STL includes. More...
Namespaces | |
| namespace | Function |
| namespace | Functor |
| namespace | Statistics |
| namespace | TimeSeriesDatabaseHelper |
Classes | |
| class | AffineImageToImageRegistrationMethod |
| class | AnisotropicSimilarity3DTransform |
| AnisotropicSimilarity3DTransform of a vector space (e.g. space coordinates). More... | |
| class | AnisotropicSimilarityLandmarkBasedTransformInitializer |
| AnisotropicSimilarityLandmarkBasedTransformInitializer is a helper class intended to The class computes the transform that aligns the fixed and moving images given a set of landmarks. The class is templated over the Transform type. The transform computed gives the best fit transform that maps the fixed and moving images in a least squares sense. The indices are taken to correspond, so point 1 in the first set will get mapped close to point 1 in the second set, etc. An equal number of fixed and moving landmarks need to be specified using SetFixedLandmarks() SetMovingLandmarks(). Any number of landmarks may be specified. Call InitializeTransform() to initialize the transform. More... | |
| class | ApplicationBase |
| class | ApplyField |
| class | BOBFFilter |
| class | BRAINSDemonWarp |
| class | BRAINSFitHelper |
| class | BRAINSFitHelperTemplate |
| class | BRAINSROIAutoImageFilter |
| This is a class to help with identifying common tissue Regions in an image. More... | |
| class | BSplineControlPointImageFilter |
| Auxilary class for the output of the class itkBSplineScatteredDataPointSetToImageFilter. More... | |
| class | BSplineImageToImageRegistrationMethod |
| class | CommandIO |
| Read and write the "Nearly Raw Raster Data" (Nrrd) image format. The Nrrd format was developed as part of the Teem package (teem.sourceforge.net). More... | |
| class | CommandIOFactory |
| Create instances of CommandIO objects using an object factory. More... | |
| class | ComputeHistogramQuantileThresholds |
| class | ComputeRestrictedHistogram |
| Compute mean, std, min, and max of positive pixels. More... | |
| class | ComputeStatisticsWherePositiveFilter |
| Compute mean, std, min, and max of positive pixels. More... | |
| class | ConstrainedValueMultiplicationImageFilter |
| Implements pixel-wise the computation of constrained value addition. More... | |
| class | CreateField |
| class | CurveSpatialObject |
| class | CurveToStructuredPlanarMesh |
| class | DecomposedAffine3DTransform |
| DecomposedAffine3DTransform of a vector space (e.g. space coordinates). More... | |
| class | DemonsPreprocessor |
| class | DemonsRegistrator |
| class | DiffeomorphicDemonsRegistrationFilter |
| Deformably register two images using a diffeomorphic demons algorithm. More... | |
| class | DiffeomorphicDemonsRegistrationWithMaskFilter |
| Deformably register two images using a diffeomorphic demons algorithm. More... | |
| class | DifferenceDiffusionTensor3DImageFilter |
| Implements comparison between two DiffusionTensor3D images. More... | |
| class | DiffusionTensor3DAbsCorrectionFilter |
| Computes pixel-wise the absolute value of the diffusion tensor eigenvalues. More... | |
| class | DiffusionTensor3DAffineTransform |
| class | DiffusionTensor3DBSplineInterpolateImageFunction |
| class | DiffusionTensor3DExtended |
| class | DiffusionTensor3DFSAffineTransform |
| class | DiffusionTensor3DInterpolateImageFunction |
| class | DiffusionTensor3DInterpolateImageFunctionReimplementation |
| class | DiffusionTensor3DLinearInterpolateFunction |
| class | DiffusionTensor3DMatrix3x3Transform |
| class | DiffusionTensor3DNearestCorrectionFilter |
| class | DiffusionTensor3DNearestNeighborInterpolateFunction |
| class | DiffusionTensor3DNonRigidTransform |
| class | DiffusionTensor3DPPDAffineTransform |
| class | DiffusionTensor3DRead |
| class | DiffusionTensor3DResample |
| class | DiffusionTensor3DRigidTransform |
| class | DiffusionTensor3DTransform |
| class | DiffusionTensor3DWindowedSincInterpolateImageFunction |
| class | DiffusionTensor3DWrite |
