Example #1
0
void WholeCellSeg::BinarizationForRealBounds(){
	if( !nuc_im_set || !cyt_im_set ){
		std::cerr<<"Complete segmenting nuclei and set input imge before starting segmentation\n";
		return;
	}

	itk::SizeValueType size1=cyt_im_inp->GetLargestPossibleRegion().GetSize()[0];
	itk::SizeValueType size2=cyt_im_inp->GetLargestPossibleRegion().GetSize()[1];

	if( ( size1 != nuclab_inp->GetLargestPossibleRegion().GetSize()[0] ) ||
      	    ( size2 != nuclab_inp->GetLargestPossibleRegion().GetSize()[1] ) )
	{
		std::cerr<<"The input images must be of the same size\n";
		return;
	}

	typedef unsigned short int UShortPixelType;

	typedef itk::ImageRegionIteratorWithIndex< UShortImageType > IteratorType;
	typedef itk::ImageRegionConstIterator< UShortImageType > ConstIteratorType;

	typedef itk::Statistics::ScalarImageToHistogramGenerator< IntImageType > ScalarImageToHistogramGeneratorType;
	typedef ScalarImageToHistogramGeneratorType::HistogramType HistogramType;
	typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > CalculatorType;
	typedef itk::RescaleIntensityImageFilter< UShortImageType, IntImageType > RescaleUsIntType;
	typedef itk::RescaleIntensityImageFilter< UShortImageType, UShortImageType > RescaleUsUsType;
	typedef itk::BinaryThresholdImageFilter< IntImageType, UShortImageType >  ThreshFilterType;
	typedef itk::BinaryThresholdImageFilter< UShortImageType, UShortImageType >  ThresholdFilterType;
	typedef itk::OrImageFilter< UShortImageType, UShortImageType, UShortImageType > OrFilterType;
 	typedef itk::BinaryBallStructuringElement< UShortPixelType, 2 > StructuringElementType;
	typedef itk::BinaryErodeImageFilter< UShortImageType, UShortImageType, StructuringElementType > ErodeFilterType;
	typedef itk::BinaryDilateImageFilter< UShortImageType, UShortImageType, StructuringElementType > DilateFilterType;

	unsigned char *in_Image;
	itk::SizeValueType ind=0;

//Call Yousef's binarization method if the number of bin levels is < 2
	if( num_levels < 2 ){
		bin_Image = (unsigned short *) malloc (size1*size2*sizeof(unsigned short));
		for(itk::SizeValueType j=0; j<size2; ++j)
			for(itk::SizeValueType i=0; i<size1; ++i)
				BIN_Image(i,j)=255;
		in_Image = (unsigned char *) malloc (size1*size2);
		if( ( in_Image == NULL ) || ( bin_Image == NULL ) ){
			std::cerr << "Memory allocation for binarization of image failed\n";
			return;
		}

		RescaleUsUsType::Pointer rescaleususfilter = RescaleUsUsType::New();
		rescaleususfilter->SetInput( cyt_im_inp );
		rescaleususfilter->SetOutputMaximum( itk::NumericTraits<unsigned char>::max() );
		rescaleususfilter->SetOutputMinimum( 0 );
		rescaleususfilter->Update();
		UShortImageType::Pointer resc_cyt_im = UShortImageType::New();
		resc_cyt_im = rescaleususfilter->GetOutput();
		ConstIteratorType pix_buf1( resc_cyt_im, resc_cyt_im->GetRequestedRegion() );
		for ( pix_buf1.GoToBegin(); !pix_buf1.IsAtEnd(); ++pix_buf1, ++ind )
		in_Image[ind]=(unsigned char)(pix_buf1.Get());

		int ok = 0;
		ok = Cell_Binarization_2D(in_Image,bin_Image, size1, size2, shift_bin);
		free( in_Image );

		if( !ok ){
			std::cerr<<"Binarization Failed\n";
			return;
		}

//copy the output binary image into the ITK image
		intermediate_bin_im_out = UShortImageType::New();
		UShortImageType::PointType origin;
		origin[0] = 0;
		origin[1] = 0;
		intermediate_bin_im_out->SetOrigin( origin );

