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ANIMA
4.0
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Classes | |
| class | AnatomicalBlockMatcher |
| class | ApproximateMCMSmoothingCostFunction |
| class | AsymmetricBMRegistrationMethod |
| class | AtlasInitializer |
| class | AxisRotationTransform |
| class | B1GammaDerivativeDistributionIntegrand |
| Integrand to compute the internal derivative integral per distribution in B1GammaMixtureT2RelaxometryCostFunction. More... | |
| class | B1GammaDistributionIntegrand |
| Integrand to compute the internal integral per distribution in B1GammaMixtureT2RelaxometryCostFunction. More... | |
| class | B1GammaMixtureT2RelaxometryCostFunction |
| class | B1GMMDistributionIntegrand |
| Integrand to compute the internal integral per distribution in B1GMMRelaxometryCostFunction. More... | |
| class | B1GMMRelaxometryCostFunction |
| Cost function for estimating B1 from T2 relaxometry acquisition, following a multi-T2 EPG decay model. The cost function includes (via variable projection) estimation of compartment weights. More... | |
| class | B1T2RelaxometryDistributionCostFunction |
| Cost function for estimating B1 from T2 relaxometry acquisition, following a multi-T2 EPG decay model. More... | |
| class | BalooExternalExtrapolateImageFilter |
| class | BalooSVFTransformAgregator |
| class | BaseAffineBlockMatcher |
| class | BaseBlockMatcher |
| class | BaseBMRegistrationMethod |
| class | BaseCompartment |
| class | BaseIsotropicCompartment |
| class | BaseMCMCost |
| Base cost function class to handle maximum likelihood estimation. More... | |
| class | BaseOrientedModelImageToImageMetric |
| class | BaseProbabilisticTractographyImageFilter |
| class | BaseRootFindingAlgorithm |
| class | BaseTractographyImageFilter |
| class | BaseTransformAgregator |
| class | BisectionRootFindingAlgorithm |
| class | BLMLambdaCostFunction |
| Levenberg-Marquardt lambda update cost function (phi) used for bounded levenberg marquardt optimizer . More... | |
| class | Block |
| class | BlockMatchingInitializer |
| class | BobyqaOptimizer |
| BOBYQA Optimizer. More... | |
| class | BoostBisectionRootFindingAlgorithm |
| class | BoundedLevenbergMarquardtOptimizer |
| Levenberg-Marquardt optimizer with lower and upper bounds on parameters Implementation of the original algorithmm, very well described in K. Madsen, H.B. Nielsen and O. Tingleff. Methods for non-linear least squares problems. 2004 http://www2.imm.dtu.dk/pubdb/views/edoc_download.php/3215/pdf/imm3215.pdf Bounded version by projection as suggested by Kanzow et al. but with a lot of modifications, including calculation of optimal lambda C. Kanzow, N. Yamashita and M. Fukushima. Levenberg-Marquardt methods with strong local convergence properties for solving nonlinear equations with convex constraints. Journal of computational and applied mathematics. 172:375-397, 2004. More... | |
| class | BracketAndSolveRootFindingAlgorithm |
| class | BrentRootFindingAlgorithm |
| class | BVLSOptimizer |
| Bounded variable least squares optimizer. Coming from Stark and Parker paper P.B. Stark and R.L. Parker. Bounded-variable least-squares: an algorithm and applications. Computational Statistics, 1995. More... | |
| class | CheckStructureNeighborFilter |
| Class removing lesions that are not sufficiently in the white matter. Intensity rules may not be enough to discard false positives, therefore we also use localization information. Considering that MS lesions are typically located in WM, we remove the detected ones that do not sufficiently achieve this condition. This filter take two entries: a lesion mask and a white matter map. More... | |
| class | CholeskyDecomposition |
| Cholesky decomposition: decomposes a symmetric matrix A in the form L D L^T, where L is lower triangular and D diagonal. May be used to solve efficiently any linear system using the solve methods. Refer to Gill, Golub et al. Methods for modifying matrix factorizations. 1974. More... | |
| class | ClassificationStrategy |
| class | ComputeMahalanobisImagesFilter |
| Compute the mahalanobis images from the NABT model. More... | |
| class | ComputeSolution |
| Class computing the 3-class GMM respresenting the NABT, where each Gaussian represents one of the brain tissues WM, GM and CSF. First a model initializer is launched, then the REM algorithm is performed using this initialization. The NABT model can be written in a csv file. More... | |
| class | DawsonIntegrand |
| class | DBlock |
| class | DekkerRootFindingAlgorithm |
| class | DenseSVFTransformAgregator |
| class | DirectionScaleSkewTransform |
| class | DirectionScaleTransform |
| class | DirectionTransform |
| class | DistortionCorrectionBlockMatcher |
| class | DistortionCorrectionBMRegistrationMethod |
| class | DistortionCorrectionImageFilter |
| class | DTIEstimationImageFilter |
| class | DTIProbabilisticTractographyImageFilter |
| class | DTIScalarMapsImageFilter |
| Applies an variance filter to an image. More... | |
| class | dtiTractographyImageFilter |
| DTI tractography image filter. Simple step by step tratpography, using advection-diffusion tricks from Weinstein et al. 1999. Tensorlines: Advection-Diffusion based Propagation through Diffusion Tensor Fields. More... | |
| class | DWISimulatorFromDTIImageFilter |
| class | EPGSignalSimulator |
| struct | errors_pair_comparator |
| class | ExpTensorImageFilter |
| class | FastCorrelationImageToImageMetric |
| class | FastMeanSquaresImageToImageMetric |
| class | FDRCorrectImageFilter |
| class | FlipTensorImageFilter |
| class | FreeWaterCompartment |
| class | FuzzyCMeansFilter |
| class | GammaMixtureT2RelaxometryEstimationImageFilter |
| class | GaussianEMEstimator |
| Gaussian Model estimator Class performing expectation-maximation algorithm. More... | |
| class | GaussianMCMCost |
| Class for computing marginal and profile costs and derivatives. This is not thread safe at all so be sure to intantiate one per thread. More... | |
| class | GaussianMCMVariableProjectionCost |
| Class for computing variable projection costs and derivatives. Right now, it is only available for Gaussian noise. By the way, this is not thread safe at all so be sure to intantiate one per thread. More... | |
| class | GaussianMCMVariableProjectionMultipleValuedCostFunction |
| class | GaussianMCMVariableProjectionSingleValuedCostFunction |
| class | GaussianREMEstimator |
| Class performing a robust expectation-maximation (REM) algorithm. Allow finding the 3-classes NABT model estimation. More... | |
| class | GaussLaguerreQuadrature |
| Computes the Gauss Laguerre quadrature of a function defined from R^+ into R. Recenters the function on the interest zone with an affine relation, then uses Gauss Legendre on the left out part of the function and computes the main part with Gauss Laguerre. More... | |
| class | GcStremMsLesionsSegmentationFilter |
| Class performing lesion segmentation. More... | |
| class | GeneralizedFAImageFilter |
| class | GMMT2RelaxometryEstimationImageFilter |
| class | GradientFileReader |
| class | Graph |
| class | Graph3DFilter |
| Class allowing the decimation of the images if necessary (if 3D graph size causes memory problems). This class just launchs NLinksFilter with appropriate image sizes. More... | |
| class | GraphCutFilter |
| Class performing grah cut segmentation. First the sources and sinks probabilities maps are computed using the TLinkFilter. Then the Graph3DFilter is called to perform the graph cut. More... | |
| class | HierarchicalInitializer |
| Class initializing a gaussian mixture with hierarchical information It uses 'a priori' knowledge of the sequences. More... | |
| class | ImageClassifierFilter |
| Classify each voxels into one of the given GMM classes. More... | |
| class | ImageDataSplitter |
| class | IsotropicRestrictedWaterCompartment |
| class | JacobianMatrixImageFilter |
| Compute the Jacobian matrix in real coordinates of a displacement field. More... | |
| class | KissingSymmetricBMRegistrationMethod |
| class | KMeansFilter |
| class | KummerIntegrand |
| class | LocalPatchCovarianceDistanceImageFilter |
| class | LocalPatchMeanDistanceImageFilter |
| class | LogEuclideanTensorCalculator |
| class | LogRigid3DTransform |
| class | LogTensorImageFilter |
| class | LowMemoryLocalPatchCovarianceDistanceBridge |
| class | LowMemoryLocalPatchMeanDistanceBridge |
| class | LowMemoryNLMeansPatientToGroupComparisonBridge |
| class | LowMemoryPatientToGroupComparisonBridge |
| class | LowMemoryPatientToGroupODFComparisonBridge |
| class | LSWTransformAgregator |
| class | LTSWTransformAgregator |
| class | MajorityLabelVotingImageFilter |
| class | MaskedImageToImageFilter |
| class | MatrixLoggerFilter |
| Class to compute many log-vectors in a multi-threaded way. More... | |
| class | MCMAverageImagesImageFilter |
| class | MCMBlockMatcher |
| class | MCMBlockMatchingInitializer |
| class | MCMCorrelationImageToImageMetric |
| class | MCMEstimatorImageFilter |
| class | MCMFileReader |
| class | MCMFileWriter |
| class | MCMImage |
| class | MCML2DistanceComputer |
| Computes a L2 distance between two MCM of any type. More... | |
| class | MCMLinearInterpolateImageFunction |
| class | MCMMeanSquaresImageToImageMetric |
| class | MCMMultipleValuedCostFunction |
| class | MCMPairingMeanSquaresImageToImageMetric |
| class | MCMResampleImageFilter |
| class | MCMScalarMapsImageFilter |
| class | MCMSingleValuedCostFunction |
| class | MCMWeightedAverager |
| Computes a weighted average of input multi-compartment models. The output model is at the same time giving the number and type of output compartments but also its parameters are erased when performing Update to get the result. More... | |
| class | MeanAndVarianceImagesFilter |
| Applies an variance filter to an image. More... | |
| class | MEstimateSVFImageFilter |
| class | MEstTransformAgregator |
| class | ModelInitializer |
| Gaussian model initializers Model Initializer represents the processes computing a gaussian model that will be used as the model initialization in an EM process. More... | |
| class | MTPairingCorrelationImageToImageMetric |
| Multi-tensor correlation similarity measure as defined by Taquet et al, based on pairing of the individual compartments. More... | |
| class | MultiCompartmentModel |
| MultiCompartmentModel: holds several diffusion compartments, ordered by type It also handles weights of the different compartments. Although there are N weights in memory for N compartments, the parameters returned and set are considered to have one less weight in them, the first one being removed. This comes from the fact that they sum up to 1. More... | |
| class | MultiCompartmentModelCreator |
| Really this class is some simplified factory that creates the MCM that it knows. More... | |
| class | MultiT2EPGRelaxometryCostFunction |
| Cost function for estimating B1 from T2 relaxometry acquisition, following a multi-T2 EPG decay model. More... | |
| class | MultiT2RelaxometryEstimationImageFilter |
| Implements multi-peak T2 relaxometry estimation (with or without regularization) More... | |
| class | MultiTensorSmoothingCostFunction |
| class | NLinksFilter |
| Class creating a 3D graph in a graph cut framework. More... | |
| class | NLMeansPatientToGroupComparisonImageFilter |
| class | NLMeansVectorPatchSearcher |
| class | NLOPTOptimizers |
| Implements an ITK wrapper for the NLOPT library. More... | |
| class | NLOPTParametersConstraintFunction |
| class | NNLSOptimizer |
| Non negative least squares optimizer. Implements Lawson et al method, of squared problem is activated, assumes we pass AtA et AtB and uses Bro and de Jong method. More... | |
