diff --git a/Modules/AlgorithmsExt/test/CMakeLists.txt b/Modules/AlgorithmsExt/test/CMakeLists.txt index 4b2f4f5be6..5c76ebf4b6 100644 --- a/Modules/AlgorithmsExt/test/CMakeLists.txt +++ b/Modules/AlgorithmsExt/test/CMakeLists.txt @@ -1,5 +1,5 @@ MITK_CREATE_MODULE_TESTS() if(TARGET ${TESTDRIVER}) - mitkAddCustomModuleTest(mitkLabeledImageToSurfaceFilterTest_BinaryBall mitkLabeledImageToSurfaceFilterTest ${MITK_DATA_DIR}/BallBinary30x30x30.pic.gz) + mitkAddCustomModuleTest(mitkLabeledImageToSurfaceFilterTest_BinaryBall mitkLabeledImageToSurfaceFilterTest ${MITK_DATA_DIR}/BallBinary30x30x30.nrrd) endif() diff --git a/Modules/Core/include/mitkCommon.h b/Modules/Core/include/mitkCommon.h index be1abe9faa..1fd400dfaf 100644 --- a/Modules/Core/include/mitkCommon.h +++ b/Modules/Core/include/mitkCommon.h @@ -1,200 +1,196 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MITK_COMMON_H_DEFINED #define MITK_COMMON_H_DEFINED #ifdef _MSC_VER // This warns about truncation to 255 characters in debug/browse info #pragma warning(disable : 4786) #pragma warning(disable : 4068) /* disable unknown pragma warnings */ #endif // add only those headers here that are really necessary for all classes! #include "itkObject.h" #include "mitkConfig.h" #include "mitkExceptionMacro.h" #include "mitkGetClassHierarchy.h" #include "mitkLogMacros.h" -#ifndef MITK_UNMANGLE_IPPIC -#define mitkIpPicDescriptor mitkIpPicDescriptor -#endif - typedef unsigned int MapperSlotId; /** From ITK 4.7 version, the TypeMacro overrides (by using the explicit attribute) the GetNameOfClass * hence the SuperClass must provide one. * * If not, use the mitkClassMacroNoParent version */ #define mitkClassMacro(className, SuperClassName) \ typedef className Self; \ typedef SuperClassName Superclass; \ typedef itk::SmartPointer Pointer; \ typedef itk::SmartPointer ConstPointer; \ static const char *GetStaticNameOfClass() { return #className; } \ virtual std::vector GetClassHierarchy() const override { return mitk::GetClassHierarchy(); } \ itkTypeMacro(className, SuperClassName); #define mitkClassMacroItkParent(className, SuperClassName) \ typedef className Self; \ typedef SuperClassName Superclass; \ typedef itk::SmartPointer Pointer; \ typedef itk::SmartPointer ConstPointer; \ static const char *GetStaticNameOfClass() { return #className; } \ virtual std::vector GetClassHierarchy() const { return mitk::GetClassHierarchy(); } \ itkTypeMacro(className, SuperClassName); /** At version 4.7 provides two type macros, the normal one expects the Superclass to provide the * GetNameOfClass explicitely, the NoParent deos not expect anything. */ #define mitkClassMacroNoParent(className) \ typedef className Self; \ typedef itk::SmartPointer Pointer; \ typedef itk::SmartPointer ConstPointer; \ static const char *GetStaticNameOfClass() { return #className; } \ virtual std::vector GetClassHierarchy() const { return mitk::GetClassHierarchy(); } \ itkTypeMacroNoParent(className) /** * Macro for Constructors with one parameter for classes derived from itk::Lightobject **/ #define mitkNewMacro1Param(classname, type) \ \ static Pointer New(type _arg) \ \ { \ Pointer smartPtr = new classname(_arg); \ smartPtr->UnRegister(); \ return smartPtr; \ } /** * Macro for Constructors with two parameters for classes derived from itk::Lightobject **/ #define mitkNewMacro2Param(classname, typea, typeb) \ \ static Pointer New(typea _arga, typeb _argb) \ \ { \ Pointer smartPtr = new classname(_arga, _argb); \ smartPtr->UnRegister(); \ return smartPtr; \ } /** * Macro for Constructors with three parameters for classes derived from itk::Lightobject **/ #define mitkNewMacro3Param(classname, typea, typeb, typec) \ \ static Pointer New(typea _arga, typeb _argb, typec _argc) \ \ { \ Pointer smartPtr = new classname(_arga, _argb, _argc); \ smartPtr->UnRegister(); \ return smartPtr; \ } /** * Macro for Constructors with four parameters for classes derived from itk::Lightobject **/ #define mitkNewMacro4Param(classname, typea, typeb, typec, typed) \ \ static Pointer New(typea _arga, typeb _argb, typec _argc, typed _argd) \ \ { \ Pointer smartPtr = new classname(_arga, _argb, _argc, _argd); \ smartPtr->UnRegister(); \ return smartPtr; \ } /** * Macro for Constructors with five parameters for classes derived from itk::Lightobject **/ #define mitkNewMacro5Param(classname, typea, typeb, typec, typed, typee) \ \ static Pointer New(typea _arga, typeb _argb, typec _argc, typed _argd, typee _arge) \ \ { \ Pointer smartPtr = new classname(_arga, _argb, _argc, _argd, _arge); \ smartPtr->UnRegister(); \ return smartPtr; \ } /** * Macro for Constructors with six parameters for classes derived from itk::Lightobject **/ #define mitkNewMacro6Param(classname, typea, typeb, typec, typed, typee, typef) \ \ static Pointer New(typea _arga, typeb _argb, typec _argc, typed _argd, typee _arge, typef _argf) \ \ { \ Pointer smartPtr = new classname(_arga, _argb, _argc, _argd, _arge, _argf); \ smartPtr->UnRegister(); \ return smartPtr; \ } /** Get a smart const pointer to an object. Creates the member * Get"name"() (e.g., GetPoints()). */ #define mitkGetObjectMacroConst(name, type) \ virtual type *Get##name() const \ { \ itkDebugMacro("returning " #name " address " << this->m_##name); \ return this->m_##name.GetPointer(); \ } /** Creates a Clone() method for "Classname". Returns a smartPtr of a clone of the calling object*/ #define mitkCloneMacro(classname) \ virtual itk::LightObject::Pointer InternalClone() const override \ \ { \ Pointer smartPtr = new classname(*this); \ smartPtr->UnRegister(); \ return smartPtr.GetPointer(); \ } /** cross-platform deprecation macro \todo maybe there is something in external toolkits (ITK, VTK,...) that we could reulse -- would be much preferable */ #ifdef MITK_NO_DEPRECATED_WARNINGS #define DEPRECATED(func) func #elif defined(__GNUC__) #define DEPRECATED(...) __VA_ARGS__ __attribute__((deprecated)) #elif defined(_MSC_VER) #define DEPRECATED(...) __declspec(deprecated)##__VA_ARGS__ #else #pragma message("WARNING: You need to implement DEPRECATED for your compiler!") #define DEPRECATED(func) func #endif /** * Mark templates as exported to generate public RTTI symbols which are * needed for GCC and Clang to support e.g. dynamic_cast between DSOs. */ #if defined(__clang__) || defined(__GNUC__) #define MITK_EXPORT __attribute__((visibility("default"))) #define MITK_IMPORT __attribute__((visibility("default"))) #define MITK_LOCAL __attribute__((visibility("hidden"))) #elif defined(WIN32) #define MITK_EXPORT __declspec(dllexport) #define MITK_IMPORT __declspec(dllimport) #define MITK_LOCAL #else #define MITK_EXPORT #define MITK_IMPORT #define MITK_LOCAL #endif #endif // MITK_COMMON_H_DEFINED diff --git a/Modules/Core/include/mitkImage.h b/Modules/Core/include/mitkImage.h index 359b536d87..c8b6f03464 100644 --- a/Modules/Core/include/mitkImage.h +++ b/Modules/Core/include/mitkImage.h @@ -1,644 +1,643 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MITKIMAGE_H_HEADER_INCLUDED_C1C2FCD2 #define MITKIMAGE_H_HEADER_INCLUDED_C1C2FCD2 #include "mitkBaseData.h" #include "mitkImageAccessorBase.h" #include "mitkImageDataItem.h" #include "mitkImageDescriptor.h" #include "mitkImageVtkAccessor.h" #include "mitkLevelWindow.h" #include "mitkPlaneGeometry.h" #include "mitkSlicedData.h" #include #include #ifndef __itkHistogram_h #include #endif class vtkImageData; namespace itk { template class MutexLockHolder; } namespace mitk { class SubImageSelector; class ImageTimeSelector; class ImageStatisticsHolder; /** * @brief Image class for storing images * - * Can be asked for header information, the data vector, - * the mitkIpPicDescriptor struct or vtkImageData objects. If not the complete - * data is required, the appropriate SubImageSelector class should be used - * for access. + * Can be asked for header information, the data vector, or vtkImageData objects. + * If not the complete data is required, the appropriate SubImageSelector class + * should be used for access. * Image organizes sets of slices (s x 2D), volumes (t x 3D) and channels (n * x ND). Channels are for different kind of data, e.g., morphology in * channel 0, velocities in channel 1. All channels must have the same Geometry! In * particular, the dimensions of all channels are the same, only the pixel-type * may differ between channels. * * For importing ITK images use of mitk::ITKImageImport is recommended, see * \ref Adaptor. * * For ITK v3.8 and older: Converting coordinates from the ITK physical * coordinate system (which does not support rotated images) to the MITK world * coordinate system should be performed via the BaseGeometry of the Image, see * BaseGeometry::WorldToItkPhysicalPoint. * * For more information, see \ref MitkImagePage . * @ingroup Data */ class MITKCORE_EXPORT Image : public SlicedData { friend class SubImageSelector; friend class ImageAccessorBase; friend class ImageVtkAccessor; friend class ImageVtkReadAccessor; friend class ImageVtkWriteAccessor; friend class ImageReadAccessor; friend class ImageWriteAccessor; public: mitkClassMacro(Image, SlicedData); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Smart Pointer type to a ImageDataItem. */ typedef itk::SmartPointer ImageDataItemPointer; typedef itk::Statistics::Histogram HistogramType; typedef mitk::ImageStatisticsHolder *StatisticsHolderPointer; /** This enum is evaluated when setting new data to an image. */ enum ImportMemoryManagementType { CopyMemory, /**< Data to be set is copied and assigned to a new memory block. Data memory block will be freed on deletion of mitk::Image. */ ManageMemory, /**< Data to be set will be referenced, and Data memory block will be freed on deletion of mitk::Image. */ ReferenceMemory, /**< Data to be set will be referenced, but Data memory block will not be freed on deletion of mitk::Image. */ DontManageMemory = ReferenceMemory }; /** * @brief Vector container of SmartPointers to ImageDataItems; * Class is only for internal usage to allow convenient access to all slices over iterators; * See documentation of ImageDataItem for details. */ typedef std::vector ImageDataItemPointerArray; public: /** * @brief Returns the PixelType of channel @a n. */ const mitk::PixelType GetPixelType(int n = 0) const; /** * @brief Get dimension of the image */ unsigned int GetDimension() const; /** * @brief Get the size of dimension @a i (e.g., i=0 results in the number of pixels in x-direction). * * @sa GetDimensions() */ unsigned int GetDimension(int i) const; public: /** * @brief Get a volume at a specific time @a t of channel @a n as a vtkImageData. */ virtual vtkImageData *GetVtkImageData(int t = 0, int n = 0); virtual const vtkImageData *GetVtkImageData(int t = 0, int n = 0) const; /** * @brief Check whether slice @a s at time @a t in channel @a n is set */ bool IsSliceSet(int s = 0, int t = 0, int n = 0) const override; /** * @brief Check whether volume at time @a t in channel @a n is set */ bool IsVolumeSet(int t = 0, int n = 0) const override; /** * @brief Check whether the channel @a n is set */ bool IsChannelSet(int n = 0) const override; /** * @brief Set @a data as slice @a s at time @a t in channel @a n. It is in * the responsibility of the caller to ensure that the data vector @a data * is really a slice (at least is not smaller than a slice), since there is * no chance to check this. * * The data is copied to an array managed by the image. If the image shall * reference the data, use SetImportSlice with ImportMemoryManagementType * set to ReferenceMemory. For importing ITK images use of mitk:: * ITKImageImport is recommended. * @sa SetPicSlice, SetImportSlice, SetImportVolume */ virtual bool SetSlice(const void *data, int s = 0, int t = 0, int n = 0); /** * @brief Set @a data as volume at time @a t in channel @a n. It is in * the responsibility of the caller to ensure that the data vector @a data * is really a volume (at least is not smaller than a volume), since there is * no chance to check this. * * The data is copied to an array managed by the image. If the image shall * reference the data, use SetImportVolume with ImportMemoryManagementType * set to ReferenceMemory. For importing ITK images use of mitk:: * ITKImageImport is recommended. * @sa SetPicVolume, SetImportVolume */ virtual bool SetVolume(const void *data, int t = 0, int n = 0); /** * @brief Set @a data in channel @a n. It is in * the responsibility of the caller to ensure that the data vector @a data * is really a channel (at least is not smaller than a channel), since there is * no chance to check this. * * The data is copied to an array managed by the image. If the image shall * reference the data, use SetImportChannel with ImportMemoryManagementType * set to ReferenceMemory. For importing ITK images use of mitk:: * ITKImageImport is recommended. * @sa SetPicChannel, SetImportChannel */ virtual bool SetChannel(const void *data, int n = 0); /** * @brief Set @a data as slice @a s at time @a t in channel @a n. It is in * the responsibility of the caller to ensure that the data vector @a data * is really a slice (at least is not smaller than a slice), since there is * no chance to check this. * * The data is managed according to the parameter \a importMemoryManagement. * @sa SetPicSlice */ virtual bool SetImportSlice( void *data, int s = 0, int t = 0, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory); /** * @brief Set @a data as volume at time @a t in channel @a n. It is in * the responsibility of the caller to ensure that the data vector @a data * is really a volume (at least is not smaller than a volume), since there is * no chance to check this. * * The data is managed according to the parameter \a importMemoryManagement. * @sa SetPicVolume */ virtual bool SetImportVolume(void *data, int t = 0, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory); virtual bool SetImportVolume(const void *const_data, int t = 0, int n = 0); /** * @brief Set @a data in channel @a n. It is in * the responsibility of the caller to ensure that the data vector @a data * is really a channel (at least is not smaller than a channel), since there is * no chance to check this. * * The data is managed according to the parameter \a importMemoryManagement. * @sa SetPicChannel */ virtual bool SetImportChannel(void *data, int n = 0, ImportMemoryManagementType importMemoryManagement = CopyMemory); /** * initialize new (or re-initialize) image information * @warning Initialize() by pic assumes a plane, evenly spaced geometry starting at (0,0,0). */ virtual void Initialize(const mitk::PixelType &type, unsigned int dimension, const unsigned int *dimensions, unsigned int channels = 1); /** * initialize new (or re-initialize) image information by a BaseGeometry * * \param type * \param geometry * \param channels * @param tDim defines the number of time steps for which the Image should be initialized */ virtual void Initialize(const mitk::PixelType &type, const mitk::BaseGeometry &geometry, unsigned int channels = 1, int tDim = 1); /** * \brief Initialize new (or re-initialize) image information by a TimeGeometry * * \param type * \param geometry * \param channels * \param tDim override time dimension if the value is bigger than 0 (Default -1) */ virtual void Initialize(const mitk::PixelType &type, const mitk::TimeGeometry &geometry, unsigned int channels = 1, int tDim = -1); /** * initialize new (or re-initialize) image information by a PlaneGeometry and number of slices * * Initializes the bounding box according to the width/height of the * PlaneGeometry and @a sDim via SlicedGeometry3D::InitializeEvenlySpaced. * The spacing is calculated from the PlaneGeometry. * \sa SlicedGeometry3D::InitializeEvenlySpaced */ virtual void Initialize(const mitk::PixelType &type, int sDim, const mitk::PlaneGeometry &geometry2d, unsigned int channels = 1, int tDim = 1); /** * initialize new (or re-initialize) image information by another * mitk-image. * Only the header is used, not the data vector! */ virtual void Initialize(const mitk::Image *image); virtual void Initialize(const mitk::ImageDescriptor::Pointer inDesc); /** * initialize new (or re-initialize) image information by @a vtkimagedata, * a vtk-image. * Only the header is used, not the data vector! Use * SetVolume(vtkimage->GetScalarPointer()) to set the data vector. * * @param vtkimagedata * @param channels * @param tDim override time dimension in @a vtkimagedata (if >0 and <) * @param sDim override z-space dimension in @a vtkimagedata (if >0 and <) * @param pDim override y-space dimension in @a vtkimagedata (if >0 and <) */ virtual void Initialize(vtkImageData *vtkimagedata, int channels = 1, int tDim = -1, int sDim = -1, int pDim = -1); /** * initialize new (or re-initialize) image information by @a itkimage, * a templated itk-image. * Only the header is used, not the data vector! Use * SetVolume(itkimage->GetBufferPointer()) to set the data vector. * * @param itkimage * @param channels * @param tDim override time dimension in @a itkimage (if >0 and <) * @param sDim override z-space dimension in @a itkimage (if >0 and <) */ template void InitializeByItk(const itkImageType *itkimage, int channels = 1, int tDim = -1, int sDim = -1) { if (itkimage == nullptr) return; MITK_DEBUG << "Initializing MITK image from ITK image."; // build array with dimensions in each direction with at least 4 entries m_Dimension = itkimage->GetImageDimension(); unsigned int i, *tmpDimensions = new unsigned int[m_Dimension > 4 ? m_Dimension : 4]; for (i = 0; i < m_Dimension; ++i) tmpDimensions[i] = itkimage->GetLargestPossibleRegion().GetSize().GetSize()[i]; if (m_Dimension < 4) { unsigned int *p; for (i = 0, p = tmpDimensions + m_Dimension; i < 4 - m_Dimension; ++i, ++p) *p = 1; } // overwrite number of slices if sDim is set if ((m_Dimension > 2) && (sDim >= 0)) tmpDimensions[2] = sDim; // overwrite number of time points if tDim is set if ((m_Dimension > 3) && (tDim >= 0)) tmpDimensions[3] = tDim; // rough initialization of Image // mitk::PixelType importType = ImportItkPixelType( itkimage::PixelType ); Initialize( MakePixelType(itkimage->GetNumberOfComponentsPerPixel()), m_Dimension, tmpDimensions, channels); const typename itkImageType::SpacingType &itkspacing = itkimage->GetSpacing(); MITK_DEBUG << "ITK spacing " << itkspacing; // access spacing of itk::Image Vector3D spacing; FillVector3D(spacing, itkspacing[0], 1.0, 1.0); if (m_Dimension >= 2) spacing[1] = itkspacing[1]; if (m_Dimension >= 3) spacing[2] = itkspacing[2]; // access origin of itk::Image Point3D origin; const typename itkImageType::PointType &itkorigin = itkimage->GetOrigin(); MITK_DEBUG << "ITK origin " << itkorigin; FillVector3D(origin, itkorigin[0], 0.0, 0.0); if (m_Dimension >= 2) origin[1] = itkorigin[1]; if (m_Dimension >= 3) origin[2] = itkorigin[2]; // access direction of itk::Imagm_PixelType = new mitk::PixelType(type);e and include spacing const typename itkImageType::DirectionType &itkdirection = itkimage->GetDirection(); MITK_DEBUG << "ITK direction " << itkdirection; mitk::Matrix3D matrix; matrix.SetIdentity(); unsigned int j, itkDimMax3 = (m_Dimension >= 3 ? 3 : m_Dimension); // check if spacing has no zero entry and itkdirection has no zero columns bool itkdirectionOk = true; mitk::ScalarType columnSum; for (j = 0; j < itkDimMax3; ++j) { columnSum = 0.0; for (i = 0; i < itkDimMax3; ++i) { columnSum += fabs(itkdirection[i][j]); } if (columnSum < mitk::eps) { itkdirectionOk = false; } if ((spacing[j] < -mitk::eps) // (normally sized) negative value && (j == 2) && (m_Dimensions[2] == 1)) { // Negative spacings can occur when reading single DICOM slices with ITK via GDCMIO // In these cases spacing is not determind by ITK correctly (because it distinguishes correctly // between slice thickness and inter slice distance -- slice distance is meaningless for // single slices). // I experienced that ITK produced something meaningful nonetheless because is is // evaluating the tag "(0018,0088) Spacing between slices" as a fallback. This tag is not // reliable (http://www.itk.org/pipermail/insight-users/2005-September/014711.html) // but gives at least a hint. // In real world cases I experienced that this tag contained the correct inter slice distance // with a negative sign, so we just invert such negative spacings. MITK_WARN << "Illegal value of itk::Image::GetSpacing()[" << j << "]=" << spacing[j] << ". Using inverted value " << -spacing[j]; spacing[j] = -spacing[j]; } else if (spacing[j] < mitk::eps) // value near zero { MITK_ERROR << "Illegal value of itk::Image::GetSpacing()[" << j << "]=" << spacing[j] << ". Using 1.0 instead."; spacing[j] = 1.0; } } if (itkdirectionOk == false) { MITK_ERROR << "Illegal matrix returned by itk::Image::GetDirection():" << itkdirection << " Using identity instead."; for (i = 0; i < itkDimMax3; ++i) for (j = 0; j < itkDimMax3; ++j) if (i == j) matrix[i][j] = spacing[j]; else matrix[i][j] = 0.0; } else { for (i = 0; i < itkDimMax3; ++i) for (j = 0; j < itkDimMax3; ++j) matrix[i][j] = itkdirection[i][j] * spacing[j]; } // re-initialize PlaneGeometry with origin and direction PlaneGeometry *planeGeometry = static_cast(GetSlicedGeometry(0)->GetPlaneGeometry(0)); planeGeometry->SetOrigin(origin); planeGeometry->GetIndexToWorldTransform()->SetMatrix(matrix); // re-initialize SlicedGeometry3D SlicedGeometry3D *slicedGeometry = GetSlicedGeometry(0); slicedGeometry->InitializeEvenlySpaced(planeGeometry, m_Dimensions[2]); slicedGeometry->SetSpacing(spacing); // re-initialize TimeGeometry ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New(); timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]); SetTimeGeometry(timeGeometry); // clean-up delete[] tmpDimensions; this->Initialize(); } /** * @brief Check whether slice @a s at time @a t in channel @a n is valid, i.e., * is (or can be) inside of the image */ virtual bool IsValidSlice(int s = 0, int t = 0, int n = 0) const; /** * @brief Check whether volume at time @a t in channel @a n is valid, i.e., * is (or can be) inside of the image */ virtual bool IsValidVolume(int t = 0, int n = 0) const; /** * @brief Check whether the channel @a n is valid, i.e., * is (or can be) inside of the image */ virtual bool IsValidChannel(int n = 0) const; /** * @brief Returns true if an image is rotated, i.e. its geometry's * transformation matrix has nonzero elements besides the diagonal. * Non-diagonal elements are checked if larger then 1/1000 of the matrix' trace. */ bool IsRotated() const; /** * @brief Get the sizes of all dimensions as an integer-array. * * @sa GetDimension(int i); */ unsigned int *GetDimensions() const; ImageDescriptor::Pointer GetImageDescriptor() const { return m_ImageDescriptor; } ChannelDescriptor GetChannelDescriptor(int id = 0) const { return m_ImageDescriptor->GetChannelDescriptor(id); } /** \brief Sets a geometry to an image. */ void SetGeometry(BaseGeometry *aGeometry3D) override; /** * @warning for internal use only */ virtual ImageDataItemPointer GetSliceData(int s = 0, int t = 0, int n = 0, void *data = nullptr, ImportMemoryManagementType importMemoryManagement = CopyMemory) const; /** * @warning for internal use only */ virtual ImageDataItemPointer GetVolumeData(int t = 0, int n = 0, void *data = nullptr, ImportMemoryManagementType importMemoryManagement = CopyMemory) const; /** * @warning for internal use only */ virtual ImageDataItemPointer GetChannelData(int n = 0, void *data = nullptr, ImportMemoryManagementType importMemoryManagement = CopyMemory) const; /** \brief Returns a pointer to the ImageStatisticsHolder object that holds all statistics information for the image. All Get-methods for statistics properties formerly accessible directly from an Image object are now moved to the new \a ImageStatisticsHolder object. */ StatisticsHolderPointer GetStatistics() const { return m_ImageStatistics; } protected: mitkCloneMacro(Self); typedef itk::MutexLockHolder MutexHolder; int GetSliceIndex(int s = 0, int t = 0, int n = 0) const; int GetVolumeIndex(int t = 0, int n = 0) const; void ComputeOffsetTable(); virtual bool IsValidTimeStep(int t) const; void Expand(unsigned int timeSteps) override; virtual ImageDataItemPointer AllocateSliceData( int s = 0, int t = 0, int n = 0, void *data = nullptr, ImportMemoryManagementType importMemoryManagement = CopyMemory) const; virtual ImageDataItemPointer AllocateVolumeData( int t = 0, int n = 0, void *data = nullptr, ImportMemoryManagementType importMemoryManagement = CopyMemory) const; virtual ImageDataItemPointer AllocateChannelData( int n = 0, void *data = nullptr, ImportMemoryManagementType importMemoryManagement = CopyMemory) const; Image(); Image(const Image &other); ~Image() override; void Clear() override; /** @warning Has to be called by every Initialize method! */ void Initialize() override; void PrintSelf(std::ostream &os, itk::Indent indent) const override; mutable ImageDataItemPointerArray m_Channels; mutable ImageDataItemPointerArray m_Volumes; mutable ImageDataItemPointerArray m_Slices; mutable itk::SimpleFastMutexLock m_ImageDataArraysLock; unsigned int m_Dimension; unsigned int *m_Dimensions; ImageDescriptor::Pointer m_ImageDescriptor; size_t *m_OffsetTable; ImageDataItemPointer m_CompleteData; // Image statistics Holder replaces the former implementation directly inside this class friend class ImageStatisticsHolder; StatisticsHolderPointer m_ImageStatistics; private: ImageDataItemPointer GetSliceData_unlocked( int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const; ImageDataItemPointer GetVolumeData_unlocked(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const; ImageDataItemPointer GetChannelData_unlocked(int n, void *data, ImportMemoryManagementType importMemoryManagement) const; ImageDataItemPointer AllocateSliceData_unlocked( int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const; ImageDataItemPointer AllocateVolumeData_unlocked(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const; ImageDataItemPointer AllocateChannelData_unlocked(int n, void *data, ImportMemoryManagementType importMemoryManagement) const; bool IsSliceSet_unlocked(int s, int t, int n) const; bool IsVolumeSet_unlocked(int t, int n) const; bool IsChannelSet_unlocked(int n) const; /** Stores all existing ImageReadAccessors */ mutable std::vector m_Readers; /** Stores all existing ImageWriteAccessors */ mutable std::vector m_Writers; /** Stores all existing ImageVtkAccessors */ mutable std::vector m_VtkReaders; /** A mutex, which needs to be locked to manage m_Readers and m_Writers */ itk::SimpleFastMutexLock m_ReadWriteLock; /** A mutex, which needs to be locked to manage m_VtkReaders */ itk::SimpleFastMutexLock m_VtkReadersLock; }; /** * @brief Equal A function comparing two images for beeing equal in meta- and imagedata * * @ingroup MITKTestingAPI * * Following aspects are tested for equality: * - dimension of the images * - size of the images * - pixel type * - pixel values : pixel values are expected to be identical at each position ( for other options see * mitk::CompareImageFilter ) * * @param rightHandSide An image to be compared * @param leftHandSide An image 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 */ MITKCORE_EXPORT bool Equal(const mitk::Image &leftHandSide, const mitk::Image &rightHandSide, ScalarType eps, bool verbose); } // namespace mitk #endif /* MITKIMAGE_H_HEADER_INCLUDED_C1C2FCD2 */ diff --git a/Modules/Core/include/mitkImageDataItem.h b/Modules/Core/include/mitkImageDataItem.h index 946879ff55..8c1a00b8be 100644 --- a/Modules/Core/include/mitkImageDataItem.h +++ b/Modules/Core/include/mitkImageDataItem.h @@ -1,166 +1,162 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef IMAGEDATAITEM_H #define IMAGEDATAITEM_H #include "mitkCommon.h" #include -//#include -//#include "mitkPixelType.h" #include "mitkImageDescriptor.h" -//#include "mitkImageVtkAccessor.h" class vtkImageData; namespace mitk { class PixelType; class ImageVtkReadAccessor; class ImageVtkWriteAccessor; class Image; //##Documentation //## @brief Internal class for managing references on sub-images //## //## ImageDataItem is a container for image data which is used internal in //## mitk::Image to handle the communication between the different data types for images - //## used in MITK (ipPicDescriptor, mitk::Image, vtkImageData). Common for these image data + //## used in MITK (mitk::Image, vtkImageData). Common for these image data //## types is the actual image data, but they differ in representation of pixel type etc. - //## The class is also used to convert ipPic images to vtkImageData. //## //## The class is mainly used to extract sub-images inside of mitk::Image, like single slices etc. //## It should not be used outside of this. //## //## @param manageMemory Determines if image data is removed while destruction of ImageDataItem or not. //## @ingroup Data class MITKCORE_EXPORT ImageDataItem : public itk::LightObject { friend class ImageAccessorBase; friend class ImageWriteAccessor; friend class ImageReadAccessor; template friend class ImagePixelAccessor; friend class Image; // template // friend class ImageToItk; public: typedef itk::SmartPointer ImagePointer; typedef itk::SmartPointer ImageConstPointer; mitkClassMacroItkParent(ImageDataItem, itk::LightObject); itkCloneMacro(ImageDataItem); itk::LightObject::Pointer InternalClone() const override; ImageDataItem(const ImageDataItem &aParent, const mitk::ImageDescriptor::Pointer desc, int timestep, unsigned int dimension, void *data = nullptr, bool manageMemory = false, size_t offset = 0); ~ImageDataItem() override; ImageDataItem(const mitk::ImageDescriptor::Pointer desc, int timestep, void *data, bool manageMemory); ImageDataItem(const mitk::PixelType &type, int timestep, unsigned int dimension, unsigned int *dimensions, void *data, bool manageMemory); ImageDataItem(const ImageDataItem &other); bool IsComplete() const { return m_IsComplete; } void SetComplete(bool complete) { m_IsComplete = complete; } int GetOffset() const { return m_Offset; } PixelType GetPixelType() const { return *m_PixelType; } void SetTimestep(int t) { m_Timestep = t; } void SetManageMemory(bool b) { m_ManageMemory = b; } int GetDimension() const { return m_Dimension; } int GetDimension(int i) const { int returnValue = 0; // return the true size if dimension available if (i < (int)m_Dimension) returnValue = m_Dimensions[i]; return returnValue; } ImageDataItem::ConstPointer GetParent() const { return m_Parent; } /** * @brief GetVtkImageAccessor Returns a vtkImageDataItem, if none is present, a new one is constructed by the * ConstructVtkImageData method. * Due to historical development of MITK and VTK, the vtkImage origin is explicitly set * to * (0, 0, 0) for 3D images. * See bug 5050 for detailed information. * @return Pointer of type ImageVtkReadAccessor */ ImageVtkReadAccessor *GetVtkImageAccessor(ImageConstPointer) const; ImageVtkWriteAccessor *GetVtkImageAccessor(ImagePointer); // Returns if image data should be deleted on destruction of ImageDataItem. bool GetManageMemory() const { return m_ManageMemory; } virtual void ConstructVtkImageData(ImageConstPointer) const; size_t GetSize() const { return m_Size; } virtual void Modified() const; protected: /**Helper function to allow friend classes to access m_Data without changing their code. * Moved to protected visibility because only friends are allowed to access m_Data directly. * Other classes should used ImageWriteAccessor::GetData() or ImageReadAccessor::GetData() * to get access.