		UShortImageType::IndexType start;
		start[0] = 0;  // first index on X
		start[1] = 0;  // first index on Y
		UShortImageType::SizeType  size;
		size[0] = size1;  // size along X
		size[1] = size2;  // size along Y

		UShortImageType::RegionType region;
		region.SetSize( size );
		region.SetIndex( start );

		intermediate_bin_im_out->SetRegions( region );
		intermediate_bin_im_out->Allocate();
		intermediate_bin_im_out->FillBuffer(0);
		intermediate_bin_im_out->Update();

		itk::SizeValueType dum,dum1;
		dum = 0;
		dum1 = USHRT_MAX;

		//unsigned int asd,asd1; asd=0; asd1=0;
		IteratorType iterator ( intermediate_bin_im_out, intermediate_bin_im_out->GetRequestedRegion() );
		for(itk::SizeValueType i=0; i < (size1*size2); ++i){
			if( bin_Image[i] )
			iterator.Set( dum1 );
			else
			iterator.Set( dum );
			++iterator;
		}
	}
//Call multi level binarization method if the number of bin levels is >= 2
	else{
		RescaleUsIntType::Pointer rescaleusintfilter = RescaleUsIntType::New();
		ScalarImageToHistogramGeneratorType::Pointer scalarImageToHistogramGenerator = ScalarImageToHistogramGeneratorType::New();
		rescaleusintfilter->SetInput( cyt_im_inp );
		rescaleusintfilter->SetOutputMaximum( itk::NumericTraits<unsigned short>::max() );
		rescaleusintfilter->SetOutputMinimum( 0 );
		rescaleusintfilter->Update();

		ThreshFilterType::Pointer threshfilter = ThreshFilterType::New();
		CalculatorType::Pointer calculator = CalculatorType::New();
		scalarImageToHistogramGenerator->SetNumberOfBins( 255 );
		calculator->SetNumberOfThresholds( num_levels );
		threshfilter->SetOutsideValue( (int)0 );
		threshfilter->SetInsideValue( (int)USHRT_MAX );
		scalarImageToHistogramGenerator->SetInput( rescaleusintfilter->GetOutput() );
		scalarImageToHistogramGenerator->Compute();
		calculator->SetInputHistogram( scalarImageToHistogramGenerator->GetOutput() );
		threshfilter->SetInput( rescaleusintfilter->GetOutput() );
		calculator->Update();
		const CalculatorType::OutputType &thresholdVector = calculator->GetOutput();
		CalculatorType::OutputType::const_iterator itNum = thresholdVector.begin();
		int lowerThreshold,upperThreshold;

		for( int i=0; i<(num_levels-num_levels_incl); ++i ) ++itNum;
		lowerThreshold = static_cast<unsigned short>(*itNum);
		upperThreshold = itk::NumericTraits<unsigned short>::max();

		threshfilter->SetLowerThreshold( lowerThreshold );
		threshfilter->SetUpperThreshold( upperThreshold );
		threshfilter->Update();

		intermediate_bin_im_out = UShortImageType::New();
		intermediate_bin_im_out = threshfilter->GetOutput();
	}

//Fill holes left by the nuclei
	ThresholdFilterType::Pointer binarythreshfilter = ThresholdFilterType::New();
	binarythreshfilter->SetInsideValue( USHRT_MAX );
	binarythreshfilter->SetOutsideValue( 0 );
	binarythreshfilter->SetLowerThreshold( 1 );
	binarythreshfilter->SetUpperThreshold( USHRT_MAX );
	binarythreshfilter->SetInput( nuclab_inp );
	OrFilterType::Pointer orfilter = OrFilterType::New();
	orfilter->SetInput1( binarythreshfilter->GetOutput() );
	orfilter->SetInput2( intermediate_bin_im_out );
//dialate and erode
	ErodeFilterType::Pointer  binaryErode  = ErodeFilterType::New();
	DilateFilterType::Pointer binaryDilate = DilateFilterType::New();
	StructuringElementType  structuringElement;
	structuringElement.SetRadius( 3 );  // 3x3 structuring element
	structuringElement.CreateStructuringElement();
	binaryErode->SetKernel( structuringElement );
	binaryErode->SetErodeValue( USHRT_MAX );
	binaryDilate->SetDilateValue( USHRT_MAX );
	binaryDilate->SetKernel( structuringElement );
	binaryErode->SetInput( binaryDilate->GetOutput() );
	binaryDilate->SetInput( orfilter->GetOutput() );
//erode and dialate
	ErodeFilterType::Pointer  binaryErode1  = ErodeFilterType::New();
	DilateFilterType::Pointer binaryDilate1 = DilateFilterType::New();
	binaryErode1->SetKernel(  structuringElement );
	binaryErode1->SetErodeValue( USHRT_MAX );
	binaryDilate1->SetDilateValue( USHRT_MAX );
	binaryDilate1->SetKernel( structuringElement );
	binaryErode1->SetInput( binaryErode->GetOutput() );
	binaryDilate1->SetInput( binaryErode1->GetOutput() );
	binaryDilate1->Update();
//Get pointer to the final binary image and return it to calling function
	UShortImageType::Pointer image_bin = UShortImageType::New();
	image_bin = binaryDilate1->GetOutput();
	bin_im_out = image_bin;
	bin_done = 1;