| class | NODDICompartment |
| class | NoiseGeneratorImageFilter |
| class | NonLocalMeansImageFilter |
| class | NonLocalMeansPatchSearcher |
| class | NonLocalMeansTemporalImageFilter |
| class | NonLocalPatchBaseSearcher |
| class | NonLocalT2DistributionPatchSearcher |
| class | NumberedThreadImageToImageFilter |
| Implements a class to handle thread number in a dynamic way for multithreaded methods needing thread numbering even for dynamic threading. More... | |
| class | ODFEstimatorImageFilter |
| class | ODFMaximaCostFunction |
| class | ODFProbabilisticTractographyImageFilter |
| class | ODFResampleImageFilter |
| class | ODFSphericalHarmonicBasis |
| class | OrientedModelBaseResampleImageFilter |
| struct | pair_decreasing_comparator |
| struct | pair_increasing_comparator |
| class | PatientToGroupComparisonImageFilter |
| Implements patient to group comparison as in http://dx.doi.org/10.1007/978-3-540-85988-8_116. More... | |
| class | PatientToGroupODFComparisonImageFilter |
| class | PyramidalBlockMatchingBridge |
| class | PyramidalDenseMCMSVFMatchingBridge |
| class | PyramidalDenseSVFMatchingBridge |
| class | PyramidalDenseTensorSVFMatchingBridge |
| class | PyramidalDistortionCorrectionBlockMatchingBridge |
| class | PyramidalSymmetryBridge |
| class | PyramidalSymmetryConstrainedRegistrationBridge |
| class | PyramidImageFilter |
| Computes a pyramid of images using the provided resampler to perform resampling. More... | |
| class | RandomInitializer |
| Class initializing ramdomly a gaussian model. More... | |
| class | RecursiveLineYvvGaussianImageFilter |
| class | RemoveTouchingBorderFilter |
| Class selecting the connected components touching a given mask border. In MRI, external CSF may contain artifacts due to fluid flow. These effects can cause voxels in the cortex or external CSF to have intensities similar to MS lesions. In order to reduce the number of false positives due to these effects, we remove all candidate lesions that are contiguous to the brain mask border. More... | |
| class | ResampleImageFilter |
| class | RootFindingFunctionBoostBridge |
| class | RootToleranceBoostBridge |
| class | SegmentationMeasuresImageFilter |
| class | SegPerfApp |
| Main class to structure application and handle command line options. More... | |
| class | SegPerfCAnalyzer |
| Class to compute various metrics to evaluate segmentation results. More... | |
| class | SegPerfLabelSetMeasures |
| class | SegPerfResults |
| Class to format and saves results. More... | |
| class | ShapesReader |
| class | ShapesWriter |
| class | SimuBlochCoherentGRE |
| class | SimuBlochGRE |
| class | SimuBlochIRGRE |
| class | SimuBlochIRSE |
| class | SimuBlochSE |
| class | SimuBlochSPGRE |
| class | SmoothingRecursiveYvvGaussianImageFilter |
| class | SpectralClusteringFilter |
| Provides an implementation of spectral clustering, as proposed in A.Y. Ng, M.I. Jordan and Y. Weiss. "On Spectral Clustering: Analysis and an Algorithm." Advances in Neural Information Processing Systems 14. 2001. More... | |
| class | SphericalHarmonic |
| class | SplitAffine3DTransform |
| class | StaniszCompartment |
| class | StationaryWaterCompartment |
| class | StickCompartment |
| class | StimulatedSpinEchoImageFilter |
| class | SVFExponentialImageFilter |
| Computes the exponentiation of a stationary velocity field using sclaing and squaring and approximated exponential integrators. More... | |
| class | SVFLieBracketImageFilter |
| Computes the Lie bracket between two fields u and v as expressed by Bossa et al. More... | |
| class | SymmetricBMRegistrationMethod |
| class | SymmetryPlaneTransform |
| class | T1RelaxometryEstimationImageFilter |
| class | T1SERelaxometryCostFunction |
| class | T1SERelaxometryEstimationImageFilter |
| class | T2EPGRelaxometryCostFunction |
| class | T2EPGRelaxometryEstimationImageFilter |
| class | T2RelaxometryCostFunction |
| class | T2RelaxometryEstimationImageFilter |
| class | TensorBlockMatcher |
| class | TensorCompartment |
| class | TensorCorrelationImageToImageMetric |
| Tensor correlation similarity measure as defined by Taquet et al. More... | |
| class | TensorGeneralizedCorrelationImageToImageMetric |
| class | TensorMeanSquaresImageToImageMetric |
| class | TensorResampleImageFilter |
| class | TLinksFilter |
| Class computing the probability maps that are used to create the t-links. More... | |
| class | TOMS748RootFindingAlgorithm |
| class | TransformSeriesReader |
| class | VectorModelLinearInterpolateImageFunction |
| class | VoxelExhaustiveOptimizer |
| class | ZeppelinCompartment |
Enumerations | |
| enum | DiffusionModelCompartmentType { FreeWater = 0, StationaryWater, IsotropicRestrictedWater, Stanisz, Stick, Zeppelin, Tensor, NODDI, DDI } |
Functions | |
| double | a0r_support (double x, unsigned int N) |
| Support function for besserl_ratio_i. More... | |
| double | ak_support (double x, unsigned int N, unsigned int k) |
| Support function for besserl_ratio_i. More... | |
| double | bessel_i_lower_bound (unsigned int N, double x) |
| Computes a lower bound of the modified Bessel function of the first kind: I_{N} (N >= 0) More... | |
| double | bessel_ratio_i (double x, unsigned int N, unsigned int approx_order=10) |
| Computes the ratio of modified Bessel functions of the first kind: I_{N} / I_{N-1} (N >= 1) More... | |
| double | bessel_ratio_i_derivative (double x, unsigned int N, unsigned int approx_order=10) |
| Computes the derivative of the ratio of modified Bessel functions of the first kind: d/dx( I_{N}(x) / I_{N-1}(x) ) (N >= 1) More... | |
| double | bessel_ratio_i_derivative_approx (double x, unsigned int N) |
| Computes fast and accurate approximation of the derivative of the ratio of modified Bessel functions of the first kind: d/dx( I_{N}(x) / I_{N-1}(x) ) (N >= 1) More... | |
| double | bessel_ratio_i_lower_bound (double x, unsigned int N) |
| Computes a lower bound of the ratio of modified Bessel functions of the first kind: I_{N} / I_{N-1} (N >= 1) More... | |
| void | BHCorrection (std::vector< double > &pvalues, double qValue) |
| void | BYCorrection (std::vector< double > &pvalues, double qValue) |
| template<class ScalarType > | |
| std::complex< double > | ComplexShRatio (const ScalarType &k, const ScalarType &alpha, const ScalarType &beta) |
| template<class ScalarType , unsigned int NDimensions> | |
| void | composeDistortionCorrections (typename rpi::DisplacementFieldTransform< ScalarType, NDimensions >::Pointer &baseTrsf, typename rpi::DisplacementFieldTransform< ScalarType, NDimensions >::Pointer &positiveAddOn, typename rpi::DisplacementFieldTransform< ScalarType, NDimensions >::Pointer &negativeAddOn, unsigned int numThreads) |
| template<class ScalarType , unsigned int NDimensions> | |
| void | composeSVF (itk::StationaryVelocityFieldTransform< ScalarType, NDimensions > *baseTrsf, itk::StationaryVelocityFieldTransform< ScalarType, NDimensions > *addonTrsf, unsigned int numThreads, unsigned int bchOrder) |
| template<class TInput , class TScalarType , unsigned int NDimensions> | |
| itk::Point< TInput, NDimensions > | computeAffineLSWFromTranslations (std::vector< itk::Point< TInput, NDimensions > > &inputOrigins, std::vector< itk::Point< TInput, NDimensions > > &inputTransformed, std::vector< TInput > &weights, typename itk::AffineTransform< TScalarType, NDimensions >::Pointer &resultTransform) |
| template<class VectorType > | |
| double | ComputeAngle (const VectorType &v1, const VectorType &v2) |
| template<class TInput , class TScalarType , unsigned int NDimensions> | |
| itk::Point< TInput, NDimensions > | computeAnisotropSimLSWFromTranslations (std::vector< itk::Point< TInput, NDimensions > > &inputOrigins, std::vector< itk::Point< TInput, NDimensions > > &inputTransformed, std::vector< TInput > &weights, typename itk::AffineTransform< TScalarType, NDimensions >::Pointer &resultTransform, vnl_matrix< double > &UMatrix) |
| template<class T1 , class T2 , unsigned int Dimension> | |
| void | computeAverageLocalCovariance (vnl_matrix< T2 > &resVariance, itk::VectorImage< T1, Dimension > *inputImage, itk::Image< unsigned char, Dimension > *maskImage, const itk::ImageRegion< Dimension > &averagingRegion, int localNeighborhood) |
| Noise estimation for a patch of a vector image. More... | |
| template<class VectorType > | |
| void | ComputeCrossProduct (const VectorType &v1, const VectorType &v2, const unsigned int NDimension, VectorType &resVec) |
| template<class ScalarType , unsigned int NDimension> | |
| void | ComputeCrossProduct (const itk::Vector< ScalarType, NDimension > &v1, const itk::Vector< ScalarType, NDimension > &v2, itk::Vector< ScalarType, NDimension > &resVec) |
| template<class ScalarType > | |
| void | ComputeCrossProduct (const itk::VariableLengthVector< ScalarType > &v1, const itk::VariableLengthVector< ScalarType > &v2, itk::VariableLengthVector< ScalarType > &resVec) |
| template<class ScalarType , unsigned int NDimension> | |
| void | ComputeCrossProduct (const itk::Point< ScalarType, NDimension > &v1, const itk::Point< ScalarType, NDimension > &v2, itk::Point< ScalarType, NDimension > &resVec) |
| template<class ScalarType > | |
| void | ComputeCrossProduct (const vnl_vector< ScalarType > &v1, const vnl_vector< ScalarType > &v2, vnl_vector< ScalarType > &resVec) |
| template<class ScalarType , unsigned int NDimension> | |
| void | ComputeCrossProduct (const vnl_vector_fixed< ScalarType, NDimension > &v1, const vnl_vector_fixed< ScalarType, NDimension > &v2, vnl_vector_fixed< ScalarType, NDimension > &resVec) |
| template<class ScalarType > | |
| void | ComputeCrossProduct (const std::vector< ScalarType > &v1, const std::vector< ScalarType > &v2, std::vector< ScalarType > &resVec) |
| template<class VectorType > | |
| double | ComputeDirectedHausdorffDistance (const std::vector< VectorType > &s1, const std::vector< VectorType > &s2) |
| template<class VectorType > | |
| double | ComputeEuclideanDistance (const VectorType &x1, const VectorType &x2, const unsigned int NDimension) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ComputeEuclideanDistance (const itk::Vector< ScalarType, NDimension > &x1, const itk::Vector< ScalarType, NDimension > &x2) |
| template<class ScalarType > | |
| double | ComputeEuclideanDistance (const itk::VariableLengthVector< ScalarType > &x1, const itk::VariableLengthVector< ScalarType > &x2) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ComputeEuclideanDistance (const itk::Point< ScalarType, NDimension > &x1, const itk::Point< ScalarType, NDimension > &x2) |
| template<class ScalarType > | |
| double | ComputeEuclideanDistance (const vnl_vector< ScalarType > &x1, const vnl_vector< ScalarType > &x2) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ComputeEuclideanDistance (const vnl_vector_fixed< ScalarType, NDimension > &x1, const vnl_vector_fixed< ScalarType, NDimension > &x2) |
| template<class ScalarType > | |
| double | ComputeEuclideanDistance (const std::vector< ScalarType > &x1, const std::vector< ScalarType > &x2) |
| template<class VectorType > | |
| double | ComputeHausdorffDistance (const std::vector< VectorType > &s1, const std::vector< VectorType > &s2) |
| template<class VectorType > | |
| void | ComputeHouseholderVector (const VectorType &inputVector, VectorType &outputVector, double &beta, unsigned int dimension) |
| template<class ScalarType > | |
| void | ComputeHouseholderVector (const std::vector< ScalarType > &inputVector, std::vector< ScalarType > &outputVector, double &beta) |
| template<class ScalarType > | |
| void | ComputeHouseholderVector (std::vector< ScalarType > &vector, double &beta) |
| template<class TInput , class TScalarType , unsigned int NDimensions> | |
