diff --git a/Modules/ImageStatistics/mitkImageStatisticsCalculator.h b/Modules/ImageStatistics/mitkImageStatisticsCalculator.h index 2ed5491176..e20d2c7c1e 100644 --- a/Modules/ImageStatistics/mitkImageStatisticsCalculator.h +++ b/Modules/ImageStatistics/mitkImageStatisticsCalculator.h @@ -1,386 +1,401 @@ /*=================================================================== The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center, Division of Medical and Biological Informatics. All rights reserved. This software is distributed WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See LICENSE.txt or http://www.mitk.org for details. ===================================================================*/ #ifndef _MITK_IMAGESTATISTICSCALCULATOR_H #define _MITK_IMAGESTATISTICSCALCULATOR_H #include #include "ImageStatisticsExports.h" #include #include #ifndef __itkHistogram_h #include #endif #include "mitkImage.h" #include "mitkImageTimeSelector.h" #include "mitkPlanarFigure.h" #include namespace mitk { /** * \brief Class for calculating statistics and histogram for an (optionally * masked) image. * * Images can be masked by either a label image (of the same dimensions as * the original image) or by a closed mitk::PlanarFigure, e.g. a circle or * polygon. When masking with a planar figure, the slice corresponding to the * plane containing the figure is extracted and then clipped with contour * defined by the figure. Planar figures need to be aligned along the main axes * of the image (axial, sagittal, coronal). Planar figures on arbitrary * rotated planes are not supported. * * For each operating mode (no masking, masking by image, masking by planar * figure), the calculated statistics and histogram are cached so that, when * switching back and forth between operation modes without modifying mask or * image, the information doesn't need to be recalculated. * + * The class also has the possibility to calculate minimum, maximum, mean + * and their corresponding indicies in the hottest spot in a given ROI / VOI. + * The size of the hotspot is defined by a sphere with a radius specified by + * the user. This procedure is required for the calculation of SUV-statistics + * in PET-images for example. + * * Note: currently time-resolved and multi-channel pictures are not properly * supported. */ class ImageStatistics_EXPORT ImageStatisticsCalculator : public itk::Object { public: enum { MASKING_MODE_NONE = 0, MASKING_MODE_IMAGE, MASKING_MODE_PLANARFIGURE }; typedef itk::Statistics::Histogram HistogramType; typedef HistogramType::ConstIterator HistogramConstIteratorType; struct Statistics { int Label; unsigned int N; double Min; double Max; double Mean; double Median; double Variance; double Sigma; double RMS; double HotspotMin; double HotspotMax; double HotspotMean; double HotspotSigma; double HotspotPeak; vnl_vector< int > MinIndex; vnl_vector< int > MaxIndex; vnl_vector HotspotMaxIndex; vnl_vector HotspotMinIndex; vnl_vector HotspotPeakIndex; void Reset() { Label = 0; N = 0; Min = 0.0; Max = 0.0; Mean = 0.0; Median = 0.0; Variance = 0.0; Sigma = 0.0; RMS = 0.0; HotspotMin = 0.0; HotspotMax = 0.0; HotspotMean = 0.0; HotspotPeak = 0.0; HotspotSigma = 0.0; } }; struct MinMaxIndex { double Max; double Min; vnl_vector MaxIndex; vnl_vector MinIndex; std::list< vnl_vector > MaxIndexList; std::list< vnl_vector > MinIndexList; }; typedef std::vector< HistogramType::ConstPointer > HistogramContainer; typedef std::vector< Statistics > StatisticsContainer; mitkClassMacro( ImageStatisticsCalculator, itk::Object ); itkNewMacro( ImageStatisticsCalculator ); /** \brief Set image from which to compute statistics. */ void SetImage( const mitk::Image *image ); /** \brief Set image for masking. */ void SetImageMask( const mitk::Image *imageMask ); /** \brief Set planar figure for masking. */ void SetPlanarFigure( mitk::PlanarFigure *planarFigure ); /** \brief Set/Get operation mode for masking */ void SetMaskingMode( unsigned int mode ); /** \brief Set/Get operation mode for masking */ itkGetMacro( MaskingMode, unsigned int ); /** \brief Set/Get operation mode for masking */ void SetMaskingModeToNone(); /** \brief Set/Get operation mode for masking */ void SetMaskingModeToImage(); /** \brief Set/Get operation mode for masking */ void SetMaskingModeToPlanarFigure(); /** \brief Set a pixel value