Authors belong to:
- University of LYON http://www.universite-lyon.fr/
- - Léon Bérard cancer center http://oncora1.lyon.fnclcc.fr
+ - Léon Bérard cancer center http://www.centreleonberard.fr
- CREATIS CNRS laboratory http://www.creatis.insa-lyon.fr
This software is distributed WITHOUT ANY WARRANTY; without even
- BSD See included LICENSE.txt file
- CeCILL-B http://www.cecill.info/licences/Licence_CeCILL-B_V1-en.html
- ======================================================================-====*/
+ ===========================================================================**/
#ifndef CLITKEXTRACTLUNGSFILTER_TXX
#define CLITKEXTRACTLUNGSFILTER_TXX
#include "clitkAutoCropFilter.h"
#include "clitkCropLikeImageFilter.h"
#include "clitkFillMaskFilter.h"
+#include "clitkMemoryUsage.h"
// itk
#include "itkBinaryThresholdImageFilter.h"
SetBackgroundValue(0); // Must be zero
SetForegroundValue(1);
SetMinimalComponentSize(100);
+ VerboseRegionGrowingFlagOff();
// Step 1 default values
SetUpperThreshold(-300);
SetMultiplierForTrachea(5);
SetThresholdStepSizeForTrachea(64);
SetNumberOfSlicesToSkipBeforeSearchingSeed(0);
+ TracheaVolumeMustBeCheckedFlagOn();
// Step 3 default values
SetNumberOfHistogramBins(500);
SetLabelizeParameters3(p3);
// Step 5
- OpenCloseOff();
+ OpenCloseFlagOff();
SetOpenCloseRadius(1);
// Step 6
- FillHolesOn();
+ FillHolesFlagOn();
+ AutoCropOn();
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
-//--------------------------------------------------------------------
-template <class ImageType>
-template<class ArgsInfoType>
-void
-clitk::ExtractLungFilter<ImageType>::
-SetArgsInfo(ArgsInfoType mArgsInfo)
-{
- SetVerboseOption_GGO(mArgsInfo);
- SetVerboseStep_GGO(mArgsInfo);
- SetWriteStep_GGO(mArgsInfo);
- SetVerboseWarningOff_GGO(mArgsInfo);
-
- SetAFDBFilename_GGO(mArgsInfo);
- SetOutputLungFilename_GGO(mArgsInfo);
- SetOutputTracheaFilename_GGO(mArgsInfo);
-
- SetUpperThreshold_GGO(mArgsInfo);
- SetLowerThreshold_GGO(mArgsInfo);
- SetNumberOfSlicesToSkipBeforeSearchingSeed_GGO(mArgsInfo);
- SetLabelizeParameters1_GGO(mArgsInfo);
- if (!mArgsInfo.remove1_given) {
- GetLabelizeParameters1()->AddLabelToRemove(2);
- if (GetVerboseOption()) VerboseOption("remove1", 2);
- }
-
- SetUpperThresholdForTrachea_GGO(mArgsInfo);
- SetMultiplierForTrachea_GGO(mArgsInfo);
- SetThresholdStepSizeForTrachea_GGO(mArgsInfo);
- AddSeed_GGO(mArgsInfo);
-
- SetMinimalComponentSize_GGO(mArgsInfo);
-
- SetNumberOfHistogramBins_GGO(mArgsInfo);
- SetLabelizeParameters2_GGO(mArgsInfo);
-
- SetRadiusForTrachea_GGO(mArgsInfo);
- SetLabelizeParameters3_GGO(mArgsInfo);
-
- SetOpenCloseRadius_GGO(mArgsInfo);
- SetOpenClose_GGO(mArgsInfo);
-
- SetFillHoles_GGO(mArgsInfo);
-}
-//--------------------------------------------------------------------
-
-
//--------------------------------------------------------------------
template <class ImageType>
void
clitk::ExtractLungFilter<ImageType>::
GenerateOutputInformation()
{
+ clitk::PrintMemory(GetVerboseMemoryFlag(), "Initial memory"); // OK
Superclass::GenerateOutputInformation();
// Read DB
// Get input pointers
input = dynamic_cast<const ImageType*>(itk::ProcessObject::GetInput(0));
- patient = GetAFDB()->template GetImage <MaskImageType>("patient");
+ patient = GetAFDB()->template GetImage <MaskImageType>("Patient");
+ PrintMemory(GetVerboseMemoryFlag(), "After reading patient"); // OK
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// Crop input like patient image (must have the same spacing)
- StartNewStep("Crop input image to 'patient' extends");
+ // It copy the input if the same are the same
+ StartNewStep("Copy and crop input image to 'patient' extends");
typedef clitk::CropLikeImageFilter<ImageType> CropImageFilter;
typename CropImageFilter::Pointer cropFilter = CropImageFilter::New();
+ // cropFilter->ReleaseDataFlagOn(); // NO=seg fault !!
