diff --git a/Modules/PhotoacousticsLib/include/mitkPAInSilicoTissueVolume.h b/Modules/PhotoacousticsLib/include/mitkPAInSilicoTissueVolume.h index 13de46dbf2..7e13506e87 100644 --- a/Modules/PhotoacousticsLib/include/mitkPAInSilicoTissueVolume.h +++ b/Modules/PhotoacousticsLib/include/mitkPAInSilicoTissueVolume.h @@ -1,140 +1,152 @@ /*=================================================================== 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 MITKPHOTOACOUSTICVOLUME_H #define MITKPHOTOACOUSTICVOLUME_H #include #include #include #include #include //Includes for smart pointer usage #include "mitkCommon.h" #include "itkLightObject.h" namespace mitk { namespace pa { class MITKPHOTOACOUSTICSLIB_EXPORT InSilicoTissueVolume : public itk::LightObject { public: mitkClassMacroItkParent(InSilicoTissueVolume, itk::LightObject) mitkNewMacro1Param(Self, TissueGeneratorParameters::Pointer) enum SegmentationType { AIR = -1, BACKGROUND = 0, VESSEL = 1, FAT = 2, SKIN = 3 }; /** * @brief ConvertToMitkImage * @return a pointer to an mitk image containing this volume. */ mitk::Image::Pointer ConvertToMitkImage(); /** * @brief SetVolumeValues sets the values for aborption, scattering and anisotropy at the specified voxel location. * * @param x * @param y * @param z * @param absorption * @param scattering * @param anisotropy * @param segmentType */ - void SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy, SegmentationType segmentType = SegmentationType::BACKGROUND); + void SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy, SegmentationType segmentType); + + /** + * @brief SetVolumeValues sets the values for aborption, scattering and anisotropy at the specified voxel location. + * + * @param x + * @param y + * @param z + * @param absorption + * @param scattering + * @param anisotropy + */ + void SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy); /** * @brief IsInsideVolume * * @param x * @param y * @param z * @return true if the voxel location is inside the volume */ bool IsInsideVolume(int x, int y, int z); /** * @brief AddDoubleProperty adds a persistent property to the volume, which will be exported to the mitk image. * * @param label * @param value */ void AddDoubleProperty(std::string label, double value); /** * @brief AddIntProperty adds a persistent property to the volume, which will be exported to the mitk image. * * @param label * @param value */ void AddIntProperty(std::string label, int value); Volume::Pointer GetAbsorptionVolume(); Volume::Pointer GetScatteringVolume(); Volume::Pointer GetAnisotropyVolume(); Volume::Pointer GetSegmentationVolume(); void FinalizeVolume(); itkGetMacro(TissueParameters, TissueGeneratorParameters::Pointer); itkGetMacro(TDim, unsigned int); static InSilicoTissueVolume::Pointer New(mitk::pa::Volume::Pointer absorptionVolume, Volume::Pointer scatteringVolume, Volume::Pointer anisotropyVolume, Volume::Pointer segmentationVolume, TissueGeneratorParameters::Pointer tissueParameters, mitk::PropertyList::Pointer propertyList); protected: InSilicoTissueVolume(TissueGeneratorParameters::Pointer parameters); InSilicoTissueVolume(Volume::Pointer absorptionVolume, Volume::Pointer scatteringVolume, Volume::Pointer anisotropyVolume, Volume::Pointer segmentationVolume, TissueGeneratorParameters::Pointer tissueParameters, mitk::PropertyList::Pointer propertyList); virtual ~InSilicoTissueVolume(); mitk::pa::Volume::Pointer m_AbsorptionVolume; mitk::pa::Volume::Pointer m_ScatteringVolume; mitk::pa::Volume::Pointer m_AnisotropyVolume; mitk::pa::Volume::Pointer m_SegmentationVolume; TissueGeneratorParameters::Pointer m_TissueParameters; unsigned int m_TDim; void RandomizeTissueCoefficients(long rngSeed, bool useRngSeed, double percentage); mitk::PropertyList::Pointer m_PropertyList; private: void FillZLayer(int x, int y, double startIdx, double endIdx, double absorption, double scattering, double anisotropy, SegmentationType segmentationType); void AddSkinAndAirLayers(); void UpdatePropertyList(); }; } } #endif // MITKPHOTOACOUSTICVOLUME_H diff --git a/Modules/PhotoacousticsLib/include/mitkPATissueGeneratorParameters.h b/Modules/PhotoacousticsLib/include/mitkPATissueGeneratorParameters.h index 63863dc3a1..6be09cc42f 100644 --- a/Modules/PhotoacousticsLib/include/mitkPATissueGeneratorParameters.h +++ b/Modules/PhotoacousticsLib/include/mitkPATissueGeneratorParameters.h @@ -1,214 +1,211 @@ /*=================================================================== 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 MITKPHOTOACOUSTICTISSUEGENERATORPARAMETERS_H #define MITKPHOTOACOUSTICTISSUEGENERATORPARAMETERS_H #include #include //Includes for smart pointer usage #include "mitkCommon.h" #include "itkLightObject.h" namespace mitk { namespace pa { class MITKPHOTOACOUSTICSLIB_EXPORT TissueGeneratorParameters : public itk::Object { public: mitkClassMacroItkParent(TissueGeneratorParameters, itk::Object) itkFactorylessNewMacro(Self) /** * Callback function definition of a VesselMeanderStrategy */ typedef void (VesselMeanderStrategy::*CalculateNewVesselPositionCallback) (Vector::Pointer, Vector::Pointer, double, std::mt19937*); itkGetMacro(XDim, int) itkGetMacro(YDim, int) itkGetMacro(ZDim, int) itkGetMacro(VoxelSpacingInCentimeters, double) - itkGetMacro(VolumeSmoothingSigma, double) - itkGetMacro(DoVolumeSmoothing, bool) + itkGetMacro(DoPartialVolume, bool) itkGetMacro(UseRngSeed, bool) itkGetMacro(RngSeed, long) itkGetMacro(RandomizePhysicalProperties, bool) itkGetMacro(RandomizePhysicalPropertiesPercentage, double) itkGetMacro(BackgroundAbsorption, double) itkGetMacro(BackgroundScattering, double) itkGetMacro(BackgroundAnisotropy, double) itkGetMacro(AirAbsorption, double) itkGetMacro(AirScattering, double) itkGetMacro(AirAnisotropy, double) itkGetMacro(AirThicknessInMillimeters, double) itkGetMacro(SkinAbsorption, double) itkGetMacro(SkinScattering, double) itkGetMacro(SkinAnisotropy, double) itkGetMacro(SkinThicknessInMillimeters, double) itkGetMacro(CalculateNewVesselPositionCallback, CalculateNewVesselPositionCallback) itkGetMacro(MinNumberOfVessels, int) itkGetMacro(MaxNumberOfVessels, int) itkGetMacro(MinVesselBending, double) itkGetMacro(MaxVesselBending, double) itkGetMacro(MinVesselAbsorption, double) itkGetMacro(MaxVesselAbsorption, double) itkGetMacro(MinVesselRadiusInMillimeters, double) itkGetMacro(MaxVesselRadiusInMillimeters, double) itkGetMacro(VesselBifurcationFrequency, int) itkGetMacro(MinVesselScattering, double) itkGetMacro(MaxVesselScattering, double) itkGetMacro(MinVesselAnisotropy, double) itkGetMacro(MaxVesselAnisotropy, double) itkGetMacro(MinVesselZOrigin, double) itkGetMacro(MaxVesselZOrigin, double) itkGetMacro(MCflag, double) itkGetMacro(MCLaunchflag, double) itkGetMacro(MCBoundaryflag, double) itkGetMacro(MCLaunchPointX, double) itkGetMacro(MCLaunchPointY, double) itkGetMacro(MCLaunchPointZ, double) itkGetMacro(MCFocusPointX, double) itkGetMacro(MCFocusPointY, double) itkGetMacro(MCFocusPointZ, double) itkGetMacro(MCTrajectoryVectorX, double) itkGetMacro(MCTrajectoryVectorY, double) itkGetMacro(MCTrajectoryVectorZ, double) itkGetMacro(MCRadius, double) itkGetMacro(MCWaist, double) itkSetMacro(XDim, int) itkSetMacro(YDim, int) itkSetMacro(ZDim, int) itkSetMacro(VoxelSpacingInCentimeters, double) - itkSetMacro(VolumeSmoothingSigma, double) - itkSetMacro(DoVolumeSmoothing, bool) + itkSetMacro(DoPartialVolume, bool) itkSetMacro(UseRngSeed, bool) itkSetMacro(RngSeed, long) itkSetMacro(RandomizePhysicalProperties, bool) itkSetMacro(RandomizePhysicalPropertiesPercentage, double) itkSetMacro(BackgroundAbsorption, double) itkSetMacro(BackgroundScattering, double) itkSetMacro(BackgroundAnisotropy, double) itkSetMacro(AirAbsorption, double) itkSetMacro(AirScattering, double) itkSetMacro(AirAnisotropy, double) itkSetMacro(AirThicknessInMillimeters, double) itkSetMacro(SkinAbsorption, double) itkSetMacro(SkinScattering, double) itkSetMacro(SkinAnisotropy, double) itkSetMacro(SkinThicknessInMillimeters, double) itkSetMacro(CalculateNewVesselPositionCallback, CalculateNewVesselPositionCallback) itkSetMacro(MinNumberOfVessels, int) itkSetMacro(MaxNumberOfVessels, int) itkSetMacro(MinVesselBending, double) itkSetMacro(MaxVesselBending, double) itkSetMacro(MinVesselAbsorption, double) itkSetMacro(MaxVesselAbsorption, double) itkSetMacro(MinVesselRadiusInMillimeters, double) itkSetMacro(MaxVesselRadiusInMillimeters, double) itkSetMacro(VesselBifurcationFrequency, int) itkSetMacro(MinVesselScattering, double) itkSetMacro(MaxVesselScattering, double) itkSetMacro(MinVesselAnisotropy, double) itkSetMacro(MaxVesselAnisotropy, double) itkSetMacro(MinVesselZOrigin, double) itkSetMacro(MaxVesselZOrigin, double) itkSetMacro(MCflag, double) itkSetMacro(MCLaunchflag, double) itkSetMacro(MCBoundaryflag, double) itkSetMacro(MCLaunchPointX, double) itkSetMacro(MCLaunchPointY, double) itkSetMacro(MCLaunchPointZ, double) itkSetMacro(MCFocusPointX, double) itkSetMacro(MCFocusPointY, double) itkSetMacro(MCFocusPointZ, double) itkSetMacro(MCTrajectoryVectorX, double) itkSetMacro(MCTrajectoryVectorY, double) itkSetMacro(MCTrajectoryVectorZ, double) itkSetMacro(MCRadius, double) itkSetMacro(MCWaist, double) protected: