diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.cpp index 1142e81514..4fa8210d7f 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.cpp +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.cpp @@ -1,264 +1,262 @@ /*=================================================================== 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. ===================================================================*/ #include "QmitkImageStatisticsCalculationJob.h" -//QT headers -#include -#include +#include "mitkImageStatisticsCalculator.h" #include #include #include QmitkImageStatisticsCalculationJob::QmitkImageStatisticsCalculationJob() : QThread() , m_StatisticsImage(nullptr) , m_BinaryMask(nullptr) , m_PlanarFigureMask(nullptr) , m_TimeStep(0) , m_IgnoreZeros(false) , m_HistogramNBins(100) , m_StatisticChanged(false) , m_CalculationSuccessful(false) { } QmitkImageStatisticsCalculationJob::~QmitkImageStatisticsCalculationJob() { } void QmitkImageStatisticsCalculationJob::Initialize( mitk::Image::ConstPointer image, mitk::Image::ConstPointer binaryImage, mitk::PlanarFigure::ConstPointer planarFig ) { // reset old values if( this->m_StatisticsImage.IsNotNull() ) this->m_StatisticsImage = nullptr; if( this->m_BinaryMask.IsNotNull() ) this->m_BinaryMask = nullptr; if( this->m_PlanarFigureMask.IsNotNull()) this->m_PlanarFigureMask = nullptr; // set new values if passed in if(image.IsNotNull()) this->m_StatisticsImage = image; if(binaryImage.IsNotNull()) this->m_BinaryMask = binaryImage; if(planarFig.IsNotNull()) this->m_PlanarFigureMask = planarFig; } void QmitkImageStatisticsCalculationJob::SetTimeStep( int times ) { this->m_TimeStep = times; } int QmitkImageStatisticsCalculationJob::GetTimeStep() const { return this->m_TimeStep; } mitk::StatisticsContainer::ConstPointer QmitkImageStatisticsCalculationJob::GetStatisticsData() const { mitk::StatisticsContainer::ConstPointer constContainer = this->m_StatisticsContainer.GetPointer(); return constContainer; } mitk::Image::ConstPointer QmitkImageStatisticsCalculationJob::GetStatisticsImage() const { return this->m_StatisticsImage; } mitk::Image::ConstPointer QmitkImageStatisticsCalculationJob::GetMaskImage() const { return this->m_BinaryMask; } mitk::PlanarFigure::ConstPointer QmitkImageStatisticsCalculationJob::GetPlanarFigure() const { return this->m_PlanarFigureMask; } void QmitkImageStatisticsCalculationJob::SetIgnoreZeroValueVoxel(bool _arg) { this->m_IgnoreZeros = _arg; } bool QmitkImageStatisticsCalculationJob::GetIgnoreZeroValueVoxel() const { return this->m_IgnoreZeros; } void QmitkImageStatisticsCalculationJob::SetHistogramNBins(unsigned int nbins) { this->m_HistogramNBins = nbins; } unsigned int QmitkImageStatisticsCalculationJob::GetHistogramNBins() const { return this->m_HistogramNBins; } std::string QmitkImageStatisticsCalculationJob::GetLastErrorMessage() const { return m_message; } QmitkImageStatisticsCalculationJob::HistogramType::ConstPointer QmitkImageStatisticsCalculationJob::GetTimeStepHistogram(unsigned int t) const { if (t >= this->m_HistogramVector.size()) return nullptr; return this->m_HistogramVector[t]; } bool QmitkImageStatisticsCalculationJob::GetStatisticsChangedFlag() const { return m_StatisticChanged; } bool QmitkImageStatisticsCalculationJob::GetStatisticsUpdateSuccessFlag() const { return m_CalculationSuccessful; } void QmitkImageStatisticsCalculationJob::run() { bool statisticCalculationSuccessful = true; mitk::ImageStatisticsCalculator::Pointer calculator = mitk::ImageStatisticsCalculator::New(); if(this->m_StatisticsImage.IsNotNull()) { calculator->SetInputImage(m_StatisticsImage->Clone()); } else { statisticCalculationSuccessful = false; } // Bug 13416 : The ImageStatistics::SetImageMask() method can throw exceptions, i.e. when the dimensionality // of the masked and input image differ, we need to catch them and mark the calculation as failed // the same holds for the ::SetPlanarFigure() try { if(this->m_BinaryMask.IsNotNull()) { mitk::ImageMaskGenerator::Pointer imgMask = mitk::ImageMaskGenerator::New(); imgMask->SetImageMask(m_BinaryMask->Clone()); calculator->SetMask(imgMask.GetPointer()); } if(this->m_PlanarFigureMask.IsNotNull()) { mitk::PlanarFigureMaskGenerator::Pointer pfMaskGen = mitk::PlanarFigureMaskGenerator::New(); pfMaskGen->SetInputImage(m_StatisticsImage->Clone()); pfMaskGen->SetPlanarFigure(m_PlanarFigureMask->Clone()); calculator->SetMask(pfMaskGen.GetPointer()); } } catch (const mitk::Exception& e) { MITK_ERROR << "MITK Exception: " << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } catch( const itk::ExceptionObject& e) { MITK_ERROR << "ITK Exception:" << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } catch ( const std::runtime_error &e ) { MITK_ERROR<< "Runtime Exception: " << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } catch ( const std::exception &e ) { MITK_ERROR<< "Standard Exception: " << e.what(); m_message = e.what(); statisticCalculationSuccessful = false; } bool statisticChanged = false; if (this->m_IgnoreZeros) { mitk::IgnorePixelMaskGenerator::Pointer ignorePixelValueMaskGen = mitk::IgnorePixelMaskGenerator::New(); ignorePixelValueMaskGen->SetIgnoredPixelValue(0); ignorePixelValueMaskGen->SetInputImage(m_StatisticsImage->Clone()); calculator->SetSecondaryMask(ignorePixelValueMaskGen.GetPointer()); } else { calculator->SetSecondaryMask(nullptr); } calculator->SetNBinsForHistogramStatistics(m_HistogramNBins); for (unsigned int i = 0; i < m_StatisticsImage->GetTimeSteps(); i++) { try { calculator->GetStatistics(i); } catch ( mitk::Exception& e) { m_message = e.GetDescription(); MITK_ERROR<< "MITK Exception: " << e.what(); statisticCalculationSuccessful = false; } catch ( const std::runtime_error &e ) { m_message = "Failure: " + std::string(e.what()); MITK_ERROR<< "Runtime Exception: " << e.what(); statisticCalculationSuccessful = false; } catch ( const std::exception &e ) { m_message = "Failure: " + std::string(e.what()); MITK_ERROR<< "Standard Exception: " << e.what(); statisticCalculationSuccessful = false; } } this->m_StatisticChanged = statisticChanged; this->m_CalculationSuccessful = statisticCalculationSuccessful; if(statisticCalculationSuccessful) { //this->m_StatisticsVector.clear(); //this->m_HistogramVector.clear(); //for (unsigned int i = 0; i < m_StatisticsImage->GetTimeSteps(); i++) //{ // this->m_StatisticsVector.push_back(calculator->GetStatistics(i).GetPointer()); // this->m_HistogramVector.push_back((HistogramType*)this->m_StatisticsVector[i]->GetHistogram().GetPointer()); //} // maybe use reset if this line does not work m_StatisticsContainer = mitk::StatisticsContainer::New(); this->m_HistogramVector.clear(); mitk::TimeGeometry::Pointer tg = m_StatisticsImage->GetTimeGeometry()->Clone(); m_StatisticsContainer->SetTimeGeometry(tg); for (unsigned int i = 0; i < m_StatisticsImage->GetTimeSteps(); i++) { this->m_StatisticsContainer->SetStatisticsForTimeStep(i, calculator->GetStatistics(i)); this->m_HistogramVector.push_back((HistogramType*) calculator->GetStatistics(i).m_Histogram.GetPointer()); } } } diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.h b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.h index cb5ad415ca..8a69133044 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.h +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkImageStatisticsCalculationJob.h @@ -1,117 +1,116 @@ /*=================================================================== 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 QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED #define QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED //QT headers #include -#include + //mitk headers #include "mitkImage.h" #include "mitkPlanarFigure.h" -#include "mitkImageStatisticsCalculator.h" +#include "mitkImageStatisticsContainer.h" #include // itk headers #ifndef __itkHistogram_h #include #endif /** /brief This class is executed as background thread for image statistics calculation. * Documentation: This class is derived from QThread and is intended to be used by QmitkImageStatisticsView to run the image statistics calculation in a background thread keepung the gui usable. */ class MITKIMAGESTATISTICSUI_EXPORT QmitkImageStatisticsCalculationJob : public QThread { Q_OBJECT public: typedef itk::Statistics::Histogram HistogramType; /*! /brief standard constructor. */ QmitkImageStatisticsCalculationJob(); /*! /brief standard destructor. */ ~QmitkImageStatisticsCalculationJob(); /*! /brief Initializes the object with necessary data. */ void Initialize( mitk::Image::ConstPointer image, mitk::Image::ConstPointer binaryImage, mitk::PlanarFigure::ConstPointer planarFig ); /*! /brief returns the calculated image statistics. */ mitk::StatisticsContainer::ConstPointer GetStatisticsData() const; mitk::Image::ConstPointer GetStatisticsImage() const; mitk::Image::ConstPointer GetMaskImage() const; mitk::PlanarFigure::ConstPointer GetPlanarFigure() const; //T25568: can be removed when deprecated image statistics plugin is removed /*! /brief Set the time step of the image you want to process. */ void SetTimeStep( int times ); /*! /brief Get the time step of the image you want to process. */ int GetTimeStep() const; /*! /brief Set flag to ignore zero valued voxels */ void SetIgnoreZeroValueVoxel( bool _arg ); /*! /brief Get status of zero value voxel ignoring. */ bool GetIgnoreZeroValueVoxel() const; /*! /brief Set bin size for histogram resolution.*/ void SetHistogramNBins( unsigned int nbins); /*! /brief Get bin size for histogram resolution.*/ unsigned int GetHistogramNBins() const; /*! /brief Returns the histogram of the currently selected time step. */ HistogramType::ConstPointer GetTimeStepHistogram(unsigned int t = 0) const; /*! /brief Returns a flag indicating if the statistics have changed during calculation */ bool GetStatisticsChangedFlag() const; /*! /brief Returns a flag the indicates if the statistics are updated successfully */ bool GetStatisticsUpdateSuccessFlag() const; /*! /brief Method called once the thread is executed. */ void run() override; std::string GetLastErrorMessage() const; private: //member declaration mitk::Image::ConstPointer m_StatisticsImage; ///< member variable holds the input image for which the statistics need to be calculated. mitk::Image::ConstPointer m_BinaryMask; ///< member variable holds the binary mask image for segmentation image statistics calculation. mitk::PlanarFigure::ConstPointer m_PlanarFigureMask; ///< member variable holds the planar figure for segmentation image statistics calculation. - //std::vector m_StatisticsVector; ///< member variable holds the result structs. mitk::StatisticsContainer::Pointer m_StatisticsContainer; //T25568: can be removed when deprecated image statistics plugin is removed int m_TimeStep; ///< member variable holds the time step for statistics calculation bool m_IgnoreZeros; ///< member variable holds flag to indicate if zero valued voxel should be suppressed unsigned int m_HistogramNBins; ///< member variable holds the bin size for histogram resolution. bool m_StatisticChanged; ///< flag set if statistics have changed bool m_CalculationSuccessful; ///< flag set if statistics calculation was successful std::vector m_HistogramVector; ///< member holds the histograms of all time steps. std::string m_message; }; #endif // QMITKIMAGESTATISTICSCALCULATIONTHREAD_H_INCLUDED