Namespaces | |
| namespace | Accumulators |
Helper classes that project a series of values into a single value. | |
| namespace | FileUtils |
Utility functions for file and directory access. | |
| namespace | Interpolators |
Interpolation kernels to be used with UniformVolumeInterpolator. | |
| namespace | MathUtil |
| namespace | Memory |
Memory-related helper functions. | |
| namespace | PointSpreadFunctions |
Point spread functions for iterative deblurring. | |
| namespace | Threads |
Thread-related utility functions and global configuration variables. | |
| namespace | Timers |
Namespace that contains functions and variables for CPU time measurements. | |
| namespace | Types |
Define float type used for coordinates. | |
| namespace | Units |
Classes for type-safe values with physical units, and automatic conversions between them. | |
| namespace | Wrappers |
Wrappers for math.h functions. | |
Classes | |
| class | ActiveDeformationModel |
| Active deformation model. More... | |
| class | ActiveShapeModel |
| Class for a three-dimensional active shape model. More... | |
| class | AffineXform |
| 3D affine transformation. More... | |
| class | AffineXformUniformVolume |
| Pre-compute transformation for grid locations in a uniform volume. More... | |
| class | AnatomicalOrientation |
| Class with helper functions for handling anatomical image orientation. More... | |
| class | AnatomicalOrientationBase |
| Base class for handling anatomical image orientation. More... | |
| class | BitVector |
| Set of binary values. More... | |
| class | ControlPoint |
| Class for control points in WarpXform and derived classes. More... | |
| class | ControlPointList |
| List of several warp control points. More... | |
| class | CubicSpline |
| Class computing cubic splines. More... | |
| class | DataGrid |
| Grid topology of data arranged in a 3D lattice. More... | |
| class | DataGridFilter |
| Filter operations for data on 3D grids. More... | |
| class | DataGridMorphologicalOperators |
| Grid topology of data arranged in a 3D lattice. More... | |
| class | DataTypeTraits |
| Data type traits. More... | |
| class | DataTypeTraits< float > |
| Data type traits for single-precision floating point. More... | |
| class | DataTypeTraits< double > |
| Data type traits for double-precision floating point. More... | |
| class | DataTypeTraits< byte > |
| Data type traits for unsigned char (byte). More... | |
| class | DataTypeTraits< char > |
| Data type traits for signed char. More... | |
| class | DataTypeTraits< signed short > |
| Data type traits for signed short. More... | |
| class | DataTypeTraits< unsigned short > |
| Data type traits for unsigned short. More... | |
| class | DataTypeTraits< int > |
| Data type traits for unsigned short. More... | |
| class | DeformationField |
| Class for pixel-wise deformation field. More... | |
| class | DirectionSet |
| A set of directions in n-dimensional space. More... | |
| class | EigenSystemSymmetricMatrix3x3 |
| Compute the eigenvectors and eigenvalues of a symmetric 3x3 matrix. More... | |
| class | FilterMaskPixel |
| Filter mask pixel entry. More... | |
| class | FilterMask |
| Filter mask. More... | |
| class | FilterVolume |
| Class for filtering volume images. More... | |
| class | FixedVector |
| Class for n-dimensional image index. More... | |
| class | FixedVectorStaticInitializer |
| Fixed vector static initializer class template. More... | |
| class | FixedVectorStaticInitializer< 3, T > |
| Fixed vector static initializer class template. More... | |
| class | Functional |
| Class defining a real-valued functional on a multi-dimensional domain. More... | |
| class | GaussianKernel |
| Utility class for generating Gaussian kernels. More... | |
| class | GeneralLinearModel |
| Pixelwise linear modeling and t statistics of data. More... | |
| class | Histogram |
| Histogram of a distribution with bins of arbitrary types. More... | |
| class | HistogramBase |
| Common (non-template) base class for all 1-D histograms. More... | |
| class | HypothesisTests |
| Statistical hypothesis testing between groups of images. More... | |
| class | ImageInterpolator |
| Class template for kernel-based volume interpolators. More... | |
| class | ImageOperation |
| Image operation base class. More... | |
| class | ImageOperationBoundaryMap |
| Image operation: create binary or multi-valued boundary map. More... | |
| class | ImageOperationConnectedComponents |
| Image operation: create connected components map. More... | |
| class | ImageOperationCropRegion |
| Image operation: crop to region. More... | |
| class | ImageOperationCropThreshold |
| Image operation: crop by threshold. More... | |
| class | ImageOperationDistanceMap |
| Compute distance map. More... | |
| class | ImageOperationDownsample |
| Image operation: grid downsampling. More... | |
| class | ImageOperationErodeDilate |
| Image operation: erode or dilate. More... | |
| class | ImageOperationConvertType |
| Image operation: convert data type. More... | |
| class | ImageOperationFlip |
| Image operation: flip. More... | |
| class | ImageOperationGaussFilter |
| Image operation: grid downsampling. More... | |
| class | ImageOperationHistogramEqualization |
| Image operation: histogram equalization with optional number of bins. More... | |
| class | ImageOperationMedialSkeleton |
| Compute medical skeleton of a (binary) mask image. More... | |
| class | ImageOperationMedianFilter |
| Image operation: grid downsampling. More... | |
| class | ImageOperationReplace |
| Image operation: replace image pixel values. More... | |
| class | ImageOperationRevert |
| Image operation: revert binary mask. More... | |
| class | ImageOperationScaleToRange |
| Image operation: scale image values to given range. More... | |
| class | ImageOperationSetPadding |
| Image operation: set padding flag and value. More... | |
| class | ImageOperationThreshold |
| Image operation: thresholding. More... | |
| class | ImageTemplate |
| Uniform volume template. More... | |
| class | Intersection |
| Utility Class for Intersection Computation. More... | |
| class | JointHistogram |
| Joint histogram of two distributions. More... | |
| class | JointHistogramBase |
| Basic (non-template) 2-D histogram functions. More... | |
| class | Landmark |
| Coordinates of an (anatomical) landmark. More... | |
| class | LandmarkList |
| List of landmarks in 3-D. More... | |
| class | LogHistogram |
| Histogram of log intensities. More... | |
| class | MatchedLandmark |
| Matched landmark (landmark with source and target location). More... | |
| class | MatchedLandmarkList |
| List of matched landmarks in 3-D. More... | |
| class | MathUtil |
| General-purpose mathematical functions and function templates. More... | |
| class | Matrix |
| Rekursive matrix template. More... | |
| class | Matrix< TElement, 1 > |
| class | Matrix2D |
| Two-dimensional matrix template. More... | |
| class | Matrix3D |
| Three-dimensional matrix template. More... | |
| class | Matrix3x3 |
| Homogeneous 3x3 transformation matrix. More... | |
| class | Matrix4x4 |
| Homogeneous 4x4 transformation matrix. More... | |
| class | MetaInformationObject |
| Meta-information associated with library objects. More... | |
| class | NumericTraits |
| Base class for numeric traits definition for primitive data types.. More... | |
| class | NumericTraits< char > |
| class | NumericTraits< unsigned char > |
| class | NumericTraits< short > |
| class | ParametricPlane |
| Class for parameterized infinite planes. More... | |
| class | Polynomial |
| Generic class template for polynomials of arbitrary degrees. More... | |
| class | Polynomial< 0, TRealType > |
| Generic class template for polynomials of degree 1. More... | |
| class | Polynomial< 1, TRealType > |
| Generic class template for polynomials of degree 1. More... | |
| class | Polynomial< 2, TRealType > |
| Generic class template for polynomials of degree 2. More... | |