cropFilter->SetInput(input);
cropFilter->SetCropLikeImage(patient);
cropFilter->Update();
working_input = cropFilter->GetOutput();
+ // cropFilter->Delete(); // NO !!!! if yes, sg fault, Cropfilter is buggy !??
StopCurrentStep<ImageType>(working_input);
-
+ PrintMemory(GetVerboseMemoryFlag(), "After crop"); // OK, slightly more than a copy of input
+
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Set background to initial image");
working_input = SetBackground<ImageType, MaskImageType>
- (working_input, patient, GetPatientMaskBackgroundValue(), -1000);
+ (working_input, patient, GetPatientMaskBackgroundValue(), -1000, true);
StopCurrentStep<ImageType>(working_input);
+ PrintMemory(GetVerboseMemoryFlag(), "After set bg"); // OK, additional mem = 0
+
+ /*
+ // We do not need patient mask anymore, release memory
+ GetAFDB()->template ReleaseImage<MaskImageType>("Patient");
+ DD(patient->GetReferenceCount());
+ PrintMemory(GetVerboseMemoryFlag(), "After delete patient"); // OK, additional mem = 0
+ patient->Delete();
+ PrintMemory(GetVerboseMemoryFlag(), "After delete patient"); // OK, additional mem = 0
+ */
//--------------------------------------------------------------------
//--------------------------------------------------------------------
}
}
// Threshold to get air
- typedef itk::BinaryThresholdImageFilter<ImageType, InternalImageType> InputBinarizeFilterType;
- typename InputBinarizeFilterType::Pointer binarizeFilter=InputBinarizeFilterType::New();
+ typedef itk::BinaryThresholdImageFilter<ImageType, MaskImageType> InputBinarizeFilterType;
+ typename InputBinarizeFilterType::Pointer binarizeFilter = InputBinarizeFilterType::New();
binarizeFilter->SetInput(working_input);
if (m_UseLowerThreshold) binarizeFilter->SetLowerThreshold(m_LowerThreshold);
+ // binarizeFilter->CanRunInPlace() is false
binarizeFilter->SetUpperThreshold(m_UpperThreshold);
- binarizeFilter ->SetInsideValue(this->GetForegroundValue());
- binarizeFilter ->SetOutsideValue(this->GetBackgroundValue());
+ binarizeFilter->SetInsideValue(this->GetForegroundValue());
+ binarizeFilter->SetOutsideValue(this->GetBackgroundValue());
binarizeFilter->Update();
- working_image = binarizeFilter->GetOutput();
-
- // Labelize and keep right labels
- working_image = Labelize<InternalImageType>(working_image, GetBackgroundValue(), true, GetMinimalComponentSize());
+ working_mask = binarizeFilter->GetOutput();
+ PrintMemory(GetVerboseMemoryFlag(), "After Binarizefilter"); // OK, additional mem is one mask image
- working_image = RemoveLabels<InternalImageType>
- (working_image, GetBackgroundValue(), GetLabelizeParameters1()->GetLabelsToRemove());
+ // Labelize and keep right labels
+ working_mask =
+ Labelize<MaskImageType>
+ (working_mask, GetBackgroundValue(), true, GetMinimalComponentSize());
+ PrintMemory(GetVerboseMemoryFlag(), "After Labelize"); // BUG ? additional mem around 1 time the input ?