TissueGeneratorParameters(); virtual ~TissueGeneratorParameters(); private: int m_XDim; int m_YDim; int m_ZDim; double m_VoxelSpacingInCentimeters; - double m_VolumeSmoothingSigma; - bool m_DoVolumeSmoothing; + bool m_DoPartialVolume; bool m_UseRngSeed; long m_RngSeed; bool m_RandomizePhysicalProperties; double m_RandomizePhysicalPropertiesPercentage; double m_BackgroundAbsorption; double m_BackgroundScattering; double m_BackgroundAnisotropy; double m_AirAbsorption; double m_AirScattering; double m_AirAnisotropy; double m_AirThicknessInMillimeters; double m_SkinAbsorption; double m_SkinScattering; double m_SkinAnisotropy; double m_SkinThicknessInMillimeters; CalculateNewVesselPositionCallback m_CalculateNewVesselPositionCallback; int m_MinNumberOfVessels; int m_MaxNumberOfVessels; double m_MinVesselBending; double m_MaxVesselBending; double m_MinVesselAbsorption; double m_MaxVesselAbsorption; double m_MinVesselRadiusInMillimeters; double m_MaxVesselRadiusInMillimeters; int m_VesselBifurcationFrequency; double m_MinVesselScattering; double m_MaxVesselScattering; double m_MinVesselAnisotropy; double m_MaxVesselAnisotropy; double m_MinVesselZOrigin; double m_MaxVesselZOrigin; double m_MCflag; double m_MCLaunchflag; double m_MCBoundaryflag; double m_MCLaunchPointX; double m_MCLaunchPointY; double m_MCLaunchPointZ; double m_MCFocusPointX; double m_MCFocusPointY; double m_MCFocusPointZ; double m_MCTrajectoryVectorX; double m_MCTrajectoryVectorY; double m_MCTrajectoryVectorZ; double m_MCRadius; double m_MCWaist; }; } } #endif // MITKPHOTOACOUSTICTISSUEGENERATORPARAMETERS_H diff --git a/Modules/PhotoacousticsLib/include/mitkPAVesselProperties.h b/Modules/PhotoacousticsLib/include/mitkPAVesselProperties.h index b73934e8e6..aef1a8b181 100644 --- a/Modules/PhotoacousticsLib/include/mitkPAVesselProperties.h +++ b/Modules/PhotoacousticsLib/include/mitkPAVesselProperties.h @@ -1,80 +1,83 @@ /*=================================================================== 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 MITKPhotoacousticVesselParameters_H #define MITKPhotoacousticVesselParameters_H #include #include //Includes for smart pointer usage #include "mitkCommon.h" #include "itkLightObject.h" namespace mitk { namespace pa { class MITKPHOTOACOUSTICSLIB_EXPORT VesselProperties : public itk::Object { public: - mitkClassMacroItkParent(VesselProperties, itk::Object) - itkFactorylessNewMacro(Self) - mitkNewMacro1Param(Self, Self::Pointer) + mitkClassMacroItkParent(VesselProperties, itk::Object); + itkFactorylessNewMacro(Self); + mitkNewMacro1Param(Self, Self::Pointer); - itkGetMacro(PositionVector, Vector::Pointer) - itkGetMacro(DirectionVector, Vector::Pointer) - itkGetMacro(RadiusInVoxel, double) - itkGetMacro(AbsorptionCoefficient, double) - itkGetMacro(ScatteringCoefficient, double) - itkGetMacro(AnisotopyCoefficient, double) - itkGetMacro(BifurcationFrequency, double) + itkGetMacro(PositionVector, Vector::Pointer); + itkGetMacro(DirectionVector, Vector::Pointer); + itkGetMacro(RadiusInVoxel, double); + itkGetMacro(AbsorptionCoefficient, double); + itkGetMacro(ScatteringCoefficient, double); + itkGetMacro(AnisotopyCoefficient, double); + itkGetMacro(BifurcationFrequency, double); + itkGetMacro(DoPartialVolume, bool); - itkSetMacro(PositionVector, Vector::Pointer) - itkSetMacro(DirectionVector, Vector::Pointer) - itkSetMacro(RadiusInVoxel, double) - itkSetMacro(AbsorptionCoefficient, double) - itkSetMacro(ScatteringCoefficient, double) - itkSetMacro(AnisotopyCoefficient, double) - itkSetMacro(BifurcationFrequency, double) + itkSetMacro(PositionVector, Vector::Pointer); + itkSetMacro(DirectionVector, Vector::Pointer); + itkSetMacro(RadiusInVoxel, double); + itkSetMacro(AbsorptionCoefficient, double); + itkSetMacro(ScatteringCoefficient, double); + itkSetMacro(AnisotopyCoefficient, double); + itkSetMacro(BifurcationFrequency, double); + itkSetMacro(DoPartialVolume, bool); protected: VesselProperties(); VesselProperties(Self::Pointer other); virtual ~VesselProperties(); private: Vector::Pointer m_PositionVector; Vector::Pointer m_DirectionVector; double m_RadiusInVoxel; double m_AbsorptionCoefficient; double m_ScatteringCoefficient; double m_AnisotopyCoefficient; double m_BifurcationFrequency; + bool m_DoPartialVolume; }; /** * @brief Equal A function comparing two VesselProperty instances for beeing equal * * @param rightHandSide A VesselProperty to be compared * @param leftHandSide A Vesselproperty to be compared * @param eps tolarence for comparison. You can use mitk::eps in most cases. * @param verbose flag indicating if the user wants detailed console output or not. * @return true, if all subsequent comparisons are true, false otherwise */ MITKPHOTOACOUSTICSLIB_EXPORT bool Equal(const VesselProperties::Pointer leftHandSide, const VesselProperties::Pointer rightHandSide, double eps, bool verbose); } } #endif // MITKPhotoacousticVesselParameters_H diff --git a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVessel.cpp b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVessel.cpp index f785185151..7caf51845c 100644 --- a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVessel.cpp +++ b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVessel.cpp @@ -1,206 +1,217 @@ /*=================================================================== 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 "mitkPAVessel.h" #include #define _USE_MATH_DEFINES #include #include mitk::pa::Vessel::Vessel(VesselProperties::Pointer initialProperties) : m_RangeDistribution(M_PI / 16, M_PI / 8), m_SignDistribution(-1, 1) { m_Finished = false; //Copy this so it may be reused for other vessels. m_VesselProperties = VesselProperties::New(initialProperties); m_RadiusRangeDistribution = std::uniform_real_distribution<>(NEW_RADIUS_MINIMUM_RELATIVE_SIZE, NEW_RADIUS_MAXIMUM_RELATIVE_SIZE); m_VesselMeanderStrategy = VesselMeanderStrategy::New(); m_WalkedDistance = 0; } mitk::pa::Vessel::~Vessel() { m_VesselProperties = nullptr; m_VesselMeanderStrategy = nullptr; } void mitk::pa::Vessel::ExpandVessel(InSilicoTissueVolume::Pointer volume, CalculateNewVesselPositionCallback calculateNewPosition, double bendingFactor, std::mt19937* rng) { Vector::Pointer oldPosition = m_VesselProperties->GetPositionVector()->Clone(); (m_VesselMeanderStrategy->*calculateNewPosition)(m_VesselProperties->GetPositionVector(), m_VesselProperties->GetDirectionVector(), bendingFactor, rng); DrawVesselInVolume(oldPosition, volume); } bool mitk::pa::Vessel::CanBifurcate() { return m_VesselProperties->GetBifurcationFrequency() < m_WalkedDistance; } int mitk::pa::Vessel::GetSign(std::mt19937 *rng) { if (m_SignDistribution(*rng) < 0) return -1; return 1; } mitk::pa::Vessel::Pointer mitk::pa::Vessel::Bifurcate(std::mt19937* rng) { VesselProperties::Pointer vesselParams = VesselProperties::New(m_VesselProperties); double thetaChange = m_RangeDistribution(*rng) * GetSign(rng); double phiChange = m_RangeDistribution(*rng) * GetSign(rng); vesselParams->GetDirectionVector()->Rotate(thetaChange, phiChange); m_VesselProperties->GetDirectionVector()->Rotate(-thetaChange, -phiChange); double newRadius = m_RadiusRangeDistribution(*rng)*m_VesselProperties->GetRadiusInVoxel(); vesselParams->SetRadiusInVoxel(newRadius); m_VesselProperties->SetRadiusInVoxel( sqrt(m_VesselProperties->GetRadiusInVoxel()*m_VesselProperties->GetRadiusInVoxel() - newRadius*newRadius)); m_WalkedDistance = 0; return Vessel::New(vesselParams); } void mitk::pa::Vessel::DrawVesselInVolume(Vector::Pointer fromPosition, InSilicoTissueVolume::Pointer volume) { Vector::Pointer diffVector = Vector::New(); Vector::Pointer toPosition = m_VesselProperties->GetPositionVector(); diffVector->SetElement(0, fromPosition->GetElement(0) - toPosition->GetElement(0)); diffVector->SetElement(1, fromPosition->GetElement(1) - toPosition->GetElement(1)); diffVector->SetElement(2, fromPosition->GetElement(2) - toPosition->GetElement(2)); //1/SCALING_FACTOR steps along the direction vector are taken and drawn into the image. Vector::Pointer stepSize = Vector::New(); stepSize->SetValue(m_VesselProperties->GetDirectionVector()); stepSize->Scale(SCALING_FACTOR); while (diffVector->GetNorm() >= SCALING_FACTOR) { m_WalkedDistance += stepSize->GetNorm(); fromPosition->SetElement(0, fromPosition->GetElement(0) + stepSize->GetElement(0)); fromPosition->SetElement(1, fromPosition->GetElement(1) + stepSize->GetElement(1)); fromPosition->SetElement(2, fromPosition->GetElement(2) + stepSize->GetElement(2)); double xPos = fromPosition->GetElement(0); double yPos = fromPosition->GetElement(1); double zPos = fromPosition->GetElement(2); if (!volume->IsInsideVolume(xPos, yPos, zPos)) { m_VesselProperties->SetRadiusInVoxel(0); break; } double radius = m_VesselProperties->GetRadiusInVoxel(); double ceiledRadius = ceil(radius); for (int x = xPos - ceiledRadius; x <= xPos + ceiledRadius; x += 1) for (int y = yPos - ceiledRadius; y <= yPos + ceiledRadius; y += 1) for (int z = zPos - ceiledRadius; z <= zPos + ceiledRadius; z += 1) { if (!volume->IsInsideVolume(x, y, z)) { continue; } double xDiff = x - xPos; double yDiff = y - yPos; double zDiff = z - zPos; double vectorLengthDiff = radius*radius - (xDiff*xDiff + yDiff*yDiff + zDiff*zDiff); if (vectorLengthDiff > 0) { volume->SetVolumeValues(x, y, z, m_VesselProperties->GetAbsorptionCoefficient(), m_VesselProperties->GetScatteringCoefficient(), m_VesselProperties->GetAnisotopyCoefficient(), mitk::pa::InSilicoTissueVolume::SegmentationType::VESSEL); } else { - double backgroundFraction = abs(sqrt((xDiff*xDiff + yDiff*yDiff + zDiff*zDiff)) - radius); - double vesselFraction = 1.0 - backgroundFraction; - auto type = mitk::pa::InSilicoTissueVolume::SegmentationType::BACKGROUND; - if (vesselFraction >= 0.5) + if (m_VesselProperties->GetDoPartialVolume()) { - type = mitk::pa::InSilicoTissueVolume::SegmentationType::VESSEL; + double backgroundFraction = abs(sqrt(xDiff*xDiff + yDiff*yDiff + zDiff*zDiff) - radius); + if (backgroundFraction <= 1 && backgroundFraction >= 0) + { + double vesselFraction = 1.0 - backgroundFraction; + + double absorption = backgroundFraction * volume->GetAbsorptionVolume()->GetData( + x, y, z) + + vesselFraction * m_VesselProperties->GetAbsorptionCoefficient(); + double scattering = backgroundFraction * volume->GetScatteringVolume()->GetData( + x, y, z) + + vesselFraction * m_VesselProperties->GetScatteringCoefficient(); + double anisotropy = backgroundFraction * volume->GetAnisotropyVolume()->GetData( + x, y, z) + + vesselFraction * m_VesselProperties->GetAnisotopyCoefficient(); + + if (vesselFraction >= 0.5) + { + volume->SetVolumeValues(x, y, z, + absorption, + scattering, + anisotropy, + InSilicoTissueVolume::SegmentationType::VESSEL); + } + else + { + volume->SetVolumeValues(x, y, z, + absorption, + scattering, + anisotropy); + } + } } - double absorption = backgroundFraction * volume->GetAbsorptionVolume()->GetData( - x, y, z) - + vesselFraction * m_VesselProperties->GetAbsorptionCoefficient(); - double scattering = backgroundFraction * volume->GetScatteringVolume()->GetData( - x, y, z) - + vesselFraction * m_VesselProperties->GetScatteringCoefficient(); - double anisotropy = backgroundFraction * volume->GetAnisotropyVolume()->GetData( - x, y, z) - + vesselFraction * m_VesselProperties->GetAnisotopyCoefficient(); - - volume->SetVolumeValues(x, y, z, - absorption, - scattering, - anisotropy, - type - ); } } diffVector->SetElement(0, fromPosition->GetElement(0) - toPosition->GetElement(0)); diffVector->SetElement(1, fromPosition->GetElement(1) - toPosition->GetElement(1)); diffVector->SetElement(2, fromPosition->GetElement(2) - toPosition->GetElement(2)); } } bool mitk::pa::Vessel::IsFinished() { return m_VesselProperties->GetRadiusInVoxel() < MINIMUM_VESSEL_RADIUS; } bool mitk::pa::Equal(const Vessel::Pointer leftHandSide, const Vessel::Pointer rightHandSide, double eps, bool verbose) { MITK_INFO(verbose) << "=== mitk::pa::Vessel Equal ==="; if (rightHandSide.IsNull() || leftHandSide.IsNull()) { MITK_INFO(verbose) << "Cannot compare nullpointers"; return false; } if (leftHandSide->IsFinished() != rightHandSide->IsFinished()) { MITK_INFO(verbose) << "Not same finished state."; return false; } if (leftHandSide->CanBifurcate() != rightHandSide->CanBifurcate()) { MITK_INFO(verbose) << "Not same bifurcation state."; return false; } if (!Equal(leftHandSide->GetVesselProperties(), rightHandSide->GetVesselProperties(), eps, verbose)) { MITK_INFO(verbose) << "Vesselproperties not equal"; return false; } return true; } diff --git a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselProperties.cpp b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselProperties.cpp index 63ebd6de6d..c3800ef171 100644 --- a/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselProperties.cpp +++ b/Modules/PhotoacousticsLib/src/Domain/Vessel/mitkPAVesselProperties.cpp @@ -1,101 +1,109 @@ /*=================================================================== 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 "mitkPAVesselProperties.h" mitk::pa::VesselProperties::VesselProperties() { m_PositionVector = Vector::New(); m_DirectionVector = Vector::New(); m_RadiusInVoxel = 0; m_AbsorptionCoefficient = 0; m_ScatteringCoefficient = 0; m_AnisotopyCoefficient = 0; m_BifurcationFrequency = 0; + m_DoPartialVolume = false; } mitk::pa::VesselProperties::VesselProperties(Self::Pointer other) { m_PositionVector = other->GetPositionVector()->Clone(); m_DirectionVector = other->GetDirectionVector()->Clone(); m_RadiusInVoxel = other->GetRadiusInVoxel(); m_AbsorptionCoefficient = other->GetAbsorptionCoefficient(); m_ScatteringCoefficient = other->GetScatteringCoefficient(); m_AnisotopyCoefficient = other->GetAnisotopyCoefficient(); m_BifurcationFrequency = other->GetBifurcationFrequency(); + m_DoPartialVolume = other->GetDoPartialVolume(); } mitk::pa::VesselProperties::~VesselProperties() { m_PositionVector = nullptr; m_DirectionVector = nullptr; } bool mitk::pa::Equal(const VesselProperties::Pointer leftHandSide, const VesselProperties::Pointer rightHandSide, double eps, bool verbose) { MITK_INFO(verbose) << "=== mitk::pa::VesselProperties Equal ==="; if (rightHandSide.IsNull() || leftHandSide.IsNull()) { MITK_INFO(verbose) << "Cannot compare nullpointers"; return false; } if (leftHandSide->GetAbsorptionCoefficient() - rightHandSide->GetAbsorptionCoefficient() > eps) { MITK_INFO(verbose) << "Not the same AbsorptionCoefficient."; return false; } if (leftHandSide->GetAnisotopyCoefficient() - rightHandSide->GetAnisotopyCoefficient() > eps) { MITK_INFO(verbose) << "Not the same AnisotropyCoefficient."; return false; } if (leftHandSide->GetBifurcationFrequency() - rightHandSide->GetBifurcationFrequency() > eps) { MITK_INFO(verbose) << "Not the same BifurcationFrequency."; return false; } if (leftHandSide->GetRadiusInVoxel() - rightHandSide->GetRadiusInVoxel() > eps) { MITK_INFO(verbose) << "Not the same RadiusInVoxel."; return false; } if (leftHandSide->GetScatteringCoefficient() - rightHandSide->GetScatteringCoefficient() > eps) { MITK_INFO(verbose) << "Not the same ScatteringCoefficient."; return false; } if (!Equal(leftHandSide->GetPositionVector(), rightHandSide->GetPositionVector(), eps, verbose)) { MITK_INFO(verbose) << "PositionVector not equal"; return false; } if (!Equal(leftHandSide->GetDirectionVector(), rightHandSide->GetDirectionVector(), eps, verbose)) { - MITK_INFO(verbose) << "PositionVector not equal"; + MITK_INFO(verbose) << "DirectionVector not equal"; + return false; + } + + if (!