ImageType::Pointer SBFilterUtils::ThresholdImage(ImageType::Pointer image, int lowerThreshold, int upperThreshold, int insideValue, int outsideValue)
{
BinaryThresholdFilterType::Pointer thresholdFilter = BinaryThresholdFilterType::New();
thresholdFilter->SetInput(image);
thresholdFilter->SetLowerThreshold(lowerThreshold);
thresholdFilter->SetUpperThreshold(upperThreshold);
thresholdFilter->SetOutsideValue(outsideValue);
thresholdFilter->SetInsideValue(insideValue);
thresholdFilter->Update();
return thresholdFilter->GetOutput();
}
void BinaryThresholdFilterDialog::on_pushButtonApply_clicked()
{
ImageLayer *imageLayer = ImageLayer::instance();
int insideValue = ui->spinBoxInsideValue->value();
int outsideValue = ui->spinBoxOutsideValue->value();
int lowerThreshold = ui->spinBoxLowerThreshold->value();
int upperThreshold = ui->spinBoxUpperThreshold->value();
imageLayer->resizeImageVector(2);
typedef itk::BinaryThresholdImageFilter<ImageLayer::GrayImageType, ImageLayer::GrayImageType> BinaryThresholdFilterType;
BinaryThresholdFilterType::Pointer binaryThresholdFilter = BinaryThresholdFilterType::New();
binaryThresholdFilter->SetInsideValue(insideValue);
binaryThresholdFilter->SetOutsideValue(outsideValue);
binaryThresholdFilter->SetLowerThreshold(lowerThreshold);
binaryThresholdFilter->SetUpperThreshold(upperThreshold);
binaryThresholdFilter->SetInput(imageLayer->grayImagePointer(0));
binaryThresholdFilter->Update();
imageLayer->setGrayImage(1, binaryThresholdFilter->GetOutput());
}
bool ShowSegmentationAsSmoothedSurface::ThreadedUpdateFunction()
{
Image::Pointer image;
GetPointerParameter("Input", image);
float smoothing;
GetParameter("Smoothing", smoothing);
float decimation;
GetParameter("Decimation", decimation);
float closing;
GetParameter("Closing", closing);
int timeNr = 0;
GetParameter("TimeNr", timeNr);
if (image->GetDimension() == 4)
MITK_INFO << "CREATING SMOOTHED POLYGON MODEL (t = " << timeNr << ')';
else
MITK_INFO << "CREATING SMOOTHED POLYGON MODEL";
MITK_INFO << " Smoothing = " << smoothing;
MITK_INFO << " Decimation = " << decimation;
MITK_INFO << " Closing = " << closing;
Geometry3D::Pointer geometry = dynamic_cast<Geometry3D *>(image->GetGeometry()->Clone().GetPointer());
// Make ITK image out of MITK image
typedef itk::Image<unsigned char, 3> CharImageType;
typedef itk::Image<unsigned short, 3> ShortImageType;
typedef itk::Image<float, 3> FloatImageType;
if (image->GetDimension() == 4)
{
ImageTimeSelector::Pointer imageTimeSelector = ImageTimeSelector::New();
imageTimeSelector->SetInput(image);
imageTimeSelector->SetTimeNr(timeNr);
imageTimeSelector->UpdateLargestPossibleRegion();
image = imageTimeSelector->GetOutput(0);
}
ImageToItk<CharImageType>::Pointer imageToItkFilter = ImageToItk<CharImageType>::New();
try
{
imageToItkFilter->SetInput(image);
}
catch (const itk::ExceptionObject &e)
{
// Most probably the input image type is wrong. Binary images are expected to be
// >unsigned< char images.
