0);
SetObjectCCLSelectionDirection(1);
ObjectCCLSelectionIgnoreSingleCCLFlagOff();
+ VerboseSlicesFlagOff();
+ this->SetK1(std::acos(-1.0)/2);
}
//--------------------------------------------------------------------
PrintOptions(std::ostream & os)
{
os << "Slice direction = " << this->GetDirection() << std::endl
- << "BG value = " << this->GetBackgroundValue() << std::endl;
+ << "BG value = " << (int)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))
<< "ObjectCCLSelectionFlag = " << this->GetObjectCCLSelectionFlag() << std::endl
<< "ObjectCCLSelectionDimension = " << this->GetObjectCCLSelectionDimension() << std::endl
<< "ObjectCCLSelectionIgnoreSingleCCLFlag = " << this->GetObjectCCLSelectionIgnoreSingleCCLFlag() << std::endl
- << "IgnoreEmptySliceObjectFlag = " << this->GetIgnoreEmptySliceObjectFlag() << std::endl;
+ << "IgnoreEmptySliceObjectFlag = " << this->GetIgnoreEmptySliceObjectFlag() << std::endl
+ << "(RP) FastFlag = " << this->GetFastFlag() << std::endl
+ << "(RP) Radius = " << this->GetRadius() << std::endl
+ << "(RP) K1 = " << this->GetK1() << std::endl;
}
//--------------------------------------------------------------------
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);
- }
- else {
- }
+ */
+
+ // 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());
+
+ // Index can be negative in some cases, and lead to problem with
+ // some filter. So we correct it.
+ m_working_input = clitk::RemoveNegativeIndexFromRegion<ImageType>(m_working_input);
+ m_working_object = clitk::RemoveNegativeIndexFromRegion<ImageType>(m_working_object);
- /*
+ // End
+ this->template StopCurrentStep<ImageType>(m_working_input);
+ }
+
+ //--------------------------------------------------------------------
+ /* 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;
//--------------------------------------------------------------------
// Perform slice by slice relative position
- this->StartNewStep("Perform slice by slice relative position");
+ this->StartNewStep("Perform slice by slice relative position ("+toString(mInputSlices.size())+")");
for(unsigned int i=0; i<mInputSlices.size(); i++) {
// 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 (GetVerboseSlicesFlag()) {
+ std::cout << "slice " << i << " nb = " << nb << std::endl;
+ }
+
+ // 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);
// Relative position
typedef clitk::AddRelativePositionConstraintToLabelImageFilter<SliceType> RelPosFilterType;
typename RelPosFilterType::Pointer relPosFilter = RelPosFilterType::New();
-
relPosFilter->VerboseStepFlagOff();
+ if (GetVerboseSlicesFlag()) {
+ std::cout << "Slice " << i << std::endl;
+ relPosFilter->VerboseStepFlagOn();
+ //relPosFilter->WriteStepFlagOn();
+ }
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());
+ 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());
-
+ // relPosFilter->SetComputeFuzzyMapFlag(this->GetComputeFuzzyMapFlag());
+ relPosFilter->SetFastFlag(this->GetFastFlag());
+ relPosFilter->SetRadius(this->GetRadius());
+ relPosFilter->SetK1(this->GetK1());
+
// 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