(leftHandSide->GetDoPartialVolume() == rightHandSide->GetDoPartialVolume())) + { + MITK_INFO(verbose) << "GetDoPartialVolume not equal"; return false; } return true; } diff --git a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp index 034e1aa585..2b15cc3f65 100644 --- a/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp +++ b/Modules/PhotoacousticsLib/src/Domain/Volume/mitkPAInSilicoTissueVolume.cpp @@ -1,325 +1,332 @@ /*=================================================================== 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 mitk::pa::InSilicoTissueVolume::InSilicoTissueVolume(TissueGeneratorParameters::Pointer parameters) { { unsigned int xDim = parameters->GetXDim(); unsigned int yDim = parameters->GetYDim(); unsigned int zDim = parameters->GetZDim(); m_TDim = 4; unsigned int size = xDim * yDim * zDim; double* absorptionArray = new double[size]; double* scatteringArray = new double[size]; double* anisotropyArray = new double[size]; double* segmentationArray = new double[size]; for (unsigned int index = 0; index < size; index++) { absorptionArray[index] = parameters->GetBackgroundAbsorption(); scatteringArray[index] = parameters->GetBackgroundScattering(); anisotropyArray[index] = parameters->GetBackgroundAnisotropy(); segmentationArray[index] = SegmentationType::BACKGROUND; } m_AbsorptionVolume = Volume::New(absorptionArray, xDim, yDim, zDim); m_ScatteringVolume = Volume::New(scatteringArray, xDim, yDim, zDim); m_AnisotropyVolume = Volume::New(anisotropyArray, xDim, yDim, zDim); m_SegmentationVolume = Volume::New(segmentationArray, xDim, yDim, zDim); } m_TissueParameters = parameters; m_PropertyList = mitk::PropertyList::New(); UpdatePropertyList(); } void mitk::pa::InSilicoTissueVolume::UpdatePropertyList() { //Set properties AddIntProperty("mcflag", m_TissueParameters->GetMCflag()); AddIntProperty("launchflag", m_TissueParameters->GetMCLaunchflag()); AddIntProperty("boundaryflag", m_TissueParameters->GetMCBoundaryflag()); AddDoubleProperty("launchPointX", m_TissueParameters->GetMCLaunchPointX()); AddDoubleProperty("launchPointY", m_TissueParameters->GetMCLaunchPointY()); AddDoubleProperty("launchPointZ", m_TissueParameters->GetMCLaunchPointZ()); AddDoubleProperty("focusPointX", m_TissueParameters->GetMCFocusPointX()); AddDoubleProperty("focusPointY", m_TissueParameters->GetMCFocusPointY()); AddDoubleProperty("focusPointZ", m_TissueParameters->GetMCFocusPointZ()); AddDoubleProperty("trajectoryVectorX", m_TissueParameters->GetMCTrajectoryVectorX()); AddDoubleProperty("trajectoryVectorY", m_TissueParameters->GetMCTrajectoryVectorY()); AddDoubleProperty("trajectoryVectorZ", m_TissueParameters->GetMCTrajectoryVectorZ()); AddDoubleProperty("radius", m_TissueParameters->GetMCRadius()); AddDoubleProperty("waist", m_TissueParameters->GetMCWaist()); - if (m_TissueParameters->GetDoVolumeSmoothing()) - AddDoubleProperty("sigma", m_TissueParameters->GetVolumeSmoothingSigma()); - else - AddDoubleProperty("sigma", 0); + AddDoubleProperty("partialVolume", m_TissueParameters->GetDoPartialVolume()); AddDoubleProperty("standardTissueAbsorption", m_TissueParameters->GetBackgroundAbsorption()); AddDoubleProperty("standardTissueScattering", m_TissueParameters->GetBackgroundScattering()); AddDoubleProperty("standardTissueAnisotropy", m_TissueParameters->GetBackgroundAnisotropy()); AddDoubleProperty("airThickness", m_TissueParameters->GetAirThicknessInMillimeters()); AddDoubleProperty("skinThickness", m_TissueParameters->GetSkinThicknessInMillimeters()); } mitk::pa::InSilicoTissueVolume::InSilicoTissueVolume( Volume::Pointer absorptionVolume, Volume::Pointer scatteringVolume, Volume::Pointer anisotropyVolume, Volume::Pointer segmentationVolume, TissueGeneratorParameters::Pointer tissueParameters, mitk::PropertyList::Pointer propertyList) { m_AbsorptionVolume = absorptionVolume; m_ScatteringVolume = scatteringVolume; m_AnisotropyVolume = anisotropyVolume; m_SegmentationVolume = segmentationVolume; m_TissueParameters = tissueParameters; m_PropertyList = propertyList; if (m_SegmentationVolume.IsNotNull()) m_TDim = 4; else m_TDim = 3; } void mitk::pa::InSilicoTissueVolume::AddDoubleProperty(std::string label, double value) { m_PropertyList->SetDoubleProperty(label.c_str(), value); mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New(label)); } void mitk::pa::InSilicoTissueVolume::AddIntProperty(std::string label, int value) { m_PropertyList->SetIntProperty(label.c_str(), value); mitk::CoreServices::GetPropertyPersistence()->AddInfo(mitk::PropertyPersistenceInfo::New(label)); } mitk::Image::Pointer mitk::pa::InSilicoTissueVolume::ConvertToMitkImage() { mitk::Image::Pointer resultImage = mitk::Image::New(); mitk::PixelType TPixel = mitk::MakeScalarPixelType(); unsigned int* dimensionsOfImage = new unsigned int[4]; // Copy dimensions dimensionsOfImage[0] = m_TissueParameters->GetYDim(); dimensionsOfImage[1] = m_TissueParameters->GetXDim(); dimensionsOfImage[2] = m_TissueParameters->GetZDim(); dimensionsOfImage[3] = m_TDim; MITK_INFO << "Initializing image..."; resultImage->Initialize(TPixel, 4, dimensionsOfImage, 1); MITK_INFO << "Initializing image...[Done]"; mitk::Vector3D spacing; spacing.Fill(m_TissueParameters->GetVoxelSpacingInCentimeters()); resultImage->SetSpacing(spacing); MITK_INFO << "Set Import Volumes..."; //Copy memory, deal with cleaning up memory yourself! resultImage->SetImportVolume(m_AbsorptionVolume->GetData(), 0, 0, mitk::Image::CopyMemory); resultImage->SetImportVolume(m_ScatteringVolume->GetData(), 1, 0, mitk::Image::CopyMemory); resultImage->SetImportVolume(m_AnisotropyVolume->GetData(), 2, 0, mitk::Image::CopyMemory); resultImage->SetImportVolume(m_SegmentationVolume->GetData(), 3, 0, mitk::Image::CopyMemory); MITK_INFO << "Set Import Volumes...[Done]"; resultImage->SetPropertyList(m_PropertyList); return resultImage; } mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::InSilicoTissueVolume::New( Volume::Pointer absorptionVolume, Volume::Pointer scatteringVolume, Volume::Pointer anisotropyVolume, Volume::Pointer segmentationVolume, TissueGeneratorParameters::Pointer tissueParameters, mitk::PropertyList::Pointer propertyList) { InSilicoTissueVolume::Pointer smartPtr = new InSilicoTissueVolume( absorptionVolume, scatteringVolume, anisotropyVolume, segmentationVolume, tissueParameters, propertyList); smartPtr->UnRegister(); return smartPtr; } mitk::pa::InSilicoTissueVolume::~InSilicoTissueVolume() { m_AbsorptionVolume = nullptr; m_ScatteringVolume = nullptr; m_AnisotropyVolume = nullptr; m_SegmentationVolume = nullptr; m_TissueParameters = nullptr; m_PropertyList = nullptr; } +void mitk::pa::InSilicoTissueVolume::SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy) +{ + if (IsInsideVolume(x, y, z)) + { + m_AbsorptionVolume->SetData(absorption, x, y, z); + m_ScatteringVolume->SetData(scattering, x, y, z); + m_AnisotropyVolume->SetData(anisotropy, x, y, z); + } +} + void mitk::pa::InSilicoTissueVolume::SetVolumeValues(int x, int y, int z, double absorption, double scattering, double anisotropy, SegmentationType segmentType) { if (IsInsideVolume(x, y, z)) { m_AbsorptionVolume->SetData(absorption, x, y, z); m_ScatteringVolume->SetData(scattering, x, y, z); m_AnisotropyVolume->SetData(anisotropy, x, y, z); m_SegmentationVolume->SetData(segmentType, x, y, z); } } bool mitk::pa::InSilicoTissueVolume::IsInsideVolume(int x, int y, int z) { return x >= 0 && x < m_TissueParameters->GetXDim() && y >= 0 && y < m_TissueParameters->GetYDim() && z >= 0 && z < m_TissueParameters->GetZDim(); } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetAbsorptionVolume() { return m_AbsorptionVolume; } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetSegmentationVolume() { return m_SegmentationVolume; } void mitk::pa::InSilicoTissueVolume::FinalizeVolume() { AddSkinAndAirLayers(); // If specified, randomize all tissue parameters if (m_TissueParameters->GetRandomizePhysicalProperties()) RandomizeTissueCoefficients(m_TissueParameters->GetUseRngSeed(), m_TissueParameters->GetRngSeed(), m_TissueParameters->GetRandomizePhysicalPropertiesPercentage()); } void mitk::pa::InSilicoTissueVolume::AddSkinAndAirLayers() { //Calculate the index location according to thickness in cm double airvoxel = (m_TissueParameters->GetAirThicknessInMillimeters() / m_TissueParameters->GetVoxelSpacingInCentimeters()) / 10; double skinvoxel = airvoxel + (m_TissueParameters->GetSkinThicknessInMillimeters() / m_TissueParameters->GetVoxelSpacingInCentimeters()) / 10; for (int y = 0; y < m_TissueParameters->GetYDim(); y++) { for (int x = 0; x < m_TissueParameters->GetXDim(); x++) { // Add air from index 0 to airvoxel if (m_TissueParameters->GetAirThicknessInMillimeters() > mitk::eps) { FillZLayer(x, y, 0, airvoxel, m_TissueParameters->GetAirAbsorption(), m_TissueParameters->GetAirScattering(), m_TissueParameters->GetAirAnisotropy(), SegmentationType::AIR); } //Add skin from index airvoxel to skinvoxel if (m_TissueParameters->GetSkinThicknessInMillimeters() > mitk::eps) { FillZLayer(x, y, airvoxel, skinvoxel, m_TissueParameters->GetSkinAbsorption(), m_TissueParameters->GetSkinScattering(), m_TissueParameters->GetSkinAnisotropy(), SegmentationType::SKIN); } } } } void mitk::pa::InSilicoTissueVolume::FillZLayer(int x, int y, double startIdx, double endIdx, double absorption, double scattering, double anisotropy, SegmentationType segmentationType) { for (int z = startIdx; z < endIdx; z++) { if (IsInsideVolume(x, y, z)) { if (endIdx - z < 1) { //Simulate partial volume effects m_AbsorptionVolume->SetData((1 - (endIdx - z)) * m_AbsorptionVolume->GetData(x, y, z) + (endIdx - z) * absorption, x, y, z); m_ScatteringVolume->SetData((1 - (endIdx - z)) * m_ScatteringVolume->GetData(x, y, z) + (endIdx - z) * scattering, x, y, z); m_AnisotropyVolume->SetData((1 - (endIdx - z)) * m_AnisotropyVolume->GetData(x, y, z) + (endIdx - z) * anisotropy, x, y, z); if (endIdx - z > 0.5) { //Only put the segmentation label if more than half of the partial volume is the wanted tissue type m_SegmentationVolume->SetData(segmentationType, x, y, z); } } else { m_AbsorptionVolume->SetData(absorption, x, y, z); m_ScatteringVolume->SetData(scattering, x, y, z); m_AnisotropyVolume->SetData(anisotropy, x, y, z); m_SegmentationVolume->SetData(segmentationType, x, y, z); } } } } void mitk::pa::InSilicoTissueVolume::RandomizeTissueCoefficients(long rngSeed, bool useRngSeed, double percentage) { std::mt19937 rng; std::random_device randomDevice; if (useRngSeed) { rng.seed(rngSeed); } else { if (randomDevice.entropy() > 0.1) { rng.seed(randomDevice()); } else { rng.seed(std::chrono::duration_cast(std::chrono::high_resolution_clock::now().time_since_epoch()).count()); } } std::normal_distribution<> percentageDistribution(1, percentage / 100); for (int y = 0; y < m_TissueParameters->GetYDim(); y++) { for (int x = 0; x < m_TissueParameters->GetXDim(); x++) { for (int z = 0; z < m_TissueParameters->GetZDim(); z++) { m_AbsorptionVolume->SetData(m_AbsorptionVolume->GetData(x, y, z) * percentageDistribution(rng), x, y, z); m_ScatteringVolume->SetData(m_ScatteringVolume->GetData(x, y, z) * percentageDistribution(rng), x, y, z); } } } } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetScatteringVolume() { return m_ScatteringVolume; } mitk::pa::Volume::Pointer mitk::pa::InSilicoTissueVolume::GetAnisotropyVolume() { return m_AnisotropyVolume; } diff --git a/Modules/PhotoacousticsLib/src/Generator/mitkPATissueGenerator.cpp b/Modules/PhotoacousticsLib/src/Generator/mitkPATissueGenerator.cpp index c2704dce5a..6f37d0e86d 100644 --- a/Modules/PhotoacousticsLib/src/Generator/mitkPATissueGenerator.cpp +++ b/Modules/PhotoacousticsLib/src/Generator/mitkPATissueGenerator.cpp @@ -1,160 +1,157 @@ /*=================================================================== 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 "mitkPATissueGenerator.h" #include "mitkPAVector.h" #include "mitkPAVolumeManipulator.h" mitk::pa::InSilicoTissueVolume::Pointer mitk::pa::InSilicoTissueGenerator::GenerateInSilicoData( TissueGeneratorParameters::Pointer parameters) { MITK_DEBUG << "Initializing Empty Volume"; auto generatedVolume = mitk::pa::InSilicoTissueVolume::New(parameters); const double DIRECTION_VECTOR_INITIAL_VARIANCE = 0.2; std::mt19937 randomNumberGenerator; std::random_device randomDevice; if (parameters->GetUseRngSeed()) { randomNumberGenerator.seed(parameters->GetRngSeed()); } else { if (randomDevice.entropy() > 0.1) { randomNumberGenerator.seed(randomDevice()); } else { randomNumberGenerator.seed(std::chrono::duration_cast(std::chrono::high_resolution_clock::now().time_since_epoch()).count()); } } std::uniform_int_distribution randomNumVesselDistribution(parameters->GetMinNumberOfVessels(), parameters->GetMaxNumberOfVessels()); std::uniform_real_distribution randomBendingDistribution(parameters->GetMinVesselBending(), parameters->GetMaxVesselBending()); std::uniform_real_distribution randomAbsorptionDistribution(parameters->GetMinVesselAbsorption(), parameters->GetMaxVesselAbsorption()); std::uniform_real_distribution randomRadiusDistribution(parameters->GetMinVesselRadiusInMillimeters(), parameters->GetMaxVesselRadiusInMillimeters()); std::uniform_real_distribution randomScatteringDistribution(parameters->GetMinVesselScattering(), parameters->GetMaxVesselScattering()); std::uniform_real_distribution randomAnisotropyDistribution(parameters->GetMinVesselAnisotropy(), parameters->GetMaxVesselAnisotropy()); std::uniform_int_distribution borderTypeDistribution(0, 3); int numberOfBloodVessels = randomNumVesselDistribution(randomNumberGenerator); generatedVolume->AddIntProperty("numberOfVessels", numberOfBloodVessels); generatedVolume->AddIntProperty("bifurcationFrequency", parameters->GetVesselBifurcationFrequency()); MITK_INFO << "Simulating " << numberOfBloodVessels << " vessel structures"; for (int vesselNumber = 0; vesselNumber < numberOfBloodVessels; vesselNumber++) { Vector::Pointer initialPosition = Vector::New(); Vector::Pointer initialDirection = Vector::New(); double initialRadius = randomRadiusDistribution(randomNumberGenerator) / parameters->GetVoxelSpacingInCentimeters() / 10; std::stringstream radiusString; radiusString << "vessel_" << vesselNumber + 1 << "_radius"; generatedVolume->AddDoubleProperty(radiusString.str(), initialRadius); double absorptionCoefficient = randomAbsorptionDistribution(randomNumberGenerator); std::stringstream absorptionString; absorptionString << "vessel_" << vesselNumber + 1 << "_absorption"; generatedVolume->AddDoubleProperty(absorptionString.str(), absorptionCoefficient); double bendingFactor = randomBendingDistribution(randomNumberGenerator); std::stringstream bendingString; bendingString << "vessel_" << vesselNumber + 1 << "_bendingFactor"; generatedVolume->AddDoubleProperty(bendingString.str(), bendingFactor); double vesselScattering = randomScatteringDistribution(randomNumberGenerator); std::stringstream scatteringString; scatteringString << "vessel_" << vesselNumber + 1 << "_scattering"; generatedVolume->AddDoubleProperty(scatteringString.str(), vesselScattering); double vesselAnisotropy = randomAnisotropyDistribution(randomNumberGenerator); std::stringstream anisotropyString; anisotropyString << "vessel_" << vesselNumber + 1 << "_anisotropy"; generatedVolume->AddDoubleProperty(anisotropyString.str(), vesselAnisotropy); /*The vessel tree shall start at one of the 4 sides of the volume. * The vessels will always be completely contained in the volume * when starting to meander. * They will meander in a direction perpendicular to the * plane they started from (within the limits of the * DIRECTION_VECTOR_INITIAL_VARIANCE) */ int borderType = borderTypeDistribution(randomNumberGenerator); switch (borderType) { case 0: initialPosition->Randomize(0, 0, initialRadius, parameters->GetYDim() - initialRadius, parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator); initialDirection->Randomize(1, 2, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator); break; case 1: initialPosition->Randomize(parameters->GetXDim(), parameters->GetXDim(), initialRadius, parameters->GetYDim() - initialRadius, parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator); initialDirection->Randomize(-2, -1, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator); break; case 2: initialPosition->Randomize(initialRadius, parameters->GetXDim() - initialRadius, 0, 0, parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator); initialDirection->Randomize(-DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, 1, 2, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator); break; case 3: initialPosition->Randomize(initialRadius, parameters->GetXDim() - initialRadius, parameters->GetYDim(), parameters->GetYDim(), parameters->GetMinVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), parameters->GetMaxVesselZOrigin() / parameters->GetVoxelSpacingInCentimeters(), &randomNumberGenerator); initialDirection->Randomize(-DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, -2, -1, -DIRECTION_VECTOR_INITIAL_VARIANCE, DIRECTION_VECTOR_INITIAL_VARIANCE, &randomNumberGenerator); break; } VesselProperties::Pointer vesselParams = VesselProperties::New(); vesselParams->SetDirectionVector(initialDirection); vesselParams->SetPositionVector(initialPosition); vesselParams->SetRadiusInVoxel(initialRadius); vesselParams->SetAbsorptionCoefficient(absorptionCoefficient); vesselParams->SetScatteringCoefficient(vesselScattering); vesselParams->SetAnisotopyCoefficient(vesselAnisotropy); vesselParams->SetBifurcationFrequency(parameters->GetVesselBifurcationFrequency()); + vesselParams->SetDoPartialVolume(parameters->GetDoPartialVolume()); VesselTree::Pointer vesselTree = VesselTree::New(vesselParams); while (!vesselTree->IsFinished()) { vesselTree->Step(generatedVolume, parameters->GetCalculateNewVesselPositionCallback(), bendingFactor, &randomNumberGenerator); } } - mitk::pa::VolumeManipulator::GaussianBlur3D(generatedVolume->GetAbsorptionVolume(), parameters->GetVolumeSmoothingSigma()); - mitk::pa::VolumeManipulator::GaussianBlur3D(generatedVolume->GetScatteringVolume(), parameters->GetVolumeSmoothingSigma()); - mitk::pa::VolumeManipulator::GaussianBlur3D(generatedVolume->GetAnisotropyVolume(), parameters->GetVolumeSmoothingSigma()); - generatedVolume->FinalizeVolume(); return generatedVolume; } mitk::pa::InSilicoTissueGenerator::InSilicoTissueGenerator() { } mitk::pa::InSilicoTissueGenerator::~InSilicoTissueGenerator() { } diff --git