| class | DiffusionTensor3DZeroCorrectionFilter |
| class | DisplacementFieldTransform |
| Number of dimensions. More... | |
| class | DivideByConstantImageFilter |
| Divide input pixels by a constant. More... | |
| class | EMLocalCostFunctionWrapper |
| Optimizes alignment between atlas and segmentation space. More... | |
| class | EncodedTransformFileReader |
| class | EncodedTransformFileWriter |
| class | ESMDemonsRegistrationFunction |
| Fast implementation of the symmetric demons registration force. More... | |
| class | ESMDemonsRegistrationWithMaskFunction |
| Fast implementation of the symmetric demons registration force. More... | |
| class | EulerAnisotropicSimilarity3DTransform |
| EulerAnisotropicSimilarity3DTransform of a vector space (e.g. space coordinates). More... | |
| class | EulerSimilarity3DTransform |
| EulerSimilarity3DTransform of a vector space (e.g. space coordinates). More... | |
| class | ExponentialDeformationFieldImageFilter |
| Computes a diffeomorphic deformation field as the Lie group exponential of a vector field. More... | |
| class | ExponentialDeformationFieldImageFilter2 |
| Computes a diffeomorphic deformation field as the Lie group exponential of a vector field. More... | |
| class | ExtractVolumeFilter |
| class | FastSymmetricForcesDemonsRegistrationFilter |
| Deformably register two images using a symmetric forces demons algorithm. More... | |
| class | FindCenterOfBrainFilter |
| class | FixedRotationSimilarity3DTransform |
| FixedRotationSimilarity3DTransform of a vector space (e.g. space coordinates). More... | |
| struct | GetDimension |
| class | GridForwardWarpImageFilter |
| Warps a grid using an input deformation field. More... | |
| class | GridForwardWarpImageFilterNew |
| Warps a grid using an input deformation field. More... | |
| class | GrowCutSegmentationImageFilter |
| Given a mask image containing the gestures for foreground classes and their background, employs grow cut segmentation to produce segmentation. Supports passing an existing segmentation with additional gestures for editing a segmentation produced as a result of the same or different algorithm. More... | |
| class | HFieldToDeformationFieldImageFilter |
| Computes the Mean Diffusivity for every pixel of a input tensor image. More... | |
| class | ImageRegionMomentsCalculator |
| Compute moments of an n-dimensional image. More... | |
| class | ImageToHexahedronMeshFilter |
| class | ImageToHexahedronMeshSource |
| class | ImageToImageRegistrationHelper |
| class | ImageToImageRegistrationMethod |
| class | ImageToImageRegistrationMethodTestingHelper |
| class | ImageToVTKImageFilter |
| Converts an ITK image into a VTK image and plugs a itk data pipeline to a VTK datapipeline. More... | |
| class | InitialImageToImageRegistrationMethod |
| class | InverseConsistentLandmarkPoint |
| class | InverseConsistentLandmarks |
| class | ItkMeshToFEMMesh |
| class | itkMimxAbaqusMeshFileWriter |
| class | LargestForegroundFilledMaskImageFilter |
| class | LevelTracingImageFilter |
| Trace a level curve/surface given a seed point on the level curve/surface. More... | |
| class | LMMSEVectorImageFilter |
| Applies a Rician Linear Minimum Mean Square Error Filter to an Image. More... | |
| class | LMMSEVectorImageFilterStep |
| Applies a LMMSE filtering for Rician noise removal. More... | |
| class | LogDomainDeformableRegistrationFilter |
| Deformably register two images using a PDE-like algorithm where the transformation is represented as the exponential of a velocity field. More... | |
| class | LogDomainDemonsRegistrationFilter |
| Deformably register two images using a diffeomorphic demons algorithm. More... | |
| class | MaskedMeanImageFilter |
| Applies an averaging filter to an image. More... | |
| class | MatrixExtended |
| class | MeshToMeshFilter |
| MeshToMeshFilter is the base class for all process objects that output Mesh data and require mesh data as input. Specifically, this class defines the SetInput() method for defining the input to a filter. More... | |