| class | Polynomial< 3, TRealType > |
| Generic class template for polynomials of degree 3. More... | |
| class | Polynomial< 4, TRealType > |
| Generic class template for polynomials of degree 4. More... | |
| class | ProbeInfo |
| Information on volume node data. More... | |
| class | QRDecomposition |
| Compute the QRDecomposition of a matrix. More... | |
| class | Region |
| Class for n-dimensional image index. More... | |
| class | RegionIndexIterator |
| Class for n-dimensional image index. More... | |
| class | ScalarImage |
| Two-dimensional image with scalar pixel values. More... | |
| class | SegmentationLabel |
| A label (class) in a segmentation. More... | |
| class | SplineWarpXform |
| B-spline-based local deformation. More... | |
| class | SplineWarpXformUniformVolume |
| Pre-compute transformation for grid locations in a uniform volume. More... | |
| class | SurfaceNormal |
| Class that computes the surface normal. More... | |
| class | TemplateArray |
| Template for Variable-Typed Data Arrays. More... | |
| class | TransformChangeFromSpaceAffine |
| Compute affine coordinate transformation in standard space from transformation in natrive reference and floating image coordinate spaces. More... | |
| class | TransformChangeToSpaceAffine |
| Compute affine coordinate transformation between native spaces of reference and floating images. More... | |
| class | TransformedVolumeAxes |
| Class that represents pre-transformed axes samples for 3D volumes. More... | |
| class | TypedArray |
| Generic Variable-Typed Data Array. More... | |
| class | TypedArrayFunction |
| Base class for lookup classes. More... | |
| class | TypedArrayFunctionHistogramEqualization |
| Lookup class for histogram equalization. More... | |
| class | TypedArrayFunctionHistogramMatching |
| Lookup class for histogram intensity matching. More... | |
| class | TypedArrayNoiseEstimatorNaiveGaussian |
| Estimate noise level in data stored in a TypedArray. More... | |
| class | UniformDistanceMap |
| Distance map on a uniform grid. More... | |
| class | UniformVolume |
| Uniform volume. More... | |
| class | UniformVolumeFilter |
| Filter operations for 3D uniform image data. More... | |
| class | UniformVolumeInterpolator |
| Class template for kernel-based volume interpolators. More... | |
| class | UniformVolumeInterpolatorBase |
| Base class for kernel-based uniform volume. More... | |
| class | UniformVolumeInterpolatorPartialVolume |
| Partial-volume interpolation class. More... | |
| class | UniformVolumePainter |
| Class for painting in uniform volume objects. More... | |
| class | UnionFind |
| Class template for (relatively) efficient union-find algorithm. More... | |
| class | ValueSequence |
| Class for computing characteristic values of number sequences. More... | |
| class | Vector |
| Numerical vector class. More... | |
| class | Volume |
| General 3D volume. More... | |
| class | VolumeClipping |
| Utility class for volume clipping. More... | |
| class | VolumeGridToGridLookup |
| Class for grid to grid lookup tables. More... | |
| class | WarpXform |
| Common base class for free-form-deformation-based warps. More... | |
| class | Xform |
| General 3D coordinate transformation. More... | |
| class | XformList |
| A transformation list. More... | |
| class | XformListEntry |
| An entry in a transformation sequence. More... | |
| class | XformUniformVolume |
| Pre-compute transformation for grid locations in a uniform volume. More... | |
| class | DeviceArrayTemplate |
| Resource managing class template for type-specific memory allocated on a GPU device through . More... | |
| class | DeviceArrayCUDA |
| Resource managing class for raw memory allocated on a GPU device through CUDA. More... | |
| class | DeviceContextCL |
| Device context wrapper for OpenCL. More... | |
| class | DeviceHistogram |
| Device memory representation of a uniform volume with static helper functions. More... | |
| class | DeviceMemory |
| Resource managing class template for type-specific memory allocated on a GPU device through . More... | |
| class | DeviceMemoryCL |
| Resource managing class for raw memory allocated on a GPU device through OpenCL. More... | |
| class | DeviceMemoryCUDA |
| Resource managing class for raw memory allocated on a GPU device through CUDA. More... | |
| class | DeviceUniformVolume |
| Device memory representation of a uniform volume with static helper functions. More... | |
| class | DeviceUniformVolumeArray |
| Representation of a uniform volume as 3D texture in device memory. More... | |
| class | EntropyMinimizationIntensityCorrectionFunctionalDevice |
| Base class for GPU implementation entropy-minimzation MR bias correction functional using Device. More... | |
| class | ImagePairAffineRegistrationFunctionalDevice |
| Functional for affine registration of two images on the GPU. More... | |
| class | ImageSymmetryPlaneFunctionalDevice |
| Functional for finding a symmetry plane in 3-D volumes using GPU support. More... | |
| class | SimpleLevelsetDevice |
| Class for computing a simple levelset evolution on the GPU. More... | |
| struct | UniformVolumeOnDevice |
| Copy from host to device. More... | |
| class | AffineXformITKIO |
| Class for reading and writing affine transformations from and to ITK's file format. More... | |
| class | ClassStream |
| Class for writing and reading various library classes to and from disk. More... | |
| class | ClassStreamStudyList |
| StudyList with class stream file system interface. More... | |
| class | DICOM |
| Reader/writer class for DICOM images. More... | |
| struct | FileFormatMagic |
| Structure that holds information on magic file number. More... | |
| class | FileFormat |
| Identify file (and directory) formats. More... | |
| class | FileHeader |
| Access to fields in a binary file header. More... | |
| class | ImageOperationApplyMask |
| Apply mask image. More... | |
| class | PGM |
| Reader/writer class for PGM (portable graymap) files. More... | |
| class | ResourceFile |
| Resource file is a map of sections accessed by section title. More... | |
| class | ScalarImageIO |
| Read and write scalar 2d images. More... | |
| class | SplineWarpXformITKIO |
| Class for reading and writing affine transformations from and to ITK's file format. More... | |
| class | SQLite |
| Wrapper class for SQLite database. More... | |
| class | Study |
| Class for parameters of a general imaging study. More... | |
| class | StudyImageSet |
| An imaging study that is constructed from multiple 2-D images. More... | |
| class | StudyList |
| class | TypedStream |
| Class for reading and writing og "typedstream" archives. More... | |
| class | TypedStreamStudylist |
| Studylist with typedstream file system interface. More... | |
| class | VolumeFromFile |
| Class to read uniform volume from disk file(s). More... | |
| struct | FileHeaderBioRad |
| BioRad microscopy image file header. More... | |
| class | VolumeFromSlices |
| Class for building 3D fields from slice image data. More... | |
| class | VolumeFromStudy |
| Class for building 3D volumes from an Study object. More... | |
| class | VolumeIO |
| Class for input/output of 3-D image data. More... | |
| class | XformIO |
| Utility class for one-stop transformation import. More... | |
| class | XformListIO |
| Utility class to generate a list of concatenated transformation objects. More... | |
| class | ArrayFilter |
| Filter class for array inputs. More... | |
| class | Colormap |
| Class representing a configurable (HSV) colormap. More... | |
| class | Drain |
| General data drain template class. More... | |
| class | Filter |
| Basic filter class. More... | |
| class | Image |
| Class for 2D image data. More... | |
| class | ImageEdgeOperator |
| Filter class to apply edge operators to Image objects. More... | |
| class | ImageRGB |
| Class to represent ready-to-display RGB image data. More... | |
| class | ImageToImageRGB |