//Update bin array
	ind=0;
	if( draw_real_bounds ){
		ConstIteratorType pix_buf3( bin_im_out, bin_im_out->GetRequestedRegion() );
		for ( pix_buf3.GoToBegin(); !pix_buf3.IsAtEnd(); ++pix_buf3, ++ind )
		bin_Image[ind]=(pix_buf3.Get());
	}else
		free( bin_Image );
/*
	typedef itk::ImageFileWriter< UShortImageType > WriterType;
	WriterType::Pointer writer = WriterType::New();
	writer->SetFileName( "bin_info.tif" );
	writer->SetInput( bin_im_out );//RescaleIntIO1--finalO/P
	writer->Update();
*/
	return;
}
Example #2
0
void Preprocess::OtsuBinarize(int num_thresholds, int num_in_foreground, bool fgrnd_dark)
{
	//Create histogram:
	typedef itk::Statistics::ScalarImageToHistogramGenerator< ImageType3D > HistogramGeneratorType;
	typedef HistogramGeneratorType::HistogramType HistogramType;
	HistogramGeneratorType::Pointer histoGenerator = HistogramGeneratorType::New();
	histoGenerator->SetNumberOfBins( 256 );
	histoGenerator->SetInput( myImg );
	try
	{
		histoGenerator->Compute();
	}
	catch( itk::ExceptionObject & excep )
    {
		std::cerr << "    Histogram Computation: exception caught !" << std::endl;
		std::cerr << excep << std::endl;
		return;
    }

	//Estimate thresholds:
	typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > CalculatorType;
	CalculatorType::Pointer calculator = CalculatorType::New();
	calculator->SetNumberOfThresholds( num_thresholds );
	calculator->SetInputHistogram( histoGenerator->GetOutput() );
	try
	{
		calculator->Update();
	}
	catch( itk::ExceptionObject & excep )
    {
		std::cerr << "    Otsu Computation: exception caught !" << std::endl;
		std::cerr << excep << std::endl;
		return;
    }

	const CalculatorType::OutputType &thresholdVector = calculator->GetOutput();

	//Estimate Binarization thresholds:
	PixelType lowerThreshold,upperThreshold;
	if( fgrnd_dark )	//Do I want to make the foregound of the binary dark:
	{
		CalculatorType::OutputType::const_iterator itNum = thresholdVector.end();
 		for( int i=0; i<(num_thresholds-num_in_foreground+1); ++i ) 
			--itNum;
		upperThreshold = static_cast<PixelType>(*itNum);
		lowerThreshold = itk::NumericTraits<PixelType>::min();
	} 
	else
	{
		CalculatorType::OutputType::const_iterator itNum = thresholdVector.begin();
		for( int i=0; i<(num_thresholds-num_in_foreground); ++i ) 
			++itNum;
		lowerThreshold = static_cast<PixelType>(*itNum);
		upperThreshold = itk::NumericTraits<PixelType>::max();
	}