+
+ working_mask = RemoveLabels<MaskImageType>
+ (working_mask, GetBackgroundValue(), GetLabelizeParameters1()->GetLabelsToRemove());
+ PrintMemory(GetVerboseMemoryFlag(), "After RemoveLabels"); // OK additional mem = 0
- typename InternalImageType::Pointer air = KeepLabels<InternalImageType>
- (working_image,
+ working_mask = KeepLabels<MaskImageType>
+ (working_mask,
GetBackgroundValue(),
GetForegroundValue(),
GetLabelizeParameters1()->GetFirstKeep(),
GetLabelizeParameters1()->GetLastKeep(),
GetLabelizeParameters1()->GetUseLastKeep());
+ PrintMemory(GetVerboseMemoryFlag(), "After KeepLabels to create the 'air'");
// Set Air to BG
- working_input = SetBackground<ImageType, InternalImageType>
- (working_input, air, this->GetForegroundValue(), this->GetBackgroundValue());
+ working_input = SetBackground<ImageType, MaskImageType>
+ (working_input, working_mask, this->GetForegroundValue(), this->GetBackgroundValue(), true);
+ PrintMemory(GetVerboseMemoryFlag(), "After SetBackground");
// End
StopCurrentStep<ImageType>(working_input);
//--------------------------------------------------------------------
StartNewStep("Search for the trachea");
SearchForTrachea();
+ PrintMemory(GetVerboseMemoryFlag(), "After SearchForTrachea");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Extract the lung with Otsu filter");
// Automated Otsu thresholding and relabeling
- typedef itk::OtsuThresholdImageFilter<ImageType,InternalImageType> OtsuThresholdImageFilterType;
+ typedef itk::OtsuThresholdImageFilter<ImageType,MaskImageType> OtsuThresholdImageFilterType;
typename OtsuThresholdImageFilterType::Pointer otsuFilter=OtsuThresholdImageFilterType::New();
otsuFilter->SetInput(working_input);
otsuFilter->SetNumberOfHistogramBins(GetNumberOfHistogramBins());
otsuFilter->SetInsideValue(this->GetForegroundValue());
otsuFilter->SetOutsideValue(this->GetBackgroundValue());
otsuFilter->Update();
- working_image = otsuFilter->GetOutput();
+ working_mask = otsuFilter->GetOutput();
// Set output
- StopCurrentStep<InternalImageType>(working_image);
+ StopCurrentStep<MaskImageType>(working_mask);
+ PrintMemory(GetVerboseMemoryFlag(), "After Otsufilter");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Select labels");
// Keep right labels
- working_image = LabelizeAndSelectLabels<InternalImageType>
- (working_image,
+ working_mask = LabelizeAndSelectLabels<MaskImageType>
+ (working_mask,
GetBackgroundValue(),
GetForegroundValue(),
false,
GetLabelizeParameters2());
// Set output
- StopCurrentStep<InternalImageType>(working_image);
+ StopCurrentStep<MaskImageType>(working_mask);
+ PrintMemory(GetVerboseMemoryFlag(), "After LabelizeAndSelectLabels");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
if (m_Seeds.size() != 0) { // if ==0 ->no trachea found
StartNewStep("Remove the trachea");
// Set the trachea
- working_image = SetBackground<InternalImageType, InternalImageType>
- (working_image, trachea_tmp, 1, -1);
+ working_mask = SetBackground<MaskImageType, MaskImageType>
+ (working_mask, trachea, 1, -1, true);
+ PrintMemory(GetVerboseMemoryFlag(), "After SetBackground");
// Dilate the trachea
static const unsigned int Dim = ImageType::ImageDimension;
KernelType structuringElement;
structuringElement.SetRadius(GetRadiusForTrachea());
structuringElement.CreateStructuringElement();
- typedef clitk::ConditionalBinaryDilateImageFilter<InternalImageType, InternalImageType, KernelType> ConditionalBinaryDilateImageFilterType;
+ typedef clitk::ConditionalBinaryDilateImageFilter<MaskImageType, MaskImageType, KernelType> ConditionalBinaryDilateImageFilterType;
typename ConditionalBinaryDilateImageFilterType::Pointer dilateFilter = ConditionalBinaryDilateImageFilterType::New();