| Filter to convert image to RGB image using a color lookup table. More... | |
| class | MultiFilter |
| Filter with several inputs. More... | |
| class | Object |
| Base class for all reference counted objects. More... | |
| class | PipelineObject |
| Base class for all reference counted and linked objects. More... | |
| class | Plane |
| Class for 2D planes, that is uniform point meshes. More... | |
| class | PlaneSource |
| Class to generate slicing planes according to volume data. More... | |
| class | Renderer |
| General renderer template class. More... | |
| struct | RGB |
| Red, green, and blue components of one pixel. More... | |
| class | RGBA |
| RGB components plus transparency (alpha value). More... | |
| class | Slicer |
| Reformat slice image from a volume. More... | |
| class | Source |
| General data source object. More... | |
| class | VolumeWrapper |
| Class to encapsulate volume objects. More... | |
| class | QGraphicsPixmapItemEvents |
| Class that derives from Qt's pixmap graphics item and signals events it receives. More... | |
| class | QtIcons |
| Collection of general-purpose icons for Qt applications. More... | |
| class | QtImageOperators |
| A collection of 3D image operators with Qt menu. More... | |
| class | QtProgress |
| Class for interface of progress meter to Qt. More... | |
| class | QtRenderImageRGB |
| Class to render RGB images in Qt. More... | |
| class | QtScrollRenderView |
| Widget that renders an RGB image in a scrolled viewport. More... | |
| class | QtSliderEntry |
| Widget that combines a slider with a numerical entry field and labels. More... | |
| class | QtTriplanarViewer |
| Stand-alone triplanar image viewer. More... | |
| class | QtTriplanarWindow |
| Triplanar image viewer window. More... | |
| class | QtWindowLevelControls |
| Widget for a group box with Window/Level controls. More... | |
| class | QtWindowLevelDialog |
| Dialog with WIndow/Level and Colormap controls. More... | |
| class | DeblurringVolumeReconstruction |
| Class for volume reconstruction using joint iterative deblurring. More... | |
| class | InverseInterpolationVolumeReconstruction |
| Class for volume reconstruction using inverse interpolation. More... | |
| class | InverseInterpolationVolumeReconstructionBase |
| Base class for volume reconstruction using inverse interpolation. More... | |
| class | VolumeInjectionReconstruction |
| Class for volume reconstruction using volume injection. More... | |
| class | AffineMultiChannelRegistrationFunctional |
| Class for affine multi-channel registration functional. More... | |
| class | AffineRegistration |
| Class for affine multi-resolution voxel registration. More... | |
| class | AffineRegistrationCommandLine |
| Class for command line-controlled affine registration. More... | |
| class | BestDirectionOptimizer |
| Optimizer derived from BestNeighbourOptimizer. More... | |
| class | BestNeighbourOptimizer |
| Best-neighbour-search optimizer. More... | |
| class | CongealingFunctional |
| Functional base class for groupwise congealing registration. More... | |
| class | ElasticRegistration |
| Generic multiresolution voxel-registration class. More... | |
| class | ElasticRegistrationCommandLine |
| Class for command line controlled voxel registration. More... | |
| class | FunctionalAffine2D |
| Functional for the affine registration two 2D images. More... | |
| class | GroupwiseRegistrationFunctionalAffineInitializer |
| Affine initialization of groupwise registration functionals. More... | |
| class | GroupwiseRegistrationFunctionalBase |
| Base class for groupwise registration functionals. More... | |
| class | GroupwiseRegistrationFunctionalXformTemplate |
| Trannsformation-dependent class template for groupwise registration functionals. More... | |
| class | GroupwiseRegistrationFunctionalXformTemplate< AffineXform > |
| Template specialization for groupwise affine registration functionals. More... | |
| class | GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform > |
| Template specialization for groupwise nonrigid registration functionals. More... | |
| class | GroupwiseRegistrationFunctionalXformTemplateBase |
| Base class template for groupwise registration functionals. More... | |
| class | GroupwiseRegistrationOutput |
| Class for output of groupwise registration results. More... | |
| class | GroupwiseRegistrationRMIFunctional |
| Functional for groupwise registration. More... | |
| class | ImagePairAffineRegistration |
| Class for affine multi-resolution voxel registration. More... | |
| class | ImagePairAffineRegistrationCommandLine |
| Class for command line-controlled affine registration. More... | |
| class | ImagePairAffineRegistrationFunctional |
| Base-class for affine registration functionals. More... | |
| class | ImagePairAffineRegistrationFunctionalTemplate |
| Functional that evaluates a voxel-based similarity measure. More... | |
| class | ImagePairNonrigidRegistration |
| Generic multiresolution voxel-registration class. More... | |
| class | ImagePairNonrigidRegistrationCommandLine |
| Class for command line controlled voxel registration. More... | |
| class | ImagePairNonrigidRegistrationFunctional |
| Common base class for all elastic registration functionals. More... | |
| class | ImagePairNonrigidRegistrationFunctionalTemplate |
| Parallel elastic registration functional. More... | |
| class | ImagePairRegistration |
| Generic multiresolution voxel-registration class. More... | |
| class | ImagePairRegistrationFunctional |
| Base class for voxel matching functionals. More... | |
| class | ImagePairSimilarityJointHistogram |
| Base class for voxel metrics with pre-converted image data. More... | |
| class | ImagePairSimilarityMeasure |
| Base class for voxel metrics with pre-converted image data. More... | |
| class | ImagePairSimilarityMeasureCR |
| Pairwise image similarity measure "correlation ratio". More... | |
| class | ImagePairSimilarityMeasureMI |
| Base class for voxel metrics with pre-converted image data. More... | |
| class | ImagePairSimilarityMeasureMSD |
| Mean squared difference metric. More... | |
| class | ImagePairSimilarityMeasureNCC |
| Normalized Cross Correlation Metric. More... | |
| class | ImagePairSimilarityMeasureNMI |
| Base class for voxel metrics with pre-converted image data. More... | |
| class | ImagePairSimilarityMeasureRMS |
| Mean squared difference metric. More... | |
| class | ImagePairSymmetricNonrigidRegistrationFunctional |
| Symmtric-consistent elastic registration functional. More... | |
| class | ImagePairSymmetricNonrigidRegistrationFunctionalTemplate |
| Template for symmtric-consistent elastic registration functional. More... | |
| class | ImageSymmetryPlaneCommandLine |
| Class template for symmetry plane computation command line tools. More... | |
| class | ImageSymmetryPlaneCommandLineBase |
| Base class for symmetry plane computation command line tools. More... | |
| class | ImageSymmetryPlaneFunctional |
| Functional for finding a symmetry plane in 3-D volumes. More... | |
| class | ImageSymmetryPlaneFunctionalBase |
| Base class for functionals to find a symmetry plane in 3-D volumes. More... | |
| class | ImageXformDB |
| Class for image and transformation database. More... | |
| class | IterativeDirectionOptimizer |
| Iterative direction optimizer. More... | |
| class | MakeInitialAffineTransformation |
| Class for generating initial affine coordinate transformations between two images. More... | |
| class | MultiChannelHistogramRegistrationFunctional |
| Base class for multi-channel registration functionals using the Histogram metric. More... | |
| class | MultiChannelRegistrationFunctional |
| Base class for multi-channel registration functionals. More... | |
| class | MultiChannelRegistrationFunctionalBase |
| Base class for multi-channel registration functionals. More... | |
| class | MultiChannelRMIRegistrationFunctional |
| Base class for multi-channel registration functionals using the RMI metric. More... | |