MITK_ERROR << e.GetDescription() << endl;
return false;
}
imageToItkFilter->Update();
CharImageType::Pointer itkImage = imageToItkFilter->GetOutput();
// Get bounding box and relabel
MITK_INFO << "Extracting VOI...";
int imageLabel = 1;
bool roiFound = false;
CharImageType::IndexType minIndex;
minIndex.Fill(numeric_limits<CharImageType::IndexValueType>::max());
CharImageType::IndexType maxIndex;
maxIndex.Fill(numeric_limits<CharImageType::IndexValueType>::min());
itk::ImageRegionIteratorWithIndex<CharImageType> iter(itkImage, itkImage->GetLargestPossibleRegion());
for (iter.GoToBegin(); !iter.IsAtEnd(); ++iter)
{
if (iter.Get() == imageLabel)
{
roiFound = true;
iter.Set(1);
CharImageType::IndexType currentIndex = iter.GetIndex();
for (unsigned int dim = 0; dim < 3; ++dim)
{
minIndex[dim] = min(currentIndex[dim], minIndex[dim]);
maxIndex[dim] = max(currentIndex[dim], maxIndex[dim]);
}
}
else
{
iter.Set(0);
}
}
if (!roiFound)
{
ProgressBar::GetInstance()->Progress(8);
MITK_ERROR << "Didn't found segmentation labeled with " << imageLabel << "!" << endl;
return false;
}
ProgressBar::GetInstance()->Progress(1);
// Extract and pad bounding box
typedef itk::RegionOfInterestImageFilter<CharImageType, CharImageType> ROIFilterType;
ROIFilterType::Pointer roiFilter = ROIFilterType::New();
CharImageType::RegionType region;
CharImageType::SizeType size;
for (unsigned int dim = 0; dim < 3; ++dim)
{
size[dim] = maxIndex[dim] - minIndex[dim] + 1;
}
region.SetIndex(minIndex);
region.SetSize(size);
roiFilter->SetInput(itkImage);
roiFilter->SetRegionOfInterest(region);
roiFilter->ReleaseDataFlagOn();
roiFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::ConstantPadImageFilter<CharImageType, CharImageType> PadFilterType;
PadFilterType::Pointer padFilter = PadFilterType::New();
const PadFilterType::SizeValueType pad[3] = { 10, 10, 10 };
padFilter->SetInput(roiFilter->GetOutput());
padFilter->SetConstant(0);
padFilter->SetPadLowerBound(pad);
padFilter->SetPadUpperBound(pad);
padFilter->ReleaseDataFlagOn();
padFilter->ReleaseDataBeforeUpdateFlagOn();
padFilter->Update();
CharImageType::Pointer roiImage = padFilter->GetOutput();
roiImage->DisconnectPipeline();
roiFilter = nullptr;
padFilter = nullptr;
// Correct origin of real geometry (changed by cropping and padding)
typedef Geometry3D::TransformType TransformType;
TransformType::Pointer transform = TransformType::New();
TransformType::OutputVectorType translation;
for (unsigned int dim = 0; dim < 3; ++dim)
translation[dim] = (int)minIndex[dim] - (int)pad[dim];
transform->SetIdentity();
transform->Translate(translation);
geometry->Compose(transform, true);
ProgressBar::GetInstance()->Progress(1);
// Median
MITK_INFO << "Median...";
typedef itk::BinaryMedianImageFilter<CharImageType, CharImageType> MedianFilterType;
MedianFilterType::Pointer medianFilter = MedianFilterType::New();
CharImageType::SizeType radius = { 0 };
medianFilter->SetRadius(radius);
medianFilter->SetBackgroundValue(0);
medianFilter->SetForegroundValue(1);
medianFilter->SetInput(roiImage);
medianFilter->ReleaseDataFlagOn();
medianFilter->ReleaseDataBeforeUpdateFlagOn();
medianFilter->Update();
ProgressBar::GetInstance()->Progress(1);
// Intelligent closing
MITK_INFO << "Intelligent closing...";
unsigned int surfaceRatio = (unsigned int)((1.0f - closing) * 100.0f);
typedef itk::IntelligentBinaryClosingFilter<CharImageType, ShortImageType> ClosingFilterType;
ClosingFilterType::Pointer closingFilter = ClosingFilterType::New();
closingFilter->SetInput(medianFilter->GetOutput());
closingFilter->ReleaseDataFlagOn();
closingFilter->ReleaseDataBeforeUpdateFlagOn();
closingFilter->SetSurfaceRatio(surfaceRatio);
closingFilter->Update();
ShortImageType::Pointer closedImage = closingFilter->GetOutput();
closedImage->DisconnectPipeline();
roiImage = nullptr;
medianFilter = nullptr;
closingFilter = nullptr;
ProgressBar::GetInstance()->Progress(1);
// Gaussian blur
MITK_INFO << "Gauss...";
typedef itk::BinaryThresholdImageFilter<ShortImageType, FloatImageType> BinaryThresholdToFloatFilterType;
BinaryThresholdToFloatFilterType::Pointer binThresToFloatFilter = BinaryThresholdToFloatFilterType::New();
binThresToFloatFilter->SetInput(closedImage);
binThresToFloatFilter->SetLowerThreshold(1);
binThresToFloatFilter->SetUpperThreshold(1);
binThresToFloatFilter->SetInsideValue(100);
binThresToFloatFilter->SetOutsideValue(0);
binThresToFloatFilter->ReleaseDataFlagOn();
binThresToFloatFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::DiscreteGaussianImageFilter<FloatImageType, FloatImageType> GaussianFilterType;
// From the following line on, IntelliSense (VS 2008) is broken. Any idea how to fix it?
