void mitk::ImageLiveWireContourModelFilter::ItkPreProcessImage (const itk::Image<TPixel, VImageDimension>* inputImage)
{
typedef itk::Image< TPixel, VImageDimension > InputImageType;
typedef itk::CastImageFilter< InputImageType, InternalImageType > CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput(inputImage);
castFilter->Update();
m_InternalImage = castFilter->GetOutput();
m_CostFunction->SetImage( m_InternalImage );
m_ShortestPathFilter->SetInput( m_InternalImage );
}
dtkSmartPointer<medAbstractData> itkFiltersComponentSizeThresholdProcess::castToOutputType(medAbstractData* inputData)
{
//we will later label the image so we don't care about precision.
typedef itk::CastImageFilter< InputImageType, OutputImageType > CastFilterType;
typename CastFilterType::Pointer caster = CastFilterType::New();
typename InputImageType::Pointer im = static_cast<InputImageType*>(inputData->data());
caster->SetInput(im);
caster->Update();
dtkSmartPointer<medAbstractData> outputData = medAbstractDataFactory::instance()->createSmartPointer(medUtilitiesITK::itkDataImageId<OutputImageType>());
outputData->setData(caster->GetOutput());
return outputData;
}
void
mitk::ModelSignalImageGenerator::DoPrepareMask(itk::Image<TPixel, VDim>* image)
{
m_InternalMask = dynamic_cast<InternalMaskType*>(image);
if (m_InternalMask.IsNull())
{
MITK_INFO << "Parameter Fit Generator. Need to cast mask for parameter fit.";
typedef itk::Image<TPixel, VDim> InputImageType;
typedef itk::CastImageFilter< InputImageType, InternalMaskType > CastFilterType;
typename CastFilterType::Pointer spImageCaster = CastFilterType::New();
spImageCaster->SetInput(image);
m_InternalMask = spImageCaster->GetOutput();
spImageCaster->Update();
}
}
void RTDoseReader::MultiplyGridScaling(itk::Image<TPixel, VImageDimension>* image, float gridscale)
{
typedef itk::Image<Float32, VImageDimension> OutputImageType;
typedef itk::Image<TPixel, VImageDimension> InputImageType;
typedef itk::CastImageFilter<InputImageType, OutputImageType> CastFilterType;
typedef itk::ShiftScaleImageFilter<OutputImageType, OutputImageType> ScaleFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
typename ScaleFilterType::Pointer scaleFilter = ScaleFilterType::New();
castFilter->SetInput(image);
scaleFilter->SetInput(castFilter->GetOutput());
scaleFilter->SetScale(gridscale);
scaleFilter->Update();
typename OutputImageType::Pointer scaledOutput = scaleFilter->GetOutput();
this->scaledDoseImage = mitk::Image::New();
mitk::CastToMitkImage(scaledOutput, this->scaledDoseImage);
}
void DemonsRegistration::GenerateData2(const itk::Image<TPixel, VImageDimension>* itkImage1)
{
typedef typename itk::Image< TPixel, VImageDimension > FixedImageType;
typedef typename itk::Image< TPixel, VImageDimension > MovingImageType;
typedef float InternalPixelType;
typedef typename itk::Image< InternalPixelType, VImageDimension > InternalImageType;
typedef typename itk::CastImageFilter< FixedImageType,
InternalImageType > FixedImageCasterType;
typedef typename itk::CastImageFilter< MovingImageType,
InternalImageType > MovingImageCasterType;
typedef typename itk::Image< InternalPixelType, VImageDimension > InternalImageType;
typedef typename itk::Vector< float, VImageDimension > VectorPixelType;
typedef typename itk::Image< VectorPixelType, VImageDimension > DeformationFieldType;
typedef typename itk::DemonsRegistrationFilter<
InternalImageType,
InternalImageType,
DeformationFieldType> RegistrationFilterType;
typedef typename itk::WarpImageFilter<
MovingImageType,
MovingImageType,
DeformationFieldType > WarperType;
typedef typename itk::LinearInterpolateImageFunction<
MovingImageType,
double > InterpolatorType;
typedef TPixel OutputPixelType;
typedef typename itk::Image< OutputPixelType, VImageDimension > OutputImageType;
typedef typename itk::CastImageFilter<
MovingImageType,
