diff --git a/Modules/ImageStatistics/mitkIntensityProfile.cpp b/Modules/ImageStatistics/mitkIntensityProfile.cpp index 8cade2320e..f7e6d1491d 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.cpp +++ b/Modules/ImageStatistics/mitkIntensityProfile.cpp @@ -1,382 +1,387 @@ /*=================================================================== 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 #include #include #include #include #include #include #include #include "mitkIntensityProfile.h" using namespace mitk; template static void ReadPixel(const PixelType&, Image::Pointer image, const itk::Index<3>& index, ScalarType* returnValue) { switch (image->GetDimension()) { case 2: { ImagePixelReadAccessor readAccess(image, image->GetSliceData(0)); *returnValue = readAccess.GetPixelByIndex(reinterpret_cast&>(index)); break; } case 3: { ImagePixelReadAccessor readAccess(image, image->GetVolumeData(0)); *returnValue = readAccess.GetPixelByIndex(index); break; } default: *returnValue = 0; break; } } static IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, itk::PolyLineParametricPath<3>::Pointer path) { + if (image->GetDimension() == 4) + { + mitkThrow() << "computation of intensity profiles not supported for 4D images"; + } + IntensityProfile::Pointer intensityProfile = IntensityProfile::New(); itk::PolyLineParametricPath<3>::InputType input = path->StartOfInput(); BaseGeometry* imageGeometry = image->GetGeometry(); const PixelType pixelType = image->GetPixelType(); IntensityProfile::MeasurementVectorType measurementVector; itk::PolyLineParametricPath<3>::OffsetType offset; Point3D worldPoint; itk::Index<3> index; do { imageGeometry->IndexToWorld(path->Evaluate(input), worldPoint); imageGeometry->WorldToIndex(worldPoint, index); mitkPixelTypeMultiplex3(ReadPixel, pixelType, image, index, measurementVector.GetDataPointer()); intensityProfile->PushBack(measurementVector); offset = path->IncrementInput(input); } while ((offset[0] | offset[1] | offset[2]) != 0); return intensityProfile; } template static typename itk::InterpolateImageFunction::Pointer CreateInterpolateImageFunction(InterpolateImageFunction::Enum interpolator) { switch (interpolator) { case InterpolateImageFunction::NearestNeighbor: return itk::NearestNeighborInterpolateImageFunction::New().GetPointer(); case InterpolateImageFunction::Linear: return itk::LinearInterpolateImageFunction::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Blackman_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Blackman_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Blackman_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Cosine_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Cosine_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Cosine_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Hamming_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Hamming_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Hamming_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Lanczos_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Lanczos_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Lanczos_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Welch_3: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Welch_4: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); case InterpolateImageFunction::WindowedSinc_Welch_5: return itk::WindowedSincInterpolateImageFunction >::New().GetPointer(); default: return itk::NearestNeighborInterpolateImageFunction::New().GetPointer(); } } template static void ComputeIntensityProfile(itk::Image* image, itk::PolyLineParametricPath<3>::Pointer path, unsigned int numSamples, InterpolateImageFunction::Enum interpolator, IntensityProfile::Pointer intensityProfile) { typename itk::InterpolateImageFunction >::Pointer interpolateImageFunction = CreateInterpolateImageFunction >(interpolator); interpolateImageFunction->SetInputImage(image); const itk::PolyLineParametricPath<3>::InputType startOfInput = path->StartOfInput(); const itk::PolyLineParametricPath<3>::InputType delta = 1.0 / (numSamples - 1); IntensityProfile::MeasurementVectorType measurementVector; for (unsigned int i = 0; i < numSamples; ++i) { measurementVector[0] = interpolateImageFunction->EvaluateAtContinuousIndex(path->Evaluate(startOfInput + i * delta)); intensityProfile->PushBack(measurementVector); } } static IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, itk::PolyLineParametricPath<3>::Pointer path, unsigned int numSamples, InterpolateImageFunction::Enum interpolator) { IntensityProfile::Pointer intensityProfile = IntensityProfile::New(); AccessFixedDimensionByItk_n(image, ComputeIntensityProfile, 3, (path, numSamples, interpolator, intensityProfile)); return intensityProfile; } class AddPolyLineElementToPath { public: AddPolyLineElementToPath(const PlaneGeometry* planarFigureGeometry, const BaseGeometry* imageGeometry, itk::PolyLineParametricPath<3>::Pointer path) : m_PlanarFigureGeometry(planarFigureGeometry), m_ImageGeometry(imageGeometry), m_Path(path) { } void operator()(const PlanarFigure::PolyLineElement& polyLineElement) { m_PlanarFigureGeometry->Map(polyLineElement, m_WorldPoint); m_ImageGeometry->WorldToIndex(m_WorldPoint, m_ContinuousIndexPoint); m_Vertex.CastFrom(m_ContinuousIndexPoint); m_Path->AddVertex(m_Vertex); } private: const PlaneGeometry* m_PlanarFigureGeometry; const BaseGeometry* m_ImageGeometry; itk::PolyLineParametricPath<3>::Pointer m_Path; Point3D m_WorldPoint; Point3D m_ContinuousIndexPoint; itk::PolyLineParametricPath<3>::ContinuousIndexType m_Vertex; }; static itk::PolyLineParametricPath<3>::Pointer CreatePathFromPlanarFigure(BaseGeometry* imageGeometry, PlanarFigure* planarFigure) { itk::PolyLineParametricPath<3>::Pointer path = itk::PolyLineParametricPath<3>::New(); const PlanarFigure::PolyLineType polyLine = planarFigure->GetPolyLine(0); std::for_each(polyLine.begin(), polyLine.end(), AddPolyLineElementToPath(planarFigure->GetPlaneGeometry(), imageGeometry, path)); return path; } static void AddPointToPath(const BaseGeometry* imageGeometry, const Point3D& point, itk::PolyLineParametricPath<3>::Pointer path) { Point3D continuousIndexPoint; imageGeometry->WorldToIndex(point, continuousIndexPoint); itk::PolyLineParametricPath<3>::ContinuousIndexType vertex; vertex.CastFrom(continuousIndexPoint); path->AddVertex(vertex); } static itk::PolyLineParametricPath<3>::Pointer CreatePathFromPoints(BaseGeometry* imageGeometry, const