diff --git a/Modules/ImageStatistics/mitkIntensityProfile.cpp b/Modules/ImageStatistics/mitkIntensityProfile.cpp index 9199a3bc78..f899c6cd26 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.cpp +++ b/Modules/ImageStatistics/mitkIntensityProfile.cpp @@ -1,311 +1,337 @@ /*=================================================================== 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 Index3D& 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(); Geometry3D* imageGeometry = image->GetGeometry(); const PixelType pixelType = image->GetPixelType(); IntensityProfile::MeasurementVectorType measurementVector; itk::PolyLineParametricPath<3>::OffsetType offset; Point3D worldPoint; Index3D 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 AddPointToPath +class AddPolyLineElementToPath { public: - AddPointToPath(const Geometry2D* planarFigureGeometry, const Geometry3D* imageGeometry, itk::PolyLineParametricPath<3>::Pointer path) + AddPolyLineElementToPath(const Geometry2D* planarFigureGeometry, const Geometry3D* 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.Point, m_WorldPoint); m_ImageGeometry->WorldToIndex(m_WorldPoint, m_ContinuousIndexPoint); m_Vertex.CastFrom(m_ContinuousIndexPoint); m_Path->AddVertex(m_Vertex); } private: const Geometry2D* m_PlanarFigureGeometry; const Geometry3D* 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(Geometry3D* 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(), - AddPointToPath(planarFigure->GetGeometry2D(), imageGeometry, path)); + AddPolyLineElementToPath(planarFigure->GetGeometry2D(), imageGeometry, path)); + + return path; +} + +static void AddPointToPath(const Geometry3D* 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(Geometry3D* 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::MeasurementType max = -vcl_numeric_limits::max(); 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::MeasurementType 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::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; } diff --git a/Modules/ImageStatistics/mitkIntensityProfile.h b/Modules/ImageStatistics/mitkIntensityProfile.h index f4086acc9c..6c100074f2 100644 --- a/Modules/ImageStatistics/mitkIntensityProfile.h +++ b/Modules/ImageStatistics/mitkIntensityProfile.h @@ -1,115 +1,127 @@ /*=================================================================== 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 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); /** \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); /** \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