OutputImageType > CastFilterType;
typedef typename itk::ImageFileWriter< OutputImageType > WriterType;
typedef typename itk::ImageFileWriter< DeformationFieldType > FieldWriterType;
typename FixedImageType::Pointer fixedImage = FixedImageType::New();
mitk::CastToItkImage(m_ReferenceImage, fixedImage);
typename MovingImageType::ConstPointer movingImage = itkImage1;
if (fixedImage.IsNotNull() && movingImage.IsNotNull())
{
typename RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
this->AddStepsToDo(4);
typename itk::ReceptorMemberCommand<DemonsRegistration>::Pointer command = itk::ReceptorMemberCommand<DemonsRegistration>::New();
command->SetCallbackFunction(this, &DemonsRegistration::SetProgress);
filter->AddObserver( itk::IterationEvent(), command );
typename FixedImageCasterType::Pointer fixedImageCaster = FixedImageCasterType::New();
fixedImageCaster->SetInput(fixedImage);
filter->SetFixedImage( fixedImageCaster->GetOutput() );
typename MovingImageCasterType::Pointer movingImageCaster = MovingImageCasterType::New();
movingImageCaster->SetInput(movingImage);
filter->SetMovingImage(movingImageCaster->GetOutput());
filter->SetNumberOfIterations( m_Iterations );
filter->SetStandardDeviations( m_StandardDeviation );
filter->Update();
typename WarperType::Pointer warper = WarperType::New();
typename InterpolatorType::Pointer interpolator = InterpolatorType::New();
warper->SetInput( movingImage );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( fixedImage->GetSpacing() );
warper->SetOutputOrigin( fixedImage->GetOrigin() );
warper->SetOutputDirection( fixedImage->GetDirection());
warper->SetDisplacementField( filter->GetOutput() );
warper->Update();
Image::Pointer outputImage = this->GetOutput();
mitk::CastToMitkImage( warper->GetOutput(), outputImage );
typename WriterType::Pointer writer = WriterType::New();
typename CastFilterType::Pointer caster = CastFilterType::New();
writer->SetFileName( m_ResultName );
caster->SetInput( warper->GetOutput() );
writer->SetInput( caster->GetOutput() );
if(m_SaveResult)
{
writer->Update();
}
if (VImageDimension == 2)
{
typedef DeformationFieldType VectorImage2DType;
typedef typename DeformationFieldType::PixelType Vector2DType;
typename VectorImage2DType::ConstPointer vectorImage2D = filter->GetOutput();
typename VectorImage2DType::RegionType region2D = vectorImage2D->GetBufferedRegion();
typename VectorImage2DType::IndexType index2D = region2D.GetIndex();
typename VectorImage2DType::SizeType size2D = region2D.GetSize();
typedef typename itk::Vector< float, 3 > Vector3DType;
typedef typename itk::Image< Vector3DType, 3 > VectorImage3DType;
typedef typename itk::ImageFileWriter< VectorImage3DType > WriterType;
typename WriterType::Pointer writer3D = WriterType::New();
typename VectorImage3DType::Pointer vectorImage3D = VectorImage3DType::New();
typename VectorImage3DType::RegionType region3D;
typename VectorImage3DType::IndexType index3D;
typename VectorImage3DType::SizeType size3D;
index3D[0] = index2D[0];
index3D[1] = index2D[1];
index3D[2] = 0;
size3D[0] = size2D[0];
size3D[1] = size2D[1];
size3D[2] = 1;
region3D.SetSize( size3D );
region3D.SetIndex( index3D );
typename VectorImage2DType::SpacingType spacing2D = vectorImage2D->GetSpacing();
typename VectorImage3DType::SpacingType spacing3D;
spacing3D[0] = spacing2D[0];
spacing3D[1] = spacing2D[1];
spacing3D[2] = 1.0;
vectorImage3D->SetSpacing( spacing3D );
vectorImage3D->SetRegions( region3D );
vectorImage3D->Allocate();
typedef typename itk::ImageRegionConstIterator< VectorImage2DType > Iterator2DType;
typedef typename itk::ImageRegionIterator< VectorImage3DType > Iterator3DType;
Iterator2DType it2( vectorImage2D, region2D );
Iterator3DType it3( vectorImage3D, region3D );
it2.GoToBegin();
it3.GoToBegin();
Vector2DType vector2D;
Vector3DType vector3D;
vector3D[2] = 0; // set Z component to zero.