Point3D& startPoint, const Point3D& endPoint) { itk::PolyLineParametricPath<3>::Pointer path = itk::PolyLineParametricPath<3>::New(); AddPointToPath(imageGeometry, startPoint, path); AddPointToPath(imageGeometry, endPoint, path); return path; } IntensityProfile::Pointer mitk::ComputeIntensityProfile(Image::Pointer image, PlanarFigure::Pointer planarFigure) { return ::ComputeIntensityProfile(image, CreatePathFromPlanarFigure(image->GetGeometry(), planarFigure)); } IntensityProfile::Pointer mitk::ComputeIntensityProfile(Image::Pointer image, PlanarLine::Pointer planarLine, unsigned int numSamples, InterpolateImageFunction::Enum interpolator) { return ::ComputeIntensityProfile(image, CreatePathFromPlanarFigure(image->GetGeometry(), planarLine.GetPointer()), numSamples, interpolator); } IntensityProfile::Pointer mitk::ComputeIntensityProfile(Image::Pointer image, const Point3D& startPoint, const Point3D& endPoint, unsigned int numSamples, InterpolateImageFunction::Enum interpolator) { return ::ComputeIntensityProfile(image, CreatePathFromPoints(image->GetGeometry(), startPoint, endPoint), numSamples, interpolator); } IntensityProfile::InstanceIdentifier mitk::ComputeGlobalMaximum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &max) { max = -vcl_numeric_limits::min(); IntensityProfile::InstanceIdentifier maxIndex = 0; IntensityProfile::ConstIterator end = intensityProfile->End(); IntensityProfile::MeasurementType measurement; for (IntensityProfile::ConstIterator it = intensityProfile->Begin(); it != end; ++it) { measurement = it.GetMeasurementVector()[0]; if (measurement > max) { max = measurement; maxIndex = it.GetInstanceIdentifier(); } } return maxIndex; } IntensityProfile::InstanceIdentifier mitk::ComputeGlobalMinimum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &min) { min = vcl_numeric_limits::max(); IntensityProfile::InstanceIdentifier minIndex = 0; IntensityProfile::ConstIterator end = intensityProfile->End(); IntensityProfile::MeasurementType measurement; for (IntensityProfile::ConstIterator it = intensityProfile->Begin(); it != end; ++it) { measurement = it.GetMeasurementVector()[0]; if (measurement < min) { min = measurement; minIndex = it.GetInstanceIdentifier(); } } return minIndex; } IntensityProfile::InstanceIdentifier mitk::ComputeCenterOfMaximumArea(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::InstanceIdentifier radius) { //const IntensityProfile::MeasurementType min = intensityProfile->GetMeasurementVector(ComputeGlobalMinimum(intensityProfile))[0]; IntensityProfile::MeasurementType min; ComputeGlobalMinimum(intensityProfile, min); const IntensityProfile::InstanceIdentifier areaWidth = 1 + 2 * radius; IntensityProfile::MeasurementType maxArea = 0; for (IntensityProfile::InstanceIdentifier i = 0; i < areaWidth; ++i) maxArea += intensityProfile->GetMeasurementVector(i)[0] - min; const IntensityProfile::InstanceIdentifier lastIndex = intensityProfile->Size() - areaWidth; IntensityProfile::InstanceIdentifier centerOfMaxArea = radius; IntensityProfile::MeasurementType area = maxArea; for (IntensityProfile::InstanceIdentifier i = 1; i <= lastIndex; ++i) { area += intensityProfile->GetMeasurementVector(i + areaWidth - 1)[0] - min; area -= intensityProfile->GetMeasurementVector(i - 1)[0] - min; if (area > maxArea) { maxArea = area; centerOfMaxArea = i + radius; // TODO: If multiple areas in the neighborhood have the same intensity chose the middle one instead of the first one. } } return centerOfMaxArea; } std::vector mitk::CreateVectorFromIntensityProfile(IntensityProfile::ConstPointer intensityProfile) { std::vector result; result.reserve(intensityProfile->Size()); IntensityProfile::ConstIterator end = intensityProfile->End(); for (IntensityProfile::ConstIterator it = intensityProfile->Begin(); it != end; ++it) result.push_back(it.GetMeasurementVector()[0]); return result; } IntensityProfile::Pointer mitk::CreateIntensityProfileFromVector(const std::vector& vector) { const IntensityProfile::InstanceIdentifier size = vector.size(); IntensityProfile::Pointer result = IntensityProfile::New(); result->Resize(size); for (IntensityProfile::InstanceIdentifier i = 0; i < size; ++i) result->SetMeasurement(i, 0, vector[i]); return result; } void mitk::ComputeIntensityProfileStatistics(IntensityProfile::ConstPointer intensityProfile, ImageStatisticsContainer::ImageStatisticsObject& stats) { typedef std::vector StatsVecType; StatsVecType statsVec = mitk::CreateVectorFromIntensityProfile( intensityProfile ); IntensityProfile::MeasurementType min; IntensityProfile::MeasurementType max; mitk::ComputeGlobalMinimum( intensityProfile, min ); mitk::ComputeGlobalMaximum( intensityProfile, max ); auto numSamples = static_cast(statsVec.size()); double mean = 0.0; double rms = 0.0; for ( StatsVecType::const_iterator it = statsVec.begin(); it != statsVec.end(); ++it ) { double val = *it; mean += val; rms += val*val; } mean /= static_cast(numSamples); rms /= static_cast(numSamples); double var = 0.0; for ( StatsVecType::const_iterator it = statsVec.begin(); it != statsVec.end(); ++it ) { double diff = *it - mean; var += diff*diff; } var /= (static_cast(numSamples) - 1 ); rms = sqrt( rms ); stats.AddStatistic(mitk::ImageStatisticsConstants::MINIMUM(), min); stats.AddStatistic(mitk::ImageStatisticsConstants::MAXIMUM(), max); stats.AddStatistic(mitk::ImageStatisticsConstants::NUMBEROFVOXELS(), numSamples); stats.AddStatistic(mitk::ImageStatisticsConstants::MEAN(), mean); stats.AddStatistic(mitk::ImageStatisticsConstants::STANDARDDEVIATION(), sqrt(var)); stats.AddStatistic(mitk::ImageStatisticsConstants::VARIANCE(), var); stats.AddStatistic(mitk::ImageStatisticsConstants::RMS(), rms); } diff --git a/Modules/ImageStatistics/mitkIntensityProfile.h b/Modules/ImageStatistics/mitkIntensityProfile.h index 60207dff01..361ef34268 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.h +++ b/Modules/ImageStatistics/mitkIntensityProfile.h @@ -1,137 +1,139 @@ /*=================================================================== 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 mitkIntensityProfile_h #define mitkIntensityProfile_h #include #include #include #include #include namespace mitk { typedef itk::Statistics::ListSample::MeasurementVectorType> IntensityProfile; /** \brief Compute intensity profile of an image for each pixel along the first PolyLine of a given planar figure. * * \param[in] image A two or three-dimensional image which