| void | computeLogEuclideanAverage (std::vector< vnl_matrix< TInput > > &inputTransforms, std::vector< TInput > &weights, typename itk::AffineTransform< TScalarType, NDimensions >::Pointer &resultTransform) |
| template<class VectorType > | |
| double | ComputeModifiedDirectedHausdorffDistance (const std::vector< VectorType > &s1, const std::vector< VectorType > &s2) |
| template<class VectorType > | |
| double | ComputeModifiedHausdorffDistance (const std::vector< VectorType > &s1, const std::vector< VectorType > &s2) |
| template<class VectorType > | |
| double | ComputeNorm (const VectorType &v) |
| template<class VectorType > | |
| double | ComputeOrientationAngle (const VectorType &v1, const VectorType &v2) |
| template<class T1 , class T2 , unsigned int Dimension> | |
| unsigned int | computePatchMeanAndCovariance (const itk::VectorImage< T1, Dimension > *inputImage, const itk::ImageRegion< Dimension > &patchRegion, itk::VariableLengthVector< T2 > &patchMean, vnl_matrix< T2 > &patchCov) |
| Computes the average and covariance matrix from a patch of a vector image. More... | |
| template<class VectorType > | |
| double | ComputePointToSetDistance (const VectorType &x, const std::vector< VectorType > &s) |
| template<class TInput , class TScalarType , unsigned int NDimensions> | |
| void | computeRigidLSWFromTranslations (std::vector< itk::Point< TInput, NDimensions > > &inputOrigins, std::vector< itk::Point< TInput, NDimensions > > &inputTransformed, std::vector< TInput > &weights, typename itk::AffineTransform< TScalarType, NDimensions >::Pointer &resultTransform) |
| template<class TInput , class TOutput > | |
| vnl_matrix< TOutput > | computeRotationFromQuaternion (vnl_vector< TInput > eigenVector) |
| template<class VectorType > | |
| double | ComputeScalarProduct (const VectorType &v1, const VectorType &v2, const unsigned int NDimension) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ComputeScalarProduct (const itk::Vector< ScalarType, NDimension > &v1, const itk::Vector< ScalarType, NDimension > &v2) |
| template<class ScalarType > | |
| double | ComputeScalarProduct (const itk::VariableLengthVector< ScalarType > &v1, const itk::VariableLengthVector< ScalarType > &v2) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ComputeScalarProduct (const itk::Point< ScalarType, NDimension > &v1, const itk::Point< ScalarType, NDimension > &v2) |
| template<class ScalarType > | |
| double | ComputeScalarProduct (const vnl_vector< ScalarType > &v1, const vnl_vector< ScalarType > &v2) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ComputeScalarProduct (const vnl_vector_fixed< ScalarType, NDimension > &v1, const vnl_vector_fixed< ScalarType, NDimension > &v2) |
| template<class ScalarType > | |
| double | ComputeScalarProduct (const std::vector< ScalarType > &v1, const std::vector< ScalarType > &v2) |
| template<class ScalarType > | |
| void | ComputeSphericalCentroid (const std::vector< std::vector< ScalarType > > &dataPoints, std::vector< ScalarType > ¢roidValue, const std::vector< ScalarType > &initPoint, const std::vector< ScalarType > &weights, std::vector< ScalarType > *workLogVector=0, std::vector< ScalarType > *workVector=0, double tol=1.0e-4) |
| template<class TInput , class TScalarType , unsigned int NDimensions> | |
| void | computeTranslationLSWFromTranslations (std::vector< itk::Point< TInput, NDimensions > > &inputOrigins, std::vector< itk::Point< TInput, NDimensions > > &inputTransformed, std::vector< TInput > &weights, typename itk::AffineTransform< TScalarType, NDimensions >::Pointer &resultTransform) |
| template<class VectorType , class ScalarType > | |
| double | ComputeVMFPdf (const VectorType &v, const VectorType &meanDirection, const ScalarType &kappa) |
| template<class T > | |
| T | Cubic (T x0, T x1, T x2, T x3, T y0, T y1, T y2, T y3, T x) |
| template<class T > | |
| void | CubicInterpolator (std::vector< T > &transfVect, std::vector< T > &scale, std::vector< T > &outputVect, T LengthLine) |
| void | EstimateLocalODFRotationMatrix (vnl_matrix< double > &resVal, unsigned int l, double alpha, double beta, double gamma) |
| double | EvaluateDawsonFunction (double x) |
| compute Dawson(x) = sqrt(pi)/2 * exp(-x^2) * erfi(x) More... | |
| double | EvaluateDawsonFunctionNR (double x) |
| Numerical recipes implementation of Dawson integral. More... | |
| double | EvaluateDawsonIntegral (const double x, const bool scaled) |
| template<class VectorType , class ScalarType > | |
| double | EvaluateWatsonPDF (const VectorType &v, const VectorType &meanAxis, const ScalarType &kappa) |
| template<class ScalarType > | |
| double | EvaluateWatsonPDF (const vnl_vector_fixed< ScalarType, 3 > &v, const vnl_vector_fixed< ScalarType, 3 > &meanAxis, const ScalarType &kappa) |
| template<class ScalarType > | |
| double | EvaluateWatsonPDF (const itk::Point< ScalarType, 3 > &v, const itk::Point< ScalarType, 3 > &meanAxis, const ScalarType &kappa) |
| template<class ScalarType > | |
| double | EvaluateWatsonPDF (const itk::Vector< ScalarType, 3 > &v, const itk::Vector< ScalarType, 3 > &meanAxis, const ScalarType &kappa) |
| double | EvaluateWImFunction (double x) |
| double | EvaluateWImY100Function (double y100, double x) |
| template<class VectorType > | |
| double | ExponentialSum (const VectorType &x, const unsigned int NDimension) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ExponentialSum (const itk::Vector< ScalarType, NDimension > &x) |
| template<class ScalarType > | |
| double | ExponentialSum (const itk::VariableLengthVector< ScalarType > &x) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ExponentialSum (const itk::Point< ScalarType, NDimension > &x) |
| template<class ScalarType > | |
| double | ExponentialSum (const vnl_vector< ScalarType > &x) |
| template<class ScalarType , unsigned int NDimension> | |
| double | ExponentialSum (const vnl_vector_fixed< ScalarType, NDimension > &x) |
| template<class ScalarType > | |
| double | ExponentialSum (const std::vector< ScalarType > &x) |
| template<typename RealType , typename MatrixType > | |
| void | ExtractPPDRotationFromJacobianMatrix (vnl_matrix< RealType > &jacobianMatrix, vnl_matrix< RealType > &rotationMatrix, MatrixType &eigenVectors) |
| template<typename RealType > | |
| void | ExtractRotationFromJacobianMatrix (vnl_matrix< RealType > &jacobianMatrix, vnl_matrix< RealType > &rotationMatrix, vnl_matrix< RealType > &tmpMat) |
| double | gammaHalfMinusN (unsigned int n) |
| double | gammaHalfPlusN (unsigned int n) |
| template<class T > | |
| void | Get3DRotationExponential (const std::vector< T > &angles, vnl_matrix< T > &outputRotation) |
| Computation of a 3D rotation matrix exponential. Rodrigues' explicit formula. More... | |
| template<class T > | |
| void | Get3DRotationLogarithm (const vnl_matrix< T > &rotationMatrix, std::vector< T > &outputAngles) |
| Computation of a 3D rotation matrix logarithm. Rodrigues' explicit formula. More... | |
| double | GetBValueFromAcquisitionParameters (double smallDelta, double bigDelta, double gradientStrength) |
| Given gyromagnetic ratio in rad/s/T, gradient strength in T/mm and deltas in s, computes b-value in s/mm^2. More... | |
| double | GetDValue (unsigned int l, int m, int mp, double angle) |
| void | GetEulerAnglesFromRotationMatrix (vnl_matrix< double > &R, std::vector< double > &resVal) |
| template<class T > | |
| vnl_matrix< T > | GetExponential (const vnl_matrix< T > &m, const int numApprox=1) |
| Computation of the matrix exponential. Algo: classical scaling and squaring, as in Matlab. See Higham, SIAM Matr. Anal., 2004. More... | |
| double | GetGradientStrengthFromBValue (double bValue, double smallDelta, double bigDelta) |
| Given b-value in s/mm^2 and deltas in s, computes gradient strength in T/mm. More... | |
| template<class InputImageType , class OutputImageType > | |
| std::vector< itk::SmartPointer< OutputImageType > > | getImagesFromHigherDimensionImage (InputImageType *inputImage) |
| Get a vector of input images from a higher dimensional image. More... | |
| double | GetKummerFunctionValue (const double &x, const double &a, const double &b, const unsigned int maxIter=1000, const double tol=1.0e-8) |
| Computes the confluent hypergeometric function 1F1 also known as the Kummer function M. It calls Kummer function core to get the value. More... | |
| template<class T > | |
| vnl_matrix< T > | GetLogarithm (const vnl_matrix< T > &m, const double precision=0.00000000001, const int numApprox=1) |
| Computation of the matrix logarithm. Algo: inverse scaling and squaring, variant proposed by Cheng et al., SIAM Matrix Anal., 2001. More... | |
| itk::ImageIOBase::IOComponentType ANIMAMCM_EXPORT | GetMCMComponentType (std::string fileName) |
| template<class T > | |
| vnl_matrix< T > | GetPadeLogarithm (const vnl_matrix< double > &m, const int numApprox) |
| Final part of the computation of the log. Estimates the log with a Pade approximation for a matrix m such that |m-Id| <= 0.5. More... | |
| template<class T > | |
| vnl_matrix< T > | GetPadeLogarithm (const vnl_matrix< T > &m, const int numApprox) |
| template<typename ScalarType > | |
| void | GetQMatrixQRPivoDecomposition (vnl_matrix< ScalarType > &qrMatrix, std::vector< ScalarType > &houseBetaValues, vnl_matrix< ScalarType > &qMatrix, unsigned int rank) |
| template<typename ScalarType > | |
| void | GetQMatrixQRPivotDecomposition (vnl_matrix< ScalarType > &qrMatrix, std::vector< ScalarType > &houseBetaValues, vnl_matrix< ScalarType > &qMatrix, unsigned int rank) |
| template<typename ScalarType > | |
| void | GetQtBFromQRPivotDecomposition (vnl_matrix< ScalarType > &qrMatrix, vnl_vector< ScalarType > &bVector, std::vector< ScalarType > &houseBetaValues, unsigned int rank) |
| template<class VectorType > | |
| itk::Matrix< double, 3, 3 > | GetRotationMatrixFromVectors (const VectorType &first_direction, const VectorType &second_direction, const unsigned int dimension) |
| template<class ScalarType > | |
| itk::Matrix< double, 3, 3 > | GetRotationMatrixFromVectors (const itk::Point< ScalarType > &first_direction, const itk::Point< ScalarType > &second_direction) |
| template<class ScalarType , unsigned int NDimension> | |
| itk::Matrix< double, 3, 3 > | GetRotationMatrixFromVectors (const itk::Vector< ScalarType, NDimension > &first_direction, const itk::Vector< ScalarType, NDimension > &second_direction) |
| template<class ScalarType , unsigned int NDimension> | |
| itk::Matrix< double, 3, 3 > | GetRotationMatrixFromVectors (const vnl_vector_fixed< ScalarType, NDimension > &first_direction, const vnl_vector_fixed< ScalarType, NDimension > &second_direction) |
| double | GetScaledKummerFunctionValue (const double &x, const double &a, const double &b, const unsigned int maxIter=1000, const double tol=1.0e-8) |
| Computes the confluent hypergeometric function 1F1 also known as the Kummer function M. It returns a scaled value: exp(-x) * M(x,a,b). More... | |
| template<class ScalarType > | |
| void | GetSphereEvenSampling (std::vector< std::vector< ScalarType > > &spherePoints, unsigned int numSamples) |
| template<class T > | |
| vnl_matrix< T > | GetSquareRoot (const vnl_matrix< T > &m, const double precision, vnl_matrix< T > &resultM) |
| Gets the square root of matrix m. More... | |
| template<class ScalarType > | |
| void | GetStandardWatsonSHCoefficients (const ScalarType k, std::vector< ScalarType > &coefficients, std::vector< ScalarType > &derivatives) |
| template<class ScalarType , unsigned int NDimensions> | |
| void | GetSVFExponential (itk::StationaryVelocityFieldTransform< ScalarType, NDimensions > *baseTrsf, rpi::DisplacementFieldTransform< ScalarType, NDimensions > *resultTransform, unsigned int exponentiationOrder, unsigned int numThreads, bool invert) |
