diff --git a/Modules/ImageStatistics/mitkIntensityProfile.cpp b/Modules/ImageStatistics/mitkIntensityProfile.cpp index 6b8f70f61e..eb93ca2bb7 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.cpp +++ b/Modules/ImageStatistics/mitkIntensityProfile.cpp @@ -1,337 +1,381 @@ /*=================================================================== 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 "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) { 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::Pointer intensityProfile) +IntensityProfile::InstanceIdentifier mitk::ComputeGlobalMaximum(IntensityProfile::Pointer intensityProfile, IntensityProfile::MeasurementType &max) { - IntensityProfile::MeasurementType max = -vcl_numeric_limits::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::Pointer intensityProfile) +IntensityProfile::InstanceIdentifier mitk::ComputeGlobalMinimum(IntensityProfile::Pointer intensityProfile, IntensityProfile::MeasurementType &min) { - IntensityProfile::MeasurementType min = vcl_numeric_limits::max(); + 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::Pointer intensityProfile, IntensityProfile::InstanceIdentifier radius) { - const IntensityProfile::MeasurementType min = intensityProfile->GetMeasurementVector(ComputeGlobalMinimum(intensityProfile))[0]; + //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::Pointer 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::Pointer intensityProfile, ImageStatisticsCalculator::Statistics &stats) +{ + typedef std::vector StatsVecType; + + StatsVecType statsVec = mitk::CreateVectorFromIntensityProfile( intensityProfile ); + + IntensityProfile::MeasurementType min; + IntensityProfile::MeasurementType max; + mitk::ComputeGlobalMinimum( intensityProfile, min ); + mitk::ComputeGlobalMaximum( intensityProfile, max ); + StatsVecType::size_type numSamples = 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 /= numSamples; + rms /= numSamples; + + double var = 0.0; + for ( StatsVecType::const_iterator it = statsVec.begin(); it != statsVec.end(); ++it ) + { + double diff = *it - mean; + var += diff*diff; + } + var /= ( numSamples - 1 ); + + double stdDev = sqrt( var ); + rms = sqrt( rms ); + + stats.SetMin( static_cast( min ) ); + stats.SetMax( static_cast( max ) ); + stats.SetN( numSamples ); + stats.SetMean( mean ); + stats.SetVariance( var ); + stats.SetRMS( rms ); +} diff --git a/Modules/ImageStatistics/mitkIntensityProfile.h b/Modules/ImageStatistics/mitkIntensityProfile.h index acb4c7ba07..c0ba4bb96d 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.h +++ b/Modules/ImageStatistics/mitkIntensityProfile.h @@ -1,127 +1,137 @@ /*=================================================================== 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. * * \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. * * \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::Pointer intensityProfile); + MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeGlobalMaximum(IntensityProfile::Pointer 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::Pointer intensityProfile); + MITKIMAGESTATISTICS_EXPORT IntensityProfile::InstanceIdentifier ComputeGlobalMinimum(IntensityProfile::Pointer 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::Pointer intensityProfile, ImageStatisticsCalculator::Statistics &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::Pointer 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::Pointer 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/QtWidgetsExt/include/QmitkHistogramJSWidget.h b/Modules/QtWidgetsExt/include/QmitkHistogramJSWidget.h index bd295b41ce..10bbc449a3 100644 --- a/Modules/QtWidgetsExt/include/QmitkHistogramJSWidget.h +++ b/Modules/QtWidgetsExt/include/QmitkHistogramJSWidget.h @@ -1,278 +1,286 @@ /*=================================================================== 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 QMITKHISTOGRAMJSWIDGET_H #define QMITKHISTOGRAMJSWIDGET_H #include #include #include #include "MitkQtWidgetsExtExports.h" #include #include "mitkImage.h" #include "mitkPlanarFigure.h" #include +#include #include /** * \brief Widget which shows a histogram using JavaScript. * * This class is a QWebView. It shows the histogram for a selected image * or segmentation. It also can display an intensity profile for * path elements, which lais over an image. */ class MITKQTWIDGETSEXT_EXPORT QmitkHistogramJSWidget : public QWebView { Q_OBJECT /** * \brief Measurement property. * * This property is used in JavaScript as member of the current object. * It holds a QList, containing the measurements of the current histogram. * @see GetMeasurement() */ Q_PROPERTY(QList measurement READ GetMeasurement) /** * \brief Frequency property. * * This property is used in JavaScript as member of the current object. * It holds a QList, containing the frequencies of the current histogram. * @see GetFrequency() */ Q_PROPERTY(QList frequency READ GetFrequency) /** * \brief Line graph property. * * This property is used in JavaScript as member of the current object. * It holds a boolean, which sais wether to use a line or not. * @see GetUseLineGraph() */ Q_PROPERTY(bool useLineGraph READ GetUseLineGraph) /** * @brief intensity profile property. * * This property is used in JavaScript as member of the current object. * It holds a boolean, which says whether to use an intensity profile or not. * @see GetIntensityProfile() */ Q_PROPERTY(bool intensityProfile READ GetIntensityProfile) public: typedef mitk::Image::HistogramType HistogramType; typedef mitk::Image::HistogramType::ConstIterator HistogramConstIteratorType; typedef itk::PolyLineParametricPath< 3 > ParametricPathType; typedef itk::ParametricPath< 3 >::Superclass PathType; typedef mitk::PlanarFigure::PolyLineType VertexContainerType; explicit QmitkHistogramJSWidget(QWidget *parent = nullptr); ~QmitkHistogramJSWidget(); /** * \brief