*/ void* GetData() const { return m_Data; } unsigned char *m_Data; PixelType *m_PixelType; bool m_ManageMemory; mutable vtkImageData *m_VtkImageData; mutable ImageVtkReadAccessor *m_VtkImageReadAccessor; ImageVtkWriteAccessor *m_VtkImageWriteAccessor; int m_Offset; bool m_IsComplete; size_t m_Size; private: void ComputeItemSize(const unsigned int *dimensions, unsigned int dimension); ImageDataItem::ConstPointer m_Parent; unsigned int m_Dimension; unsigned int m_Dimensions[MAX_IMAGE_DIMENSIONS]; int m_Timestep; }; } // namespace mitk #endif /* IMAGEDATAITEM_H */ diff --git a/Modules/Core/include/mitkImageDescriptor.h b/Modules/Core/include/mitkImageDescriptor.h index 48986781eb..e9e082a3d7 100644 --- a/Modules/Core/include/mitkImageDescriptor.h +++ b/Modules/Core/include/mitkImageDescriptor.h @@ -1,122 +1,122 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef MITKIMAGEDESCRIPTOR_H #define MITKIMAGEDESCRIPTOR_H #include #include #include #include "mitkChannelDescriptor.h" #include "mitkCommon.h" -/// Defines the maximum of 8 dimensions per image channel taken from ipPicDescriptor +/// Defines the maximum of 8 dimensions per image channel #define MAX_IMAGE_DIMENSIONS 8 namespace mitk { /** \brief An object to hold all essential information about an Image object The ImageDescriptor holds an std::vector of pointers to ChannelDescriptor together with the information about the image's dimensions. The general assumption ist, that each channel of an image has to have the same geometry. \sa Image, ChannelDescriptor */ class MITKCORE_EXPORT ImageDescriptor : public itk::Object { public: mitkClassMacroItkParent(ImageDescriptor, itk::Object); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /** Insert new channel @param ptype Pixel Type @param name channel's name */ void AddNewChannel(mitk::PixelType ptype, const char *name = nullptr); /** \brief Initialize the image descriptor by the dimensions */ void Initialize(const unsigned int *dims, const unsigned int dim); /** \brief Initialize the descriptor by an referenced Descriptor */ void Initialize(const ImageDescriptor::Pointer refDescriptor, unsigned int channel = 0); /** \brief Get the C-array of unsigned int holding the size for each dimension of the image The C-array has allways lenght of MAX_IMAGE_DIMENSIONS */ const unsigned int *GetDimensions() const { return m_Dimensions; } /** \brief Get the number dimensions used (e.g. non-zero size) The return value does not exceed MAX_IMAGE_DIMENSIONS */ unsigned int GetNumberOfDimensions() const { return m_NumberOfDimensions; } /** \brief Get the name of selected channel If the name of the channel wasn't initialized, the string returned is set to "Unnamed [ ]" \sa PixelType, ChannelDescriptor */ const std::string GetChannelName(unsigned int id) const; /** \brief Get the pixel type of a channel specified by its name Returns an uninitialized PixelType object if no channel with given name was found */ PixelType GetChannelTypeByName(const char *name) const; /** \brief Get the pixel type of a channel specified by its id Returns an uninitialized PixelType object if no channel with given id was found */ PixelType GetChannelTypeById(unsigned int id) const; /** \brief Get the ChannelDescriptor for a channel specified by its id */ ChannelDescriptor GetChannelDescriptor(unsigned int id = 0) const; /** \brief Get the count of channels used */ unsigned int GetNumberOfChannels() const { return m_NumberOfChannels; } protected: /** Protected constructor */ ImageDescriptor(); /** Protected desctructor */ ~ImageDescriptor() override{}; private: /** A std::vector holding a pointer to a ChannelDescriptor for each active channel of the image */ std::vector m_ChannelDesc; /** A vector holding the names of corresponding channels */ std::vector m_ChannelNames; /** Constant iterator for traversing the vector of channel's names */ typedef std::vector::const_iterator ConstChannelNamesIter; /** Constant iterator for traversing the vector of ChannelDescriptors */ typedef std::vector::const_iterator ConstChannelsIter; unsigned int m_NumberOfChannels; unsigned int m_NumberOfDimensions; unsigned int m_Dimensions[MAX_IMAGE_DIMENSIONS]; }; } // end namespace #endif // MITKIMAGEDESCRIPTOR_H diff --git a/Modules/Core/src/DataManagement/mitkImage.cpp b/Modules/Core/src/DataManagement/mitkImage.cpp index 251e1ca36f..bd5ba5e95d 100644 --- a/Modules/Core/src/DataManagement/mitkImage.cpp +++ b/Modules/Core/src/DataManagement/mitkImage.cpp @@ -1,1369 +1,1358 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // MITK #include "mitkImage.h" #include "mitkCompareImageDataFilter.h" #include "mitkImageStatisticsHolder.h" #include "mitkImageVtkReadAccessor.h" #include "mitkImageVtkWriteAccessor.h" #include "mitkPixelTypeMultiplex.h" #include // VTK #include // ITK #include // Other #include #define FILL_C_ARRAY(_arr, _size, _value) \ for (unsigned int i = 0u; i < _size; i++) \ \ { \ _arr[i] = _value; \ } mitk::Image::Image() : m_Dimension(0), m_Dimensions(nullptr), m_ImageDescriptor(nullptr), m_OffsetTable(nullptr), m_CompleteData(nullptr), m_ImageStatistics(nullptr) { m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS]; FILL_C_ARRAY(m_Dimensions, MAX_IMAGE_DIMENSIONS, 0u); m_Initialized = false; } mitk::Image::Image(const Image &other) : SlicedData(other), m_Dimension(0), m_Dimensions(nullptr), m_ImageDescriptor(nullptr), m_OffsetTable(nullptr), m_CompleteData(nullptr), m_ImageStatistics(nullptr) { m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS]; FILL_C_ARRAY(m_Dimensions, MAX_IMAGE_DIMENSIONS, 0u); this->Initialize(other.GetPixelType(), other.GetDimension(), other.GetDimensions()); // Since the above called "Initialize" method doesn't take the geometry into account we need to set it // here manually TimeGeometry::Pointer cloned = other.GetTimeGeometry()->Clone(); this->SetTimeGeometry(cloned.GetPointer()); if (this->GetDimension() > 3) { const unsigned int time_steps = this->GetDimension(3); for (unsigned int i = 0u; i < time_steps; ++i) { ImageDataItemPointer volume = other.GetVolumeData(i); this->SetVolume(volume->GetData(), i); } } else { ImageDataItemPointer volume = other.GetVolumeData(0); this->SetVolume(volume->GetData(), 0); } } mitk::Image::~Image() { this->Clear(); m_ReferenceCount = 3; m_ReferenceCount = 0; delete[] m_OffsetTable; delete m_ImageStatistics; } const mitk::PixelType mitk::Image::GetPixelType(int n) const { return this->m_ImageDescriptor->GetChannelTypeById(n); } unsigned int mitk::Image::GetDimension() const { return m_Dimension; } unsigned int mitk::Image::GetDimension(int i) const { if ((i >= 0) && (i < (int)m_Dimension)) return m_Dimensions[i]; return 1; } template void AccessPixel(const mitk::PixelType ptype, void *data, const unsigned int offset, double &value) { value = 0.0; if (data == nullptr) return; if (ptype.GetBpe() != 24) { value = (double)(((T *)data)[offset]); } else { const unsigned int rgboffset = offset; double returnvalue = (((T *)data)[rgboffset]); returnvalue += (((T *)data)[rgboffset + 1]); returnvalue += (((T *)data)[rgboffset + 2]); value = returnvalue; } } vtkImageData *mitk::Image::GetVtkImageData(int t, int n) { if (m_Initialized == false) { if (GetSource().IsNull()) return nullptr; if (GetSource()->Updating() == false) GetSource()->UpdateOutputInformation(); } ImageDataItemPointer volume = GetVolumeData(t, n); return volume.GetPointer() == nullptr ? nullptr : volume->GetVtkImageAccessor(this)->GetVtkImageData(); } const vtkImageData *mitk::Image::GetVtkImageData(int t, int n) const { if (m_Initialized == false) { if (GetSource().IsNull()) return nullptr; if (GetSource()->Updating() == false) GetSource()->UpdateOutputInformation(); } ImageDataItemPointer volume = GetVolumeData(t, n); return volume.GetPointer() == nullptr ? nullptr : volume->GetVtkImageAccessor(this)->GetVtkImageData(); } mitk::Image::ImageDataItemPointer mitk::Image::GetSliceData( int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { MutexHolder lock(m_ImageDataArraysLock); return GetSliceData_unlocked(s, t, n, data, importMemoryManagement); } mitk::Image::ImageDataItemPointer mitk::Image::GetSliceData_unlocked( int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { if (IsValidSlice(s, t, n) == false) return nullptr; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // slice directly available? int pos = GetSliceIndex(s, t, n); if (m_Slices[pos].GetPointer() != nullptr) { return m_Slices[pos]; } // is slice available as part of a volume that is available? ImageDataItemPointer sl, ch, vol; vol = m_Volumes[GetVolumeIndex(t, n)]; if ((vol.GetPointer() != nullptr) && (vol->IsComplete())) { sl = new ImageDataItem(*vol, m_ImageDescriptor, t, 2, data, importMemoryManagement == ManageMemory, ((size_t)s) * m_OffsetTable[2] * (ptypeSize)); sl->SetComplete(true); return m_Slices[pos] = sl; } // is slice available as part of a channel that is available? ch = m_Channels[n]; if ((ch.GetPointer() != nullptr) && (ch->IsComplete())) { sl = new ImageDataItem(*ch, m_ImageDescriptor, t, 2, data, importMemoryManagement == ManageMemory, (((size_t)s) * m_OffsetTable[2] + ((size_t)t) * m_OffsetTable[3]) * (ptypeSize)); sl->SetComplete(true); return m_Slices[pos] = sl; } // slice is unavailable. Can we calculate it? if ((GetSource().IsNotNull()) && (GetSource()->Updating() == false)) { // ... wir mussen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, s); m_RequestedRegion.SetIndex(3, t); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, 1); m_RequestedRegion.SetSize(3, 1); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized = true; GetSource()->Update(); if (IsSliceSet_unlocked(s, t, n)) // yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetSliceData_unlocked(s, t, n, data, importMemoryManagement); else return nullptr; } else { ImageDataItemPointer item = AllocateSliceData_unlocked(s, t, n, data, importMemoryManagement); item->SetComplete(true); return item; } } mitk::Image::ImageDataItemPointer mitk::Image::GetVolumeData(int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { MutexHolder lock(m_ImageDataArraysLock); return GetVolumeData_unlocked(t, n, data, importMemoryManagement); } mitk::Image::ImageDataItemPointer mitk::Image::GetVolumeData_unlocked( int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { if (IsValidVolume(t, n) == false) return nullptr; ImageDataItemPointer ch, vol; // volume directly available? int pos = GetVolumeIndex(t, n); vol = m_Volumes[pos]; if ((vol.GetPointer() != nullptr) && (vol->IsComplete())) return vol; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // is volume available as part of a channel that is available? ch = m_Channels[n]; if ((ch.GetPointer() != nullptr) && (ch->IsComplete())) { vol = new ImageDataItem(*ch, m_ImageDescriptor, t, 3, data, importMemoryManagement == ManageMemory, (((size_t)t) * m_OffsetTable[3]) * (ptypeSize)); vol->SetComplete(true); return m_Volumes[pos] = vol; } // let's see if all slices of the volume are set, so that we can (could) combine them to a volume bool complete = true; unsigned int s; for (s = 0; s < m_Dimensions[2]; ++s) { if (m_Slices[GetSliceIndex(s, t, n)].GetPointer() == nullptr) { complete = false; break; } } if (complete) { // if there is only single slice we do not need to combine anything if (m_Dimensions[2] <= 1) { ImageDataItemPointer sl; sl = GetSliceData_unlocked(0, t, n, data, importMemoryManagement); vol = new ImageDataItem(*sl, m_ImageDescriptor, t, 3, data, importMemoryManagement == ManageMemory); vol->SetComplete(true); } else { mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n); vol = m_Volumes[pos]; // ok, let's combine the slices! if (vol.GetPointer() == nullptr) { vol = new ImageDataItem(chPixelType, t, 3, m_Dimensions, nullptr, true); } vol->SetComplete(true); size_t size = m_OffsetTable[2] * (ptypeSize); for (s = 0; s < m_Dimensions[2]; ++s) { int posSl; ImageDataItemPointer sl; posSl = GetSliceIndex(s, t, n); sl = m_Slices[posSl]; if (sl->GetParent() != vol) { // copy data of slices in volume size_t offset = ((size_t)s) * size; std::memcpy(static_cast(vol->GetData()) + offset, sl->GetData(), size); - // FIXME mitkIpPicDescriptor * pic = sl->GetPicDescriptor(); - // replace old slice with reference to volume sl = new ImageDataItem( *vol, m_ImageDescriptor, t, 2, data, importMemoryManagement == ManageMemory, ((size_t)s) * size); sl->SetComplete(true); - // mitkIpFuncCopyTags(sl->GetPicDescriptor(), pic); m_Slices[posSl] = sl; } } - // if(vol->GetPicDescriptor()->info->tags_head==nullptr) - // mitkIpFuncCopyTags(vol->GetPicDescriptor(), m_Slices[GetSliceIndex(0,t,n)]->GetPicDescriptor()); } return m_Volumes[pos] = vol; } // volume is unavailable. Can we calculate it? if ((GetSource().IsNotNull()) && (GetSource()->Updating() == false)) { // ... wir muessen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, 0); m_RequestedRegion.SetIndex(3, t); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, m_Dimensions[2]); m_RequestedRegion.SetSize(3, 1); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized = true; GetSource()->Update(); if (IsVolumeSet_unlocked(t, n)) // yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetVolumeData_unlocked(t, n, data, importMemoryManagement); else return nullptr; } else { ImageDataItemPointer item = AllocateVolumeData_unlocked(t, n, data, importMemoryManagement); item->SetComplete(true); return item; } } mitk::Image::ImageDataItemPointer mitk::Image::GetChannelData(int n, void *data, ImportMemoryManagementType importMemoryManagement) const { MutexHolder lock(m_ImageDataArraysLock); return GetChannelData_unlocked(n, data, importMemoryManagement); } mitk::Image::ImageDataItemPointer mitk::Image::GetChannelData_unlocked( int n, void *data, ImportMemoryManagementType importMemoryManagement) const { if (IsValidChannel(n) == false) return nullptr; ImageDataItemPointer ch, vol; ch = m_Channels[n]; if ((ch.GetPointer() != nullptr) && (ch->IsComplete())) return ch; // let's see if all volumes are set, so that we can (could) combine them to a channel if (IsChannelSet_unlocked(n)) { // if there is only one time frame we do not need to combine anything if (m_Dimensions[3] <= 1) { vol = GetVolumeData_unlocked(0, n, data, importMemoryManagement); ch = new ImageDataItem(*vol, m_ImageDescriptor, 0, m_ImageDescriptor->GetNumberOfDimensions(), data, importMemoryManagement == ManageMemory); ch->SetComplete(true); } else { const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ch = m_Channels[n]; // ok, let's combine the volumes! if (ch.GetPointer() == nullptr) ch = new ImageDataItem(this->m_ImageDescriptor, -1, nullptr, true); ch->SetComplete(true); size_t size = m_OffsetTable[m_Dimension - 1] * (ptypeSize); unsigned int t; auto slicesIt = m_Slices.begin() + n * m_Dimensions[2] * m_Dimensions[3]; for (t = 0; t < m_Dimensions[3]; ++t) { int posVol; ImageDataItemPointer vol; posVol = GetVolumeIndex(t, n); vol = GetVolumeData_unlocked(t, n, data, importMemoryManagement); if (vol->GetParent() != ch) { // copy data of volume in channel size_t offset = ((size_t)t) * m_OffsetTable[3] * (ptypeSize); std::memcpy(static_cast(ch->GetData()) + offset, vol->GetData(), size); - // REVEIW FIX mitkIpPicDescriptor * pic = vol->GetPicDescriptor(); - // replace old volume with reference to channel vol = new ImageDataItem(*ch, m_ImageDescriptor, t, 3, data, importMemoryManagement == ManageMemory, offset); vol->SetComplete(true); - // mitkIpFuncCopyTags(vol->GetPicDescriptor(), pic); m_Volumes[posVol] = vol; // get rid of slices - they may point to old volume ImageDataItemPointer dnull = nullptr; for (unsigned int i = 0; i < m_Dimensions[2]; ++i, ++slicesIt) { assert(slicesIt != m_Slices.end()); *slicesIt = dnull; } } } - // REVIEW FIX - // if(ch->GetPicDescriptor()->info->tags_head==nullptr) - // mitkIpFuncCopyTags(ch->GetPicDescriptor(), m_Volumes[GetVolumeIndex(0,n)]->GetPicDescriptor()); } return m_Channels[n] = ch; } // channel is unavailable. Can we calculate it? if ((GetSource().IsNotNull()) && (GetSource()->Updating() == false)) { // ... wir muessen rechnen!!! .... m_RequestedRegion.SetIndex(0, 0); m_RequestedRegion.SetIndex(1, 0); m_RequestedRegion.SetIndex(2, 0); m_RequestedRegion.SetIndex(3, 0); m_RequestedRegion.SetIndex(4, n); m_RequestedRegion.SetSize(0, m_Dimensions[0]); m_RequestedRegion.SetSize(1, m_Dimensions[1]); m_RequestedRegion.SetSize(2, m_Dimensions[2]); m_RequestedRegion.SetSize(3, m_Dimensions[3]); m_RequestedRegion.SetSize(4, 1); m_RequestedRegionInitialized = true; GetSource()->Update(); // did it work? if (IsChannelSet_unlocked(n)) // yes: now we can call ourselves without the risk of a endless loop (see "if" above) return GetChannelData_unlocked(n, data, importMemoryManagement); else return nullptr; } else { ImageDataItemPointer item = AllocateChannelData_unlocked(n, data, importMemoryManagement); item->SetComplete(true); return item; } } bool mitk::Image::IsSliceSet(int s, int t, int n) const { MutexHolder lock(m_ImageDataArraysLock); return IsSliceSet_unlocked(s, t, n); } bool mitk::Image::IsSliceSet_unlocked(int s, int t, int n) const { if (IsValidSlice(s, t, n) == false) return false; if (m_Slices[GetSliceIndex(s, t, n)].GetPointer() != nullptr) { return true; } ImageDataItemPointer ch, vol; vol = m_Volumes[GetVolumeIndex(t, n)]; if ((vol.GetPointer() != nullptr) && (vol->IsComplete())) { return true; } ch = m_Channels[n]; if ((ch.GetPointer() != nullptr) && (ch->IsComplete())) { return true; } return false; } bool mitk::Image::IsVolumeSet(int t, int n) const { MutexHolder lock(m_ImageDataArraysLock); return IsVolumeSet_unlocked(t, n); } bool mitk::Image::IsVolumeSet_unlocked(int t, int n) const { if (IsValidVolume(t, n) == false) return false; ImageDataItemPointer ch, vol; // volume directly available? vol = m_Volumes[GetVolumeIndex(t, n)]; if ((vol.GetPointer() != nullptr) && (vol->IsComplete())) return true; // is volume available as part of a channel that is available? ch = m_Channels[n]; if ((ch.GetPointer() != nullptr) && (ch->IsComplete())) return true; // let's see if all slices of the volume are set, so that we can (could) combine them to a volume unsigned int s; for (s = 0; s < m_Dimensions[2]; ++s) { if (m_Slices[GetSliceIndex(s, t, n)].GetPointer() == nullptr) { return false; } } return true; } bool mitk::Image::IsChannelSet(int n) const { MutexHolder lock(m_ImageDataArraysLock); return IsChannelSet_unlocked(n); } bool mitk::Image::IsChannelSet_unlocked(int n) const { if (IsValidChannel(n) == false) return false; ImageDataItemPointer ch, vol; ch = m_Channels[n]; if ((ch.GetPointer() != nullptr) && (ch->IsComplete())) return true; // let's see if all volumes are set, so that we can (could) combine them to a channel unsigned int t; for (t = 0; t < m_Dimensions[3]; ++t) { if (IsVolumeSet_unlocked(t, n) == false) { return false; } } return true; } bool mitk::Image::SetSlice(const void *data, int s, int t, int n) { // const_cast is no risk for ImportMemoryManagementType == CopyMemory return SetImportSlice(const_cast(data), s, t, n, CopyMemory); } bool mitk::Image::SetVolume(const void *data, int t, int n) { // const_cast is no risk for ImportMemoryManagementType == CopyMemory return SetImportVolume(const_cast(data), t, n, CopyMemory); } bool mitk::Image::SetChannel(const void *data, int n) { // const_cast is no risk for ImportMemoryManagementType == CopyMemory return SetImportChannel(const_cast(data), n, CopyMemory); } bool mitk::Image::SetImportSlice(void *data, int s, int t, int n, ImportMemoryManagementType importMemoryManagement) { if (IsValidSlice(s, t, n) == false) return false; ImageDataItemPointer sl; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); if (IsSliceSet(s, t, n)) { sl = GetSliceData(s, t, n, data, importMemoryManagement); if (sl->GetManageMemory() == false) { sl = AllocateSliceData(s, t, n, data, importMemoryManagement); if (sl.GetPointer() == nullptr) return false; } if (sl->GetData() != data) std::memcpy(sl->GetData(), data, m_OffsetTable[2] * (ptypeSize)); sl->Modified(); // we have changed the data: call Modified()! Modified(); } else { sl = AllocateSliceData(s, t, n, data, importMemoryManagement); if (sl.GetPointer() == nullptr) return false; if (sl->GetData() != data) std::memcpy(sl->GetData(), data, m_OffsetTable[2] * (ptypeSize)); // we just added a missing slice, which is not regarded as modification. // Therefore, we do not call Modified()! } return true; } bool mitk::Image::SetImportVolume(void *data, int t, int n, ImportMemoryManagementType importMemoryManagement) { if (IsValidVolume(t, n) == false) return false; const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ImageDataItemPointer vol; if (IsVolumeSet(t, n)) { vol = GetVolumeData(t, n, data, importMemoryManagement); if (vol->GetManageMemory() == false) { vol = AllocateVolumeData(t, n, data, importMemoryManagement); if (vol.GetPointer() == nullptr) return false; } if (vol->GetData() != data) std::memcpy(vol->GetData(), data, m_OffsetTable[3] * (ptypeSize)); vol->Modified(); vol->SetComplete(true); // we have changed the data: call Modified()! Modified(); } else { vol = AllocateVolumeData(t, n, data, importMemoryManagement); if (vol.GetPointer() == nullptr) return false; if (vol->GetData() != data) { std::memcpy(vol->GetData(), data, m_OffsetTable[3] * (ptypeSize)); } vol->SetComplete(true); this->m_ImageDescriptor->GetChannelDescriptor(n).SetData(vol->GetData()); // we just added a missing Volume, which is not regarded as modification. // Therefore, we do not call Modified()! } return true; } bool mitk::Image::SetImportVolume(const void *const_data, int t, int n) { return this->SetImportVolume(const_cast(const_data), t, n, CopyMemory); } bool mitk::Image::SetImportChannel(void *data, int n, ImportMemoryManagementType importMemoryManagement) { if (IsValidChannel(n) == false) return false; // channel descriptor const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ImageDataItemPointer ch; if (IsChannelSet(n)) { ch = GetChannelData(n, data, importMemoryManagement); if (ch->GetManageMemory() == false) { ch = AllocateChannelData(n, data, importMemoryManagement); if (ch.GetPointer() == nullptr) return false; } if (ch->GetData() != data) std::memcpy(ch->GetData(), data, m_OffsetTable[4] * (ptypeSize)); ch->Modified(); ch->SetComplete(true); // we have changed the data: call Modified()! Modified(); } else { ch = AllocateChannelData(n, data, importMemoryManagement); if (ch.GetPointer() == nullptr) return false; if (ch->GetData() != data) std::memcpy(ch->GetData(), data, m_OffsetTable[4] * (ptypeSize)); ch->SetComplete(true); this->m_ImageDescriptor->GetChannelDescriptor(n).SetData(ch->GetData()); // we just added a missing Channel, which is not regarded as modification. // Therefore, we do not call Modified()! } return true; } void mitk::Image::Initialize() { ImageDataItemPointerArray::iterator it, end; for (it = m_Slices.begin(), end = m_Slices.end(); it != end; ++it) { (*it) = nullptr; } for (it = m_Volumes.begin(), end = m_Volumes.end(); it != end; ++it) { (*it) = nullptr; } for (it = m_Channels.begin(), end = m_Channels.end(); it != end; ++it) { (*it) = nullptr; } m_CompleteData = nullptr; if (m_ImageStatistics == nullptr) { m_ImageStatistics = new mitk::ImageStatisticsHolder(this); } SetRequestedRegionToLargestPossibleRegion(); } void mitk::Image::Initialize(const mitk::ImageDescriptor::Pointer inDesc) { // store the descriptor this->m_ImageDescriptor = inDesc; // initialize image this->Initialize( inDesc->GetChannelDescriptor(0).GetPixelType(), inDesc->GetNumberOfDimensions(), inDesc->GetDimensions(), 1); } void mitk::Image::Initialize(const mitk::PixelType &type, unsigned int dimension, const unsigned int *dimensions, unsigned int channels) { Clear(); m_Dimension = dimension; if (!dimensions) itkExceptionMacro(<< "invalid zero dimension image"); unsigned int i; for (i = 0; i < dimension; ++i) { if (dimensions[i] < 1) itkExceptionMacro(<< "invalid dimension[" << i << "]: " << dimensions[i]); } // create new array since the old was deleted m_Dimensions = new unsigned int[MAX_IMAGE_DIMENSIONS]; // initialize the first four dimensions to 1, the remaining 4 to 0 FILL_C_ARRAY(m_Dimensions, 4, 1u); FILL_C_ARRAY((m_Dimensions + 4), 4, 0u); // copy in the passed dimension information std::memcpy(m_Dimensions, dimensions, sizeof(unsigned int) * m_Dimension); this->m_ImageDescriptor = mitk::ImageDescriptor::New(); this->m_ImageDescriptor->Initialize(this->m_Dimensions, this->m_Dimension); for (i = 0; i < 4; ++i) { m_LargestPossibleRegion.SetIndex(i, 0); m_LargestPossibleRegion.SetSize(i, m_Dimensions[i]); } m_LargestPossibleRegion.SetIndex(i, 0); m_LargestPossibleRegion.SetSize(i, channels); if (m_LargestPossibleRegion.GetNumberOfPixels() == 0) { delete[] m_Dimensions; m_Dimensions = nullptr; return; } for (unsigned int i = 0u; i < channels; i++) { this->m_ImageDescriptor->AddNewChannel(type); } PlaneGeometry::Pointer planegeometry = PlaneGeometry::New(); planegeometry->InitializeStandardPlane(m_Dimensions[0], m_Dimensions[1]); SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New(); slicedGeometry->InitializeEvenlySpaced(planegeometry, m_Dimensions[2]); ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New(); timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]); for (TimeStepType step = 0; step < timeGeometry->CountTimeSteps(); ++step) { timeGeometry->GetGeometryForTimeStep(step)->ImageGeometryOn(); } SetTimeGeometry(timeGeometry); ImageDataItemPointer dnull = nullptr; m_Channels.assign(GetNumberOfChannels(), dnull); m_Volumes.assign(GetNumberOfChannels() * m_Dimensions[3], dnull); m_Slices.assign(GetNumberOfChannels() * m_Dimensions[3] * m_Dimensions[2], dnull); ComputeOffsetTable(); Initialize(); m_Initialized = true; } void mitk::Image::Initialize(const mitk::PixelType &type, const mitk::BaseGeometry &geometry, unsigned int channels, int tDim) { mitk::ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New(); timeGeometry->Initialize(geometry.Clone(), tDim); this->Initialize(type, *timeGeometry, channels, tDim); } void mitk::Image::Initialize(const mitk::PixelType &type, const mitk::TimeGeometry &geometry, unsigned int channels, int tDim) { unsigned int dimensions[5]; dimensions[0] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(0) + 0.5); dimensions[1] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(1) + 0.5); dimensions[2] = (unsigned int)(geometry.GetGeometryForTimeStep(0)->GetExtent(2) + 0.5); dimensions[3] = (tDim > 0) ? tDim : geometry.CountTimeSteps(); dimensions[4] = 0; unsigned int dimension = 2; if (dimensions[2] > 1) dimension = 3; if (dimensions[3] > 1) dimension = 4; Initialize(type, dimension, dimensions, channels); if (geometry.CountTimeSteps() > 1) { TimeGeometry::Pointer cloned = geometry.Clone(); SetTimeGeometry(cloned.GetPointer()); // make sure the image geometry flag is properly set for all time steps for (TimeStepType step = 0; step < cloned->CountTimeSteps(); ++step) { if (!cloned->GetGeometryCloneForTimeStep(step)->GetImageGeometry()) { MITK_WARN("Image.3DnT.Initialize") << " Attempt to initialize an image with a non-image geometry. " "Re-interpretting the initialization geometry for timestep " << step << " as image geometry, the original geometry remains unchanged."; cloned->GetGeometryForTimeStep(step)->ImageGeometryOn(); } } } else { // make sure the image geometry coming from outside has proper value of the image geometry flag BaseGeometry::Pointer cloned = geometry.GetGeometryCloneForTimeStep(0)->Clone(); if (!cloned->GetImageGeometry()) { MITK_WARN("Image.Initialize") << " Attempt to initialize an image with a non-image geometry. Re-interpretting " "the initialization geometry as image geometry, the original geometry remains " "unchanged."; cloned->ImageGeometryOn(); } Superclass::SetGeometry(cloned); } } void mitk::Image::Initialize(const mitk::PixelType &type, int sDim, const mitk::PlaneGeometry &geometry2d, unsigned int channels, int tDim) { SlicedGeometry3D::Pointer slicedGeometry = SlicedGeometry3D::New(); slicedGeometry->InitializeEvenlySpaced(geometry2d.Clone(), sDim); Initialize(type, *slicedGeometry, channels, tDim); } void mitk::Image::Initialize(const mitk::Image *image) { Initialize(image->GetPixelType(), *image->GetTimeGeometry()); } void mitk::Image::Initialize(vtkImageData *vtkimagedata, int channels, int tDim, int sDim, int pDim) { if (vtkimagedata == nullptr) return; m_Dimension = vtkimagedata->GetDataDimension(); unsigned int i, *tmpDimensions = new unsigned int[m_Dimension > 4 ? m_Dimension : 4]; for (i = 0; i < m_Dimension; ++i) tmpDimensions[i] = vtkimagedata->GetDimensions()[i]; if (m_Dimension < 4) { unsigned int *p; for (i = 0, p = tmpDimensions + m_Dimension; i < 4 - m_Dimension; ++i, ++p) *p = 1; } if (pDim >= 0) { tmpDimensions[1] = pDim; if (m_Dimension < 2) m_Dimension = 2; } if (sDim >= 0) { tmpDimensions[2] = sDim; if (m_Dimension < 3) m_Dimension = 3; } if (tDim >= 0) { tmpDimensions[3] = tDim; if (m_Dimension < 4) m_Dimension = 4; } mitk::PixelType pixelType(MakePixelType(vtkimagedata)); Initialize(pixelType, m_Dimension, tmpDimensions, channels); const double *spacinglist = vtkimagedata->GetSpacing(); Vector3D spacing; FillVector3D(spacing, spacinglist[0], 1.0, 1.0); if (m_Dimension >= 2) spacing[1] = spacinglist[1]; if (m_Dimension >= 3) spacing[2] = spacinglist[2]; // access origin of vtkImage Point3D origin; double vtkorigin[3]; vtkimagedata->GetOrigin(vtkorigin); FillVector3D(origin, vtkorigin[0], 0.0, 0.0); if (m_Dimension >= 2) origin[1] = vtkorigin[1]; if (m_Dimension >= 3) origin[2] = vtkorigin[2]; SlicedGeometry3D *slicedGeometry = GetSlicedGeometry(0); // re-initialize PlaneGeometry with origin and direction auto *planeGeometry = static_cast(slicedGeometry->GetPlaneGeometry(0)); planeGeometry->SetOrigin(origin); // re-initialize SlicedGeometry3D slicedGeometry->SetOrigin(origin); slicedGeometry->SetSpacing(spacing); ProportionalTimeGeometry::Pointer timeGeometry = ProportionalTimeGeometry::New(); timeGeometry->Initialize(slicedGeometry, m_Dimensions[3]); SetTimeGeometry(timeGeometry); delete[] tmpDimensions; } bool mitk::Image::IsValidSlice(int s, int t, int n) const { if (m_Initialized) return ((s >= 0) && (s < (int)m_Dimensions[2]) && (t >= 0) && (t < (int)m_Dimensions[3]) && (n >= 0) && (n < (int)GetNumberOfChannels())); else return false; } bool mitk::Image::IsValidVolume(int t, int n) const { if (m_Initialized) return IsValidSlice(0, t, n); else return false; } bool mitk::Image::IsValidChannel(int n) const { if (m_Initialized) return IsValidSlice(0, 0, n); else return false; } void mitk::Image::ComputeOffsetTable() { if (m_OffsetTable != nullptr) delete[] m_OffsetTable; m_OffsetTable = new size_t[m_Dimension > 4 ? m_Dimension + 1 : 4 + 1]; unsigned int i; size_t num = 1; m_OffsetTable[0] = 1; for (i = 0; i < m_Dimension; ++i) { num *= m_Dimensions[i]; m_OffsetTable[i + 1] = num; } for (; i < 4; ++i) m_OffsetTable[i + 1] = num; } bool mitk::Image::IsValidTimeStep(int t) const { return ((m_Dimension >= 4 && t <= (int)m_Dimensions[3] && t > 0) || (t == 0)); } void mitk::Image::Expand(unsigned int timeSteps) { if (timeSteps < 1) itkExceptionMacro(<< "Invalid timestep in Image!"); Superclass::Expand(timeSteps); } int mitk::Image::GetSliceIndex(int s, int t, int n) const { if (IsValidSlice(s, t, n) == false) return false; return ((size_t)s) + ((size_t)t) * m_Dimensions[2] + ((size_t)n) * m_Dimensions[3] * m_Dimensions[2]; //?? } int mitk::Image::GetVolumeIndex(int t, int n) const { if (IsValidVolume(t, n) == false) return false; return ((size_t)t) + ((size_t)n) * m_Dimensions[3]; //?? } mitk::Image::ImageDataItemPointer mitk::Image::AllocateSliceData( int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { MutexHolder lock(m_ImageDataArraysLock); return AllocateSliceData_unlocked(s, t, n, data, importMemoryManagement); } mitk::Image::ImageDataItemPointer mitk::Image::AllocateSliceData_unlocked( int s, int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { int pos; pos = GetSliceIndex(s, t, n); const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // is slice available as part of a volume that is available? ImageDataItemPointer sl, ch, vol; vol = m_Volumes[GetVolumeIndex(t, n)]; if (vol.GetPointer() != nullptr) { sl = new ImageDataItem(*vol, m_ImageDescriptor, t, 2, data, importMemoryManagement == ManageMemory, ((size_t)s) * m_OffsetTable[2] * (ptypeSize)); sl->SetComplete(true); return m_Slices[pos] = sl; } // is slice available as part of a channel that is available? ch = m_Channels[n]; if (ch.GetPointer() != nullptr) { sl = new ImageDataItem(*ch, m_ImageDescriptor, t, 2, data, importMemoryManagement == ManageMemory, (((size_t)s) * m_OffsetTable[2] + ((size_t)t) * m_OffsetTable[3]) * (ptypeSize)); sl->SetComplete(true); return m_Slices[pos] = sl; } // allocate new volume (instead of a single slice to keep data together!) m_Volumes[GetVolumeIndex(t, n)] = vol = AllocateVolumeData_unlocked(t, n, nullptr, importMemoryManagement); sl = new ImageDataItem(*vol, m_ImageDescriptor, t, 2, data, importMemoryManagement == ManageMemory, ((size_t)s) * m_OffsetTable[2] * (ptypeSize)); sl->SetComplete(true); return m_Slices[pos] = sl; ////ALTERNATIVE: //// allocate new slice // sl=new ImageDataItem(*m_PixelType, 2, m_Dimensions); // m_Slices[pos]=sl; // return vol; } mitk::Image::ImageDataItemPointer mitk::Image::AllocateVolumeData( int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { MutexHolder lock(m_ImageDataArraysLock); return AllocateVolumeData_unlocked(t, n, data, importMemoryManagement); } mitk::Image::ImageDataItemPointer mitk::Image::AllocateVolumeData_unlocked( int t, int n, void *data, ImportMemoryManagementType importMemoryManagement) const { int pos; pos = GetVolumeIndex(t, n); const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); // is volume available as part of a channel that is available? ImageDataItemPointer ch, vol; ch = m_Channels[n]; if (ch.GetPointer() != nullptr) { vol = new ImageDataItem(*ch, m_ImageDescriptor, t, 3, data, importMemoryManagement == ManageMemory, (((size_t)t) * m_OffsetTable[3]) * (ptypeSize)); return m_Volumes[pos] = vol; } mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(n); // allocate new volume if (importMemoryManagement == CopyMemory) { vol = new ImageDataItem(chPixelType, t, 3, m_Dimensions, nullptr, true); if (data != nullptr) std::memcpy(vol->GetData(), data, m_OffsetTable[3] * (ptypeSize)); } else { vol = new ImageDataItem(chPixelType, t, 3, m_Dimensions, data, importMemoryManagement == ManageMemory); } m_Volumes[pos] = vol; return vol; } mitk::Image::ImageDataItemPointer mitk::Image::AllocateChannelData( int n, void *data, ImportMemoryManagementType importMemoryManagement) const { MutexHolder lock(m_ImageDataArraysLock); return AllocateChannelData_unlocked(n, data, importMemoryManagement); } mitk::Image::ImageDataItemPointer mitk::Image::AllocateChannelData_unlocked( int n, void *data, ImportMemoryManagementType importMemoryManagement) const { ImageDataItemPointer ch; // allocate new channel if (importMemoryManagement == CopyMemory) { const size_t ptypeSize = this->m_ImageDescriptor->GetChannelTypeById(n).GetSize(); ch = new ImageDataItem(this->m_ImageDescriptor, -1, nullptr, true); if (data != nullptr) std::memcpy(ch->GetData(), data, m_OffsetTable[4] * (ptypeSize)); } else { ch = new ImageDataItem(this->m_ImageDescriptor, -1, data, importMemoryManagement == ManageMemory); } m_Channels[n] = ch; return ch; } unsigned int *mitk::Image::GetDimensions() const { return m_Dimensions; } void mitk::Image::Clear() { Superclass::Clear(); delete[] m_Dimensions; m_Dimensions = nullptr; } void mitk::Image::SetGeometry(BaseGeometry *aGeometry3D) { // Please be aware of the 0.5 offset/pixel-center issue! See Geometry documentation for further information if (aGeometry3D->GetImageGeometry() == false) { MITK_INFO << "WARNING: Applied a non-image geometry onto an image. Please be SURE that this geometry is " "pixel-center-based! If it is not, you need to call " "Geometry3D->ChangeImageGeometryConsideringOriginOffset(true) before calling image->setGeometry(..)\n"; } Superclass::SetGeometry(aGeometry3D); for (TimeStepType step = 0; step < GetTimeGeometry()->CountTimeSteps(); ++step) GetTimeGeometry()->GetGeometryForTimeStep(step)->ImageGeometryOn(); } void mitk::Image::PrintSelf(std::ostream &os, itk::Indent indent) const { if (m_Initialized) { unsigned char i; os << indent << " Dimension: " << m_Dimension << std::endl; os << indent << " Dimensions: "; for (i = 0; i < m_Dimension; ++i) os << GetDimension(i) << " "; os << std::endl; for (unsigned int ch = 0; ch < this->m_ImageDescriptor->GetNumberOfChannels(); ch++) { mitk::PixelType chPixelType = this->m_ImageDescriptor->GetChannelTypeById(ch); os << indent << " Channel: " << this->m_ImageDescriptor->GetChannelName(ch) << std::endl; os << indent << " PixelType: " << chPixelType.GetPixelTypeAsString() << std::endl; os << indent << " BytesPerElement: " << chPixelType.GetSize() << std::endl; os << indent << " ComponentType: " << chPixelType.GetComponentTypeAsString() << std::endl; os << indent << " NumberOfComponents: " << chPixelType.GetNumberOfComponents() << std::endl; os << indent << " BitsPerComponent: " << chPixelType.GetBitsPerComponent() << std::endl; } } else { os << indent << " Image not initialized: m_Initialized: false" << std::endl; } Superclass::PrintSelf(os, indent); } bool mitk::Image::IsRotated() const { const mitk::BaseGeometry *geo = this->GetGeometry(); bool ret = false; if (geo) { const vnl_matrix_fixed &mx = geo->GetIndexToWorldTransform()->GetMatrix().GetVnlMatrix(); mitk::ScalarType ref = 0; for (short k = 0; k < 3; ++k) ref += mx[k][k]; ref /= 1000; // Arbitrary value; if a non-diagonal (nd) element is bigger then this, matrix is considered nd. for (short i = 0; i < 3; ++i) { for (short j = 0; j < 3; ++j) { if (i != j) { if (std::abs(mx[i][j]) > ref) // matrix is nd ret = true; } } } } return ret; } bool mitk::Equal(const mitk::Image &leftHandSide, const mitk::Image &rightHandSide, ScalarType eps, bool verbose) { bool returnValue = true; // Dimensionality if (rightHandSide.GetDimension() != leftHandSide.GetDimension()) { if (verbose) { MITK_INFO << "[( Image )] Dimensionality differs."; MITK_INFO << "leftHandSide is " << leftHandSide.GetDimension() << "rightHandSide is " << rightHandSide.GetDimension(); } returnValue = false; } // Pair-wise dimension (size) comparison unsigned int minDimensionality = std::min(rightHandSide.GetDimension(), leftHandSide.GetDimension()); for (unsigned int i = 0; i < minDimensionality; ++i) { if (rightHandSide.GetDimension(i) != leftHandSide.GetDimension(i)) { returnValue = false; if (verbose) { MITK_INFO << "[( Image )] dimension differs."; MITK_INFO << "leftHandSide->GetDimension(" << i << ") is " << leftHandSide.GetDimension(i) << "rightHandSide->GetDimension(" << i << ") is " << rightHandSide.GetDimension(i); } } } // Pixeltype mitk::PixelType pixelTypeRightHandSide = rightHandSide.GetPixelType(); mitk::PixelType pixelTypeLeftHandSide = leftHandSide.GetPixelType(); if (!