| template<class T1 , class T2 > | |
| void | GetTensorFromVectorRepresentation (const itk::VariableLengthVector< T1 > &vector, vnl_matrix< T2 > &tensor, unsigned int tensDim=0, bool scale=false) |
| template<class T1 , class T2 > | |
| void | GetVectorRepresentation (const vnl_matrix< T1 > &tensor, itk::VariableLengthVector< T2 > &vector, unsigned int vecDim=0, bool scale=false) |
| template<class ScalarType > | |
| double | GetVonMisesConcentrationMLE (const ScalarType rbar) |
| Maximum likelihood estimation of the concentration parameter of the 2D von Mises distribution according to Mardia, Statistics of Directional Data, 1972. More... | |
| std::vector< std::vector< double > > | InitializeSampleDirections (unsigned int nbTheta, unsigned int nbPhi, std::string sampleDirFileName) |
| template<class T > | |
| void | InverseCubicInterpolator (std::vector< T > &inputVect, std::vector< T > &outputVect, T step) |
| template<class T > | |
| double | jfour (const T &k) |
| template<class T > | |
| double | jtwo (const T &k) |
| double | KummerIntegrandMethod (const double &x, const double &a, const double &b) |
| According to Muller, K. E. (2001) ‘Computing the confluent hypergeometric function, M (a, b, x)’, Numerische Mathematik, pp. 179–196. Method with integral if b > a > 0. More... | |
| double | KummerMethod1 (const double &x, const double &a, const double &b, const unsigned int maxIter=1000, const double tol=1.0e-8) |
| According to Muller, K. E. (2001) ‘Computing the confluent hypergeometric function, M (a, b, x)’, Numerische Mathematik, pp. 179–196. Method 1.C, p.5. More... | |
| double | KummerMethod2 (const double &x, const double &a, const double &b, const unsigned int maxIter=1000, const double tol=1.0e-8) |
| According to Muller, K. E. (2001) ‘Computing the confluent hypergeometric function, M (a, b, x)’, Numerische Mathematik, pp. 179–196. Method 2, p.6. More... | |
| double | legendre_first_derivative (int L, int M, double value) |
| double | legendre_second_derivative (int L, int M, double value) |
| double | log_bessel_i (unsigned int N, double x) |
| Computes the log of modified Bessel function of the first kind: I_{N} (N >= 0) More... | |
| double | log_bessel_i_lower_bound (unsigned int N, double x) |
| Computes a lower bound of the log of modified Bessel function of the first kind: I_{N} (N >= 0) More... | |
| double | log_bessel_order_derivative_i (double x, unsigned int order, double emc, unsigned int approx_order=50) |
| Computes the derivative of the log of modified Bessel function of the first kind w.r.t. its order (emc is the Euler-Mascheroni constant) More... | |
| template<class ScalarType , class VectorType > | |
| void | LowerTriangularSolver (vnl_matrix< ScalarType > &matrix, VectorType &rhs, VectorType &result, unsigned int rank=0) |
| template<class VectorType > | |
| void | Normalize (const VectorType &v, const unsigned int NDimension, VectorType &resVec) |
| template<class ScalarType , unsigned int NDimension> | |
| void | Normalize (const itk::Vector< ScalarType, NDimension > &v, itk::Vector< ScalarType, NDimension > &resVec) |
| template<class ScalarType > | |
| void | Normalize (const itk::VariableLengthVector< ScalarType > &v, itk::VariableLengthVector< ScalarType > &resVec) |
| template<class ScalarType , unsigned int NDimension> | |
| void | Normalize (const itk::Point< ScalarType, NDimension > &v, itk::Point< ScalarType, NDimension > &resVec) |
| template<class ScalarType > | |
| void | Normalize (const vnl_vector< ScalarType > &v, vnl_vector< ScalarType > &resVec) |
| template<class ScalarType , unsigned int NDimension> | |
| void | Normalize (const vnl_vector_fixed< ScalarType, NDimension > &v, vnl_vector_fixed< ScalarType, NDimension > &resVec) |
| template<class ScalarType > | |
| void | Normalize (const std::vector< ScalarType > &v, std::vector< ScalarType > &resVec) |
| template<class T1 > | |
| double | ovlScore (vnl_diag_matrix< T1 > &eigsX, vnl_matrix< T1 > &eigVecsX, vnl_diag_matrix< T1 > &eigsY, vnl_matrix< T1 > &eigVecsY) |
| template<class TInput , class TOutput , unsigned int NDimensions> | |
| void | pairingToQuaternion (const vnl_vector_fixed< TInput, NDimensions > &inputPoint, const vnl_vector_fixed< TInput, NDimensions > &inputTransformedPoint, vnl_matrix< TOutput > &outputMatrix) |
| template<class TInput , class TOutput , unsigned int NDimensions> | |
| void | pairingToQuaternion (const itk::Vector< TInput, NDimensions > &inputPoint, const itk::Vector< TInput, NDimensions > &inputTransformedPoint, vnl_matrix< TOutput > &outputMatrix) |
| template<class PointType , class TOutput > | |
| void | pairingToQuaternion (const PointType &inputPoint, const PointType &inputTransformedPoint, vnl_matrix< TOutput > &outputMatrix, unsigned int ndim) |
| template<class TInput , class TOutput , unsigned int NDimensions> | |
| void | pairingToQuaternionScalingsDerivative (const vnl_vector_fixed< TInput, NDimensions > &inputPoint, const vnl_vector_fixed< TInput, NDimensions > &inputTransformedPoint, vnl_matrix< TOutput > &outputMatrix, const int &dimScal) |
| template<class TInput , class TOutput , unsigned int NDimensions> | |
| void | pairingToQuaternionScalingsDerivative (const itk::Vector< TInput, NDimensions > &inputPoint, const itk::Vector< TInput, NDimensions > &inputTransformedPoint, vnl_matrix< TOutput > &outputMatrix, const int &dimScal) |
| template<class PointType , class TOutput > | |
| void | pairingToQuaternionScalingsDerivative (const PointType &inputPoint, const PointType &inputTransformedPoint, vnl_matrix< TOutput > &outputMatrix, unsigned int ndim, const int &dimScal) |
| double | PochHammer (const double &x, const unsigned int n) |
| template<class T1 , class T2 , class T3 > | |
| void | ProjectOnOrthogonalPlane (const std::vector< T1 > &v, const std::vector< T2 > &normalVec, std::vector< T3 > &resVec) |
| template<class T > | |
| void | ProjectOnTensorSpace (const vnl_matrix< T > &matrix, vnl_matrix< T > &tensor) |
| double | psi_function (unsigned int n, double emc) |
| template<typename ScalarType > | |
| void | QRGivensDecomposition (vnl_matrix< ScalarType > &aMatrix, vnl_vector< ScalarType > &bVector) |
| template<typename ScalarType > | |
| void | QRPivotDecomposition (vnl_matrix< ScalarType > &aMatrix, std::vector< unsigned int > &pivotVector, std::vector< ScalarType > &houseBetaValues, unsigned int &rank) |
| template<class ImageType > | |
| itk::SmartPointer< ImageType > | readImage (std::string filename) |
| template<class T1 , class T2 > | |
| void | RecomposeTensor (vnl_diag_matrix< T1 > &eigs, vnl_matrix< T1 > &eigVecs, vnl_matrix< T2 > &resMatrix) |
| Recompose tensor from values extracted using SymmetricEigenAnalysis (vnl_symmetric_eigensystem transposes all this) More... | |
| template<class ImageType > | |
| itk::SmartPointer< ImageType > | reorient3DImage (typename itk::SmartPointer< ImageType > input, itk::SpatialOrientation::ValidCoordinateOrientationFlags orientation) |
| template<class ImageType , class GradientType > | |
| void | reorientGradients (typename itk::SmartPointer< ImageType > input, std::vector< GradientType > &gradients) |
| template<class ImageType > | |
| itk::SmartPointer< ImageType > | reorientImage (typename itk::SmartPointer< ImageType > input, itk::SpatialOrientation::ValidCoordinateOrientationFlags orientation) |
| template<class VectorType > | |
| void | Revert (const VectorType &v, const unsigned int vSize, VectorType &resVec) |
| template<class ScalarType > | |
| void | Revert (const std::vector< ScalarType > &v, std::vector< ScalarType > &resVec) |
| template<class ScalarType > | |
| void | Revert (const itk::Point< ScalarType > &v, itk::Point< ScalarType > &resVec) |
| template<class ScalarType , unsigned int NDimension> | |
| void | Revert (const vnl_vector_fixed< ScalarType, NDimension > &v, vnl_vector_fixed< ScalarType, NDimension > &resVec) |
| template<class T1 , class T2 , class T3 , class T4 > | |
| void | RotateAroundAxis (const std::vector< T1 > &v, const T2 &phi, const std::vector< T3 > &normalVec, std::vector< T4 > &resVec) |
| template<class Vector3DType , class ScalarType > | |
| void | RotateAroundAxis (const Vector3DType &v, const ScalarType &phi, const Vector3DType &normalVec, Vector3DType &resVec) |
| template<class T1 , class T2 , class T3 > | |
| void | RotateSymmetricMatrix (T1 &tensor, T2 &rotationMatrix, T3 &rotated_tensor, unsigned int tensorDim) |
| Rotates a symmetric matrix by performing R^T D R where R is a rotation matrix and D the symmetric matrix. More... | |
| template<class T1 , class T2 > | |
| void | RotateSymmetricMatrix (vnl_matrix< T1 > &tensor, vnl_matrix< T2 > &rotationMatrix, vnl_matrix< T2 > &rotated_tensor) |
| template<class T1 , class T2 , unsigned int NDim> | |
| void | RotateSymmetricMatrix (itk::Matrix< T1, NDim, NDim > &tensor, itk::Matrix< T2, NDim, NDim > &rotationMatrix, itk::Matrix< T2, NDim, NDim > &rotated_tensor) |
| template<class ScalarType > | |
| double | safe_log (const ScalarType x) |
| template<class T > | |
| unsigned int | SampleFromBernoulliDistribution (const T &p, std::mt19937 &generator) |
| template<class T > | |
| double | SampleFromGaussianDistribution (const T &mean, const T &std, std::mt19937 &generator) |
| template<class VectorType , class ScalarType > | |
| void | SampleFromMultivariateGaussianDistribution (const VectorType &mean, const vnl_matrix< ScalarType > &mat, VectorType &resVec, std::mt19937 &generator, bool isMatCovariance=true) |
| template<class T > | |
| double | SampleFromUniformDistribution (const T &a, const T &b, std::mt19937 &generator) |
| template<class VectorType > | |
| void | SampleFromUniformDistributionOn2Sphere (std::mt19937 &generator, VectorType &resVec) |
| template<class VectorType , class ScalarType > | |
| void | SampleFromVMFDistribution (const ScalarType &kappa, const VectorType &meanDirection, VectorType &resVec, std::mt19937 &generator) |
| template<class VectorType , class ScalarType > | |
| void | SampleFromVMFDistributionNumericallyStable (const ScalarType &kappa, const VectorType &meanDirection, VectorType &resVec, std::mt19937 &generator) |
| template<class ScalarType , class VectorType > | |
| void | SampleFromWatsonDistribution (const ScalarType &kappa, const VectorType &meanDirection, VectorType &resVec, unsigned int DataDimension, std::mt19937 &generator) |
| template<class ScalarType , unsigned int DataDimension> | |
| void | SampleFromWatsonDistribution (const ScalarType &kappa, const vnl_vector_fixed< ScalarType, DataDimension > &meanDirection, vnl_vector_fixed< ScalarType, DataDimension > &resVec, std::mt19937 &generator) |
| template<class ScalarType , unsigned int DataDimension> | |
| void | SampleFromWatsonDistribution (const ScalarType &kappa, const itk::Point< ScalarType, DataDimension > &meanDirection, itk::Point< ScalarType, DataDimension > &resVec, std::mt19937 &generator) |
| template<class ScalarType , unsigned int DataDimension> | |
| void | SampleFromWatsonDistribution (const ScalarType &kappa, const itk::Vector< ScalarType, DataDimension > &meanDirection, itk::Vector< ScalarType, DataDimension > &resVec, std::mt19937 &generator) |
| template<class InputImageType , class ImageFilterType > | |
| unsigned int | setMultipleImageFilterInputsFromFileName (std::string &fileName, ImageFilterType *filter) |
| Set inputs of an image to image filter from a file name containing either a list of files or a higher dimensional image. More... | |
| template<class T > | |
| double | ShOverId (const T &x) |
| template<class T1 , class T2 , class T3 > | |
| double | ShRatio (const T1 &k, const T2 &alpha, const T3 &beta) |
