X-Git-Url: https://git.creatis.insa-lyon.fr/pubgit/?a=blobdiff_plain;f=itk%2FclitkSliceBySliceRelativePositionFilter.txx;h=16571ea7a224df6b17d87425d7cf8bde619a66b0;hb=3a823a03d4a2217e41e4dd3b05a8ea825bb762a5;hp=0df2987312797c94f34fb72365359fda82b4043a;hpb=c84464b925114176d46e882f73a00c5c10d18ff1;p=clitk.git diff --git a/itk/clitkSliceBySliceRelativePositionFilter.txx b/itk/clitkSliceBySliceRelativePositionFilter.txx index 0df2987..16571ea 100644 --- a/itk/clitkSliceBySliceRelativePositionFilter.txx +++ b/itk/clitkSliceBySliceRelativePositionFilter.txx @@ -42,6 +42,8 @@ SliceBySliceRelativePositionFilter(): SetObjectCCLSelectionDimension(0); SetObjectCCLSelectionDirection(1); ObjectCCLSelectionIgnoreSingleCCLFlagOff(); + VerboseSlicesFlagOff(); + this->SetK1(vcl_acos(-1.0)/2); } //-------------------------------------------------------------------- @@ -77,7 +79,7 @@ clitk::SliceBySliceRelativePositionFilter:: 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; iGetNumberOfAngles(); i++) { os << "Orientation = " << this->GetOrientationTypeString()[i] << std::endl; os << "Angles = " << clitk::rad2deg(this->GetAngle1InRad(i)) @@ -95,7 +97,10 @@ PrintOptions(std::ostream & os) << "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; } //-------------------------------------------------------------------- @@ -127,9 +132,13 @@ GenerateOutputInformation() PrintOptions(); } + // if (this->GetFuzzyMapOnlyFlag()) this->ComputeFuzzyMapFlagOn(); + // Get input pointer input = dynamic_cast(itk::ProcessObject::GetInput(0)); object = dynamic_cast(itk::ProcessObject::GetInput(1)); + m_working_object = object; + m_working_input = input; //-------------------------------------------------------------------- // Resample object to the same spacing than input @@ -138,36 +147,67 @@ GenerateOutputInformation() m_working_object = clitk::ResampleImageSpacing(object, input->GetSpacing()); this->template StopCurrentStep(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(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(m_working_object, - input, - this->GetObjectBackgroundValue()); + input, + this->GetObjectBackgroundValue()); this->template StopCurrentStep(m_working_object); - } - else { - } + */ + + // Compute union of bounding boxes in X and Y + static const unsigned int dim = ImageType::ImageDimension; + typedef itk::BoundingBox BBType; + typename BBType::Pointer bb1 = BBType::New(); + ComputeBBFromImageRegion(m_working_object, m_working_object->GetLargestPossibleRegion(), bb1); + typename BBType::Pointer bb2 = BBType::New(); + ComputeBBFromImageRegion(input, input->GetLargestPossibleRegion(), bb2); + typename BBType::Pointer bbo = BBType::New(); + ComputeBBUnion(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(input, bbo, this->GetBackgroundValue()); + m_working_object = clitk::ResizeImageLike(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(m_working_input); + m_working_object = clitk::RemoveNegativeIndexFromRegion(m_working_object); - /* + // End + this->template StopCurrentStep(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 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; @@ -179,7 +219,7 @@ GenerateOutputInformation() // 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 mObjectSlices; @@ -193,14 +233,18 @@ GenerateOutputInformation() //-------------------------------------------------------------------- // 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(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]); @@ -208,10 +252,10 @@ GenerateOutputInformation() 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(mObjectSlices[i], 0, 1, 1, 1, true); @@ -253,32 +297,37 @@ GenerateOutputInformation() // Relative position typedef clitk::AddRelativePositionConstraintToLabelImageFilter 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; jGetNumberOfAngles(); 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(); @@ -287,17 +336,19 @@ GenerateOutputInformation() mFuzzyMapSlices[i] = relPosFilter->GetFuzzyMap(); // writeImage(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(mInputSlices[i], 0, true, 1); mInputSlices[i] = KeepLabels(mInputSlices[i], 0, 1, 1, 1, true); - } - + } } } + /* // Select unique CC according to the most in a given direction if (GetUniqueConnectedComponentBySliceAccordingToADirection()) { @@ -307,20 +358,22 @@ GenerateOutputInformation() ComputeCentroids } */ - } - } + + } // End nb!=0 || GetComputeFuzzyMapFlagOFF + + } // end for i mInputSlices + + // Join the slices + m_working_input = clitk::JoinSlices(mInputSlices, m_working_input, GetDirection()); + this->template StopCurrentStep(m_working_input); // Join the fuzzy map if needed if (this->GetFuzzyMapOnlyFlag()) { - this->m_FuzzyMap = clitk::JoinSlices(mFuzzyMapSlices, input, GetDirection()); + this->m_FuzzyMap = clitk::JoinSlices(mFuzzyMapSlices, m_working_input, GetDirection()); this->template StopCurrentStep(this->m_FuzzyMap); - return; + if (this->GetFuzzyMapOnlyFlag()) return; } - // Join the slices - m_working_input = clitk::JoinSlices(mInputSlices, input, GetDirection()); - this->template StopCurrentStep(m_working_input); - //-------------------------------------------------------------------- // Step 7: autocrop if (this->GetAutoCropFlag()) {