while( !it2.IsAtEnd() )
{
vector2D = it2.Get();
vector3D[0] = vector2D[0];
vector3D[1] = vector2D[1];
it3.Set( vector3D );
++it2;
++it3;
}
writer3D->SetInput( vectorImage3D );
m_DeformationField = vectorImage3D;
writer3D->SetFileName( m_FieldName );
try
{
if(m_SaveField)
{
writer3D->Update();
}
}
catch( itk::ExceptionObject & excp )
{
MITK_ERROR << excp << std::endl;
}
}
else
{
typename FieldWriterType::Pointer fieldwriter = FieldWriterType::New();
fieldwriter->SetFileName(m_FieldName);
fieldwriter->SetInput( filter->GetOutput() );
m_DeformationField = (itk::Image<itk::Vector<float, 3>,3> *)(filter->GetOutput());
if(m_SaveField)
{
fieldwriter->Update();
}
}
this->SetRemainingProgress(4);
}
}
void PartialVolumeAnalysisClusteringCalculator::InternalQuantify(
const itk::Image< TPixel, VImageDimension > *image,
mitk::Image::Pointer clusteredImage, double* retval, mitk::Image::Pointer mask ) const
{
typedef itk::Image< TPixel, VImageDimension > ImageType;
typedef itk::Image< float, VImageDimension > ProbImageType;
typedef itk::Image< unsigned char, VImageDimension > MaskImageType;
typedef mitk::ImageToItk<ProbImageType> CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput( clusteredImage );
castFilter->Update();
typename ProbImageType::Pointer clusterImage = castFilter->GetOutput();
typename MaskImageType::Pointer itkmask = 0;
if(mask.IsNotNull())
{
typedef mitk::ImageToItk<MaskImageType> CastFilterType2;
typename CastFilterType2::Pointer castFilter2 = CastFilterType2::New();
castFilter2->SetInput( mask );
castFilter2->Update();
itkmask = castFilter2->GetOutput();
}
else
{
itkmask = MaskImageType::New();
itkmask->SetSpacing( clusterImage->GetSpacing() ); // Set the image spacing
itkmask->SetOrigin( clusterImage->GetOrigin() ); // Set the image origin
itkmask->SetDirection( clusterImage->GetDirection() ); // Set the image direction
itkmask->SetRegions( clusterImage->GetLargestPossibleRegion() );
itkmask->Allocate();
itkmask->FillBuffer(1);
}
itk::ImageRegionConstIterator<ImageType>
itimage(image, image->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<ProbImageType>
itprob(clusterImage, clusterImage->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<MaskImageType>
itmask(itkmask, itkmask->GetLargestPossibleRegion());
itimage.GoToBegin();
itprob.GoToBegin();
itmask.GoToBegin();
double totalProb = 0;
double measurement = 0;
double error = 0;
while( !itimage.IsAtEnd() && !itprob.IsAtEnd() && !itmask.IsAtEnd() )
{
double valImag = itimage.Get();
double valProb = itprob.Get();
double valMask = itmask.Get();
typename ProbImageType::PixelType prop = valProb * valMask;
totalProb += prop;
measurement += valImag * prop;
error += valImag * valImag * prop;
++itimage;
++itprob;
++itmask;
}
measurement = measurement / totalProb;
error = error / totalProb;
retval[0] = measurement;
retval[1] = sqrt( error - measurement*measurement );
}
void PartialVolumeAnalysisClusteringCalculator::InternalGenerateRGB( HelperStructRGBChannels *rgbin, mitk::Image::Pointer retval ) const
{
typedef itk::Image< float, VImageDimension > ProbImageType;
typedef itk::Image< typename itk::RGBAPixel<unsigned char>, VImageDimension > RGBImageType;
typedef mitk::ImageToItk<ProbImageType> CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput( rgbin->r );
castFilter->Update();
typename ProbImageType::Pointer r = castFilter->GetOutput();
castFilter = CastFilterType::New();
castFilter->SetInput( rgbin->g );
castFilter->Update();
typename ProbImageType::Pointer g = castFilter->GetOutput();
typename RGBImageType::Pointer rgb = RGBImageType::New();