| class | MultiLevelOptimizer |
| Multi-level optimizer. More... | |
| class | Optimizer |
| Abstract optimizer. More... | |
| class | OptimizerBase |
| Base class for all optimizers and meta optimizers. More... | |
| class | ParallelElasticFunctional |
| Parallel elastic registration functional. More... | |
| class | ProtocolCallback |
| Callback object with protocol functionality. More... | |
| class | ReformatVolume |
| Utility class for reformatting volume data. More... | |
| class | Registration2d2d |
| Class for registration of two 2D images. More... | |
| class | RegistrationCallback |
| Generic callback class. More... | |
| class | RegistrationDatabaseUpdater |
| Class for updating the image/transformation database with a newly computed registration. More... | |
| class | RegistrationJointHistogram |
| 2-D histogram for entropy-based image similarity measures. More... | |
| class | ScalarImageSimilarityMemory |
| Memory for image similarity computation. More... | |
| class | ScalarImageSimilarity |
| Class with operators to compute various 2-D image similarity measures. More... | |
| class | ScaleHistogramValueTrait |
| Histogram kernel scaling traits. More... | |
| class | ScaleHistogramValueTrait< int > |
| class | ScaleHistogramValueTrait< unsigned int > |
| class | SearchTrace |
| Class for traces in the optimization search space. More... | |
| class | SplineWarpCongealingFunctional |
| Functional for spline warp congealing. More... | |
| class | SplineWarpGroupwiseRegistrationRMIFunctional |
| Functional for spline warp groupwise registration. More... | |
| class | SplineWarpMultiChannelIntensityCorrectionRegistrationFunctional |
| Class for spline warp multi-channel registration functional. More... | |
| class | SplineWarpMultiChannelRegistrationFunctional |
| Class for spline warp multi-channel registration functional. More... | |
| class | SymmetricElasticFunctional |
| Symmtric-consistent elastic registration functional. More... | |
| class | SymmetricElasticFunctional_Template |
| Template for symmtric-consistent elastic registration functional. More... | |
| class | SymmetryPlaneFunctional |
| Functional for finding a symmetry plane in 3-D volumes. More... | |
| class | TemplateMultiChannelRegistrationFunctional |
| Class for transformation-templated multi-channel registration functional. More... | |
| class | TypedArraySimilarity |
| Class with operators to compute various pixel similarity measures. More... | |
| class | TypedArraySimilarityMemory |
| Memory for typed array similarity computation. More... | |
| class | VoxelMatchingAffineFunctional |
| Base-class for affine registration functionals. More... | |
| class | VoxelMatchingAffineFunctionalTemplate |
| Functional that evaluates a voxel-based similarity measure. More... | |
| class | VoxelMatchingCorrRatio |
| Voxel metric "correlation ratio". More... | |
| class | VoxelMatchingCrossCorrelation |
| Normalized Cross Correlation Metric. More... | |
| class | VoxelMatchingElasticFunctional |
| Common base class for all elastic registration functionals. More... | |
| class | VoxelMatchingElasticFunctional_WarpTemplate |
| Template class for elastic registration functional. More... | |
| class | VoxelMatchingElasticFunctional_Template |
| Functional that evaluates a voxel-based similarity measure. More... | |
| class | VoxelMatchingFunctional |
| Base class for voxel matching functionals. More... | |
| class | VoxelMatchingFunctional_Template |
| Functional that evaluates a voxel-based similarity measure. More... | |
| class | VoxelMatchingMeanSquaredDifference |
| Mean squared difference metric. More... | |
| class | VoxelMatchingMetric |
| Base class for voxel metrics with pre-converted image data. More... | |
| class | VoxelMatchingMetric_Type |
| Base class for voxel metrics with pre-converted image data. More... | |
| class | VoxelMatchingMutInf |
| Voxel metric "mutual information". More... | |
| class | VoxelMatchingNormMutInf |
| Voxel metric "normalized mutual information". More... | |
| class | VoxelRegistration |
| Generic multiresolution voxel-registration class. More... | |
| class | AtlasSegmentation |
| class | EntropyMinimizationIntensityCorrectionFunctional |
| Functional to correct MR intensity bias by miniming image entropy. More... | |
| class | EntropyMinimizationIntensityCorrectionFunctionalBase |
| Base class for entropy-minimzation MR bias correction functional. More... | |
| class | LabelCombinationMultiClassSTAPLE |
| Multi-class STAPLE label combination. More... | |
| class | LabelCombinationSTAPLE |
| Binary STAPLE label combination. More... | |
| class | LabelCombinationVoting |
| Label voting image combination. More... | |
| class | OverlapMeasures |
| Class for overlap measures between multiple segmentations. More... | |
| class | SimpleLevelset |
| Class for computing a simple two-phase levelset evolution. More... | |
| class | SimpleLevelsetCommandLine |
| Command line interface class template for simple levelset segmentation with a particular implementation (CPU or GPU). More... | |
| class | SimpleLevelsetCommandLineBase |
| Command line interface base class for simple levelset segmentation. More... | |
| class | CannotBeCopied |
| Base class to prevent copying of derived classes. More... | |
| class | CommandLine |
| Command line argument parser. More... | |
| class | CommandLineTypeTraitsBase |
| class | CommandLineTypeTraits |
| Template for traits to handle command line arguments of different types. More... | |
| class | CommandLineTypeTraits< const char * > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< std::string > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< std::vector< std::string > > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< int > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< unsigned int > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< short > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< unsigned short > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< signed char > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< unsigned char > |
| class | CommandLineTypeTraits< float > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< double > |
| Inherit generic template members. More... | |
| class | CommandLineTypeTraits< bool > |
| Inherit generic template members. More... | |
| class | CompressedStream |
| Stream with on-the-fly decompression. More... | |
| class | ConditionVariable |
| Condition variable for thread synchronization. More... | |
| class | Console |
| Standard error output console for library. More... | |
| class | Exception |
| Exception class. More... | |
| class | ExitException |
| Program exit exception class. More... | |
| class | LockingPtr |
| Class for mutually exclusive access to objects. More... | |
| class | MountPoints |
| Directory translation. More... | |
| class | MutexLock |
| Generic mutex lock. More... | |
| class | Progress |
| Generic class for progress indication. More... | |
| class | ProgressConsole |
| Progress indicator with console output. More... | |
| class | SafeCounter |
| Thread-safe counter. More... | |
| class | SmartConstPointer |
| Smart pointer with reference counting. More... | |
| class | SmartPointer |
| Smart pointer with reference counting. More... | |
| class | StackBacktrace |
| Class for printing stack backtrace in the event of a crash. More... | |
| class | TestFunctionMap |
| Map from test name to test function. More... | |
| class | ThreadParameterArray |
| Array of thread parameters. More... | |
| class | ThreadParameters |
| Base class for thread parameter blocks. More... | |
| class | ThreadPool |
| Class that provides a pool of continuously running threads that can be used for reducing overhead in SMP computations. More... | |
| class | ThreadSemaphore |
| Semaphore for thread synchronization. More... | |
| class | TypedArrayNoiseEstimatorBrummer |
| Estimate noise level in data stored in a TypedArray. More... | |