consists of single component pixels. * \param[in] planarFigure A planar figure from which the first PolyLine is used to evaluate the intensity profile. * * \return The computed intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, PlanarFigure::Pointer planarFigure); namespace InterpolateImageFunction { enum Enum { NearestNeighbor, Linear, WindowedSinc_Blackman_3, WindowedSinc_Blackman_4, WindowedSinc_Blackman_5, WindowedSinc_Cosine_3, WindowedSinc_Cosine_4, WindowedSinc_Cosine_5, WindowedSinc_Hamming_3, WindowedSinc_Hamming_4, WindowedSinc_Hamming_5, WindowedSinc_Lanczos_3, WindowedSinc_Lanczos_4, WindowedSinc_Lanczos_5, WindowedSinc_Welch_3, WindowedSinc_Welch_4, WindowedSinc_Welch_5 }; } /** \brief Compute intensity profile of an image for each sample along a planar line. * * \param[in] image A three-dimensional image which consists of single component pixels. * \param[in] planarLine A planar line along which the intensity profile will be evaluated. * \param[in] numSamples Number of samples along the planar line (must be at least 2). * \param[in] interpolator Image interpolation function which is used to read each sample. + * \throw if image is 4D * * \return The computed intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, PlanarLine::Pointer planarLine, unsigned int numSamples, InterpolateImageFunction::Enum interpolator = InterpolateImageFunction::NearestNeighbor); /** \brief Compute intensity profile of an image for each sample between two points. * * \param[in] image A three-dimensional image which consists of single component pixels. * \param[in] startPoint A point at which the first sample is to be read. * \param[in] endPoint A point at which the last sample is to be read. * \param[in] numSamples Number of samples between startPoint and endPoint (must be at least 2). * \param[in] interpolator Image interpolation function which is used to read each sample. + * \throw if image is 4D * * \return The computed intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer ComputeIntensityProfile(Image::Pointer image, const Point3D& startPoint, const Point3D& endPoint, unsigned int numSamples, InterpolateImageFunction::Enum interpolator = InterpolateImageFunction::NearestNeighbor); /** \brief Compute global maximum of an intensity profile. * * \param[in] intensityProfile An intensity profile. * * \return Index of the global maximum. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeGlobalMaximum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &max); /** \brief Compute global minimum of an intensity profile. * * \param[in] intensityProfile An intensity profile. * * \return Index of the global minimum. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeGlobalMinimum(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::MeasurementType &min); /** \brief Compute statistics of an intensity profile. * * \param[in] intensityProfile An intensity profile. * * \param[in] stats An ImageStatisticsCalculator::Statistics object to hold the calculated statistics. * */ MITKIMAGESTATISTICS_EXPORT void ComputeIntensityProfileStatistics(IntensityProfile::ConstPointer intensityProfile, ImageStatisticsContainer::ImageStatisticsObject& stats); /** \brief Compute center of maximum area under the curve of an intensity profile. * * \param[in] intensityProfile An intensity profile. * \param[in] radius Radius of the area (width of area equals 1 + 2 * radius). * * \return Index of the maximum area center. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeCenterOfMaximumArea(IntensityProfile::ConstPointer intensityProfile, IntensityProfile::InstanceIdentifier radius); /** \brief Convert an intensity profile to a standard library vector. * * \param[in] intensityProfile An intensity profile. * * \return Standard library vector which contains the input intensity profile measurements. */ MITKIMAGESTATISTICS_EXPORT std::vector CreateVectorFromIntensityProfile(IntensityProfile::ConstPointer intensityProfile); /** \brief Convert a standard library vector to an intensity profile. * * \param[in] vector An standard library vector which contains intensity profile measurements. * * \return An intensity profile. */ MITKIMAGESTATISTICS_EXPORT IntensityProfile::Pointer CreateIntensityProfileFromVector(const std::vector& vector); } #endif diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp index eef9c21873..cf33da8a09 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkHistogramVisualizationWidget.cpp @@ -1,195 +1,196 @@ /*=================================================================== 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 "QmitkHistogramVisualizationWidget.h" #include QmitkHistogramVisualizationWidget::QmitkHistogramVisualizationWidget(QWidget* parent) : QWidget(parent) { m_Controls.setupUi(this); m_Controls.checkBoxShowSubchart->setChecked(false); m_Controls.spinBoxNBins->setValue(m_DefaultNBins); m_Controls.spinBoxNBins->setMinimum(m_MinNBins); m_Controls.spinBoxNBins->setMaximum(m_MaxNBins); SetGUIElementsEnabled(false); CreateConnections(); } void QmitkHistogramVisualizationWidget::SetHistogram(itk::Statistics::Histogram::ConstPointer histogram, const std::string& dataLabel) { if (histogram == nullptr) return; m_Histogram = histogram; m_Controls.chartWidget->AddData2D(ConvertHistogramToMap(m_Histogram), dataLabel); m_Controls.chartWidget->SetChartType(dataLabel, QmitkChartWidget::ChartType::bar); m_Controls.chartWidget->SetXAxisLabel("Gray value"); m_Controls.chartWidget->SetYAxisLabel("Frequency"); + m_Controls.chartWidget->SetShowLegend(false); m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); SetGUIElementsEnabled(true); } void QmitkHistogramVisualizationWidget::Reset() { m_Controls.chartWidget->Clear(); SetGUIElementsEnabled(false); } int QmitkHistogramVisualizationWidget::GetBins() { return m_Controls.spinBoxNBins->value(); } void QmitkHistogramVisualizationWidget::ResetDefault() { m_Controls.checkBoxUseDefaultNBins->setChecked(true); m_Controls.spinBoxNBins->setEnabled(false); m_Controls.spinBoxNBins->setValue(100); m_Controls.checkBoxShowSubchart->setChecked(false); } void QmitkHistogramVisualizationWidget::SetTheme(QmitkChartWidget::ColorTheme style) { m_Controls.chartWidget->SetTheme(style); } void