rgb->SetSpacing( g->GetSpacing() ); // Set the image spacing
rgb->SetOrigin( g->GetOrigin() ); // Set the image origin
rgb->SetDirection( g->GetDirection() ); // Set the image direction
rgb->SetRegions( g->GetLargestPossibleRegion() );
rgb->Allocate();
itk::ImageRegionConstIterator<ProbImageType>
itr(r, r->GetLargestPossibleRegion());
itk::ImageRegionConstIterator<ProbImageType>
itg(g, g->GetLargestPossibleRegion());
itk::ImageRegionIterator<RGBImageType>
itrgb(rgb, rgb->GetLargestPossibleRegion());
itr.GoToBegin();
itg.GoToBegin();
float maxr = 0;
float maxg = 0;
while( !itr.IsAtEnd() )
{
typename ProbImageType::PixelType pr = itr.Get();
typename ProbImageType::PixelType pg = itg.Get();
if(pr > maxr)
{
maxr = pr;
}
if(pg > maxg)
{
maxg = pg;
}
++itr;
++itg;
}
itr.GoToBegin();
itg.GoToBegin();
itrgb.GoToBegin();
while( !itr.IsAtEnd() )
{
typename ProbImageType::PixelType pr = itr.Get();
typename ProbImageType::PixelType pg = itg.Get();
typename RGBImageType::PixelType prgb;
float valr = (pr/maxr)*255.0f;
float valg = (pg/maxg)*255.0f;
float alpha = valr>valg ? valr : valg;
prgb.Set(valr, valg, 0.0f, alpha);
itrgb.Set(prgb);
++itr;
++itg;
++itrgb;
}
retval->InitializeByItk(rgb.GetPointer());
retval->SetVolume(rgb->GetBufferPointer());
}
template <class inputType, unsigned int Dimension> medAbstractJob::medJobExitStatus medItkBiasCorrectionProcess::N4BiasCorrectionCore()
{
medJobExitStatus eRes = medAbstractJob::MED_JOB_EXIT_SUCCESS;
typedef itk::Image<inputType, Dimension > ImageType;
typedef itk::Image <float, Dimension> OutputImageType;
typedef itk::Image<unsigned char, Dimension> MaskImageType;
typedef itk::N4BiasFieldCorrectionImageFilter<OutputImageType, MaskImageType, OutputImageType> BiasFilter;
typedef itk::ConstantPadImageFilter<OutputImageType, OutputImageType> PadderType;
typedef itk::ConstantPadImageFilter<MaskImageType, MaskImageType> MaskPadderType;
typedef itk::ShrinkImageFilter<OutputImageType, OutputImageType> ShrinkerType;
typedef itk::ShrinkImageFilter<MaskImageType, MaskImageType> MaskShrinkerType;
typedef itk::BSplineControlPointImageFilter<typename BiasFilter::BiasFieldControlPointLatticeType, typename BiasFilter::ScalarImageType> BSplinerType;
typedef itk::ExpImageFilter<OutputImageType, OutputImageType> ExpFilterType;
typedef itk::DivideImageFilter<OutputImageType, OutputImageType, OutputImageType> DividerType;
typedef itk::ExtractImageFilter<OutputImageType, OutputImageType> CropperType;
unsigned int uiThreadNb = static_cast<unsigned int>(m_poUIThreadNb->value());
unsigned int uiShrinkFactors = static_cast<unsigned int>(m_poUIShrinkFactors->value());
unsigned int uiSplineOrder = static_cast<unsigned int>(m_poUISplineOrder->value());
float fWienerFilterNoise = static_cast<float>(m_poFWienerFilterNoise->value());
float fbfFWHM = static_cast<float>(m_poFbfFWHM->value());
float fConvergenceThreshold = static_cast<float>(m_poFConvergenceThreshold->value());
float fSplineDistance = static_cast<float>(m_poFSplineDistance->value());
float fProgression = 0;
QStringList oListValue = m_poSMaxIterations->value().split("x");
std::vector<unsigned int> oMaxNumbersIterationsVector(oListValue.size());
std::vector<float> oInitialMeshResolutionVect(Dimension);
for (int i=0; i<oMaxNumbersIterationsVector.size(); ++i)
{
oMaxNumbersIterationsVector[i] = (unsigned int)oListValue[i].toInt();
}
oInitialMeshResolutionVect[0] = static_cast<float>(m_poFInitialMeshResolutionVect1->value());
oInitialMeshResolutionVect[1] = static_cast<float>(m_poFInitialMeshResolutionVect2->value());