for pixels that will be ignored in the statistics */ void SetIgnorePixelValue(double value); /** \brief Get the pixel value for pixels that will be ignored in the statistics */ double GetIgnorePixelValue(); - /** \brief Set wether a pixel value should be ignored in the statistics */ + /** \brief Set whether a pixel value should be ignored in the statistics */ void SetDoIgnorePixelValue(bool doit); - /** \brief Get wether a pixel value will be ignored in the statistics */ + /** \brief Get whether a pixel value will be ignored in the statistics */ bool GetDoIgnorePixelValue(); + /** \brief Sets the radius for the hotspot */ void SetHotspotSize (double hotspotRadiusInMM); + /** \brief Returns the radius of the hotspot */ double GetHotspotSize(); + /** \brief Sets whether the hotspot should be calculated */ void SetCalculateHotspot(bool calculateHotspot); + /** \brief Returns true whether the hotspot should be calculated, otherwise false */ bool IsHotspotCalculated(); /** \brief Compute statistics (together with histogram) for the current * masking mode. * * Computation is not executed if statistics is already up to date. In this * case, false is returned; otherwise, true.*/ virtual bool ComputeStatistics( unsigned int timeStep = 0 ); /** \brief Retrieve the histogram depending on the current masking mode. * * \param label The label for which to retrieve the histogram in multi-label situations (ascending order). */ const HistogramType *GetHistogram( unsigned int timeStep = 0, unsigned int label = 0 ) const; /** \brief Retrieve the histogram depending on the current masking mode (for all image labels. */ const HistogramContainer &GetHistogramVector( unsigned int timeStep = 0 ) const; /** \brief Retrieve statistics depending on the current masking mode. * * \param label The label for which to retrieve the statistics in multi-label situations (ascending order). */ const Statistics &GetStatistics( unsigned int timeStep = 0, unsigned int label = 0 ) const; - /** \brief Retrieve statistics depending on the current masking mode. - * TODO: Kommentare anpassen! - * \param label The label for which to retrieve the statistics in multi-label situations (ascending order). - */ - const Statistics &GetHotspotStatistics( unsigned int timeStep = 0, unsigned int label = 0 ) const; /** \brief Retrieve statistics depending on the current masking mode (for all image labels). */ const StatisticsContainer &GetStatisticsVector( unsigned int timeStep = 0 ) const; protected: typedef std::vector< HistogramContainer > HistogramVector; typedef std::vector< StatisticsContainer > StatisticsVector; typedef std::vector< itk::TimeStamp > TimeStampVectorType; typedef std::vector< bool > BoolVectorType; - - typedef itk::Image< unsigned short, 3 > MaskImage3DType; typedef itk::Image< unsigned short, 2 > MaskImage2DType; ImageStatisticsCalculator(); virtual ~ImageStatisticsCalculator(); /** \brief Depending on the masking mode, the image and mask from which to * calculate statistics is extracted from the original input image and mask * data. * * For example, a when using a PlanarFigure as mask, the 2D image slice * corresponding to the PlanarFigure will be extracted from the original * image. If masking is disabled, the original image is simply passed * through. */ void ExtractImageAndMask( unsigned int timeStep = 0 ); /** \brief If the passed vector matches any of the three principal axes * of the passed geometry, the ínteger value corresponding to the axis * is set and true is returned. */ bool GetPrincipalAxis( const Geometry3D *geometry, Vector3D vector, unsigned int &axis ); template < typename TPixel, unsigned int VImageDimension > void InternalCalculateStatisticsUnmasked( const itk::Image< TPixel, VImageDimension > *image, StatisticsContainer* statisticsContainer, HistogramContainer *histogramContainer ); template < typename TPixel, unsigned int VImageDimension > void InternalCalculateStatisticsMasked( const itk::Image< TPixel, VImageDimension > *image, itk::Image< unsigned short, VImageDimension > *maskImage, StatisticsContainer* statisticsContainer, HistogramContainer* histogramContainer ); template < typename TPixel, unsigned int VImageDimension > void InternalCalculateMaskFromPlanarFigure( const itk::Image< TPixel, VImageDimension > *image, unsigned int axis ); template < typename TPixel, unsigned