(pixelTypeRightHandSide == pixelTypeLeftHandSide)) { if (verbose) { MITK_INFO << "[( Image )] PixelType differs."; MITK_INFO << "leftHandSide is " << pixelTypeLeftHandSide.GetTypeAsString() << "rightHandSide is " << pixelTypeRightHandSide.GetTypeAsString(); } returnValue = false; } // Geometries if (!mitk::Equal(*leftHandSide.GetGeometry(), *rightHandSide.GetGeometry(), eps, verbose)) { if (verbose) { MITK_INFO << "[( Image )] Geometries differ."; } returnValue = false; } // Pixel values - default mode [ 0 threshold in difference ] // compare only if all previous checks were successfull, otherwise the ITK filter will throw an exception if (returnValue) { mitk::CompareImageDataFilter::Pointer compareFilter = mitk::CompareImageDataFilter::New(); compareFilter->SetInput(0, &rightHandSide); compareFilter->SetInput(1, &leftHandSide); compareFilter->SetTolerance(eps); compareFilter->Update(); if ((!compareFilter->GetResult())) { returnValue = false; if (verbose) { MITK_INFO << "[(Image)] Pixel values differ: "; compareFilter->GetCompareResults().PrintSelf(); } } } return returnValue; } diff --git a/Modules/Core/src/mitkCoreObjectFactoryBase.cpp b/Modules/Core/src/mitkCoreObjectFactoryBase.cpp index 32cf6111ca..08d0443af4 100644 --- a/Modules/Core/src/mitkCoreObjectFactoryBase.cpp +++ b/Modules/Core/src/mitkCoreObjectFactoryBase.cpp @@ -1,67 +1,67 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkCoreObjectFactoryBase.h" void mitk::CoreObjectFactoryBase::CreateFileExtensions(MultimapType fileExtensionsMap, std::string &fileExtensions) { std::map aMap; // group the extensions by extension-group // e.g. aMap["DICOM files"] = "*.dcm *.DCM *.dc3 *.DC3 *.gdcm" for (auto it = fileExtensionsMap.begin(); it != fileExtensionsMap.end(); ++it) { std::string aValue = aMap[(*it).second]; if (aValue.compare("") != 0) { aValue.append(" "); } aValue.append((*it).first); aMap[(*it).second] = aValue; } // build the "all" entry (it contains all the extensions) // and add it to the string in the first position // e.g. "all (*.dcm *.DCM *.dc3 *.DC3 *.gdcm *.ima *.mhd ... *.vti *.hdr *.nrrd *.nhdr );;" fileExtensions = "known extensions ("; std::string lastKey = ""; for (auto it = fileExtensionsMap.begin(); it != fileExtensionsMap.end(); ++it) { std::string aKey = (*it).first; if (aKey.compare(lastKey) != 0) { if (lastKey.compare("") != 0) { fileExtensions.append(" "); } fileExtensions.append(aKey); } lastKey = aKey; } fileExtensions.append(");;all (*);;"); // build the entry for each extension-group - // e.g. "Sets of 2D slices (*.pic *.pic.gz *.bmp *.png *.dcm *.gdcm *.ima *.tiff);;" + // e.g. "Sets of 2D slices (*.bmp *.png *.dcm *.gdcm *.ima *.tiff);;" for (auto it = aMap.begin(); it != aMap.end(); ++it) { // cout << " [" << (*it).first << ", " << (*it).second << "]" << endl; std::string aKey = (*it).first; if (aKey.compare("") != 0) { fileExtensions.append((*it).first); fileExtensions.append(" ("); fileExtensions.append((*it).second); fileExtensions.append(");;"); } } } diff --git a/Modules/Core/test/CMakeLists.txt b/Modules/Core/test/CMakeLists.txt index 7839cb73bd..61f89dd6b6 100644 --- a/Modules/Core/test/CMakeLists.txt +++ b/Modules/Core/test/CMakeLists.txt @@ -1,177 +1,177 @@ # The core tests need relaxed compiler flags... # TODO fix core tests to compile without these additional no-error flags if(MSVC_VERSION) # disable deprecated warnings (they would lead to errors) mitkFunctionCheckCAndCXXCompilerFlags("/wd4996" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) else() mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) mitkFunctionCheckCAndCXXCompilerFlags("-Wno-error=deprecated-declarations" CMAKE_C_FLAGS CMAKE_CXX_FLAGS) endif() MITK_CREATE_MODULE_TESTS() if(TARGET ${TESTDRIVER}) mitk_use_modules(TARGET ${TESTDRIVER} PACKAGES ITK|IONRRD VTK|TestingRendering tinyxml2) mitkAddCustomModuleTest(mitkVolumeCalculatorTest_Png2D-bw mitkVolumeCalculatorTest ${MITK_DATA_DIR}/Png2D-bw.png ${MITK_DATA_DIR}/Pic2DplusT.nrrd ) mitkAddCustomModuleTest(mitkEventConfigTest_CreateObjectInDifferentWays mitkEventConfigTest ${MITK_SOURCE_DIR}/Modules/Core/test/resource/Interactions/StatemachineConfigTest.xml ) mitkAddCustomModuleTest(mitkDataStorageTest_US4DCyl mitkDataStorageTest ${MITK_DATA_DIR}/US4DCyl.nrrd ) mitkAddCustomModuleTest(mitkPointSetReaderTest mitkPointSetReaderTest ${MITK_DATA_DIR}/PointSetReaderTestData.mps ) mitkAddCustomModuleTest(mitkImageTest_4DImageData mitkImageTest ${MITK_DATA_DIR}/US4DCyl.nrrd ) mitkAddCustomModuleTest(mitkImageTest_2D+tImageData mitkImageTest ${MITK_DATA_DIR}/Pic2DplusT.nrrd ) mitkAddCustomModuleTest(mitkImageTest_3DImageData mitkImageTest ${MITK_DATA_DIR}/Pic3D.nrrd ) mitkAddCustomModuleTest(mitkImageEqualTest mitkImageEqualTest) mitkAddCustomModuleTest(mitkImageTest_brainImage mitkImageTest ${MITK_DATA_DIR}/brain.mhd ) mitkAddCustomModuleTest(mitkMultiComponentImageDataComparisonFilterTest mitkMultiComponentImageDataComparisonFilterTest ${MITK_DATA_DIR}/NrrdWritingTestImage.jpg ) mitkAddCustomModuleTest(mitkImageToItkTest mitkImageToItkTest ${MITK_DATA_DIR}/Pic3D.nrrd ) mitkAddCustomModuleTest(mitkImageSliceSelectorTest mitkImageSliceSelectorTest ${MITK_DATA_DIR}/Pic2DplusT.nrrd ) mitkAddCustomModuleTest(mitkRotatedSlice4DTest mitkRotatedSlice4DTest ${MITK_DATA_DIR}/UltrasoundImages/4D_TEE_Data_MV.dcm ) mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_rgbaImage640x480 mitkImageVtkMapper2DTest ${MITK_DATA_DIR}/RenderingTestData/rgbaImage.png #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/rgbaImage640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3d640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3d640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3dColorBlue640x480 mitkImageVtkMapper2DColorTest #test for color property (=blue) Pic3D sagittal slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dColorBlue640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3dLevelWindow640x480 mitkImageVtkMapper2DLevelWindowTest #test for levelwindow property (=blood) #Pic3D sagittal slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dLevelWindowBlood640x480REF.png #corresponding reference #screenshot ) mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_pic3dSwivel640x480 mitkImageVtkMapper2DSwivelTest #test for a randomly chosen Pic3D swivelled slice ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dSwivel640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_openMeAlone640x480 mitkPointSetVtkMapper2DTest ${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAlone640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_Pic3DPointSetForPic3D640x480 mitkPointSetVtkMapper2DImageTest ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/RenderingTestData/PointSetForPic3D.mps #input point set and image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Pic3DPointSetForPic3D640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_openMeAloneGlyphType640x480 mitkPointSetVtkMapper2DGlyphTypeTest ${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAloneGlyphType640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkPointSetVtkMapper2D_openMeAloneTransformed640x480 mitkPointSetVtkMapper2DTransformedPointsTest ${MITK_DATA_DIR}/RenderingTestData/openMeAlone.mps #input point set to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/openMeAloneTransformedPoints640x480REF.png #corresponding reference screenshot ) # Currently not working on windows because of a rendering timing issue # see bug 18083 for details if(NOT WIN32) mitkAddCustomModuleRenderingTest(mitkSurfaceDepthSortingTransparency_StanfordBunnySTL640x480 mitkSurfaceDepthSortingTest ${MITK_DATA_DIR}/RenderingTestData/Stanford_bunny.stl -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Stanford_bunnySTLDepthSorting640x480REF.png) endif() # BUG 18695 - tests deactivated, because win 32 bit continuous renders images slightly different. TODO! #Test reslice interpolation #note: nearest mode is already tested by swivel test #mitkAddCustomModuleRenderingTest(ResliceInterpolationIsLinear mitkImageVtkMapper2DResliceInterpolationPropertyTest # 1 #linear # ${MITK_DATA_DIR}/Pic3D.nrrd # -V # ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefLinear.png #corresponding reference screenshot LINEAR #) #mitkAddCustomModuleRenderingTest(ResliceInterpolationIsCubic mitkImageVtkMapper2DResliceInterpolationPropertyTest # 3 #cubic # ${MITK_DATA_DIR}/Pic3D.nrrd # -V # ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/pic3dRefCubic.png #corresponding reference screenshot CUBIC #) #End test reslice interpolation # Testing of the rendering of binary images #mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_binaryTestImage640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice # ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage # -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImage640x480REF.png #corresponding reference screenshot #) #mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2D_binaryTestImageWithRef640x480 mitkImageVtkMapper2DTest #test for standard Pic3D axial slice # ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/RenderingTestData/binaryImage.nrrd #input image to load in data storage # -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/binaryImageWithRef640x480REF.png #corresponding reference screenshot #) # End of binary image tests mitkAddCustomModuleRenderingTest(mitkSurfaceVtkMapper3DTest_TextureProperty mitkSurfaceVtkMapper3DTest ${MITK_DATA_DIR}/RenderingTestData/earth.jpg -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/texturedSphere640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2DTransferFunctionTest_Png2D-bw mitkImageVtkMapper2DTransferFunctionTest ${MITK_DATA_DIR}/Png2D-bw.png -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-TransferFunctionRGBImage640x480REF.png #corresponding reference screenshot ) mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2DOpacityTransferFunctionTest_Png2D-bw mitkImageVtkMapper2DOpacityTransferFunctionTest ${MITK_DATA_DIR}/Png2D-bw.png -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-OpacityTransferFunctionRGBImage640x480REF.png #corresponding reference screenshot ) ############################## DISABLED TESTS mitkAddCustomModuleRenderingTest(mitkImageVtkMapper2DLookupTableTest_Png2D-bw mitkImageVtkMapper2DLookupTableTest ${MITK_DATA_DIR}/Png2D-bw.png -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/Png2D-bw-LookupTableRGBImage640x480REF.png #corresponding reference screenshot ) #mitkAddCustomModuleRenderingTest(mitkImageTest_color2DImage mitkImageTest # ${MITK_DATA_DIR}/NrrdWritingTestImage.jpg #) #mitkAddCustomModuleRenderingTest(mitkNodeDependentPointSetInteractorTest mitkNodeDependentPointSetInteractorTest - # ${MITK_DATA_DIR}/Pic3D.pic.gz ${MITK_DATA_DIR}/BallBinary30x30x30.pic.gz + # ${MITK_DATA_DIR}/Pic3D.nrrd ${MITK_DATA_DIR}/BallBinary30x30x30.nrrd #) mitkAddCustomModuleRenderingTest(mitkPlaneGeometryDataMapper2DTest mitkPlaneGeometryDataMapper2DTest ${MITK_DATA_DIR}/Pic3D.nrrd #input image to load in data storage -V ${MITK_DATA_DIR}/RenderingTestData/ReferenceScreenshots/PlaneGeometryMapper640x480REF.png #corresponding reference screenshot ) endif() # TARGET ${TESTDRIVER} diff --git a/Modules/Core/test/mitkImageSliceSelectorTest.cpp b/Modules/Core/test/mitkImageSliceSelectorTest.cpp index 6881f5cdbd..98c0285616 100644 --- a/Modules/Core/test/mitkImageSliceSelectorTest.cpp +++ b/Modules/Core/test/mitkImageSliceSelectorTest.cpp @@ -1,207 +1,138 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include int mitkImageSliceSelectorTest(int argc, char *argv[]) { int slice_nr = 1; std::cout << "Loading file: "; if (argc == 0) { std::cout << "no file specified [FAILED]" << std::endl; return EXIT_FAILURE; } mitk::Image::Pointer image; try { image = mitk::IOUtil::Load(argv[1]); } catch (const mitk::Exception &) { std::cout << "file not an image - test will not be applied [PASSED]" << std::endl; std::cout << "[TEST DONE]" << std::endl; return EXIT_SUCCESS; } catch ( const itk::ExceptionObject &ex ) { std::cout << "Exception: " << ex.GetDescription() << "[FAILED]" << std::endl; return EXIT_FAILURE; } if (image->GetDimension(2) < 2) slice_nr = 0; // Take a slice mitk::ImageSliceSelector::Pointer slice = mitk::ImageSliceSelector::New(); slice->SetInput(image); slice->SetSliceNr(slice_nr); slice->Update(); std::cout << "Testing IsInitialized(): "; if (slice->GetOutput()->IsInitialized() == false) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; std::cout << "Testing IsSliceSet(): "; if (slice->GetOutput()->IsSliceSet(0) == false) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; - /* deactivated because IpPic is not available any more (see bug 16662) - if(itksys::SystemTools::LowerCase(itksys::SystemTools::GetFilenameExtension(argv[1])).find(".pic")!=std::string::npos) - { - std::cout << "Testing whether the slice is identical with a slice loaded by mitkIpPicGetSlice:"; - mitkIpPicDescriptor *picslice = mitkIpPicGetSlice(argv[1], nullptr, (image->GetDimension(2)-1-slice_nr)+1); - int i, size = _mitkIpPicSize(picslice); - char * p1 = (char*)slice->GetPic()->data; - char * p2 = (char*)picslice->data; - //picslice->info->write_protect=mitkIpFalse; - //mitkIpPicPut("C:\\1aaaaIPPIC.pic", picslice); - //mitkIpPicPut("C:\\1aaaaSEL.pic", slice->GetPic()); - for(i=0; iSetInput(image); - //the output size of this filter is smaller than the of the input!! - cyl2cart->SetTargetXSize( 64 ); - - //Use the same slice-selector again, this time to take a slice of the filtered image - //which is smaller than the one of the old input!! - slice->SetInput(cyl2cart->GetOutput()); - slice->SetSliceNr(1); - - //The requested region is still the old one, - //therefore the following results in most ITK versions - //in an exception! - slice->Update(); - - //If no exception occured, check that the requested region is now - //the one of the smaller image - if(cyl2cart->GetOutput()->GetLargestPossibleRegion().GetSize()[0]!=64) - { - std::cout<<"Part 1 [FAILED]"<GetOutput()->GetDimensions()[0]!=64) || (cyl2cart->GetOutput()->GetDimensions()[1]!=64)) - { - std::cout<<"Part 1b [FAILED]"<ResetPipeline(); - } - */ try { slice->UpdateLargestPossibleRegion(); } catch (const itk::ExceptionObject &) { std::cout << "Part 2 [FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "Part 2 [PASSED]" << std::endl; std::cout << "Testing IsInitialized(): "; if (slice->GetOutput()->IsInitialized() == false) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; std::cout << "Testing IsSliceSet(): "; if (slice->GetOutput()->IsSliceSet(0) == false) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; if (image->GetDimension(3) > 1) { int time = image->GetDimension(3) - 1; std::cout << "Testing 3D+t: Setting time to " << time << ": "; slice->SetTimeNr(time); if (slice->GetTimeNr() != time) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; std::cout << "Testing 3D+t: Updating slice: "; slice->Update(); if (slice->GetOutput()->IsInitialized() == false) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; std::cout << "Testing 3D+t: IsSliceSet(): "; if (slice->GetOutput()->IsSliceSet(0) == false) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; std::cout << "Testing 3D+t: First slice in reader available: "; if (image->IsSliceSet(0, time) == false) { std::cout << "[FAILED]" << std::endl; return EXIT_FAILURE; } std::cout << "[PASSED]" << std::endl; } std::cout << "[TEST DONE]" << std::endl; return EXIT_SUCCESS; } diff --git a/Modules/Core/test/mitkImageTest.cpp b/Modules/Core/test/mitkImageTest.cpp index bd86398541..18abf3c780 100644 --- a/Modules/Core/test/mitkImageTest.cpp +++ b/Modules/Core/test/mitkImageTest.cpp @@ -1,552 +1,538 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // mitk includes #include "mitkException.h" #include "mitkIOUtil.h" #include "mitkImageGenerator.h" #include "mitkImagePixelReadAccessor.h" #include "mitkImageReadAccessor.h" #include "mitkPixelTypeMultiplex.h" #include #include #include #include #include #include "mitkImageSliceSelector.h" // itk includes #include #include // stl includes #include // vtk includes #include // Checks if reference count is correct after using GetVtkImageData() bool ImageVtkDataReferenceCheck(const char *fname) { const std::string filename = std::string(fname); try { mitk::Image::Pointer image = mitk::IOUtil::Load(filename); MITK_TEST_CONDITION_REQUIRED(image.IsNotNull(), "Non-nullptr image") vtkImageData *vtk = image->GetVtkImageData(); if (vtk == nullptr) return false; } catch (...) { MITK_TEST_FAILED_MSG(<< "Could not read file for testing: " << filename); return false; } return true; } template void TestRandomPixelAccess(const mitk::PixelType /*ptype*/, mitk::Image::Pointer image, mitk::Point3D &point, mitk::ScalarType &value) { // generate a random point in world coordinates mitk::Point3D xMax, yMax, zMax, xMaxIndex, yMaxIndex, zMaxIndex; xMaxIndex.Fill(0.0f); yMaxIndex.Fill(0.0f); zMaxIndex.Fill(0.0f); xMaxIndex[0] = image->GetLargestPossibleRegion().GetSize()[0]; yMaxIndex[1] = image->GetLargestPossibleRegion().GetSize()[1]; zMaxIndex[2] = image->GetLargestPossibleRegion().GetSize()[2]; image->GetGeometry()->IndexToWorld(xMaxIndex, xMax); image->GetGeometry()->IndexToWorld(yMaxIndex, yMax); image->GetGeometry()->IndexToWorld(zMaxIndex, zMax); MITK_INFO << "Origin " << image->GetGeometry()->GetOrigin()[0] << " " << image->GetGeometry()->GetOrigin()[1] << " " << image->GetGeometry()->GetOrigin()[2] << ""; MITK_INFO << "MaxExtend " << xMax[0] << " " << yMax[1] << " " << zMax[2] << ""; itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randomGenerator = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); randomGenerator->Initialize(std::rand()); // initialize with random value, to get sensible random points for the image point[0] = randomGenerator->GetUniformVariate(image->GetGeometry()->GetOrigin()[0], xMax[0]); point[1] = randomGenerator->GetUniformVariate(image->GetGeometry()->GetOrigin()[1], yMax[1]); point[2] = randomGenerator->GetUniformVariate(image->GetGeometry()->GetOrigin()[2], zMax[2]); MITK_INFO << "RandomPoint " << point[0] << " " << point[1] << " " << point[2] << ""; // test values and max/min mitk::ScalarType imageMin = image->GetStatistics()->GetScalarValueMin(); mitk::ScalarType imageMax = image->GetStatistics()->GetScalarValueMax(); // test accessing PixelValue with coordinate leading to a negative index const mitk::Point3D geom_origin = image->GetGeometry()->GetOrigin(); const mitk::Point3D geom_center = image->GetGeometry()->GetCenter(); // shift position from origin outside of the image ( in the opposite direction to [center-origin] vector which points // in the inside) mitk::Point3D position = geom_origin + (geom_origin - geom_center); MITK_INFO << "Testing access outside of the image"; unsigned int dim = image->GetDimension(); if (dim == 3 || dim == 4) { mitk::ImagePixelReadAccessor imAccess3(image, image->GetVolumeData(0)); // Comparison ?>=0 not needed since all position[i] and timestep are unsigned int // (position[0]>=0 && position[1] >=0 && position[2]>=0 && timestep>=0) // bug-11978 : we still need to catch index with negative values if (point[0] < 0 || point[1] < 0 || point[2] < 0) { MITK_WARN << "Given position (" << point << ") is out of image range, returning 0."; } else { value = static_cast(imAccess3.GetPixelByWorldCoordinates(point)); MITK_TEST_CONDITION((value >= imageMin && value <= imageMax), "Value returned is between max/min"); } itk::Index<3> itkIndex; image->GetGeometry()->WorldToIndex(position, itkIndex); MITK_TEST_FOR_EXCEPTION_BEGIN(mitk::Exception); imAccess3.GetPixelByIndexSafe(itkIndex); MITK_TEST_FOR_EXCEPTION_END(mitk::Exception); } MITK_INFO << imageMin << " " << imageMax << " " << value << ""; } class mitkImageTestClass { public: void SetClonedGeometry_None_ClonedEqualInput() { mitk::Image::Pointer image = mitk::ImageGenerator::GenerateRandomImage(100, 100, 100, 1, 0.2, 0.3, 0.4); //----------------- // geometry information for image mitk::Point3D origin; mitk::Vector3D right, bottom; mitk::Vector3D spacing; mitk::FillVector3D(origin, 17.0, 19.92, 7.83); mitk::FillVector3D(right, 1.0, 2.0, 3.0); mitk::FillVector3D(bottom, 0.0, -3.0, 2.0); mitk::FillVector3D(spacing, 0.78, 0.91, 2.23); // InitializeStandardPlane(rightVector, downVector, spacing) mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); planegeometry->InitializeStandardPlane(100, 100, right, bottom, &spacing); planegeometry->SetOrigin(origin); planegeometry->ChangeImageGeometryConsideringOriginOffset(true); image->SetClonedGeometry(planegeometry); mitk::BaseGeometry::Pointer imageGeometry = image->GetGeometry(); MITK_ASSERT_EQUAL(imageGeometry, planegeometry, "Matrix elements of cloned matrix equal original matrix"); } }; int mitkImageTest(int argc, char *argv[]) { MITK_TEST_BEGIN(mitkImageTest); mitkImageTestClass tester; tester.SetClonedGeometry_None_ClonedEqualInput(); // Create Image out of nowhere mitk::Image::Pointer imgMem = mitk::Image::New(); mitk::PixelType pt = mitk::MakeScalarPixelType(); unsigned int dim[] = {100, 100, 20}; MITK_TEST_CONDITION_REQUIRED(imgMem.IsNotNull(), "An image was created. "); // Initialize image imgMem->Initialize(pt, 3, dim); MITK_TEST_CONDITION_REQUIRED(imgMem->IsInitialized(), "Image::IsInitialized() ?"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetPixelType() == pt, "PixelType was set correctly."); int *p = nullptr; int *p2 = nullptr; try { mitk::ImageReadAccessor imgMemAcc(imgMem); p = (int *)imgMemAcc.GetData(); } catch ( const mitk::Exception &e ) { MITK_ERROR << e.what(); } MITK_TEST_CONDITION(p != nullptr, "GetData() returned not-nullptr pointer."); // filling image const unsigned int size = dim[0] * dim[1] * dim[2]; for (unsigned int i = 0; i < size; ++i, ++p) *p = (signed int)i; // Getting it again and compare with filled values: try { mitk::ImageReadAccessor imgMemAcc(imgMem); p2 = (int *)imgMemAcc.GetData(); } catch ( const mitk::Exception &e ) { MITK_ERROR << e.what(); } MITK_TEST_CONDITION(p2 != nullptr, "GetData() returned not-nullptr pointer."); bool isEqual = true; for (unsigned int i = 0; i < size; ++i, ++p2) { if (*p2 != (signed int)i) { isEqual = false; } } MITK_TEST_CONDITION(isEqual, "The values previously set as data are correct [pixelwise comparison]."); // Testing GetSliceData() and compare with filled values: try { mitk::ImageReadAccessor imgMemAcc(imgMem, imgMem->GetSliceData(dim[2] / 2)); p2 = (int *)imgMemAcc.GetData(); } catch ( const mitk::Exception &e ) { MITK_ERROR << e.what(); } MITK_TEST_CONDITION_REQUIRED(p2 != nullptr, "Valid slice data returned"); unsigned int xy_size = dim[0] * dim[1]; unsigned int start_mid_slice = (dim[2] / 2) * xy_size; isEqual = true; for (unsigned int i = 0; i < xy_size; ++i, ++p2) { if (*p2 != (signed int)(i + start_mid_slice)) { isEqual = false; } } MITK_TEST_CONDITION(isEqual, "The SliceData are correct [pixelwise comparison]. "); imgMem = mitk::Image::New(); // testing re-initialization of test image mitk::PixelType pType = mitk::MakePixelType(); imgMem->Initialize(pType, 3, dim); MITK_TEST_CONDITION_REQUIRED(imgMem->GetDimension() == 3, "Testing initialization parameter dimension!"); MITK_TEST_CONDITION_REQUIRED(imgMem->GetPixelType() == pType, "Testing initialization parameter pixeltype!"); MITK_TEST_CONDITION_REQUIRED( imgMem->GetDimension(0) == dim[0] && imgMem->GetDimension(1) == dim[1] && imgMem->GetDimension(2) == dim[2], "Testing initialization of dimensions!"); MITK_TEST_CONDITION(imgMem->IsInitialized(), "Image is initialized."); // Setting volume again: try { mitk::ImageReadAccessor imgMemAcc(imgMem); imgMem->SetVolume(imgMemAcc.GetData()); } catch ( const mitk::Exception &e ) { MITK_ERROR << e.what(); } //----------------- // geometry information for image mitk::Point3D origin; mitk::Vector3D right, bottom; mitk::Vector3D spacing; mitk::FillVector3D(origin, 17.0, 19.92, 7.83); mitk::FillVector3D(right, 1.0, 2.0, 3.0); mitk::FillVector3D(bottom, 0.0, -3.0, 2.0); mitk::FillVector3D(spacing, 0.78, 0.91, 2.23); // InitializeStandardPlane(rightVector, downVector, spacing) mitk::PlaneGeometry::Pointer planegeometry = mitk::PlaneGeometry::New(); planegeometry->InitializeStandardPlane(100, 100, right, bottom, &spacing); planegeometry->SetOrigin(origin); planegeometry->SetImageGeometry(true); // Testing Initialize(const mitk::PixelType& type, const mitk::Geometry3D& geometry, unsigned int slices) with // PlaneGeometry and GetData(): "; imgMem->Initialize(mitk::MakePixelType(), *planegeometry); MITK_TEST_CONDITION_REQUIRED( imgMem->GetGeometry()->GetOrigin() == static_cast(planegeometry)->GetOrigin(), "Testing correct setting of geometry via initialize!"); try { mitk::ImageReadAccessor imgMemAcc(imgMem); p = (int *)imgMemAcc.GetData(); } catch ( const mitk::Exception &e ) { MITK_ERROR << e.what(); } MITK_TEST_CONDITION_REQUIRED(p != nullptr, "GetData() returned valid pointer."); // Testing Initialize(const mitk::PixelType& type, int sDim, const mitk::PlaneGeometry& geometry) and GetData(): "; imgMem->Initialize(mitk::MakePixelType(), 40, *planegeometry); try { mitk::ImageReadAccessor imgMemAcc(imgMem); p = (int *)imgMemAcc.GetData(); } catch ( const mitk::Exception &e ) { MITK_ERROR << e.what(); } MITK_TEST_CONDITION_REQUIRED(p != nullptr, "GetData() returned valid pointer."); //----------------- // testing origin information and methods MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin), "Testing correctness of origin via GetGeometry()->GetOrigin(): "); // Setting origin via SetOrigin(origin): "; mitk::FillVector3D(origin, 37.0, 17.92, 27.83); imgMem->SetOrigin(origin); // Test origin MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetGeometry()->GetOrigin(), origin), "Testing correctness of changed origin via GetGeometry()->GetOrigin(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetSlicedGeometry()->GetPlaneGeometry(0)->GetOrigin(), origin), "Testing correctness of changed origin via GetSlicedGeometry()->GetPlaneGeometry(0)->GetOrigin(): "); //----------------- // testing spacing information and methodsunsigned int dim[]={100,100,20}; MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing), "Testing correct spacing from Geometry3D!"); mitk::FillVector3D(spacing, 7.0, 0.92, 1.83); imgMem->SetSpacing(spacing); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(imgMem->GetGeometry()->GetSpacing(), spacing), "Testing correctness of changed spacing via GetGeometry()->GetSpacing(): "); MITK_TEST_CONDITION_REQUIRED( mitk::Equal(imgMem->GetSlicedGeometry()->GetPlaneGeometry(0)->GetSpacing(), spacing), "Testing correctness of changed spacing via GetSlicedGeometry()->GetPlaneGeometry(0)->GetSpacing(): "); mitk::Image::Pointer vecImg = mitk::Image::New(); try { mitk::ImageReadAccessor imgMemAcc(imgMem); vecImg->Initialize(imgMem->GetPixelType(), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/); vecImg->SetImportChannel(const_cast(imgMemAcc.GetData()), 0, mitk::Image::CopyMemory); vecImg->SetImportChannel(const_cast(imgMemAcc.GetData()), 1, mitk::Image::CopyMemory); mitk::ImageReadAccessor vecImgAcc(vecImg); mitk::ImageReadAccessor vecImgAcc0(vecImg, vecImg->GetChannelData(0)); mitk::ImageReadAccessor vecImgAcc1(vecImg, vecImg->GetChannelData(1)); MITK_TEST_CONDITION_REQUIRED(vecImgAcc0.GetData() != nullptr && vecImgAcc1.GetData() != nullptr, "Testing set and return of channel data!"); MITK_TEST_CONDITION_REQUIRED(vecImg->IsValidSlice(0, 0, 1), ""); MITK_TEST_OUTPUT(<< " Testing whether CopyMemory worked"); MITK_TEST_CONDITION_REQUIRED(imgMemAcc.GetData() != vecImgAcc.GetData(), ""); MITK_TEST_OUTPUT(<< " Testing destruction after SetImportChannel"); vecImg = nullptr; MITK_TEST_CONDITION_REQUIRED(vecImg.IsNull(), "testing destruction!"); } catch ( const mitk::Exception &e ) { MITK_ERROR << e.what(); } //----------------- MITK_TEST_OUTPUT(<< "Testing initialization via vtkImageData"); MITK_TEST_OUTPUT(<< " Setting up vtkImageData"); vtkImageData *vtkimage = vtkImageData::New(); vtkimage->Initialize(); vtkimage->SetDimensions(2, 3, 4); double vtkorigin[] = {-350, -358.203, -1363.5}; vtkimage->SetOrigin(vtkorigin); mitk::Point3D vtkoriginAsMitkPoint; mitk::vtk2itk(vtkorigin, vtkoriginAsMitkPoint); double vtkspacing[] = {1.367, 1.367, 2}; vtkimage->SetSpacing(vtkspacing); vtkimage->AllocateScalars(VTK_SHORT, 1); std::cout << "[PASSED]" << std::endl; MITK_TEST_OUTPUT(<< " Testing mitk::Image::Initialize(vtkImageData*, ...)"); mitk::Image::Pointer mitkByVtkImage = mitk::Image::New(); mitkByVtkImage->Initialize(vtkimage); MITK_TEST_CONDITION_REQUIRED(mitkByVtkImage->IsInitialized(), ""); vtkimage->Delete(); MITK_TEST_OUTPUT(<< " Testing whether spacing has been correctly initialized from vtkImageData"); mitk::Vector3D spacing2 = mitkByVtkImage->GetGeometry()->GetSpacing(); mitk::Vector3D vtkspacingAsMitkVector; mitk::vtk2itk(vtkspacing, vtkspacingAsMitkVector); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(spacing2, vtkspacingAsMitkVector), ""); MITK_TEST_OUTPUT( << " Testing whether GetSlicedGeometry(0)->GetOrigin() has been correctly initialized from vtkImageData"); mitk::Point3D origin2 = mitkByVtkImage->GetSlicedGeometry(0)->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2, vtkoriginAsMitkPoint), ""); MITK_TEST_OUTPUT(<< " Testing whether GetGeometry()->GetOrigin() has been correctly initialized from vtkImageData"); origin2 = mitkByVtkImage->GetGeometry()->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(origin2, vtkoriginAsMitkPoint), ""); MITK_TEST_OUTPUT(<< " Testing if vtkOrigin is (0, 0, 0). This behaviour is due to historical development of MITK. " "Aslo see bug 5050!"); vtkImageData *vtkImage = imgMem->GetVtkImageData(); auto vtkOrigin = vtkImage->GetOrigin(); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(vtkOrigin[0], 0), "testing vtkOrigin[0] to be 0"); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(vtkOrigin[1], 0), "testing vtkOrigin[1] to be 0"); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(vtkOrigin[2], 0), "testing vtkOrigin[2] to be 0"); - // TODO test the following initializers on channel-incorporation - // void mitk::Image::Initialize(const mitk::PixelType& type, unsigned int dimension, unsigned int *dimensions, - // unsigned int channels) - // void mitk::Image::Initialize(const mitk::PixelType& type, int sDim, const mitk::PlaneGeometry& geometry2d, bool - // flipped, unsigned int channels, int tDim ) - // void mitk::Image::Initialize(const mitk::Image* image) - // void mitk::Image::Initialize(const mitkIpPicDescriptor* pic, int channels, int tDim, int sDim) - - // mitk::Image::Pointer vecImg = mitk::Image::New(); - // vecImg->Initialize(PixelType(typeid(float), 6, itk::ImageIOBase::SYMMETRICSECONDRANKTENSOR), - // *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, false /*shiftBoundingBoxMinimumToZero*/ ); - // vecImg->Initialize(PixelType(typeid(itk::Vector)), *imgMem->GetGeometry(), 2 /* #channels */, 0 /*tDim*/, - // false /*shiftBoundingBoxMinimumToZero*/ ); - // testing access by index coordinates and by world coordinates MITK_TEST_CONDITION_REQUIRED(argc == 2, "Check if test image is accessible!"); const std::string filename = std::string(argv[1]); mitk::Image::Pointer image; try { image = mitk::IOUtil::Load(filename); MITK_TEST_CONDITION_REQUIRED(image.IsNotNull(), "Non-nullptr image") } catch (...) { MITK_TEST_FAILED_MSG(<< "Could not read file for testing: " << filename); return 0; } mitk::Point3D point; mitk::ScalarType value = -1.; mitkPixelTypeMultiplex3( TestRandomPixelAccess, image->GetImageDescriptor()->GetChannelTypeById(0), image, point, value) { // testing the clone method of mitk::Image mitk::Image::Pointer cloneImage = image->Clone(); MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension() == image->GetDimension(), "Clone (testing dimension)"); MITK_TEST_CONDITION_REQUIRED(cloneImage->GetPixelType() == image->GetPixelType(), "Clone (testing pixel type)"); // After cloning an image the geometry of both images should be equal too MITK_TEST_CONDITION_REQUIRED(cloneImage->GetGeometry()->GetOrigin() == image->GetGeometry()->GetOrigin(), "Clone (testing origin)"); MITK_TEST_CONDITION_REQUIRED(cloneImage->GetGeometry()->GetSpacing() == image->GetGeometry()->GetSpacing(), "Clone (testing spacing)"); MITK_TEST_CONDITION_REQUIRED( mitk::MatrixEqualElementWise(cloneImage->GetGeometry()->GetIndexToWorldTransform()->GetMatrix(), image->GetGeometry()->GetIndexToWorldTransform()->GetMatrix()), "Clone (testing transformation matrix)"); MITK_TEST_CONDITION_REQUIRED( mitk::MatrixEqualElementWise(cloneImage->GetTimeGeometry() ->GetGeometryForTimeStep(cloneImage->GetDimension(3) - 1) ->GetIndexToWorldTransform() ->GetMatrix(), cloneImage->GetTimeGeometry() ->GetGeometryForTimeStep(image->GetDimension(3) - 1) ->GetIndexToWorldTransform() ->GetMatrix()), "Clone(testing time sliced geometry)"); for (unsigned int i = 0u; i < cloneImage->GetDimension(); ++i) { MITK_TEST_CONDITION_REQUIRED(cloneImage->GetDimension(i) == image->GetDimension(i), "Clone (testing dimension " << i << ")"); } } // access via itk if (image->GetDimension() > 3) // CastToItk only works with 3d images so we need to check for 4d images { mitk::ImageTimeSelector::Pointer selector = mitk::ImageTimeSelector::New(); selector->SetTimeNr(0); selector->SetInput(image); selector->Update(); image = selector->GetOutput(); } if (image->GetDimension() == 3) { typedef itk::Image ItkFloatImage3D; ItkFloatImage3D::Pointer itkimage; try { mitk::CastToItkImage(image, itkimage); MITK_TEST_CONDITION_REQUIRED(itkimage.IsNotNull(), "Test conversion to itk::Image!"); } catch ( const std::exception &e ) { MITK_INFO << e.what(); } mitk::Point3D itkPhysicalPoint; image->GetGeometry()->WorldToItkPhysicalPoint(point, itkPhysicalPoint); MITK_INFO << "ITKPoint " << itkPhysicalPoint[0] << " " << itkPhysicalPoint[1] << " " << itkPhysicalPoint[2] << ""; mitk::Point3D backTransformedPoint; image->GetGeometry()->ItkPhysicalPointToWorld(itkPhysicalPoint, backTransformedPoint); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(point, backTransformedPoint), "Testing world->itk-physical->world consistency"); itk::Index<3> idx; bool status = itkimage->TransformPhysicalPointToIndex(itkPhysicalPoint, idx); MITK_INFO << "ITK Index " << idx[0] << " " << idx[1] << " " << idx[2] << ""; if (status && value != -1.) { float valByItk = itkimage->GetPixel(idx); MITK_TEST_CONDITION_REQUIRED(mitk::Equal(valByItk, value), "Compare value of pixel returned by mitk in comparison to itk"); } else { MITK_WARN << "Index is out buffered region!"; } } else { MITK_INFO << "Image does not contain three dimensions, some test cases are skipped!"; } // clone generated 3D image with one slice in z direction (cf. bug 11058) auto *threeDdim = new unsigned int[3]; threeDdim[0] = 100; threeDdim[1] = 200; threeDdim[2] = 1; mitk::Image::Pointer threeDImage = mitk::Image::New(); threeDImage->Initialize(mitk::MakeScalarPixelType(), 3, threeDdim); mitk::Image::Pointer cloneThreeDImage = threeDImage->Clone(); // check that the clone image has the same dimensionality as the source image MITK_TEST_CONDITION_REQUIRED(cloneThreeDImage->GetDimension() == 3, "Testing if the clone image initializes with 3D!"); MITK_TEST_CONDITION_REQUIRED(ImageVtkDataReferenceCheck(argv[1]), "Checking reference count of Image after using GetVtkImageData()"); MITK_TEST_END(); } diff --git a/Modules/SceneSerialization/src/mitkImageSerializer.cpp b/Modules/SceneSerialization/src/mitkImageSerializer.cpp index 82ded44882..6d262f9322 100644 --- a/Modules/SceneSerialization/src/mitkImageSerializer.cpp +++ b/Modules/SceneSerialization/src/mitkImageSerializer.cpp @@ -1,57 +1,57 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkImageSerializer.h" #include "mitkIOUtil.h" #include "mitkImage.h" #include MITK_REGISTER_SERIALIZER(ImageSerializer) mitk::ImageSerializer::ImageSerializer() { } mitk::ImageSerializer::~ImageSerializer() { } std::string mitk::ImageSerializer::Serialize() { const auto *image = dynamic_cast(m_Data.GetPointer()); if (!image) { MITK_ERROR << " Object at " << (const void *)this->m_Data << " is not an mitk::Image. Cannot serialize as image."; return ""; } std::string filename(this->GetUniqueFilenameInWorkingDirectory()); std::cout << "creating file " << filename << " in " << m_WorkingDirectory << std::endl; filename += "_"; filename += m_FilenameHint; std::string fullname(m_WorkingDirectory); fullname += Poco::Path::separator(); fullname += filename + ".nrrd"; try { IOUtil::Save(image, fullname); } catch (std::exception &e) { MITK_ERROR << " Error serializing object at " << (const void *)this->m_Data << " to " << fullname << ": " << e.what(); return ""; } - return Poco::Path(fullname).getFileName(); // + ".pic"; + return Poco::Path(fullname).getFileName(); } diff --git a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp index 0fa978346e..2bc6b9c576 100644 --- a/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp +++ b/Modules/Segmentation/Interactions/mitkRegionGrowingTool.cpp @@ -1,573 +1,510 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "mitkRegionGrowingTool.h" #include "mitkBaseRenderer.h" #include "mitkImageToContourModelFilter.h" #include "mitkRegionGrowingTool.xpm" #include "mitkRenderingManager.h" #include "mitkToolManager.h" // us #include #include #include #include // ITK #include "mitkITKImageImport.h" #include "mitkImageAccessByItk.h" #include #include #include #include #include namespace mitk { MITK_TOOL_MACRO(MITKSEGMENTATION_EXPORT, RegionGrowingTool, "Region growing tool"); } #define ROUND(a) ((a) > 0 ? (int)((a) + 0.5) : -(int)(0.5 - (a))) mitk::RegionGrowingTool::RegionGrowingTool() : FeedbackContourTool("PressMoveRelease"), m_SeedValue(0), m_ScreenYDifference(0), m_ScreenXDifference(0), m_MouseDistanceScaleFactor(0.5), m_PaintingPixelValue(0), m_FillFeedbackContour(true), m_ConnectedComponentValue(1) { } mitk::RegionGrowingTool::~RegionGrowingTool() { } void