oInitialMeshResolutionVect[2] = static_cast<float>(m_poFInitialMeshResolutionVect3->value());
typename ImageType::Pointer image = dynamic_cast<ImageType *>((itk::Object*)(this->input()->data()));
typedef itk::CastImageFilter <ImageType, OutputImageType> CastFilterType;
typename CastFilterType::Pointer castFilter = CastFilterType::New();
castFilter->SetInput(image);
/********************************************************************************/
/***************************** PREPARING STARTING *******************************/
/********************************************************************************/
/*** 0 ******************* Create filter and accessories ******************/
ABORT_CHECKING(m_bAborting);
typename BiasFilter::Pointer filter = BiasFilter::New();
typename BiasFilter::ArrayType oNumberOfControlPointsArray;
m_filter = filter;
/*** 1 ******************* Read input image *******************************/
ABORT_CHECKING(m_bAborting);
fProgression = 1;
updateProgression(fProgression);
/*** 2 ******************* Creating Otsu mask *****************************/
ABORT_CHECKING(m_bAborting);
itk::TimeProbe timer;
timer.Start();
typename MaskImageType::Pointer maskImage = ITK_NULLPTR;
typedef itk::OtsuThresholdImageFilter<OutputImageType, MaskImageType> ThresholderType;
typename ThresholderType::Pointer otsu = ThresholderType::New();
m_filter = otsu;
otsu->SetInput(castFilter->GetOutput());
otsu->SetNumberOfHistogramBins(200);
otsu->SetInsideValue(0);
otsu->SetOutsideValue(1);
otsu->SetNumberOfThreads(uiThreadNb);
otsu->Update();
updateProgression(fProgression);
maskImage = otsu->GetOutput();
/*** 3A *************** Set Maximum number of Iterations for the filter ***/
ABORT_CHECKING(m_bAborting);
typename BiasFilter::VariableSizeArrayType itkTabMaximumIterations;
itkTabMaximumIterations.SetSize(oMaxNumbersIterationsVector.size());
for (int i = 0; i < oMaxNumbersIterationsVector.size(); ++i)
{
itkTabMaximumIterations[i] = oMaxNumbersIterationsVector[i];
}
filter->SetMaximumNumberOfIterations(itkTabMaximumIterations);
/*** 3B *************** Set Fitting Levels for the filter *****************/
typename BiasFilter::ArrayType oFittingLevelsTab;
oFittingLevelsTab.Fill(oMaxNumbersIterationsVector.size());
filter->SetNumberOfFittingLevels(oFittingLevelsTab);
updateProgression(fProgression);
/*** 4 ******************* Save image's index, size, origine **************/
ABORT_CHECKING(m_bAborting);
typename ImageType::IndexType oImageIndex = image->GetLargestPossibleRegion().GetIndex();
typename ImageType::SizeType oImageSize = image->GetLargestPossibleRegion().GetSize();
typename ImageType::PointType newOrigin = image->GetOrigin();
typename OutputImageType::Pointer outImage = castFilter->GetOutput();
if (fSplineDistance > 0)
{
/*** 5 ******************* Compute number of control points **************/
ABORT_CHECKING(m_bAborting);
itk::SizeValueType lowerBound[3];
itk::SizeValueType upperBound[3];
for (unsigned int i = 0; i < 3; i++)
{
float domain = static_cast<float>(image->GetLargestPossibleRegion().GetSize()[i] - 1) * image->GetSpacing()[i];
unsigned int numberOfSpans = static_cast<unsigned int>(std::ceil(domain / fSplineDistance));
unsigned long extraPadding = static_cast<unsigned long>((numberOfSpans * fSplineDistance - domain) / image->GetSpacing()[i] + 0.5);
lowerBound[i] = static_cast<unsigned long>(0.5 * extraPadding);
upperBound[i] = extraPadding - lowerBound[i];
newOrigin[i] -= (static_cast<float>(lowerBound[i]) * image->GetSpacing()[i]);
oNumberOfControlPointsArray[i] = numberOfSpans + filter->GetSplineOrder();