dilateFilter->SetBoundaryToForeground(false);
dilateFilter->SetKernel(structuringElement);
dilateFilter->SetBackgroundValue (1);
dilateFilter->SetForegroundValue (-1);
- dilateFilter->SetInput (working_image);
+ dilateFilter->SetInput (working_mask);
dilateFilter->Update();
- working_image = dilateFilter->GetOutput();
+ working_mask = dilateFilter->GetOutput();
+ PrintMemory(GetVerboseMemoryFlag(), "After dilate");
// Set trachea with dilatation
- trachea_tmp = SetBackground<InternalImageType, InternalImageType>
- (trachea_tmp, working_image, -1, this->GetForegroundValue());
+ trachea = SetBackground<MaskImageType, MaskImageType>
+ (trachea, working_mask, -1, this->GetForegroundValue(), true);
// Remove the trachea
- working_image = SetBackground<InternalImageType, InternalImageType>
- (working_image, working_image, -1, this->GetBackgroundValue());
+ working_mask = SetBackground<MaskImageType, MaskImageType>
+ (working_mask, working_mask, -1, this->GetBackgroundValue(), true);
// Label
- working_image = LabelizeAndSelectLabels<InternalImageType>
- (working_image,
+ working_mask = LabelizeAndSelectLabels<MaskImageType>
+ (working_mask,
GetBackgroundValue(),
GetForegroundValue(),
false,
GetLabelizeParameters3());
// Set output
- StopCurrentStep<InternalImageType>(working_image);
+ StopCurrentStep<MaskImageType>(working_mask);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
- typedef clitk::AutoCropFilter<InternalImageType> AutoCropFilterType;
- typename AutoCropFilterType::Pointer autocropFilter = AutoCropFilterType::New();
+ PrintMemory(GetVerboseMemoryFlag(), "before autocropfilter");
if (m_Seeds.size() != 0) { // if ==0 ->no trachea found
- StartNewStep("Cropping trachea");
- autocropFilter->SetInput(trachea_tmp);
- autocropFilter->Update(); // Needed
- typedef itk::CastImageFilter<InternalImageType, MaskImageType> CastImageFilterType;
- typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
- caster->SetInput(autocropFilter->GetOutput());
- caster->Update();
- trachea = caster->GetOutput();
+ if (GetAutoCrop())
+ trachea = clitk::AutoCrop<MaskImageType>(trachea, GetBackgroundValue());
StopCurrentStep<MaskImageType>(trachea);
+ PrintMemory(GetVerboseMemoryFlag(), "after delete trachea");
}
+ PrintMemory(GetVerboseMemoryFlag(), "after delete trachea");
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Cropping lung");
- typename AutoCropFilterType::Pointer autocropFilter2 = AutoCropFilterType::New(); // Needed to reset pipeline
- autocropFilter2->SetInput(working_image);
- autocropFilter2->Update();
- working_image = autocropFilter2->GetOutput();
- StopCurrentStep<InternalImageType>(working_image);
+ PrintMemory(GetVerboseMemoryFlag(), "Before Autocropfilter");
+ if (GetAutoCrop())
+ working_mask = clitk::AutoCrop<MaskImageType>(working_mask, GetBackgroundValue());
+ StopCurrentStep<MaskImageType>(working_mask);
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// Final OpenClose
- if (GetOpenClose()) {
+ if (GetOpenCloseFlag()) {
StartNewStep("Open/Close");
-
+ PrintMemory(GetVerboseMemoryFlag(), "Before OpenClose");
+
// Structuring element
typedef itk::BinaryBallStructuringElement<InternalPixelType, ImageDimension> KernelType;
KernelType structuringElement;
structuringElement.CreateStructuringElement();
// Open
- typedef itk::BinaryMorphologicalOpeningImageFilter<InternalImageType, InternalImageType, KernelType> OpenFilterType;
+ typedef itk::BinaryMorphologicalOpeningImageFilter<MaskImageType, InternalImageType, KernelType> OpenFilterType;
typename OpenFilterType::Pointer openFilter = OpenFilterType::New();
- openFilter->SetInput(working_image);
+ openFilter->SetInput(working_mask);