mitk::RegionGrowingTool::ConnectActionsAndFunctions() { CONNECT_FUNCTION("PrimaryButtonPressed", OnMousePressed); CONNECT_FUNCTION("Move", OnMouseMoved); CONNECT_FUNCTION("Release", OnMouseReleased); } const char **mitk::RegionGrowingTool::GetXPM() const { return mitkRegionGrowingTool_xpm; } us::ModuleResource mitk::RegionGrowingTool::GetIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("RegionGrowing_48x48.png"); return resource; } us::ModuleResource mitk::RegionGrowingTool::GetCursorIconResource() const { us::Module *module = us::GetModuleContext()->GetModule(); us::ModuleResource resource = module->GetResource("RegionGrowing_Cursor_32x32.png"); return resource; } const char *mitk::RegionGrowingTool::GetName() const { return "Region Growing"; } void mitk::RegionGrowingTool::Activated() { Superclass::Activated(); } void mitk::RegionGrowingTool::Deactivated() { Superclass::Deactivated(); } // Get the average pixel value of square/cube with radius=neighborhood around index template void mitk::RegionGrowingTool::GetNeighborhoodAverage(const itk::Image *itkImage, const itk::Index& index, ScalarType *result, unsigned int neighborhood) { // maybe assert that image dimension is only 2 or 3? auto neighborhoodInt = (int)neighborhood; TPixel averageValue(0); unsigned int numberOfPixels = (2 * neighborhood + 1) * (2 * neighborhood + 1); if (imageDimension == 3) { numberOfPixels *= (2 * neighborhood + 1); } MITK_DEBUG << "Getting neighborhood of " << numberOfPixels << " pixels around " << index; itk::Index currentIndex; for (int i = (0 - neighborhoodInt); i <= neighborhoodInt; ++i) { currentIndex[0] = index[0] + i; for (int j = (0 - neighborhoodInt); j <= neighborhoodInt; ++j) { currentIndex[1] = index[1] + j; if (imageDimension == 3) { for (int k = (0 - neighborhoodInt); k <= neighborhoodInt; ++k) { currentIndex[2] = index[2] + k; if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex)) { averageValue += itkImage->GetPixel(currentIndex); } else { numberOfPixels -= 1; } } } else { if (itkImage->GetLargestPossibleRegion().IsInside(currentIndex)) { averageValue += itkImage->GetPixel(currentIndex); } else { numberOfPixels -= 1; } } } } *result = (ScalarType)averageValue; *result /= numberOfPixels; } // Check whether index lies inside a segmentation template void mitk::RegionGrowingTool::IsInsideSegmentation(const itk::Image *itkImage, const itk::Index& index, bool *result) { if (itkImage->GetPixel(index) > 0) { *result = true; } else { *result = false; } } // Do the region growing (i.e. call an ITK filter that does it) template void mitk::RegionGrowingTool::StartRegionGrowing(const itk::Image *inputImage, const itk::Index& seedIndex, const std::array& thresholds, mitk::Image::Pointer &outputImage) { MITK_DEBUG << "Starting region growing at index " << seedIndex << " with lower threshold " << thresholds[0] << " and upper threshold " << thresholds[1]; typedef itk::Image InputImageType; typedef itk::Image OutputImageType; typedef itk::ConnectedThresholdImageFilter RegionGrowingFilterType; typename RegionGrowingFilterType::Pointer regionGrower = RegionGrowingFilterType::New(); // perform region growing in desired segmented region regionGrower->SetInput(inputImage); regionGrower->SetSeed(seedIndex); regionGrower->SetLower(thresholds[0]); regionGrower->SetUpper(thresholds[1]); try { regionGrower->Update(); } catch (...) { return; // Should we do something? } typename OutputImageType::Pointer resultImage = regionGrower->GetOutput(); // Smooth result: Every pixel is replaced by the majority of the neighborhood typedef itk::NeighborhoodIterator NeighborhoodIteratorType; typedef itk::ImageRegionIterator ImageIteratorType; typename NeighborhoodIteratorType::RadiusType radius; radius.Fill(2); // for now, maybe make this something the user can adjust in the preferences? typedef itk::ImageDuplicator< OutputImageType > DuplicatorType; typename DuplicatorType::Pointer duplicator = DuplicatorType::New(); duplicator->SetInputImage(resultImage); duplicator->Update(); typename OutputImageType::Pointer resultDup = duplicator->GetOutput(); NeighborhoodIteratorType neighborhoodIterator(radius, resultDup, resultDup->GetRequestedRegion()); ImageIteratorType imageIterator(resultImage, resultImage->GetRequestedRegion()); for (neighborhoodIterator.GoToBegin(), imageIterator.GoToBegin(); !neighborhoodIterator.IsAtEnd(); ++neighborhoodIterator, ++imageIterator) { DefaultSegmentationDataType voteYes(0); DefaultSegmentationDataType voteNo(0); for (unsigned int i = 0; i < neighborhoodIterator.Size(); ++i) { if (neighborhoodIterator.GetPixel(i) > 0) { voteYes += 1; } else { voteNo += 1; } } if (voteYes > voteNo) { imageIterator.Set(1); } else { imageIterator.Set(0); } } if (resultImage.IsNull()) { MITK_DEBUG << "Region growing result is empty."; } // Can potentially have multiple regions, use connected component image filter to label disjunct regions typedef itk::ConnectedComponentImageFilter ConnectedComponentImageFilterType; typename ConnectedComponentImageFilterType::Pointer connectedComponentFilter = ConnectedComponentImageFilterType::New(); connectedComponentFilter->SetInput(resultImage); connectedComponentFilter->Update(); typename OutputImageType::Pointer resultImageCC = connectedComponentFilter->GetOutput(); m_ConnectedComponentValue = resultImageCC->GetPixel(seedIndex); outputImage = mitk::GrabItkImageMemory(resultImageCC); } template void mitk::RegionGrowingTool::CalculateInitialThresholds(const itk::Image*) { LevelWindow levelWindow; this->GetToolManager()->GetReferenceData(0)->GetLevelWindow(levelWindow); m_ThresholdExtrema[0] = static_cast(std::numeric_limits::lowest()); m_ThresholdExtrema[1] = static_cast(std::numeric_limits::max()); const ScalarType lowerWindowBound = std::max(m_ThresholdExtrema[0], levelWindow.GetLowerWindowBound()); const ScalarType upperWindowBound = std::min(m_ThresholdExtrema[1], levelWindow.GetUpperWindowBound()); if (m_SeedValue < lowerWindowBound) { m_InitialThresholds = { m_ThresholdExtrema[0], lowerWindowBound }; } else if (m_SeedValue > upperWindowBound) { m_InitialThresholds = { upperWindowBound, m_ThresholdExtrema[1] }; } else { const ScalarType range = 0.1 * (upperWindowBound - lowerWindowBound); // 10% of the visible window m_InitialThresholds[0] = std::min(std::max(lowerWindowBound, m_SeedValue - 0.5 * range), upperWindowBound - range); m_InitialThresholds[1] = m_InitialThresholds[0] + range; } } void mitk::RegionGrowingTool::OnMousePressed(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (!positionEvent) return; m_LastEventSender = positionEvent->GetSender(); m_LastEventSlice = m_LastEventSender->GetSlice(); m_LastScreenPosition = Point2I(positionEvent->GetPointerPositionOnScreen()); // ReferenceSlice is from the underlying image, WorkingSlice from the active segmentation (can be empty) m_ReferenceSlice = FeedbackContourTool::GetAffectedReferenceSlice(positionEvent); m_WorkingSlice = FeedbackContourTool::GetAffectedWorkingSlice(positionEvent); if (m_WorkingSlice.IsNotNull()) // can't do anything without a working slice (i.e. a possibly empty segmentation) { // 2. Determine if the user clicked inside or outside of the segmentation/working slice (i.e. the whole volume) mitk::BaseGeometry::Pointer workingSliceGeometry; workingSliceGeometry = m_WorkingSlice->GetGeometry(); workingSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), m_SeedPoint); itk::Index<2> indexInWorkingSlice2D; indexInWorkingSlice2D[0] = m_SeedPoint[0]; indexInWorkingSlice2D[1] = m_SeedPoint[1]; if (workingSliceGeometry->IsIndexInside(m_SeedPoint)) { MITK_DEBUG << "OnMousePressed: point " << positionEvent->GetPositionInWorld() << " (index coordinates " << m_SeedPoint << ") is inside working slice"; // 3. determine the pixel value under the last click to determine what to do bool inside(true); AccessFixedDimensionByItk_2(m_WorkingSlice, IsInsideSegmentation, 2, indexInWorkingSlice2D, &inside); m_PaintingPixelValue = inside ? 0 : 1; if (inside) { MITK_DEBUG << "Clicked inside segmentation"; // For now, we're doing nothing when the user clicks inside the segmentation. Behaviour can be implemented via // OnMousePressedInside() // When you do, be sure to remove the m_PaintingPixelValue check in OnMouseMoved() and OnMouseReleased() return; } else { MITK_DEBUG << "Clicked outside of segmentation"; OnMousePressedOutside(nullptr, interactionEvent); } } } } // Use this to implement a behaviour for when the user clicks inside a segmentation (for example remove something) -// Old IpPic code is kept as comment for reference void mitk::RegionGrowingTool::OnMousePressedInside() { - // mitk::InteractionPositionEvent* positionEvent = dynamic_cast( interactionEvent - // ); - // //const PositionEvent* positionEvent = dynamic_cast(stateEvent->GetEvent()); // checked in - // OnMousePressed - // // 3.1.1. Create a skeletonization of the segmentation and try to find a nice cut - // // apply the skeletonization-and-cut algorithm - // // generate contour to remove - // // set m_ReferenceSlice = nullptr so nothing will happen during mouse move - // // remember to fill the contour with 0 in mouserelease - // mitkIpPicDescriptor* segmentationHistory = ipMITKSegmentationCreateGrowerHistory( workingPicSlice, - // m_LastWorkingSeed, nullptr ); // free again - // if (segmentationHistory) - // { - // tCutResult cutContour = ipMITKSegmentationGetCutPoints( workingPicSlice, segmentationHistory, - // initialWorkingOffset ); // tCutResult is a ipSegmentation type - // mitkIpPicFree( segmentationHistory ); - // if (cutContour.cutIt) - // { - // int timestep = positionEvent->GetSender()->GetTimeStep(); - // // 3.1.2 copy point from float* to mitk::Contour - // ContourModel::Pointer contourInImageIndexCoordinates = ContourModel::New(); - // contourInImageIndexCoordinates->Expand(timestep + 1); - // contourInImageIndexCoordinates->SetClosed(true, timestep); - // Point3D newPoint; - // for (int index = 0; index < cutContour.deleteSize; ++index) - // { - // newPoint[0] = cutContour.deleteCurve[ 2 * index + 0 ] - 0.5;//correction is needed because the - // output of the algorithm is center based - // newPoint[1] = cutContour.deleteCurve[ 2 * index + 1 ] - 0.5;//and we want our contour displayed - // corner based. - // newPoint[2] = 0.0; - - // contourInImageIndexCoordinates->AddVertex( newPoint, timestep ); - // } - - // free(cutContour.traceline); - // free(cutContour.deleteCurve); // perhaps visualize this for fun? - // free(cutContour.onGradient); - - // ContourModel::Pointer contourInWorldCoordinates = FeedbackContourTool::BackProjectContourFrom2DSlice( - // m_WorkingSlice->GetGeometry(), contourInImageIndexCoordinates, true ); // true: sub 0.5 for - // ipSegmentation correction - - // FeedbackContourTool::SetFeedbackContour( contourInWorldCoordinates ); - // FeedbackContourTool::SetFeedbackContourVisible(true); - // mitk::RenderingManager::GetInstance()->RequestUpdate( positionEvent->GetSender()->GetRenderWindow() ); - // m_FillFeedbackContour = true; - // } - // else - // { - // m_FillFeedbackContour = false; - // } - - // } - // else - // { - // m_FillFeedbackContour = false; - // } - - // m_ReferenceSlice = nullptr; - - // return true; } void mitk::RegionGrowingTool::OnMousePressedOutside(StateMachineAction *, InteractionEvent *interactionEvent) { auto *positionEvent = dynamic_cast(interactionEvent); if (positionEvent) { // Get geometry and indices mitk::BaseGeometry::Pointer workingSliceGeometry; workingSliceGeometry = m_WorkingSlice->GetGeometry(); itk::Index<2> indexInWorkingSlice2D; indexInWorkingSlice2D[0] = m_SeedPoint[0]; indexInWorkingSlice2D[1] = m_SeedPoint[1]; mitk::BaseGeometry::Pointer referenceSliceGeometry; referenceSliceGeometry = m_ReferenceSlice->GetGeometry(); itk::Index<3> indexInReferenceSlice; itk::Index<2> indexInReferenceSlice2D; referenceSliceGeometry->WorldToIndex(positionEvent->GetPositionInWorld(), indexInReferenceSlice); indexInReferenceSlice2D[0] = indexInReferenceSlice[0]; indexInReferenceSlice2D[1] = indexInReferenceSlice[1]; // Get seed neighborhood ScalarType averageValue(0); AccessFixedDimensionByItk_3(m_ReferenceSlice, GetNeighborhoodAverage, 2, indexInReferenceSlice2D, &averageValue, 1); m_SeedValue = averageValue; MITK_DEBUG << "Seed value is " << m_SeedValue; // Calculate initial thresholds AccessFixedDimensionByItk(m_ReferenceSlice, CalculateInitialThresholds, 2); m_Thresholds[0] = m_InitialThresholds[0]; m_Thresholds[1] = m_InitialThresholds[1]; // Perform region growing mitk::Image::Pointer resultImage = mitk::Image::New(); AccessFixedDimensionByItk_3( m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage); resultImage->SetGeometry(workingSliceGeometry); // Extract contour if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1) { float isoOffset = 0.33; mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New(); contourExtractor->SetInput(resultImage); contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset); contourExtractor->Update(); ContourModel::Pointer resultContour = ContourModel::New(); resultContour = contourExtractor->GetOutput(); // Show contour if (resultContour.IsNotNull()) { ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice( workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour)); FeedbackContourTool::UpdateCurrentFeedbackContour(resultContourWorld); FeedbackContourTool::SetFeedbackContourVisible(true); mitk::RenderingManager::GetInstance()->RequestUpdate(m_LastEventSender->GetRenderWindow()); } } } } void mitk::RegionGrowingTool::OnMouseMoved(StateMachineAction *, InteractionEvent *interactionEvent) { // Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0, // i.e. when the user clicked inside the segmentation if (m_PaintingPixelValue == 0) { return; } auto *positionEvent = dynamic_cast(interactionEvent); if (m_ReferenceSlice.IsNotNull() && positionEvent) { // Get geometry and indices mitk::BaseGeometry::Pointer workingSliceGeometry; workingSliceGeometry = m_WorkingSlice->GetGeometry(); itk::Index<2> indexInWorkingSlice2D; indexInWorkingSlice2D[0] = m_SeedPoint[0]; indexInWorkingSlice2D[1] = m_SeedPoint[1]; m_ScreenYDifference += positionEvent->GetPointerPositionOnScreen()[1] - m_LastScreenPosition[1]; m_ScreenXDifference += positionEvent->GetPointerPositionOnScreen()[0] - m_LastScreenPosition[0]; m_LastScreenPosition = Point2I(positionEvent->GetPointerPositionOnScreen()); // Moving the mouse up and down adjusts the width of the threshold window, // moving it left and right shifts the threshold window m_Thresholds[0] = std::min(m_SeedValue, m_InitialThresholds[0] - (m_ScreenYDifference - m_ScreenXDifference) * m_MouseDistanceScaleFactor); m_Thresholds[1] = std::max(m_SeedValue, m_InitialThresholds[1] + (m_ScreenYDifference + m_ScreenXDifference) * m_MouseDistanceScaleFactor); // Do not exceed the pixel type extrema of the reference slice, though m_Thresholds[0] = std::max(m_ThresholdExtrema[0], m_Thresholds[0]); m_Thresholds[1] = std::min(m_ThresholdExtrema[1], m_Thresholds[1]); // Perform region growing again and show the result mitk::Image::Pointer resultImage = mitk::Image::New(); AccessFixedDimensionByItk_3( m_ReferenceSlice, StartRegionGrowing, 2, indexInWorkingSlice2D, m_Thresholds, resultImage); resultImage->SetGeometry(workingSliceGeometry); // Update the contour if (resultImage.IsNotNull() && m_ConnectedComponentValue >= 1) { float isoOffset = 0.33; mitk::ImageToContourModelFilter::Pointer contourExtractor = mitk::ImageToContourModelFilter::New(); contourExtractor->SetInput(resultImage); contourExtractor->SetContourValue(m_ConnectedComponentValue - isoOffset); contourExtractor->Update(); ContourModel::Pointer resultContour = ContourModel::New(); resultContour = contourExtractor->GetOutput(); // Show contour if (resultContour.IsNotNull()) { ContourModel::Pointer resultContourWorld = FeedbackContourTool::BackProjectContourFrom2DSlice( workingSliceGeometry, FeedbackContourTool::ProjectContourTo2DSlice(m_WorkingSlice, resultContour)); FeedbackContourTool::UpdateCurrentFeedbackContour(resultContourWorld); FeedbackContourTool::SetFeedbackContourVisible(true); mitk::RenderingManager::GetInstance()->ForceImmediateUpdate(positionEvent->GetSender()->GetRenderWindow()); } } } } void mitk::RegionGrowingTool::OnMouseReleased(StateMachineAction *, InteractionEvent *interactionEvent) { // Until OnMousePressedInside() implements a behaviour, we're just returning here whenever m_PaintingPixelValue is 0, // i.e. when the user clicked inside the segmentation if (m_PaintingPixelValue == 0) { return; } auto *positionEvent = dynamic_cast(interactionEvent); if (m_WorkingSlice.IsNotNull() && m_FillFeedbackContour && positionEvent) { this->WriteBackFeedbackContourAsSegmentationResult(positionEvent, m_PaintingPixelValue); m_ScreenYDifference = 0; m_ScreenXDifference = 0; } } diff --git a/Modules/ToFHardware/CMakeLists.txt b/Modules/ToFHardware/CMakeLists.txt index f6f70f68c1..004d65c850 100644 --- a/Modules/ToFHardware/CMakeLists.txt +++ b/Modules/ToFHardware/CMakeLists.txt @@ -1,32 +1,32 @@ #Define the platform string mitkMacroGetPMDPlatformString(_PLATFORM_STRING) MITK_CREATE_MODULE( - DEPENDS MitkOpenCVVideoSupport MitkIGTBase MitkCameraCalibration MitkIpPic + DEPENDS MitkOpenCVVideoSupport MitkIGTBase MitkCameraCalibration PACKAGE_DEPENDS PRIVATE ITK|IONRRD ADDITIONAL_LIBS ${ADDITIONAL_LIBS} ) # set(tofHardware_srcs ) # usFunctionEmbedResources(tofHardware_srcs # LIBRARY_NAME mitkToFHardware # ROOT_DIR ${MITK_DATA_DIR}/ToF-Data/CalibrationFiles # FILES Default_Parameters.xml Kinect_IR_camera.xml Kinect_RGB_camera.xml Mesa-SR4000_Camera.xml PMDCamBoard_camera.xml PMDCamCube2_camera.xml PMDCamCube3_camera.xml # ) add_subdirectory(Testing) add_subdirectory(Kinect) add_subdirectory(KinectV2) add_subdirectory(PMD) add_subdirectory(MesaSR4000) # Install external libraries which are not directly linked to a MITK module include(${CMAKE_CURRENT_SOURCE_DIR}/mitkToFHardwareInstallRules.cmake) CONFIGURE_FILE(${CMAKE_CURRENT_SOURCE_DIR}/mitkToFHardwareInstallRules.cmake ${PROJECT_BINARY_DIR}/mitkToFHardwareInstallRules.cmake COPYONLY) CONFIGURE_FILE(mitkToFConfig.h.in ${PROJECT_BINARY_DIR}/mitkToFConfig.h @ONLY) #foreach(tofhardwaresubfolder_dir ${tofhardwaresubfolder_dirs}) # add_subdirectory(${tofhardwaresubfolder_dirs}) #endforeach() diff --git a/Modules/ToFHardware/PMD/Testing/mitkToFCameraPMDMITKPlayerControllerTest.cpp b/Modules/ToFHardware/PMD/Testing/mitkToFCameraPMDMITKPlayerControllerTest.cpp index 0a86e43654..8abfe50ec6 100644 --- a/Modules/ToFHardware/PMD/Testing/mitkToFCameraPMDMITKPlayerControllerTest.cpp +++ b/Modules/ToFHardware/PMD/Testing/mitkToFCameraPMDMITKPlayerControllerTest.cpp @@ -1,61 +1,61 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include /**Documentation * test for the class "ToFCameraPMDMITKPlayerController". */ int mitkToFCameraPMDMITKPlayerControllerTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("ToFCameraPMDMITKPlayerController"); mitk::ToFCameraPMDMITKPlayerController::Pointer testObject = mitk::ToFCameraPMDMITKPlayerController::New(); MITK_TEST_CONDITION_REQUIRED(!(testObject.GetPointer() == nullptr) ,"Testing initialization class"); MITK_TEST_CONDITION_REQUIRED(testObject->GetCaptureHeight()== 200 ,"Testing initialization of CaptureHeight"); MITK_TEST_CONDITION_REQUIRED(testObject->GetCaptureWidth()== 200 ,"Testing initialization of CaptureWidth"); // test empty file behavior std::string testFile = ""; testObject->SetInputFileName(testFile); MITK_TEST_CONDITION_REQUIRED(testObject->OpenCameraConnection(),"Testing open camera without valid data"); //MITK_TEST_CONDITION_REQUIRED(!testObject->CloseCameraConnection(),"Testing closing of connection"); //test valid data behavior //CAVE: The following test cases are valid once rawData recording is fixed. Currently the // functionality is not working therefor the test cases are excluded!! //std::string filePath = MITK_TOF_DATA_DIR; - //testFile = "/aa_raw.pic"; + //testFile = "/aa_raw.nrrd"; //filePath.append(testFile); //testObject->SetInputFileName(filePath); //MITK_TEST_CONDITION_REQUIRED( testObject->OpenCameraConnection(),"Testing open camera with valid data"); //MITK_TEST_CONDITION_REQUIRED( testObject->GetIntegrationTime() == 2500,"Testing correct setting of integration time!"); //MITK_TEST_CONDITION_REQUIRED( testObject->GetModulationFrequency() == 20,"Testing correct setting of modulation frequency!"); // ////test source data passing and updating! //int size = testObject->GetSourceDataStructSize(); //MITK_TEST_CONDITION_REQUIRED( size != 0 , "Testing correct setting of source data size!" ) //char* sourceData = nullptr; //testObject->GetSourceData( sourceData ); //MITK_TEST_CONDITION_REQUIRED( sourceData == nullptr, "Testing setting of source data without update camera!"); //testObject->UpdateCamera(); //sourceData = new char[size]; //testObject->GetSourceData(sourceData); //MITK_TEST_CONDITION_REQUIRED( sourceData != nullptr, "Testing setting of source data with update camera!"); //delete[] sourceData; MITK_TEST_CONDITION( testObject->CloseCameraConnection(),"Closing Connection!"); MITK_TEST_END(); }git st diff --git a/Modules/ToFHardware/Testing/mitkToFCameraMITKPlayerControllerTest.cpp b/Modules/ToFHardware/Testing/mitkToFCameraMITKPlayerControllerTest.cpp index e5f521c196..7ef5d926c1 100644 --- a/Modules/ToFHardware/Testing/mitkToFCameraMITKPlayerControllerTest.cpp +++ b/Modules/ToFHardware/Testing/mitkToFCameraMITKPlayerControllerTest.cpp @@ -1,184 +1,180 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include namespace mitk { class ToFCameraMITKPlayerDeviceImpl : public ToFCameraMITKPlayerDevice { public: inline ToFCameraMITKPlayerController::Pointer GetController(){return m_Controller;}; inline ToFCameraMITKPlayerDeviceImpl(){}; inline ~ToFCameraMITKPlayerDeviceImpl(){}; private: }; } // end namespace mitk /**Documentation * test for the class "ToFCameraMITKPlayerController". */ void ReadFileFormatTestCase(std::string extension, mitk::ToFImageGrabber::Pointer grabber) { MITK_INFO<<"Checking image processing with file format " << extension.c_str(); //create some test image unsigned int* dim = new unsigned int[3]; dim[0] = 100; dim[1] = 100; dim[2] = 1; int end = dim[0]*dim[1]*dim[2]; float* data = new float[end]; int index = 0; while(index != end) { data[index] = (float) index; index++; } mitk::Image::Pointer testImage = mitk::Image::New(); mitk::PixelType FloatType = mitk::MakeScalarPixelType(); testImage->Initialize( FloatType, 3, dim); testImage->SetVolume(data); // save image as dist, ampl and inten image to file. std::string distanceImageFileName("distTestImage"); std::string amplitudeImageFileName("amplTestImage"); std::string intensityImageFileName("intenTestImage"); mitk::ImageWriter::Pointer writer = mitk::ImageWriter::New(); writer->SetInput(testImage); writer->SetExtension(extension); writer->SetFileName(distanceImageFileName); writer->Update(); writer->SetFileName(amplitudeImageFileName); writer->Update(); writer->SetFileName(intensityImageFileName); writer->Update(); // load the files from directory grabber->SetStringProperty("DistanceImageFileName", (distanceImageFileName.append(extension)).c_str()); grabber->SetStringProperty("AmplitudeImageFileName", (amplitudeImageFileName.append(extension)).c_str()); grabber->SetStringProperty("IntensityImageFileName", (intensityImageFileName.append(extension)).c_str()); MITK_TEST_CONDITION_REQUIRED(grabber->ConnectCamera() ,"Are the image files loaded correctly?"); mitk::ToFCameraMITKPlayerController::Pointer testObject = static_cast(grabber->GetCameraDevice())->GetController(); // test load image from image grabber testObject->UpdateCamera(); index = 0; bool distOK = true; bool amplOK = true; bool intenOK = true; float* dist = new float[end]; float* ampl = new float[end]; float* inten = new float[end]; testObject->GetDistances( dist ); testObject->GetAmplitudes( ampl ); testObject->GetIntensities( inten ); while( index != end ) { if( dist[index] != data[index]) { distOK = false; } if( ampl[index] != data[index]) { amplOK = false; } if( inten[index] != data[index]) { intenOK = false; } index++; } MITK_TEST_CONDITION_REQUIRED(distOK ,"Testing correct loading and passing of distance image information!"); MITK_TEST_CONDITION_REQUIRED(amplOK ,"Testing correct loading and passing of amplitude image information!"); MITK_TEST_CONDITION_REQUIRED(intenOK ,"Testing correct loading and passing of intensity image information!"); MITK_TEST_CONDITION_REQUIRED(testObject->CloseCameraConnection(),"Testing disconnection of controller"); //clean up and delete saved image files if(remove(distanceImageFileName.c_str())!=0) { MITK_ERROR<<"File: "<SetCameraDevice(deviceImpl); MITK_TEST_CONDITION_REQUIRED(!(testObject.GetPointer() == nullptr) ,"Testing initialization class"); MITK_TEST_CONDITION_REQUIRED(testObject->GetCaptureHeight()== 0 ,"Testing initialization of CaptureHeight"); MITK_TEST_CONDITION_REQUIRED(testObject->GetCaptureWidth()== 0 ,"Testing initialization of CaptureWidth"); //test correct order of file name member testObject->SetDistanceImageFileName("distTest"); testObject->SetAmplitudeImageFileName("amplTest"); testObject->SetIntensityImageFileName("intenTest"); MITK_TEST_CONDITION_REQUIRED(testObject->GetDistanceImageFileName()== "distTest" ,"Testing correct filename passing - Dist"); MITK_TEST_CONDITION_REQUIRED(testObject->GetAmplitudeImageFileName()== "amplTest" ,"Testing correct filename passing - Ampl"); MITK_TEST_CONDITION_REQUIRED(testObject->GetIntensityImageFileName()== "intenTest" ,"Testing correct filename passing - Inten"); //test passing of file name from image grabber imageGrabber->SetStringProperty("DistanceImageFileName", "distPropertyTestName"); imageGrabber->SetStringProperty("AmplitudeImageFileName", "amplPropertyTestName"); imageGrabber->SetStringProperty("IntensityImageFileName", "intenPropertyTestName"); testObject = deviceImpl->GetController(); MITK_TEST_CONDITION_REQUIRED(testObject->GetDistanceImageFileName()== "distPropertyTestName" ,"Testing correct filename passing from Image Grabber- Dist"); MITK_TEST_CONDITION_REQUIRED(testObject->GetAmplitudeImageFileName()== "amplPropertyTestName" ,"Testing correct filename passing from Image Grabber- Ampl"); MITK_TEST_CONDITION_REQUIRED(testObject->GetIntensityImageFileName()== "intenPropertyTestName" ,"Testing correct filename passing from Image Grabber- Inten"); - // PIC Format is deprecated - // ReadFileFormatTestCase(".pic", imageGrabber); ReadFileFormatTestCase(".nrrd", imageGrabber); deviceImpl->Delete(); // end of test MITK_TEST_END(); } - - diff --git a/Modules/ToFHardware/Testing/mitkToFImageGrabberTest.cpp b/Modules/ToFHardware/Testing/mitkToFImageGrabberTest.cpp index 177d50a7a2..3e7858a398 100644 --- a/Modules/ToFHardware/Testing/mitkToFImageGrabberTest.cpp +++ b/Modules/ToFHardware/Testing/mitkToFImageGrabberTest.cpp @@ -1,186 +1,186 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include #include #include /** * @brief The mitkToFImageGrabberTestSuite class is a test-suite for mitkToFImageGrabber. * * Test data is retrieved from MITK-Data. */ class mitkToFImageGrabberTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkToFImageGrabberTestSuite); MITK_TEST(GetterAndSetterTests); MITK_TEST(ConnectCamera_InvalidFileName_ThrowsException); MITK_TEST(ConnectCamera_ValidFileName_ReturnsTrue); MITK_TEST(IsCameraActive_DifferentStates_ReturnsCorrectResult); MITK_TEST(Update_2DData_ImagesAreEqual); MITK_TEST(Update_CamCubeData_PropertiesAreTrue); CPPUNIT_TEST_SUITE_END(); private: std::string m_KinectDepthImagePath; std::string m_KinectColorImagePath; std::string m_CamCubeDepthImagePath; std::string m_CamCubeIntensityImagePath; std::string m_CamCubeAmplitudeImagePath; mitk::ToFImageGrabber::Pointer m_ToFImageGrabber; public: void setUp() override { std::string dirName = MITK_TOF_DATA_DIR; std::string depthImagePath = dirName + "/" + "Kinect_Lego_Phantom_DistanceImage.nrrd"; std::string colorImagePath = dirName + "/" + "Kinect_Lego_Phantom_RGBImage.nrrd"; - std::string distanceImageP = dirName + "/" + "PMDCamCube2_MF0_IT0_1Images_DistanceImage.pic"; - std::string amplitudeImage = dirName + "/" + "PMDCamCube2_MF0_IT0_1Images_AmplitudeImage.pic"; - std::string intensityImage = dirName + "/" + "PMDCamCube2_MF0_IT0_1Images_IntensityImage.pic"; + std::string distanceImageP = dirName + "/" + "PMDCamCube2_MF0_IT0_1Images_DistanceImage.nrrd"; + std::string amplitudeImage = dirName + "/" + "PMDCamCube2_MF0_IT0_1Images_AmplitudeImage.nrrd"; + std::string intensityImage = dirName + "/" + "PMDCamCube2_MF0_IT0_1Images_IntensityImage.nrrd"; m_KinectDepthImagePath = GetTestDataFilePath(depthImagePath); m_KinectColorImagePath = GetTestDataFilePath(colorImagePath); m_CamCubeDepthImagePath = GetTestDataFilePath(distanceImageP); m_CamCubeIntensityImagePath = GetTestDataFilePath(amplitudeImage); m_CamCubeAmplitudeImagePath = GetTestDataFilePath(intensityImage); m_ToFImageGrabber = mitk::ToFImageGrabber::New(); //The Grabber always needs a device mitk::ToFCameraMITKPlayerDevice::Pointer tofCameraMITKPlayerDevice = mitk::ToFCameraMITKPlayerDevice::New(); m_ToFImageGrabber->SetCameraDevice(tofCameraMITKPlayerDevice); } void tearDown() override { if(m_ToFImageGrabber->IsCameraActive()) { m_ToFImageGrabber->StopCamera(); m_ToFImageGrabber->DisconnectCamera(); } m_ToFImageGrabber = nullptr; } /** * @brief GetterAndSetterTests Testing getters and setters of mitkToFImageGrabber, because * they internally contain logic. */ void GetterAndSetterTests() { int modulationFrequency = 20; m_ToFImageGrabber->SetModulationFrequency(modulationFrequency); CPPUNIT_ASSERT(modulationFrequency==m_ToFImageGrabber->GetModulationFrequency()); int integrationTime = 500; m_ToFImageGrabber->SetIntegrationTime(integrationTime); CPPUNIT_ASSERT(integrationTime==m_ToFImageGrabber->GetIntegrationTime()); } void ConnectCamera_InvalidFileName_ThrowsException() { MITK_TEST_FOR_EXCEPTION(std::logic_error, m_ToFImageGrabber->ConnectCamera()); m_ToFImageGrabber->StartCamera(); m_ToFImageGrabber->StopCamera(); CPPUNIT_ASSERT_MESSAGE("Test DisconnectCamera() with no file name set", !m_ToFImageGrabber->DisconnectCamera()); } void ConnectCamera_ValidFileName_ReturnsTrue() { m_ToFImageGrabber->SetProperty("DistanceImageFileName",mitk::StringProperty::New(m_KinectDepthImagePath)); m_ToFImageGrabber->SetProperty("RGBImageFileName",mitk::StringProperty::New(m_KinectColorImagePath)); CPPUNIT_ASSERT(m_ToFImageGrabber->ConnectCamera() == true); } void Update_2DData_ImagesAreEqual() { try { m_ToFImageGrabber->SetProperty("DistanceImageFileName",mitk::StringProperty::New(m_KinectDepthImagePath)); m_ToFImageGrabber->ConnectCamera(); m_ToFImageGrabber->StartCamera(); mitk::Image::Pointer expectedResultImage = mitk::IOUtil::Load(m_KinectDepthImagePath); m_ToFImageGrabber->Update(); //Select 2D slice to make it comparable in diminsion mitk::ImageSliceSelector::Pointer selector = mitk::ImageSliceSelector::New(); selector->SetSliceNr(0); selector->SetTimeNr(0); selector->SetInput( m_ToFImageGrabber->GetOutput(0) ); selector->Update(); mitk::Image::Pointer distanceImage = selector->GetOutput(0); MITK_ASSERT_EQUAL( expectedResultImage, distanceImage, "Test data is 2D. Results should be equal."); } catch(std::exception &e) { MITK_ERROR << e.what(); } } void IsCameraActive_DifferentStates_ReturnsCorrectResult() { m_ToFImageGrabber->SetProperty("DistanceImageFileName",mitk::StringProperty::New(m_KinectDepthImagePath)); m_ToFImageGrabber->SetProperty("RGBImageFileName",mitk::StringProperty::New(m_KinectColorImagePath)); m_ToFImageGrabber->ConnectCamera(); CPPUNIT_ASSERT(m_ToFImageGrabber->IsCameraActive() == false); m_ToFImageGrabber->StartCamera(); CPPUNIT_ASSERT(m_ToFImageGrabber->IsCameraActive() == true); m_ToFImageGrabber->StopCamera(); CPPUNIT_ASSERT(m_ToFImageGrabber->IsCameraActive() == false); m_ToFImageGrabber->StartCamera(); CPPUNIT_ASSERT(m_ToFImageGrabber->IsCameraActive() == true); m_ToFImageGrabber->StopCamera(); CPPUNIT_ASSERT(m_ToFImageGrabber->IsCameraActive() == false); m_ToFImageGrabber->DisconnectCamera(); CPPUNIT_ASSERT(m_ToFImageGrabber->IsCameraActive() == false); } void Update_CamCubeData_PropertiesAreTrue() { m_ToFImageGrabber->SetProperty("DistanceImageFileName",mitk::StringProperty::New(m_CamCubeDepthImagePath)); m_ToFImageGrabber->SetProperty("AmplitudeImageFileName",mitk::StringProperty::New(m_CamCubeAmplitudeImagePath)); m_ToFImageGrabber->SetProperty("IntensityImageFileName",mitk::StringProperty::New(m_CamCubeIntensityImagePath)); m_ToFImageGrabber->ConnectCamera(); m_ToFImageGrabber->StartCamera(); m_ToFImageGrabber->Update(); CPPUNIT_ASSERT( m_ToFImageGrabber->GetBoolProperty("HasAmplitudeImage") == true); CPPUNIT_ASSERT( m_ToFImageGrabber->GetBoolProperty("HasIntensityImage") == true); CPPUNIT_ASSERT( m_ToFImageGrabber->GetOutput(1) != nullptr ); CPPUNIT_ASSERT( m_ToFImageGrabber->GetOutput(2) != nullptr ); } }; MITK_TEST_SUITE_REGISTRATION(mitkToFImageGrabber) diff --git a/Modules/ToFHardware/Testing/mitkToFImageRecorderFilterTest.cpp b/Modules/ToFHardware/Testing/mitkToFImageRecorderFilterTest.cpp index 1b61990333..0d0930706e 100644 --- a/Modules/ToFHardware/Testing/mitkToFImageRecorderFilterTest.cpp +++ b/Modules/ToFHardware/Testing/mitkToFImageRecorderFilterTest.cpp @@ -1,163 +1,163 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include #include #include #include mitk::Image::Pointer CreateTestImage(unsigned int dimX, unsigned int dimY) { typedef itk::Image ItkImageType2D; typedef itk::ImageRegionIterator ItkImageRegionIteratorType2D; ItkImageType2D::Pointer image = ItkImageType2D::New(); ItkImageType2D::IndexType start; start[0] = 0; start[1] = 0; ItkImageType2D::SizeType size; size[0] = dimX; size[1] = dimY; ItkImageType2D::RegionType region; region.SetSize(size); region.SetIndex( start); ItkImageType2D::SpacingType spacing; spacing[0] = 1.0; spacing[1] = 1.0; image->SetRegions( region ); image->SetSpacing ( spacing ); image->Allocate(); //Obtaining image data from ToF camera// //Correlate inten values to PixelIndex// ItkImageRegionIteratorType2D imageIterator(image,image->GetLargestPossibleRegion()); imageIterator.GoToBegin(); itk::Statistics::MersenneTwisterRandomVariateGenerator::Pointer randomGenerator = itk::Statistics::MersenneTwisterRandomVariateGenerator::New(); while (!imageIterator.IsAtEnd()) { double pixelValue = randomGenerator->GetUniformVariate(0.0,1000.0); imageIterator.Set(pixelValue); ++imageIterator; } mitk::Image::Pointer mitkImage = mitk::Image::New(); mitk::CastToMitkImage(image,mitkImage); return mitkImage; } static bool CompareImages(mitk::Image::Pointer image1, mitk::Image::Pointer image2) { //check if epsilon is exceeded unsigned int sliceDimension = image1->GetDimension(0)*image1->GetDimension(1); bool picturesEqual = true; float* floatArray1 = (float*)image1->GetSliceData(0, 0, 0)->GetData(); float* floatArray2 = (float*)image2->GetSliceData(0, 0, 0)->GetData(); for(unsigned int i = 0; i < sliceDimension; i++) { if(!