a/Modules/PhotoacousticsLib/src/Utils/mitkPATissueGeneratorParameters.cpp b/Modules/PhotoacousticsLib/src/Utils/mitkPATissueGeneratorParameters.cpp index d6e1637a34..b7f8a22f78 100644 --- a/Modules/PhotoacousticsLib/src/Utils/mitkPATissueGeneratorParameters.cpp +++ b/Modules/PhotoacousticsLib/src/Utils/mitkPATissueGeneratorParameters.cpp @@ -1,79 +1,78 @@ /*=================================================================== 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 "mitkPATissueGeneratorParameters.h" mitk::pa::TissueGeneratorParameters::TissueGeneratorParameters() { m_XDim = 50; m_YDim = 50; m_ZDim = 50; m_VoxelSpacingInCentimeters = 1; - m_VolumeSmoothingSigma = 0; - m_DoVolumeSmoothing = false; + m_DoPartialVolume = false; m_UseRngSeed = false; m_RngSeed = 1337L; m_RandomizePhysicalProperties = false; m_RandomizePhysicalPropertiesPercentage = 0; m_BackgroundAbsorption = 0.1; m_BackgroundScattering = 15; m_BackgroundAnisotropy = 0.9; m_AirAbsorption = 0.0001; m_AirScattering = 1; m_AirAnisotropy = 1; m_AirThicknessInMillimeters = 0; m_SkinAbsorption = 0.1; m_SkinScattering = 15; m_SkinAnisotropy = 0.9; m_SkinThicknessInMillimeters = 0; m_CalculateNewVesselPositionCallback = &VesselMeanderStrategy::CalculateRandomlyDivergingPosition; m_MinNumberOfVessels = 0; m_MaxNumberOfVessels = 0; m_MinVesselBending = 0; m_MaxVesselBending = 0.1; m_MinVesselAbsorption = 1; m_MaxVesselAbsorption = 8; m_MinVesselRadiusInMillimeters = 1; m_MaxVesselRadiusInMillimeters = 3; m_VesselBifurcationFrequency = 25; m_MinVesselScattering = 15; m_MaxVesselScattering = 15; m_MinVesselAnisotropy = 0.9; m_MaxVesselAnisotropy = 0.9; m_MinVesselZOrigin = 10; m_MaxVesselZOrigin = 40; m_MCflag = 1; m_MCLaunchflag = 0; m_MCBoundaryflag = 2; m_MCLaunchPointX = 25; m_MCLaunchPointY = 25; m_MCLaunchPointZ = 2; m_MCFocusPointX = 25; m_MCFocusPointY = 25; m_MCFocusPointZ = 25; m_MCTrajectoryVectorX = 0; m_MCTrajectoryVectorY = 0; m_MCTrajectoryVectorZ = 1; m_MCRadius = 2; m_MCWaist = 4; } mitk::pa::TissueGeneratorParameters::~TissueGeneratorParameters() { } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.cpp b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.cpp index c9c4bf1e75..c35200cc00 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.cpp +++ b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.cpp @@ -1,276 +1,255 @@ /*=================================================================== 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. ===================================================================*/ // Blueberry #include #include // Qmitk #include "PASimulator.h" // Qt #include #include #include // mitk #include #include #include #include #include const std::string PASimulator::VIEW_ID = "org.mitk.views.pasimulator"; void PASimulator::SetFocus() { m_Controls.pushButtonShowRandomTissue->setFocus(); } void PASimulator::CreateQtPartControl(QWidget *parent) { m_Controls.setupUi(parent); connect(m_Controls.pushButtonShowRandomTissue, SIGNAL(clicked()), this, SLOT(DoImageProcessing())); - connect(m_Controls.checkBoxGauss, SIGNAL(stateChanged(int)), this, SLOT(ClickedGaussBox())); connect(m_Controls.pushButtonOpenPath, SIGNAL(clicked()), this, SLOT(OpenFolder())); connect(m_Controls.pushButtonOpenBinary, SIGNAL(clicked()), this, SLOT(OpenBinary())); connect(m_Controls.checkBoxGenerateBatch, SIGNAL(clicked()), this, SLOT(UpdateVisibilityOfBatchCreation())); connect(m_Controls.pushButtonAjustWavelength, SIGNAL(clicked()), this, SLOT(UpdateParametersAccordingToWavelength())); connect(m_Controls.checkBoxRngSeed, SIGNAL(clicked()), this, SLOT(ClickedCheckboxFixedSeed())); connect(m_Controls.checkBoxRandomizeParameters, SIGNAL(clicked()), this, SLOT(ClickedRandomizePhysicalParameters())); - m_Controls.spinboxSigma->setEnabled(false); - m_Controls.labelSigma->setEnabled(false); - auto home = std::getenv("HOME"); std::string home_env = ""; if (home != nullptr) { home_env = std::string(home); } else { home = std::getenv("HOMEPATH"); if (home != nullptr) { home_env = std::string(home); } } m_Controls.label_NrrdFilePath->setText(home_env.c_str()); m_PhotoacousticPropertyCalculator = mitk::pa::PropertyCalculator::New(); UpdateVisibilityOfBatchCreation(); ClickedRandomizePhysicalParameters(); ClickedCheckboxFixedSeed(); - ClickedGaussBox(); } void PASimulator::ClickedRandomizePhysicalParameters() { m_Controls.spinboxRandomizeParameters->setEnabled(m_Controls.checkBoxRandomizeParameters->isChecked()); } void PASimulator::ClickedCheckboxFixedSeed() { m_Controls.spinBoxRngSeed->setEnabled(m_Controls.checkBoxRngSeed->isChecked()); } void PASimulator::UpdateParametersAccordingToWavelength() { int wavelength = m_Controls.spinboxWavelength->value(); double bloodOxygenation = m_Controls.spinboxBloodOxygenSaturation->value() / 100; auto result = m_PhotoacousticPropertyCalculator->CalculatePropertyForSpecificWavelength( mitk::pa::PropertyCalculator::TissueType::BLOOD, wavelength, bloodOxygenation); m_Controls.spinboxMaxAbsorption->setValue(result.mua); m_Controls.spinboxMinAbsorption->setValue(result.mua); m_Controls.spinboxBloodVesselScatteringMinimum->setValue(result.mus); m_Controls.spinboxBloodVesselScatteringMaximum->setValue(result.mus); m_Controls.spinboxBloodVesselAnisotropyMinimum->setValue(result.g); m_Controls.spinboxBloodVesselAnisotropyMaximum->setValue(result.g); result = m_PhotoacousticPropertyCalculator->CalculatePropertyForSpecificWavelength( mitk::pa::PropertyCalculator::TissueType::EPIDERMIS, wavelength, bloodOxygenation); m_Controls.spinboxSkinAbsorption->setValue(result.mua); m_Controls.spinboxSkinScattering->setValue(result.mus); m_Controls.spinboxSkinAnisotropy->setValue(result.g); result = m_PhotoacousticPropertyCalculator->CalculatePropertyForSpecificWavelength( mitk::pa::PropertyCalculator::TissueType::STANDARD_TISSUE, wavelength, bloodOxygenation); m_Controls.spinboxBackgroundAbsorption->setValue(result.mua); m_Controls.spinboxBackgroundScattering->setValue(result.mus); m_Controls.spinboxBackgroundAnisotropy->setValue(result.g); } void PASimulator::UpdateVisibilityOfBatchCreation() { m_Controls.widgetBatchFile->setVisible(m_Controls.checkBoxGenerateBatch->isChecked()); } mitk::pa::TissueGeneratorParameters::Pointer PASimulator::GetParametersFromUIInput() { auto parameters = mitk::pa::TissueGeneratorParameters::New(); // Getting settings from UI // General settings parameters->SetXDim(m_Controls.spinboxXDim->value()); parameters->SetYDim(m_Controls.spinboxYDim->value()); parameters->SetZDim(m_Controls.spinboxZDim->value()); - parameters->SetDoVolumeSmoothing(m_Controls.checkBoxGauss->isChecked()); - if (parameters->GetDoVolumeSmoothing()) - parameters->SetVolumeSmoothingSigma(m_Controls.spinboxSigma->value()); + parameters->SetDoPartialVolume(m_Controls.checkBoxPartialVolume->isChecked()); parameters->SetRandomizePhysicalProperties(m_Controls.checkBoxRandomizeParameters->isChecked()); parameters->SetRandomizePhysicalPropertiesPercentage(m_Controls.spinboxRandomizeParameters->value()); parameters->SetVoxelSpacingInCentimeters(m_Controls.spinboxSpacing->value()); parameters->SetUseRngSeed(m_Controls.checkBoxRngSeed->isChecked()); parameters->SetRngSeed(m_Controls.spinBoxRngSeed->value()); // Monte Carlo simulation parameters parameters->SetMCflag(m_Controls.spinboxMcFlag->value()); parameters->SetMCLaunchflag(m_Controls.spinboxLaunchFlag->value()); parameters->SetMCBoundaryflag(m_Controls.spinboxboundaryFlag->value()); parameters->SetMCLaunchPointX(m_Controls.spinboxLaunchpointX->value()); parameters->SetMCLaunchPointY(m_Controls.spinboxLaunchpointY->value()); parameters->SetMCLaunchPointZ(m_Controls.spinboxLaunchpointZ->value()); parameters->SetMCFocusPointX(m_Controls.spinboxFocuspointX->value()); parameters->SetMCFocusPointY(m_Controls.spinboxFocuspointY->value()); parameters->SetMCFocusPointZ(m_Controls.spinboxFocuspointZ->value()); parameters->SetMCTrajectoryVectorX(m_Controls.spinboxTrajectoryVectorX->value()); parameters->SetMCTrajectoryVectorY(m_Controls.spinboxTrajectoryVectorY->value()); parameters->SetMCTrajectoryVectorZ(m_Controls.spinboxTrajectoryVectorZ->value()); parameters->SetMCRadius(m_Controls.spinboxRadius->value()); parameters->SetMCWaist(m_Controls.spinboxWaist->value()); // Vessel settings