Event which notifies a change of the widget size. * * Reimplemented from QWebView::resizeEvent(), * reloads the webframe */ void resizeEvent(QResizeEvent* resizeEvent) override; /** * \brief Calculates the histogram. * * This function removes all frequencies of 0 until the first bin and behind the last bin. * It writes the measurement and frequency, which are given from the HistogramType, into * m_Measurement and m_Frequency. * The SignalDataChanged is called, to update the information, which is displayed in the webframe. */ void ComputeHistogram(HistogramType* histogram); /** * \brief Calculates the intensityprofile. * * If an image and a pathelement are set, this function * calculates an intensity profile for a pathelement which lies over an image. * Sets m_IntensityProfile and m_UseLineGraph to true. * The SignalDataChanged is called, to update the information, which is displayed in the webframe. */ - void ComputeIntensityProfile(unsigned int timeStep = 0); + void ComputeIntensityProfile(unsigned int timeStep = 0, bool computeStatistics = false ); /** * \brief Clears the Histogram. * * This function clears the data and calls SignalDataChanged to update * the displayed information in the webframe. */ void ClearHistogram(); /** * \brief Getter for measurement. * * @return List of measurements. */ QList GetMeasurement(); /** * \brief Getter for frequency. * * @return List of frequencies. */ QList GetFrequency(); /** * \brief Getter for uselineGraph. * * @return True if a linegraph should be used. */ bool GetUseLineGraph(); /** * \brief Getter for intensity profile. * * @return True if current histogram is an intensityprofile */ bool GetIntensityProfile(); + mitk::ImageStatisticsCalculator::Statistics& GetStatistics() + { + return m_Statistics; + }; + /** * \brief Setter for reference image. * * @param image The corresponding image for an intensity profile. */ void SetImage(mitk::Image* image); /** * \brief Setter for planarFigure. * * @param planarFigure The pathelement for an intensity profile. */ void SetPlanarFigure(const mitk::PlanarFigure* planarFigure); private: /** * \brief List of frequencies. * * A QList which holds the frequencies of the current histogram * or holds the intesities of current intensity profile. */ QList m_Frequency; /** * \brief List of measurements. * * A QList which holds the measurements of the current histogram * or holds the distances of current intensity profile. */ QList m_Measurement; + mitk::ImageStatisticsCalculator::Statistics m_Statistics; + /** * \brief Reference image. * * Holds the image to calculate an intensity profile. */ mitk::Image::Pointer m_Image; /** * \brief Pathelement. * * Holds a not closed planar figure to calculate an intensity profile. */ mitk::PlanarFigure::ConstPointer m_PlanarFigure; bool m_UseLineGraph; bool m_IntensityProfile; /** * Holds the current histogram */ HistogramType::ConstPointer m_Histogram; /** * Path derived either form user-specified path or from PlanarFigure-generated * path */ PathType::ConstPointer m_DerivedPath; /** * Parametric path as generated from PlanarFigure */ ParametricPathType::Pointer m_ParametricPath; /** * \brief Clears data. * * Clears the QLists m_Measurement and m_Frequency */ void ClearData(); QmitkJSWebPage* m_Page; private slots: /** * \brief Adds an object to JavaScript. * * Adds an object of the widget to JavaScript. * By using this object JavaScript can react to the signals of the widget * and can access the QProperties as members of the object. */ void AddJSObject(); public slots: /** * \brief Slot for radiobutton m_barRadioButton. * * Sets m_UseLineGraph to false. * Calls signal GraphChanged to update the graph in the webframe. */ void OnBarRadioButtonSelected(); /** * \brief Slot for radiobutton m_lineRadioButton. * * Sets m_UseLineGraph to true. * Calls signal GraphChanged to update the graph in the webframe. */ void OnLineRadioButtonSelected(); signals: /** * \brief Signal data has changed. * * It has to be called when the data of the histogram or intensity profile has changed. */ void SignalDataChanged(); /** * \brief Signal graph has changed. * * It has to be called when the graph changed from barchart to linegraph. Vice versa. */ void SignalGraphChanged(); }; #endif diff --git a/Modules/QtWidgetsExt/src/QmitkHistogramJSWidget.cpp b/Modules/QtWidgetsExt/src/QmitkHistogramJSWidget.cpp index a03468b6f3..7d8382bff8 100644 --- a/Modules/QtWidgetsExt/src/QmitkHistogramJSWidget.cpp +++ b/Modules/QtWidgetsExt/src/QmitkHistogramJSWidget.cpp @@ -1,242 +1,247 @@ /*=================================================================== 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 "QmitkHistogramJSWidget.h" #include "mitkPixelTypeMultiplex.h" #include #include #include "mitkRenderingManager.h" #include "mitkBaseRenderer.h" #include "mitkImageTimeSelector.h" #include "mitkExtractSliceFilter.h" #include QmitkHistogramJSWidget::QmitkHistogramJSWidget(QWidget *parent) : QWebView(parent) { // set histogram type to barchart in first instance m_UseLineGraph = false; m_Page = new QmitkJSWebPage(this); setPage(m_Page); // set html from source connect(page()->mainFrame(), SIGNAL(javaScriptWindowObjectCleared()), this, SLOT(AddJSObject())); QUrl myUrl = QUrl("qrc:///QtWidgetsExt/Histogram.html"); setUrl(myUrl); // set Scrollbars to be always disabled page()->mainFrame()->setScrollBarPolicy(Qt::Horizontal, Qt::ScrollBarAlwaysOff); page()->mainFrame()->setScrollBarPolicy(Qt::Vertical, Qt::ScrollBarAlwaysOff); m_ParametricPath = ParametricPathType::New(); } QmitkHistogramJSWidget::~QmitkHistogramJSWidget() { } // adds an Object of Type QmitkHistogramJSWidget to the JavaScript, using QtWebkitBridge void QmitkHistogramJSWidget::AddJSObject() { page()->mainFrame()->addToJavaScriptWindowObject(QString("histogramData"), this); } // reloads WebView, everytime its size has been changed, so the size of the Histogram fits