	//std::cerr << "Binarization Thresholds: " << lowerThreshold << "  " << upperThreshold << std::endl;

	typedef itk::BinaryThresholdImageFilter< ImageType3D, ImageType3D >  ThreshFilterType;
	ThreshFilterType::Pointer threshfilter = ThreshFilterType::New();
	threshfilter->SetOutsideValue( 0 );
	threshfilter->SetInsideValue( (int)itk::NumericTraits<PixelType>::max() );
	threshfilter->SetInput( myImg );
	threshfilter->SetLowerThreshold( lowerThreshold );
	threshfilter->SetUpperThreshold( upperThreshold );

	try
	{
		threshfilter->Update();
	}
	catch( itk::ExceptionObject & excep )
    {
		std::cerr << "    Threshold: exception caught !" << std::endl;
		std::cerr << excep << std::endl;
		return;
    }

	myImg = threshfilter->GetOutput();
}
Example #3
0
USImageType::PixelType returnthresh( itk::SmartPointer<USImageType> input_image,
			     int num_bin_levs, int num_in_fg ){
	//Instantiate the different image and filter types that will be used
	typedef itk::ImageRegionConstIterator< USImageType > ConstIteratorType;
	typedef itk::Statistics::Histogram< float > HistogramType;
	typedef itk::OtsuMultipleThresholdsCalculator< HistogramType > CalculatorType;

	std::cout<<"Starting threshold computation\n";

	//Create a temporary histogram container:
	const int numBins = itk::NumericTraits<USImageType::PixelType>::max();
	double *tempHist;
	tempHist = (double*) malloc( sizeof(double) * numBins );
	for(USImageType::PixelType i=0; i<numBins; ++i)
		tempHist[i] = 0;

	USImageType::PixelType maxval = itk::NumericTraits<USImageType::PixelType>::ZeroValue();
	USImageType::PixelType minval = itk::NumericTraits<USImageType::PixelType>::max();
	//Populate the histogram (assume pixel type is actually is some integer type):
	ConstIteratorType it( input_image, input_image->GetRequestedRegion() );
	for ( it.GoToBegin(); !it.IsAtEnd(); ++it ){
		USImageType::PixelType pix = it.Get();
		++tempHist[pix];
		if( pix > maxval ) maxval = pix;
		if( pix < minval ) minval = pix;
	}
	//return max of type if there is no variation in the staining
	if( (maxval-minval)<3 ) return itk::NumericTraits<USImageType::PixelType>::max(); 
	const USImageType::PixelType numBinsPresent = maxval+1;
	
	//Find max value in the histogram
	double floatIntegerMax = itk::NumericTraits<USImageType::PixelType>::max();
	double max = 0.0;
	for(USImageType::PixelType i=0; i<numBinsPresent; ++i)
		if( tempHist[i] > max )
			max = tempHist[i];

	double scaleFactor = 1;
	if(max >= floatIntegerMax)
		scaleFactor = floatIntegerMax / max;

	HistogramType::Pointer histogram = HistogramType::New() ;
	// initialize histogram
	HistogramType::SizeType size;
	HistogramType::MeasurementVectorType lowerBound;
	HistogramType::MeasurementVectorType upperBound;

	lowerBound.SetSize(1);
	upperBound.SetSize(1);
	size.SetSize(1);

	lowerBound.Fill(0.0);
	upperBound.Fill((double)maxval);
	size.Fill(numBinsPresent);

	histogram->SetMeasurementVectorSize(1);
	histogram->Initialize(size, lowerBound, upperBound ) ;

	USImageType::PixelType i=0;
	for (HistogramType::Iterator iter = histogram->Begin(); iter != histogram->End(); ++iter ){
		float norm_freq = (float)(tempHist[i] * scaleFactor);
		iter.SetFrequency(norm_freq);
		++i;
	}

	std::cout<<"Histogram computed\n";

	CalculatorType::Pointer calculator = CalculatorType::New();
	calculator->SetNumberOfThresholds( num_bin_levs );
	calculator->SetInputHistogram( histogram );
	calculator->Update();
	const CalculatorType::OutputType &thresholdVector = calculator->GetOutput(); 
	CalculatorType::OutputType::const_iterator itNum = thresholdVector.begin();

	float thresh;

	for(USImageType::PixelType i=0; i < num_in_fg; ++itNum, ++i)
		thresh = (static_cast<float>(*itNum));

	std::cout<<"Threshold computed: "<<thresh<<std::endl;

	return (USImageType::PixelType)(thresh+0.5);
}