| class | MGHImageIO |
| class | MGHImageIOFactory |
| class | MimxImageToVtkUnstructuredGridFilter |
| class | mimxRegisterBSplineFilter |
| class | mimxRegisterVersorRigidFilter |
| class | mimxTransformIO |
| Convience functions for transform I/O. These were required for building on Windows Visual studio because the object sizes from the templated code. More... | |
| class | MRMLIDImageIO |
| ImageIO object for reading and writing imaegs from a MRML scene. More... | |
| class | MRMLIDImageIOFactory |
| Create instances of MRMLIDImageIO objects using an object factory. More... | |
| class | MultiModal3DMutualRegistrationHelper |
| class | MultiModeHistogramThresholdBinaryImageFilter |
| class | MultiplyByConstantImageFilter |
| Multiply input pixels by a constant. More... | |
| class | MultiResolutionLogDomainDeformableRegistration |
| Framework for performing multi-resolution log-domain deformable registration. More... | |
| class | MultiResolutionPDEDeformableRegistration2 |
| Framework for performing multi-resolution PDE deformable registration ( with linear interpolation and NN extrapolation ). More... | |
| class | N3BiasFieldScaleCostFunction |
| class | N3MRIBiasFieldCorrectionImageFilter |
| class | N4MRIBiasFieldCorrectionImageFilter |
| class | NewOtsuThresholdImageCalculator |
| Computes the Otsu's threshold for an image. More... | |
| class | NewOtsuThresholdImageFilter |
| Threshold an image using the Otsu Threshold. More... | |
| class | OppositeImageFilter |
| Take the opposite of the input pixels. More... | |
| class | OptimizedImageToImageRegistrationMethod |
| class | OtsuHistogramMatchingImageFilter |
| Normalize the grayscale values between two image by histogram matching. More... | |
| class | OtsuStatistics |
| Applies a LMMSE filtering for Rician noise removal. More... | |
| class | OtsuThreshold |
| class | ParameterCostFunction |
| class | PluginFilterWatcher |
| Simple mechanism for monitoring the pipeline events of a filter and reporting these events to std::cout. Formats reports with xml. More... | |
| class | Polygon2DSpatialObject |
| class | Polygon3DSpatialObject |
| class | ReadHistogramBinValuesFilter |
| class | RebinHexahedronMeshTraitDataInPlaceFilter |
| class | RigidImageToImageRegistrationMethod |
| class | SeparateComponentsOfADiffusionTensorImage |
| class | SlicerBoxSpatialObject |
| The class may be used to represent N-dimensional boxes. In two dimensions it is a rectangle, In three dimensions it is a cuboid... More... | |
| class | SlicerOutputWindow |
| class | SymmetricLogDomainDemonsRegistrationFilter |
| Deformably register two images using a diffeomorphic demons algorithm and a symmetrized optimization scheme. More... | |
| class | ThirionRegistration |
| class | TimeSeriesDatabase |
| class | TransformAdaptor |
| class | TransformDeformationFieldFilter |
| class | UNLMFilter |
| class | ValidationInputParser |
| class | VBRAINSDemonWarp |
| class | VDemonsPreprocessor |
| class | VDemonsRegistrator |
| class | VectorCentralDifferenceImageFunction |
| Calculate the derivative by central differencing. More... | |
| class | VectorDiffeomorphicDemonsRegistrationFilter |
| class | VectorESMDemonsRegistrationFunction |
| class | VectorImageCastFilter |
| class | VectorLinearInterpolateNearestNeighborExtrapolateImageFunction |
| Linearly interpolate or NN extrapolate a vector image at specified positions. More... | |
| class | VectorMultiResolutionPDEDeformableRegistration |
| Framework for performing multi-resolution PDE deformable registration ( with linear interpolation and NN extrapolation ). More... | |
| class | VelocityFieldBCHCompositionFilter |
| Compute Baker-Campbell-Hausdorff formula on two vector fields. More... | |
| class | VelocityFieldLieBracketFilter |
| Compute the Lie bracket of two vector fields using the formula [v,u](p) = Jac(v)(p).u(p) − Jac(u)(p).v(p) (1). More... | |
| class | VTKImageToImageFilter |