GaussianFilterType::Pointer gaussFilter = GaussianFilterType::New();
gaussFilter->SetInput(binThresToFloatFilter->GetOutput());
gaussFilter->SetUseImageSpacing(true);
gaussFilter->SetVariance(smoothing);
gaussFilter->ReleaseDataFlagOn();
gaussFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::BinaryThresholdImageFilter<FloatImageType, CharImageType> BinaryThresholdFromFloatFilterType;
BinaryThresholdFromFloatFilterType::Pointer binThresFromFloatFilter = BinaryThresholdFromFloatFilterType::New();
binThresFromFloatFilter->SetInput(gaussFilter->GetOutput());
binThresFromFloatFilter->SetLowerThreshold(50);
binThresFromFloatFilter->SetUpperThreshold(255);
binThresFromFloatFilter->SetInsideValue(1);
binThresFromFloatFilter->SetOutsideValue(0);
binThresFromFloatFilter->ReleaseDataFlagOn();
binThresFromFloatFilter->ReleaseDataBeforeUpdateFlagOn();
binThresFromFloatFilter->Update();
CharImageType::Pointer blurredImage = binThresFromFloatFilter->GetOutput();
blurredImage->DisconnectPipeline();
closedImage = nullptr;
binThresToFloatFilter = nullptr;
gaussFilter = nullptr;
ProgressBar::GetInstance()->Progress(1);
// Fill holes
MITK_INFO << "Filling cavities...";
typedef itk::ConnectedThresholdImageFilter<CharImageType, CharImageType> ConnectedThresholdFilterType;
ConnectedThresholdFilterType::Pointer connectedThresFilter = ConnectedThresholdFilterType::New();
CharImageType::IndexType corner;
corner[0] = 0;
corner[1] = 0;
corner[2] = 0;
connectedThresFilter->SetInput(blurredImage);
connectedThresFilter->SetSeed(corner);
connectedThresFilter->SetLower(0);
connectedThresFilter->SetUpper(0);
connectedThresFilter->SetReplaceValue(2);
connectedThresFilter->ReleaseDataFlagOn();
connectedThresFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::BinaryThresholdImageFilter<CharImageType, CharImageType> BinaryThresholdFilterType;
BinaryThresholdFilterType::Pointer binThresFilter = BinaryThresholdFilterType::New();
binThresFilter->SetInput(connectedThresFilter->GetOutput());
binThresFilter->SetLowerThreshold(0);
binThresFilter->SetUpperThreshold(0);
binThresFilter->SetInsideValue(50);
binThresFilter->SetOutsideValue(0);
binThresFilter->ReleaseDataFlagOn();
binThresFilter->ReleaseDataBeforeUpdateFlagOn();
typedef itk::AddImageFilter<CharImageType, CharImageType, CharImageType> AddFilterType;
AddFilterType::Pointer addFilter = AddFilterType::New();
addFilter->SetInput1(blurredImage);
addFilter->SetInput2(binThresFilter->GetOutput());
addFilter->ReleaseDataFlagOn();
addFilter->ReleaseDataBeforeUpdateFlagOn();
addFilter->Update();
ProgressBar::GetInstance()->Progress(1);
// Surface extraction
MITK_INFO << "Surface extraction...";
Image::Pointer filteredImage = Image::New();
CastToMitkImage(addFilter->GetOutput(), filteredImage);
filteredImage->SetGeometry(geometry);
ImageToSurfaceFilter::Pointer imageToSurfaceFilter = ImageToSurfaceFilter::New();
imageToSurfaceFilter->SetInput(filteredImage);
imageToSurfaceFilter->SetThreshold(50);
imageToSurfaceFilter->SmoothOn();
imageToSurfaceFilter->SetDecimate(ImageToSurfaceFilter::NoDecimation);
m_Surface = imageToSurfaceFilter->GetOutput(0);
ProgressBar::GetInstance()->Progress(1);
// Mesh decimation
if (decimation > 0.0f && decimation < 1.0f)
{
MITK_INFO << "Quadric mesh decimation...";