}
updateProgression(fProgression);
/*** 6 ******************* Padder ****************************************/
ABORT_CHECKING(m_bAborting);
typename PadderType::Pointer imagePadder = PadderType::New();
m_filter = imagePadder;
imagePadder->SetInput(castFilter->GetOutput());
imagePadder->SetPadLowerBound(lowerBound);
imagePadder->SetPadUpperBound(upperBound);
imagePadder->SetConstant(0);
imagePadder->SetNumberOfThreads(uiThreadNb);
imagePadder->Update();
updateProgression(fProgression);
outImage = imagePadder->GetOutput();
/*** 7 ******************** Handle the mask image *************************/
ABORT_CHECKING(m_bAborting);
typename MaskPadderType::Pointer maskPadder = MaskPadderType::New();
m_filter = maskPadder;
maskPadder->SetInput(maskImage);
maskPadder->SetPadLowerBound(lowerBound);
maskPadder->SetPadUpperBound(upperBound);
maskPadder->SetConstant(0);
maskPadder->SetNumberOfThreads(uiThreadNb);
maskPadder->Update();
updateProgression(fProgression);
maskImage = maskPadder->GetOutput();
/*** 8 ******************** SetNumber Of Control Points *******************/
ABORT_CHECKING(m_bAborting);
filter->SetNumberOfControlPoints(oNumberOfControlPointsArray);
}
else if (oInitialMeshResolutionVect.size() == 3)
{
/*** 9 ******************** SetNumber Of Control Points alternative *******/
ABORT_CHECKING(m_bAborting);
for (unsigned i = 0; i < 3; i++)
{
oNumberOfControlPointsArray[i] = static_cast<unsigned int>(oInitialMeshResolutionVect[i]) + filter->GetSplineOrder();
}
filter->SetNumberOfControlPoints(oNumberOfControlPointsArray);
updateProgression(fProgression, 3);
}
else
{
fProgression = 0;
updateProgression(fProgression);
std::cout << "No BSpline distance and Mesh Resolution is ignored because not 3 dimensions" << std::endl;
}
/*** 10 ******************* Shrinker image ********************************/
ABORT_CHECKING(m_bAborting);
typename ShrinkerType::Pointer imageShrinker = ShrinkerType::New();
m_filter = imageShrinker;
imageShrinker->SetInput(outImage);
/*** 11 ******************* Shrinker mask *********************************/
ABORT_CHECKING(m_bAborting);
typename MaskShrinkerType::Pointer maskShrinker = MaskShrinkerType::New();
m_filter = maskShrinker;
maskShrinker->SetInput(maskImage);
/*** 12 ******************* Shrink mask and image *************************/
ABORT_CHECKING(m_bAborting);
imageShrinker->SetShrinkFactors(uiShrinkFactors);
maskShrinker->SetShrinkFactors(uiShrinkFactors);
imageShrinker->SetNumberOfThreads(uiThreadNb);
maskShrinker->SetNumberOfThreads(uiThreadNb);
imageShrinker->Update();
updateProgression(fProgression);
maskShrinker->Update();
updateProgression(fProgression);
/*** 13 ******************* Filter setings ********************************/
ABORT_CHECKING(m_bAborting);
filter->SetSplineOrder(uiSplineOrder);
filter->SetWienerFilterNoise(fWienerFilterNoise);
filter->SetBiasFieldFullWidthAtHalfMaximum(fbfFWHM);
filter->SetConvergenceThreshold(fConvergenceThreshold);
filter->SetInput(imageShrinker->GetOutput());
filter->SetMaskImage(maskShrinker->GetOutput());
/*** 14 ******************* Apply filter **********************************/
ABORT_CHECKING(m_bAborting);
try
{
filter->SetNumberOfThreads(uiThreadNb);
filter->Update();
updateProgression(fProgression, 5);
}
catch (itk::ExceptionObject & err)
{
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
eRes = medAbstractJob::MED_JOB_EXIT_FAILURE;
return eRes;
}
/**
* Reconstruct the bias field at full image resolution. Divide
* the original input image by the bias field to get the final
* corrected image.