(mitk::Equal(floatArray1[i], floatArray2[i]))) { picturesEqual = false; } } return picturesEqual; } /**Documentation * test for the class "ToFImageRecorderFilter". */ int mitkToFImageRecorderFilterTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("ToFImageRecorder"); mitk::ToFImageRecorderFilter::Pointer tofImageRecorderFilter = mitk::ToFImageRecorderFilter::New(); std::string dirName = MITK_TOF_DATA_DIR; MITK_TEST_OUTPUT(<< "Test SetFileName()"); - std::string testFileName = dirName + "test.pic"; + std::string testFileName = dirName + "test.nrrd"; MITK_TEST_FOR_EXCEPTION_BEGIN(std::logic_error); tofImageRecorderFilter->SetFileName(testFileName); MITK_TEST_FOR_EXCEPTION_END(std::logic_error); testFileName = dirName + "test.nrrd"; tofImageRecorderFilter->SetFileName(testFileName); mitk::ToFImageWriter::Pointer tofImageWriter = tofImageRecorderFilter->GetToFImageWriter(); std::string requiredName = dirName + "test_DistanceImage.nrrd"; std::string name = tofImageWriter->GetDistanceImageFileName(); MITK_TEST_CONDITION_REQUIRED(requiredName==name,"Test for distance image file name"); requiredName = dirName + "test_AmplitudeImage.nrrd"; name = tofImageWriter->GetAmplitudeImageFileName(); MITK_TEST_CONDITION_REQUIRED(requiredName==name,"Test for amplitude image file name"); requiredName = dirName + "test_IntensityImage.nrrd"; name = tofImageWriter->GetIntensityImageFileName(); MITK_TEST_CONDITION_REQUIRED(requiredName==name,"Test for intensity image file name"); mitk::Image::Pointer testDistanceImage = CreateTestImage(200,200); mitk::Image::Pointer testAmplitudeImage = CreateTestImage(200,200); mitk::Image::Pointer testIntensityImage = CreateTestImage(200,200); MITK_TEST_OUTPUT(<< "Apply filter"); tofImageRecorderFilter->StartRecording(); tofImageRecorderFilter->SetInput(0,testDistanceImage); tofImageRecorderFilter->SetInput(1,testAmplitudeImage); tofImageRecorderFilter->SetInput(2,testIntensityImage); tofImageRecorderFilter->Update(); MITK_TEST_OUTPUT(<< "Test outputs of filter"); mitk::Image::Pointer outputDistanceImage = tofImageRecorderFilter->GetOutput(); MITK_TEST_CONDITION_REQUIRED(CompareImages(testDistanceImage,outputDistanceImage),"Test output 0 (distance image)"); mitk::Image::Pointer outputAmplitudeImage = tofImageRecorderFilter->GetOutput(1); MITK_TEST_CONDITION_REQUIRED(CompareImages(testAmplitudeImage,outputAmplitudeImage),"Test output 1 (amplitude image)"); mitk::Image::Pointer outputIntensityImage = tofImageRecorderFilter->GetOutput(2); MITK_TEST_CONDITION_REQUIRED(CompareImages(testIntensityImage,outputIntensityImage),"Test output 2 (intensity image)"); tofImageRecorderFilter->StopRecording(); MITK_TEST_OUTPUT(<< "Test content of written files"); mitk::ItkImageFileReader::Pointer imageReader = mitk::ItkImageFileReader::New(); std::string testDistanceImageName = dirName + "test_DistanceImage.nrrd"; imageReader->SetFileName(testDistanceImageName); imageReader->Update(); mitk::Image::Pointer loadedDistanceImage = imageReader->GetOutput(); MITK_TEST_CONDITION_REQUIRED(CompareImages(testDistanceImage,loadedDistanceImage),"Test loaded image 0 (distance image)"); std::string testAmplitudeImageName = dirName + "test_AmplitudeImage.nrrd"; imageReader->SetFileName(testAmplitudeImageName); imageReader->Update(); mitk::Image::Pointer loadedAmplitudeImage = imageReader->GetOutput(); MITK_TEST_CONDITION_REQUIRED(CompareImages(testAmplitudeImage,loadedAmplitudeImage),"Test loaded image 1 (amplitude image)"); std::string testIntensityImageName = dirName + "test_IntensityImage.nrrd"; imageReader->SetFileName(testIntensityImageName); imageReader->Update(); mitk::Image::Pointer loadedIntensityImage = imageReader->GetOutput(); MITK_TEST_CONDITION_REQUIRED(CompareImages(testIntensityImage,loadedIntensityImage),"Test loaded image 2 (intensity image)"); //clean up and delete saved image files if( remove( testDistanceImageName.c_str() ) != 0 ) { MITK_ERROR<<"File: test_DistanceImage.nrrd not successfully deleted!"; } if( remove( testAmplitudeImageName.c_str() ) != 0 ) { MITK_ERROR<<"File: test_AmplitudeImage.nrrd not successfully deleted!"; } if( remove( testIntensityImageName.c_str() ) != 0 ) { MITK_ERROR<<"File: test_IntensityImage.nrrd not successfully deleted!"; } MITK_TEST_END(); } diff --git a/Modules/ToFHardware/Testing/mitkToFImageRecorderTest.cpp b/Modules/ToFHardware/Testing/mitkToFImageRecorderTest.cpp index aee449e21f..87d6b72f1c 100644 --- a/Modules/ToFHardware/Testing/mitkToFImageRecorderTest.cpp +++ b/Modules/ToFHardware/Testing/mitkToFImageRecorderTest.cpp @@ -1,155 +1,155 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include #include #include class mitkToFImageRecorderTestSuite : public mitk::TestFixture { CPPUNIT_TEST_SUITE(mitkToFImageRecorderTestSuite); //See bug #12997 // MITK_TEST(StartRecording_ValidDepthImage_WritesImageToFile); // MITK_TEST(StartRecording_ValidAmplitudeImage_WritesImageToFile); // MITK_TEST(StartRecording_ValidIntensityImage_WritesImageToFile); CPPUNIT_TEST_SUITE_END(); private: /** Members used inside the different (sub-)tests. All members are initialized via setUp(). * Every recorder needs a device. Here we use a player device. * The player device needs data to load. The ground truth is loaded via IOUtil. */ mitk::ToFImageRecorder::Pointer m_ToFImageRecorder; mitk::ToFCameraMITKPlayerDevice::Pointer m_PlayerDevice; std::string m_DistanceImageName; std::string m_AmplitudeImageName; std::string m_IntensityImageName; mitk::Image::Pointer m_GroundTruthDepthImage; mitk::Image::Pointer m_GroundTruthIntensityImage; mitk::Image::Pointer m_GroundTruthAmplitudeImage; public: /** * @brief Setup a recorder including a device. Here, we use a player, because in an automatic test * hardware is not useful. */ void setUp() override { m_ToFImageRecorder = mitk::ToFImageRecorder::New(); m_DistanceImageName = mitk::IOUtil::CreateTemporaryFile(); m_AmplitudeImageName = mitk::IOUtil::CreateTemporaryFile(); m_IntensityImageName = mitk::IOUtil::CreateTemporaryFile(); //The recorder would automatically append the default extension ".nrrd" //but we have to append it here, because the data is later loaded with //IOUtil which does not know what kind of data to load/look for. m_DistanceImageName.append("Distance.nrrd"); m_AmplitudeImageName.append("Amplitude.nrrd"); m_IntensityImageName.append("Intensity.nrrd"); m_PlayerDevice = mitk::ToFCameraMITKPlayerDevice::New(); m_ToFImageRecorder->SetCameraDevice(m_PlayerDevice); //the test data set has 20 frames, so we record 20 per default m_ToFImageRecorder->SetNumOfFrames(20); m_ToFImageRecorder->SetRecordMode(mitk::ToFImageRecorder::PerFrames); std::string dirName = MITK_TOF_DATA_DIR; - std::string distanceFileName = dirName + "/PMDCamCube2_MF0_IT0_20Images_DistanceImage.pic"; - std::string amplitudeFileName = dirName + "/PMDCamCube2_MF0_IT0_20Images_AmplitudeImage.pic"; - std::string intensityFileName = dirName + "/PMDCamCube2_MF0_IT0_20Images_IntensityImage.pic"; + std::string distanceFileName = dirName + "/PMDCamCube2_MF0_IT0_20Images_DistanceImage.nrrd"; + std::string amplitudeFileName = dirName + "/PMDCamCube2_MF0_IT0_20Images_AmplitudeImage.nrrd"; + std::string intensityFileName = dirName + "/PMDCamCube2_MF0_IT0_20Images_IntensityImage.nrrd"; m_PlayerDevice->SetProperty("DistanceImageFileName",mitk::StringProperty::New(distanceFileName)); m_PlayerDevice->SetProperty("AmplitudeImageFileName",mitk::StringProperty::New(amplitudeFileName)); m_PlayerDevice->SetProperty("IntensityImageFileName",mitk::StringProperty::New(intensityFileName)); //comparing against IOUtil seems fair enough m_GroundTruthDepthImage = mitk::IOUtil::Load(distanceFileName); m_GroundTruthAmplitudeImage = mitk::IOUtil::Load(amplitudeFileName); m_GroundTruthIntensityImage = mitk::IOUtil::Load(intensityFileName); m_PlayerDevice->ConnectCamera(); m_PlayerDevice->StartCamera(); } void tearDown() override { m_PlayerDevice->StopCamera(); m_PlayerDevice->DisconnectCamera(); } void StartRecording_ValidDepthImage_WritesImageToFile() { m_ToFImageRecorder->SetDistanceImageFileName(m_DistanceImageName); m_ToFImageRecorder->StartRecording(); m_ToFImageRecorder->WaitForThreadBeingTerminated(); m_ToFImageRecorder->StopRecording(); mitk::Image::Pointer recordedImage = mitk::IOUtil::Load(m_DistanceImageName); MITK_ASSERT_EQUAL( m_GroundTruthDepthImage, recordedImage, "Recorded image should be equal to the test data."); //delete the tmp image if( remove( m_DistanceImageName.c_str() ) != 0 ) { MITK_ERROR<<"File: "<< m_DistanceImageName << " not successfully deleted!"; } } void StartRecording_ValidAmplitudeImage_WritesImageToFile() { m_ToFImageRecorder->SetAmplitudeImageFileName(m_AmplitudeImageName); m_ToFImageRecorder->SetAmplitudeImageSelected(true); m_ToFImageRecorder->SetDistanceImageSelected(false); m_ToFImageRecorder->StartRecording(); m_ToFImageRecorder->WaitForThreadBeingTerminated(); m_ToFImageRecorder->StopRecording(); mitk::Image::Pointer recordedImage = mitk::IOUtil::Load(m_AmplitudeImageName); MITK_ASSERT_EQUAL( m_GroundTruthAmplitudeImage, recordedImage, "Recorded image should be equal to the test data."); //delete the tmp image if( remove( m_AmplitudeImageName.c_str() ) != 0 ) { MITK_ERROR<<"File: "<< m_AmplitudeImageName << " not successfully deleted!"; } } void StartRecording_ValidIntensityImage_WritesImageToFile() { m_ToFImageRecorder->SetIntensityImageFileName(m_IntensityImageName); m_ToFImageRecorder->SetIntensityImageSelected(true); m_ToFImageRecorder->SetDistanceImageSelected(false); m_ToFImageRecorder->StartRecording(); m_ToFImageRecorder->WaitForThreadBeingTerminated(); m_ToFImageRecorder->StopRecording(); mitk::Image::Pointer recordedImage = mitk::IOUtil::Load(m_IntensityImageName); MITK_ASSERT_EQUAL( m_GroundTruthIntensityImage, recordedImage, "Recorded image should be equal to the test data."); //delete the tmp image if( remove( m_IntensityImageName.c_str() ) != 0 ) { MITK_ERROR<<"File: "<< m_IntensityImageName << " not successfully deleted!"; } } }; MITK_TEST_SUITE_REGISTRATION(mitkToFImageRecorder) diff --git a/Modules/ToFHardware/Testing/mitkToFImageWriterTest.cpp b/Modules/ToFHardware/Testing/mitkToFImageWriterTest.cpp index 85aeebe0b0..96fe92b6ee 100644 --- a/Modules/ToFHardware/Testing/mitkToFImageWriterTest.cpp +++ b/Modules/ToFHardware/Testing/mitkToFImageWriterTest.cpp @@ -1,78 +1,78 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include /**Documentation * test for the class "ToFImageWriter". */ int mitkToFImageWriterTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("ToFImageWriter"); //testing initialization of object mitk::ToFImageWriter::Pointer tofWriter = mitk::ToFImageWriter::New(); MITK_TEST_CONDITION_REQUIRED(tofWriter.GetPointer(), "Testing initialization of test object!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetExtension()!= "", "Test initialization of member extension!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetDistanceImageFileName()== "", "Test initialization of member distanceImageFileName!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetAmplitudeImageFileName()== "", "Test initialization of member amplitudeImageFileName!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetIntensityImageFileName()== "", "Test initialization of member intnensityImageFileName!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetDistanceImageSelected()==true, "Test initialization of member distanceImageSelected!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetAmplitudeImageSelected()==false, "Test initialization of member amplitudeImageSelected!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetIntensityImageSelected()==false, "Test initialization of member intensityImageSelected!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetRGBImageSelected()==false, "Test initialization of member rgbImageSelected!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetToFCaptureWidth()== 200, "Test initialization of member captureWidth!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetToFCaptureHeight()== 200, "Test initialization of member captureHeight!"); MITK_TEST_CONDITION_REQUIRED(tofWriter->GetToFImageType()== mitk::ToFImageWriter::ToFImageType3D, "Test initialization of member ToFImageType!"); //set member parameter and test again int dimX = 255; int dimY = 188; - std::string distanceImageFileName("distImg.pic"); - std::string amplitudeImageFileName("amplImg.pic"); - std::string intensityImageFileName("intImg.pic"); - std::string rgbImageFileName("rgbImg.pic"); + std::string distanceImageFileName("distImg.nrrd"); + std::string amplitudeImageFileName("amplImg.nrrd"); + std::string intensityImageFileName("intImg.nrrd"); + std::string rgbImageFileName("rgbImg.nrrd"); std::string fileExtension(".test"); bool distanceImageSelected = false; bool amplitudeImageSelected = false; bool intensityImageSelected = false; bool rgbImageSelected = false; tofWriter->SetToFCaptureWidth(dimX); tofWriter->SetToFCaptureHeight(dimY); tofWriter->SetDistanceImageFileName(distanceImageFileName); tofWriter->SetAmplitudeImageFileName(amplitudeImageFileName); tofWriter->SetIntensityImageFileName(intensityImageFileName); tofWriter->SetRGBImageFileName(rgbImageFileName); tofWriter->SetExtension(fileExtension); tofWriter->SetDistanceImageSelected(distanceImageSelected); tofWriter->SetAmplitudeImageSelected(amplitudeImageSelected); tofWriter->SetIntensityImageSelected(intensityImageSelected); tofWriter->SetRGBImageSelected(rgbImageSelected); tofWriter->SetToFImageType(mitk::ToFImageWriter::ToFImageType2DPlusT); MITK_TEST_CONDITION_REQUIRED(distanceImageFileName==tofWriter->GetDistanceImageFileName(), "Testing set/get distance image file name"); MITK_TEST_CONDITION_REQUIRED(amplitudeImageFileName==tofWriter->GetAmplitudeImageFileName(), "Testing set/get amplitude image file name"); MITK_TEST_CONDITION_REQUIRED(intensityImageFileName==tofWriter->GetIntensityImageFileName(), "Testing set/get intensity image file name"); MITK_TEST_CONDITION_REQUIRED(rgbImageFileName==tofWriter->GetRGBImageFileName(), "Testing set/get rgb image file name"); MITK_TEST_CONDITION_REQUIRED(dimX==tofWriter->GetToFCaptureWidth(), "Testing set/get CaptureWidth"); MITK_TEST_CONDITION_REQUIRED(dimY==tofWriter->GetToFCaptureHeight(), "Testing set/get CaptureHeight"); MITK_TEST_CONDITION_REQUIRED(distanceImageSelected==tofWriter->GetDistanceImageSelected(), "Testing set/get distance image selection"); MITK_TEST_CONDITION_REQUIRED(amplitudeImageSelected==tofWriter->GetAmplitudeImageSelected(), "Testing set/get amplitude image selection"); MITK_TEST_CONDITION_REQUIRED(intensityImageSelected==tofWriter->GetIntensityImageSelected(), "Testing set/get intensity image selection"); MITK_TEST_CONDITION_REQUIRED(rgbImageSelected==tofWriter->GetRGBImageSelected(), "Testing set/get rgb image selection"); MITK_TEST_CONDITION_REQUIRED(fileExtension==tofWriter->GetExtension(), "Testing set/get file extension"); MITK_TEST_CONDITION_REQUIRED(mitk::ToFImageWriter::ToFImageType2DPlusT==tofWriter->GetToFImageType(), "Testing set/get ToFImageType"); MITK_TEST_END(); } diff --git a/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp b/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp index fec7edbeea..2c650eeab1 100644 --- a/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp +++ b/Modules/ToFHardware/Testing/mitkToFOpenCVImageGrabberTest.cpp @@ -1,97 +1,97 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include #include #include #include #include #include static bool CompareImages(mitk::Image::Pointer mitkImage, cv::Mat openCVImage) { float equal = true; if (static_cast(mitkImage->GetDimension(0)) != openCVImage.cols || static_cast(mitkImage->GetDimension(1)) != openCVImage.rows) { equal = false; } mitk::ImagePixelReadAccessor imageAcces(mitkImage, mitkImage->GetSliceData(0)); for(int i=0; i currentIndex; currentIndex[0] = i; currentIndex[1] = j; float mitkImageValue = imageAcces.GetPixelByIndex(currentIndex); float openCVImageValue = openCVImage.at(j,i); if (!mitk::Equal(mitkImageValue,openCVImageValue)) { equal = false; } } } return equal; } /**Documentation * test for the class "ToFOpenCVImageGrabber". */ int mitkToFOpenCVImageGrabberTest(int /* argc */, char* /*argv*/[]) { MITK_TEST_BEGIN("ToFOpenCVImageGrabber"); std::string dirName = MITK_TOF_DATA_DIR; mitk::ToFImageGrabber::Pointer tofImageGrabber = mitk::ToFImageGrabber::New(); tofImageGrabber->SetCameraDevice(mitk::ToFCameraMITKPlayerDevice::New()); - std::string distanceFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_DistanceImage.pic"; + std::string distanceFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_DistanceImage.nrrd"; tofImageGrabber->SetProperty("DistanceImageFileName",mitk::StringProperty::New(distanceFileName)); - std::string amplitudeFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_AmplitudeImage.pic"; + std::string amplitudeFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_AmplitudeImage.nrrd"; tofImageGrabber->SetProperty("AmplitudeImageFileName",mitk::StringProperty::New(amplitudeFileName)); - std::string intensityFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_IntensityImage.pic"; + std::string intensityFileName = dirName + "/PMDCamCube2_MF0_IT0_1Images_IntensityImage.nrrd"; tofImageGrabber->SetProperty("IntensityImageFileName",mitk::StringProperty::New(intensityFileName)); tofImageGrabber->Update(); mitk::Image::Pointer image = mitk::IOUtil::Load(distanceFileName); try { mitk::ToFOpenCVImageGrabber::Pointer tofOpenCVImageGrabber = mitk::ToFOpenCVImageGrabber::New(); tofOpenCVImageGrabber->SetToFImageGrabber(tofImageGrabber); MITK_TEST_CONDITION_REQUIRED(tofImageGrabber==tofOpenCVImageGrabber->GetToFImageGrabber(),"Test Set/GetToFImageGrabber()"); MITK_TEST_OUTPUT(<<"Call StartCapturing()"); tofOpenCVImageGrabber->StartCapturing(); cv::Mat cvImage = tofOpenCVImageGrabber->GetImage(); MITK_TEST_CONDITION_REQUIRED(CompareImages(image,cvImage),"Test distance image"); image = mitk::IOUtil::Load(amplitudeFileName); tofOpenCVImageGrabber->SetImageType(1); cvImage = tofOpenCVImageGrabber->GetImage(); MITK_TEST_CONDITION_REQUIRED(CompareImages(image,cvImage),"Test amplitude image"); image = mitk::IOUtil::Load(intensityFileName); tofOpenCVImageGrabber->SetImageType(2); cvImage = tofOpenCVImageGrabber->GetImage(); MITK_TEST_CONDITION_REQUIRED(CompareImages(image,cvImage),"Test intensity image"); MITK_TEST_OUTPUT(<<"Call StopCapturing()"); tofOpenCVImageGrabber->StopCapturing(); } catch(std::exception &e) { MITK_INFO << "Exception is: " << e.what(); } MITK_TEST_END(); } diff --git a/Modules/ToFHardware/mitkToFCameraMITKPlayerController.cpp b/Modules/ToFHardware/mitkToFCameraMITKPlayerController.cpp index c09e18eaa6..f825a93c61 100644 --- a/Modules/ToFHardware/mitkToFCameraMITKPlayerController.cpp +++ b/Modules/ToFHardware/mitkToFCameraMITKPlayerController.cpp @@ -1,333 +1,332 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include #include // mitk includes #include "mitkIOUtil.h" -#include #include "mitkImageReadAccessor.h" namespace mitk { ToFCameraMITKPlayerController::ToFCameraMITKPlayerController() : m_PixelNumber(0), m_RGBPixelNumber(0), m_NumberOfBytes(0), m_NumberOfRGBBytes(0), m_CaptureWidth(0), m_CaptureHeight(0), m_RGBCaptureWidth(0), m_RGBCaptureHeight(0), m_ConnectionCheck(false), m_InputFileName(""), m_ToFImageType(ToFImageType3D), m_DistanceImage(nullptr), m_AmplitudeImage(nullptr), m_IntensityImage(nullptr), m_RGBImage(nullptr), m_DistanceInfile(nullptr), m_AmplitudeInfile(nullptr), m_IntensityInfile(nullptr), m_RGBInfile(nullptr), m_IntensityArray(nullptr), m_DistanceArray(nullptr), m_AmplitudeArray(nullptr), m_RGBArray(nullptr), m_DistanceImageFileName(""), m_AmplitudeImageFileName(""), m_IntensityImageFileName(""), m_RGBImageFileName(""), m_PixelStartInFile(0), m_CurrentFrame(-1), m_NumOfFrames(0) { m_ImageStatus = std::vector(4,true); } ToFCameraMITKPlayerController::~ToFCameraMITKPlayerController() { this->CleanUp(); } void ToFCameraMITKPlayerController::CleanUp() { if(m_DistanceImage.IsNotNull()) { m_DistanceImage->ReleaseData(); m_DistanceImage = nullptr; } if(m_AmplitudeImage.IsNotNull()) { m_AmplitudeImage->ReleaseData(); m_AmplitudeImage = nullptr; } if(m_IntensityImage.IsNotNull()) { m_IntensityImage->ReleaseData(); m_IntensityImage = nullptr; } if(m_RGBImage.IsNotNull()) { m_RGBImage->ReleaseData(); m_RGBImage = nullptr; } delete[] this->m_DistanceArray; this->m_DistanceArray = nullptr; delete[] this->m_AmplitudeArray; this->m_AmplitudeArray = nullptr; delete[] this->m_IntensityArray; this->m_IntensityArray = nullptr; delete[] this->m_RGBArray; this->m_RGBArray = nullptr; this->m_DistanceImageFileName = ""; this->m_AmplitudeImageFileName = ""; this->m_IntensityImageFileName = ""; this->m_RGBImageFileName = ""; } bool ToFCameraMITKPlayerController::OpenCameraConnection() { if(!this->m_ConnectionCheck) { // reset the image status before connection m_ImageStatus = std::vector(4,true); try { if (this->m_DistanceImageFileName.empty() && this->m_AmplitudeImageFileName.empty() && this->m_IntensityImageFileName.empty() && this->m_RGBImageFileName.empty()) { throw std::logic_error("No image data file names set"); } if (!this->m_DistanceImageFileName.empty()) { m_DistanceImage = mitk::IOUtil::Load(this->m_DistanceImageFileName); } else { MITK_ERROR << "ToF distance image data file empty"; } if (!this->m_AmplitudeImageFileName.empty()) { m_AmplitudeImage = mitk::IOUtil::Load(this->m_AmplitudeImageFileName); } else { MITK_WARN << "ToF amplitude image data file empty"; } if (!this->m_IntensityImageFileName.empty()) { m_IntensityImage = mitk::IOUtil::Load(this->m_IntensityImageFileName); } else { MITK_WARN << "ToF intensity image data file empty"; } if (!this->m_RGBImageFileName.empty()) { m_RGBImage = mitk::IOUtil::Load(this->m_RGBImageFileName); } else { MITK_WARN << "ToF RGB image data file empty"; } // check if the opened files contained data if(m_DistanceImage.IsNull()) { m_ImageStatus.at(0) = false; } if(m_AmplitudeImage.IsNull()) { m_ImageStatus.at(1) = false; } if(m_IntensityImage.IsNull()) { m_ImageStatus.at(2) = false; } if(m_RGBImage.IsNull()) { m_ImageStatus.at(3) = false; } // Check for dimension type mitk::Image::Pointer infoImage = nullptr; if(m_ImageStatus.at(0)) { infoImage = m_DistanceImage; } else if (m_ImageStatus.at(1)) { infoImage = m_AmplitudeImage; } else if(m_ImageStatus.at(2)) { infoImage = m_IntensityImage; } else if(m_ImageStatus.at(3)) { infoImage = m_RGBImage; } if (infoImage->GetDimension() == 2) this->m_ToFImageType = ToFImageType2DPlusT; else if (infoImage->GetDimension() == 3) this->m_ToFImageType = ToFImageType3D; else if (infoImage->GetDimension() == 4) this->m_ToFImageType = ToFImageType2DPlusT; else throw std::logic_error("Error opening ToF data file: Invalid dimension."); this->m_CaptureWidth = infoImage->GetDimension(0); this->m_CaptureHeight = infoImage->GetDimension(1); this->m_PixelNumber = this->m_CaptureWidth*this->m_CaptureHeight; this->m_NumberOfBytes = this->m_PixelNumber * sizeof(float); if(m_RGBImage) { m_RGBCaptureWidth = m_RGBImage->GetDimension(0); m_RGBCaptureHeight = m_RGBImage->GetDimension(1); m_RGBPixelNumber = m_RGBCaptureWidth * m_RGBCaptureHeight; m_NumberOfRGBBytes = m_RGBPixelNumber * 3; } if (this->m_ToFImageType == ToFImageType2DPlusT) { this->m_NumOfFrames = infoImage->GetDimension(3); } else { this->m_NumOfFrames = infoImage->GetDimension(2); } // allocate buffer this->m_DistanceArray = new float[this->m_PixelNumber]; for(int i=0; im_PixelNumber; i++) {this->m_DistanceArray[i]=0.0;} this->m_AmplitudeArray = new float[this->m_PixelNumber]; for(int i=0; im_PixelNumber; i++) {this->m_AmplitudeArray[i]=0.0;} this->m_IntensityArray = new float[this->m_PixelNumber]; for(int i=0; im_PixelNumber; i++) {this->m_IntensityArray[i]=0.0;} this->m_RGBArray = new unsigned char[m_NumberOfRGBBytes]; for(int i=0; im_RGBArray[i]=0.0;} MITK_INFO << "NumOfFrames: " << this->m_NumOfFrames; this->m_ConnectionCheck = true; return this->m_ConnectionCheck; } catch(std::exception& e) { MITK_ERROR << "Error opening ToF data file " << this->m_InputFileName << " " << e.what(); throw std::logic_error("Error opening ToF data file"); return false; } } else return this->m_ConnectionCheck; } bool ToFCameraMITKPlayerController::CloseCameraConnection() { if (this->m_ConnectionCheck) { this->CleanUp(); this->m_ConnectionCheck = false; return true; } return false; } void ToFCameraMITKPlayerController::UpdateCamera() { this->m_CurrentFrame++; if(this->m_CurrentFrame >= this->m_NumOfFrames) { this->m_CurrentFrame = 0; } if(this->m_ImageStatus.at(0)) { this->AccessData(this->m_CurrentFrame, this->m_DistanceImage, this->m_DistanceArray); } if(this->m_ImageStatus.at(1)) { this->AccessData(this->m_CurrentFrame, this->m_AmplitudeImage, this->m_AmplitudeArray); } if(this->m_ImageStatus.at(2)) { this->AccessData(this->m_CurrentFrame, this->m_IntensityImage, this->m_IntensityArray); } if(this->m_ImageStatus.at(3)) { if(!this->m_ToFImageType) { ImageReadAccessor rgbAcc(m_RGBImage, m_RGBImage->GetSliceData(m_CurrentFrame)); memcpy(m_RGBArray, rgbAcc.GetData(), m_NumberOfRGBBytes ); } else if(this->m_ToFImageType) { ImageReadAccessor rgbAcc(m_RGBImage, m_RGBImage->GetVolumeData(m_CurrentFrame)); memcpy(m_RGBArray, rgbAcc.GetData(), m_NumberOfRGBBytes); } } itksys::SystemTools::Delay(50); } void ToFCameraMITKPlayerController::AccessData(int frame, Image::Pointer image, float* &data) { if(!this->m_ToFImageType) { ImageReadAccessor imgAcc(image, image->GetSliceData(frame)); memcpy(data, imgAcc.GetData(), this->m_NumberOfBytes ); } else if(this->m_ToFImageType) { ImageReadAccessor imgAcc(image, image->GetVolumeData(frame)); memcpy(data, imgAcc.GetData(), this->m_NumberOfBytes); } } void ToFCameraMITKPlayerController::GetAmplitudes(float* amplitudeArray) { memcpy(amplitudeArray, this->m_AmplitudeArray, this->m_NumberOfBytes); } void ToFCameraMITKPlayerController::GetIntensities(float* intensityArray) { memcpy(intensityArray, this->m_IntensityArray, this->m_NumberOfBytes); } void ToFCameraMITKPlayerController::GetDistances(float* distanceArray) { memcpy(distanceArray, this->m_DistanceArray, this->m_NumberOfBytes); } void ToFCameraMITKPlayerController::GetRgb(unsigned char* rgbArray) { memcpy(rgbArray, this->m_RGBArray, m_NumberOfRGBBytes); } void ToFCameraMITKPlayerController::SetInputFileName(std::string inputFileName) { this->m_InputFileName = inputFileName; } } diff --git a/Modules/ToFHardware/mitkToFCameraMITKPlayerController.h b/Modules/ToFHardware/mitkToFCameraMITKPlayerController.h index 49dbb49184..eb1eb707a6 100644 --- a/Modules/ToFHardware/mitkToFCameraMITKPlayerController.h +++ b/Modules/ToFHardware/mitkToFCameraMITKPlayerController.h @@ -1,142 +1,142 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef __mitkToFCameraMITKPlayerController_h #define __mitkToFCameraMITKPlayerController_h #include #include "mitkCommon.h" #include "mitkFileReader.h" #include "mitkImage.h" #include "itkObject.h" #include "itkObjectFactory.h" namespace mitk { /** - * @brief Controller for playing ToF images saved in MITK (.pic) format + * @brief Controller for playing ToF images saved in NRRD format * * @ingroup ToFHardware */ class MITKTOFHARDWARE_EXPORT ToFCameraMITKPlayerController : public itk::Object { public: mitkClassMacroItkParent( ToFCameraMITKPlayerController , itk::Object ); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /*! \brief opens a connection to the ToF camera \return Returns 'true' if connection could be established and 'false' otherwise */ virtual bool OpenCameraConnection(); /*! \brief closes the connection to the camera \return Returns 'true' if connection could be closed (i.e. only if a connection was established before) and 'false' otherwise */ virtual bool CloseCameraConnection(); /*! \brief gets the current amplitude frame from the input These values can be used to determine the quality of the distance values. The higher the amplitude value, the higher the accuracy of the according distance value */ virtual void GetAmplitudes(float* amplitudeArray); /*! \brief gets the current intensity frame from the input as a greyscale image */ virtual void GetIntensities(float* intensityArray); /*! \brief gets the current distance frame from the inpug measuring the distance between the camera and the different object points in millimeters */ virtual void GetDistances(float* distanceArray); /*! \brief gets the current RGB frame from the input if available */ virtual void GetRgb(unsigned char* rgbArray); /*! \brief updates the current image frames from input */ virtual void UpdateCamera(); virtual void SetInputFileName(std::string inputFileName); itkGetMacro(PixelNumber, int); itkGetMacro(RGBPixelNumber, int); itkGetMacro(CaptureWidth, int); itkGetMacro(CaptureHeight, int); itkGetMacro(RGBCaptureWidth, int); itkGetMacro(RGBCaptureHeight, int); itkGetMacro( DistanceImageFileName, std::string ); itkGetMacro( AmplitudeImageFileName, std::string ); itkGetMacro( IntensityImageFileName, std::string ); itkGetMacro( RGBImageFileName, std::string ); itkSetMacro( DistanceImageFileName, std::string ); itkSetMacro( AmplitudeImageFileName, std::string ); itkSetMacro( IntensityImageFileName, std::string ); itkSetMacro( RGBImageFileName, std::string ); enum ToFImageType{ ToFImageType3D, ToFImageType2DPlusT }; protected: ToFCameraMITKPlayerController(); ~ToFCameraMITKPlayerController() override; int m_PixelNumber; ///< holds the number of pixels contained in the image int m_RGBPixelNumber; ///< same for RGB image int m_NumberOfBytes; ///< holds the number of bytes contained in the image int m_NumberOfRGBBytes; ///< same for RGB image int m_CaptureWidth; ///< holds the width of the image int m_CaptureHeight; ///< holds the height of the image int m_RGBCaptureWidth; ///< same for RGB image which can be different then depth etc. int m_RGBCaptureHeight; ///< same for RGB image which can be different then depth etc. bool m_ConnectionCheck; ///< flag showing whether the camera is connected (true) or not (false) std::string m_InputFileName; ToFImageType m_ToFImageType; ///< type of the ToF image to be played: 3D Volume (ToFImageType3D), temporal 2D image stack (ToFImageType2DPlusT) Image::Pointer m_DistanceImage; Image::Pointer m_AmplitudeImage; Image::Pointer m_IntensityImage; Image::Pointer m_RGBImage; std::vector m_ImageStatus; FILE* m_DistanceInfile; ///< file holding the distance data FILE* m_AmplitudeInfile; ///< file holding the amplitude data FILE* m_IntensityInfile; ///< file holding the intensity data FILE* m_RGBInfile; ///< file holding the rgb data float* m_IntensityArray; ///< member holding the current intensity frame float* m_DistanceArray; ///< member holding the current distance frame float* m_AmplitudeArray; ///< member holding the current amplitude frame unsigned char* m_RGBArray; ///< member holding the current rgb frame std::string m_DistanceImageFileName; ///< file name of the distance image to be played std::string m_AmplitudeImageFileName; ///< file name of the amplitude image to be played std::string m_IntensityImageFileName; ///< file name of the intensity image to be played std::string m_RGBImageFileName; ///< file name of the rgb image to be played long m_PixelStartInFile; int m_CurrentFrame; int m_NumOfFrames; private: void AccessData(int frame, Image::Pointer image, float* &data); void CleanUp(); }; } //END mitk namespace #endif diff --git a/Modules/ToFHardware/mitkToFImageWriter.h b/Modules/ToFHardware/mitkToFImageWriter.h index 3d499612d5..33e7f49fef 100644 --- a/Modules/ToFHardware/mitkToFImageWriter.h +++ b/Modules/ToFHardware/mitkToFImageWriter.h @@ -1,130 +1,130 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef __mitkToFImageWriter_h #define __mitkToFImageWriter_h #include #include "mitkCommon.h" #include "mitkToFImageGrabber.h" #include "itkObject.h" #include "itkObjectFactory.h" namespace mitk { /** * @brief Writer class for ToF images * - * This writer class allows streaming of ToF data into a file. The .pic file format is used for writing the data. - * Image information is included in the header of the pic file. + * This writer class allows streaming of ToF data into a file. + * Image information is included in the header of the nrrd file. * Writer can simultaneously save "distance", "intensity" and "amplitude" image. * Images can be written as 3D volume (ToFImageType::ToFImageType3D) or temporal image stack (ToFImageType::ToFImageType2DPlusT) * * @ingroup ToFHardware */ class MITKTOFHARDWARE_EXPORT ToFImageWriter : public itk::Object { public: ToFImageWriter(); ~ToFImageWriter() override; mitkClassMacroItkParent( ToFImageWriter , itk::Object ); itkFactorylessNewMacro(Self); itkCloneMacro(Self); itkGetMacro( DistanceImageFileName, std::string ); itkGetMacro( AmplitudeImageFileName, std::string ); itkGetMacro( IntensityImageFileName, std::string ); itkGetMacro( RGBImageFileName, std::string ); itkGetMacro( Extension, std::string ); itkGetMacro( ToFCaptureWidth, int ); itkGetMacro( ToFCaptureHeight, int ); itkGetMacro( RGBCaptureWidth, int ); itkGetMacro( RGBCaptureHeight, int ); itkGetMacro( DistanceImageSelected, bool ); itkGetMacro( AmplitudeImageSelected, bool ); itkGetMacro( IntensityImageSelected, bool ); itkGetMacro( RGBImageSelected, bool ); itkSetMacro( DistanceImageFileName, std::string ); itkSetMacro( AmplitudeImageFileName, std::string ); itkSetMacro( IntensityImageFileName, std::string ); itkSetMacro( RGBImageFileName, std::string ); itkSetMacro( Extension, std::string ); itkSetMacro( ToFCaptureWidth, int ); itkSetMacro( ToFCaptureHeight, int ); itkSetMacro( RGBCaptureWidth, int ); itkSetMacro( RGBCaptureHeight, int ); itkSetMacro( DistanceImageSelected, bool ); itkSetMacro( AmplitudeImageSelected, bool ); itkSetMacro( IntensityImageSelected, bool ); itkSetMacro( RGBImageSelected, bool ); enum ToFImageType{ ToFImageType3D, ToFImageType2DPlusT }; /*! \brief Get the type of image to be written \return ToF image type: ToFImageType3D (0) or ToFImageType2DPlusT (1) */ ToFImageWriter::ToFImageType GetToFImageType(); /*! \brief Set the type of image to be written \param toFImageType type of the ToF image: ToFImageType3D (0) or ToFImageType2DPlusT (1) */ void SetToFImageType(ToFImageWriter::ToFImageType toFImageType); /*! \brief Open file(s) for writing */ virtual void Open(){}; /*! - \brief Close file(s) add .pic header and write + \brief Close file(s) add header and write */ virtual void Close(){}; /*! \brief Add new data to file. */ virtual void Add(float* /*distanceFloatData*/, float* /*amplitudeFloatData*/, float* /*intensityFloatData*/, unsigned char* /*rgbData*/=nullptr){}; protected: /*! \brief Checks file name if file extension exists. If not an error message is returned */ void CheckForFileExtension(std::string& fileName); // member variables std::string m_Extension; ///< file extension used for saving images std::string m_DistanceImageFileName; ///< file name for saving the distance image std::string m_AmplitudeImageFileName; ///< file name for saving the amplitude image std::string m_IntensityImageFileName; ///< file name for saving the intensity image std::string m_RGBImageFileName; ///< file name for saving the RGB image int m_NumOfFrames; ///< number of frames written to the image. Used for pic header. bool m_DistanceImageSelected; ///< flag indicating if distance image should be recorded bool m_AmplitudeImageSelected; ///< flag indicating if amplitude image should be recorded bool m_IntensityImageSelected; ///< flag indicating if intensity image should be recorded bool m_RGBImageSelected; ///< flag indicating if RGB image should be recorded int m_ToFCaptureWidth; ///< width (x-dimension) of the images to record. int m_ToFCaptureHeight; ///< height (y-dimension) of the images to record. int m_RGBCaptureWidth; ///< width (x-dimension) of the images to record. int m_RGBCaptureHeight; ///< height (y-dimension) of the images to record. int m_ToFPixelNumber; ///< number of pixels (widht*height) of the images to record int m_ToFImageSizeInBytes; ///< size of the image to save in bytes int m_RGBPixelNumber; ///< number of pixels (widht*height) of the images to record int m_RGBImageSizeInBytes; ///< size of the image to save in bytes ToFImageWriter::ToFImageType m_ToFImageType; ///< type of image to be recorded: ToFImageType3D (0) or ToFImageType2DPlusT (1) }; } //END mitk namespace #endif // __mitkToFImageWriter_h diff --git a/Modules/ToFHardware/mitkToFNrrdImageWriter.h b/Modules/ToFHardware/mitkToFNrrdImageWriter.h index c6872000c8..f940eaf9d1 100644 --- a/Modules/ToFHardware/mitkToFNrrdImageWriter.h +++ b/Modules/ToFHardware/mitkToFNrrdImageWriter.h @@ -1,77 +1,77 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #ifndef __mitkToFNrrdImageWriter_h #define __mitkToFNrrdImageWriter_h #include #include "mitkToFImageWriter.h" #include namespace mitk { /** * @brief Writer class for ToF nrrd images * * This writer class allows streaming of ToF data into a nrrd file. This class uses the itkNrrdImageIO class * Writer can simultaneously save "distance", "intensity" and "amplitude" image. * Images