| class | TypedArrayNoiseEstimatorMaximumLikelihood |
| Estimate noise level in data stored in a TypedArray. More... | |
Typedefs | |
| typedef ActiveDeformationModel < SplineWarpXform > | SplineActiveDeformationModel |
| Spline warp active deformation model. | |
| typedef Matrix3x3 < Types::Coordinate > | CoordinateMatrix3x3 |
| Define coordinate matrix. | |
| typedef std::map< int, SegmentationLabel > | SegmentationLabelMap |
| Map from numerical IDs to labels. | |
| typedef Vector< Types::Coordinate > | CoordinateVector |
| Shortcut definition. | |
| typedef Vector< float > | FloatVector |
| Shortcut definition. | |
| typedef FixedVector < 3, Types::Coordinate > | Vector3D |
| Convenience typedef: vectors in 3D coordinate space. | |
| typedef DeviceArrayTemplate < DeviceArrayCL > | DeviceArray |
| typedef std::list< std::string > | ResourceSection |
| Resource file section is a list of strings. | |
| typedef std::multimap < Study::SmartPtr, Xform::SmartPtr > | StudyToXform |
| typedef std::map < Study::SmartPtr, StudyToXform > | StudyToStudyToXform |
| typedef CongealingFunctional < AffineXform > | AffineCongealingFunctional |
| Functional for affine congealing. | |
| typedef GroupwiseRegistrationRMIFunctional < AffineXform > | AffineGroupwiseRegistrationRMIFunctional |
| Functional for affine groupwise registration using "RMI" metric. | |
| typedef VoxelMatchingCorrRatio < Interpolators::LINEAR > | VoxelMatchingCorrRatio_Trilinear |
| Correlation ratio with trilinear interpolation. | |
| typedef VoxelMatchingCorrRatio < Interpolators::NEAREST_NEIGHBOR > | VoxelMatchingCorrRatio_NearestNeighbor |
| Correlation ratio with nearest-neighbor interpolation. | |
| typedef VoxelMatchingMetric < short, TYPE_SHORT > | VoxelMatchingMetricShort |
| Convenience typedef. | |
| typedef VoxelMatchingMetric < byte, TYPE_BYTE > | VoxelMatchingMetricByte |
| Convenience typedef. | |
| typedef VoxelMatchingMetric < short, TYPE_SHORT, Interpolators::NEAREST_NEIGHBOR > | VoxelMatchingMetricShort_NN |
| Convenience typedef. | |
| typedef VoxelMatchingMetric < byte, TYPE_BYTE, Interpolators::NEAREST_NEIGHBOR > | VoxelMatchingMetricByte_NN |
| Convenience typedef. | |
| typedef VoxelMatchingMutInf < Interpolators::LINEAR > | VoxelMatchingMutInf_Trilinear |
| Mutual information with trilinear interpolation. | |
| typedef VoxelMatchingMutInf < Interpolators::NEAREST_NEIGHBOR > | VoxelMatchingMutInf_NearestNeighbor |
| Mutual information with nearest-neighbor interpolation. | |
| typedef VoxelMatchingNormMutInf < Interpolators::LINEAR > | VoxelMatchingNormMutInf_Trilinear |
| Normalized mutual information with trilinear interpolation. | |
| typedef VoxelMatchingNormMutInf < Interpolators::NEAREST_NEIGHBOR > | VoxelMatchingNormMutInf_NearestNeighbor |
| Normalized mutual information with nearest-neighbor interpolation. | |
| typedef int | ThreadIDType |
| Dummy definition for non-threading builds. | |
| typedef CMTK_THREAD_RETURN_TYPE(* | ThreadFunction )(CMTK_THREAD_ARG_TYPE) |
| Type of thread function. | |
Shortcut class typedefs for typed arrays. | |
| typedef TemplateArray< byte > | ByteArray |
| Array of (unsigned) byte values. | |
| typedef TemplateArray< char > | CharArray |
| Array of (signed) char values. | |
| typedef TemplateArray< short > | ShortArray |
| Array of signed short values. | |
| typedef TemplateArray < unsigned short > | UShortArray |
| Array of unsigned short values. | |
| typedef TemplateArray< int > | IntArray |
| Array of (signed) integer values. | |
| typedef TemplateArray< float > | FloatArray |
| Array of single-precision float values. | |
| typedef TemplateArray< double > | DoubleArray |
| Array of double-precision float values. | |
Enumerations | |
| enum | { AXIS_X = 0, AXIS_Y = 1, AXIS_Z = 2 } |
Identifiers for coordinate axes. More... | |
| enum | DataClass { DATACLASS_GREY, DATACLASS_LABEL, DATACLASS_UNKNOWN } |
Class of image data. More... | |
| enum | ScalarDataType { TYPE_BYTE = 0, TYPE_CHAR = 1, TYPE_SHORT = 2, TYPE_USHORT = 3, TYPE_INT = 4, TYPE_UINT = 5, TYPE_FLOAT = 6, TYPE_DOUBLE = 7, TYPE_NONE = -1 } |
Scalar data type identifiers. More... | |
| enum | AnalyzeDataType { ANALYZE_TYPE_NONE = 0, ANALYZE_TYPE_BINARY = 1, ANALYZE_TYPE_UNSIGNED_CHAR = 2, ANALYZE_TYPE_SIGNED_SHORT = 4, ANALYZE_TYPE_SIGNED_INT = 8, ANALYZE_TYPE_FLOAT = 16, ANALYZE_TYPE_COMPLEX = 32, ANALYZE_TYPE_DOUBLE = 64, ANALYZE_TYPE_RGB = 128, ANALYZE_TYPE_USHORT = 132, ANALYZE_TYPE_UINT = 136, ANALYZE_TYPE_ALL = 255 } |
IDs for data types in Analyze image file. More... | |
| enum | AnalyzeOrientation { ANALYZE_AXIAL = 0, ANALYZE_CORONAL = 1, ANALYZE_SAGITTAL = 2, ANALYZE_AXIAL_FLIP = 3, ANALYZE_CORONAL_FLIP = 4, ANALYZE_SAGITTAL_FLIP = 5, ANALYZE_UNKNOWN = 255 } |
IDs for slice orientations in Analyze image file. More... | |
| enum | FileFormatID { FILEFORMAT_NEXIST = 0, FILEFORMAT_COMPRESSED_ARCHIVE = 1, FILEFORMAT_STUDY = 2, FILEFORMAT_STUDYLIST = 3, FILEFORMAT_TYPEDSTREAM = 4, FILEFORMAT_PGM = 5, FILEFORMAT_DICOM = 6, FILEFORMAT_VANDERBILT = 7, FILEFORMAT_AMIRA = 8, FILEFORMAT_RAW = 9, FILEFORMAT_RAW3D = 10, FILEFORMAT_BIORAD = 11, FILEFORMAT_NIFTI_DETACHED = 12, FILEFORMAT_NIFTI_SINGLEFILE = 13, FILEFORMAT_ANALYZE_AVW = 14, FILEFORMAT_METAIMAGE = 15, FILEFORMAT_NRRD = 16, FILEFORMAT_ANALYZE_HDR = 17, FILEFORMAT_ANALYZE_HDR_BIGENDIAN = 18, FILEFORMAT_ITK_TFM = 19, FILEFORMAT_UNKNOWN } |
ID codes for known file formats. More... | |
| enum | { PALETTE_GRAY = 0, PALETTE_RED = 1, PALETTE_GREEN = 2, PALETTE_BLUE = 3, PALETTE_RAINBOW = 4, PALETTE_LABELS = 5 } |
Constants to identify color table. More... | |
| enum | ImageAlphaToggle { IMAGE_RGB, IMAGE_RGBA } |
Type definition for the status of the alpha-channel presence flag. More... | |
| enum | CallbackResult { CALLBACK_OK = 0, CALLBACK_INTERRUPT = 1, CALLBACK_TIMEOUT = 2, CALLBACK_FAILED = 3 } |
Status code returned by Execute() methods. More... | |
TypedStream.h | |
| enum | TypedStreamMode { TYPEDSTREAM_READ, TYPEDSTREAM_WRITE, TYPEDSTREAM_WRITE_ZLIB, TYPEDSTREAM_APPEND } |
Access modes for archives. More... | |
| enum | TypedStreamCondition { TYPEDSTREAM_ERROR, TYPEDSTREAM_OK } |
Condition upon function return. More... | |
| enum | TypedStreamStatus { TYPEDSTREAM_ERROR_NONE, TYPEDSTREAM_ERROR_UNKNOWN, TYPEDSTREAM_ERROR_SYSTEM, TYPEDSTREAM_ERROR_FORMAT, TYPEDSTREAM_ERROR_ARG, TYPEDSTREAM_ERROR_MODE, TYPEDSTREAM_ERROR_TYPE, TYPEDSTREAM_ERROR_LIMIT, TYPEDSTREAM_ERROR_LEVEL, TYPEDSTREAM_ERROR_INVALID, TYPEDSTREAM_ERROR_MAX } |
Classes of error conditions. More... | |
| enum | TypedStreamType { TYPEDSTREAM_TYPE_INT, TYPEDSTREAM_TYPE_BOOL, TYPEDSTREAM_TYPE_BINARYBOOL, TYPEDSTREAM_TYPE_FLOAT, TYPEDSTREAM_TYPE_DOUBLE, TYPEDSTREAM_TYPE_STRING } |
Identifiers for supported primitive data types. More... | |
| enum | TypedStreamToken { TYPEDSTREAM_EOF, TYPEDSTREAM_BEGIN, TYPEDSTREAM_END, TYPEDSTREAM_KEY, TYPEDSTREAM_VALUE, TYPEDSTREAM_COMMENT } |
Identifiers for tokens in archives. More... | |
| enum | TypedStreamDebugFlag { TYPEDSTREAM_DEBUG_OFF, TYPEDSTREAM_DEBUG_ON } |
Debug flag values. More... | |
Functions | |
| void | printBlock (Types::DataItem block[COUPE_BLOCK_SIZE]) |
| template<size_t NDIM, typename T > | |
| const FixedVector< NDIM, T > | operator+ (const FixedVector< NDIM, T > &lhs, const FixedVector< NDIM, T > &rhs) |
| Addition operator. | |
| template<size_t NDIM, typename T > | |
| const FixedVector< NDIM, T > | operator- (const FixedVector< NDIM, T > &lhs, const FixedVector< NDIM, T > &rhs) |
| Subtraction operator. | |
| template<size_t NDIM, typename T > | |
| T | operator* (const FixedVector< NDIM, T > &lhs, const FixedVector< NDIM, T > &rhs) |
| Scalar product operator. | |
| template<size_t NDIM, typename T , typename T2 > | |
| const FixedVector< NDIM, T > | operator* (const T2 lhs, const FixedVector< NDIM, T > &rhs) |
| Scalar multiplication operator. | |
| template<size_t NDIM, typename T > | |
| std::ofstream & | operator<< (std::ofstream &stream, const FixedVector< NDIM, T > &index) |