QmitkHistogramVisualizationWidget::CreateConnections() { connect(m_Controls.buttonCopyHistogramToClipboard, &QPushButton::clicked, this, &QmitkHistogramVisualizationWidget::OnClipboardButtonClicked); connect(m_Controls.checkBoxUseDefaultNBins, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnDefaultNBinsCheckBoxChanged); connect(m_Controls.spinBoxNBins, &QSpinBox::editingFinished, this, &QmitkHistogramVisualizationWidget::OnNBinsSpinBoxValueChanged); connect(m_Controls.checkBoxShowSubchart, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnShowSubchartCheckBoxChanged); connect(m_Controls.checkBoxViewMinMax, &QCheckBox::clicked, this, &QmitkHistogramVisualizationWidget::OnViewMinMaxCheckBoxChanged); connect(m_Controls.doubleSpinBoxMaxValue, &QSpinBox::editingFinished, this, &QmitkHistogramVisualizationWidget::OnMaxValueSpinBoxValueChanged); connect(m_Controls.doubleSpinBoxMinValue, &QSpinBox::editingFinished, this, &QmitkHistogramVisualizationWidget::OnMinValueSpinBoxValueChanged); } void QmitkHistogramVisualizationWidget::SetGUIElementsEnabled(bool enabled) { this->setEnabled(enabled); m_Controls.tabWidgetPlot->setEnabled(enabled); m_Controls.checkBoxShowSubchart->setEnabled(enabled); m_Controls.checkBoxUseDefaultNBins->setEnabled(enabled); m_Controls.spinBoxNBins->setEnabled(!m_Controls.checkBoxUseDefaultNBins->isChecked()); m_Controls.buttonCopyHistogramToClipboard->setEnabled(enabled); m_Controls.checkBoxViewMinMax->setEnabled(enabled); m_Controls.doubleSpinBoxMaxValue->setEnabled(m_Controls.checkBoxViewMinMax->isChecked()); m_Controls.doubleSpinBoxMinValue->setEnabled(m_Controls.checkBoxViewMinMax->isChecked()); } std::map QmitkHistogramVisualizationWidget::ConvertHistogramToMap(itk::Statistics::Histogram::ConstPointer histogram) const { std::map histogramMap; if (histogram) { auto endIt = histogram->End(); auto it = histogram->Begin(); // generating Lists of measurement and frequencies for (; it != endIt; ++it) { double frequency = it.GetFrequency(); double measurement = it.GetMeasurementVector()[0]; histogramMap.emplace(measurement, frequency); } } return histogramMap; } void QmitkHistogramVisualizationWidget::OnClipboardButtonClicked() { if (m_Histogram) { QApplication::clipboard()->clear(); QString clipboard("Measurement \t Frequency\n"); auto iter = m_Histogram->Begin(); auto iterEnd = m_Histogram->End(); for (; iter != iterEnd; ++iter) { clipboard = clipboard.append("%L1 \t %L2\n") .arg(iter.GetMeasurementVector()[0], 0, 'f', 2) .arg(iter.GetFrequency()); } QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); } } void QmitkHistogramVisualizationWidget::OnDefaultNBinsCheckBoxChanged() { if (m_Controls.checkBoxUseDefaultNBins->isChecked()) { m_Controls.spinBoxNBins->setEnabled(false); if (m_Controls.spinBoxNBins->value() != static_cast(m_DefaultNBins) ) { m_Controls.spinBoxNBins->setValue(m_DefaultNBins); OnNBinsSpinBoxValueChanged(); } } else { m_Controls.spinBoxNBins->setEnabled(true); } } void QmitkHistogramVisualizationWidget::OnNBinsSpinBoxValueChanged() { emit RequestHistogramUpdate(m_Controls.spinBoxNBins->value()); } void QmitkHistogramVisualizationWidget::OnShowSubchartCheckBoxChanged() { m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); } void QmitkHistogramVisualizationWidget::OnViewMinMaxCheckBoxChanged() { double min = m_Histogram->GetBinMin(0, 0); auto maxVector = m_Histogram->GetDimensionMaxs(0); double max; if (m_Controls.checkBoxUseDefaultNBins->isChecked()) max = maxVector[m_DefaultNBins - 1]; else max = maxVector[m_Controls.spinBoxNBins->value() - 1]; if (!m_Controls.checkBoxViewMinMax->isChecked()) { m_Controls.doubleSpinBoxMaxValue->setEnabled(false); m_Controls.doubleSpinBoxMinValue->setEnabled(false); m_Controls.chartWidget->Reload(); } else { m_Controls.doubleSpinBoxMinValue->setMinimum(min); m_Controls.doubleSpinBoxMaxValue->setMaximum(max); m_Controls.doubleSpinBoxMaxValue->setEnabled(true); m_Controls.doubleSpinBoxMinValue->setEnabled(true); } } void QmitkHistogramVisualizationWidget::OnMinValueSpinBoxValueChanged() { m_Controls.doubleSpinBoxMaxValue->setMinimum(m_Controls.doubleSpinBoxMinValue->value()+1); m_Controls.chartWidget->UpdateMinMaxValueView(m_Controls.doubleSpinBoxMinValue->value(),m_Controls.doubleSpinBoxMaxValue->value()); } void QmitkHistogramVisualizationWidget::OnMaxValueSpinBoxValueChanged() { m_Controls.doubleSpinBoxMinValue->setMaximum(m_Controls.doubleSpinBoxMaxValue->value()-1); m_Controls.chartWidget->UpdateMinMaxValueView(m_Controls.doubleSpinBoxMinValue->value(),m_Controls.doubleSpinBoxMaxValue->value()); } \ No newline at end of file diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.cpp b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.cpp index 16b6ecc019..9af758ca5b 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.cpp +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.cpp @@ -1,117 +1,117 @@ /*=================================================================== 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 "QmitkIntensityProfileVisualizationWidget.h" #include QmitkIntensityProfileVisualizationWidget::QmitkIntensityProfileVisualizationWidget(QWidget* parent) : QWidget(parent) { m_Controls.setupUi(this); m_Controls.checkBoxShowSubchart->setChecked(false); CreateConnections(); } void QmitkIntensityProfileVisualizationWidget::SetIntensityProfile(mitk::IntensityProfile::ConstPointer intensityProfile, const std::string& dataLabel) { if (intensityProfile == nullptr) return; m_IntensityProfileList = mitk::CreateVectorFromIntensityProfile(intensityProfile); if (m_IntensityProfileList.empty()) return; m_Controls.chartWidget->AddData1D(m_IntensityProfileList, dataLabel); m_Controls.chartWidget->SetChartType(dataLabel, QmitkChartWidget::ChartType::line); m_Controls.chartWidget->SetXAxisLabel("Distance"); m_Controls.chartWidget->SetYAxisLabel("Intensity"); + m_Controls.chartWidget->SetShowLegend(false); m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); SetGUIElementsEnabled(true); } void QmitkIntensityProfileVisualizationWidget::Reset() { m_Controls.chartWidget->Clear(); SetGUIElementsEnabled(false); m_IntensityProfileList.clear(); } void QmitkIntensityProfileVisualizationWidget::SetTheme(QmitkChartWidget::ColorTheme style) { m_ChartStyle = style; } void QmitkIntensityProfileVisualizationWidget::CreateConnections() { connect(m_Controls.checkBoxShowSubchart, &QCheckBox::clicked, this, &QmitkIntensityProfileVisualizationWidget::OnShowSubchartCheckBoxChanged); connect(m_Controls.buttonCopyToClipboard, &QPushButton::clicked, this, &QmitkIntensityProfileVisualizationWidget::OnClipboardButtonClicked); connect(m_Controls.chartWidget, &QmitkChartWidget::PageSuccessfullyLoaded, this, &QmitkIntensityProfileVisualizationWidget::OnPageSuccessfullyLoaded); } void