openFilter->SetBackgroundValue(GetBackgroundValue());
openFilter->SetForegroundValue(GetForegroundValue());
openFilter->SetKernel(structuringElement);
// Close
- typedef itk::BinaryMorphologicalClosingImageFilter<InternalImageType, InternalImageType, KernelType> CloseFilterType;
+ typedef itk::BinaryMorphologicalClosingImageFilter<MaskImageType, MaskImageType, KernelType> CloseFilterType;
typename CloseFilterType::Pointer closeFilter = CloseFilterType::New();
closeFilter->SetInput(openFilter->GetOutput());
closeFilter->SetSafeBorder(true);
closeFilter->SetForegroundValue(GetForegroundValue());
closeFilter->SetKernel(structuringElement);
closeFilter->Update();
- working_image = closeFilter->GetOutput();
+ working_mask = closeFilter->GetOutput();
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
// Fill Lungs
- if (GetFillHoles()) {
+ if (GetFillHolesFlag()) {
StartNewStep("Fill Holes");
- /*
+ PrintMemory(GetVerboseMemoryFlag(), "Before Fill Holes");
+ typedef clitk::FillMaskFilter<MaskImageType> FillMaskFilterType;
typename FillMaskFilterType::Pointer fillMaskFilter = FillMaskFilterType::New();
- fillMaskFilter(working_image);
+ fillMaskFilter->SetInput(working_mask);
+ fillMaskFilter->AddDirection(2);
+ //fillMaskFilter->AddDirection(1);
fillMaskFilter->Update();
- working_image = fillMaskFilter->GetOutput();
- StopCurrentStep<InternalImageType>(working_image);
- */
+ working_mask = fillMaskFilter->GetOutput();
+ StopCurrentStep<MaskImageType>(working_mask);
}
//--------------------------------------------------------------------
//--------------------------------------------------------------------
StartNewStep("Separate Left/Right lungs");
+ PrintMemory(GetVerboseMemoryFlag(), "Before Separate");
// Initial label
- working_image = Labelize<InternalImageType>(working_image,
- GetBackgroundValue(),
- false,
- GetMinimalComponentSize());
+ working_mask = Labelize<MaskImageType>(working_mask,
+ GetBackgroundValue(),
+ false,
+ GetMinimalComponentSize());
+
+ PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
// Count the labels
- typedef itk::StatisticsImageFilter<InternalImageType> StatisticsImageFilterType;
+ typedef itk::StatisticsImageFilter<MaskImageType> StatisticsImageFilterType;
typename StatisticsImageFilterType::Pointer statisticsImageFilter=StatisticsImageFilterType::New();
- statisticsImageFilter->SetInput(working_image);
+ statisticsImageFilter->SetInput(working_mask);
statisticsImageFilter->Update();
unsigned int initialNumberOfLabels = statisticsImageFilter->GetMaximum();
- working_image = statisticsImageFilter->GetOutput();
+ working_mask = statisticsImageFilter->GetOutput();
+
+ PrintMemory(GetVerboseMemoryFlag(), "After count label");
// Decompose the first label
static const unsigned int Dim = ImageType::ImageDimension;
// Structuring element radius
typename ImageType::SizeType radius;
for (unsigned int i=0;i<Dim;i++) radius[i]=1;
- typedef clitk::DecomposeAndReconstructImageFilter<InternalImageType,InternalImageType> DecomposeAndReconstructFilterType;
+ typedef clitk::DecomposeAndReconstructImageFilter<MaskImageType,MaskImageType> DecomposeAndReconstructFilterType;
typename DecomposeAndReconstructFilterType::Pointer decomposeAndReconstructFilter=DecomposeAndReconstructFilterType::New();
- decomposeAndReconstructFilter->SetInput(working_image);
+ decomposeAndReconstructFilter->SetInput(working_mask);
decomposeAndReconstructFilter->SetVerbose(false);
decomposeAndReconstructFilter->SetRadius(radius);
decomposeAndReconstructFilter->SetMaximumNumberOfLabels(2);
decomposeAndReconstructFilter->SetFullyConnected(true);
decomposeAndReconstructFilter->SetNumberOfNewLabels(1);