to the size of the widget void QmitkHistogramJSWidget::resizeEvent(QResizeEvent* resizeEvent) { QWebView::resizeEvent(resizeEvent); // workaround for Qt Bug: https://bugs.webkit.org/show_bug.cgi?id=75984 page()->mainFrame()->evaluateJavaScript("disconnectSignals()"); this->reload(); } // method to expose data to JavaScript by using properties void QmitkHistogramJSWidget::ComputeHistogram(HistogramType* histogram) { m_Histogram = histogram; HistogramConstIteratorType startIt = m_Histogram->End(); HistogramConstIteratorType endIt = m_Histogram->End(); HistogramConstIteratorType it = m_Histogram->Begin(); ClearData(); unsigned int i = 0; bool firstValue = false; // removes frequencies of 0, which are outside the first and last bin for (; it != m_Histogram->End(); ++it) { if (it.GetFrequency() > 0.0) { endIt = it; if (!firstValue) { firstValue = true; startIt = it; } } } ++endIt; // generating Lists of measurement and frequencies for (it = startIt ; it != endIt; ++it, ++i) { QVariant frequency = QVariant::fromValue(it.GetFrequency()); QVariant measurement = it.GetMeasurementVector()[0]; m_Frequency.insert(i, frequency); m_Measurement.insert(i, measurement); } m_IntensityProfile = false; this->SignalDataChanged(); } void QmitkHistogramJSWidget::ClearData() { m_Frequency.clear(); m_Measurement.clear(); } void QmitkHistogramJSWidget::ClearHistogram() { this->ClearData(); this->SignalDataChanged(); } QList QmitkHistogramJSWidget::GetFrequency() { return m_Frequency; } QList QmitkHistogramJSWidget::GetMeasurement() { return m_Measurement; } bool QmitkHistogramJSWidget::GetUseLineGraph() { return m_UseLineGraph; } void QmitkHistogramJSWidget::OnBarRadioButtonSelected() { if (m_UseLineGraph) { m_UseLineGraph = false; this->SignalGraphChanged(); } } void QmitkHistogramJSWidget::OnLineRadioButtonSelected() { if (!m_UseLineGraph) { m_UseLineGraph = true; this->SignalGraphChanged(); } } void QmitkHistogramJSWidget::SetImage(mitk::Image* image) { m_Image = image; } void QmitkHistogramJSWidget::SetPlanarFigure(const mitk::PlanarFigure* planarFigure) { m_PlanarFigure = planarFigure; } template void ReadPixel(mitk::PixelType, mitk::Image::Pointer image, itk::Index<3> indexPoint, double& value) { if (image->GetDimension() == 2) { mitk::ImagePixelReadAccessor readAccess(image, image->GetSliceData(0)); itk::Index<2> idx; idx[0] = indexPoint[0]; idx[1] = indexPoint[1]; value = readAccess.GetPixelByIndex(idx); } else if (image->GetDimension() == 3) { mitk::ImagePixelReadAccessor readAccess(image, image->GetVolumeData(0)); itk::Index<3> idx; idx[0] = indexPoint[0]; idx[1] = indexPoint[1]; idx[2] = indexPoint[2]; value = readAccess.GetPixelByIndex(idx); } else { //unhandled } } -void QmitkHistogramJSWidget::ComputeIntensityProfile(unsigned int timeStep) +void QmitkHistogramJSWidget::ComputeIntensityProfile(unsigned int timeStep, bool computeStatistics) { this->ClearData(); m_ParametricPath->Initialize(); if (m_PlanarFigure.IsNull()) { mitkThrow() << "PlanarFigure not set!"; } if (m_Image.IsNull()) { mitkThrow() << "Image not set!"; } mitk::Image::Pointer image; if (m_Image->GetDimension() == 4) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(m_Image); timeSelector->SetTimeNr(timeStep); timeSelector->Update(); image = timeSelector->GetOutput(); } else { image = m_Image; } mitk::IntensityProfile::Pointer intensityProfile = mitk::ComputeIntensityProfile(image, const_cast(m_PlanarFigure.GetPointer())); m_Frequency.clear(); m_Measurement.clear(); int i = -1; mitk::IntensityProfile::ConstIterator end = intensityProfile->End(); for (mitk::IntensityProfile::ConstIterator it = intensityProfile->Begin(); it != end; ++it) { m_Frequency.push_back(it.GetMeasurementVector()[0]); m_Measurement.push_back(++i); } + if ( computeStatistics ) + { + mitk::ComputeIntensityProfileStatistics( intensityProfile, m_Statistics ); + } + m_IntensityProfile = true; m_UseLineGraph = true; this->SignalDataChanged(); } bool QmitkHistogramJSWidget::GetIntensityProfile() { return m_IntensityProfile; } 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 2cb326cee8..69fc1370fb 100644 --- a/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp +++ b/Plugins/org.mitk.gui.qt.measurementtoolbox/src/internal/QmitkImageStatisticsView.cpp @@ -1,999 +1,1064 @@ /*=================================================================== 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" // Qt includes #include #include // berry includes #include // mitk includes #include "mitkNodePredicateDataType.h" #include "mitkPlanarFigureInteractor.h" // itk includes #include "itksys/SystemTools.hxx" #include #include const std::string QmitkImageStatisticsView::VIEW_ID = "org.mitk.views.imagestatistics"; const int QmitkImageStatisticsView::STAT_TABLE_BASE_HEIGHT = 180; QmitkImageStatisticsView::QmitkImageStatisticsView(QObject* /*parent*/, const char* /*name*/) : m_Controls( NULL ), m_TimeStepperAdapter( NULL ), m_SelectedImage( NULL ), m_SelectedImageMask( NULL ), m_SelectedPlanarFigure( NULL ), m_ImageObserverTag( -1 ), m_ImageMaskObserverTag( -1 ), m_PlanarFigureObserverTag( -1 ), m_TimeObserverTag( -1 ), m_CurrentStatisticsValid( false ), m_StatisticsUpdatePending( false ), m_DataNodeSelectionChanged ( false ), m_Visible(false) { this->m_CalculationThread = new QmitkImageStatisticsCalculationThread; } QmitkImageStatisticsView::~QmitkImageStatisticsView() { if ( m_SelectedImage != NULL ) m_SelectedImage->RemoveObserver( m_ImageObserverTag ); if ( m_SelectedImageMask != NULL ) m_SelectedImageMask->RemoveObserver( m_ImageMaskObserverTag ); if ( m_SelectedPlanarFigure != NULL ) m_SelectedPlanarFigure->RemoveObserver( m_PlanarFigureObserverTag ); while(this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } delete this->m_CalculationThread; } void QmitkImageStatisticsView::CreateQtPartControl(QWidget *parent) { if (m_Controls == NULL) { m_Controls = new