QmitkIntensityProfileVisualizationWidget::SetGUIElementsEnabled(bool enabled) { this->setEnabled(enabled); m_Controls.groupBoxIntensityProfile->setEnabled(enabled); m_Controls.groupBoxPlot->setEnabled(enabled); m_Controls.buttonCopyToClipboard->setEnabled(enabled); m_Controls.checkBoxShowSubchart->setEnabled(enabled); m_Controls.chartWidget->setEnabled(enabled); - m_Controls.labelInfo->setEnabled(enabled); } std::vector QmitkIntensityProfileVisualizationWidget::ConvertIntensityProfileToVector(mitk::IntensityProfile::ConstPointer intensityProfile) const { std::vector intensityProfileList; if (intensityProfile != nullptr) { auto end = intensityProfile->End(); for (auto it = intensityProfile->Begin(); it != end; ++it) { intensityProfileList.push_back(it.GetMeasurementVector()[0]); } } return intensityProfileList; } void QmitkIntensityProfileVisualizationWidget::OnClipboardButtonClicked() { if (m_IntensityProfileList.empty()) return; QApplication::clipboard()->clear(); QString clipboard("Pixel \t Intensity\n"); for (unsigned int i = 0; i < m_IntensityProfileList.size(); i++) { clipboard = clipboard.append("%L1 \t %L2\n") .arg(QString::number(i)) .arg(QString::number(m_IntensityProfileList.at(i))); } QApplication::clipboard()->setText(clipboard, QClipboard::Clipboard); } void QmitkIntensityProfileVisualizationWidget::OnShowSubchartCheckBoxChanged() { m_Controls.chartWidget->Show(m_Controls.checkBoxShowSubchart->isChecked()); } void QmitkIntensityProfileVisualizationWidget::OnPageSuccessfullyLoaded() { m_Controls.chartWidget->SetTheme(m_ChartStyle); } diff --git a/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.ui b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.ui index 6b98ce7a12..dd3a6f4c0a 100644 --- a/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.ui +++ b/Modules/ImageStatisticsUI/Qmitk/QmitkIntensityProfileVisualizationWidget.ui @@ -1,140 +1,133 @@ QmitkIntensityProfileControls 0 0 540 468 Form false false false 0 0 0 0 16777215 16777215 Plot Show Subchart true - - - - - - - 0 0 0 0 0 0 0 Copy to Clipboard Qt::Horizontal 40 20 QmitkChartWidget QWidget
QmitkChartWidget.h
 diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp index 9d90a7ad54..eef0f5a6a8 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,508 +1,545 @@ /*=================================================================== 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 "QmitkImageStatisticsView.h" #include // berry includes #include #include #include #include #include #include #include #include #include #include #include #include #include +#include #include "mitkImageStatisticsContainerManager.h" #include const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; QmitkImageStatisticsView::QmitkImageStatisticsView(QObject * /*parent*/, const char * /*name*/) { - this->m_CalculationThread = new QmitkImageStatisticsCalculationJob(); + this->m_CalculationJob = new QmitkImageStatisticsCalculationJob(); } QmitkImageStatisticsView::~QmitkImageStatisticsView() { if (m_selectedPlanarFigure) m_selectedPlanarFigure->RemoveObserver(m_PlanarFigureObserverTag); } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { m_Controls.setupUi(parent); m_Controls.widget_histogram->SetTheme(this->GetColorTheme()); m_Controls.widget_intensityProfile->SetTheme(this->GetColorTheme()); m_Controls.groupBox_histogram->setVisible(true); m_Controls.groupBox_intensityProfile->setVisible(false); m_Controls.label_currentlyComputingStatistics->setVisible(false); m_Controls.sliderWidget_histogram->setPrefix("Time: "); m_Controls.sliderWidget_histogram->setDecimals(0); m_Controls.sliderWidget_histogram->setVisible(false); + m_Controls.sliderWidget_intensityProfile->setPrefix("Time: "); + m_Controls.sliderWidget_intensityProfile->setDecimals(0); + m_Controls.sliderWidget_intensityProfile->setVisible(false); ResetGUI(); PrepareDataStorageComboBoxes(); m_Controls.widget_statistics->SetDataStorage(this->GetDataStorage()); CreateConnections(); } void QmitkImageStatisticsView::CreateConnections() { - connect(this->m_CalculationThread, + connect(this->m_CalculationJob, &QmitkImageStatisticsCalculationJob::finished, this, &QmitkImageStatisticsView::OnStatisticsCalculationEnds, Qt::QueuedConnection); connect(this->m_Controls.checkBox_ignoreZero, &QCheckBox::stateChanged, this, &QmitkImageStatisticsView::OnCheckBoxIgnoreZeroStateChanged); connect(this->m_Controls.sliderWidget_histogram, &ctkSliderWidget::valueChanged, this, &QmitkImageStatisticsView::OnSliderWidgetHistogramChanged); + connect(this->m_Controls.sliderWidget_intensityProfile, + &ctkSliderWidget::valueChanged, + this, + &QmitkImageStatisticsView::OnSliderWidgetIntensityProfileChanged); connect(this->m_Controls.imageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsView::OnImageSelectorChanged); connect(this->m_Controls.maskImageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsView::OnMaskSelectorChanged); } void QmitkImageStatisticsView::OnCheckBoxIgnoreZeroStateChanged(int state) { m_ForceRecompute = true; if (state != Qt::Unchecked) { - this->m_CalculationThread->SetIgnoreZeroValueVoxel(true); + this->m_CalculationJob->SetIgnoreZeroValueVoxel(true); } else { - this->m_CalculationThread->SetIgnoreZeroValueVoxel(false); + this->m_CalculationJob->SetIgnoreZeroValueVoxel(false); } CalculateOrGetStatistics(); } void QmitkImageStatisticsView::OnSliderWidgetHistogramChanged(double value) { unsigned int timeStep = static_cast(value); auto mask = m_selectedMaskNode ? m_selectedMaskNode->GetData() : nullptr; auto imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics( this->GetDataStorage(), m_selectedImageNode->GetData(), mask); HistogramType::ConstPointer histogram = imageStatistics->GetStatisticsForTimeStep(timeStep).m_Histogram; - if (histogram.IsNotNull() && this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) + if (histogram.IsNotNull() && this->m_CalculationJob->GetStatisticsUpdateSuccessFlag()) { this->FillHistogramWidget({histogram}, {m_selectedImageNode->GetName()}); } } +void QmitkImageStatisticsView::OnSliderWidgetIntensityProfileChanged(double value) +{ + //intensity profile is always computed on request, not stored as node in DataStorage + auto image = dynamic_cast(m_selectedImageNode->GetData()); + auto planarFigure = dynamic_cast(m_selectedMaskNode->GetData()); + + if (image && planarFigure && this->m_CalculationJob->GetStatisticsUpdateSuccessFlag()) + { + this->ComputeAndDisplayIntensityProfile(image, planarFigure); + } +} + void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer &) {} void QmitkImageStatisticsView::FillHistogramWidget(const std::vector &histogram, - const std::vector &dataLabels) + const std::vector &dataLabels) { m_Controls.groupBox_histogram->setVisible(true); m_Controls.widget_histogram->SetTheme(this->GetColorTheme()); m_Controls.widget_histogram->Reset(); m_Controls.widget_histogram->SetHistogram(histogram.front(), dataLabels.front()); connect(m_Controls.widget_histogram, &QmitkHistogramVisualizationWidget::RequestHistogramUpdate, this, &QmitkImageStatisticsView::OnRequestHistogramUpdate); } QmitkChartWidget::ColorTheme QmitkImageStatisticsView::GetColorTheme() const { ctkPluginContext *context = berry::WorkbenchPlugin::GetDefault()->GetPluginContext(); ctkServiceReference styleManagerRef = context->getServiceReference(); if (styleManagerRef) { auto styleManager = context->getService(styleManagerRef); if (styleManager->GetStyle().name == "Dark") { return QmitkChartWidget::ColorTheme::darkstyle; } else { return QmitkChartWidget::ColorTheme::lightstyle; } } return QmitkChartWidget::ColorTheme::darkstyle; } void QmitkImageStatisticsView::OnImageSelectorChanged() { auto selectedImageNode = m_Controls.imageSelector->GetSelectedNode(); if (selectedImageNode != m_selectedImageNode) { m_selectedImageNode = selectedImageNode; if (m_selectedImageNode.IsNotNull()) { ResetGUIDefault(); auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto hasSameGeometry = mitk::NodePredicateGeometry::New(m_selectedImageNode->GetData()->GetGeometry()); hasSameGeometry->SetCheckPrecision(1e-10); auto isMaskWithGeometryPredicate = mitk::NodePredicateAnd::New(isMaskPredicate, hasSameGeometry); auto isMaskOrPlanarFigureWithGeometryPredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskWithGeometryPredicate); // prevent triggering of computation as the predicate triggers a signalChanged event m_Controls.maskImageSelector->disconnect(); m_Controls.maskImageSelector->SetPredicate(isMaskOrPlanarFigureWithGeometryPredicate); // reset mask to m_Controls.maskImageSelector->SetZeroEntryText(""); m_Controls.checkBox_ignoreZero->setEnabled(true); m_selectedMaskNode = nullptr; m_Controls.widget_statistics->SetMaskNodes({}); CalculateOrGetStatistics(); m_Controls.widget_statistics->SetImageNodes({m_selectedImageNode.GetPointer()}); connect(this->m_Controls.maskImageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsView::OnMaskSelectorChanged); } else { m_Controls.widget_statistics->SetImageNodes({}); m_Controls.widget_statistics->SetMaskNodes({}); - m_Controls.widget_statistics->Reset(); + m_Controls.widget_statistics->Reset(); m_Controls.widget_histogram->Reset(); ResetGUI(); } } } void QmitkImageStatisticsView::OnMaskSelectorChanged() { auto selectedMaskNode = m_Controls.maskImageSelector->GetSelectedNode(); if (selectedMaskNode != m_selectedMaskNode) { m_selectedMaskNode = selectedMaskNode; if (m_selectedMaskNode.IsNotNull()) { m_Controls.widget_statistics->SetMaskNodes({m_selectedMaskNode.GetPointer()}); } else { m_Controls.widget_statistics->SetMaskNodes({}); } CalculateOrGetStatistics(); } } void QmitkImageStatisticsView::CalculateOrGetStatistics() { if (this->m_selectedPlanarFigure) { this->m_selectedPlanarFigure->RemoveObserver(this->m_PlanarFigureObserverTag); this->m_selectedPlanarFigure = nullptr; } m_Controls.groupBox_intensityProfile->setVisible(false); m_Controls.widget_statistics->setEnabled(m_selectedImageNode.IsNotNull()); if (m_selectedImageNode != nullptr) { auto image = dynamic_cast(m_selectedImageNode->GetData()); mitk::Image::Pointer mask = nullptr; mitk::PlanarFigure::Pointer maskPlanarFigure = nullptr; if (image->GetDimension() == 4) { m_Controls.sliderWidget_histogram->setVisible(true); unsigned int maxTimestep = image->GetTimeSteps(); m_Controls.sliderWidget_histogram->setMaximum(maxTimestep - 1); } else { m_Controls.sliderWidget_histogram->setVisible(false); } if (m_selectedMaskNode != nullptr) { mask = dynamic_cast(m_selectedMaskNode->GetData()); if (mask == nullptr) { maskPlanarFigure = dynamic_cast(m_selectedMaskNode->GetData()); } } mitk::ImageStatisticsContainer::ConstPointer imageStatistics; if (mask) { imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(this->GetDataStorage(), image, mask.GetPointer()); } else if (maskPlanarFigure) { m_selectedPlanarFigure = maskPlanarFigure; ITKCommandType::Pointer changeListener = ITKCommandType::New(); changeListener->SetCallbackFunction(this, &QmitkImageStatisticsView::CalculateOrGetStatistics); this->m_PlanarFigureObserverTag = m_selectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); if (!maskPlanarFigure->IsClosed()) { ComputeAndDisplayIntensityProfile(image, maskPlanarFigure); } imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics( this->GetDataStorage(), image, maskPlanarFigure.GetPointer()); } else { imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics(this->GetDataStorage(), image); } - - bool imageStatisticsOlderThanInputs = false; if (imageStatistics && (imageStatistics->GetMTime() < image->GetMTime() || (mask && imageStatistics->GetMTime() < mask->GetMTime()) || (maskPlanarFigure && imageStatistics->GetMTime() < maskPlanarFigure->GetMTime()))) { imageStatisticsOlderThanInputs = true; } if (imageStatistics) { // triggers recomputation when switched between images and the newest one has not 100 bins (default) auto calculatedBins = imageStatistics->GetStatisticsForTimeStep(0).m_Histogram.GetPointer()->Size(); - if (calculatedBins != 100) + if (calculatedBins != 100) { OnRequestHistogramUpdate(m_Controls.widget_histogram->GetBins()); } } - //statistics need to be computed - if (!imageStatistics || imageStatisticsOlderThanInputs || m_ForceRecompute) { + // statistics need to be computed + if (!imageStatistics || imageStatisticsOlderThanInputs || m_ForceRecompute) + { CalculateStatistics(image, mask.GetPointer(), maskPlanarFigure.GetPointer()); } // statistics already computed else { // Not an open planar figure: show histogram (intensity profile already shown) if (!