decomposeAndReconstructFilter->Update();
- working_image = decomposeAndReconstructFilter->GetOutput();
+ working_mask = decomposeAndReconstructFilter->GetOutput();
}
+ PrintMemory(GetVerboseMemoryFlag(), "After decomposeAndReconstructFilter");
// Retain labels ('1' is largset lung, so right. '2' is left)
- typedef itk::ThresholdImageFilter<InternalImageType> ThresholdImageFilterType;
+ typedef itk::ThresholdImageFilter<MaskImageType> ThresholdImageFilterType;
typename ThresholdImageFilterType::Pointer thresholdFilter = ThresholdImageFilterType::New();
- thresholdFilter->SetInput(working_image);
+ thresholdFilter->SetInput(working_mask);
thresholdFilter->ThresholdAbove(2);
thresholdFilter->SetOutsideValue(this->GetBackgroundValue());
thresholdFilter->Update();
- working_image = thresholdFilter->GetOutput();
- StopCurrentStep<InternalImageType> (working_image);
-
- // Final Cast
- StartNewStep("Cast the lung mask");
- typedef itk::CastImageFilter<InternalImageType, MaskImageType> CastImageFilterType;
- typename CastImageFilterType::Pointer caster= CastImageFilterType::New();
- caster->SetInput(working_image);
- caster->Update();
- output = caster->GetOutput();
+ working_mask = thresholdFilter->GetOutput();
+ StopCurrentStep<MaskImageType> (working_mask);
+ PrintMemory(GetVerboseMemoryFlag(), "After Thresholdfilter");
// Update output info
- this->GetOutput(0)->SetRegions(output->GetLargestPossibleRegion());
+ // output = working_mask;
+ //this->GetOutput(0)->SetRegions(output->GetLargestPossibleRegion());
+
+ // this->GetOutput(0)->SetRegions(working_mask->GetLargestPossibleRegion());
+
+}
+//--------------------------------------------------------------------
+
+
+//--------------------------------------------------------------------
+template <class TImageType>
+void
+clitk::ExtractLungFilter<TImageType>::
+GenerateInputRequestedRegion() {
+ // DD("GenerateInputRequestedRegion (nothing?)");
}
//--------------------------------------------------------------------
GenerateData()
{
// Set the output
- this->GraftOutput(output); // not SetNthOutput
+ // this->GraftOutput(output); // not SetNthOutput
+ this->GraftOutput(working_mask); // not SetNthOutput
// Store image filenames into AFDB
- GetAFDB()->SetImageFilename("lungs", this->GetOutputLungFilename());
- GetAFDB()->SetImageFilename("trachea", this->GetOutputTracheaFilename());
+ GetAFDB()->SetImageFilename("Lungs", this->GetOutputLungFilename());
+ GetAFDB()->SetImageFilename("Trachea", this->GetOutputTracheaFilename());
WriteAFDB();
}
//--------------------------------------------------------------------
// if we do not found : restart
stop = (m_Seeds.size() != 0);
if (!stop) {
- if (GetVerboseStep()) {
+ if (GetVerboseStepFlag()) {
std::cout << "\t No seed found this time. I skip some slices and restart." << std::endl;
}
if (skip > 0.5 * working_input->GetLargestPossibleRegion().GetSize()[2]) {
}
skip += 5;
}
+ else {
+ // DD(m_Seeds[0]);
+ // DD(m_Seeds.size());
+ }
}
}
return (m_Seeds.size() != 0);
TracheaRegionGrowing()
{
// Explosion controlled region growing
- typedef clitk::ExplosionControlledThresholdConnectedImageFilter<ImageType, InternalImageType> ImageFilterType;
+ PrintMemory(GetVerboseMemoryFlag(), "Before ExplosionControlledThresholdConnectedImageFilter");
+ typedef clitk::ExplosionControlledThresholdConnectedImageFilter<ImageType, MaskImageType> ImageFilterType;
typename ImageFilterType::Pointer f= ImageFilterType::New();
f->SetInput(working_input);
- f->SetVerbose(false);
f->SetLower(-2000);
f->SetUpper(GetUpperThresholdForTrachea());
f->SetMinimumLowerThreshold(-2000);
- f->SetMaximumUpperThreshold(0);
+ // f->SetMaximumUpperThreshold(0); // MAYBE TO CHANGE ???