Ui::QmitkImageStatisticsViewControls; m_Controls->setupUi(parent); CreateConnections(); m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); m_Controls->m_BinSizeFrame->setVisible(false); } } void QmitkImageStatisticsView::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(this->m_Controls->m_ButtonCopyHistogramToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardHistogramButtonClicked()) ); connect( (QObject*)(this->m_Controls->m_ButtonCopyStatisticsToClipboard), SIGNAL(clicked()),(QObject*) this, SLOT(OnClipboardStatisticsButtonClicked()) ); connect( (QObject*)(this->m_Controls->m_IgnoreZerosCheckbox), SIGNAL(clicked()),(QObject*) this, SLOT(OnIgnoreZerosCheckboxClicked()) ); connect( (QObject*) this->m_CalculationThread, SIGNAL(finished()),this, SLOT( OnThreadedStatisticsCalculationEnds()),Qt::QueuedConnection); connect( (QObject*) this, SIGNAL(StatisticsUpdate()),this, SLOT( RequestStatisticsUpdate()), Qt::QueuedConnection); connect( (QObject*) this->m_Controls->m_StatisticsTable, SIGNAL(cellDoubleClicked(int,int)),this, SLOT( JumpToCoordinates(int,int)) ); connect( (QObject*) (this->m_Controls->m_barRadioButton), SIGNAL(clicked()), (QObject*) (this->m_Controls->m_JSHistogram), SLOT(OnBarRadioButtonSelected())); connect( (QObject*) (this->m_Controls->m_lineRadioButton), SIGNAL(clicked()), (QObject*) (this->m_Controls->m_JSHistogram), SLOT(OnLineRadioButtonSelected())); connect( (QObject*) (this->m_Controls->m_HistogramBinSizeSpinbox), SIGNAL(editingFinished()), this, SLOT(OnHistogramBinSizeBoxValueChanged())); connect( (QObject*)(this->m_Controls->m_UseDefaultBinSizeBox), SIGNAL(clicked()),(QObject*) this, SLOT(OnDefaultBinSizeBoxChanged()) ); } } void QmitkImageStatisticsView::OnDefaultBinSizeBoxChanged() { if (m_CalculationThread!=NULL) m_Controls->m_HistogramBinSizeSpinbox->setValue(m_CalculationThread->GetHistogramBinSize()); if (m_Controls->m_UseDefaultBinSizeBox->isChecked()) m_Controls->m_BinSizeFrame->setVisible(false); else m_Controls->m_BinSizeFrame->setVisible(true); } void QmitkImageStatisticsView::PartClosed(const berry::IWorkbenchPartReference::Pointer& ) { } void QmitkImageStatisticsView::OnTimeChanged(const itk::EventObject& e) { if (this->m_SelectedDataNodes.isEmpty() || this->m_SelectedImage == NULL) return; const mitk::SliceNavigationController::GeometryTimeEvent* timeEvent = dynamic_cast(&e); assert(timeEvent != NULL); unsigned int timestep = timeEvent->GetPos(); if (this->m_SelectedImage->GetTimeSteps() > 1) { for (unsigned int x = 0; x < this->m_Controls->m_StatisticsTable->columnCount(); x++) { for (unsigned int y = 0; y < this->m_Controls->m_StatisticsTable->rowCount(); y++) { QTableWidgetItem* item = this->m_Controls->m_StatisticsTable->item(y, x); if (item == NULL) break; if (x == timestep) { item->setBackgroundColor(Qt::yellow); } else { if (y % 2 == 0) item->setBackground(this->m_Controls->m_StatisticsTable->palette().base()); else item->setBackground(this->m_Controls->m_StatisticsTable->palette().alternateBase()); } } } this->m_Controls->m_StatisticsTable->viewport()->update(); } if ((this->m_SelectedImage->GetTimeSteps() == 1 && timestep == 0) || this->m_SelectedImage->GetTimeSteps() > 1) { // display histogram for selected timestep this->m_Controls->m_JSHistogram->ClearHistogram(); QmitkImageStatisticsCalculationThread::HistogramType::Pointer histogram = this->m_CalculationThread->GetTimeStepHistogram(timestep); if (histogram.IsNotNull()) { - this->m_Controls->m_JSHistogram->ComputeHistogram(histogram.GetPointer()); + bool closedFigure = this->m_CalculationThread->GetStatisticsUpdateSuccessFlag(); + + if ( closedFigure ) + { + this->m_Controls->m_JSHistogram->ComputeHistogram(histogram.GetPointer()); + } + //this->m_Controls->m_JSHistogram->ComputeHistogram(histogram.GetPointer()); + /*else + { + m_Controls->m_JSHistogram->ComputeIntensityProfile(timestep, true); + }*/ + // this->m_Controls->m_JSHistogram->SignalGraphChanged(); // hacky way to make sure the protected SignalGraphChanged() is called if (this->m_Controls->m_JSHistogram->GetUseLineGraph()) { this->m_Controls->m_JSHistogram->OnBarRadioButtonSelected(); this->m_Controls->m_JSHistogram->OnLineRadioButtonSelected(); } else { this->m_Controls->m_JSHistogram->OnLineRadioButtonSelected(); this->m_Controls->m_JSHistogram->OnBarRadioButtonSelected(); } } } } void QmitkImageStatisticsView::JumpToCoordinates(int row ,int col) { if(m_SelectedDataNodes.isEmpty()) { MITK_WARN("QmitkImageStatisticsView") << "No data node selected for statistics calculation." ; return; } mitk::Point3D world; if (row==4 && !m_WorldMinList.empty()) world = m_WorldMinList[col]; else if (row==3 && !m_WorldMaxList.empty()) world = m_WorldMaxList[col]; else return; mitk::IRenderWindowPart* part = this->GetRenderWindowPart(); if (part) { part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("sagittal")->GetSliceNavigationController()->SelectSliceByPoint(world); part->GetQmitkRenderWindow("coronal")->GetSliceNavigationController()->SelectSliceByPoint(world); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), col); part->GetQmitkRenderWindow("axial")->GetSliceNavigationController()->SetGeometryTime(timeEvent); } } void QmitkImageStatisticsView::OnIgnoreZerosCheckboxClicked() { emit StatisticsUpdate(); } void QmitkImageStatisticsView::OnClipboardHistogramButtonClicked() { if ( m_CurrentStatisticsValid ) { const unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); typedef mitk::ImageStatisticsCalculator::HistogramType HistogramType; const HistogramType *histogram = this->m_CalculationThread->GetTimeStepHistogram(t).GetPointer(); QString clipboard( "Measurement \t Frequency\n" ); for ( HistogramType::ConstIterator it = histogram->Begin(); it != histogram->End(); ++it ) { if( m_Controls->m_HistogramBinSizeSpinbox->value() == 1.0) { clipboard = clipboard.append( "%L1 \t %L2\n" ) .arg( it.GetMeasurementVector()[0], 0, 'f', 0 ) .arg( it.GetFrequency() ); } else { clipboard = clipboard.append( "%L1 \t %L2\n" ) .arg( it.GetMeasurementVector()[0], 0, 'f', 2 ) .arg( it.GetFrequency() ); } } QApplication::clipboard()->setText( clipboard, QClipboard::Clipboard ); } else { QApplication::clipboard()->clear(); } } void QmitkImageStatisticsView::OnClipboardStatisticsButtonClicked() { QLocale tempLocal; QLocale::setDefault(QLocale(QLocale::English, QLocale::UnitedStates)); if ( this->m_CurrentStatisticsValid ) { const std::vector &statistics = this->m_CalculationThread->GetStatisticsData(); const unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> GetPos(); // Copy statistics to clipboard ("%Ln" will use the default locale for // number formatting) QString clipboard( "Mean \t StdDev \t RMS \t Max \t Min \t N \t V (mm³)\n" ); clipboard = clipboard.append("%L1 \t %L2 \t %L3 \t %L4 \t %L5 \t %L6 \t %L7") .arg(statistics[t].GetMean(), 0, 'f', 10) .arg(statistics[t].GetSigma(), 0, 'f', 10) .arg(statistics[t].GetRMS(), 0, 'f', 10) .arg(statistics[t].GetMax(), 0, 'f', 10) .arg(statistics[t].GetMin(), 0, 'f', 10) .arg(statistics[t].GetN()) .arg( m_Controls->m_StatisticsTable->item(6, 0)->data(Qt::DisplayRole).toDouble(), 0, 'f', 10); QApplication::clipboard()->setText( clipboard, QClipboard::Clipboard ); } else { QApplication::clipboard()->clear(); } QLocale::setDefault(tempLocal); } void QmitkImageStatisticsView::OnSelectionChanged( berry::IWorkbenchPart::Pointer /*part*/, const QList &selectedNodes ) { if (this->m_Visible) { this->SelectionChanged( selectedNodes ); } else { this->m_DataNodeSelectionChanged = true; } } void QmitkImageStatisticsView::SelectionChanged(const QList &selectedNodes) { if( this->m_StatisticsUpdatePending ) { this->m_DataNodeSelectionChanged = true; return; // not ready for new data now! } if (selectedNodes.size() == this->m_SelectedDataNodes.size()) { int i = 0; for (; i < selectedNodes.size(); ++i) { if (selectedNodes.at(i) != this->m_SelectedDataNodes.at(i)) { break; } } // node selection did not change if (i == selectedNodes.size()) return; } //reset the feature image and image mask field m_Controls->m_SelectedFeatureImageLabel->setText("None"); m_Controls->m_SelectedMaskLabel->setText("None"); this->ReinitData(); if (selectedNodes.isEmpty()) { m_Controls->m_JSHistogram->ClearHistogram(); m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); // m_Controls->m_HistogramBinSizeLabel->setEnabled(true); m_Controls->m_InfoLabel->setText(QString("")); // m_Controls->horizontalLayout_3->setEnabled(false); m_Controls->groupBox->setEnabled(false); m_Controls->groupBox_3->setEnabled(false); } else { // m_Controls->horizontalLayout_3->setEnabled(true); m_Controls->groupBox->setEnabled(true); m_Controls->groupBox_3->setEnabled(true); } if(selectedNodes.size() == 1 || selectedNodes.size() == 2) { bool isBinary = false; selectedNodes.value(0)->GetBoolProperty("binary",isBinary); if(isBinary) { m_Controls->m_JSHistogram->ClearHistogram(); m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); // m_Controls->m_HistogramBinSizeLabel->setEnabled(true); m_Controls->m_InfoLabel->setText(QString("")); } for (int i= 0; i< selectedNodes.size(); ++i) { this->m_SelectedDataNodes.push_back(selectedNodes.at(i)); } this->m_DataNodeSelectionChanged = false; this->m_Controls->m_ErrorMessageLabel->setText( "" ); this->m_Controls->m_ErrorMessageLabel->hide(); emit StatisticsUpdate(); } else { this->m_DataNodeSelectionChanged = false; } } void QmitkImageStatisticsView::ReinitData() { while( this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } if(this->m_SelectedImage != NULL) { this->m_SelectedImage->RemoveObserver( this->m_ImageObserverTag); this->m_SelectedImage = NULL; } if(this->m_SelectedImageMask != NULL) { this->m_SelectedImageMask->RemoveObserver( this->m_ImageMaskObserverTag); this->m_SelectedImageMask = NULL; } if(this->m_SelectedPlanarFigure != NULL) { this->m_SelectedPlanarFigure->RemoveObserver( this->m_PlanarFigureObserverTag); this->m_SelectedPlanarFigure = NULL; } this->m_SelectedDataNodes.clear(); this->m_StatisticsUpdatePending = false; m_Controls->m_ErrorMessageLabel->setText( "" ); m_Controls->m_ErrorMessageLabel->hide(); this->InvalidateStatisticsTableView(); m_Controls->m_JSHistogram->ClearHistogram(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); } void QmitkImageStatisticsView::OnThreadedStatisticsCalculationEnds() { std::stringstream message; message << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->hide(); this->WriteStatisticsToGUI(); } void QmitkImageStatisticsView::UpdateStatistics() { mitk::IRenderWindowPart* renderPart = this->GetRenderWindowPart(); if ( renderPart == NULL ) { this->m_StatisticsUpdatePending = false; return; } m_WorldMinList.clear(); m_WorldMaxList.clear(); // classify selected nodes mitk::NodePredicateDataType::Pointer imagePredicate = mitk::NodePredicateDataType::New("Image"); std::string maskName = std::string(); std::string maskType = std::string(); std::string featureImageName = std::string(); unsigned int maskDimension = 0; // reset data from last run ITKCommandType::Pointer changeListener = ITKCommandType::New(); changeListener->SetCallbackFunction( this, &QmitkImageStatisticsView::SelectedDataModified ); mitk::DataNode::Pointer planarFigureNode; for( int i= 0 ; i < this->m_SelectedDataNodes.size(); ++i) { mitk::PlanarFigure::Pointer planarFig = dynamic_cast(this->m_SelectedDataNodes.at(i)->GetData()); if( imagePredicate->CheckNode(this->m_SelectedDataNodes.at(i)) ) { bool isMask = false; this->m_SelectedDataNodes.at(i)->GetPropertyValue("binary", isMask); if( this->m_SelectedImageMask == NULL && isMask) { this->m_SelectedImageMask = dynamic_cast(this->m_SelectedDataNodes.at(i)->GetData()); this->m_ImageMaskObserverTag = this->m_SelectedImageMask->AddObserver(itk::ModifiedEvent(), changeListener); maskName = this->m_SelectedDataNodes.at(i)->GetName(); maskType = m_SelectedImageMask->GetNameOfClass(); maskDimension = 3; } else if( !isMask ) { if(this->m_SelectedImage == NULL) { this->m_SelectedImage = static_cast(this->m_SelectedDataNodes.at(i)->GetData()); this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener); } featureImageName = this->m_SelectedDataNodes.at(i)->GetName(); } } else if (planarFig.IsNotNull()) { if(this->m_SelectedPlanarFigure == NULL) { this->m_SelectedPlanarFigure = planarFig; this->m_PlanarFigureObserverTag = this->m_SelectedPlanarFigure->AddObserver(mitk::EndInteractionPlanarFigureEvent(), changeListener); maskName = this->m_SelectedDataNodes.at(i)->GetName(); maskType = this->m_SelectedPlanarFigure->GetNameOfClass(); maskDimension = 2; planarFigureNode = m_SelectedDataNodes.at(i); } } else { std::stringstream message; message << "" << "Invalid data node type!" << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); } } if(maskName == "") { maskName = "None"; maskType = ""; maskDimension = 0; } if(featureImageName == "") { featureImageName = "None"; } if (m_SelectedPlanarFigure != NULL && m_SelectedImage == NULL) { mitk::DataStorage::SetOfObjects::ConstPointer parentSet = this->GetDataStorage()->GetSources(planarFigureNode); for (int i=0; iSize(); i++) { mitk::DataNode::Pointer node = parentSet->ElementAt(i); if( imagePredicate->CheckNode(node) ) { bool isMask = false; node->GetPropertyValue("binary", isMask); if( !isMask ) { if(this->m_SelectedImage == NULL) { this->m_SelectedImage = static_cast(node->GetData()); this->m_ImageObserverTag = this->m_SelectedImage->AddObserver(itk::ModifiedEvent(), changeListener); } } } } } unsigned int timeStep = renderPart->GetTimeNavigationController()->GetTime()->GetPos(); if ( m_SelectedImage != NULL && m_SelectedImage->IsInitialized()) { // Check if a the selected image is a multi-channel image. If yes, statistics // cannot be calculated currently. if ( m_SelectedImage->GetPixelType().GetNumberOfComponents() > 1 ) { std::stringstream message; message << "Multi-component images not supported."; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); m_Controls->m_JSHistogram->ClearHistogram(); m_CurrentStatisticsValid = false; this->m_StatisticsUpdatePending = false; m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); // m_Controls->m_HistogramBinSizeLabel->setEnabled(true); m_Controls->m_InfoLabel->setText(QString("")); return; } std::stringstream maskLabel; maskLabel << maskName; if ( maskDimension > 0 ) { maskLabel << " [" << maskDimension << "D " << maskType << "]"; } m_Controls->m_SelectedMaskLabel->setText( maskLabel.str().c_str() ); m_Controls->m_SelectedFeatureImageLabel->setText(featureImageName.c_str()); // check time step validity if(m_SelectedImage->GetDimension() <= 3 && timeStep > m_SelectedImage->GetDimension(3)-1) { timeStep = m_SelectedImage->GetDimension(3)-1; } // Add the used mask time step to the mask label so the user knows which mask time step was used // if the image time step is bigger than the total number of mask time steps (see // ImageStatisticsCalculator::ExtractImageAndMask) if (m_SelectedImageMask != NULL) { unsigned int maskTimeStep = timeStep; if (maskTimeStep >= m_SelectedImageMask->GetTimeSteps()) { maskTimeStep = m_SelectedImageMask->GetTimeSteps() - 1; } m_Controls->m_SelectedMaskLabel->setText(m_Controls->m_SelectedMaskLabel->text() + QString(" (t=") + QString::number(maskTimeStep) + QString(")")); } //// initialize thread and trigger it this->m_CalculationThread->SetIgnoreZeroValueVoxel( m_Controls->m_IgnoreZerosCheckbox->isChecked() ); this->m_CalculationThread->Initialize( m_SelectedImage, m_SelectedImageMask, m_SelectedPlanarFigure ); this->m_CalculationThread->SetTimeStep( timeStep ); this->m_CalculationThread->SetHistogramBinSize(m_Controls->m_HistogramBinSizeSpinbox->value()); std::stringstream message; message << "Calculating statistics..."; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); try { // Compute statistics this->m_CalculationThread->SetUseDefaultBinSize(m_Controls->m_UseDefaultBinSizeBox->isChecked()); this->m_CalculationThread->start(); } catch ( const mitk::Exception& e) { std::stringstream message; message << "" << e.GetDescription() << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } catch ( const std::runtime_error &e ) { // In case of exception, print error message on GUI std::stringstream message; message << "" << e.what() << ""; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } catch ( const std::exception &e ) { MITK_ERROR << "Caught exception: " << e.what(); // In case of exception, print error message on GUI std::stringstream message; message << "Error! Unequal Dimensions of Image and Segmentation. No recompute possible "; m_Controls->m_ErrorMessageLabel->setText( message.str().c_str() ); m_Controls->m_ErrorMessageLabel->show(); this->m_StatisticsUpdatePending = false; } } else { this->m_StatisticsUpdatePending = false; } } void QmitkImageStatisticsView::SelectedDataModified() { if( !m_StatisticsUpdatePending ) { emit StatisticsUpdate(); } } void QmitkImageStatisticsView::NodeRemoved(const mitk::DataNode *node) { while(this->m_CalculationThread->isRunning()) // wait until thread has finished { itksys::SystemTools::Delay(100); } if (node->GetData() == m_SelectedImage) { m_SelectedImage = NULL; } } void QmitkImageStatisticsView::RequestStatisticsUpdate() { if ( !m_StatisticsUpdatePending ) { if(this->m_DataNodeSelectionChanged) { this->SelectionChanged(this->GetCurrentSelection()); } else { this->m_StatisticsUpdatePending = true; this->UpdateStatistics(); } } if (this->GetRenderWindowPart()) this->GetRenderWindowPart()->RequestUpdate(); } void QmitkImageStatisticsView::OnHistogramBinSizeBoxValueChanged() { this->UpdateStatistics(); } void QmitkImageStatisticsView::WriteStatisticsToGUI() { m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); // m_Controls->m_HistogramBinSizeLabel->setEnabled(true); m_Controls->m_InfoLabel->setText(QString("")); if(m_DataNodeSelectionChanged) { this->m_StatisticsUpdatePending = false; this->RequestStatisticsUpdate(); return; // stop visualization of results and calculate statistics of new selection } if ( this->m_CalculationThread->GetStatisticsUpdateSuccessFlag()) { if ( this->m_CalculationThread->GetStatisticsChangedFlag() ) { // Do not show any error messages m_Controls->m_ErrorMessageLabel->hide(); m_CurrentStatisticsValid = true; } if (m_Controls->m_barRadioButton->isChecked()) { m_Controls->m_JSHistogram->OnBarRadioButtonSelected(); } m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); m_Controls->m_HistogramBinSizeSpinbox->setValue( this->m_CalculationThread->GetHistogramBinSize() ); //m_Controls->m_JSHistogram->ComputeHistogram( this->m_CalculationThread->GetTimeStepHistogram(this->m_CalculationThread->GetTimeStep()).GetPointer() ); this->FillStatisticsTableView( this->m_CalculationThread->GetStatisticsData(), this->m_CalculationThread->GetStatisticsImage()); } else { m_Controls->m_SelectedMaskLabel->setText( "None" ); m_Controls->m_ErrorMessageLabel->setText( m_CalculationThread->GetLastErrorMessage().c_str() ); m_Controls->m_ErrorMessageLabel->show(); // Clear statistics and histogram this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); //m_Controls->m_JSHistogram->clearHistogram(); m_CurrentStatisticsValid = false; // If a (non-closed) PlanarFigure is selected, display a line profile widget if ( m_SelectedPlanarFigure != NULL ) { // Check if the (closed) planar figure is out of bounds and so no image mask could be calculated--> Intensity Profile can not be calculated bool outOfBounds = false; if ( m_SelectedPlanarFigure->IsClosed() && m_SelectedImageMask == NULL) { outOfBounds = true; std::stringstream message; message << "Planar figure is on a rotated image plane or outside the image bounds."; m_Controls->m_InfoLabel->setText(message.str().c_str()); } // check whether PlanarFigure is initialized const mitk::PlaneGeometry *planarFigurePlaneGeometry = m_SelectedPlanarFigure->GetPlaneGeometry(); if ( planarFigurePlaneGeometry == NULL || outOfBounds) { // Clear statistics, histogram, and GUI this->InvalidateStatisticsTableView(); m_Controls->m_StatisticsWidgetStack->setCurrentIndex( 0 ); m_Controls->m_JSHistogram->ClearHistogram(); m_CurrentStatisticsValid = false; m_Controls->m_ErrorMessageLabel->hide(); m_Controls->m_SelectedMaskLabel->setText( "None" ); this->m_StatisticsUpdatePending = false; m_Controls->m_lineRadioButton->setEnabled(true); m_Controls->m_barRadioButton->setEnabled(true); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(true); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(true); // m_Controls->m_HistogramBinSizeLabel->setEnabled(true); if (!outOfBounds) m_Controls->m_InfoLabel->setText(QString("")); return; } unsigned int timeStep = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()->GetPos(); m_Controls->m_JSHistogram->SetImage(this->m_CalculationThread->GetStatisticsImage()); m_Controls->m_JSHistogram->SetPlanarFigure(m_SelectedPlanarFigure); - m_Controls->m_JSHistogram->ComputeIntensityProfile(timeStep); + m_Controls->m_JSHistogram->ComputeIntensityProfile(timeStep, true); + //m_Controls->m_JSHistogram->ComputeIntensityProfile(timeStep); m_Controls->m_lineRadioButton->setEnabled(false); m_Controls->m_barRadioButton->setEnabled(false); m_Controls->m_HistogramBinSizeSpinbox->setEnabled(false); m_Controls->m_HistogramBinSizeCaptionLabel->setEnabled(false); // m_Controls->m_HistogramBinSizeLabel->setEnabled(false); + + this->FillLinearProfileStatisticsTableView( this->m_CalculationThread->GetStatisticsImage() ); + std::stringstream message; message << "Only linegraph available for an intensity profile!"; m_Controls->m_InfoLabel->setText(message.str().c_str()); } } this->m_StatisticsUpdatePending = false; } void QmitkImageStatisticsView::FillStatisticsTableView( const std::vector &s, const mitk::Image *image ) { this->m_Controls->m_StatisticsTable->setColumnCount(image->GetTimeSteps()); this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(image->GetTimeSteps() > 1); int decimals = 2; mitk::PixelType doublePix = mitk::MakeScalarPixelType< double >(); mitk::PixelType floatPix = mitk::MakeScalarPixelType< float >(); if (image->GetPixelType()==doublePix || image->GetPixelType()==floatPix) { decimals = 5; } for (unsigned int t = 0; t < image->GetTimeSteps(); t++) { this->m_Controls->m_StatisticsTable->setHorizontalHeaderItem(t, new QTableWidgetItem(QString::number(t))); if (s[t].GetMaxIndex().size()==3) { mitk::Point3D index, max, min; index[0] = s[t].GetMaxIndex()[0]; index[1] = s[t].GetMaxIndex()[1]; index[2] = s[t].GetMaxIndex()[2]; m_SelectedImage->GetGeometry()->IndexToWorld(index, max); this->m_WorldMaxList.push_back(max); index[0] = s[t].GetMinIndex()[0]; index[1] = s[t].GetMinIndex()[1]; index[2] = s[t].GetMinIndex()[2]; m_SelectedImage->GetGeometry()->IndexToWorld(index, min); this->m_WorldMinList.push_back(min); } this->m_Controls->m_StatisticsTable->setItem( 0, t, new QTableWidgetItem( QString("%1").arg(s[t].GetMean(), 0, 'f', decimals) ) ); this->m_Controls->m_StatisticsTable->setItem( 1, t, new QTableWidgetItem( QString("%1").arg(s[t].GetSigma(), 0, 'f', decimals) ) ); this->m_Controls->m_StatisticsTable->setItem( 2, t, new QTableWidgetItem( QString("%1").arg(s[t].GetRMS(), 0, 'f', decimals) ) ); QString max; max.append(QString("%1").arg(s[t].GetMax(), 0, 'f', decimals)); max += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 3, t, new QTableWidgetItem( max ) ); QString min; min.append(QString("%1").arg(s[t].GetMin(), 0, 'f', decimals)); min += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 4, t, new QTableWidgetItem( min ) ); this->m_Controls->m_StatisticsTable->setItem( 5, t, new QTableWidgetItem( QString("%1").arg(s[t].GetN()) ) ); const mitk::BaseGeometry *geometry = image->GetGeometry(); if ( geometry != NULL ) { const