can be written as 3D volume (ToFImageType::ToFImageType3D) or temporal image stack (ToFImageType::ToFImageType2DPlusT) * * @ingroup ToFHardware */ class MITKTOFHARDWARE_EXPORT ToFNrrdImageWriter : public ToFImageWriter { public: mitkClassMacro( ToFNrrdImageWriter , ToFImageWriter ); itkFactorylessNewMacro(Self); itkCloneMacro(Self); /*! \brief Open file(s) for writing */ void Open() override; /*! - \brief Close file(s) add .pic header and write + \brief Close file(s) add header and write */ void Close() override; /*! \brief Add new data to file. */ void Add(float* distanceFloatData, float* amplitudeFloatData, float* intensityFloatData, unsigned char* rgbData=nullptr) override; protected: std::ofstream m_DistanceOutfile; ///< file for distance image std::ofstream m_AmplitudeOutfile; ///< file for amplitude image std::ofstream m_IntensityOutfile; ///< file for intensity image std::ofstream m_RGBOutfile; ///< file for intensity image private: ToFNrrdImageWriter(); ~ToFNrrdImageWriter() override; /*! \brief Open file by filename to gain write access to it. */ void OpenStreamFile(std::ofstream &outfile, std::string outfileName); /*! \brief Close file after work on it is finished. */ void CloseStreamFile(std::ofstream &outfile, std::string fileName); /*! \brief Write image information to the NrrdFile. */ void ConvertStreamToNrrdFormat( std::string fileName ); }; } //END mitk namespace #endif // __mitkToFNrrdImageWriter_h diff --git a/Modules/ToFProcessing/Testing/CMakeLists.txt b/Modules/ToFProcessing/Testing/CMakeLists.txt index 237d89c83a..201eeca560 100644 --- a/Modules/ToFProcessing/Testing/CMakeLists.txt +++ b/Modules/ToFProcessing/Testing/CMakeLists.txt @@ -1,10 +1,10 @@ MITK_CREATE_MODULE_TESTS() if(TARGET ${TESTDRIVER}) mitkAddCustomModuleTest(mitkKinectReconstructionTest_LegoPhantom mitkKinectReconstructionTest ${MITK_DATA_DIR}/ToF-Data/CalibrationFiles/Kinect_RGB_camera.xml #camera intrinsics ${MITK_DATA_DIR}/ToF-Data/Kinect_Lego_Phantom_DistanceImage.nrrd #kinect distance image ) - #mitkAddCustomModuleTest(mitkToFImageDownsamplingFilterTest_20 mitkToFImageDownsamplingFilterTest PMDCamCube2_MF0_IT0_20Images_DistanceImage.pic) - #mitkAddCustomModuleTest(mitkToFImageDownsamplingFilterTest_1 mitkToFImageDownsamplingFilterTest PMDCamCube2_MF0_IT0_1Images_DistanceImage.pic) + #mitkAddCustomModuleTest(mitkToFImageDownsamplingFilterTest_20 mitkToFImageDownsamplingFilterTest PMDCamCube2_MF0_IT0_20Images_DistanceImage.nrrd) + #mitkAddCustomModuleTest(mitkToFImageDownsamplingFilterTest_1 mitkToFImageDownsamplingFilterTest PMDCamCube2_MF0_IT0_1Images_DistanceImage.nrrd) endif() diff --git a/Modules/ToFProcessing/Testing/mitkToFImageDownsamplingFilterTest.cpp b/Modules/ToFProcessing/Testing/mitkToFImageDownsamplingFilterTest.cpp index 2b2cc6c754..34976928ed 100644 --- a/Modules/ToFProcessing/Testing/mitkToFImageDownsamplingFilterTest.cpp +++ b/Modules/ToFProcessing/Testing/mitkToFImageDownsamplingFilterTest.cpp @@ -1,92 +1,81 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ //mitk includes #include #include #include #include #include "mitkToFImageDownsamplingFilter.h" // creator class that provides pre-configured ToFCameraDevices int mitkToFImageDownsamplingFilterTest(int argc , char* argv[]) { MITK_TEST_BEGIN("mitkToFImageDownSamplingFilterFilter"); MITK_TEST_CONDITION_REQUIRED(argc>=1, "Missing Parameters"); //Defining constants const int XDIM = 127; const int YDIM = 96; const int ZDIM = 19; // always start with this // create a new instance of filter and new image mitk::ToFImageDownsamplingFilter::Pointer testDownSampler = mitk::ToFImageDownsamplingFilter::New(); // make sure new filter ins't null MITK_TEST_CONDITION_REQUIRED(testDownSampler.IsNotNull(), "Testing instantiation!"); // Load ToF image MITK_INFO<<"Loading test image file: " << argv[1] << "\n"; // update with proper path and figure out how iti s passed from the test driver mitk::PicFileReader::Pointer reader = mitk::PicFileReader::New(); std::string filename = MITK_TOF_DATA_DIR; filename.append("/"); filename.append(argv[1]); reader->SetFileName(filename); reader->Update(); mitk::Image::Pointer image = reader->GetOutput(); MITK_TEST_CONDITION_REQUIRED(image.IsNotNull(), "Testing image reading"); MITK_INFO << "Original image dimensions " << image->GetDimension (0)<<" " << image->GetDimension(1)<< " " << image->GetDimension(2) ; //call filter testDownSampler->SetInput(image); testDownSampler->SetResampledX(XDIM); testDownSampler->SetResampledY(YDIM); testDownSampler->SetResampledZ(ZDIM); if(image->GetDimension(0) >= XDIM && image->GetDimension(1)>=YDIM && image->GetDimension(2)>=ZDIM && (image->GetDimension()==2 || image->GetDimension()==3)) { testDownSampler->Update(); mitk::Image::Pointer resultImage = testDownSampler->GetOutput(); MITK_TEST_CONDITION_REQUIRED(resultImage->GetDimension(0) == XDIM && resultImage->GetDimension(1)==YDIM &&resultImage->GetDimension(2)==ZDIM, "Test result image dimensions with 3D image"); MITK_INFO << "new image dimensions " << resultImage->GetDimension (0)<<" " << resultImage->GetDimension(1)<<" " << resultImage->GetDimension(2) ; } else { MITK_TEST_FOR_EXCEPTION_BEGIN(itk::ExceptionObject); testDownSampler->Update(); MITK_TEST_FOR_EXCEPTION_END(itk::ExceptionObject); } - - - // Mean for debugging purposes if you want to write the resutling image to a file - //mitk::PicFileWriter::Pointer writer = mitk::PicFileWriter::New(); - //writer->SetInputImage( resultImage); - //writer->SetFileName( "tofResult1.pic" ); - - //writer->Update(); - - // always end with this! MITK_TEST_END(); } - diff --git a/Modules/ToFUI/Qmitk/QmitkToFConnectionWidget.cpp b/Modules/ToFUI/Qmitk/QmitkToFConnectionWidget.cpp index 4566a20c8f..611eb548a0 100644 --- a/Modules/ToFUI/Qmitk/QmitkToFConnectionWidget.cpp +++ b/Modules/ToFUI/Qmitk/QmitkToFConnectionWidget.cpp @@ -1,393 +1,393 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ //#define _USE_MATH_DEFINES #include //QT headers #include #include #include //mitk headers #include "mitkToFConfig.h" #include "mitkCameraIntrinsics.h" #include "mitkCameraIntrinsicsProperty.h" //itk headers #include //Setting the View_ID const std::string QmitkToFConnectionWidget::VIEW_ID = "org.mitk.views.qmitktofconnectionwidget2"; //Constructor of QmitkToFConnectionWidget QmitkToFConnectionWidget::QmitkToFConnectionWidget(QWidget* parent, Qt::WindowFlags f): QWidget(parent, f) , m_Controls(nullptr) , m_IntegrationTime(0) , m_ModulationFrequency(0) , m_SelectedCameraName("") { this->m_ToFImageGrabber = mitk::ToFImageGrabber::New(); //Calling CreateQtPartControl CreateQtPartControl(this); } //Destructor of QmitkToFConnectionWidget QmitkToFConnectionWidget::~QmitkToFConnectionWidget() { //MitkServiceListWidget must not be deinizialized here. Qmitk methods destroy their children automatically before self-destruction } void QmitkToFConnectionWidget::CreateQtPartControl(QWidget *parent) //Definition of CreateQtPartControll-Methode in QmitkToFConnectionWidget; Input= Pointer { if (!m_Controls) //Define if not alreaddy exists { // create GUI widgets m_Controls = new Ui::QmitkToFConnectionWidgetControls2; m_Controls->setupUi(parent); //and hide them on startup this->HideAllParameterWidgets(); // initzializing MitkServiceListWidget here std::string empty= ""; m_Controls->m_DeviceList->Initialize("ToFDeviceName", empty);// the empty could just be any kind of filter this->CreateConnections(); } } //Creating the SIGNAL-SLOT-Connectuions void QmitkToFConnectionWidget::CreateConnections() { if ( m_Controls ) { //ConnectCameraButton as a trigger for OnConnectCamera() connect( (QObject*)(m_Controls->m_ConnectCameraButton), SIGNAL(clicked()),(QObject*) this, SLOT(OnConnectCamera()) ); //QmitkServiceListWidget::ServiceSelectionChanged as a Signal for the OnSlectCamera() slot connect( m_Controls->m_DeviceList, SIGNAL(ServiceSelectionChanged(us::ServiceReferenceU)), this, SLOT(OnSelectCamera())); /*Creating an other Datanode structur for Kinect is done here: As soon as a Kinect is connected, the KinectParameterWidget is enabled, which can be used to trigger the KinectAcqusitionModeChanged-Method, to create a working Data-Node-structure*/ connect( m_Controls->m_KinectParameterWidget, SIGNAL(AcquisitionModeChanged()), this, SIGNAL(KinectAcquisitionModeChanged()) ); } } mitk::ToFImageGrabber::Pointer QmitkToFConnectionWidget::GetToFImageGrabber() { return m_ToFImageGrabber; } //The OnSelectCamer-Method is in charge of activating the appropiate ParameterWidgets void QmitkToFConnectionWidget::OnSelectCamera() { //Here we are getting our decvie through the QmitkServiceListWidget-Instance m_DeviceList through the GetSelectedService-Method mitk::ToFCameraDevice* device = m_Controls->m_DeviceList->GetSelectedService(); //getting the selectedCamera through a static Method used to transform the device->GetNameOfClass QString selectedCamera = QString::fromStdString(device->GetNameOfClass()); this->HideAllParameterWidgets(); //reactivating the Widgets on slecting a device if (selectedCamera.contains("PMD")) //Check if selectedCamera string contains ".." for each device { this->m_Controls->m_PMDParameterWidget->show(); //and activate the correct widget } else if (selectedCamera.contains("MESA")) { this->m_Controls->m_MESAParameterWidget->show(); } else if (selectedCamera.contains("Kinect")) { this->m_Controls->m_KinectParameterWidget->show(); } else if (selectedCamera.contains("Structure")) { this->m_Controls->m_StructureParameterWidget->show(); } m_Controls->m_ConnectCameraButton->setEnabled(true); //ConnectCameraButton gets enabled m_SelectedCameraName = selectedCamera; } //This Methods hides all Widgets (later each widget is activated on its own) void QmitkToFConnectionWidget::HideAllParameterWidgets() { this->m_Controls->m_PMDParameterWidget->hide(); this->m_Controls->m_MESAParameterWidget->hide(); this->m_Controls->m_KinectParameterWidget->hide(); this->m_Controls->m_StructureParameterWidget->hide(); } //OnConnectCamera-Method; represents one of the main parts of ToFConnectionWidget2. void QmitkToFConnectionWidget::OnConnectCamera() { //After connecting a device if (m_Controls->m_ConnectCameraButton->text()=="Connect") { //Getting the device- and the slectedCamera-variables using the ServiceListWidget as we did it in the CameraSelect-Method mitk::ToFCameraDevice* device = m_Controls->m_DeviceList->GetSelectedService(); if (device) { QString tmpFileName(""); QString fileFilter(""); QString selectedCamera = QString::fromStdString(device->GetNameOfClass()); emit ToFCameraSelected(selectedCamera); //Feeding it with the Info from ServiceListWidget this->m_ToFImageGrabber->SetCameraDevice(device); if (selectedCamera.contains("Kinect") ) { //If the particular property is selected, the suitable data-node will be generated this->m_ToFImageGrabber->SetBoolProperty("RGB", m_Controls->m_KinectParameterWidget->IsAcquisitionModeRGB()); this->m_ToFImageGrabber->SetBoolProperty("IR", m_Controls->m_KinectParameterWidget->IsAcquisitionModeIR()); } if (selectedCamera.contains("Structure") ) { this->m_ToFImageGrabber->SetIntProperty("RGBResolution", m_Controls->m_StructureParameterWidget->GetSelectedResolution()); this->m_ToFImageGrabber->SetIntProperty("DepthResolution", m_Controls->m_StructureParameterWidget->GetSelectedResolution()); } //Activation of "PlayerMode". If the selectedCamera String contains "Player", we start the Player Mode if (selectedCamera.contains("Player")) { //IF PMD-Player selected if (selectedCamera.contains("PMD")) { fileFilter.append("PMD Files (*.pmd)"); //And seting the corresponding fileFilter } else { - fileFilter.append("NRRD Images (*.nrrd);;PIC Images - deprecated (*.pic)"); + fileFilter.append("NRRD Images (*.nrrd)"); } //open a QFileDialog to chose the corresponding file from the disc tmpFileName = QFileDialog::getOpenFileName(nullptr, "Play Image From...", "", fileFilter); //If no fileName is returned by the Dialog,Button and Widget have to return to default(disconnected) + Opening a MessageBox if (tmpFileName.isEmpty()) { m_Controls->m_ConnectCameraButton->setChecked(false); m_Controls->m_ConnectCameraButton->setEnabled(true); //re-enabling the ConnectCameraButton m_Controls->m_DeviceList->setEnabled(true); //Reactivating ServiceListWidget this->OnSelectCamera(); //Calling the OnSelctCamera-Method -> Hides all Widget and just activates the needed ones QMessageBox::information( this, "Template functionality", "Please select a valid image before starting some action."); return; } if(selectedCamera.contains("PMDPlayer")) //If PMD-Player is selected, set ToFImageGrabberProperty correspondingly { this->m_ToFImageGrabber->SetStringProperty("PMDFileName", tmpFileName.toStdString().c_str() ); } else //Default action { std::string msg = ""; try { //get 3 corresponding file names std::string dir = itksys::SystemTools::GetFilenamePath( tmpFileName.toStdString() ); std::string baseFilename = itksys::SystemTools::GetFilenameWithoutLastExtension( tmpFileName.toStdString() ); std::string extension = itksys::SystemTools::GetFilenameLastExtension( tmpFileName.toStdString() ); - //"Incorrect format"-warning while using .nrrd or .pic files - if (extension != ".pic" && extension != ".nrrd") + //"Incorrect format"-warning while using .nrrd files + if (extension != ".nrrd") { msg = msg + "Invalid file format, please select a \".nrrd\"-file"; throw std::logic_error(msg.c_str()); } //Checking for npos. If available, check for the Amplitude-, Intensity- and RGBImage int found = baseFilename.rfind("_DistanceImage"); //Defining "found" variable+checking if baseFilname contains "_DistanceImage". If not, found == npos(0) if (found == static_cast(std::string::npos)) //If found =0 { found = baseFilename.rfind("_AmplitudeImage"); //If "_AmplitudeImage" is found, the found variable is 1-> the next if statment is false } if (found == static_cast(std::string::npos)) { found = baseFilename.rfind("_IntensityImage"); //found = true if baseFilename cotains "_IntesityImage" } if (found == static_cast(std::string::npos)) { found = baseFilename.rfind("_RGBImage"); } if (found == static_cast(std::string::npos)) //If none of the Nodes is found, display an error { msg = msg + "Input file name must end with \"_DistanceImage\", \"_AmplitudeImage\", \"_IntensityImage\" or \"_RGBImage\"!"; throw std::logic_error(msg.c_str()); } std::string baseFilenamePrefix = baseFilename.substr(0,found);//Set the baseFilenamePrefix as a substring from baseFilname //Set corresponding FileNames std::string distanceImageFileName = dir + "/" + baseFilenamePrefix + "_DistanceImage" + extension; //Set the name as: directory+FilenamePrefix+""+extension std::string amplitudeImageFileName = dir + "/" + baseFilenamePrefix + "_AmplitudeImage" + extension; std::string intensityImageFileName = dir + "/" + baseFilenamePrefix + "_IntensityImage" + extension; std::string rgbImageFileName = dir + "/" + baseFilenamePrefix + "_RGBImage" + extension; if (!itksys::SystemTools::FileExists(distanceImageFileName.c_str(), true)) { this->m_ToFImageGrabber->SetStringProperty("DistanceImageFileName", ""); } else { this->m_ToFImageGrabber->SetStringProperty("DistanceImageFileName", distanceImageFileName.c_str()); } if (!itksys::SystemTools::FileExists(amplitudeImageFileName.c_str(), true)) { } else { this->m_ToFImageGrabber->SetStringProperty("AmplitudeImageFileName", amplitudeImageFileName.c_str()); } if (!itksys::SystemTools::FileExists(intensityImageFileName.c_str(), true)) { this->m_ToFImageGrabber->SetStringProperty("IntensityImageFileName", ""); } else { this->m_ToFImageGrabber->SetStringProperty("IntensityImageFileName", intensityImageFileName.c_str()); } if (!itksys::SystemTools::FileExists(rgbImageFileName.c_str(), true)) { this->m_ToFImageGrabber->SetStringProperty("RGBImageFileName", ""); } else { this->m_ToFImageGrabber->SetStringProperty("RGBImageFileName", rgbImageFileName.c_str()); } } catch (std::exception &e) { MITK_ERROR << e.what(); QMessageBox::critical( this, "Error", e.what() ); m_Controls->m_ConnectCameraButton->setChecked(false); m_Controls->m_ConnectCameraButton->setEnabled(true); m_Controls->m_DeviceList->setEnabled(true); this->OnSelectCamera(); return; } } } //End "PlayerMode" //Reset the ConnectCameraButton to disconnected m_Controls->m_ConnectCameraButton->setText("Disconnect"); //if a connection could be established try { if (this->m_ToFImageGrabber->ConnectCamera()) { this->m_Controls->m_PMDParameterWidget->SetToFImageGrabber(this->m_ToFImageGrabber); this->m_Controls->m_MESAParameterWidget->SetToFImageGrabber(this->m_ToFImageGrabber); this->m_Controls->m_KinectParameterWidget->SetToFImageGrabber(this->m_ToFImageGrabber); this->m_Controls->m_StructureParameterWidget->SetToFImageGrabber(this->m_ToFImageGrabber); //Activating the respective widgets if (selectedCamera.contains("PMD")) { this->m_Controls->m_PMDParameterWidget->ActivateAllParameters(); } else if (selectedCamera.contains("MESA")) { this->m_Controls->m_MESAParameterWidget->ActivateAllParameters(); } else if (selectedCamera.contains("Kinect")) { this->m_Controls->m_KinectParameterWidget->ActivateAllParameters(); } else if (selectedCamera.contains("Structure")) { this->m_Controls->m_StructureParameterWidget->ActivateAllParameters(); } else { this->HideAllParameterWidgets(); } // send connect signal to the caller functionality emit ToFCameraConnected(); } else //##### TODO: Remove this else part once all controllers are throwing exceptions //if they cannot to any device! { //Throw an error if the Connection failed and reset the Widgets <- better catch an exception! QMessageBox::critical( this, "Error", "Connection failed. Check if you have installed the latest driver for your system." ); m_Controls->m_ConnectCameraButton->setChecked(false); m_Controls->m_ConnectCameraButton->setEnabled(true); m_Controls->m_ConnectCameraButton->setText("Connect"); m_Controls->m_DeviceList->setEnabled(true); //Reactivating ServiceListWidget this->OnSelectCamera(); return; } }catch(std::exception &e) { //catch exceptions of camera which cannot connect give a better reason QMessageBox::critical( this, "Connection failed.", e.what() ); m_Controls->m_ConnectCameraButton->setChecked(false); m_Controls->m_ConnectCameraButton->setEnabled(true); m_Controls->m_ConnectCameraButton->setText("Connect"); m_Controls->m_DeviceList->setEnabled(true); //Reactivating ServiceListWidget this->OnSelectCamera(); return; } m_Controls->m_ConnectCameraButton->setEnabled(true); // ask wether camera parameters (intrinsics, ...) should be loaded if (QMessageBox::question(this,"Camera parameters","Do you want to specify your own camera intrinsics?",QMessageBox::Yes,QMessageBox::No)==QMessageBox::Yes) { try { QString fileName = QFileDialog::getOpenFileName(this,"Open camera intrinsics","/","*.xml"); mitk::CameraIntrinsics::Pointer cameraIntrinsics = mitk::CameraIntrinsics::New(); cameraIntrinsics->FromXMLFile(fileName.toStdString()); this->m_ToFImageGrabber->SetProperty("CameraIntrinsics",mitk::CameraIntrinsicsProperty::New(cameraIntrinsics)); } catch ( std::exception &e ) { MITK_WARN << "Error loading camera intrinsics: " << e.what(); } } ////Reset the status of some GUI-Elements m_Controls->m_DeviceList->setEnabled(false); //Deactivating the Instance of QmitkServiceListWidget //repaint the widget this->repaint(); } else { QMessageBox::information(this,"Camera connection","No camera selected, please select a range camera"); m_Controls->m_ConnectCameraButton->setChecked(false); } } else if (m_Controls->m_ConnectCameraButton->text()=="Disconnect") { this->m_ToFImageGrabber->StopCamera(); this->m_ToFImageGrabber->DisconnectCamera(); m_Controls->m_ConnectCameraButton->setText("Connect"); m_Controls->m_DeviceList->setEnabled(true); //Reactivating ServiceListWidget this->OnSelectCamera(); // send disconnect signal to the caller functionality emit ToFCameraDisconnected(); } } void QmitkToFConnectionWidget::ConnectCamera() { this->m_Controls->m_ConnectCameraButton->animateClick(); } diff --git a/Modules/ToFUI/Qmitk/QmitkToFRecorderWidget.cpp b/Modules/ToFUI/Qmitk/QmitkToFRecorderWidget.cpp index db6e4ff9a2..a33addeb80 100644 --- a/Modules/ToFUI/Qmitk/QmitkToFRecorderWidget.cpp +++ b/Modules/ToFUI/Qmitk/QmitkToFRecorderWidget.cpp @@ -1,423 +1,415 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #define _USE_MATH_DEFINES #include "QmitkToFRecorderWidget.h" //QT headers #include #include #include #include #include #include #include //mitk headers #include //itk headers #pragma GCC visibility push(default) #include #pragma GCC visibility pop #include struct QFileDialogArgs; class QFileDialogPrivate; const std::string QmitkToFRecorderWidget::VIEW_ID = "org.mitk.views.qmitktofrecorderwidget"; QmitkToFRecorderWidget::QmitkToFRecorderWidget(QWidget* parent, Qt::WindowFlags f): QWidget(parent, f) { this->m_ToFImageRecorder = nullptr; this->m_ToFImageGrabber = nullptr; this->m_RecordMode = mitk::ToFImageRecorder::PerFrames; this-> m_Controls = nullptr; CreateQtPartControl(this); } QmitkToFRecorderWidget::~QmitkToFRecorderWidget() { } void QmitkToFRecorderWidget::CreateQtPartControl(QWidget *parent) { if (!m_Controls) { // create GUI widgets this->m_Controls = new Ui::QmitkToFRecorderWidgetControls; this->m_Controls->setupUi(parent); this->CreateConnections(); } } void QmitkToFRecorderWidget::CreateConnections() { if ( m_Controls ) { connect( (QObject*)(m_Controls->m_PlayButton), SIGNAL(clicked()),(QObject*) this, SLOT(OnPlay()) ); connect( (QObject*)(m_Controls->m_StopButton), SIGNAL(clicked()),(QObject*) this, SLOT(OnStop()) ); connect( (QObject*)(m_Controls->m_StartRecordingButton), SIGNAL(clicked()),(QObject*) this, SLOT(OnStartRecorder()) ); connect( (QObject*)(m_Controls->m_RecordModeComboBox), SIGNAL(currentIndexChanged(int)),(QObject*) this, SLOT(OnChangeRecordModeComboBox(int)) ); connect(this, SIGNAL(RecordingStopped()), this, SLOT(OnRecordingStopped()), Qt::BlockingQueuedConnection); } } void QmitkToFRecorderWidget::SetParameter(mitk::ToFImageGrabber* toFImageGrabber, mitk::ToFImageRecorder* toFImageRecorder) { this->m_ToFImageGrabber = toFImageGrabber; this->m_ToFImageRecorder = toFImageRecorder; this->m_StopRecordingCommand = CommandType::New(); this->m_StopRecordingCommand->SetCallbackFunction(this, &QmitkToFRecorderWidget::StopRecordingCallback); this->m_ToFImageRecorder->RemoveAllObservers(); this->m_ToFImageRecorder->AddObserver(itk::AbortEvent(), this->m_StopRecordingCommand); m_Controls->m_PlayButton->setChecked(false); m_Controls->m_PlayButton->setEnabled(true); m_Controls->m_StartRecordingButton->setChecked(false); m_Controls->m_RecorderGroupBox->setEnabled(true); } void QmitkToFRecorderWidget::StopRecordingCallback() { emit RecordingStopped(); } void QmitkToFRecorderWidget::ResetGUIToInitial() { m_Controls->m_PlayButton->setChecked(false); m_Controls->m_PlayButton->setEnabled(true); m_Controls->m_RecorderGroupBox->setEnabled(false); } void QmitkToFRecorderWidget::OnRecordingStopped() { m_Controls->m_StartRecordingButton->setChecked(false); m_Controls->m_RecorderGroupBox->setEnabled(true); } void QmitkToFRecorderWidget::OnStop() { StopCamera(); StopRecorder(); ResetGUIToInitial(); emit ToFCameraStopped(); } void QmitkToFRecorderWidget::OnPlay() { m_Controls->m_PlayButton->setChecked(true); m_Controls->m_PlayButton->setEnabled(false); m_Controls->m_RecorderGroupBox->setEnabled(true); this->repaint(); StartCamera(); emit ToFCameraStarted(); } void QmitkToFRecorderWidget::StartCamera() { if (!m_ToFImageGrabber->IsCameraActive()) { m_ToFImageGrabber->StartCamera(); } } void QmitkToFRecorderWidget::StopCamera() { if( m_ToFImageGrabber.IsNotNull() ) m_ToFImageGrabber->StopCamera(); } void QmitkToFRecorderWidget::StopRecorder() { if( m_ToFImageRecorder.IsNotNull() ) { this->m_ToFImageRecorder->StopRecording(); } } void QmitkToFRecorderWidget::OnStartRecorder() { m_Controls->m_StartRecordingButton->setChecked(true); m_Controls->m_RecorderGroupBox->setEnabled(false); this->repaint(); int numOfFrames = m_Controls->m_NumOfFramesSpinBox->value(); try { bool fileOK = true; bool distanceImageSelected = true; bool amplitudeImageSelected = false; bool intensityImageSelected = false; bool rgbImageSelected = false; bool rawDataSelected = false; //Set check boxes in dialog according to device properties m_ToFImageGrabber->GetCameraDevice()->GetBoolProperty("HasAmplitudeImage",amplitudeImageSelected); m_ToFImageGrabber->GetCameraDevice()->GetBoolProperty("HasIntensityImage",intensityImageSelected); m_ToFImageGrabber->GetCameraDevice()->GetBoolProperty("HasRGBImage",rgbImageSelected); QString tmpFileName(""); QString selectedFilter(""); QString imageFileName(""); mitk::ToFImageWriter::ToFImageType tofImageType; tmpFileName = QmitkToFRecorderWidget::getSaveFileName(tofImageType, distanceImageSelected, amplitudeImageSelected, intensityImageSelected, rgbImageSelected, rawDataSelected, - nullptr, "Save Image To...", imageFileName, "NRRD Images (*.nrrd);;PIC Images - deprecated (*.pic);;Text (*.csv)", &selectedFilter); + nullptr, "Save Image To...", imageFileName, "NRRD Images (*.nrrd);;Text (*.csv)", &selectedFilter); if (tmpFileName.isEmpty()) { fileOK = false; } else { imageFileName = tmpFileName; } if (fileOK) { std::string dir = itksys::SystemTools::GetFilenamePath( imageFileName.toStdString() ); std::string baseFilename = itksys::SystemTools::GetFilenameWithoutLastExtension( imageFileName.toStdString() ); std::string extension = itksys::SystemTools::GetFilenameLastExtension( imageFileName.toStdString() ); int integrationTime = this->m_ToFImageGrabber->GetIntegrationTime(); int modulationFreq = this->m_ToFImageGrabber->GetModulationFrequency(); QString integrationTimeStr; integrationTimeStr.setNum(integrationTime); QString modulationFreqStr; modulationFreqStr.setNum(modulationFreq); QString numOfFramesStr(""); if (this->m_RecordMode == mitk::ToFImageRecorder::PerFrames) { numOfFramesStr.setNum(numOfFrames); } std::string distImageFileName = prepareFilename(dir, baseFilename, modulationFreqStr.toStdString(), integrationTimeStr.toStdString(), numOfFramesStr.toStdString(), extension, "_DistanceImage"); MITK_INFO << "Save distance data to: " << distImageFileName; std::string amplImageFileName = prepareFilename(dir, baseFilename, modulationFreqStr.toStdString(), integrationTimeStr.toStdString(), numOfFramesStr.toStdString(), extension, "_AmplitudeImage"); MITK_INFO << "Save amplitude data to: " << amplImageFileName; std::string intenImageFileName = prepareFilename(dir, baseFilename, modulationFreqStr.toStdString(), integrationTimeStr.toStdString(), numOfFramesStr.toStdString(), extension, "_IntensityImage"); MITK_INFO << "Save intensity data to: " << intenImageFileName; std::string rgbImageFileName = prepareFilename(dir, baseFilename, modulationFreqStr.toStdString(), integrationTimeStr.toStdString(), numOfFramesStr.toStdString(), extension, "_RGBImage"); MITK_INFO << "Save intensity data to: " << rgbImageFileName; if (selectedFilter.compare("Text (*.csv)") == 0) { this->m_ToFImageRecorder->SetFileFormat(".csv"); } - else if (selectedFilter.compare("PIC Images - deprecated (*.pic)") == 0) - { - //default - this->m_ToFImageRecorder->SetFileFormat(".pic"); - - QMessageBox::warning(nullptr, "Deprecated File Format!", - "Please note that *.pic file format is deprecated and not longer supported! The suggested file format for images is *.nrrd!"); - } else if (selectedFilter.compare("NRRD Images (*.nrrd)") == 0) { this->m_ToFImageRecorder->SetFileFormat(".nrrd"); } else { QMessageBox::warning(nullptr, "Unsupported file format!", "Please specify one of the supported file formats *.nrrd, *.csv!"); return; } numOfFrames = m_Controls->m_NumOfFramesSpinBox->value(); this->m_ToFImageRecorder->SetDistanceImageFileName(distImageFileName); this->m_ToFImageRecorder->SetAmplitudeImageFileName(amplImageFileName); this->m_ToFImageRecorder->SetIntensityImageFileName(intenImageFileName); this->m_ToFImageRecorder->SetRGBImageFileName(rgbImageFileName); this->m_ToFImageRecorder->SetToFImageType(tofImageType); this->m_ToFImageRecorder->SetDistanceImageSelected(distanceImageSelected); this->m_ToFImageRecorder->SetAmplitudeImageSelected(amplitudeImageSelected); this->m_ToFImageRecorder->SetIntensityImageSelected(intensityImageSelected); this->m_ToFImageRecorder->SetRGBImageSelected(rgbImageSelected); this->m_ToFImageRecorder->SetRecordMode(this->m_RecordMode); this->m_ToFImageRecorder->SetNumOfFrames(numOfFrames); emit RecordingStarted(); this->m_ToFImageRecorder->StartRecording(); } else { this->OnRecordingStopped(); } } catch(std::exception& e) { QMessageBox::critical(nullptr, "Error", QString(e.what())); this->OnRecordingStopped(); } } QString QmitkToFRecorderWidget::getSaveFileName(mitk::ToFImageWriter::ToFImageType& tofImageType, bool& distanceImageSelected, bool& amplitudeImageSelected, bool& intensityImageSelected, bool& rgbImageSelected, bool& rawDataSelected, QWidget *parent, const QString &caption, const QString &dir, const QString &filter, QString *selectedFilter, QFileDialog::Options ) { QString selectedFileName = ""; QComboBox* combo = new QComboBox; combo->addItem("3D"); combo->addItem("2D + t"); QHBoxLayout* checkBoxGroup = new QHBoxLayout(); QCheckBox* distanceImageCheckBox = new QCheckBox; distanceImageCheckBox->setText("Distance image"); distanceImageCheckBox->setChecked(distanceImageSelected); QCheckBox* amplitudeImageCheckBox = new QCheckBox; amplitudeImageCheckBox->setText("Amplitude image"); amplitudeImageCheckBox->setChecked(amplitudeImageSelected); amplitudeImageCheckBox->setEnabled(amplitudeImageSelected); if(!amplitudeImageSelected) amplitudeImageCheckBox->setToolTip(QString("This device does not provide amplitude data.")); QCheckBox* intensityImageCheckBox = new QCheckBox; intensityImageCheckBox->setText("Intensity image"); intensityImageCheckBox->setChecked(intensityImageSelected); intensityImageCheckBox->setEnabled(intensityImageSelected); if(!intensityImageSelected) intensityImageCheckBox->setToolTip(QString("This device does not provide intensity data.")); QCheckBox* rgbImageCheckBox = new QCheckBox; rgbImageCheckBox->setText("RGB image"); rgbImageCheckBox->setChecked(rgbImageSelected); rgbImageCheckBox->setEnabled(rgbImageSelected); if(!rgbImageSelected) rgbImageCheckBox->setToolTip(QString("This device does not provide RGB data.")); QCheckBox* rawDataCheckBox = new QCheckBox; rawDataCheckBox->setText("Raw data"); rawDataCheckBox->setChecked(false); rawDataCheckBox->setEnabled(false); checkBoxGroup->addWidget(distanceImageCheckBox); checkBoxGroup->addWidget(amplitudeImageCheckBox); checkBoxGroup->addWidget(intensityImageCheckBox); checkBoxGroup->addWidget(rgbImageCheckBox); checkBoxGroup->addWidget(rawDataCheckBox); QFileDialog* fileDialog = new QFileDialog(parent, caption, dir, filter); QLayout* layout = fileDialog->layout(); QGridLayout* gridbox = qobject_cast(layout); if (gridbox) { gridbox->addWidget(new QLabel("ToF-Image type:")); gridbox->addWidget(combo); int lastRow = gridbox->rowCount(); gridbox->addLayout(checkBoxGroup, lastRow, 0, 1, -1); } fileDialog->setLayout(gridbox); fileDialog->setAcceptMode(QFileDialog::AcceptSave); if (selectedFilter) { fileDialog->selectNameFilter(*selectedFilter); } if (fileDialog->exec() == QDialog::Accepted) { if (selectedFilter) { *selectedFilter = fileDialog->selectedNameFilter(); } if (combo->currentIndex() == 0) { tofImageType = mitk::ToFImageWriter::ToFImageType3D; } else { tofImageType = mitk::ToFImageWriter::ToFImageType2DPlusT; } distanceImageSelected = distanceImageCheckBox->isChecked(); amplitudeImageSelected = amplitudeImageCheckBox->isChecked(); intensityImageSelected = intensityImageCheckBox->isChecked(); rgbImageSelected = rgbImageCheckBox->isChecked(); rawDataSelected = rawDataCheckBox->isChecked(); selectedFileName = fileDialog->selectedFiles().value(0); } delete fileDialog; return selectedFileName; } std::string QmitkToFRecorderWidget::prepareFilename(std::string dir, std::string baseFilename, std::string modulationFreq, std::string integrationTime, std::string numOfFrames, std::string extension, std::string imageType) { std::string filenName(""); filenName.append(dir); filenName.append("/"); filenName.append(baseFilename); filenName.append("_MF"); filenName.append(modulationFreq); filenName.append("_IT"); filenName.append(integrationTime); filenName.append("_"); filenName.append(numOfFrames); filenName.append("Images"); filenName.append(imageType); filenName.append(extension); return filenName; } void QmitkToFRecorderWidget::OnChangeRecordModeComboBox(int index) { if (index == 0) { this->m_RecordMode = mitk::ToFImageRecorder::PerFrames; m_Controls->m_NumOfFramesSpinBox->setEnabled(true); } else { this->m_RecordMode = mitk::ToFImageRecorder::Infinite; m_Controls->m_NumOfFramesSpinBox->setEnabled(false); } } diff --git a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp index 1790e3da27..f6cc560a7e 100644 --- a/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp +++ b/Plugins/org.mitk.gui.qt.basicimageprocessing/src/internal/QmitkBasicImageProcessingView.cpp @@ -1,1345 +1,1345 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkBasicImageProcessingView.h" // QT includes (GUI) #include #include #include #include #include #include #include // MITK includes (general) #include #include #include #include #include #include #include #include #include #include // Includes for image casting between ITK and MITK #include #include // ITK includes (general) #include #include // Morphological Operations #include #include #include #include #include // Smoothing #include #include #include // Threshold #include // Inversion #include // Derivatives #include #include #include // Resampling #include #include #include #include #include // Image Arithmetics #include #include #include #include // Boolean operations #include #include #include // Flip Image #include #include #include // Convenient Definitions typedef itk::Image ImageType; typedef itk::Image SegmentationImageType; typedef itk::Image DoubleImageType; typedef itk::Image, 3> VectorImageType; typedef itk::BinaryBallStructuringElement BallType; typedef itk::GrayscaleDilateImageFilter DilationFilterType; typedef itk::GrayscaleErodeImageFilter ErosionFilterType; typedef itk::GrayscaleMorphologicalOpeningImageFilter OpeningFilterType; typedef itk::GrayscaleMorphologicalClosingImageFilter ClosingFilterType; typedef itk::MedianImageFilter< ImageType, ImageType > MedianFilterType; typedef itk::DiscreteGaussianImageFilter< ImageType, ImageType> GaussianFilterType; typedef itk::TotalVariationDenoisingImageFilter TotalVariationFilterType; typedef itk::TotalVariationDenoisingImageFilter VectorTotalVariationFilterType; typedef itk::BinaryThresholdImageFilter< ImageType, ImageType > ThresholdFilterType; typedef itk::InvertIntensityImageFilter< ImageType, ImageType > InversionFilterType; typedef itk::GradientMagnitudeRecursiveGaussianImageFilter< ImageType, ImageType > GradientFilterType; typedef itk::LaplacianImageFilter< DoubleImageType, DoubleImageType > LaplacianFilterType; typedef itk::SobelEdgeDetectionImageFilter< DoubleImageType, DoubleImageType > SobelFilterType; typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType; typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType2; typedef itk::CastImageFilter< ImageType, DoubleImageType > ImagePTypeToFloatPTypeCasterType; typedef itk::AddImageFilter< ImageType, ImageType, ImageType > AddFilterType; typedef itk::SubtractImageFilter< ImageType, ImageType, ImageType > SubtractFilterType; typedef itk::MultiplyImageFilter< ImageType, ImageType, ImageType > MultiplyFilterType; typedef itk::DivideImageFilter< ImageType, ImageType, DoubleImageType > DivideFilterType; typedef itk::OrImageFilter< ImageType, ImageType > OrImageFilterType; typedef itk::AndImageFilter< ImageType, ImageType > AndImageFilterType; typedef itk::XorImageFilter< ImageType, ImageType > XorImageFilterType; typedef itk::FlipImageFilter< ImageType > FlipImageFilterType; typedef itk::LinearInterpolateImageFunction< ImageType, double > LinearInterpolatorType; typedef itk::NearestNeighborInterpolateImageFunction< ImageType, double > NearestInterpolatorType; const std::string QmitkBasicImageProcessing::VIEW_ID = "org.mitk.views.basicimageprocessing"; QmitkBasicImageProcessing::QmitkBasicImageProcessing() : QmitkAbstractView() , m_Controls(new Ui::QmitkBasicImageProcessingViewControls) , m_TimeStepperAdapter(nullptr) { auto isImage = mitk::TNodePredicateDataType::New(); auto isNotHelperObject = mitk::NodePredicateNot::New( mitk::NodePredicateProperty::New("helper object", mitk::BoolProperty::New(true))); auto dimensionPredicate = mitk::NodePredicateOr::New( mitk::NodePredicateDimension::New(3), mitk::NodePredicateDimension::New(4)); m_IsImagePredicate = mitk::NodePredicateAnd::New( isImage, isNotHelperObject, dimensionPredicate); } QmitkBasicImageProcessing::~QmitkBasicImageProcessing() { } void QmitkBasicImageProcessing::CreateQtPartControl(QWidget *parent) { m_Controls->setupUi(parent); m_Controls->selectedImageWidget->SetDataStorage(this->GetDataStorage()); m_Controls->selectedImageWidget->SetNodePredicate(m_IsImagePredicate); m_Controls->selectedImageWidget->SetSelectionIsOptional(true); m_Controls->selectedImageWidget->SetAutoSelectNewNodes(true); m_Controls->selectedImageWidget->SetEmptyInfo(QString("Please select a 3D / 4D image")); m_Controls->selectedImageWidget->SetPopUpTitel(QString("Select an image")); m_Controls->selectedImageWidget_2->SetDataStorage(this->GetDataStorage()); m_Controls->selectedImageWidget_2->SetNodePredicate(m_IsImagePredicate); m_Controls->selectedImageWidget_2->SetSelectionIsOptional(true); m_Controls->selectedImageWidget_2->SetAutoSelectNewNodes(true); m_Controls->selectedImageWidget_2->SetEmptyInfo(QString("Please select a 3D / 4D image")); m_Controls->selectedImageWidget_2->SetPopUpTitel(QString("Select an image")); m_Controls->gbTwoImageOps->hide(); m_Controls->cbWhat1->clear(); m_Controls->cbWhat1->insertItem(NOACTIONSELECTED, "Please select an operation"); m_Controls->cbWhat1->insertItem(CATEGORY_DENOISING, "--- Denoising ---"); m_Controls->cbWhat1->insertItem(GAUSSIAN, "Gaussian"); m_Controls->cbWhat1->insertItem(MEDIAN, "Median"); m_Controls->cbWhat1->insertItem(TOTALVARIATION, "Total Variation"); m_Controls->cbWhat1->insertItem(CATEGORY_MORPHOLOGICAL, "--- Morphological ---"); m_Controls->cbWhat1->insertItem(DILATION, "Dilation"); m_Controls->cbWhat1->insertItem(EROSION, "Erosion"); m_Controls->cbWhat1->insertItem(OPENING, "Opening"); m_Controls->cbWhat1->insertItem(CLOSING, "Closing"); m_Controls->cbWhat1->insertItem(CATEGORY_EDGE_DETECTION, "--- Edge Detection ---"); m_Controls->cbWhat1->insertItem(GRADIENT, "Gradient"); m_Controls->cbWhat1->insertItem(LAPLACIAN, "Laplacian (2nd Derivative)"); m_Controls->cbWhat1->insertItem(SOBEL, "Sobel Operator"); m_Controls->cbWhat1->insertItem(CATEGORY_MISC, "--- Misc ---"); m_Controls->cbWhat1->insertItem(THRESHOLD, "Threshold"); m_Controls->cbWhat1->insertItem(INVERSION, "Image Inversion"); m_Controls->cbWhat1->insertItem(DOWNSAMPLING, "Downsampling"); m_Controls->cbWhat1->insertItem(FLIPPING, "Flipping"); m_Controls->cbWhat1->insertItem(RESAMPLING, "Resample to"); m_Controls->cbWhat1->insertItem(RESCALE, "Rescale values to interval"); m_Controls->cbWhat1->insertItem(RESCALE2, "Rescale values by scalar"); m_Controls->cbWhat2->clear(); m_Controls->cbWhat2->insertItem(TWOIMAGESNOACTIONSELECTED, "Please select an operation"); m_Controls->cbWhat2->insertItem(CATEGORY_ARITHMETIC, "--- Arithmetric operations ---"); m_Controls->cbWhat2->insertItem(ADD, "Add to Image 1:"); m_Controls->cbWhat2->insertItem(SUBTRACT, "Subtract from Image 1:"); m_Controls->cbWhat2->insertItem(MULTIPLY, "Multiply with Image 1:"); m_Controls->cbWhat2->insertItem(RESAMPLE_TO, "Resample Image 1 to fit geometry:"); m_Controls->cbWhat2->insertItem(DIVIDE, "Divide Image 1 by:"); m_Controls->cbWhat2->insertItem(CATEGORY_BOOLEAN, "--- Boolean operations ---"); m_Controls->cbWhat2->insertItem(AND, "AND"); m_Controls->cbWhat2->insertItem(OR, "OR"); m_Controls->cbWhat2->insertItem(XOR, "XOR"); m_Controls->cbParam4->clear(); m_Controls->cbParam4->insertItem(LINEAR, "Linear"); m_Controls->cbParam4->insertItem(NEAREST, "Nearest neighbor"); m_Controls->dsbParam1->hide(); m_Controls->dsbParam2->hide(); m_Controls->dsbParam3->hide(); m_Controls->tlParam3->hide(); m_Controls->tlParam4->hide(); m_Controls->cbParam4->hide(); this->CreateConnections(); } void QmitkBasicImageProcessing::CreateConnections() { connect(m_Controls->cbWhat1, QOverload::of(&QComboBox::activated), this, &QmitkBasicImageProcessing::SelectAction); connect(m_Controls->btnDoIt, &QPushButton::clicked, this, &QmitkBasicImageProcessing::StartButtonClicked); connect(m_Controls->cbWhat2, QOverload::of(&QComboBox::activated), this, &QmitkBasicImageProcessing::SelectAction2); connect(m_Controls->btnDoIt2, &QPushButton::clicked, this, &QmitkBasicImageProcessing::StartButton2Clicked); connect(m_Controls->rBOneImOp, &QRadioButton::clicked, this, &QmitkBasicImageProcessing::ChangeGUI); connect(m_Controls->rBTwoImOp, &QRadioButton::clicked, this, &QmitkBasicImageProcessing::ChangeGUI); connect(m_Controls->cbParam4, QOverload::of(&QComboBox::activated), this, &QmitkBasicImageProcessing::SelectInterpolator); connect(m_Controls->selectedImageWidget, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkBasicImageProcessing::OnCurrentSelectionChanged); connect(m_Controls->selectedImageWidget_2, &QmitkAbstractNodeSelectionWidget::CurrentSelectionChanged, this, &QmitkBasicImageProcessing::OnCurrentSelectionChanged); } void QmitkBasicImageProcessing::InternalGetTimeNavigationController() { auto renwin_part = GetRenderWindowPart(); if( renwin_part != nullptr ) { auto tnc = renwin_part->GetTimeNavigationController(); if( tnc != nullptr ) { m_TimeStepperAdapter = new QmitkStepperAdapter((QObject*) m_Controls->sliceNavigatorTime, tnc->GetTime(), "sliceNavigatorTimeFromBIP"); } } } void QmitkBasicImageProcessing::SetFocus() { m_Controls->rBOneImOp->setFocus(); } void QmitkBasicImageProcessing::OnCurrentSelectionChanged(const QList& nodes) { if (nodes.empty() || nodes.front().IsNull()) { m_Controls->sliceNavigatorTime->setEnabled(false); m_Controls->tlTime->setEnabled(false); m_Controls->tlWhat1->setEnabled(false); m_Controls->cbWhat1->setEnabled(false); m_Controls->tlWhat2->setEnabled(false); m_Controls->cbWhat2->setEnabled(false); return; } auto selectedImage = dynamic_cast(nodes.front()->GetData()); if (nullptr == selectedImage) { return; } if (selectedImage->GetDimension() > 3) { // try to retrieve the TNC (for 4-D Processing ) this->InternalGetTimeNavigationController(); m_Controls->sliceNavigatorTime->setEnabled(true); m_Controls->tlTime->setEnabled(true); } m_Controls->tlWhat1->setEnabled(true); m_Controls->cbWhat1->setEnabled(true); m_Controls->tlWhat2->setEnabled(true); m_Controls->cbWhat2->setEnabled(true); } void QmitkBasicImageProcessing::ChangeGUI() { if(m_Controls->rBOneImOp->isChecked()) { m_Controls->gbTwoImageOps->hide(); m_Controls->gbOneImageOps->show(); } else if(m_Controls->rBTwoImOp->isChecked()) { m_Controls->gbOneImageOps->hide(); m_Controls->gbTwoImageOps->show(); } } void QmitkBasicImageProcessing::ResetParameterPanel() { m_Controls->tlParam->setEnabled(false); m_Controls->tlParam1->setEnabled(false); m_Controls->tlParam2->setEnabled(false); m_Controls->tlParam3->setEnabled(false); m_Controls->tlParam4->setEnabled(false); m_Controls->sbParam1->setEnabled(false); m_Controls->sbParam2->setEnabled(false); m_Controls->dsbParam1->setEnabled(false); m_Controls->dsbParam2->setEnabled(false); m_Controls->dsbParam3->setEnabled(false); m_Controls->cbParam4->setEnabled(false); m_Controls->sbParam1->setValue(0); m_Controls->sbParam2->setValue(0); m_Controls->dsbParam1->setValue(0); m_Controls->dsbParam2->setValue(0); m_Controls->dsbParam3->setValue(0); m_Controls->sbParam1->show(); m_Controls->sbParam2->show(); m_Controls->dsbParam1->hide(); m_Controls->dsbParam2->hide(); m_Controls->dsbParam3->hide(); m_Controls->cbParam4->hide(); m_Controls->tlParam3->hide(); m_Controls->tlParam4->hide(); } void QmitkBasicImageProcessing::SelectAction(int action) { auto selectedImage = m_Controls->selectedImageWidget->GetSelectedNode(); if (selectedImage.IsNull()) { return; } // Prepare GUI this->ResetParameterPanel(); m_Controls->btnDoIt->setEnabled(false); m_Controls->cbHideOrig->setEnabled(false); QString text1 = tr("No Parameters"); QString text2 = text1; QString text3 = text1; QString text4 = text1; if (action != 19) { m_Controls->dsbParam1->hide(); m_Controls->dsbParam2->hide(); m_Controls->dsbParam3->hide(); m_Controls->tlParam1->show(); m_Controls->tlParam2->show(); m_Controls->tlParam3->hide(); m_Controls->tlParam4->hide(); m_Controls->sbParam1->show(); m_Controls->sbParam2->show(); m_Controls->cbParam4->hide(); } switch (action) { case 2: { m_SelectedAction = GAUSSIAN; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->hide(); m_Controls->dsbParam1->show(); m_Controls->dsbParam1->setEnabled(true); text1 = tr("&Variance:"); m_Controls->tlParam2->hide(); m_Controls->sbParam2->hide(); m_Controls->dsbParam1->setMinimum( 0 ); m_Controls->dsbParam1->setMaximum( 200 ); m_Controls->dsbParam1->setValue( 2 ); break; } case 3: { m_SelectedAction = MEDIAN; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); text1 = tr("&Radius:"); m_Controls->sbParam1->setMinimum( 0 ); m_Controls->sbParam1->setMaximum( 200 ); m_Controls->sbParam1->setValue( 3 ); break; } case 4: { m_SelectedAction = TOTALVARIATION; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); m_Controls->tlParam2->setEnabled(true); m_Controls->sbParam2->setEnabled(true); text1 = tr("Number Iterations:"); text2 = tr("Regularization\n(Lambda/1000):"); m_Controls->sbParam1->setMinimum( 1 ); m_Controls->sbParam1->setMaximum( 1000 ); m_Controls->sbParam1->setValue( 40 ); m_Controls->sbParam2->setMinimum( 0 ); m_Controls->sbParam2->setMaximum( 100000 ); m_Controls->sbParam2->setValue( 1 ); break; } case 6: { m_SelectedAction = DILATION; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); text1 = tr("&Radius:"); m_Controls->sbParam1->setMinimum( 0 ); m_Controls->sbParam1->setMaximum( 200 ); m_Controls->sbParam1->setValue( 3 ); break; } case 7: { m_SelectedAction = EROSION; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); text1 = tr("&Radius:"); m_Controls->sbParam1->setMinimum( 0 ); m_Controls->sbParam1->setMaximum( 200 ); m_Controls->sbParam1->setValue( 3 ); break; } case 8: { m_SelectedAction = OPENING; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); text1 = tr("&Radius:"); m_Controls->sbParam1->setMinimum( 0 ); m_Controls->sbParam1->setMaximum( 200 ); m_Controls->sbParam1->setValue( 3 ); break; } case 9: { m_SelectedAction = CLOSING; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); text1 = tr("&Radius:"); m_Controls->sbParam1->setMinimum( 0 ); m_Controls->sbParam1->setMaximum( 200 ); m_Controls->sbParam1->setValue( 3 ); break; } case 11: { m_SelectedAction = GRADIENT; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->hide(); m_Controls->dsbParam1->show(); m_Controls->dsbParam1->setEnabled(true); text1 = tr("Sigma of Gaussian Kernel:\n(in Image Spacing Units)"); m_Controls->tlParam2->hide(); m_Controls->sbParam2->hide(); m_Controls->dsbParam1->setMinimum( 0 ); m_Controls->dsbParam1->setMaximum( 200 ); m_Controls->dsbParam1->setValue( 2 ); break; } case 12: { m_SelectedAction = LAPLACIAN; break; } case 13: { m_SelectedAction = SOBEL; break; } case 15: { m_SelectedAction = THRESHOLD; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); m_Controls->tlParam2->setEnabled(true); m_Controls->sbParam2->setEnabled(true); text1 = tr("Lower threshold:"); text2 = tr("Upper threshold:"); m_Controls->sbParam1->setMinimum( -100000 ); m_Controls->sbParam1->setMaximum( 100000 ); m_Controls->sbParam1->setValue( 0 ); m_Controls->sbParam2->setMinimum( -100000 ); m_Controls->sbParam2->setMaximum( 100000 ); m_Controls->sbParam2->setValue( 300 ); break; } case 16: { m_SelectedAction = INVERSION; break; } case 17: { m_SelectedAction = DOWNSAMPLING; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); text1 = tr("Downsampling by Factor:"); m_Controls->sbParam1->setMinimum( 1 ); m_Controls->sbParam1->setMaximum( 100 ); m_Controls->sbParam1->setValue( 2 ); break; } case 18: { m_SelectedAction = FLIPPING; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(true); text1 = tr("Flip across axis:"); m_Controls->sbParam1->setMinimum( 0 ); m_Controls->sbParam1->setMaximum( 2 ); m_Controls->sbParam1->setValue( 1 ); break; } case 19: { m_SelectedAction = RESAMPLING; m_Controls->tlParam1->setEnabled(true); m_Controls->sbParam1->setEnabled(false); m_Controls->sbParam1->hide(); m_Controls->dsbParam1->show(); m_Controls->dsbParam1->setEnabled(true); m_Controls->tlParam2->setEnabled(true); m_Controls->sbParam2->setEnabled(false); m_Controls->sbParam2->hide(); m_Controls->dsbParam2->show(); m_Controls->dsbParam2->setEnabled(true); m_Controls->tlParam3->show(); m_Controls->tlParam3->setEnabled(true); m_Controls->dsbParam3->show(); m_Controls->dsbParam3->setEnabled(true); m_Controls->tlParam4->show(); m_Controls->tlParam4->setEnabled(true); m_Controls->cbParam4->show(); m_Controls->cbParam4->setEnabled(true); m_Controls->dsbParam1->setMinimum(0.01); m_Controls->dsbParam1->setMaximum(10.0); m_Controls->dsbParam1->setSingleStep(0.1); m_Controls->dsbParam1->setValue(0.3); m_Controls->dsbParam2->setMinimum(0.01); m_Controls->dsbParam2->setMaximum(10.0); m_Controls->dsbParam2->setSingleStep(0.1); m_Controls->dsbParam2->setValue(0.3); m_Controls->dsbParam3->setMinimum(0.01); m_Controls->dsbParam3->setMaximum(10.0); m_Controls->dsbParam3->setSingleStep(0.1); m_Controls->dsbParam3->setValue(1.5); text1 = tr("x-spacing:"); text2 = tr("y-spacing:"); text3 = tr("z-spacing:"); text4 = tr("Interplation:"); break; } case 20: { m_SelectedAction = RESCALE; m_Controls->dsbParam1->show(); m_Controls->tlParam1->show(); m_Controls->dsbParam1->setEnabled(true); m_Controls->tlParam1->setEnabled(true); m_Controls->dsbParam2->show(); m_Controls->tlParam2->show(); m_Controls->dsbParam2->setEnabled(true); m_Controls->tlParam2->setEnabled(true); text1 = tr("Output minimum:"); text2 = tr("Output maximum:"); break; } case 21: { m_SelectedAction = RESCALE2; m_Controls->dsbParam1->show(); m_Controls->tlParam1->show(); m_Controls->dsbParam1->setEnabled(true); m_Controls->tlParam1->setEnabled(true); text1 = tr("Scaling value:"); break; } default: return; } m_Controls->tlParam->setEnabled(true); m_Controls->tlParam1->setText(text1); m_Controls->tlParam2->setText(text2); m_Controls->tlParam3->setText(text3); m_Controls->tlParam4->setText(text4); m_Controls->btnDoIt->setEnabled(true); m_Controls->cbHideOrig->setEnabled(true); } void QmitkBasicImageProcessing::StartButtonClicked() { auto selectedNode = m_Controls->selectedImageWidget->GetSelectedNode(); if (selectedNode.IsNull()) { return; } this->BusyCursorOn(); mitk::Image::Pointer newImage; try { newImage = dynamic_cast(selectedNode->GetData()); } catch ( std::exception &e ) { QString exceptionString = tr("An error occured during image loading:\n"); exceptionString.append( e.what() ); QMessageBox::warning( nullptr, "Basic Image Processing", exceptionString , QMessageBox::Ok, QMessageBox::NoButton ); this->BusyCursorOff(); return; } // check if input image is valid, casting does not throw exception when casting from 'nullptr-Object' if ( (! newImage) || (newImage->IsInitialized() == false) ) { this->BusyCursorOff(); QMessageBox::warning( nullptr, "Basic Image Processing", tr("Input image is broken or not initialized. Returning."), QMessageBox::Ok, QMessageBox::NoButton ); return; } // check if operation is done on 4D a image time step if(newImage->GetDimension() > 3) { auto timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(newImage); timeSelector->SetTimeNr( ((QmitkSliderNavigatorWidget*)m_Controls->sliceNavigatorTime)->GetPos() ); timeSelector->Update(); newImage = timeSelector->GetOutput(); } // check if image or vector image auto itkImage = ImageType::New(); auto itkVecImage = VectorImageType::New(); int isVectorImage = newImage->GetPixelType().GetNumberOfComponents(); if(isVectorImage > 1) { CastToItkImage( newImage, itkVecImage ); } else { CastToItkImage( newImage, itkImage ); } std::stringstream nameAddition(""); int param1 = m_Controls->sbParam1->value(); int param2 = m_Controls->sbParam2->value(); double dparam1 = m_Controls->dsbParam1->value(); double dparam2 = m_Controls->dsbParam2->value(); double dparam3 = m_Controls->dsbParam3->value(); try { switch (m_SelectedAction) { case GAUSSIAN: { GaussianFilterType::Pointer gaussianFilter = GaussianFilterType::New(); gaussianFilter->SetInput( itkImage ); gaussianFilter->SetVariance( dparam1 ); gaussianFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(gaussianFilter->GetOutput())->Clone(); nameAddition << "_Gaussian_var_" << dparam1; std::cout << "Gaussian filtering successful." << std::endl; break; } case MEDIAN: { MedianFilterType::Pointer medianFilter = MedianFilterType::New(); MedianFilterType::InputSizeType size; size.Fill(param1); medianFilter->SetRadius( size ); medianFilter->SetInput(itkImage); medianFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(medianFilter->GetOutput())->Clone(); nameAddition << "_Median_radius_" << param1; std::cout << "Median Filtering successful." << std::endl; break; } case TOTALVARIATION: { if(isVectorImage > 1) { VectorTotalVariationFilterType::Pointer TVFilter = VectorTotalVariationFilterType::New(); TVFilter->SetInput( itkVecImage.GetPointer() ); TVFilter->SetNumberIterations(param1); TVFilter->SetLambda(double(param2)/1000.); TVFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(TVFilter->GetOutput())->Clone(); } else { ImagePTypeToFloatPTypeCasterType::Pointer floatCaster = ImagePTypeToFloatPTypeCasterType::New(); floatCaster->SetInput( itkImage ); floatCaster->Update(); DoubleImageType::Pointer fImage = floatCaster->GetOutput(); TotalVariationFilterType::Pointer TVFilter = TotalVariationFilterType::New(); TVFilter->SetInput( fImage.GetPointer() ); TVFilter->SetNumberIterations(param1); TVFilter->SetLambda(double(param2)/1000.); TVFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(TVFilter->GetOutput())->Clone(); } nameAddition << "_TV_Iter_" << param1 << "_L_" << param2; std::cout << "Total Variation Filtering successful." << std::endl; break; } case DILATION: { BallType binaryBall; binaryBall.SetRadius( param1 ); binaryBall.CreateStructuringElement(); DilationFilterType::Pointer dilationFilter = DilationFilterType::New(); dilationFilter->SetInput( itkImage ); dilationFilter->SetKernel( binaryBall ); dilationFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(dilationFilter->GetOutput())->Clone(); nameAddition << "_Dilated_by_" << param1; std::cout << "Dilation successful." << std::endl; break; } case EROSION: { BallType binaryBall; binaryBall.SetRadius( param1 ); binaryBall.CreateStructuringElement(); ErosionFilterType::Pointer erosionFilter = ErosionFilterType::New(); erosionFilter->SetInput( itkImage ); erosionFilter->SetKernel( binaryBall ); erosionFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(erosionFilter->GetOutput())->Clone(); nameAddition << "_Eroded_by_" << param1; std::cout << "Erosion successful." << std::endl; break; } case OPENING: { BallType binaryBall; binaryBall.SetRadius( param1 ); binaryBall.CreateStructuringElement(); OpeningFilterType::Pointer openFilter = OpeningFilterType::New(); openFilter->SetInput( itkImage ); openFilter->SetKernel( binaryBall ); openFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(openFilter->GetOutput())->Clone(); nameAddition << "_Opened_by_" << param1; std::cout << "Opening successful." << std::endl; break; } case CLOSING: { BallType binaryBall; binaryBall.SetRadius( param1 ); binaryBall.CreateStructuringElement(); ClosingFilterType::Pointer closeFilter = ClosingFilterType::New(); closeFilter->SetInput( itkImage ); closeFilter->SetKernel( binaryBall ); closeFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(closeFilter->GetOutput())->Clone(); nameAddition << "_Closed_by_" << param1; std::cout << "Closing successful." << std::endl; break; } case GRADIENT: { GradientFilterType::Pointer gradientFilter = GradientFilterType::New(); gradientFilter->SetInput( itkImage ); gradientFilter->SetSigma( dparam1 ); gradientFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(gradientFilter->GetOutput())->Clone(); nameAddition << "_Gradient_sigma_" << dparam1; std::cout << "Gradient calculation successful." << std::endl; break; } case LAPLACIAN: { // the laplace filter requires a float type image as input, we need to cast the itkImage // to correct type ImagePTypeToFloatPTypeCasterType::Pointer caster = ImagePTypeToFloatPTypeCasterType::New(); caster->SetInput( itkImage ); caster->Update(); DoubleImageType::Pointer fImage = caster->GetOutput(); LaplacianFilterType::Pointer laplacianFilter = LaplacianFilterType::New(); laplacianFilter->SetInput( fImage ); laplacianFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(laplacianFilter->GetOutput())->Clone(); nameAddition << "_Second_Derivative"; std::cout << "Laplacian filtering successful." << std::endl; break; } case SOBEL: { // the sobel filter requires a float type image as input, we need to cast the itkImage // to correct type ImagePTypeToFloatPTypeCasterType::Pointer caster = ImagePTypeToFloatPTypeCasterType::New(); caster->SetInput( itkImage ); caster->Update(); DoubleImageType::Pointer fImage = caster->GetOutput(); SobelFilterType::Pointer sobelFilter = SobelFilterType::New(); sobelFilter->SetInput( fImage ); sobelFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(sobelFilter->GetOutput())->Clone(); nameAddition << "_Sobel"; std::cout << "Edge Detection successful." << std::endl; break; } case THRESHOLD: { ThresholdFilterType::Pointer thFilter = ThresholdFilterType::New(); thFilter->SetLowerThreshold(param1 < param2 ? param1 : param2); thFilter->SetUpperThreshold(param2 > param1 ? param2 : param1); thFilter->SetInsideValue(1); thFilter->SetOutsideValue(0); thFilter->SetInput(itkImage); thFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(thFilter->GetOutput())->Clone(); nameAddition << "_Threshold"; std::cout << "Thresholding successful." << std::endl; break; } case INVERSION: { InversionFilterType::Pointer invFilter = InversionFilterType::New(); mitk::ScalarType min = newImage->GetStatistics()->GetScalarValueMin(); mitk::ScalarType max = newImage->GetStatistics()->GetScalarValueMax(); invFilter->SetMaximum( max + min ); invFilter->SetInput(itkImage); invFilter->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(invFilter->GetOutput())->Clone(); nameAddition << "_Inverted"; std::cout << "Image inversion successful." << std::endl; break; } case DOWNSAMPLING: { ResampleImageFilterType::Pointer downsampler = ResampleImageFilterType::New(); downsampler->SetInput( itkImage ); NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New(); downsampler->SetInterpolator( interpolator ); downsampler->SetDefaultPixelValue( 0 ); ResampleImageFilterType::SpacingType spacing = itkImage->GetSpacing(); spacing *= (double) param1; downsampler->SetOutputSpacing( spacing ); downsampler->SetOutputOrigin( itkImage->GetOrigin() ); downsampler->SetOutputDirection( itkImage->GetDirection() ); ResampleImageFilterType::SizeType size = itkImage->GetLargestPossibleRegion().GetSize(); for ( int i = 0; i < 3; ++i ) { size[i] /= param1; } downsampler->SetSize( size ); downsampler->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(downsampler->GetOutput())->Clone(); nameAddition << "_Downsampled_by_" << param1; std::cout << "Downsampling successful." << std::endl; break; } case FLIPPING: { FlipImageFilterType::Pointer flipper = FlipImageFilterType::New(); flipper->SetInput( itkImage ); itk::FixedArray flipAxes; for(int i=0; i<3; ++i) { if(i == param1) { flipAxes[i] = true; } else { flipAxes[i] = false; } } flipper->SetFlipAxes(flipAxes); flipper->UpdateLargestPossibleRegion(); newImage = mitk::ImportItkImage(flipper->GetOutput())->Clone(); std::cout << "Image flipping successful." << std::endl; break; } case RESAMPLING: { std::string selectedInterpolator; ResampleImageFilterType::Pointer resampler = ResampleImageFilterType::New(); switch (m_SelectedInterpolation) { case LINEAR: { LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Linear"; break; } case NEAREST: { NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Nearest"; break; } default: { LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Linear"; break; } } resampler->SetInput( itkImage ); resampler->SetOutputOrigin( itkImage->GetOrigin() ); ImageType::SizeType input_size = itkImage->GetLargestPossibleRegion().GetSize(); ImageType::SpacingType input_spacing = itkImage->GetSpacing(); ImageType::SizeType output_size; ImageType::SpacingType output_spacing; output_size[0] = input_size[0] * (input_spacing[0] / dparam1); output_size[1] = input_size[1] * (input_spacing[1] / dparam2); output_size[2] = input_size[2] * (input_spacing[2] / dparam3); output_spacing [0] = dparam1; output_spacing [1] = dparam2; output_spacing [2] = dparam3; resampler->SetSize( output_size ); resampler->SetOutputSpacing( output_spacing ); resampler->SetOutputDirection( itkImage->GetDirection() ); resampler->UpdateLargestPossibleRegion(); ImageType::Pointer resampledImage = resampler->GetOutput(); newImage = mitk::ImportItkImage( resampledImage )->Clone(); nameAddition << "_Resampled_" << selectedInterpolator; std::cout << "Resampling successful." << std::endl; break; } case RESCALE: { DoubleImageType::Pointer floatImage = DoubleImageType::New(); CastToItkImage( newImage, floatImage ); itk::RescaleIntensityImageFilter::Pointer filter = itk::RescaleIntensityImageFilter::New(); filter->SetInput(0, floatImage); filter->SetOutputMinimum(dparam1); filter->SetOutputMaximum(dparam2); filter->Update(); floatImage = filter->GetOutput(); newImage = mitk::Image::New(); newImage->InitializeByItk(floatImage.GetPointer()); newImage->SetVolume(floatImage->GetBufferPointer()); nameAddition << "_Rescaled"; std::cout << "Rescaling successful." << std::endl; break; } case RESCALE2: { DoubleImageType::Pointer floatImage = DoubleImageType::New(); CastToItkImage( newImage, floatImage ); itk::ShiftScaleImageFilter::Pointer filter = itk::ShiftScaleImageFilter::New(); filter->SetInput(0, floatImage); filter->SetScale(dparam1); filter->Update(); floatImage = filter->GetOutput(); newImage = mitk::Image::New(); newImage->InitializeByItk(floatImage.GetPointer()); newImage->SetVolume(floatImage->GetBufferPointer()); nameAddition << "_Rescaled"; std::cout << "Rescaling successful." << std::endl; break; } default: this->BusyCursorOff(); return; } } catch (...) { this->BusyCursorOff(); QMessageBox::warning(nullptr, "Warning", "Problem when applying filter operation. Check your input..."); return; } newImage->DisconnectPipeline(); // adjust level/window to new image mitk::LevelWindow levelwindow; levelwindow.SetAuto( newImage ); auto levWinProp = mitk::LevelWindowProperty::New(); levWinProp->SetLevelWindow( levelwindow ); // compose new image name std::string name = selectedNode->GetName(); - if (name.find(".pic.gz") == name.size() -7 ) + if (name.find(".nrrd") == name.size() -5 ) { - name = name.substr(0,name.size() -7); + name = name.substr(0,name.size() -5); } name.append( nameAddition.str() ); // create final result MITK data storage node auto result = mitk::DataNode::New(); result->SetProperty( "levelwindow", levWinProp ); result->SetProperty( "name", mitk::StringProperty::New( name.c_str() ) ); result->SetData( newImage ); // for vector images, a different mapper is needed if(isVectorImage > 1) { auto mapper = mitk::VectorImageMapper2D::New(); result->SetMapper(1,mapper); } // add new image to data storage and set as active to ease further processing GetDataStorage()->Add(result, selectedNode); if (m_Controls->cbHideOrig->isChecked() == true) { selectedNode->SetProperty("visible", mitk::BoolProperty::New(false)); } // show the results mitk::RenderingManager::GetInstance()->RequestUpdateAll(); this->BusyCursorOff(); } void QmitkBasicImageProcessing::SelectAction2(int operation) { switch (operation) { case 2: m_SelectedOperation = ADD; break; case 3: m_SelectedOperation = SUBTRACT; break; case 4: m_SelectedOperation = MULTIPLY; break; case 5: m_SelectedOperation = DIVIDE; break; case 6: m_SelectedOperation = RESAMPLE_TO; break; case 8: m_SelectedOperation = AND; break; case 9: m_SelectedOperation = OR; break; case 10: m_SelectedOperation = XOR; break; default: return; } m_Controls->selectedImageLabel_2->setEnabled(true); m_Controls->selectedImageWidget_2->setEnabled(true); m_Controls->btnDoIt2->setEnabled(true); } void QmitkBasicImageProcessing::StartButton2Clicked() { auto selectedNode = m_Controls->selectedImageWidget->GetSelectedNode(); if (selectedNode.IsNull()) { return; } auto selectedNode2 = m_Controls->selectedImageWidget_2->GetSelectedNode(); if (selectedNode2.IsNull()) { return; } mitk::Image::Pointer newImage1 = dynamic_cast(selectedNode->GetData()); mitk::Image::Pointer newImage2 = dynamic_cast(selectedNode2->GetData()); // check if images are valid if(newImage1.IsNull() || newImage2.IsNull() || false == newImage1->IsInitialized() || false == newImage2->IsInitialized()) { itkGenericExceptionMacro(<< "At least one of the input images is broken or not initialized."); return; } this->BusyCursorOn(); // check if 4D image and use filter on correct time step if(newImage1->GetDimension() > 3) { auto timeSelector = mitk::ImageTimeSelector::New(); auto sn_widget = static_cast( m_Controls->sliceNavigatorTime ); int time = 0; if( sn_widget != nullptr ) time = sn_widget->GetPos(); timeSelector->SetInput(newImage1); timeSelector->SetTimeNr( time ); timeSelector->UpdateLargestPossibleRegion(); newImage1 = timeSelector->GetOutput(); newImage1->DisconnectPipeline(); timeSelector->SetInput(newImage2); timeSelector->SetTimeNr( time ); timeSelector->UpdateLargestPossibleRegion(); newImage2 = timeSelector->GetOutput(); newImage2->DisconnectPipeline(); } auto itkImage1 = ImageType::New(); auto itkImage2 = ImageType::New(); CastToItkImage( newImage1, itkImage1 ); CastToItkImage( newImage2, itkImage2 ); std::string nameAddition = ""; try { switch (m_SelectedOperation) { case ADD: { AddFilterType::Pointer addFilter = AddFilterType::New(); addFilter->SetInput1( itkImage1 ); addFilter->SetInput2( itkImage2 ); addFilter->UpdateLargestPossibleRegion(); newImage1 = mitk::ImportItkImage(addFilter->GetOutput())->Clone(); nameAddition = "_Added"; } break; case SUBTRACT: { SubtractFilterType::Pointer subFilter = SubtractFilterType::New(); subFilter->SetInput1( itkImage1 ); subFilter->SetInput2( itkImage2 ); subFilter->UpdateLargestPossibleRegion(); newImage1 = mitk::ImportItkImage(subFilter->GetOutput())->Clone(); nameAddition = "_Subtracted"; } break; case MULTIPLY: { MultiplyFilterType::Pointer multFilter = MultiplyFilterType::New(); multFilter->SetInput1( itkImage1 ); multFilter->SetInput2( itkImage2 ); multFilter->UpdateLargestPossibleRegion(); newImage1 = mitk::ImportItkImage(multFilter->GetOutput())->Clone(); nameAddition = "_Multiplied"; } break; case DIVIDE: { DivideFilterType::Pointer divFilter = DivideFilterType::New(); divFilter->SetInput1( itkImage1 ); divFilter->SetInput2( itkImage2 ); divFilter->UpdateLargestPossibleRegion(); newImage1 = mitk::ImportItkImage(divFilter->GetOutput())->Clone(); nameAddition = "_Divided"; } break; case AND: { AndImageFilterType::Pointer andFilter = AndImageFilterType::New(); andFilter->SetInput1( itkImage1 ); andFilter->SetInput2( itkImage2 ); andFilter->UpdateLargestPossibleRegion(); newImage1 = mitk::ImportItkImage(andFilter->GetOutput())->Clone(); nameAddition = "_AND"; break; } case OR: { OrImageFilterType::Pointer orFilter = OrImageFilterType::New(); orFilter->SetInput1( itkImage1 ); orFilter->SetInput2( itkImage2 ); orFilter->UpdateLargestPossibleRegion(); newImage1 = mitk::ImportItkImage(orFilter->GetOutput())->Clone(); nameAddition = "_OR"; break; } case XOR: { XorImageFilterType::Pointer xorFilter = XorImageFilterType::New(); xorFilter->SetInput1( itkImage1 ); xorFilter->SetInput2( itkImage2 ); xorFilter->UpdateLargestPossibleRegion(); newImage1 = mitk::ImportItkImage(xorFilter->GetOutput())->Clone(); nameAddition = "_XOR"; break; } case RESAMPLE_TO: { itk::BSplineInterpolateImageFunction::Pointer bspl_interpolator = itk::BSplineInterpolateImageFunction::New(); bspl_interpolator->SetSplineOrder( 3 ); itk::NearestNeighborInterpolateImageFunction< DoubleImageType >::Pointer nn_interpolator = itk::NearestNeighborInterpolateImageFunction< DoubleImageType>::New(); DoubleImageType::Pointer itkImage1 = DoubleImageType::New(); DoubleImageType::Pointer itkImage2 = DoubleImageType::New(); CastToItkImage( newImage1, itkImage1 ); CastToItkImage( newImage2, itkImage2 ); itk::ResampleImageFilter< DoubleImageType, DoubleImageType >::Pointer resampleFilter = itk::ResampleImageFilter< DoubleImageType, DoubleImageType >::New(); resampleFilter->SetInput( itkImage1 ); resampleFilter->SetReferenceImage( itkImage2 ); resampleFilter->SetUseReferenceImage( true ); // use NN interp with binary images if(selectedNode->GetProperty("binary") ) resampleFilter->SetInterpolator( nn_interpolator ); else resampleFilter->SetInterpolator( bspl_interpolator ); resampleFilter->SetDefaultPixelValue( 0 ); try { resampleFilter->UpdateLargestPossibleRegion(); } catch( const itk::ExceptionObject &e) { MITK_WARN << "Updating resampling filter failed. "; MITK_WARN << "REASON: " << e.what(); } DoubleImageType::Pointer resampledImage = resampleFilter->GetOutput(); newImage1 = mitk::ImportItkImage( resampledImage )->Clone(); nameAddition = "_Resampled"; break; } default: std::cout << "Something went wrong..." << std::endl; this->BusyCursorOff(); return; } } catch (const itk::ExceptionObject& e ) { this->BusyCursorOff(); QMessageBox::warning(nullptr, "ITK Exception", e.what() ); QMessageBox::warning(nullptr, "Warning", tr("Problem when applying arithmetic operation to two images. Check dimensions of input images.")); return; } // disconnect pipeline; images will not be reused newImage1->DisconnectPipeline(); itkImage1 = nullptr; itkImage2 = nullptr; // adjust level/window to new image and compose new image name mitk::LevelWindow levelwindow; levelwindow.SetAuto( newImage1 ); auto levWinProp = mitk::LevelWindowProperty::New(); levWinProp->SetLevelWindow( levelwindow ); std::string name = selectedNode->GetName(); - if (name.find(".pic.gz") == name.size() -7 ) + if (name.find(".nrrd") == name.size() -5 ) { - name = name.substr(0,name.size() -7); + name = name.substr(0,name.size() -5); } // create final result MITK data storage node auto result = mitk::DataNode::New(); result->SetProperty( "levelwindow", levWinProp ); result->SetProperty( "name", mitk::StringProperty::New( (name + nameAddition ).c_str() )); result->SetData( newImage1 ); this->GetDataStorage()->Add(result, selectedNode); if (m_Controls->cbHideOrig->isChecked() == true) { selectedNode->SetProperty("visible", mitk::BoolProperty::New(false)); selectedNode2->SetProperty("visible", mitk::BoolProperty::New(false)); } // show the newly created image mitk::RenderingManager::GetInstance()->RequestUpdateAll(); this->BusyCursorOff(); } void QmitkBasicImageProcessing::SelectInterpolator(int interpolator) { switch (interpolator) { case 0: { m_SelectedInterpolation = LINEAR; break; } case 1: { m_SelectedInterpolation = NEAREST; break; } } } diff --git a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox index 505f2ac4bb..f9c36fce44 100644 --- a/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox +++ b/Plugins/org.mitk.gui.qt.datamanager/documentation/UserManual/QmitkDatamanager.dox @@ -1,194 +1,194 @@ /** \page org_mitk_views_datamanager The Data Manager View \imageMacro{data-manager-dox.svg,"Icon of the Data Manager", 2.00} \tableofcontents \section DataManagerIntroduction Introduction The Datamanager is the central component to manage medical data like images, segmentation masks, registrations, surfaces, point sets, annotations, measurements, etc..