| template<class T > | |
| double | SinOverId (const T &x) |
| template<class ScalarType > | |
| void | sphere_exp_map (const std::vector< ScalarType > &p, const std::vector< ScalarType > &x, std::vector< ScalarType > &expValue) |
| template<class ScalarType > | |
| void | sphere_log_map (const std::vector< ScalarType > &p, const std::vector< ScalarType > &x, std::vector< ScalarType > &logValue) |
| template<class VectorType > | |
| void | TransformCartesianToSphericalCoordinates (const VectorType &v, VectorType &resVec) |
| template<class VectorType > | |
| void | TransformSphericalToCartesianCoordinates (const VectorType &v, VectorType &resVec) |
| template<class VectorType > | |
| void | TransformSphericalToCartesianCoordinates (double theta, double phi, double vectorNorm, VectorType &resVec) |
| template<class ScalarType , class VectorType > | |
| void | UpperTriangularSolver (const vnl_matrix< ScalarType > &matrix, const VectorType &rhs, VectorType &result, unsigned int rank=0) |
| template<class T > | |
| double | VectorCovarianceTest (vnl_matrix< T > &logRefPatchCov, vnl_matrix< T > &movingPatchCov) |
| Test if covariance matrices are different (returns distance) More... | |
| template<class T > | |
| double | VectorMeansTest (itk::VariableLengthVector< T > &refPatchMean, itk::VariableLengthVector< T > &movingPatchMean, const unsigned int &refPatchNumElts, const unsigned int &movingPatchNumElts, vnl_matrix< T > &refPatchCov, vnl_matrix< T > &movingPatchCov) |
| Test if vector means are different (returns distance) More... | |
| template<class ScalarType , unsigned int Dimension> | |
| double | VMFDistance (const itk::Point< ScalarType, Dimension > &muFirst, const double &kappaFirst, const itk::Point< ScalarType, Dimension > &muSec, const double &kappaSec) |
| template<class OutputImageType > | |
| void | writeImage (std::string filename, OutputImageType *img) |
| template<class T > | |
| double | xi (const T &k) |
Variables | |
| const double | DiffusionBigDelta = 40.0e-3 |
| Default big delta value (classical values) More... | |
| const double | DiffusionGyromagneticRatio = 267.513e6 |
| Gyromagnetic ratio (in rad/s/T), from Nelson, J., Nuclear Magnetic Resonance Spectroscopy, Prentice Hall, Londres, 2003. More... | |
| const double | DiffusionSmallDelta = 10.0e-3 |
| Default small delta value (classical values) More... | |
| const double | MCMAxialDiffusivityAddonLowerBound = 5.0e-4 |
| Axial diffusivity add on to lower bound (used to ensure a minimal anisotropy to the anisotropic compartments) More... | |
| const double | MCMAzimuthAngleUpperBound = 2.0 * M_PI |
| Azimuth angle upper bound. More... | |
| const double | MCMCompartmentsFractionUpperBound = 1.0e7 |
| Compartment fractions upper bound (B0 times weight) More... | |
| const double | MCMConcentrationUpperBound = 128.0 |
| Concentration upper bound (used in NODDI and DDI) More... | |
| const double | MCMDiffusivityLowerBound = 1.0e-6 |
| Diffusivity lower bound for estimation. More... | |
| const double | MCMDiffusivityUpperBound = 3.0e-3 |
| Diffusivity upper bound. More... | |
| const double | MCMEpsilon = 1.0e-2 |
| Epsilon value in case we do not want to have parameters reaching their true bounds (used for now in DDI) More... | |
| const double | MCMFractionUpperBound = 1.0 |
| Fraction upper bound (intra/extra axonal) More... | |
| const double | MCMFreeWaterDiffusivityLowerBound = 2.0e-3 |
| Free water diffusivity lower bound. More... | |
| const double | MCMFreeWaterDiffusivityUpperBound = 4.0e-3 |
| Free water diffusivity upper bound. More... | |
| const double | MCMIsotropicRestrictedWaterDiffusivityLowerBound = 0.25e-4 |
| Isotropic restricted water diffusivity lower bound. More... | |
| const double | MCMIsotropicRestrictedWaterDiffusivityUpperBound = 2.0e-3 |
| Isotropic restricted water diffusivity upper bound. More... | |
| const double | MCMPolarAngleUpperBound = M_PI |
| Polar angle upper bound (used in tensor for now) More... | |
| const double | MCMRadialDiffusivityUpperBound = 1.0e-3 |
| Radial diffusivity upper bound. More... | |
| const double | MCMTissueRadiusLowerBound = 1.0e-4 |
| Tissue radius lower bound (in Stanisz for now) More... | |
| const double | MCMTissueRadiusUpperBound = 4.01e-2 |
| Tissue radius upper bound (in Stanisz for now) More... | |
| const double | MCMZeroLowerBound = 0.0 |
| Default zero lower bound (in case we want something else than zero one day) More... | |
| Enumerator | |
|---|---|
| FreeWater | |
| StationaryWater | |
| IsotropicRestrictedWater | |
| Stanisz | |
| Stick | |
| Zeppelin | |
| Tensor | |
| NODDI | |
| DDI | |
Definition at line 17 of file animaBaseCompartment.h.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::a0r_support | ( | double | x, |
| unsigned int | N | ||
| ) |
Support function for besserl_ratio_i.
Definition at line 155 of file animaBesselFunctions.cxx.
Referenced by bessel_ratio_i().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::ak_support | ( | double | x, |
| unsigned int | N, | ||
| unsigned int | k | ||
| ) |
Support function for besserl_ratio_i.
Definition at line 160 of file animaBesselFunctions.cxx.
Referenced by bessel_ratio_i().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::bessel_i_lower_bound | ( | unsigned int | N, |
| double | x | ||
| ) |
Computes a lower bound of the modified Bessel function of the first kind: I_{N} (N >= 0)
Definition at line 50 of file animaBesselFunctions.cxx.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::bessel_ratio_i | ( | double | x, |
| unsigned int | N, | ||
| unsigned int | approx_order | ||
| ) |
Computes the ratio of modified Bessel functions of the first kind: I_{N} / I_{N-1} (N >= 1)
Definition at line 76 of file animaBesselFunctions.cxx.
References a0r_support(), and ak_support().
Referenced by bessel_ratio_i_derivative(), and log_bessel_i().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::bessel_ratio_i_derivative | ( | double | x, |
| unsigned int | N, | ||
| unsigned int | approx_order | ||
| ) |
Computes the derivative of the ratio of modified Bessel functions of the first kind: d/dx( I_{N}(x) / I_{N-1}(x) ) (N >= 1)
Definition at line 110 of file animaBesselFunctions.cxx.
References bessel_ratio_i().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::bessel_ratio_i_derivative_approx | ( | double | x, |
| unsigned int | N | ||
| ) |
Computes fast and accurate approximation of the derivative of the ratio of modified Bessel functions of the first kind: d/dx( I_{N}(x) / I_{N-1}(x) ) (N >= 1)
Definition at line 120 of file animaBesselFunctions.cxx.
References bessel_ratio_i_lower_bound().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::bessel_ratio_i_lower_bound | ( | double | x, |
| unsigned int | N | ||
| ) |
Computes a lower bound of the ratio of modified Bessel functions of the first kind: I_{N} / I_{N-1} (N >= 1)
Definition at line 103 of file animaBesselFunctions.cxx.
Referenced by bessel_ratio_i_derivative_approx().
| ANIMASTATISTICALTESTS_EXPORT void anima::BHCorrection | ( | std::vector< double > & | pvalues, |
| double | qValue | ||
| ) |
In place correction of p-values according to Benjamini Hochberg FDR method Output is a thresholded list at the specified q-value Eq. (1) of Y. Benjamini and Y. Hochberg. Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society. Series B (Methodological) Vol. 57, No. 1 (1995), pp. 289-300
Definition at line 8 of file animaFDRCorrection.cxx.
Referenced by anima::FDRCorrectImageFilter< PixelScalarType >::GenerateData(), and anima::pair_increasing_comparator::operator()().
| ANIMASTATISTICALTESTS_EXPORT void anima::BYCorrection | ( | std::vector< double > & | pvalues, |
| double | qValue | ||
| ) |
Definition at line 33 of file animaFDRCorrection.cxx.
Referenced by anima::FDRCorrectImageFilter< PixelScalarType >::GenerateData(), and anima::pair_increasing_comparator::operator()().
| std::complex< double > anima::ComplexShRatio | ( | const ScalarType & | k, |
| const ScalarType & | alpha, | ||
| const ScalarType & | beta | ||
| ) |
Definition at line 20 of file animaHyperbolicFunctions.hxx.
| void anima::composeDistortionCorrections | ( | typename rpi::DisplacementFieldTransform< ScalarType, NDimensions >::Pointer & | baseTrsf, |
| typename rpi::DisplacementFieldTransform< ScalarType, NDimensions >::Pointer & | positiveAddOn, | ||
| typename rpi::DisplacementFieldTransform< ScalarType, NDimensions >::Pointer & | negativeAddOn, | ||
| unsigned int | numThreads | ||
| ) |
Compose distortion correction opposite updates, ensures opposite symmetry baseTrsf is replaced by the result !
Definition at line 251 of file animaVelocityUtils.hxx.
| void anima::composeSVF | ( | itk::StationaryVelocityFieldTransform< ScalarType, NDimensions > * | baseTrsf, |
| itk::StationaryVelocityFieldTransform< ScalarType, NDimensions > * | addonTrsf, | ||
| unsigned int | numThreads, | ||
| unsigned int | bchOrder | ||
| ) |
Performs BCH approximation to composition of exp(baseTrsf) and exp(addonTrsf). As explained in M. Bossa et al. "Contributions to 3D diffeomorphic atlas estimation : application to brain images.", MICCAI 2007, p. 667–674.
Definition at line 16 of file animaVelocityUtils.hxx.
Referenced by anima::BaseBMRegistrationMethod< TInputImageType >::ComposeAddOnWithTransform(), and main().
| itk::Point< TInput, NDimensions > anima::computeAffineLSWFromTranslations | ( | std::vector< itk::Point< TInput, NDimensions > > & | inputOrigins, |
| std::vector< itk::Point< TInput, NDimensions > > & | inputTransformed, | ||
| std::vector< TInput > & | weights, | ||
| typename itk::AffineTransform< TScalarType, NDimensions >::Pointer & | resultTransform | ||
| ) |
Definition at line 296 of file animaLinearTransformEstimationTools.hxx.
| double anima::ComputeAngle | ( | const VectorType & | v1, |
| const VectorType & | v2 | ||
| ) |
Definition at line 422 of file animaVectorOperations.hxx.
References ComputeNorm(), and ComputeScalarProduct().
| itk::Point< TInput, NDimensions > anima::computeAnisotropSimLSWFromTranslations | ( | std::vector< itk::Point< TInput, NDimensions > > & | inputOrigins, |
| std::vector< itk::Point< TInput, NDimensions > > & | inputTransformed, | ||
| std::vector< TInput > & | weights, | ||
| typename itk::AffineTransform< TScalarType, NDimensions >::Pointer & | resultTransform, | ||
| vnl_matrix< double > & | UMatrix | ||
| ) |
Definition at line 131 of file animaLinearTransformEstimationTools.hxx.
References pairingToQuaternion(), and pairingToQuaternionScalingsDerivative().
| void anima::computeAverageLocalCovariance | ( | vnl_matrix< T2 > & | resVariance, |
| itk::VectorImage< T1, Dimension > * | inputImage, | ||
| itk::Image< unsigned char, Dimension > * | maskImage, | ||
| const itk::ImageRegion< Dimension > & | averagingRegion, | ||
| int | localNeighborhood | ||
| ) |
Noise estimation for a patch of a vector image.
Definition at line 65 of file animaVectorImagePatchStatistics.hxx.
Referenced by anima::LowMemoryNLMeansPatientToGroupComparisonBridge::BuildAndWrite(), and anima::NLMeansVectorPatchSearcher< ImageScalarType, DataImageType >::ComputeInputProperties().
| void anima::ComputeCrossProduct | ( | const VectorType & | v1, |
| const VectorType & | v2, | ||
| const unsigned int | NDimension, | ||
| VectorType & | resVec | ||
| ) |
Definition at line 254 of file animaVectorOperations.hxx.
Referenced by ComputeCrossProduct(), and SampleFromWatsonDistribution().
| void anima::ComputeCrossProduct | ( | const itk::Vector< ScalarType, NDimension > & | v1, |
| const itk::Vector< ScalarType, NDimension > & | v2, | ||
| itk::Vector< ScalarType, NDimension > & | resVec | ||
| ) |
Definition at line 264 of file animaVectorOperations.hxx.