(maskPlanarFigure && !maskPlanarFigure->IsClosed())) { if (imageStatistics->TimeStepExists(0)) { auto histogram = imageStatistics->GetStatisticsForTimeStep(0).m_Histogram.GetPointer(); std::string imageNodeName = m_selectedImageNode->GetName(); this->FillHistogramWidget({histogram}, {imageNodeName}); } } } } else { ResetGUI(); } m_ForceRecompute = false; } void QmitkImageStatisticsView::ComputeAndDisplayIntensityProfile(mitk::Image *image, - mitk::PlanarFigure::Pointer maskPlanarFigure) + mitk::PlanarFigure::Pointer maskPlanarFigure) { - auto intensityProfile = mitk::ComputeIntensityProfile(image, maskPlanarFigure); + mitk::Image::Pointer inputImage; + if (image->GetDimension() == 4) + { + m_Controls.sliderWidget_intensityProfile->setVisible(true); + unsigned int maxTimestep = image->GetTimeSteps(); + m_Controls.sliderWidget_intensityProfile->setMaximum(maxTimestep - 1); + //Intensity profile can only be calculated on 3D, so extract if 4D + mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); + int currentTimestep = static_cast(m_Controls.sliderWidget_intensityProfile->value()); + timeSelector->SetInput(image); + timeSelector->SetTimeNr(currentTimestep); + timeSelector->Update(); + + inputImage = timeSelector->GetOutput(); + } + else + { + m_Controls.sliderWidget_intensityProfile->setVisible(false); + inputImage = image; + } + + auto intensityProfile = mitk::ComputeIntensityProfile(inputImage, maskPlanarFigure); // Don't show histogram for intensity profiles m_Controls.groupBox_histogram->setVisible(false); m_Controls.groupBox_intensityProfile->setVisible(true); m_Controls.widget_intensityProfile->Reset(); m_Controls.widget_intensityProfile->SetIntensityProfile(intensityProfile.GetPointer(), "Intensity Profile of " + m_selectedImageNode->GetName()); } void QmitkImageStatisticsView::ResetGUI() { m_Controls.widget_statistics->Reset(); - m_Controls.widget_statistics->setEnabled(false); m_Controls.widget_histogram->Reset(); + m_Controls.widget_statistics->setEnabled(false); + m_Controls.widget_histogram->Reset(); m_Controls.widget_histogram->setEnabled(false); m_Controls.checkBox_ignoreZero->setEnabled(false); } void QmitkImageStatisticsView::ResetGUIDefault() { MITK_INFO << "reset GUI"; m_Controls.widget_histogram->ResetDefault(); m_Controls.checkBox_ignoreZero->setChecked(false); } void QmitkImageStatisticsView::OnStatisticsCalculationEnds() { mitk::StatusBar::GetInstance()->Clear(); - if (this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) + if (this->m_CalculationJob->GetStatisticsUpdateSuccessFlag()) { - auto statistic = m_CalculationThread->GetStatisticsData(); - auto image = m_CalculationThread->GetStatisticsImage(); + auto statistic = m_CalculationJob->GetStatisticsData(); + auto image = m_CalculationJob->GetStatisticsImage(); mitk::BaseData::ConstPointer mask = nullptr; auto statisticNonConst = statistic->Clone(); auto imageRule = mitk::StatisticsToImageRelationRule::New(); imageRule->Connect(statisticNonConst.GetPointer(), image); - if (m_CalculationThread->GetMaskImage()) + if (m_CalculationJob->GetMaskImage()) { auto maskRule = mitk::StatisticsToMaskRelationRule::New(); - mask = m_CalculationThread->GetMaskImage(); + mask = m_CalculationJob->GetMaskImage(); maskRule->Connect(statisticNonConst.GetPointer(), mask); } - else if (m_CalculationThread->GetPlanarFigure()) + else if (m_CalculationJob->GetPlanarFigure()) { auto planarFigureRule = mitk::StatisticsToMaskRelationRule::New(); - mask = m_CalculationThread->GetPlanarFigure(); + mask = m_CalculationJob->GetPlanarFigure(); planarFigureRule->Connect(statisticNonConst.GetPointer(), mask); } - auto imageStatistics = mitk::ImageStatisticsContainerManager::GetImageStatistics( - this->GetDataStorage(), image, mask); + auto imageStatistics = + mitk::ImageStatisticsContainerManager::GetImageStatistics(this->GetDataStorage(), image, mask); - //if statistics base data already exist: add to existing node + // if statistics base data already exist: add to existing node if (imageStatistics) { auto allDataNodes = this->GetDataStorage()->GetAll()->CastToSTLConstContainer(); for (auto node : allDataNodes) { auto nodeData = node->GetData(); - if (nodeData && nodeData->GetUID() ==imageStatistics->GetUID()) + if (nodeData && nodeData->GetUID() == imageStatistics->GetUID()) { node->SetData(statisticNonConst); } } } - //statistics base data does not exist: add new node + // statistics base data does not exist: add new node else { auto statisticsNodeName = m_selectedImageNode->GetName(); if (m_selectedMaskNode) { statisticsNodeName += "_" + m_selectedMaskNode->GetName(); } statisticsNodeName += "_statistics"; auto statisticsNode = mitk::CreateImageStatisticsNode(statisticNonConst, statisticsNodeName); this->GetDataStorage()->Add(statisticsNode); } if (!m_selectedPlanarFigure || m_selectedPlanarFigure->IsClosed()) { - this->FillHistogramWidget({m_CalculationThread->GetTimeStepHistogram()}, {m_selectedImageNode->GetName()}); + this->FillHistogramWidget({m_CalculationJob->GetTimeStepHistogram()}, {m_selectedImageNode->GetName()}); } } else { - mitk::StatusBar::GetInstance()->DisplayErrorText(m_CalculationThread->GetLastErrorMessage().c_str()); + mitk::StatusBar::GetInstance()->DisplayErrorText(m_CalculationJob->GetLastErrorMessage().c_str()); m_Controls.widget_histogram->setEnabled(false); } m_Controls.label_currentlyComputingStatistics->setVisible(false); } void QmitkImageStatisticsView::OnRequestHistogramUpdate(unsigned int nBins) { - m_CalculationThread->SetHistogramNBins(nBins); - m_CalculationThread->start(); + m_CalculationJob->SetHistogramNBins(nBins); + m_CalculationJob->start(); } void QmitkImageStatisticsView::CalculateStatistics(mitk::Image::ConstPointer image, - mitk::Image::ConstPointer mask, - mitk::PlanarFigure::ConstPointer maskPlanarFigure) + mitk::Image::ConstPointer mask, + mitk::PlanarFigure::ConstPointer maskPlanarFigure) { - this->m_StatisticsUpdatePending = true; - this->m_CalculationThread->Initialize(image, mask, maskPlanarFigure); + this->m_CalculationJob->Initialize(image, mask, maskPlanarFigure); try { // Compute statistics - this->m_CalculationThread->start(); + this->m_CalculationJob->start(); m_Controls.label_currentlyComputingStatistics->setVisible(true); } catch (const mitk::Exception &e) { mitk::StatusBar::GetInstance()->DisplayErrorText(e.GetDescription()); - this->m_StatisticsUpdatePending = false; m_Controls.label_currentlyComputingStatistics->setVisible(false); } catch (const std::runtime_error &e) { mitk::StatusBar::GetInstance()->DisplayErrorText(e.what()); - this->m_StatisticsUpdatePending = false; m_Controls.label_currentlyComputingStatistics->setVisible(false); } catch (const std::exception &e) { mitk::StatusBar::GetInstance()->DisplayErrorText(e.what()); - this->m_StatisticsUpdatePending = false; m_Controls.label_currentlyComputingStatistics->setVisible(false); } } void QmitkImageStatisticsView::OnSelectionChanged(berry::IWorkbenchPart::Pointer part, - const QList &nodes) + const QList &nodes) { Q_UNUSED(part); Q_UNUSED(nodes); } void QmitkImageStatisticsView::PrepareDataStorageComboBoxes() { auto isPlanarFigurePredicate = mitk::GetImageStatisticsPlanarFigurePredicate(); auto isMaskPredicate = mitk::GetImageStatisticsMaskPredicate(); auto isImagePredicate = mitk::GetImageStatisticsImagePredicate(); auto isMaskOrPlanarFigurePredicate = mitk::NodePredicateOr::New(isPlanarFigurePredicate, isMaskPredicate); m_Controls.imageSelector->SetDataStorage(GetDataStorage()); m_Controls.imageSelector->SetPredicate(isImagePredicate); m_Controls.maskImageSelector->SetDataStorage(GetDataStorage()); m_Controls.maskImageSelector->SetPredicate(isMaskOrPlanarFigurePredicate); m_Controls.maskImageSelector->SetZeroEntryText(""); } void QmitkImageStatisticsView::Activated() {} void QmitkImageStatisticsView::Deactivated() {} void QmitkImageStatisticsView::Visible() { connect(this->m_Controls.imageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsView::OnImageSelectorChanged); connect(this->m_Controls.maskImageSelector, static_cast(&QComboBox::currentIndexChanged), this, &QmitkImageStatisticsView::OnMaskSelectorChanged); OnImageSelectorChanged(); OnMaskSelectorChanged(); } void QmitkImageStatisticsView::Hidden() { m_Controls.imageSelector->disconnect(); m_Controls.maskImageSelector->disconnect(); } void QmitkImageStatisticsView::SetFocus() {} diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h index 6390f25e7f..ab26512747 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.h @@ -1,112 +1,112 @@ /*=================================================================== 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 QmitkImageStatisticsView_H__INCLUDED #define QmitkImageStatisticsView_H__INCLUDED #include "ui_QmitkImageStatisticsViewControls.h" // Qmitk includes #include #include #include #include #include #include /*! \brief QmitkImageStatisticsView is a bundle that allows statistics calculation from images. Three modes are supported: 1. Statistics of one image, 2. Statistics of an image and a segmentation, 3. Statistics of an image and a Planar Figure. The statistics calculation is realized in a separate thread to keep the gui accessible during calculation. \ingroup Plugins/org.mitk.gui.qt.measurementtoolbox */ class QmitkImageStatisticsView : public QmitkAbstractView, public mitk::ILifecycleAwarePart, public berry::IPartListener { Q_OBJECT public: using HistogramType = mitk::ImageStatisticsContainer::HistogramType; /*! \brief default constructor */ QmitkImageStatisticsView(QObject *parent = nullptr, const char *name = nullptr); /*! \brief default destructor */ virtual ~QmitkImageStatisticsView(); /*! \brief method for creating the widget containing the application controls, like sliders, buttons etc. */ virtual void CreateQtPartControl(QWidget *parent) override; /*! \brief method for creating the connections of main and control widget */ virtual void CreateConnections(); /*! \brief Is called from the selection mechanism once the data manager selection has changed*/ void OnSelectionChanged(berry::IWorkbenchPart::Pointer part, const QList &selectedNodes) override; void PrepareDataStorageComboBoxes(); static const std::string VIEW_ID; void FillHistogramWidget(const std::vector& histogram, const std::vector& dataLabels); QmitkChartWidget::ColorTheme GetColorTheme() const; protected: virtual void Activated() override; virtual void Deactivated() override; virtual void Visible() override; virtual void Hidden() override; virtual void SetFocus() override; /** \brief Is called right before the view closes (before the destructor) */ virtual void PartClosed(const berry::IWorkbenchPartReference::Pointer&) override; /** \brief Required for berry::IPartListener */ virtual Events::Types GetPartEventTypes() const override { return Events::CLOSED; } void OnImageSelectorChanged(); void OnMaskSelectorChanged(); void CalculateOrGetStatistics(); void ComputeAndDisplayIntensityProfile(mitk::Image * image, mitk::PlanarFigure::Pointer maskPlanarFigure); void ResetGUI(); void ResetGUIDefault(); void OnStatisticsCalculationEnds(); void OnRequestHistogramUpdate(unsigned int nBins); void OnCheckBoxIgnoreZeroStateChanged(int state); void OnSliderWidgetHistogramChanged(double value); + void OnSliderWidgetIntensityProfileChanged(double value); void CalculateStatistics(mitk::Image::ConstPointer image, mitk::Image::ConstPointer mask=nullptr, mitk::PlanarFigure::ConstPointer maskPlanarFigure = nullptr); // member variables Ui::QmitkImageStatisticsViewControls m_Controls; private: typedef itk::SimpleMemberCommand< QmitkImageStatisticsView > ITKCommandType; - QmitkImageStatisticsCalculationJob * m_CalculationThread = nullptr; - bool m_StatisticsUpdatePending=false; + QmitkImageStatisticsCalculationJob * m_CalculationJob = nullptr; mitk::DataNode::ConstPointer m_selectedImageNode = nullptr, m_selectedMaskNode = nullptr; mitk::PlanarFigure::Pointer m_selectedPlanarFigure=nullptr; long m_PlanarFigureObserverTag; bool m_ForceRecompute = false; }; #endif // QmitkImageStatisticsView_H__INCLUDED diff --git a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui index 82459f65dd..ca07213aba 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsViewControls.ui @@ -1,469 +1,472 @@ QmitkImageStatisticsViewControls true 0 0 419 1016 Form QLayout::SetMinimumSize 4 0 0 false 255 0 0 0 0 0 255 0 0 0 0 0 120 120 120 120 120 120 Calculating statistics... 0 0 0 0 0 0 0 0 120 120 120 Mask image: 0 0 0 0 0 0 0 0 120 120 120 Image: 0 0 false Ignore zero-valued voxels 0 200 Statistics 3 3 3 3 255 0 0 255 0 0 255 0 0 255 0 0 255 0 0 255 0 0 120 120 120 120 120 120 120 120 120 0 200 Histogram Qt::Vertical 20 40 0 200 Intensity Profile + + + Qt::Vertical 20 40 QmitkImageStatisticsWidget QWidget
QmitkImageStatisticsWidget.h
1 QmitkDataStorageComboBox QComboBox
QmitkDataStorageComboBox.h
 QmitkHistogramVisualizationWidget QWidget
QmitkHistogramVisualizationWidget.h
1 QmitkDataStorageComboBoxWithSelectNone QComboBox
QmitkDataStorageComboBoxWithSelectNone.h
 QmitkIntensityProfileVisualizationWidget QWidget
QmitkIntensityProfileVisualizationWidget.h
1 ctkSliderWidget QWidget
ctkSliderWidget.h
1