int VImageDimension > void InternalMaskIgnoredPixels( const itk::Image< TPixel, VImageDimension > *image, itk::Image< unsigned short, VImageDimension > *maskImage ); + /** \brief Calculates minimum, maximum, mean value and their + * corresponding indices in a given ROI. As input the function + * needs an image, a mask and for limiting the searched value + * minimum- and maximum boundaries. The boundaries are set + * to the extent of float by default. It returns a + * MinMaxIndex-struct with the calculated values. */ template MinMaxIndex CalculateMinMaxIndex( const itk::Image *inputImage, itk::Image *maskImage, float minBoundary, float maxBoundary); template < typename TPixel, unsigned int VImageDimension> Statistics CalculateHotspotStatistics( const itk::Image *inputImage, itk::Image *maskImage, double radiusInMM); + /** \brief Calculates if a sphere is located within an image. + * As input the function needs an image for whose region should + * be check if the sphere is inside and an image of the sphere. + * To ensure speed only 14 points on the surface of the sphere + * are checked: six on the axis of coordinates and eight more. + * The functions returns true if every point is in the region. */ template < typename TPixel, unsigned int VImageDimension> bool IsSphereInsideRegion( const itk::Image *inputImage, itk::Image *sphereImage); /** Connection from ITK to VTK */ template void ConnectPipelines(ITK_Exporter exporter, vtkSmartPointer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } /** Connection from VTK to ITK */ template void ConnectPipelines(vtkSmartPointer exporter, ITK_Importer importer) { importer->SetUpdateInformationCallback(exporter->GetUpdateInformationCallback()); importer->SetPipelineModifiedCallback(exporter->GetPipelineModifiedCallback()); importer->SetWholeExtentCallback(exporter->GetWholeExtentCallback()); importer->SetSpacingCallback(exporter->GetSpacingCallback()); importer->SetOriginCallback(exporter->GetOriginCallback()); importer->SetScalarTypeCallback(exporter->GetScalarTypeCallback()); importer->SetNumberOfComponentsCallback(exporter->GetNumberOfComponentsCallback()); importer->SetPropagateUpdateExtentCallback(exporter->GetPropagateUpdateExtentCallback()); importer->SetUpdateDataCallback(exporter->GetUpdateDataCallback()); importer->SetDataExtentCallback(exporter->GetDataExtentCallback()); importer->SetBufferPointerCallback(exporter->GetBufferPointerCallback()); importer->SetCallbackUserData(exporter->GetCallbackUserData()); } void UnmaskedStatisticsProgressUpdate(); void MaskedStatisticsProgressUpdate(); /** m_Image contains the input image (e.g. 2D, 3D, 3D+t)*/ mitk::Image::ConstPointer m_Image; mitk::Image::ConstPointer m_ImageMask; mitk::PlanarFigure::Pointer m_PlanarFigure; HistogramVector m_ImageHistogramVector; HistogramVector m_MaskedImageHistogramVector; HistogramVector m_PlanarFigureHistogramVector; HistogramType::Pointer m_EmptyHistogram; HistogramContainer m_EmptyHistogramContainer; StatisticsVector m_ImageStatisticsVector; StatisticsVector m_MaskedImageStatisticsVector; StatisticsVector m_PlanarFigureStatisticsVector; StatisticsVector m_MaskedImageHotspotStatisticsVector; Statistics m_EmptyStatistics; StatisticsContainer m_EmptyStatisticsContainer; unsigned int m_MaskingMode; bool m_MaskingModeChanged; /** m_InternalImage contains a image volume at one time step (e.g. 2D, 3D)*/ mitk::Image::ConstPointer m_InternalImage; MaskImage3DType::Pointer m_InternalImageMask3D; MaskImage2DType::Pointer m_InternalImageMask2D; TimeStampVectorType m_ImageStatisticsTimeStampVector; TimeStampVectorType m_MaskedImageStatisticsTimeStampVector; TimeStampVectorType m_PlanarFigureStatisticsTimeStampVector; BoolVectorType m_ImageStatisticsCalculationTriggerVector; BoolVectorType m_MaskedImageStatisticsCalculationTriggerVector; BoolVectorType m_PlanarFigureStatisticsCalculationTriggerVector; double m_IgnorePixelValue; bool m_DoIgnorePixelValue; bool m_IgnorePixelValueChanged; double m_HotspotSize; bool m_CalculateHotspot; unsigned int m_PlanarFigureAxis; // Normal axis for PlanarFigure unsigned int m_PlanarFigureSlice; // Slice which contains PlanarFigure int m_PlanarFigureCoordinate0; // First plane-axis for PlanarFigure int m_PlanarFigureCoordinate1; // Second plane-axis for PlanarFigure }; } #endif // #define _MITK_IMAGESTATISTICSCALCULATOR_H