+ f->SetMaximumUpperThreshold(-800); // MAYBE TO CHANGE ???
f->SetAdaptLowerBorder(false);
f->SetAdaptUpperBorder(true);
f->SetMinimumSize(5000);
f->SetMultiplier(GetMultiplierForTrachea());
f->SetThresholdStepSize(GetThresholdStepSizeForTrachea());
f->SetMinimumThresholdStepSize(1);
+ f->SetVerbose(GetVerboseRegionGrowingFlag());
for(unsigned int i=0; i<m_Seeds.size();i++) {
f->AddSeed(m_Seeds[i]);
// DD(m_Seeds[i]);
}
f->Update();
-
+ PrintMemory(GetVerboseMemoryFlag(), "After RG update");
+
// take first (main) connected component
- trachea_tmp = Labelize<InternalImageType>(f->GetOutput(),
- GetBackgroundValue(),
- true,
- GetMinimalComponentSize());
- trachea_tmp = KeepLabels<InternalImageType>(trachea_tmp,
+ trachea = Labelize<MaskImageType>(f->GetOutput(),
+ GetBackgroundValue(),
+ true,
+ 1000);//GetMinimalComponentSize());
+ PrintMemory(GetVerboseMemoryFlag(), "After Labelize");
+ trachea = KeepLabels<MaskImageType>(trachea,
GetBackgroundValue(),
GetForegroundValue(),
1, 1, false);
+ PrintMemory(GetVerboseMemoryFlag(), "After KeepLabels");
}
//--------------------------------------------------------------------
ComputeTracheaVolume()
{
typedef itk::ImageRegionConstIterator<InternalImageType> IteratorType;
- IteratorType iter(trachea_tmp, trachea_tmp->GetLargestPossibleRegion());
+ IteratorType iter(trachea, trachea->GetLargestPossibleRegion());
iter.GoToBegin();
double volume = 0.0;
while (!iter.IsAtEnd()) {
++iter;
}
- double voxelsize = trachea_tmp->GetSpacing()[0]*trachea_tmp->GetSpacing()[1]*trachea_tmp->GetSpacing()[2];
+ double voxelsize = trachea->GetSpacing()[0]*trachea->GetSpacing()[1]*trachea->GetSpacing()[2];
return volume*voxelsize;
}
//--------------------------------------------------------------------
if (stop) {
TracheaRegionGrowing();
volume = ComputeTracheaVolume()/1000; // assume mm3, so divide by 1000 to get cc
- if ((volume > 10) && (volume < 55 )) { // it is ok
- // Typical volume 22.59 cm 3 (± 7.69 cm 3 ) [ Leader 2004 ]
- if (GetVerboseStep()) {
- std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl;
- }
- stop = true;
+ if (GetWriteStepFlag()) {
+ writeImage<MaskImageType>(trachea, "step-trachea-"+toString(skip)+".mhd");
+ }
+ if (GetTracheaVolumeMustBeCheckedFlag()) {
+ if ((volume > 10) && (volume < 65 )) { // depend on image size ...
+ // Typical volume 22.59 cm 3 (± 7.69 cm 3 ) [ Leader 2004 ]
+ if (GetVerboseStepFlag()) {
+ std::cout << "\t Found trachea with volume " << volume << " cc." << std::endl;
+ }
+ stop = true;
+ }
+ else {
+ if (GetVerboseStepFlag()) {
+ std::cout << "\t The volume of the trachea (" << volume
+ << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds."
+ << std::endl;
+ }
+ skip += 5;
+ stop = false;
+ // empty the list of seed
+ m_Seeds.clear();
+ }
}
else {
- if (GetVerboseStep()) {
- std::cout << "\t The volume of the trachea (" << volume
- << " cc) seems not correct. I skip some slices (" << skip << ") and restart to find seeds."
- << std::endl;
- }
- skip += 5;
- stop = false;
- // empty the list of seed
- m_Seeds.clear();
+ stop = true;
}
}
}
if (volume != 0.0) {
// Set output
- StopCurrentStep<InternalImageType>(trachea_tmp);
+ StopCurrentStep<MaskImageType>(trachea);
}
else { // Trachea not found
this->SetWarning("* WARNING * No seed found for trachea.");
git://git.creatis.insa-lyon.fr / clitk.git / blobdiff