vtkQuadricDecimation *quadricDecimation = vtkQuadricDecimation::New();
quadricDecimation->SetInputData(m_Surface->GetVtkPolyData());
quadricDecimation->SetTargetReduction(decimation);
quadricDecimation->AttributeErrorMetricOn();
quadricDecimation->GlobalWarningDisplayOff();
quadricDecimation->Update();
vtkCleanPolyData* cleaner = vtkCleanPolyData::New();
cleaner->SetInputConnection(quadricDecimation->GetOutputPort());
cleaner->PieceInvariantOn();
cleaner->ConvertLinesToPointsOn();
cleaner->ConvertStripsToPolysOn();
cleaner->PointMergingOn();
cleaner->Update();
m_Surface->SetVtkPolyData(cleaner->GetOutput());
}
ProgressBar::GetInstance()->Progress(1);
// Compute Normals
vtkPolyDataNormals* computeNormals = vtkPolyDataNormals::New();
computeNormals->SetInputData(m_Surface->GetVtkPolyData());
computeNormals->SetFeatureAngle(360.0f);
computeNormals->FlipNormalsOff();
computeNormals->Update();
m_Surface->SetVtkPolyData(computeNormals->GetOutput());
return true;
}
void WholeCellSeg::SyntheticBoundaries(){
typedef itk::RescaleIntensityImageFilter< UShortImageType, IntImageType > RescaleIOIntType;
typedef itk::RescaleIntensityImageFilter< FltImageType, IntImageType > RescaleFltIntType;
typedef itk::CastImageFilter< UShortImageType, IntImageType > CastUSIntType;
typedef itk::CastImageFilter< IntImageType, UShortImageType > CastIntUSType;
typedef itk::BinaryThresholdImageFilter< IntImageType, IntImageType > BinaryThresholdFilterType;
typedef itk::BinaryThresholdImageFilter< FltImageType, IntImageType > BinaryThresholdFilterTypeFI;
typedef itk::AndImageFilter< IntImageType, IntImageType, IntImageType > AndFilterType;
typedef itk::SignedMaurerDistanceMapImageFilter< IntImageType, FltImageType > SignedMaurerDistanceMapFilterType;
typedef itk::MorphologicalWatershedFromMarkersImageFilter< IntImageType, IntImageType > WatershedFilterType;
typedef itk::ImageRegionIteratorWithIndex< UShortImageType > IteratorType;
typedef itk::ImageRegionIteratorWithIndex< IntImageType > IteratorType1;
//Rescale and Threshold input label image
RescaleIOIntType::Pointer RescaleIOInt = RescaleIOIntType::New();
RescaleIOInt->SetOutputMaximum( INT_MAX );
RescaleIOInt->SetOutputMinimum( 0 );
RescaleIOInt->SetInput( nuclab_inp );
if( draw_real_bounds && remove_small_objs )
RescaleIOInt->SetInput( nuclab_inp_cpy );
else
RescaleIOInt->SetInput( nuclab_inp );
RescaleIOInt->Update();
BinaryThresholdFilterType::Pointer binarythreshfilter = BinaryThresholdFilterType::New();
binarythreshfilter->SetInsideValue( INT_MAX );
binarythreshfilter->SetOutsideValue( 0 );
binarythreshfilter->SetLowerThreshold( 1 );
binarythreshfilter->SetUpperThreshold( INT_MAX );
binarythreshfilter->SetInput( RescaleIOInt->GetOutput() );
binarythreshfilter->Update();
//Distance map for synthetic boundaries around nuclei that do not have any marker around them
SignedMaurerDistanceMapFilterType::Pointer distancemapfilter = SignedMaurerDistanceMapFilterType::New();
distancemapfilter->SetInput(binarythreshfilter->GetOutput());
distancemapfilter->SquaredDistanceOff();
distancemapfilter->Update();
//Threshold the map to limit the max distance to the radius limit set by the user
BinaryThresholdFilterTypeFI::Pointer binarythreshfilterfi = BinaryThresholdFilterTypeFI::New();
binarythreshfilterfi->SetInsideValue( INT_MAX );