| Stream input operator. | |
| template<size_t NDIM, typename T > | |
| std::ifstream & | operator>> (std::ifstream &stream, FixedVector< NDIM, T > &index) |
| Stream output operator. | |
| template<class T > | |
| Console & | operator<< (Console &stream, const Matrix3x3< T > &m) |
| Output object to console. | |
| template<class T , class T2 > | |
| FixedVector< 3, T2 > & | operator*= (FixedVector< 3, T2 > &u, const Matrix4x4< T > &M) |
| In-place multiplication with 3d vector operation (will implicitly be made homogeneous). | |
| template<class T , class T2 > | |
| FixedVector< 3, T2 > | operator* (const FixedVector< 3, T2 > &u, const Matrix4x4< T > &M) |
| Multiplication with 3d vector operation (will implicitly be made homogeneous). | |
| template<class T > | |
| Console & | operator<< (Console &stream, const Matrix4x4< T > &m) |
| Output object to console. | |
| template<size_t NDIM, typename T > | |
| std::ofstream & | operator<< (std::ofstream &stream, const Region< NDIM, T > ®ion) |
| Stream input operator. | |
| template<size_t NDIM, typename T > | |
| std::ifstream & | operator>> (std::ifstream &stream, Region< NDIM, T > ®ion) |
| Stream output operator. | |
| ScalarImage * | operator- (const ScalarImage &image0, const ScalarImage &image1) |
| void | CreateSystemLabelColorMap (SegmentationLabelMap &map) |
| Create system label map. | |
| DataClass | StringToDataClass (const char *dataClassStr) |
| Convert string to data class identifier. | |
| const char * | DataClassToString (const DataClass dataClass) |
| Convert data class identifier to string. | |
| size_t | TypeItemSize (const ScalarDataType dtype) |
| Return item size for given scalar data type. | |
| ScalarDataType | SelectDataTypeInteger (const byte itemSize, const bool signBit) |
| Select integer data type based on item size and sign bit. | |
| ScalarDataType | GetSignedDataType (const ScalarDataType dtype) |
| Return signed datatype ID corresponding to given datatype. | |
| ScalarDataType | GetDifferenceDataType (const ScalarDataType dtype1, const ScalarDataType dtype2) |
| Return difference datatype ID for given pair of datatypes. | |
| ScalarDataType | GetUnsignedDataType (const ScalarDataType dtype) |
| Return unsigned datatype ID corresponding to given datatype. | |
| template<class T > | |
| ValueSequence< T > | operator+ (const ValueSequence< T > &a, const ValueSequence< T > &b) |
| template<class T > | |
| Vector< T > | operator+ (const Vector< T > &p, const Vector< T > &delta) |
| Vector addition operator. | |
| template<class T > | |
| Vector< T > | operator- (const Vector< T > &p, const Vector< T > &delta) |
| Vector subtraction operator. | |
| template<class T > | |
| Vector< T > | operator* (const T c, const Vector< T > &p) |
| Scalar-to-vector multiplication operator. | |
| template<class T > | |
| Vector< T > | CoordMult (const Vector< T > &p, const Vector< T > &q) |
| Coordinatewise multiplication operator. | |
| template<class T > | |
| T | operator* (const Vector< T > &p, const Vector< T > &q) |
| Scalar product. | |
| void | DeviceImageConvolution (float *dest, const int *dims3, void *array, const int kernelLengthX, const float *kernelX, const int kernelLengthY, const float *kernelY, const int kernelLengthZ, const float *kernelZ) |
| Convolution of a 3D image (CUDA array) with a separable 3D kernel. | |
| void | DeviceImageConvolutionInPlace (const int *dims3, void *array, const int kernelLengthX, const float *kernelX, const int kernelLengthY, const float *kernelY, const int kernelLengthZ, const float *kernelZ) |
| In-place convolution of a 3D image (CUDA array) with a separable 3D kernel. | |
| void | DeviceThresholdData (float *dest, const int n, const float lowerThreshold, const float upperThreshold) |
| Threshold data on device. | |
| template<unsigned int NDegreeMul> | |
| EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr | CreateEntropyMinimizationIntensityCorrectionFunctionalDevice (const unsigned int polynomialDegreeAdd) |
| Create functional templated over polynomial degrees. | |
| EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr | CreateEntropyMinimizationIntensityCorrectionFunctionalDevice (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul) |
| Create functional templated over polynomial degrees. | |
| EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr | CreateEntropyMinimizationIntensityCorrectionFunctionalDevice (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul, EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr oldFunctional) |
| Create functional templated over polynomial degrees with initialization from old functional. | |
| void | EntropyMinimizationIntensityCorrectionFunctionalDeviceUpdateOutputImage (float *output, float *input, const int dims0, const int dims1, const int dims2, const int degree, const int multiply, const int nargs, const float *weights, const float *corrections) |
| Update output image using either additive or multiplicative bias field. | |
| float | ImagePairAffineRegistrationFunctionalDeviceEvaluateMSD (const int *fixedDims3, void *fixedArray, const int *movingDims3, void *movingArray, const float matrix[4][4]) |
| Evaluate Mean Squared Difference for symmetry plane computation on GPU. | |
| void | SimpleLevelsetDeviceUpdateInsideOutside (float *levelset, float *volume, const int nPixels, float *insideSum, float *outsideSum, int *nInside) |
| Count inside pixels and compute the sums of inside and outside pixels. | |
| void | SimpleLevelsetDeviceUpdateLevelset (float *levelset, float *volume, const int nPixels, const float mInside, const float mOutside, const float ratioInOut, const float timeDelta, const float levelsetThreshold) |
| Update levelset based on mean values in inside and outside regions, then threshold the result. | |
| template<class T > | |
| T | SumReduction (T *data, const int n) |
| Compute sum reduction of data. | |
| ClassStream & | operator<< (ClassStream &stream, const AffineXform &affineXform) |
| Write affine transformation object. | |
| ClassStream & | operator>> (ClassStream &stream, AffineXform::SmartPtr &affineXform) |
| Read affine transformation. | |
| ClassStream & | operator>> (ClassStream &stream, AffineXform &affineXform) |
| Read affine transformation. | |
| template<class TMetricFunctionalType > | |
| ClassStream & | operator<< (ClassStream &stream, const AffineMultiChannelRegistrationFunctional< TMetricFunctionalType > &functional) |
| Write file names and transformations from affine multi-channel registration functional. | |
| template<class TMetricFunctionalType > | |
| ClassStream & | operator>> (ClassStream &stream, AffineMultiChannelRegistrationFunctional< TMetricFunctionalType > &functional) |
| Read file names and transformations from archive to multi-channel affine registration functional. | |
| template<class TMetricFunctionalType > | |
| ClassStream & | operator<< (ClassStream &stream, const SplineWarpMultiChannelRegistrationFunctional< TMetricFunctionalType > &functional) |
| Write file names and transformations from spline warp multi-channel registration functional. | |
| ClassStream & | operator<< (ClassStream &stream, const Xform &xform) |
| Write transformation object. | |
| ClassStream & | operator<< (ClassStream &stream, const GroupwiseRegistrationFunctionalBase &func) |
| ClassStream & | operator>> (ClassStream &stream, GroupwiseRegistrationFunctionalBase &func) |
| std::istream & | operator>> (std::istream &stream, SegmentationLabelMap &lblMap) |
| Operator to read a list of label IDs from a C++ stream. | |
| ClassStream & | operator<< (ClassStream &stream, const GroupwiseRegistrationFunctionalXformTemplate< AffineXform > &func) |
| ClassStream & | operator>> (ClassStream &stream, GroupwiseRegistrationFunctionalXformTemplate< AffineXform > &func) |
| ClassStream & | operator<< (ClassStream &stream, const GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform > &func) |
