ImageStatisticsCalculator::ImageStatisticsCalculator()
: m_MaskingMode( MASKING_MODE_NONE ),
m_MaskingModeChanged( false ),
m_IgnorePixelValue(0.0),
m_DoIgnorePixelValue(false),
m_IgnorePixelValueChanged(false)
{
m_EmptyHistogram = HistogramType::New();
HistogramType::SizeType histogramSize;
histogramSize.Fill( 256 );
m_EmptyHistogram->Initialize( histogramSize );
m_EmptyStatistics.Reset();
}
PartialVolumeAnalysisHistogramCalculator::PartialVolumeAnalysisHistogramCalculator()
: m_MaskingMode( MASKING_MODE_NONE ),
m_MaskingModeChanged( false ),
m_NumberOfBins(256),
m_UpsamplingFactor(1),
m_GaussianSigma(0),
m_ForceUpdate(false),
m_PlanarFigureThickness(0)
{
m_EmptyHistogram = HistogramType::New();
HistogramType::SizeType histogramSize;
histogramSize.Fill( 256 );
m_EmptyHistogram->Initialize( histogramSize );
m_EmptyStatistics.Reset();
}
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);
}