| Converts a VTK image into an ITK image and plugs a vtk data pipeline to an ITK datapipeline. More... | |
| class | VValidationInputParser |
| class | WarpJacobianDeterminantFilter |
| Computes a scalar image from a vector image (e.g., deformation field) input, where each output scalar at each pixel is the Jacobian determinant of the warping at that location. More... | |
| class | WarpSmoothnessCalculator |
| Compute the harmonic energy of a deformation field. More... | |
| class | WarpTransform3D |
Typedefs | |
| typedef itk::AffineTransform < double, 3 > | AffineTransformType |
| typedef itk::FixedArray < double, 2 > | OrderType |
| typedef itk::ScaleSkewVersor3DTransform < double > | ScaleSkewVersor3DTransformType |
| typedef itk::ScaleVersor3DTransform < double > | ScaleVersor3DTransformType |
| typedef itk::VersorRigid3DTransform < double > | VersorRigid3DTransformType |
Functions | |
| void | AddExtraTransformRegister (void) |
| template<class T > | |
| void | AlignVolumeCenters (T *fixed, T *moving, typename T::PointType &origin) |
| VersorRigid3DTransformType::Pointer | ComputeRigidTransformFromGeneric (const GenericTransformType::ConstPointer genericTransformToWrite) |
| A utility function to write ITK compliant transforms to disk in a way that is compliant with the ReadTransformFromDisk. | |
| void | GetImageType (std::string fileName, ImageIOBase::IOPixelType &pixelType, ImageIOBase::IOComponentType &componentType) |
| void | GetImageTypes (std::vector< std::string > fileNames, std::vector< ImageIOBase::IOPixelType > &pixelTypes, std::vector< ImageIOBase::IOComponentType > &componentTypes) |
| itkConceptMacro (OutputOStreamWritableCheck,(Concept::OStreamWritable< OutputImagePixelType >)) | |
| itkConceptMacro (IntConvertibleToInputCheck,(Concept::Convertible< int, InputImagePixelType >)) | |
| itkConceptMacro (SameDimensionCheck,(Concept::SameDimension< InputImageDimension, OutputImageDimension >)) | |
| itkConceptMacro (InputEqualityComparableCheck,(Concept::EqualityComparable< InputImagePixelType >)) | |
| itkConceptMacro (OutputEqualityComparableCheck,(Concept::EqualityComparable< OutputImagePixelType >)) | |
| GenericTransformType::Pointer | ReadTransformFromDisk (const std::string initialTransform) |
| A utility function to read ITK compliant transforms to disk in a way that is compliant with the WriteTransformFromDisk. | |
| template<class IOImageType > | |
| IOImageType::Pointer | SetRigidTransformInPlace (typename VersorRigid3DTransformType::ConstPointer RigidTransform, const IOImageType *InputImage) |
| This templated function will duplicate the input image, change the direction and origin to refelect the physical space tranform that would be equivalent to calling the resample image filter. InplaceImage=SetRigidTransformInPlace(RigidTransform,InputImage); ResampleImage(InplaceImage,Identity); should produce the same result as ResampleImage(InputImage,RigidTransform);. | |
| bool | UNLM_gradientDistance_smaller (OrderType e1, OrderType e2) |
| BRAINSCommonLib_EXPORT void | ValidateTransformRankOrdering (const std::vector< std::string > &transformType) |
| int | WriteBothTransformsToDisk (const GenericTransformType::ConstPointer genericTransformToWrite, const std::string &outputTransform, const std::string &strippedOutputTransform) |
| Special purpose convenience function -- should not have a public interface. | |
| bool | WriteEncodedDoubleVector (std::ostream &out, vnl_vector< double > &VectorBuffer) |
| int | WriteStrippedRigidTransformToDisk (const GenericTransformType::ConstPointer genericTransformToWrite, const std::string &strippedOutputTransform) |
| Special purpose convenience function -- should not have a public interface. | |
| void | WriteTransformToDisk (GenericTransformType const *const genericTransformToWrite, const std::string outputTransform) |
| A utility function to write ITK compliant transforms to disk in a way that is compliant with the ReadTransformFromDisk. | |
STL includes.