*/
ABORT_CHECKING(m_bAborting);
typename BSplinerType::Pointer bspliner = BSplinerType::New();
m_filter = bspliner;
bspliner->SetInput(filter->GetLogBiasFieldControlPointLattice());
bspliner->SetSplineOrder(filter->GetSplineOrder());
bspliner->SetSize(image->GetLargestPossibleRegion().GetSize());
bspliner->SetOrigin(newOrigin);
bspliner->SetDirection(image->GetDirection());
bspliner->SetSpacing(image->GetSpacing());
bspliner->SetNumberOfThreads(uiThreadNb);
bspliner->Update();
updateProgression(fProgression);
/*********************** Logarithm phase ***************************/
ABORT_CHECKING(m_bAborting);
typename OutputImageType::Pointer logField = OutputImageType::New();
logField->SetOrigin(image->GetOrigin());
logField->SetSpacing(image->GetSpacing());
logField->SetRegions(image->GetLargestPossibleRegion());
logField->SetDirection(image->GetDirection());
logField->Allocate();
itk::ImageRegionIterator<typename BiasFilter::ScalarImageType> IB(bspliner->GetOutput(), bspliner->GetOutput()->GetLargestPossibleRegion());
itk::ImageRegionIterator<OutputImageType> IF(logField, logField->GetLargestPossibleRegion());
for (IB.GoToBegin(), IF.GoToBegin(); !IB.IsAtEnd(); ++IB, ++IF)
{
IF.Set(IB.Get()[0]);
}
/*********************** Exponential phase *************************/
ABORT_CHECKING(m_bAborting);
typename ExpFilterType::Pointer expFilter = ExpFilterType::New();
m_filter = expFilter;
expFilter->SetInput(logField);
expFilter->SetNumberOfThreads(uiThreadNb);
expFilter->Update();
updateProgression(fProgression);
/************************ Dividing phase ***************************/
ABORT_CHECKING(m_bAborting);
typename DividerType::Pointer divider = DividerType::New();
m_filter = divider;
divider->SetInput1(castFilter->GetOutput());
divider->SetInput2(expFilter->GetOutput());
divider->SetNumberOfThreads(uiThreadNb);
divider->Update();
updateProgression(fProgression);
/******************** Prepare cropping phase ***********************/
ABORT_CHECKING(m_bAborting);
typename ImageType::RegionType inputRegion;
inputRegion.SetIndex(oImageIndex);
inputRegion.SetSize(oImageSize);
/************************ Cropping phase ***************************/
ABORT_CHECKING(m_bAborting);
typename CropperType::Pointer cropper = CropperType::New();
m_filter = cropper;
cropper->SetInput(divider->GetOutput());
cropper->SetExtractionRegion(inputRegion);
cropper->SetDirectionCollapseToSubmatrix();
cropper->SetNumberOfThreads(uiThreadNb);
cropper->Update();
updateProgression(fProgression);
/********************** Write output image *************************/
ABORT_CHECKING(m_bAborting);
medAbstractImageData *out = qobject_cast<medAbstractImageData *>(medAbstractDataFactory::instance()->create("itkDataImageFloat3"));
out->setData(cropper->GetOutput());
this->setOutput(out);
m_filter = 0;
return eRes;
}