mitk::Vector3D &spacing = image->GetGeometry()->GetSpacing(); double volume = spacing[0] * spacing[1] * spacing[2] * (double) s[t].GetN(); this->m_Controls->m_StatisticsTable->setItem( 6, t, new QTableWidgetItem( QString("%1").arg(volume, 0, 'f', decimals) ) ); } else { this->m_Controls->m_StatisticsTable->setItem( 6, t, new QTableWidgetItem( "NA" ) ); } } this->m_Controls->m_StatisticsTable->resizeColumnsToContents(); int height = STAT_TABLE_BASE_HEIGHT; if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height(); if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible()) height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height(); this->m_Controls->m_StatisticsTable->setMinimumHeight(height); // make sure the current timestep's column is highlighted (and the correct histogram is displayed) unsigned int t = this->GetRenderWindowPart()->GetTimeNavigationController()->GetTime()-> GetPos(); mitk::SliceNavigationController::GeometryTimeEvent timeEvent(this->m_SelectedImage->GetTimeGeometry(), t); this->OnTimeChanged(timeEvent); t = std::min(image->GetTimeSteps() - 1, t); // See bug 18340 /*QString hotspotMean; hotspotMean.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMean(), 0, 'f', decimals)); hotspotMean += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 7, t, new QTableWidgetItem( hotspotMean ) ); QString hotspotMax; hotspotMax.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMax(), 0, 'f', decimals)); hotspotMax += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 8, t, new QTableWidgetItem( hotspotMax ) ); QString hotspotMin; hotspotMin.append(QString("%1").arg(s[t].GetHotspotStatistics().GetMin(), 0, 'f', decimals)); hotspotMin += " ("; for (int i=0; im_Controls->m_StatisticsTable->setItem( 9, t, new QTableWidgetItem( hotspotMin ) );*/ } +void QmitkImageStatisticsView::FillLinearProfileStatisticsTableView( const mitk::Image *image ) +{ + this->m_Controls->m_StatisticsTable->setColumnCount(1); + this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false); + + int decimals = 2; + + mitk::PixelType doublePix = mitk::MakeScalarPixelType< double >(); + mitk::PixelType floatPix = mitk::MakeScalarPixelType< float >(); + if (image->GetPixelType()==doublePix || image->GetPixelType()==floatPix) + { + decimals = 5; + } + + mitk::ImageStatisticsCalculator::Statistics &stats = m_Controls->m_JSHistogram->GetStatistics(); + + this->m_Controls->m_StatisticsTable->setItem( 0, 0, new QTableWidgetItem( + QString("%1").arg(stats.GetMean(), 0, 'f', decimals) ) ); + + double stdDev = sqrt( stats.GetVariance() ); + this->m_Controls->m_StatisticsTable->setItem( 1, 0, new QTableWidgetItem( QString("%1").arg( stdDev, 0, 'f', decimals) ) ); + + double rms = stats.GetRMS(); + this->m_Controls->m_StatisticsTable->setItem( 2, 0, new QTableWidgetItem( + QString("%1").arg( rms, 0, 'f', decimals) ) ); + + QString max; max.append(QString("%1").arg(stats.GetMax(), 0, 'f', decimals)); + + this->m_Controls->m_StatisticsTable->setItem( 3, 0, new QTableWidgetItem( max ) ); + + QString min; min.append(QString("%1").arg(stats.GetMin(), 0, 'f', decimals)); + + this->m_Controls->m_StatisticsTable->setItem( 4, 0, new QTableWidgetItem( min ) ); + + this->m_Controls->m_StatisticsTable->setItem( 5, 0, new QTableWidgetItem( QString("%1").arg(stats.GetN()) ) ); + + this->m_Controls->m_StatisticsTable->setItem( 6, 0, new QTableWidgetItem( "NA" ) ); + + this->m_Controls->m_StatisticsTable->resizeColumnsToContents(); + int height = STAT_TABLE_BASE_HEIGHT; + + if (this->m_Controls->m_StatisticsTable->horizontalHeader()->isVisible()) + height += this->m_Controls->m_StatisticsTable->horizontalHeader()->height(); + + if (this->m_Controls->m_StatisticsTable->horizontalScrollBar()->isVisible()) + height += this->m_Controls->m_StatisticsTable->horizontalScrollBar()->height(); + + this->m_Controls->m_StatisticsTable->setMinimumHeight(height); + } + void QmitkImageStatisticsView::InvalidateStatisticsTableView() { this->m_Controls->m_StatisticsTable->horizontalHeader()->setVisible(false); this->m_Controls->m_StatisticsTable->setColumnCount(1); for ( unsigned int i = 0; i < this->m_Controls->m_StatisticsTable->rowCount(); ++i ) { { this->m_Controls->m_StatisticsTable->setItem( i, 0, new QTableWidgetItem( "NA" ) ); } } this->m_Controls->m_StatisticsTable->setMinimumHeight(STAT_TABLE_BASE_HEIGHT); } void QmitkImageStatisticsView::Activated() { } void QmitkImageStatisticsView::Deactivated() { } void QmitkImageStatisticsView::Visible() { m_Visible = true; mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { itk::ReceptorMemberCommand::Pointer cmdTimeEvent = itk::ReceptorMemberCommand::New(); cmdTimeEvent->SetCallbackFunction(this, &QmitkImageStatisticsView::OnTimeChanged); // It is sufficient to add the observer to the axial render window since the GeometryTimeEvent // is always triggered by all views. m_TimeObserverTag = renderWindow->GetQmitkRenderWindow("axial")-> GetSliceNavigationController()-> AddObserver(mitk::SliceNavigationController::GeometryTimeEvent(NULL, 0), cmdTimeEvent); } if (m_DataNodeSelectionChanged) { if (this->IsCurrentSelectionValid()) { this->SelectionChanged(this->GetCurrentSelection()); } else { this->SelectionChanged(this->GetDataManagerSelection()); } m_DataNodeSelectionChanged = false; } } void QmitkImageStatisticsView::Hidden() { m_Visible = false; // The slice navigation controller observer is removed here instead of in the destructor. // If it was called in the destructor, the application would freeze because the view's // destructor gets called after the render windows have been destructed. if ( m_TimeObserverTag != NULL ) { mitk::IRenderWindowPart* renderWindow = GetRenderWindowPart(); if (renderWindow) { renderWindow->GetQmitkRenderWindow("axial")->GetSliceNavigationController()-> RemoveObserver( m_TimeObserverTag ); } m_TimeObserverTag = NULL; } } void QmitkImageStatisticsView::SetFocus() { }