parameters->SetMaxVesselAbsorption(m_Controls.spinboxMaxAbsorption->value()); parameters->SetMinVesselAbsorption(m_Controls.spinboxMinAbsorption->value()); parameters->SetMaxVesselBending(m_Controls.spinboxMaxBending->value()); parameters->SetMinVesselBending(m_Controls.spinboxMinBending->value()); parameters->SetMaxVesselRadiusInMillimeters(m_Controls.spinboxMaxDiameter->value()); parameters->SetMinVesselRadiusInMillimeters(m_Controls.spinboxMinDiameter->value()); parameters->SetMaxNumberOfVessels(m_Controls.spinboxMaxVessels->value()); parameters->SetMinNumberOfVessels(m_Controls.spinboxMinVessels->value()); parameters->SetMinVesselScattering(m_Controls.spinboxBloodVesselScatteringMinimum->value()); parameters->SetMaxVesselScattering(m_Controls.spinboxBloodVesselScatteringMaximum->value()); parameters->SetMinVesselAnisotropy(m_Controls.spinboxBloodVesselAnisotropyMinimum->value()); parameters->SetMaxVesselAnisotropy(m_Controls.spinboxBloodVesselAnisotropyMaximum->value()); parameters->SetVesselBifurcationFrequency(m_Controls.spinboxBifurcationFrequency->value()); parameters->SetMinVesselZOrigin(m_Controls.spinboxMinSpawnDepth->value()); parameters->SetMaxVesselZOrigin(m_Controls.spinboxMaxSpawnDepth->value()); // Background tissue settings parameters->SetBackgroundAbsorption(m_Controls.spinboxBackgroundAbsorption->value()); parameters->SetBackgroundScattering(m_Controls.spinboxBackgroundScattering->value()); parameters->SetBackgroundAnisotropy(m_Controls.spinboxBackgroundAnisotropy->value()); // Air settings parameters->SetAirThicknessInMillimeters(m_Controls.spinboxAirThickness->value()); //Skin tissue settings parameters->SetSkinThicknessInMillimeters(m_Controls.spinboxSkinThickness->value()); parameters->SetSkinAbsorption(m_Controls.spinboxSkinAbsorption->value()); parameters->SetSkinScattering(m_Controls.spinboxSkinScattering->value()); parameters->SetSkinAnisotropy(m_Controls.spinboxSkinAnisotropy->value()); parameters->SetCalculateNewVesselPositionCallback(&mitk::pa::VesselMeanderStrategy::CalculateRandomlyDivergingPosition); return parameters; } void PASimulator::DoImageProcessing() { int numberOfVolumes = 1; if (m_Controls.checkBoxGenerateBatch->isChecked()) { if (m_Controls.labelBinarypath->text().isNull() || m_Controls.labelBinarypath->text().isEmpty()) { QMessageBox::warning(nullptr, QString("Warning"), QString("You need to specify the binary first!")); return; } numberOfVolumes = m_Controls.spinboxNumberVolumes->value(); if (numberOfVolumes < 1) { QMessageBox::warning(nullptr, QString("Warning"), QString("You need to create at least one volume!")); return; } } auto tissueParameters = GetParametersFromUIInput(); for (int volumeIndex = 0; volumeIndex < numberOfVolumes; volumeIndex++) { mitk::pa::InSilicoTissueVolume::Pointer volume = mitk::pa::InSilicoTissueGenerator::GenerateInSilicoData(tissueParameters); mitk::Image::Pointer tissueVolume = volume->ConvertToMitkImage(); if (m_Controls.checkBoxGenerateBatch->isChecked()) { std::string nrrdFilePath = m_Controls.label_NrrdFilePath->text().toStdString(); std::string tissueName = m_Controls.lineEditTissueName->text().toStdString(); std::string binaryPath = m_Controls.labelBinarypath->text().toStdString(); long numberOfPhotons = m_Controls.spinboxNumberPhotons->value() * 1000L; auto batchParameters = mitk::pa::SimulationBatchGeneratorParameters::New(); batchParameters->SetBinaryPath(binaryPath); batchParameters->SetNrrdFilePath(nrrdFilePath); batchParameters->SetNumberOfPhotons(numberOfPhotons); batchParameters->SetTissueName(tissueName); batchParameters->SetVolumeIndex(volumeIndex); batchParameters->SetYOffsetLowerThresholdInCentimeters(m_Controls.spinboxFromValue->value()); batchParameters->SetYOffsetUpperThresholdInCentimeters(m_Controls.spinboxToValue->value()); batchParameters->SetYOffsetStepInCentimeters(m_Controls.spinboxStepValue->value()); mitk::pa::SimulationBatchGenerator::WriteBatchFileAndSaveTissueVolume(batchParameters, tissueVolume); } else { mitk::DataNode::Pointer dataNode = mitk::DataNode::New(); dataNode->SetData(tissueVolume); dataNode->SetName(m_Controls.lineEditTissueName->text().toStdString()); this->GetDataStorage()->Add(dataNode); mitk::RenderingManager::GetInstance()->InitializeViewsByBoundingObjects(this->GetDataStorage()); } } } -void PASimulator::ClickedGaussBox() -{ - if (m_Controls.checkBoxGauss->isChecked()) - { - m_Controls.spinboxSigma->setEnabled(true); - m_Controls.labelSigma->setEnabled(true); - } - else - { - m_Controls.spinboxSigma->setEnabled(false); - m_Controls.labelSigma->setEnabled(false); - } -} - void PASimulator::OpenFolder() { m_Controls.label_NrrdFilePath->setText(QFileDialog::getExistingDirectory().append("/")); } void PASimulator::OpenBinary() { m_Controls.labelBinarypath->setText(QFileDialog::getOpenFileName()); } diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.h b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.h index b002562b30..d6f8492faa 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.h +++ b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulator.h @@ -1,77 +1,76 @@ /*=================================================================== 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 PASimulator_h #define PASimulator_h #include #include #include "ui_PASimulatorControls.h" #include "mitkPATissueGenerator.h" #include "mitkPATissueGeneratorParameters.h" #include "mitkPAInSilicoTissueVolume.h" #include "mitkPAPropertyCalculator.h" #include "mitkPASimulationBatchGenerator.h" /** \brief PASimulator \warning This class is not yet documented. Use "git blame" and ask the author to provide basic documentation. \sa QmitkAbstractView \ingroup ${plugin_target}_internal */ class PASimulator : public QmitkAbstractView { // this is needed for all Qt objects that should have a Qt meta-object // (everything that derives from QObject and wants to have signal/slots) Q_OBJECT public: static const std::string VIEW_ID; protected slots: /// \brief Called when the user clicks the GUI button void DoImageProcessing(); - void ClickedGaussBox(); void ClickedCheckboxFixedSeed(); void ClickedRandomizePhysicalParameters(); void OpenFolder(); void OpenBinary(); void UpdateVisibilityOfBatchCreation(); void UpdateParametersAccordingToWavelength(); protected: virtual void CreateQtPartControl(QWidget *parent) override; virtual void SetFocus() override; Ui::PASimulatorControls m_Controls; mitk::pa::PropertyCalculator::Pointer m_PhotoacousticPropertyCalculator; private: mitk::pa::TissueGeneratorParameters::Pointer GetParametersFromUIInput(); }; #endif // PASimulator_h diff --git a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulatorControls.ui b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulatorControls.ui index 8e0876504b..505c73e918 100644 --- a/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulatorControls.ui +++ b/Plugins/org.mitk.gui.qt.photoacoustics.simulation/src/internal/PASimulatorControls.ui @@ -1,4793 +1,4725 @@ PASimulatorControls 0 0 437 655 0 0 Ubuntu Qt::NoContextMenu QmitkTemplate :/org.mitk.gui.qt.photoacousticsimulation/resources/icon.xpm:/org.mitk.gui.qt.photoacousticsimulation/resources/icon.xpm 0 0 415 600 Ubuntu 0 Generator 10 10 391 581 0 0 391 581 0 0 0 0 75 true Volume parameters 0 0 0 25 16777215 25 Tissue name: 0 0 0 25 16777215 25 Size x: 0 0 0 25 16777215 25 50 false Spacing: 0 0 0 25 16777215 25 PhotoacousticTissue 0 0 0 25 16777215 25 1 9999 140 0 0 0 25 16777215 25 y: 0 0 0 25 16777215 25 9999 200 0 0 0 25 16777215 25 z: 0 0 0 25 16777215 25 9999 200 0 0 0 25 16777215 25 voxels Qt::Horizontal 40 20 0 0 0 25 16777215 25 2 0.010000000000000 0.030000000000000 0 0 0 25 16777215 25 cm Qt::Horizontal 40 20 0 0 0 25 16777215 25 Randomize: - + 0 0 0 25 16777215 25 - Partial volume effects: + Custom seed: - + 0 0 0 25 16777215 25 - Custom seed: + Partial volume effects: + + + + + + + Generate batch file output: 0 0 0 25 16777215 25 false - + true 0 0 0 25 16777215 25 - - false - - + true 0 0 0 25 16777215 25 + + true + + + + + + + + + + false + 0 0 0 25 16777215 25 sigma: 0 0 0 25 16777215 25 0 100.000000000000000 0.010000000000000 2.000000000000000 0 0 0 25 16777215 25 % Qt::Horizontal 40 20 - - - - - - 0 - 0 - - - - - 0 - 25 - - - - - 16777215 - 25 - - - - sigma: - - - + - + 0 0 0 25 16777215 25 - 10.000000000000000 - - - 0.100000000000000 + 999999999 - 1.000000000000000 - - - - - - - - 0 - 0 - - - - - 0 - 25 - - - - - 16777215 - 25 - - - - voxels + 170704057 - + Qt::Horizontal 40 20 - + - - - - 0 - 0 - - - - - 0 - 25 - + + + Qt::Horizontal - + - 16777215 - 25 + 40 + 20 - - 999999999 - - - 170704057 - - + + + + + - + Qt::Horizontal 40 20 - - - - - - Generate batch file output: - - - - - - - - - - false - - - - - Number of volumes to generate: 1 9999999 1 Qt::Horizontal 40 20 Save generated tissue path: 0 0 50 0 50 16777215 open Path to MitkMcxyz binary: 0 0 50 0 50 16777215 open From (cm): 0 0 0 25 16777215 25 -100000.000000000000000 100000.000000000000000 0.100000000000000 -1.800000000000000 To (cm): 0 0 0 25 16777215 25 -10000.000000000000000 10000.000000000000000 0.100000000000000 1.800000000000000 Step: 0 0 0 25 16777215 25 -10000.000000000000000 10000.000000000000000 0.010000000000000 0.120000000000000 Number of Photons (x1000): 0 999999999 1 100000 0 0 Generate Tissue Qt::Vertical 20 40 Tissue 10 10 391 581 0 0 391 581 0 0 0 0 0 0 0 25 16777215 25 11 75 false true false Air Parameters 0 0 0 25 16777215 25 50 false Thickness: 0 0 0 10 16777215 10 11 75 true 0 0 0 25 16777215 25 75 false true false Background Parameters 0 0 0 25 16777215 25 Absorption coefficient: 0 0 0 25 16777215 25 Scattering coefficient: 0 0 0 25 16777215 25 Anisotropy facor: 0 0 0 10 16777215 10 11 75 true 0 0 0 25 16777215 25 75 false true false Skin Parameters 0 0 0 25 16777215 25 Thickness: 0 0 0 25 16777215 25 Absorption coefficient: 0 0 0 25 16777215 25 Scattering coefficient: 0 0 0 25 16777215 25 Anisotropy facor: 0 0 0 10 16777215 10 11 75 true 0 0 0 25 16777215 25 11 75 true 0 0 0 25 16777215 25 999.990000000000009 0.100000000000000 12.000000000000000 0 0 0 25 16777215 25 mm Qt::Horizontal 40 20 0 0 0 10 16777215 10 11 75 true 0 0 0 25 16777215 25 75 true 0 0 0 25 16777215 25 5 0.010000000000000 0.100000000000000 0.100000000000000 0 0 0 25 16777215 25 per cm Qt::Horizontal 40 20 0 0 0 25 16777215 25 5 0.010000000000000 1000.000000000000000 0.500000000000000 15.000000000000000 0 0 0 25 16777215 25 per cm Qt::Horizontal 40 20 0 0 0 25 16777215 25 5 0.010000000000000 1.000000000000000 0.010000000000000 0.900000000000000 Qt::Horizontal 40 20 0 0 0 10 16777215 10 11 75 true 0 0 0 25 16777215 25 75 true 0 0 0 25 16777215 25 0.100000000000000 0.000000000000000 0 0 0 25 16777215 25 mm Qt::Horizontal 40 20 0 0 0 25 16777215 25 5 0.010000000000000 0.100000000000000 3.000000000000000 0 0 0 25 16777215 25 per cm Qt::Horizontal 40 20 0 0 0 25 16777215 25 5 0.010000000000000 1000.000000000000000 0.500000000000000 20.000000000000000 0 0 0 25 16777215 25 per cm Qt::Horizontal 40 20 0 0 0 25 16777215 25 5 0.010000000000000 1.000000000000000 0.010000000000000 0.900000000000000 Qt::Horizontal 40 20 0 0 0 10 16777215 10 11 75 true Qt::Vertical 20 40 Vessels 10 10 391 581 0 0 391 581 0 0 0 0 75 true Vessel Parameters 0 25 16777215 25 The number of bloos vessels to generate Count: Qt::AlignLeading|Qt::AlignLeft|Qt::AlignVCenter 0 25 16777215 25 The radius of the blood vessels in mm Radius: 0 25 16777215 25 the absorption coefficient refers to the number of absorption events per centimeter. Absorption: 0 25 16777215 25 The reduced scattering coefficient. It refers to the amount of scattering events per centimeter. Scattering: 0 25 16777215 25 The anisotropy factor is the probability of a photon to not change its direction after a scattering event. Anisotropy factor: 0 25 16777215 25 The bifurcation frequency determines how often the vessel should bifurcate. The vessel will bifurcate after meandering a mean of the specified amount of voxels. When given a value of 0, the vessel will never bifurcate. Bifurcation frequency: 0 25 16777215 25 The curvedness it a setting to determine how much the vessel is allowed to bend during creation. A value of 0 refers to no bending at all and a value of 5 is the maximum. Curvedness: 0 25 16777215 25 The spawn depth defines the depth range in which the vessels enter the volume. Spawn depth: 0 25 16777215 25 The minimum number of blood vessels 0 1 0 25 16777215 25 to 0 25 16777215 25 The maximum number of blood vessels 1 0 25 16777215 25 Vessels Qt::Horizontal QSizePolicy::Expanding 60 20 0 25 16777215 25 The minimum radius 5 2.250000000000000 0 25 16777215 25 to 0 25 16777215 25 The maximum radius 5 4.050000000000000 0 25 16777215 25 mm Qt::Horizontal QSizePolicy::Expanding 60 20 0 25 16777215 25 The minimum absorption coefficient 5 0.010000000000000 2.000000000000000 0 25 16777215 25 to 0 25 16777215 25 The maximum absorption coefficient 5 0.010000000000000 8.000000000000000 0 25 16777215 25 per cm Qt::Horizontal QSizePolicy::Expanding 60 20 0 25 16777215 25 The minimum scattering 5 0.010000000000000 999.000000000000000 1.000000000000000 15.000000000000000 0 25 16777215 25 to 0 25 16777215 25 The minimum scattering 5 0.010000000000000 999.000000000000000 1.000000000000000 15.000000000000000 0 25 16777215 25 per cm Qt::Horizontal QSizePolicy::Expanding 60 20 0 25 16777215 25 The minimum anisotropy factor 5 0.010000000000000 1.000000000000000 0.100000000000000 0.900000000000000 0 25 16777215 25 to 0 25 16777215 25 The maximum anisotropy factor 5 0.010000000000000 1.000000000000000 0.100000000000000 0.900000000000000 Qt::Horizontal QSizePolicy::Expanding 60 20 0 25 16777215 25 The bifurcation frequency determines how often the vessel should bifurcate. The vessel will bifurcate after meandering a mean of the specified amount of voxels. When given a value of 0, the vessel will never bifurcate. 0 1.000000000000000 999999999.000000000000000 5.000000000000000 50.000000000000000 0 25 16777215 25 voxels Qt::Horizontal QSizePolicy::Expanding 60 20 0 25 16777215 25 The minimal curvedness of the vessel. A value of 0 refers to no bending at all and a value of 5 is the maximum. 5.000000000000000 0.000000000000000 0 25 16777215 25 to 0 25 16777215 25 The maximal curvedness of the vessel. A value of 0 refers to no bending at all and a value of 5 is the maximum. 5.000000000000000 0.010000000000000 0.200000000000000 0 25 16777215 25 A.U. Qt::Horizontal QSizePolicy::Expanding 60 20 0 25 16777215 25 The minimum spawn depth 5 0.010000000000000 2.200000000000000 0 25 16777215 25 to 0 25 16777215 25 the maximum spawn depth 5 0.010000000000000 4.200000000000000 0 25 16777215 25 cm Qt::Horizontal QSizePolicy::Expanding 60 20 Qt::Vertical 20 40 Monte Carlo 10 10 391 581 0 0 391 581 0 0 0 0 75 true Monte Carlo Parameters 0 25 16777215 25 50 false General: 0 0 0 25 16777215 25 Mcflag: 0 0 0 25 16777215 25 Launchflag: 0 0 0 25 16777215 25 Boundaryflag: 0 0 0 25 16777215 25 1 4 Qt::Horizontal 40 20 0 0 0 25 16777215 25 0 0 Qt::Horizontal 40 20 0 0 0 25 16777215 25 1 2 Qt::Horizontal 40 20 0 25 16777215 25 50 false Initial launch point: 0 25 16777215 25 x 0 25 16777215 25 4 1000000.000000000000000 0.000000000000000 0 25 16777215 25 y 0 25 16777215 25 4 1000000.000000000000000 0.000000000000000 0 25 16777215 25 z 0 25 16777215 25 4 1000000.000000000000000 0.000000000000000 Qt::Horizontal 40 20 0 25 16777215 25 50 false Focus point: 0 25 16777215 25 x 0 25 16777215 25 4 1000000.000000000000000 0.000000000000000 0 25 16777215 25 y 0 25 16777215 25 4 1000000.000000000000000 0.000000000000000 0 25 16777215 25 z 0 25 16777215 25 4 1000000.000000000000000 0.000000000000000 Qt::Horizontal 40 20 0 25 16777215 25 50 false Trajectory vector: 0 25 16777215 25 x 0 25 16777215 25 4 1000000.000000000000000 0.000000000000000 0 25 16777215 25 y 0 25 16777215 25 4 1000000.000000000000000 0.342000000000000 0 25 16777215 25 z 0 25 16777215 25 4 1000000.000000000000000 0.939700000000000 Qt::Horizontal 40 20 radius: waist: 4 1000.000000000000000 0.500000000000000 Qt::Horizontal 40 20 4 1000.000000000000000 0.010000000000000 Qt::Horizontal 40 20 Qt::Vertical 20 40 Wavelength 10 10 391 581 0 0 391 581 Qt::NoContextMenu 0 0 0 0 75 true Adjust physical properties by wavelength false 16777215 250 <!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0//EN" "http://www.w3.org/TR/REC-html40/strict.dtd"> <html><head><meta name="qrichtext" content="1" /><style type="text/css"> p, li { white-space: pre-wrap; } </style></head><body style=" font-family:'Ubuntu'; font-size:7.8pt; font-weight:400; font-style:normal;"> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">This widget enables the adjustment of the physical properties of the tissue according to a selected wavelength of the light and the oxygen saturation of the blood.</span></p> <p style="-qt-paragraph-type:empty; margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px; font-size:11pt;"><br /></p> <p style=" margin-top:0px; margin-bottom:0px; margin-left:0px; margin-right:0px; -qt-block-indent:0; text-indent:0px;"><span style=" font-size:11pt;">The algorithm and measurements were provided by the publication </span><span style=" font-size:11pt; font-weight:600;">Optical properties of biological tissues: a review </span><span style=" font-size:11pt;">by Steve L. Jacques.</span></p></body></html> 0 0 0 25 16777215 25 Wavelength: 0 0 0 25 16777215 25 Vessel oxygen saturation: 0 0 0 25 16777215 25 0 300.000000000000000 1000.000000000000000 650.000000000000000 Qt::Horizontal 40 20 0 0 0 25 16777215 25 0 100.000000000000000 75.000000000000000 0 0 0 25 16777215 25 % Qt::Horizontal 40 20 Adjust tissue properties Qt::Vertical 20 40