References ComputeCrossProduct().
| void anima::ComputeCrossProduct | ( | const itk::VariableLengthVector< ScalarType > & | v1, |
| const itk::VariableLengthVector< ScalarType > & | v2, | ||
| itk::VariableLengthVector< ScalarType > & | resVec | ||
| ) |
Definition at line 269 of file animaVectorOperations.hxx.
References ComputeCrossProduct().
| void anima::ComputeCrossProduct | ( | const itk::Point< ScalarType, NDimension > & | v1, |
| const itk::Point< ScalarType, NDimension > & | v2, | ||
| itk::Point< ScalarType, NDimension > & | resVec | ||
| ) |
Definition at line 280 of file animaVectorOperations.hxx.
References ComputeCrossProduct().
| void anima::ComputeCrossProduct | ( | const vnl_vector< ScalarType > & | v1, |
| const vnl_vector< ScalarType > & | v2, | ||
| vnl_vector< ScalarType > & | resVec | ||
| ) |
Definition at line 285 of file animaVectorOperations.hxx.
References ComputeCrossProduct().
| void anima::ComputeCrossProduct | ( | const vnl_vector_fixed< ScalarType, NDimension > & | v1, |
| const vnl_vector_fixed< ScalarType, NDimension > & | v2, | ||
| vnl_vector_fixed< ScalarType, NDimension > & | resVec | ||
| ) |
Definition at line 296 of file animaVectorOperations.hxx.
References ComputeCrossProduct().
| void anima::ComputeCrossProduct | ( | const std::vector< ScalarType > & | v1, |
| const std::vector< ScalarType > & | v2, | ||
| std::vector< ScalarType > & | resVec | ||
| ) |
Definition at line 301 of file animaVectorOperations.hxx.
References ComputeCrossProduct().
| double anima::ComputeDirectedHausdorffDistance | ( | const std::vector< VectorType > & | s1, |
| const std::vector< VectorType > & | s2 | ||
| ) |
Definition at line 92 of file animaVectorOperations.hxx.
References ComputePointToSetDistance().
Referenced by ComputeHausdorffDistance().
| double anima::ComputeEuclideanDistance | ( | const VectorType & | x1, |
| const VectorType & | x2, | ||
| const unsigned int | NDimension | ||
| ) |
Definition at line 14 of file animaVectorOperations.hxx.
Referenced by ComputeEuclideanDistance(), ComputePointToSetDistance(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::UpdateClassesMemberships().
| double anima::ComputeEuclideanDistance | ( | const itk::Vector< ScalarType, NDimension > & | x1, |
| const itk::Vector< ScalarType, NDimension > & | x2 | ||
| ) |
Definition at line 26 of file animaVectorOperations.hxx.
References ComputeEuclideanDistance().
| double anima::ComputeEuclideanDistance | ( | const itk::VariableLengthVector< ScalarType > & | x1, |
| const itk::VariableLengthVector< ScalarType > & | x2 | ||
| ) |
Definition at line 31 of file animaVectorOperations.hxx.
References ComputeEuclideanDistance().
| double anima::ComputeEuclideanDistance | ( | const itk::Point< ScalarType, NDimension > & | x1, |
| const itk::Point< ScalarType, NDimension > & | x2 | ||
| ) |
Definition at line 41 of file animaVectorOperations.hxx.
References ComputeEuclideanDistance().
| double anima::ComputeEuclideanDistance | ( | const vnl_vector< ScalarType > & | x1, |
| const vnl_vector< ScalarType > & | x2 | ||
| ) |
Definition at line 46 of file animaVectorOperations.hxx.
References ComputeEuclideanDistance().
| double anima::ComputeEuclideanDistance | ( | const vnl_vector_fixed< ScalarType, NDimension > & | x1, |
| const vnl_vector_fixed< ScalarType, NDimension > & | x2 | ||
| ) |
Definition at line 57 of file animaVectorOperations.hxx.
References ComputeEuclideanDistance().
| double anima::ComputeEuclideanDistance | ( | const std::vector< ScalarType > & | x1, |
| const std::vector< ScalarType > & | x2 | ||
| ) |
Definition at line 62 of file animaVectorOperations.hxx.
References ComputeEuclideanDistance().
| double anima::ComputeHausdorffDistance | ( | const std::vector< VectorType > & | s1, |
| const std::vector< VectorType > & | s2 | ||
| ) |
Definition at line 110 of file animaVectorOperations.hxx.
References ComputeDirectedHausdorffDistance().
| void anima::ComputeHouseholderVector | ( | const VectorType & | inputVector, |
| VectorType & | outputVector, | ||
| double & | beta, | ||
| unsigned int | dimension | ||
| ) |
Definition at line 376 of file animaVectorOperations.hxx.
Referenced by ComputeHouseholderVector(), and QRPivotDecomposition().
| void anima::ComputeHouseholderVector | ( | const std::vector< ScalarType > & | inputVector, |
| std::vector< ScalarType > & | outputVector, | ||
| double & | beta | ||
| ) |
Definition at line 406 of file animaVectorOperations.hxx.
References ComputeHouseholderVector().
| void anima::ComputeHouseholderVector | ( | std::vector< ScalarType > & | vector, |
| double & | beta | ||
| ) |
Definition at line 415 of file animaVectorOperations.hxx.
References ComputeHouseholderVector().
| void anima::computeLogEuclideanAverage | ( | std::vector< vnl_matrix< TInput > > & | inputTransforms, |
| std::vector< TInput > & | weights, | ||
| typename itk::AffineTransform< TScalarType, NDimensions >::Pointer & | resultTransform | ||
| ) |
Definition at line 261 of file animaLinearTransformEstimationTools.hxx.
References GetExponential().
| double anima::ComputeModifiedDirectedHausdorffDistance | ( | const std::vector< VectorType > & | s1, |
| const std::vector< VectorType > & | s2 | ||
| ) |
Definition at line 119 of file animaVectorOperations.hxx.
References ComputePointToSetDistance().
Referenced by ComputeModifiedHausdorffDistance(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::UpdateClassesMemberships().
| double anima::ComputeModifiedHausdorffDistance | ( | const std::vector< VectorType > & | s1, |
| const std::vector< VectorType > & | s2 | ||
| ) |
Definition at line 132 of file animaVectorOperations.hxx.
References ComputeModifiedDirectedHausdorffDistance().
| double anima::ComputeNorm | ( | const VectorType & | v | ) |
Definition at line 314 of file animaVectorOperations.hxx.
References ComputeScalarProduct().
Referenced by ComputeAngle(), ComputeOrientationAngle(), ComputeVMFPdf(), Normalize(), SampleFromWatsonDistribution(), TransformCartesianToSphericalCoordinates(), anima::GradientFileReader< GradientType, BValueScalarType >::Update(), and anima::NODDICompartment::UpdateSignals().
| double anima::ComputeOrientationAngle | ( | const VectorType & | v1, |
| const VectorType & | v2 | ||
| ) |
Definition at line 437 of file animaVectorOperations.hxx.
References ComputeNorm(), and ComputeScalarProduct().
Referenced by anima::BaseTractographyImageFilter::ComputeFiber(), and anima::ODFProbabilisticTractographyImageFilter::FindODFMaxima().
| unsigned int anima::computePatchMeanAndCovariance | ( | const itk::VectorImage< T1, Dimension > * | inputImage, |
| const itk::ImageRegion< Dimension > & | patchRegion, | ||
| itk::VariableLengthVector< T2 > & | patchMean, | ||
| vnl_matrix< T2 > & | patchCov | ||
| ) |
Computes the average and covariance matrix from a patch of a vector image.
Definition at line 11 of file animaVectorImagePatchStatistics.hxx.
Referenced by anima::NLMeansVectorPatchSearcher< ImageScalarType, DataImageType >::ComputeComparisonProperties(), anima::NLMeansVectorPatchSearcher< ImageScalarType, DataImageType >::ComputeInputProperties(), anima::LocalPatchCovarianceDistanceImageFilter< PixelScalarType >::DynamicThreadedGenerateData(), and anima::LocalPatchMeanDistanceImageFilter< PixelScalarType >::DynamicThreadedGenerateData().
| double anima::ComputePointToSetDistance | ( | const VectorType & | x, |
| const std::vector< VectorType > & | s | ||
| ) |
Definition at line 74 of file animaVectorOperations.hxx.
References ComputeEuclideanDistance().
Referenced by ComputeDirectedHausdorffDistance(), ComputeModifiedDirectedHausdorffDistance(), and anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::UpdateClassesMemberships().
| void anima::computeRigidLSWFromTranslations | ( | std::vector< itk::Point< TInput, NDimensions > > & | inputOrigins, |
| std::vector< itk::Point< TInput, NDimensions > > & | inputTransformed, | ||
| std::vector< TInput > & | weights, | ||
| typename itk::AffineTransform< TScalarType, NDimensions >::Pointer & | resultTransform | ||
| ) |
Definition at line 63 of file animaLinearTransformEstimationTools.hxx.
References pairingToQuaternion().
| vnl_matrix< TOutput > anima::computeRotationFromQuaternion | ( | vnl_vector< TInput > | eigenVector | ) |
Definition at line 363 of file animaLinearTransformEstimationTools.hxx.
| double anima::ComputeScalarProduct | ( | const VectorType & | v1, |
| const VectorType & | v2, | ||
| const unsigned int | NDimension | ||
| ) |
Definition at line 196 of file animaVectorOperations.hxx.
Referenced by ComputeAngle(), anima::BaseTractographyImageFilter::ComputeFiber(), ComputeNorm(), ComputeOrientationAngle(), ComputeScalarProduct(), ComputeVMFPdf(), EvaluateWatsonPDF(), anima::NODDICompartment::GetLogDiffusionProfile(), anima::StickCompartment::GetLogDiffusionProfile(), anima::ZeppelinCompartment::GetLogDiffusionProfile(), anima::dtiTractographyImageFilter::GetNextDirection(), anima::NODDICompartment::GetSignalAttenuationJacobian(), anima::TensorCompartment::GetSignalAttenuationJacobian(), anima::DTIProbabilisticTractographyImageFilter::InitializeFirstIterationFromModel(), anima::ODFProbabilisticTractographyImageFilter::InitializeFirstIterationFromModel(), anima::BaseCompartment::IsEqual(), ProjectOnOrthogonalPlane(), anima::DTIProbabilisticTractographyImageFilter::ProposeNewDirection(), anima::ODFProbabilisticTractographyImageFilter::ProposeNewDirection(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks(), and anima::NODDICompartment::UpdateSignals().
| double anima::ComputeScalarProduct | ( | const itk::Vector< ScalarType, NDimension > & | v1, |
| const itk::Vector< ScalarType, NDimension > & | v2 | ||
| ) |
Definition at line 206 of file animaVectorOperations.hxx.
References ComputeScalarProduct().
| double anima::ComputeScalarProduct | ( | const itk::VariableLengthVector< ScalarType > & | v1, |
| const itk::VariableLengthVector< ScalarType > & | v2 | ||
| ) |
Definition at line 211 of file animaVectorOperations.hxx.
References ComputeScalarProduct().
| double anima::ComputeScalarProduct | ( | const itk::Point< ScalarType, NDimension > & | v1, |
| const itk::Point< ScalarType, NDimension > & | v2 | ||
| ) |
Definition at line 221 of file animaVectorOperations.hxx.
References ComputeScalarProduct().
| double anima::ComputeScalarProduct | ( | const vnl_vector< ScalarType > & | v1, |
| const vnl_vector< ScalarType > & | v2 | ||
| ) |
Definition at line 226 of file animaVectorOperations.hxx.
References ComputeScalarProduct().
| double anima::ComputeScalarProduct | ( | const vnl_vector_fixed< ScalarType, NDimension > & | v1, |
| const vnl_vector_fixed< ScalarType, NDimension > & | v2 | ||
| ) |
Definition at line 236 of file animaVectorOperations.hxx.
References ComputeScalarProduct().
| double anima::ComputeScalarProduct | ( | const std::vector< ScalarType > & | v1, |
| const std::vector< ScalarType > & | v2 | ||
| ) |
Definition at line 241 of file animaVectorOperations.hxx.