After loading data into the Datamanager the data is shown in the four-view window, the so-called Standard Display. The user can now start working on the data by interacting with the data inside the Standard Display, by using the MITK-plugins such as Segmentation or Basic Image Processing or by using the context menu inside the data manager. \section DataManagerLoadingData Loading Data There are several ways of loading data into the Datamanager as so-called data nodes:
  • drag and drop data (e.g. from a file explorer or desktop) into the Datamanager
  • drag and drop data (e.g. from a file explorer or desktop) into one of the four windows of the Standard Display
  • use the keyboard shortcut Ctrl + o
  • use the Open File Button in the left upper corner and use the Open Dialog
  • use File -> Open File... from the top menu
A lot of file-formats can be loaded into MITK, for example:
    -
  • 2D-images / 3D-volumes with or without several time steps (*.dcm, *.ima, *.pic, *.nrrd, ...) +
  • 2D-images / 3D-volumes with or without several time steps (*.dcm, *.ima, *.nrrd, ...)
  • Surfaces (*.stl, *.vtk, ...)
  • Point sets (*.mps)
  • and many more
The user can also load a series of 2D images (e.g. image001.png, image002.png ...) to a MITK 3D volume. To do this, just drag and drop one of those 2D data files into the Datamanager by holding the ALT key. Note: What really happens is that the data nodes are stored inside a "Data storage" and the Datamanager is just a visual representation of the data inside the "Data storage". That's why the documentation sometimes uses the term "Data storage" instead of "Datamanager". \section DataManagerSavingData Saving Data There are several ways of saving data from the Datamanager:
  • use the keyboard shortcut Ctrl + s on a single data node
  • use the keyboard shortcut Ctrl + s on multiple data nodes
  • use the context menu right-click -> Save on a single data node
  • use the context menu right-click -> Save on multiple data nodes
  • use File -> Save... from the top menu on a single data node
  • use File -> Save... from the top menu on multiple data nodes
\section DataManagerWorking Working with the Datamanager After loading data into the Datamanager the data appears as data nodes in a sorted list inside the Datamanager. The user can change the order of the data nodes manually by dragging one or multiple data nodes and dropping them at any position inside the Datamanager. Data nodes can also be sorted hierarchically as a parent-child-relation. For example after using the Segmentation-Plugin to create a segmentation on DataNode, the result is created as ChildNode, which is a child of DataNode (see \ref ParentChild "Parent-Child-Relation" screenshot).
A parent-child-relation can be changed by dragging a child of a data node and dropping it onto another data node. For this the Property Allow changing of parent nodes needs to be enabled (see \ref DataManagerPreferences "Preferences"). \anchor ParentChild \imageMacro{QmitkDatamanager_ParentChild.png, "Parent-Child-Relation", 16.00} \subsection DataManagerNodeVisibility Visibility of data nodes By default all loaded data nodes are visible in the Standard Display. The visibility is indicated by the checkbox in front of the data node name in the Datamanager. If a data node is visible, the checkbox is filled - an empty checkbox indicates a hidden data node (see \ref ParentChild "Parent-Child-Relation" screenshot). Hint: The data nodes are rendered on top of each other, such that the topmost visible data node is always displayed on top of other data nodes. By hiding the topmost visible data node the next data node becomes the topmost visible data node and the hidden data node is not rendered anymore. Note: "Visible" does not mean that the node is correctly displayed inside the render windows. The user might have to re-initialize a data node to have it correctly displayed. \subsection DataManagerNodeSelection Selection of data nodes Some MITK-plugins contain widgets to control the data nodes that are used for plugin-specific data processing. These widgets can be configured such that they listen to the current selection of the Datamanager. Having such a plugin active each selection change of data nodes inside the data manager will change the respective selection of the plugin. The data node selection widgets can have specific node predicates, which means that only specific data nodes can be controlled by the widgets. It might happen that a selected data node will not be represented in such a selection widget or that the selection widget will be emptied. \subsection DataManagerNodeRenaming Renaming data nodes There are two ways of changing the name of a data node inside the Datamanager:
  • use the F2 key on a single data node
  • double-click on a single data node
In both cases the new name can be accepted by hitting Enter or by clicking somewhere else. \section DataManagerContextMenu Context Menu The Datamanager provides a context menu for each data node that can be opened by right-clicking on a data node. An example of the context-menu can be seen in the \ref ContextMenu "Context menu" screenshot. The context menu allows to quickly perform common actions on data nodes. These actions differ according to the data type. Some of these actions are described here. For more actions see the respective modules and plugins (e.g. QmitkCreatePolygonModelAction inside the org_mitk_gui_qt_segmentation-plugin.
  • Global Reinit: Re-initializes the render windows to the common bounding box of all data nodes of the data storage that
    • have not set "includeInBoundingBox" to false
    • are "visible".
    In this case it does not matter on which node this action is performed.
  • Reinit: Re-initializes the render windows to the common bounding box of all selected data nodes of the data storage that
    • have not set "includeInBoundingBox" to false
    • are "visible".
  • Save: see \ref DataManagerSavingData "Saving Data" section
  • Remove: Removes all selected data nodes from the data storage.
  • Show only selected nodes: Enables the visibility of all selected data nodes and hides all other data nodes.
  • Toggle visibility: Shows / hides each selected data node according to each node's current visibility state.
  • Show details: Opens a pop-up window with detailed information about each node, like data type, geometry, DICOM information, file path etc.
  • Opacity: Sets the opacity via a slider for the rendering of the selected data node.
  • Color: Opens a pop-up window that allows to pick an arbitrary color for the rendering of all selected data nodes.
  • Colormap: Opens another submenu with a list of different colormaps that can be chosen for the rendering of all selected data nodes.
  • Component: Sets the currently visible data component for the rendering of this particular component of the selected data node.
  • Texture Interpolation: Smooths the data visualization for rendering of a selected data node.
  • Surface Representation: Opens another submenu with the following entries:
    • Points: Visually represents a surface (a data type) as a set of points.
    • Wireframe: Visually represents a surface (a data type) as a wireframe model.
    • Surface: Visually represents a surface (a data type) as a solid surface.
As the description of the actions showed, it is possible to open / use the context menu with a single data node or with a set of selected data nodes. If the data types of multiple selected data nodes differ, the actions might not appear / work as expected. Also some actions are not available for a set of selected data nodes. \anchor ContextMenu \imageMacro{QmitkDatamanager_ContextMenu.png, "Context menu", 16.00} \section DataManagerPreferences Preferences The MITK Workbench provides a preference page for specific plugins. The preference page provided for the Datamanager can be seen in the \ref PreferencePage "Preference page" screenshot. The user can open the preference page by
  • using the keyboard shortcut Ctrl + p
  • using Window -> Preferences... from the top menu.
It allows to set the following preferences for the Datamanager, which define the behavior of the Datamanager:
  • Place new nodes on top: If enabled, newly added data nodes will be inserted at the top of the list of data nodes inside the Datamanager. If disabled, newly added nodes will be inserted at the bottom of the list.
  • Show helper objects: If enabled, data nodes that have set "helper object" to true will be displayed in the Datamanager. If disabled, data nodes that have set "helper object" to true will not be visible in the Datamanager.
  • Show nodes containing no data: If enabled, data nodes that have no underlying base data defined will be displayed in the Datamanager. If disabled, data nodes that have no underlying base data defined will not be visible in the Datamanager.
  • Use surface decimation: If enabled, a newly created surface will be decimated to reduce the number of triangles in the triangle mesh. Such a surface can be created as a polygon model from a segmentation (see \ref DataManagerContextMenu "Context Menu"). If disabled, the surface will have its original number of triangles in the triangle mesh.
  • Allow changing of parent node: If enabled, the user can change the hierarchy of the data nodes manually by dragging one or multiple data nodes and dropping them at any position inside the Datamanager (see \ref DataManagerWorking "Working with the Datamanager") for changing the order of the data nodes manually).
\anchor PreferencePage \imageMacro{QmitkDatamanager_PreferencePage.png, "Preference page", 16.00} \section DataManagerHotkeys Hotkeys The MITK Workbench provides hotkeys for specific plugins. The hotkeys provided for the Datamanager can be seen in the \ref Hotkeys "Hotkeys" screenshot. They allow to expedite common operations in relation to data nodes or the Datamanager. The user can customize the hotkeys by accessing the preference page:
  • using the keyboard shortcut Ctrl + p
  • useing Window -> Preferences... from the top menu
  • Delete selected nodes Removes all selected data nodes from the data storage.
  • Global reinit Re-initializes the render windows to the common bounding box of all data nodes of the data storage that
    • have not set "includeInBoundingBox" to false
    • are "visible"
    In this case it does not matter on which node this action is performed.
  • Make all nodes invisible Hides all data nodes of the data storage.
  • Reinit selected nodes Re-initializes the render windows to the common bounding box of all selected data nodes of the data storage that
    • have not set "includeInBoundingBox" to false
    • are "visible"
  • Show node information Opens a pop-up window with detailed information about each node, like data type, geometry, DICOM information, file path etc.
  • Toggle visibility of selected nodes: Shows / hides each selected data node according to each node's current visibility state.
\anchor Hotkeys \imageMacro{QmitkDatamanager_Hotkeys.png, "Hotkeys", 16.00} */ diff --git a/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp b/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp index 738ef2b5fb..0befa8495d 100644 --- a/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp +++ b/Plugins/org.mitk.gui.qt.preprocessing.resampling/src/internal/QmitkPreprocessingResamplingView.cpp @@ -1,457 +1,457 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ #include "QmitkPreprocessingResamplingView.h" // QT includes (GUI) #include #include #include #include #include #include #include // Berry includes (selection service) #include #include // MITK includes (GUI) #include "QmitkStdMultiWidget.h" #include "QmitkDataNodeSelectionProvider.h" #include "mitkDataNodeObject.h" // MITK includes (general) #include "mitkNodePredicateDataType.h" #include "mitkNodePredicateDimension.h" #include "mitkNodePredicateAnd.h" #include "mitkImageTimeSelector.h" #include "mitkVectorImageMapper2D.h" #include "mitkProperties.h" #include "mitkLevelWindowProperty.h" // Includes for image casting between ITK and MITK #include "mitkImageCast.h" #include "mitkITKImageImport.h" // ITK includes (general) #include #include // Resampling #include #include #include #include #include #include #include // STD #include // Convenient Definitions typedef itk::Image ImageType; typedef itk::Image SegmentationImageType; typedef itk::Image DoubleImageType; typedef itk::Image, 3> VectorImageType; typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType; typedef itk::ResampleImageFilter< ImageType, ImageType > ResampleImageFilterType2; typedef itk::CastImageFilter< ImageType, DoubleImageType > ImagePTypeToFloatPTypeCasterType; typedef itk::LinearInterpolateImageFunction< ImageType, double > LinearInterpolatorType; typedef itk::NearestNeighborInterpolateImageFunction< ImageType, double > NearestInterpolatorType; typedef itk::BSplineInterpolateImageFunction BSplineInterpolatorType; QmitkPreprocessingResampling::QmitkPreprocessingResampling() : QmitkAbstractView(), m_Controls(nullptr), m_SelectedImageNode(nullptr), m_TimeStepperAdapter(nullptr) { } QmitkPreprocessingResampling::~QmitkPreprocessingResampling() { } void QmitkPreprocessingResampling::CreateQtPartControl(QWidget *parent) { if (m_Controls == nullptr) { m_Controls = new Ui::QmitkPreprocessingResamplingViewControls; m_Controls->setupUi(parent); this->CreateConnections(); mitk::NodePredicateDimension::Pointer dimensionPredicate = mitk::NodePredicateDimension::New(3); mitk::NodePredicateDataType::Pointer imagePredicate = mitk::NodePredicateDataType::New("Image"); } m_SelectedImageNode = mitk::DataStorageSelection::New(this->GetDataStorage(), false); // Setup Controls this->m_Controls->cbParam4->clear(); this->m_Controls->cbParam4->insertItem(LINEAR, "Linear"); this->m_Controls->cbParam4->insertItem(NEAREST, "Nearest neighbor"); this->m_Controls->cbParam4->insertItem(SPLINE, "B-Spline"); } void QmitkPreprocessingResampling::CreateConnections() { if ( m_Controls ) { connect((QObject*)(m_Controls->btnDoIt), SIGNAL(clicked()), (QObject*) this, SLOT(StartButtonClicked())); connect((QObject*)(m_Controls->buttonExecuteOnMultipleImages), SIGNAL(clicked()), (QObject*) this, SLOT(StartMultipleImagesButtonClicked())); connect( (QObject*)(m_Controls->cbParam4), SIGNAL( activated(int) ), this, SLOT( SelectInterpolator(int) ) ); } } void QmitkPreprocessingResampling::InternalGetTimeNavigationController() { auto renwin_part = GetRenderWindowPart(); if( renwin_part != nullptr ) { auto tnc = renwin_part->GetTimeNavigationController(); if( tnc != nullptr ) { m_TimeStepperAdapter = new QmitkStepperAdapter((QObject*) m_Controls->sliceNavigatorTime, tnc->GetTime(), "sliceNavigatorTimeFromBIP"); } } } void QmitkPreprocessingResampling::SetFocus() { } //datamanager selection changed void QmitkPreprocessingResampling::OnSelectionChanged(berry::IWorkbenchPart::Pointer, const QList& nodes) { ResetOneImageOpPanel(); //any nodes there? if (!nodes.empty()) { // reset GUI m_Controls->sliceNavigatorTime->setEnabled(false); m_Controls->leImage1->setText(tr("Select an Image in Data Manager")); m_SelectedNodes.clear(); for (mitk::DataNode* _DataNode : nodes) { m_SelectedImageNode->RemoveAllNodes(); *m_SelectedImageNode = _DataNode; mitk::Image::Pointer tempImage = dynamic_cast(m_SelectedImageNode->GetNode()->GetData()); //no image if (tempImage.IsNull() || (tempImage->IsInitialized() == false)) { if (m_SelectedNodes.size() < 1) { m_Controls->leImage1->setText(tr("Not an image.")); } continue; } //2D image if (tempImage->GetDimension() < 3) { if (m_SelectedNodes.size() < 1) { m_Controls->leImage1->setText(tr("2D images are not supported.")); } continue; } if (m_SelectedNodes.size() < 1) { m_Controls->leImage1->setText(QString(m_SelectedImageNode->GetNode()->GetName().c_str())); mitk::Vector3D aSpacing = tempImage->GetGeometry()->GetSpacing(); std::string text("x-spacing (" + std::to_string(aSpacing[0]) + ")"); m_Controls->tlParam1->setText(text.c_str()); text = "y-spacing (" + std::to_string(aSpacing[1]) + ")"; m_Controls->tlParam2->setText(text.c_str()); text = "z-spacing (" + std::to_string(aSpacing[2]) + ")"; m_Controls->tlParam3->setText(text.c_str()); if (tempImage->GetDimension() > 3) { // try to retrieve the TNC (for 4-D Processing ) this->InternalGetTimeNavigationController(); m_Controls->sliceNavigatorTime->setEnabled(true); m_Controls->tlTime->setEnabled(true); } } m_SelectedNodes.push_back(_DataNode); } if (m_SelectedNodes.size() > 0) { *m_SelectedImageNode = m_SelectedNodes[0]; } ResetParameterPanel(); } } void QmitkPreprocessingResampling::ResetOneImageOpPanel() { m_Controls->tlTime->setEnabled(false); m_Controls->btnDoIt->setEnabled(false); m_Controls->buttonExecuteOnMultipleImages->setEnabled(false); m_Controls->cbHideOrig->setEnabled(false); m_Controls->leImage1->setText(tr("Select an Image in Data Manager")); m_Controls->tlParam1->setText("x-spacing"); m_Controls->tlParam1->setText("y-spacing"); m_Controls->tlParam1->setText("z-spacing"); } void QmitkPreprocessingResampling::ResetParameterPanel() { m_Controls->btnDoIt->setEnabled(true); m_Controls->buttonExecuteOnMultipleImages->setEnabled(true); m_Controls->cbHideOrig->setEnabled(true); } void QmitkPreprocessingResampling::ResetTwoImageOpPanel() { } void QmitkPreprocessingResampling::StartMultipleImagesButtonClicked() { for (auto currentSelectedNode : m_SelectedNodes) { m_SelectedImageNode->RemoveAllNodes(); *m_SelectedImageNode = currentSelectedNode; StartButtonClicked(); } } void QmitkPreprocessingResampling::StartButtonClicked() { if(!m_SelectedImageNode->GetNode()) return; this->BusyCursorOn(); mitk::Image::Pointer newImage; try { newImage = dynamic_cast(m_SelectedImageNode->GetNode()->GetData()); } catch ( std::exception &e ) { QString exceptionString = tr("An error occured during image loading:\n"); exceptionString.append( e.what() ); QMessageBox::warning( nullptr, "Preprocessing - Resampling: ", exceptionString , QMessageBox::Ok, QMessageBox::NoButton ); this->BusyCursorOff(); return; } // check if input image is valid, casting does not throw exception when casting from 'NULL-Object' if ( (! newImage) || (newImage->IsInitialized() == false) ) { this->BusyCursorOff(); QMessageBox::warning( nullptr, "Preprocessing - Resampling", tr("Input image is broken or not initialized. Returning."), QMessageBox::Ok, QMessageBox::NoButton ); return; } // check if operation is done on 4D a image time step if(newImage->GetDimension() > 3) { mitk::ImageTimeSelector::Pointer timeSelector = mitk::ImageTimeSelector::New(); timeSelector->SetInput(newImage); timeSelector->SetTimeNr( ((QmitkSliderNavigatorWidget*)m_Controls->sliceNavigatorTime)->GetPos() ); timeSelector->Update(); newImage = timeSelector->GetOutput(); } // check if image or vector image ImageType::Pointer itkImage = ImageType::New(); VectorImageType::Pointer itkVecImage = VectorImageType::New(); int isVectorImage = newImage->GetPixelType().GetNumberOfComponents(); if(isVectorImage > 1) { CastToItkImage( newImage, itkVecImage ); } else { CastToItkImage( newImage, itkImage ); } std::stringstream nameAddition(""); double dparam1 = m_Controls->dsbParam1->value(); double dparam2 = m_Controls->dsbParam2->value(); double dparam3 = m_Controls->dsbParam3->value(); try{ std::string selectedInterpolator; ResampleImageFilterType::Pointer resampler = ResampleImageFilterType::New(); switch (m_SelectedInterpolation) { case LINEAR: { LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Linear"; break; } case NEAREST: { NearestInterpolatorType::Pointer interpolator = NearestInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Nearest"; break; } case SPLINE: { BSplineInterpolatorType::Pointer interpolator = BSplineInterpolatorType::New(); interpolator->SetSplineOrder(3); resampler->SetInterpolator(interpolator); selectedInterpolator = "B-Spline"; break; } default: { LinearInterpolatorType::Pointer interpolator = LinearInterpolatorType::New(); resampler->SetInterpolator(interpolator); selectedInterpolator = "Linear"; break; } } resampler->SetInput( itkImage ); resampler->SetOutputOrigin( itkImage->GetOrigin() ); ImageType::SizeType input_size = itkImage->GetLargestPossibleRegion().GetSize(); ImageType::SpacingType input_spacing = itkImage->GetSpacing(); ImageType::SizeType output_size; ImageType::SpacingType output_spacing; if (dparam1 > 0) { output_size[0] = std::ceil(input_size[0] * (input_spacing[0] / dparam1)); output_spacing[0] = dparam1; } else { output_size[0] = std::ceil(input_size[0] * (-1.0 / dparam1)); output_spacing[0] = -1.0*input_spacing[0] * dparam1; } if (dparam2 > 0) { output_size[1] = std::ceil(input_size[1] * (input_spacing[1] / dparam2)); output_spacing[1] = dparam2; } else { output_size[1] = std::ceil(input_size[1] * (-1.0 / dparam2)); output_spacing[1] = -1.0*input_spacing[1] * dparam2; } if (dparam3 > 0) { output_size[2] = std::ceil(input_size[2] * (input_spacing[2] / dparam3)); output_spacing[2] = dparam3; } else { output_size[2] = std::ceil(input_size[2] * (-1.0 / dparam3)); output_spacing[2] = -1.0*input_spacing[2] * dparam3; } resampler->SetSize( output_size ); resampler->SetOutputSpacing( output_spacing ); resampler->SetOutputDirection( itkImage->GetDirection() ); resampler->UpdateLargestPossibleRegion(); ImageType::Pointer resampledImage = resampler->GetOutput(); newImage = mitk::ImportItkImage( resampledImage )->Clone(); nameAddition << "_Resampled_" << selectedInterpolator; std::cout << "Resampling successful." << std::endl; } catch (...) { this->BusyCursorOff(); QMessageBox::warning(nullptr, "Warning", "Problem when applying filter operation. Check your input..."); return; } newImage->DisconnectPipeline(); // adjust level/window to new image mitk::LevelWindow levelwindow; levelwindow.SetAuto( newImage ); mitk::LevelWindowProperty::Pointer levWinProp = mitk::LevelWindowProperty::New(); levWinProp->SetLevelWindow( levelwindow ); // compose new image name std::string name = m_SelectedImageNode->GetNode()->GetName(); - if (name.find(".pic.gz") == name.size() -7 ) + if (name.find(".nrrd") == name.size() -5 ) { - name = name.substr(0,name.size() -7); + name = name.substr(0,name.size() -5); } name.append( nameAddition.str() ); // create final result MITK data storage node mitk::DataNode::Pointer result = mitk::DataNode::New(); result->SetProperty( "levelwindow", levWinProp ); result->SetProperty( "name", mitk::StringProperty::New( name.c_str() ) ); result->SetData( newImage ); // for vector images, a different mapper is needed if(isVectorImage > 1) { mitk::VectorImageMapper2D::Pointer mapper = mitk::VectorImageMapper2D::New(); result->SetMapper(1,mapper); } // add new image to data storage and set as active to ease further processing GetDataStorage()->Add( result, m_SelectedImageNode->GetNode() ); if ( m_Controls->cbHideOrig->isChecked() == true ) m_SelectedImageNode->GetNode()->SetProperty( "visible", mitk::BoolProperty::New(false) ); // show the results mitk::RenderingManager::GetInstance()->RequestUpdateAll(); this->BusyCursorOff(); } void QmitkPreprocessingResampling::SelectInterpolator(int interpolator) { switch (interpolator) { case 0: { m_SelectedInterpolation = LINEAR; break; } case 1: { m_SelectedInterpolation = NEAREST; break; } case 2: { m_SelectedInterpolation = SPLINE; } } } diff --git a/Plugins/org.mitk.gui.qt.toftutorial/src/internal/QmitkToFTutorialView.cpp b/Plugins/org.mitk.gui.qt.toftutorial/src/internal/QmitkToFTutorialView.cpp index add81e5aca..c2984e620e 100644 --- a/Plugins/org.mitk.gui.qt.toftutorial/src/internal/QmitkToFTutorialView.cpp +++ b/Plugins/org.mitk.gui.qt.toftutorial/src/internal/QmitkToFTutorialView.cpp @@ -1,183 +1,183 @@ /*============================================================================ The Medical Imaging Interaction Toolkit (MITK) Copyright (c) German Cancer Research Center (DKFZ) All rights reserved. Use of this source code is governed by a 3-clause BSD license that can be found in the LICENSE file. ============================================================================*/ // Blueberry #include #include // Qmitk #include "QmitkToFTutorialView.h" // Qt #include // mitk includes #include // class holding the intrinsic parameters of the according camera #include // MITK-ToF related includes #include #include // configuration file holding e.g. plugin paths or path to test file directory #include // filter from module ToFProcessing that calculates a surface from the given range image #include // allows access to images provided by the ToF camera const std::string QmitkToFTutorialView::VIEW_ID = "org.mitk.views.toftutorial"; QmitkToFTutorialView::QmitkToFTutorialView() : QmitkAbstractView() , m_Controls( nullptr ) { } QmitkToFTutorialView::~QmitkToFTutorialView() { } void QmitkToFTutorialView::CreateQtPartControl( QWidget *parent ) { // build up qt view, unless already done if ( !m_Controls ) { // create GUI widgets from the Qt Designer's .ui file m_Controls = new Ui::QmitkToFTutorialViewControls; m_Controls->setupUi( parent ); connect( m_Controls->step1Button, SIGNAL(clicked()), this, SLOT(OnStep1()) ); connect( m_Controls->step2Button, SIGNAL(clicked()), this, SLOT(OnStep2()) ); } } void QmitkToFTutorialView::SetFocus() { m_Controls->step1Button->setFocus(); } void QmitkToFTutorialView::OnStep1() { // clean up data storage RemoveAllNodesFromDataStorage(); // Create an instance of ToFImageGrabber that holds a ToFCameraMITKPlayerDevice for playing ToF data mitk::ToFImageGrabber::Pointer tofImageGrabber = mitk::ToFImageGrabber::New(); tofImageGrabber->SetCameraDevice(mitk::ToFCameraMITKPlayerDevice::New()); // set paths to test data std::string distanceFileName = MITK_TOF_DATA_DIR; - distanceFileName.append("/PMDCamCube2_MF0_IT0_20Images_DistanceImage.pic"); + distanceFileName.append("/PMDCamCube2_MF0_IT0_20Images_DistanceImage.nrrd"); std::string amplitudeFileName = MITK_TOF_DATA_DIR; - amplitudeFileName.append("/PMDCamCube2_MF0_IT0_20Images_AmplitudeImage.pic"); + amplitudeFileName.append("/PMDCamCube2_MF0_IT0_20Images_AmplitudeImage.nrrd"); std::string intensityFileName = MITK_TOF_DATA_DIR; - intensityFileName.append("/PMDCamCube2_MF0_IT0_20Images_IntensityImage.pic"); + intensityFileName.append("/PMDCamCube2_MF0_IT0_20Images_IntensityImage.nrrd"); // set file name property in image grabber. This will be propagated to the corresponding device and controller class tofImageGrabber->SetProperty("DistanceImageFileName",mitk::StringProperty::New(distanceFileName)); tofImageGrabber->SetProperty("AmplitudeImageFileName",mitk::StringProperty::New(amplitudeFileName)); tofImageGrabber->SetProperty("IntensityImageFileName",mitk::StringProperty::New(intensityFileName)); // connect to device if (tofImageGrabber->ConnectCamera()) { //// start camera (internally starts thread that continuously grabs images from the camera) tofImageGrabber->StartCamera(); // update image grabber which itself represents the source of a MITK filter pipeline tofImageGrabber->Update(); // grab distance image mitk::Image::Pointer distanceImage = tofImageGrabber->GetOutput(); // grab amplitude image mitk::Image::Pointer amplitudeImage = tofImageGrabber->GetOutput(1); // grab intensity image mitk::Image::Pointer intensityImage = tofImageGrabber->GetOutput(2); //add distance image to data storage mitk::DataNode::Pointer distanceNode = mitk::DataNode::New(); distanceNode->SetName("Distance Image"); distanceNode->SetData(distanceImage); this->GetDataStorage()->Add(distanceNode); //add amplitude image to data storage mitk::DataNode::Pointer amplitudeNode = mitk::DataNode::New(); amplitudeNode->SetName("Amplitude Image"); amplitudeNode->SetData(amplitudeImage); this->GetDataStorage()->Add(amplitudeNode); //add intensity image to data storage mitk::DataNode::Pointer intensityNode = mitk::DataNode::New(); intensityNode->SetName("Intensity Image"); intensityNode->SetData(intensityImage); this->GetDataStorage()->Add(intensityNode); // stop camera (terminate internally used thread) tofImageGrabber->StopCamera(); //// disconnect from camera tofImageGrabber->DisconnectCamera(); // adjust views to new data in DataStorage mitk::RenderingManager::GetInstance()->InitializeViews(distanceImage->GetGeometry()); } else { MITK_ERROR<<"Connection to ToF camera could not be established"; } } void QmitkToFTutorialView::OnStep2() { // Check if distance image is available mitk::DataNode::Pointer distanceNode = this->GetDataStorage()->GetNamedNode("Distance Image"); if (distanceNode.IsNotNull()) { // get distance image from node and check if node contains image mitk::Image::Pointer distanceImage = dynamic_cast(distanceNode->GetData()); if (distanceImage.IsNotNull()) { // create object of CameraIntrinsics that holds intrinsic parameters of the ToF camera mitk::CameraIntrinsics::Pointer cameraIntrinsics = mitk::CameraIntrinsics::New(); // set focal length in pixel cameraIntrinsics->SetFocalLength(295.8,296.1); // set principal point in pixel cameraIntrinsics->SetPrincipalPoint(113.2,97.1); // set up filter for surface calculation mitk::ToFDistanceImageToSurfaceFilter::Pointer surfaceFilter = mitk::ToFDistanceImageToSurfaceFilter::New(); // apply intrinsic parameters to filter surfaceFilter->SetCameraIntrinsics(cameraIntrinsics); // set distance between pixels on chip in mm (in this example squared pixel) mitk::ToFProcessingCommon::ToFPoint2D interPixelDistance; interPixelDistance[0] = 0.045; interPixelDistance[1] = 0.045; surfaceFilter->SetInterPixelDistance(interPixelDistance); // set distance image as input surfaceFilter->SetInput(distanceImage); // update the filter surfaceFilter->Update(); // get surface from filter mitk::Surface::Pointer surface = surfaceFilter->GetOutput(); // add surface to data storage mitk::DataNode::Pointer surfaceNode = mitk::DataNode::New(); surfaceNode->SetName("ToF surface"); surfaceNode->SetData(surface); this->GetDataStorage()->Add(surfaceNode); // adjust views to new data in DataStorage mitk::RenderingManager::GetInstance()->InitializeViews(surface->GetGeometry()); mitk::RenderingManager::GetInstance()->InitializeViews(surface->GetGeometry()); } else { QMessageBox::warning(nullptr,"ToF Tutorial","Node 'Distance Image' contains no image"); } } else { QMessageBox::warning(nullptr,"ToF Tutorial","Perform Step 1 first to acquire a distance image"); } } void QmitkToFTutorialView::RemoveAllNodesFromDataStorage() { mitk::DataStorage::SetOfObjects::ConstPointer allNodes = this->GetDataStorage()->GetAll(); this->GetDataStorage()->Remove(allNodes); }