ITK includes
vtkITKNumericTraits - Extra itk::NumericTraits instantiations for VTK
vtkITKNumericTraits provides extra instantiations for itk::NumericTraits for VTK scalar types.
| typedef itk::AffineTransform< double, 3 > itk::AffineTransformType |
| typedef itk::FixedArray< double, 2 > itk::OrderType |
| typedef itk::ScaleSkewVersor3DTransform< double > itk::ScaleSkewVersor3DTransformType |
| typedef itk::ScaleVersor3DTransform< double > itk::ScaleVersor3DTransformType |
| typedef itk::VersorRigid3DTransform< double > itk::VersorRigid3DTransformType |
| BRAINSCommonLib_EXPORT void itk::AddExtraTransformRegister | ( | void | ) |
Referenced by BRAINSDemonWarpPrimary(), BRAINSFitIGTPrimary(), BRAINSFitPrimary(), and BRAINSResamplePrimary().
| void itk::AlignVolumeCenters | ( | T * | fixed, | |
| T * | moving, | |||
| typename T::PointType & | origin | |||
| ) | [inline] |
References ImageDimension, j, and slicerget::size.
| BRAINSCommonLib_EXPORT VersorRigid3DTransformType::Pointer itk::ComputeRigidTransformFromGeneric | ( | const GenericTransformType::ConstPointer | genericTransformToWrite | ) |
A utility function to write ITK compliant transforms to disk in a way that is compliant with the ReadTransformFromDisk.
| genericTransformToWrite | A pointer to baseclass itk::Transform<double,3,3> that is polymorphically cast to a real class like (i.e. itk::VersorRigid, itk::Affine, itk::BSpline, or similar) | |
| outputTransform | the filename of the output transform.
//To convert from non-const smart pointers ploymorphically to the smart *ConstPointer up the class tree, use the GetPointer AffineTransformType::Pointer myAffine=AffineTransformType::New(); //NOTE: This is not a const smart pointer WriteTransformToDisk(myAffine.GetPointer(), "myAffineFile.mat"); |
| void itk::GetImageType | ( | std::string | fileName, | |
| ImageIOBase::IOPixelType & | pixelType, | |||
| ImageIOBase::IOComponentType & | componentType | |||
| ) |
Referenced by GetImageTypes(), and main().
| void itk::GetImageTypes | ( | std::vector< std::string > | fileNames, | |
| std::vector< ImageIOBase::IOPixelType > & | pixelTypes, | |||
| std::vector< ImageIOBase::IOComponentType > & | componentTypes | |||
| ) |
References GetImageType().
| itk::itkConceptMacro | ( | OutputOStreamWritableCheck | , | |
| (Concept::OStreamWritable< OutputImagePixelType >) | ||||
| ) |
| itk::itkConceptMacro | ( | IntConvertibleToInputCheck | , | |
| (Concept::Convertible< int, InputImagePixelType >) | ||||
| ) |
| itk::itkConceptMacro | ( | SameDimensionCheck | , | |
| (Concept::SameDimension< InputImageDimension, OutputImageDimension >) | ||||
| ) |
| itk::itkConceptMacro | ( | InputEqualityComparableCheck | , | |
| (Concept::EqualityComparable< InputImagePixelType >) | ||||
| ) |
| itk::itkConceptMacro | ( | OutputEqualityComparableCheck | , | |
| (Concept::EqualityComparable< OutputImagePixelType >) | ||||
| ) |
/** Begin concept checking
| BRAINSCommonLib_EXPORT GenericTransformType::Pointer itk::ReadTransformFromDisk | ( | const std::string | initialTransform | ) |
A utility function to read ITK compliant transforms to disk in a way that is compliant with the WriteTransformFromDisk.