| ClassStream & | operator>> (ClassStream &stream, GroupwiseRegistrationFunctionalXformTemplate< SplineWarpXform > &func) |
| SymmetricElasticFunctional * | CreateSymmetricElasticFunctional (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume) |
| Constructor function. | |
| VoxelMatchingElasticFunctional * | CreateElasticFunctional (const int metric, UniformVolume::SmartPtr &refVolume, UniformVolume::SmartPtr &fltVolume) |
| Create functional from matching template. | |
| template<unsigned int NDegreeMul> | |
| EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr | CreateEntropyMinimizationIntensityCorrectionFunctional (const unsigned int polynomialDegreeAdd) |
| Create functional templated over polynomial degrees. | |
| EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr | CreateEntropyMinimizationIntensityCorrectionFunctional (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul) |
| Create functional templated over polynomial degrees. | |
| EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr | CreateEntropyMinimizationIntensityCorrectionFunctional (const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul, EntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr oldFunctional) |
| Create functional templated over polynomial degrees with initialization from old functional. | |
| Console & | operator<< (Console &console, CommandLine::Exception e) |
| Output of command line exception. | |
| template<> | |
| std::vector< std::string > | CommandLine::Item::Convert< std::vector< std::string > > (const char *str) |
| Convert string to vector. | |
| const char * | cmtkWhitespaceWriteMiniXML (mxml_node_t *, int where) |
| Console & | operator<< (Console &console, Exception e) |
| Output of command line exception. | |
| int | StrCmp (const char *s1, const char *s2) |
| Safe string comparison. | |
| void | StrReplace (char *&s1, const char *s2) |
| Replace a string. | |
| void | StrFree (char *const s) |
| Safe deallocation of strings. | |
| int | StrPrefixCmp (const char *s, const char *prefix) |
| Compare string prefix. | |
| const char * | StrDir (const char *path) |
| Extract directory component from a complete filesystem path. | |
| const char * | StrFName (const char *path) |
| Extract filename component from a complete filesystem path. | |
| std::string | StrReplace (const std::string &str, const std::map< std::string, std::string > &rules, const bool multiple=false) |
| Replace string components. | |
Variables | |
| const char *const | META_FS_PATH = "FILESYSTEM_PATH" |
| const char *const | META_FILEFORMAT_ORIGINAL = "FILEFORMAT_ORIGINAL" |
| const char *const | META_SPACE = "SPACE" |
| const char *const | META_SPACE_ORIGINAL = "SPACE_ORIGINAL" |
| const char *const | META_SPACE_UNITS_STRING = "SPACE_UNITS_STRING" |
| const char *const | META_EXTERNAL_SPACE_ID = "SPACE_ID_EXTERNAL" |
| const char *const | META_IMAGE_ORIENTATION = "IMAGE_ORIENTATION" |
| const char *const | META_IMAGE_ORIENTATION_ORIGINAL = "IMAGE_ORIENTATION_ORIGINAL" |
| const char *const | META_IMAGE_DIRECTION_VECTORS = "IMAGE_DIRECTION_VECTORS" |
| const char *const | META_XFORM_FIXED_IMAGE_PATH = "XFORM_FIXED_IMAGE_PATH" |
| const char *const | META_XFORM_MOVING_IMAGE_PATH = "XFORM_MOVING_IMAGE_PATH" |
| const char * | DataClassString [] |
| const char * | DataTypeName [] |
| Names of scalar data types. | |
| const ScalarDataType | TYPE_ITEM = TYPE_DOUBLE |
| const ScalarDataType | TYPE_COORDINATE = TYPE_DOUBLE |
| static StackBacktrace | StackBacktraceInstance |
| const FileFormatMagic | FileFormatMagicNumbers [] |
| Magic number records for known file types. | |
| const char * | FileFormatName [] |
| Table of file format ID names. | |
| const char *const | CMTK_LEGACY_ANALYZE_IO = "CMTK_LEGACY_ANALYZE_IO" |
| Environment variable that turns on legacy Analyze I/O with incorrect anatomical orientations. | |
| const char *const | IGS_LEGACY_ANALYZE_IO = "IGS_LEGACY_ANALYZE_IO" |
| Legacy environment variable that turns on legacy Analyze I/O with incorrect anatomical orientations. | |
| const char *const | CMTK_LEGACY_WRITE_IMAGES_RAS = "CMTK_LEGACY_WRITE_IMAGES_RAS" |
| Environment variable that turns off writing output images in the array order of the input images. | |
| static bool | InterruptSignalReceived |
| Flag that is set upon SIGINT signal. | |
| Console | StdErr (std::cerr) |
| Standard error output for the library. | |
| Console | StdOut (std::cout) |
| Standard output for the library. | |
| const char *const | CMTK_MOUNTPOINTSVAR = "CMTK_MOUNTPOINTS" |
| Name of the shell variable defining the directory translation. | |
| const char *const | IGS_MOUNTPOINTSVAR = "IGS_MOUNTPOINTS" |
| Legacy environment variable. | |
| static char | StrBuffer [PATH_MAX] |
igsCurrentTime | |
Static counter representing the current (discrete) processing time. This variable is incremented with every query using Object::GetCurrentTime(). Direct access MUST NOT occur in order to prevent inconsistent object times.
| |
| long | CurrentTime = 1 |
| void cmtk::EntropyMinimizationIntensityCorrectionFunctionalDeviceUpdateOutputImage | ( | float * | output, |
| float * | input, | ||
| const int | dims0, | ||
| const int | dims1, | ||
| const int | dims2, | ||
| const int | degree, | ||
| const int | multiply, | ||
| const int | nargs, | ||
| const float * | weights, | ||
| const float * | corrections | ||
| ) |
Update output image using either additive or multiplicative bias field.
Referenced by cmtk::EntropyMinimizationIntensityCorrectionFunctionalDevice< NOrderAdd, NOrderMul >::UpdateOutputImageDevice().
| float cmtk::ImagePairAffineRegistrationFunctionalDeviceEvaluateMSD | ( | const int * | fixedDims3, |
| void * | fixedArray, | ||
| const int * | movingDims3, | ||
| void * | movingArray, | ||
| const float | matrix[4][4] | ||
| ) |
Evaluate Mean Squared Difference for symmetry plane computation on GPU.
| fixedDims3 | Fixed volume dimensions |
| fixedArray | Device array with fixed volume data |
| movingDims3 | Movingvolume dimensions |
| movingArray | Device array with moving volume data |
| matrix | Mirror matrix: from index to image coordinates, then mirror, then to normalized [0..1] coordinates |
Referenced by cmtk::ImageSymmetryPlaneFunctionalDevice::Evaluate(), and cmtk::ImagePairAffineRegistrationFunctionalDevice::Evaluate().
| const FixedVector<NDIM,T> cmtk::operator* | ( | const T2 | lhs, |
| const FixedVector< NDIM, T > & | rhs | ||
| ) |
Scalar multiplication operator.
Definition at line 304 of file cmtkFixedVector.h.
| T cmtk::operator* | ( | const FixedVector< NDIM, T > & | lhs, |
| const FixedVector< NDIM, T > & | rhs | ||
| ) |
Scalar product operator.
Definition at line 293 of file cmtkFixedVector.h.
| const FixedVector<NDIM,T> cmtk::operator+ | ( | const FixedVector< NDIM, T > & | lhs, |
| const FixedVector< NDIM, T > & | rhs | ||
| ) |
Addition operator.
Definition at line 277 of file cmtkFixedVector.h.
| const FixedVector<NDIM,T> cmtk::operator- | ( | const FixedVector< NDIM, T > & | lhs, |
| const FixedVector< NDIM, T > & | rhs | ||
| ) |
Subtraction operator.
Definition at line 285 of file cmtkFixedVector.h.
| Console& cmtk::operator<< | ( | Console & | console, |
| Exception | e | ||
| ) |
Output of command line exception.
| std::ofstream& cmtk::operator<< | ( | std::ofstream & | stream, |
| const Region< NDIM, T > & | region | ||
| ) |
Stream input operator.
Definition at line 132 of file cmtkRegion.h.
| std::ofstream& cmtk::operator<< | ( | std::ofstream & | stream, |
| const FixedVector< NDIM, T > & | index | ||
| ) |
Stream input operator.
Definition at line 314 of file cmtkFixedVector.h.
| std::ifstream& cmtk::operator>> | ( | std::ifstream & | stream, |
| FixedVector< NDIM, T > & | index | ||
| ) |
Stream output operator.
Definition at line 323 of file cmtkFixedVector.h.
| std::ifstream& cmtk::operator>> | ( | std::ifstream & | stream, |
| Region< NDIM, T > & | region | ||
| ) |
Stream output operator.
Definition at line 139 of file cmtkRegion.h.