References ComputeScalarProduct().
| void anima::ComputeSphericalCentroid | ( | const std::vector< std::vector< ScalarType > > & | dataPoints, |
| std::vector< ScalarType > & | centroidValue, | ||
| const std::vector< ScalarType > & | initPoint, | ||
| const std::vector< ScalarType > & | weights, | ||
| std::vector< ScalarType > * | workLogVector = 0, |
||
| std::vector< ScalarType > * | workVector = 0, |
||
| double | tol = 1.0e-4 |
||
| ) |
Computes the weighted average of several points on the hyper-sphere.
| dataPoints | List of points on the sphere |
| initPoint | Starting point for average computation |
| weights | Weights for each point |
| workLogVector | Optional work variable (for speed up) to compute the logarithms, to avoid creating it inside this function |
| workVector | Optional work variable (for speed up), to avoid creating it inside this function |
| tol | Tolerance for convergence |
Definition at line 55 of file animaLogExpMapsUnitSphere.hxx.
References sphere_exp_map(), and sphere_log_map().
Referenced by anima::FuzzyCMeansFilter< double >::ComputeCentroids(), and main().
| void anima::computeTranslationLSWFromTranslations | ( | std::vector< itk::Point< TInput, NDimensions > > & | inputOrigins, |
| std::vector< itk::Point< TInput, NDimensions > > & | inputTransformed, | ||
| std::vector< TInput > & | weights, | ||
| typename itk::AffineTransform< TScalarType, NDimensions >::Pointer & | resultTransform | ||
| ) |
Definition at line 17 of file animaLinearTransformEstimationTools.hxx.
| double anima::ComputeVMFPdf | ( | const VectorType & | v, |
| const VectorType & | meanDirection, | ||
| const ScalarType & | kappa | ||
| ) |
Definition at line 15 of file animaVMFDistribution.hxx.
References ComputeNorm(), and ComputeScalarProduct().
| T anima::Cubic | ( | T | x0, |
| T | x1, | ||
| T | x2, | ||
| T | x3, | ||
| T | y0, | ||
| T | y1, | ||
| T | y2, | ||
| T | y3, | ||
| T | x | ||
| ) |
Definition at line 9 of file animaCubicInterpolation.hxx.
Referenced by InverseCubicInterpolator().
| void anima::CubicInterpolator | ( | std::vector< T > & | transfVect, |
| std::vector< T > & | scale, | ||
| std::vector< T > & | outputVect, | ||
| T | LengthLine | ||
| ) |
Definition at line 81 of file animaCubicInterpolation.hxx.
| ANIMASHTOOLS_EXPORT void anima::EstimateLocalODFRotationMatrix | ( | vnl_matrix< double > & | resVal, |
| unsigned int | l, | ||
| double | alpha, | ||
| double | beta, | ||
| double | gamma | ||
| ) |
Definition at line 154 of file animaODFFunctions.cxx.
References GetDValue().
Referenced by anima::ODFResampleImageFilter< TImageType, TInterpolatorPrecisionType >::ReorientInterpolatedModel().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::EvaluateDawsonFunction | ( | double | x | ) |
compute Dawson(x) = sqrt(pi)/2 * exp(-x^2) * erfi(x)
Definition at line 57 of file animaErrorFunctions.cxx.
References EvaluateWImFunction().
Referenced by anima::DawsonIntegrand::operator()().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::EvaluateDawsonFunctionNR | ( | double | x | ) |
Numerical recipes implementation of Dawson integral.
Definition at line 20 of file animaErrorFunctions.cxx.
Referenced by EvaluateWatsonPDF(), and anima::DawsonIntegrand::operator()().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::EvaluateDawsonIntegral | ( | const double | x, |
| const bool | scaled | ||
| ) |
Definition at line 11 of file animaErrorFunctions.cxx.
References anima::DawsonIntegrand::SetXValue().
Referenced by GetStandardWatsonSHCoefficients(), anima::DawsonIntegrand::operator()(), and anima::NODDICompartment::UpdateKappaValues().
| double anima::EvaluateWatsonPDF | ( | const VectorType & | v, |
| const VectorType & | meanAxis, | ||
| const ScalarType & | kappa | ||
| ) |
Definition at line 17 of file animaWatsonDistribution.hxx.
References ComputeScalarProduct(), and EvaluateDawsonFunctionNR().
Referenced by anima::DTIProbabilisticTractographyImageFilter::ComputeLogWeightUpdate(), anima::ODFProbabilisticTractographyImageFilter::ComputeLogWeightUpdate(), anima::DTIProbabilisticTractographyImageFilter::ProposeNewDirection(), and anima::ODFProbabilisticTractographyImageFilter::ProposeNewDirection().
| double anima::EvaluateWatsonPDF | ( | const vnl_vector_fixed< ScalarType, 3 > & | v, |
| const vnl_vector_fixed< ScalarType, 3 > & | meanAxis, | ||
| const ScalarType & | kappa | ||
| ) |
Definition at line 56 of file animaWatsonDistribution.hxx.
| double anima::EvaluateWatsonPDF | ( | const itk::Point< ScalarType, 3 > & | v, |
| const itk::Point< ScalarType, 3 > & | meanAxis, | ||
| const ScalarType & | kappa | ||
| ) |
Definition at line 65 of file animaWatsonDistribution.hxx.
| double anima::EvaluateWatsonPDF | ( | const itk::Vector< ScalarType, 3 > & | v, |
| const itk::Vector< ScalarType, 3 > & | meanAxis, | ||
| const ScalarType & | kappa | ||
| ) |
Definition at line 74 of file animaWatsonDistribution.hxx.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::EvaluateWImFunction | ( | double | x | ) |
Definition at line 63 of file animaErrorFunctions.cxx.
References EvaluateWImY100Function().
Referenced by EvaluateDawsonFunction(), and anima::DawsonIntegrand::operator()().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::EvaluateWImY100Function | ( | double | y100, |
| double | x | ||
| ) |
Definition at line 96 of file animaErrorFunctions.cxx.
Referenced by EvaluateWImFunction(), and anima::DawsonIntegrand::operator()().
| double anima::ExponentialSum | ( | const VectorType & | x, |
| const unsigned int | NDimension | ||
| ) |
Definition at line 142 of file animaVectorOperations.hxx.
Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::ComputeFiber(), and ExponentialSum().
| double anima::ExponentialSum | ( | const itk::Vector< ScalarType, NDimension > & | x | ) |
Definition at line 160 of file animaVectorOperations.hxx.
References ExponentialSum().
| double anima::ExponentialSum | ( | const itk::VariableLengthVector< ScalarType > & | x | ) |
Definition at line 165 of file animaVectorOperations.hxx.
References ExponentialSum().
| double anima::ExponentialSum | ( | const itk::Point< ScalarType, NDimension > & | x | ) |
Definition at line 171 of file animaVectorOperations.hxx.
References ExponentialSum().
| double anima::ExponentialSum | ( | const vnl_vector< ScalarType > & | x | ) |
Definition at line 176 of file animaVectorOperations.hxx.
References ExponentialSum().
| double anima::ExponentialSum | ( | const vnl_vector_fixed< ScalarType, NDimension > & | x | ) |
Definition at line 182 of file animaVectorOperations.hxx.
References ExponentialSum().
| double anima::ExponentialSum | ( | const std::vector< ScalarType > & | x | ) |
Definition at line 187 of file animaVectorOperations.hxx.
References ExponentialSum().
| void anima::ExtractPPDRotationFromJacobianMatrix | ( | vnl_matrix< RealType > & | jacobianMatrix, |
| vnl_matrix< RealType > & | rotationMatrix, | ||
| MatrixType & | eigenVectors | ||
| ) |
Definition at line 192 of file animaBaseTensorTools.hxx.
References GetRotationMatrixFromVectors(), and Normalize().
Referenced by anima::TensorMeanSquaresImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorGeneralizedCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorCompartment::Reorient(), and anima::TensorResampleImageFilter< TImageType, TInterpolatorPrecisionType >::ReorientInterpolatedModel().
| void anima::ExtractRotationFromJacobianMatrix | ( | vnl_matrix< RealType > & | jacobianMatrix, |
| vnl_matrix< RealType > & | rotationMatrix, | ||
| vnl_matrix< RealType > & | tmpMat | ||
| ) |
Definition at line 157 of file animaBaseTensorTools.hxx.
References RecomposeTensor().
Referenced by anima::OrientedModelBaseResampleImageFilter< TImageType, TInterpolatorPrecisionType >::ComputeRotationParametersFromReorientationMatrix(), and anima::BaseOrientedModelImageToImageMetric< anima::MCMImage< TFixedImagePixelType, ImageDimension >, anima::MCMImage< TMovingImagePixelType, ImageDimension > >::SetTransformParameters().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::gammaHalfMinusN | ( | unsigned int | n | ) |
Definition at line 33 of file animaGammaFunctions.cxx.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::gammaHalfPlusN | ( | unsigned int | n | ) |
Definition at line 23 of file animaGammaFunctions.cxx.
| void anima::Get3DRotationExponential | ( | const std::vector< T > & | angles, |
| vnl_matrix< T > & | outputRotation | ||
| ) |
Computation of a 3D rotation matrix exponential. Rodrigues' explicit formula.
Definition at line 300 of file animaMatrixLogExp.hxx.
References anima::MatrixLoggerFilter< TInputScalarType, TOutputScalarType, NDimensions, NDegreesOfFreedom >::Update().
Referenced by anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::ComputeCostAtPosition(), anima::SplitAffine3DTransform< TScalarType >::ComputeMatrix(), and anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DynamicThreadedGenerateData().
| void anima::Get3DRotationLogarithm | ( | const vnl_matrix< T > & | rotationMatrix, |
| std::vector< T > & | outputAngles | ||
| ) |
Computation of a 3D rotation matrix logarithm. Rodrigues' explicit formula.
Definition at line 272 of file animaMatrixLogExp.hxx.
Referenced by anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DynamicThreadedGenerateData().
|
inline |
Given gyromagnetic ratio in rad/s/T, gradient strength in T/mm and deltas in s, computes b-value in s/mm^2.
Definition at line 13 of file animaMCMConstants.h.
Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::CheckComputationMask(), anima::ApproximateMCMSmoothingCostFunction::GetDerivative(), anima::BaseIsotropicCompartment::GetFourierTransformedDiffusionProfile(), anima::NODDICompartment::GetFourierTransformedDiffusionProfile(), anima::StickCompartment::GetFourierTransformedDiffusionProfile(), anima::ZeppelinCompartment::GetFourierTransformedDiffusionProfile(), anima::TensorCompartment::GetFourierTransformedDiffusionProfile(), anima::BaseIsotropicCompartment::GetSignalAttenuationJacobian(), anima::NODDICompartment::GetSignalAttenuationJacobian(), anima::StaniszCompartment::GetSignalAttenuationJacobian(), anima::StickCompartment::GetSignalAttenuationJacobian(), anima::ZeppelinCompartment::GetSignalAttenuationJacobian(), anima::TensorCompartment::GetSignalAttenuationJacobian(), anima::ApproximateMCMSmoothingCostFunction::GetValue(), anima::MCML2DistanceComputer::UpdateSphereWeights(), and anima::MCMCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::UpdateSphereWeights().
| ANIMASHTOOLS_EXPORT double anima::GetDValue | ( | unsigned int | l, |
| int | m, | ||
| int | mp, | ||
| double | angle | ||
| ) |
Definition at line 99 of file animaODFFunctions.cxx.
Referenced by EstimateLocalODFRotationMatrix().
| ANIMASHTOOLS_EXPORT void anima::GetEulerAnglesFromRotationMatrix | ( | vnl_matrix< double > & | R, |
| std::vector< double > & | resVal | ||
| ) |
Definition at line 74 of file animaODFFunctions.cxx.
Referenced by anima::ODFResampleImageFilter< TImageType, TInterpolatorPrecisionType >::ReorientInterpolatedModel().
| vnl_matrix< T > anima::GetExponential | ( | const vnl_matrix< T > & | m, |
| const int | numApprox = 1 |
||
| ) |
Computation of the matrix exponential. Algo: classical scaling and squaring, as in Matlab. See Higham, SIAM Matr. Anal., 2004.
Definition at line 198 of file animaMatrixLogExp.hxx.
Referenced by computeLogEuclideanAverage(), anima::LogRigid3DTransform< TScalarType >::ComputeMatrix(), main(), anima::SymmetricBMRegistrationMethod< TInputImageType >::PerformOneIteration(), and anima::KissingSymmetricBMRegistrationMethod< TInputImageType >::PerformOneIteration().
|
inline |
Given b-value in s/mm^2 and deltas in s, computes gradient strength in T/mm.
Definition at line 20 of file animaMCMConstants.h.