| outputTransform | the filename of the output transform. |
//To convert from non-const smart pointers ploymorphically to the smart *ConstPointer up the class tree, use the GetPointer GenericTransformType::Pointer *myGenericTransform=ReadTransformFromDisk(myAffine.GetPointer(), *"myAffineFile.mat"); VersorRigid3DTransformType::Pointer myVersorRigid3D=NULL; { const std::string transformFileType = myGenericTransform->GetNameOfClass(); if ( transformFileType == "VersorRigid3DTransform" ) { myVersorRigid3D->SetParameters( versorRigid->GetParameters() ); myVersorRigid3D->SetFixedParameters( versorRigid->GetFixedParameters() ); } NOTE: It is more safe to copy parameters into the concrete class rather *than attempting to dynamically cast the base classes. The reason is that the smart pointer management *becomes very unweildy and is hard to keep straight between the pointer that may delete the base *class, and the pointer that is the derived class. }
Referenced by BRAINSFitIGTPrimary(), BRAINSFitPrimary(), and ResampleTransformOrDeformationField().
| IOImageType::Pointer itk::SetRigidTransformInPlace | ( | typename VersorRigid3DTransformType::ConstPointer | RigidTransform, | |
| const IOImageType * | InputImage | |||
| ) | [inline] |
This templated function will duplicate the input image, change the direction and origin to refelect the physical space tranform that would be equivalent to calling the resample image filter. InplaceImage=SetRigidTransformInPlace(RigidTransform,InputImage); ResampleImage(InplaceImage,Identity); should produce the same result as ResampleImage(InputImage,RigidTransform);.
| RigidTransform | -- Currently must be a VersorRigid3D | |
| InputImage | The image to be duplicated and modified to incorporate the rigid transform. |
Wei: The output image will have exact the same index contents but with modified image info so that the index-to-physical mapping makes the image in the physical space AC-PC aligned
| bool itk::UNLM_gradientDistance_smaller | ( | OrderType | e1, | |
| OrderType | e2 | |||
| ) |
| BRAINSCommonLib_EXPORT void itk::ValidateTransformRankOrdering | ( | const std::vector< std::string > & | transformType | ) |
Method for verifying that the ordering of the transformTypes is consistent with converting routines.
Referenced by BRAINSFitIGTPrimary(), and BRAINSFitPrimary().
| BRAINSCommonLib_EXPORT int itk::WriteBothTransformsToDisk | ( | const GenericTransformType::ConstPointer | genericTransformToWrite, | |
| const std::string & | outputTransform, | |||
| const std::string & | strippedOutputTransform | |||
| ) |
Special purpose convenience function -- should not have a public interface.
Referenced by BRAINSFitIGTPrimary(), and BRAINSFitPrimary().
| bool itk::WriteEncodedDoubleVector | ( | std::ostream & | out, | |
| vnl_vector< double > & | VectorBuffer | |||
| ) |
References double().
Referenced by itk::EncodedTransformFileWriter::Update().
| BRAINSCommonLib_EXPORT int itk::WriteStrippedRigidTransformToDisk | ( | const GenericTransformType::ConstPointer | genericTransformToWrite, | |
| const std::string & | strippedOutputTransform | |||
| ) |
Special purpose convenience function -- should not have a public interface.
| BRAINSCommonLib_EXPORT void itk::WriteTransformToDisk | ( | GenericTransformType const *const | genericTransformToWrite, | |
| const std::string | outputTransform | |||
| ) |
A utility function to write ITK compliant transforms to disk in a way that is compliant with the ReadTransformFromDisk.
| genericTransformToWrite | A pointer to baseclass itk::Transform<double,3,3> that is polymorphically cast to a real class like (i.e. itk::VersorRigid, itk::Affine, itk::BSpline, or similar) | |
| outputTransform | the filename of the output transform.
//To convert from non-const smart pointers ploymorphically to the smart *ConstPointer up the class tree, use the GetPointer AffineTransformType::Pointer myAffine=AffineTransformType::New(); //NOTE: This is not a const smart pointer WriteTransformToDisk(myAffine.GetPointer(), "myAffineFile.mat"); |
Referenced by BRAINSFitIGTPrimary().
1.6.1