binarythreshfilterfi->SetOutsideValue( 0 );
binarythreshfilterfi->SetLowerThreshold( 1 );
binarythreshfilterfi->SetUpperThreshold( radius_of_synth_bounds );
binarythreshfilterfi->SetInput( distancemapfilter->GetOutput() );
RescaleFltIntType::Pointer rescalefltint = RescaleFltIntType::New();
rescalefltint->SetOutputMaximum( INT_MAX );
rescalefltint->SetOutputMinimum( 0 );
rescalefltint->SetInput( distancemapfilter->GetOutput() );
AndFilterType::Pointer andfilter1 = AndFilterType::New();
andfilter1->SetInput1( rescalefltint->GetOutput() );
andfilter1->SetInput2( binarythreshfilterfi->GetOutput() );
AndFilterType::Pointer andfilter2 = AndFilterType::New();
andfilter2->SetInput1( andfilter1->GetOutput() );
andfilter2->SetInput2( binarythreshfilterfi->GetOutput() );
andfilter2->Update();
CastUSIntType::Pointer castUSIntfilter = CastUSIntType::New();
if( draw_real_bounds && remove_small_objs )
castUSIntfilter->SetInput( nuclab_inp_cpy );
else
castUSIntfilter->SetInput( nuclab_inp );
castUSIntfilter->Update();
IntImageType::Pointer nuclab_inp_int = IntImageType::New();
nuclab_inp_int = castUSIntfilter->GetOutput();
IntImageType::Pointer image2=andfilter2->GetOutput();
IteratorType1 pix_bufed2( image2, image2->GetRequestedRegion() );
pix_bufed2.GoToBegin();
IteratorType1 pix_bufed3( nuclab_inp_int, nuclab_inp_int->GetRequestedRegion() );
pix_bufed3.GoToBegin();
while( !pix_bufed2.IsAtEnd() || !pix_bufed3.IsAtEnd() ){
if( !pix_bufed2.Get() )
if( !pix_bufed3.Get() )
pix_bufed2.Set( INT_MIN );
++pix_bufed2; ++pix_bufed3;
}
//Draw synthetic boundaries using the seeded Watershed algorithm
WatershedFilterType::Pointer watershedfilter = WatershedFilterType::New();
watershedfilter->SetInput1( image2 );
watershedfilter->SetInput2( nuclab_inp_int );
watershedfilter->SetMarkWatershedLine( 1 );
watershedfilter->Update();
CastIntUSType::Pointer castIntUSfilter = CastIntUSType::New();
castIntUSfilter->SetInput( watershedfilter->GetOutput() );
castIntUSfilter->Update();
if( draw_real_bounds ){
UShortImageType::Pointer image1=castIntUSfilter->GetOutput();
IteratorType pix_bufed( image1, image1->GetRequestedRegion() );
pix_bufed.GoToBegin();
IteratorType pix_bufed1( seg_im_out, seg_im_out->GetRequestedRegion() );
pix_bufed1.GoToBegin();
while( !pix_bufed1.IsAtEnd() ){
if( !pix_bufed1.Get() )
pix_bufed1.Set( pix_bufed.Get());
++pix_bufed; ++pix_bufed1;
}
}
else
seg_im_out = castIntUSfilter->GetOutput();
/* IteratorType1 pix_bufed33( image2, image2->GetRequestedRegion() );
pix_bufed33.GoToBegin();
while( !pix_bufed33.IsAtEnd() ){
if( 0 > pix_bufed33.Get() )
pix_bufed33.Set(0);
++pix_bufed33;
}
typedef itk::RescaleIntensityImageFilter< IntImageType, UShortImageType > RescaleIntIOType;
RescaleIntIOType::Pointer RescaleIntIO1 = RescaleIntIOType::New();
RescaleIntIO1->SetOutputMaximum( USHRT_MAX );
RescaleIntIO1->SetOutputMinimum( 0 );
RescaleIntIO1->SetInput( image2 ); //watershedfilter->GetOutput() image1
RescaleIntIO1->Update();
typedef itk::ImageFileWriter< UShortImageType > WriterType;
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( "dist_map.tif" );
writer->SetInput( RescaleIntIO1->GetOutput() );//RescaleIntIO1--finalO/P
writer->Update();
*/
if( ( !remove_small_objs ) || ( draw_real_bounds && remove_small_objs ) )
seg_done = 1;
}
