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());
}
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;
}