References cmtk::Region< NDIM, T >::From(), and cmtk::Region< NDIM, T >::To().
| void cmtk::SimpleLevelsetDeviceUpdateInsideOutside | ( | float * | levelset, |
| float * | volume, | ||
| const int | nPixels, | ||
| float * | insideSum, | ||
| float * | outsideSum, | ||
| int * | nInside | ||
| ) |
Count inside pixels and compute the sums of inside and outside pixels.
| levelset | Input: current levelset |
| volume | Input: image data |
| nPixels | Input: number of pixels |
| insideSum | Output: sum of data values in the "inside" region |
| outsideSum | Output: sum of data values in the "outside" region |
| nInside | Output: number of pixels in the "inside" region |
Referenced by cmtk::SimpleLevelsetDevice::Evolve().
| void cmtk::SimpleLevelsetDeviceUpdateLevelset | ( | float * | levelset, |
| float * | volume, | ||
| const int | nPixels, | ||
| const float | mInside, | ||
| const float | mOutside, | ||
| const float | ratioInOut, | ||
| const float | timeDelta, | ||
| const float | levelsetThreshold | ||
| ) |
Update levelset based on mean values in inside and outside regions, then threshold the result.
| levelset | Input/output: current levelset, is updated by this function |
| volume | Input: image data |
| nPixels | Input: number of pixels |
| mInside | Input: mean value of data in the "inside" region |
| mOutside | Input: mean value of data in the "outside" region |
| ratioInOut | Input: ratio of inside and outside pixel counts. |
| timeDelta | Input: levelset evolution time constant |
| levelsetThreshold | Input: levelset threshold |
Referenced by cmtk::SimpleLevelsetDevice::Evolve().
| T cmtk::SumReduction | ( | T * | data, |
| const int | n | ||
| ) |
Compute sum reduction of data.
| const char* const cmtk::CMTK_LEGACY_ANALYZE_IO = "CMTK_LEGACY_ANALYZE_IO" |
Environment variable that turns on legacy Analyze I/O with incorrect anatomical orientations.
Definition at line 62 of file cmtkVolumeFromFileAnalyze.cxx.
| const char* const cmtk::IGS_LEGACY_ANALYZE_IO = "IGS_LEGACY_ANALYZE_IO" |
Legacy environment variable that turns on legacy Analyze I/O with incorrect anatomical orientations.
Definition at line 65 of file cmtkVolumeFromFileAnalyze.cxx.
| const char* const cmtk::META_EXTERNAL_SPACE_ID = "SPACE_ID_EXTERNAL" |
Definition at line 49 of file cmtkMetaInformationObject.h.
Referenced by cmtk::MakeInitialAffineTransformation::AlignDirectionVectors().
| const char* const cmtk::META_FILEFORMAT_ORIGINAL = "FILEFORMAT_ORIGINAL" |
Definition at line 44 of file cmtkMetaInformationObject.h.
Referenced by cmtk::VolumeIO::Read().
| const char* const cmtk::META_FS_PATH = "FILESYSTEM_PATH" |
Definition at line 43 of file cmtkMetaInformationObject.h.
Referenced by operator<<(), cmtk::ImagePairAffineRegistrationCommandLine::OutputResult(), cmtk::ElasticRegistrationCommandLine::OutputResult(), cmtk::AffineRegistrationCommandLine::OutputResult(), cmtk::GroupwiseRegistrationFunctionalBase::PrepareSingleImage(), cmtk::VolumeIO::Read(), cmtk::VolumeIO::ReadGrid(), cmtk::GroupwiseRegistrationFunctionalBase::SetTemplateGrid(), cmtk::GroupwiseRegistrationFunctionalBase::Wiggle(), cmtk::VolumeIO::Write(), cmtk::GroupwiseRegistrationOutput::WriteAverageImage(), and cmtk::GroupwiseRegistrationOutput::WriteXformsSeparateArchives().
| const char* const cmtk::META_IMAGE_DIRECTION_VECTORS = "IMAGE_DIRECTION_VECTORS" |
Definition at line 54 of file cmtkMetaInformationObject.h.
| const char* const cmtk::META_IMAGE_ORIENTATION = "IMAGE_ORIENTATION" |
Definition at line 51 of file cmtkMetaInformationObject.h.
Referenced by cmtk::ImageOperationApplyMask::Apply(), cmtk::VolumeFromSlices::FinishVolume(), cmtk::UniformVolume::GetCroppedVolume(), cmtk::DataGrid::GetDownsampledAndAveraged(), cmtk::UniformVolume::GetReoriented(), cmtk::DataGrid::GetReoriented(), cmtk::VolumeFromFile::ReadAnalyzeHdr(), cmtk::VolumeIO::ReadGridOriented(), cmtk::VolumeFromFile::ReadNifti(), cmtk::VolumeIO::ReadOriented(), cmtk::VolumeFromFile::ReadVanderbilt(), cmtk::GroupwiseRegistrationFunctionalBase::SetTemplateGrid(), cmtk::VolumeIO::Write(), and cmtk::VolumeFromFile::WriteAnalyzeHdr().
| const char* const cmtk::META_IMAGE_ORIENTATION_ORIGINAL = "IMAGE_ORIENTATION_ORIGINAL" |
Definition at line 52 of file cmtkMetaInformationObject.h.
Referenced by cmtk::VolumeFromSlices::FinishVolume(), cmtk::UniformVolume::GetCroppedVolume(), cmtk::DataGrid::GetDownsampledAndAveraged(), cmtk::DataGrid::GetReoriented(), cmtk::VolumeFromFile::ReadAnalyzeHdr(), cmtk::VolumeFromFile::ReadNifti(), cmtk::VolumeFromFile::ReadVanderbilt(), cmtk::GroupwiseRegistrationFunctionalBase::SetTemplateGrid(), cmtk::VolumeIO::Write(), and cmtk::VolumeFromFile::WriteAnalyzeHdr().
| const char* const cmtk::META_SPACE = "SPACE" |
Definition at line 46 of file cmtkMetaInformationObject.h.
Referenced by cmtk::AffineRegistrationCommandLine::AffineRegistrationCommandLine(), cmtk::MakeInitialAffineTransformation::AlignDirectionVectors(), cmtk::UniformVolume::ChangeCoordinateSpace(), cmtk::ElasticRegistrationCommandLine::ElasticRegistrationCommandLine(), cmtk::VolumeFromSlices::FinishVolume(), cmtk::ClassStream::Get(), cmtk::UniformVolume::GetCroppedVolume(), cmtk::UniformVolume::GetOrientationFromDirections(), cmtk::ImagePairAffineRegistrationCommandLine::ImagePairAffineRegistrationCommandLine(), cmtk::ImagePairNonrigidRegistrationCommandLine::ImagePairNonrigidRegistrationCommandLine(), cmtk::AffineXform::MakeInverse(), operator>>(), cmtk::AffineXformITKIO::Read(), cmtk::VolumeFromFile::ReadAnalyzeHdr(), cmtk::VolumeFromFile::ReadNifti(), cmtk::GroupwiseRegistrationFunctionalBase::SetTemplateGrid(), cmtk::VolumeFromFile::WriteMetaImage(), and cmtk::Xform::Xform().
| const char* const cmtk::META_SPACE_ORIGINAL = "SPACE_ORIGINAL" |
Definition at line 47 of file cmtkMetaInformationObject.h.
Referenced by cmtk::VolumeFromSlices::FinishVolume(), cmtk::VolumeFromFile::ReadAnalyzeHdr(), cmtk::VolumeFromFile::ReadNifti(), cmtk::GroupwiseRegistrationFunctionalBase::SetTemplateGrid(), cmtk::TransformChangeFromSpaceAffine::TransformChangeFromSpaceAffine(), cmtk::TransformChangeToSpaceAffine::TransformChangeToSpaceAffine(), and cmtk::VolumeFromFile::WriteAnalyzeHdr().
| const char* const cmtk::META_SPACE_UNITS_STRING = "SPACE_UNITS_STRING" |
Definition at line 48 of file cmtkMetaInformationObject.h.
Referenced by cmtk::VolumeFromSlices::FinishVolume().
| const char* const cmtk::META_XFORM_FIXED_IMAGE_PATH = "XFORM_FIXED_IMAGE_PATH" |
Definition at line 56 of file cmtkMetaInformationObject.h.
Referenced by cmtk::AffineXform::MakeInverse(), cmtk::ClassStreamStudyList::Merge(), operator>>(), cmtk::TypedStreamStudylist::Read(), and cmtk::WarpXform::ReplaceInitialAffine().
| const char* const cmtk::META_XFORM_MOVING_IMAGE_PATH = "XFORM_MOVING_IMAGE_PATH" |
Definition at line 57 of file cmtkMetaInformationObject.h.
Referenced by cmtk::AffineXform::MakeInverse(), cmtk::ClassStreamStudyList::Merge(), operator>>(), cmtk::TypedStreamStudylist::Read(), and cmtk::WarpXform::ReplaceInitialAffine().
Definition at line 35 of file initStackBacktrace.cxx.
1.7.2