Referenced by anima::StaniszCompartment::GetLogDiffusionProfile(), and anima::GradientFileReader< GradientType, BValueScalarType >::Update().
| std::vector< itk::SmartPointer <OutputImageType> > anima::getImagesFromHigherDimensionImage | ( | InputImageType * | inputImage | ) |
Get a vector of input images from a higher dimensional image.
Definition at line 42 of file animaReadWriteFunctions.h.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::GetKummerFunctionValue | ( | const double & | x, |
| const double & | a, | ||
| const double & | b, | ||
| const unsigned int | maxIter, | ||
| const double | tol | ||
| ) |
Computes the confluent hypergeometric function 1F1 also known as the Kummer function M. It calls Kummer function core to get the value.
Definition at line 112 of file animaKummerFunctions.cxx.
References KummerIntegrandMethod(), KummerMethod1(), and KummerMethod2().
Referenced by main(), and anima::NODDICompartment::UpdateSignals().
| vnl_matrix< T > anima::GetLogarithm | ( | const vnl_matrix< T > & | m, |
| const double | precision = 0.00000000001, |
||
| const int | numApprox = 1 |
||
| ) |
Computation of the matrix logarithm. Algo: inverse scaling and squaring, variant proposed by Cheng et al., SIAM Matrix Anal., 2001.
Definition at line 145 of file animaMatrixLogExp.hxx.
References GetPadeLogarithm(), and GetSquareRoot().
Referenced by anima::MatrixLoggerFilter< TInputScalarType, TOutputScalarType, NDimensions, NDegreesOfFreedom >::InternalLogger(), main(), anima::SymmetricBMRegistrationMethod< TInputImageType >::PerformOneIteration(), anima::KissingSymmetricBMRegistrationMethod< TInputImageType >::PerformOneIteration(), anima::LSWTransformAgregator< NDimensions >::Update(), anima::MEstTransformAgregator< NDimensions >::Update(), and anima::LTSWTransformAgregator< NDimensions >::Update().
| itk::ImageIOBase::IOComponentType ANIMAMCMBASE_EXPORT anima::GetMCMComponentType | ( | std::string | fileName | ) |
Definition at line 8 of file animaMCMFileReader.cxx.
| vnl_matrix<T> anima::GetPadeLogarithm | ( | const vnl_matrix< double > & | m, |
| const int | numApprox | ||
| ) |
Final part of the computation of the log. Estimates the log with a Pade approximation for a matrix m such that |m-Id| <= 0.5.
Referenced by GetLogarithm().
| vnl_matrix<T> anima::GetPadeLogarithm | ( | const vnl_matrix< T > & | m, |
| const int | numApprox | ||
| ) |
Definition at line 65 of file animaMatrixLogExp.hxx.
| void anima::GetQMatrixQRPivoDecomposition | ( | vnl_matrix< ScalarType > & | qrMatrix, |
| std::vector< ScalarType > & | houseBetaValues, | ||
| vnl_matrix< ScalarType > & | qMatrix, | ||
| unsigned int | rank | ||
| ) |
From the results of QR decomposition, compute Q from the obtained matrix in QRPivotDecomposition, beta values
| void anima::GetQMatrixQRPivotDecomposition | ( | vnl_matrix< ScalarType > & | qrMatrix, |
| std::vector< ScalarType > & | houseBetaValues, | ||
| vnl_matrix< ScalarType > & | qMatrix, | ||
| unsigned int | rank | ||
| ) |
Definition at line 245 of file animaQRDecomposition.hxx.
Referenced by main().
| void anima::GetQtBFromQRPivotDecomposition | ( | vnl_matrix< ScalarType > & | qrMatrix, |
| vnl_vector< ScalarType > & | bVector, | ||
| std::vector< ScalarType > & | houseBetaValues, | ||
| unsigned int | rank | ||
| ) |
From the results of QR decomposition, compute QtB from the obtained matrix in QRPivotDecomposition, beta values and provided vector B
Definition at line 221 of file animaQRDecomposition.hxx.
Referenced by main(), and anima::BoundedLevenbergMarquardtOptimizer::StartOptimization().
| itk::Matrix< double, 3, 3 > anima::GetRotationMatrixFromVectors | ( | const VectorType & | first_direction, |
| const VectorType & | second_direction, | ||
| const unsigned int | dimension | ||
| ) |
Definition at line 13 of file animaMatrixOperations.hxx.
References pairingToQuaternion().
Referenced by ExtractPPDRotationFromJacobianMatrix(), GetRotationMatrixFromVectors(), SampleFromVMFDistribution(), SampleFromVMFDistributionNumericallyStable(), anima::AxisRotationTransform< TScalarType >::SetReferencePlaneNormal(), and anima::PyramidalSymmetryConstrainedRegistrationBridge< ScalarType >::SetupPyramids().
| itk::Matrix< double, 3, 3 > anima::GetRotationMatrixFromVectors | ( | const itk::Point< ScalarType > & | first_direction, |
| const itk::Point< ScalarType > & | second_direction | ||
| ) |
Definition at line 54 of file animaMatrixOperations.hxx.
References GetRotationMatrixFromVectors().
| itk::Matrix< double, 3, 3 > anima::GetRotationMatrixFromVectors | ( | const itk::Vector< ScalarType, NDimension > & | first_direction, |
| const itk::Vector< ScalarType, NDimension > & | second_direction | ||
| ) |
Definition at line 62 of file animaMatrixOperations.hxx.
References GetRotationMatrixFromVectors().
| itk::Matrix< double, 3, 3 > anima::GetRotationMatrixFromVectors | ( | const vnl_vector_fixed< ScalarType, NDimension > & | first_direction, |
| const vnl_vector_fixed< ScalarType, NDimension > & | second_direction | ||
| ) |
Definition at line 69 of file animaMatrixOperations.hxx.
References GetRotationMatrixFromVectors().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::GetScaledKummerFunctionValue | ( | const double & | x, |
| const double & | a, | ||
| const double & | b, | ||
| const unsigned int | maxIter, | ||
| const double | tol | ||
| ) |
Computes the confluent hypergeometric function 1F1 also known as the Kummer function M. It returns a scaled value: exp(-x) * M(x,a,b).
Definition at line 154 of file animaKummerFunctions.cxx.
References KummerIntegrandMethod(), KummerMethod1(), and KummerMethod2().
| void anima::GetSphereEvenSampling | ( | std::vector< std::vector< ScalarType > > & | spherePoints, |
| unsigned int | numSamples | ||
| ) |
Computes N samples almost evenly spread on the half-sphere. C.G. Koay. A simple scheme for generating nearly uniform distribution of antipodally symmetric pointson the unit sphere Journal of computer science, 2, 2011, pp. 377-381
| spherePoints | output vector containing all sampled point |
| numSamples | number of output samples required |
Definition at line 8 of file animaSphereOperations.hxx.
Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData().
| vnl_matrix< T > anima::GetSquareRoot | ( | const vnl_matrix< T > & | m, |
| const double | precision, | ||
| vnl_matrix< T > & | resultM | ||
| ) |
Gets the square root of matrix m.
Definition at line 13 of file animaMatrixLogExp.hxx.
Referenced by GetLogarithm().
| void anima::GetStandardWatsonSHCoefficients | ( | const ScalarType | k, |
| std::vector< ScalarType > & | coefficients, | ||
| std::vector< ScalarType > & | derivatives | ||
| ) |
Definition at line 83 of file animaWatsonDistribution.hxx.
References EvaluateDawsonIntegral().
Referenced by anima::NODDICompartment::UpdateKappaValues().
| void anima::GetSVFExponential | ( | itk::StationaryVelocityFieldTransform< ScalarType, NDimensions > * | baseTrsf, |
| rpi::DisplacementFieldTransform< ScalarType, NDimensions > * | resultTransform, | ||
| unsigned int | exponentiationOrder, | ||
| unsigned int | numThreads, | ||
| bool | invert | ||
| ) |
Definition at line 208 of file animaVelocityUtils.hxx.
Referenced by anima::TransformSeriesReader< TScalarType, NDimensions >::addSVFTransformation(), anima::DistortionCorrectionBMRegistrationMethod< TInputImageType >::ComposeAddOnWithTransform(), anima::PyramidalDenseSVFMatchingBridge< ImageDimension >::GetOutputDisplacementFieldTransform(), main(), anima::BaseBMRegistrationMethod< TInputImageType >::ResampleImages(), anima::PyramidalDenseSVFMatchingBridge< ImageDimension >::Update(), anima::PyramidalDenseTensorSVFMatchingBridge< ImageDimension >::Update(), and anima::PyramidalDenseMCMSVFMatchingBridge< ImageDimension >::Update().
| void anima::GetTensorFromVectorRepresentation | ( | const itk::VariableLengthVector< T1 > & | vector, |
| vnl_matrix< T2 > & | tensor, | ||
| unsigned int | tensDim = 0, |
||
| bool | scale = false |
||
| ) |
Definition at line 107 of file animaBaseTensorTools.hxx.
Referenced by anima::dtiTractographyImageFilter::CheckModelCompatibility(), anima::dtiTractographyImageFilter::ComputeAdditionalScalarMaps(), anima::DTIProbabilisticTractographyImageFilter::ComputeAdditionalScalarMaps(), anima::DTIProbabilisticTractographyImageFilter::ComputeModelValue(), anima::MCMWeightedAverager::ComputeOutputTensorCompatibleModel(), anima::ExpTensorImageFilter< TScalarType, NDimensions >::DynamicThreadedGenerateData(), anima::LogTensorImageFilter< TScalarType, NDimensions >::DynamicThreadedGenerateData(), anima::DTIScalarMapsImageFilter< ImageDimension >::DynamicThreadedGenerateData(), anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DynamicThreadedGenerateData(), anima::dtiTractographyImageFilter::GetModelPrincipalDirection(), anima::dtiTractographyImageFilter::GetNextDirection(), anima::TensorMeanSquaresImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorGeneralizedCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorResampleImageFilter< TImageType, TInterpolatorPrecisionType >::ReorientInterpolatedModel(), and anima::TensorCompartment::SetCompartmentVector().
| void anima::GetVectorRepresentation | ( | const vnl_matrix< T1 > & | tensor, |
| itk::VariableLengthVector< T2 > & | vector, | ||
| unsigned int | vecDim = 0, |
||
| bool | scale = false |
||
| ) |
Definition at line 83 of file animaBaseTensorTools.hxx.
Referenced by anima::DTIProbabilisticTractographyImageFilter::ComputeModelValue(), anima::MCMWeightedAverager::ComputeOutputTensorCompatibleModel(), anima::MCMPairingMeanSquaresImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::ComputeTensorBasedMetricPart(), anima::MCMWeightedAverager::ComputeTensorDistanceMatrix(), anima::LogTensorImageFilter< TScalarType, NDimensions >::DynamicThreadedGenerateData(), anima::ExpTensorImageFilter< TScalarType, NDimensions >::DynamicThreadedGenerateData(), anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DynamicThreadedGenerateData(), anima::TensorCompartment::GetCompartmentVector(), anima::TensorMeanSquaresImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorGeneralizedCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::MTPairingCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::MTPairingCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::PreComputeFixedValues(), anima::TensorCompartment::Reorient(), and anima::TensorResampleImageFilter< TImageType, TInterpolatorPrecisionType >::ReorientInterpolatedModel().
| double anima::GetVonMisesConcentrationMLE | ( | const ScalarType | rbar | ) |
Maximum likelihood estimation of the concentration parameter of the 2D von Mises distribution according to Mardia, Statistics of Directional Data, 1972.
Definition at line 72 of file animaVMFDistribution.hxx.
| ANIMASHTOOLS_EXPORT std::vector< std::vector< double > > anima::InitializeSampleDirections | ( | unsigned int | nbTheta, |
| unsigned int | nbPhi, | ||
| std::string | sampleDirFileName | ||
| ) |
Definition at line 15 of file animaODFFunctions.cxx.
References TransformCartesianToSphericalCoordinates().
Referenced by main().
| void anima::InverseCubicInterpolator | ( | std::vector< T > & | inputVect, |
| std::vector< T > & | outputVect, | ||
| T | step | ||
| ) |
Definition at line 30 of file animaCubicInterpolation.hxx.
References Cubic().
Referenced by anima::DistortionCorrectionImageFilter< TInputImage >::DynamicThreadedGenerateData().
| double anima::jfour | ( | const T & | k | ) |
Definition at line 66 of file animaHyperbolicFunctions.hxx.
| double anima::jtwo | ( | const T & | k | ) |
Definition at line 54 of file animaHyperbolicFunctions.hxx.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::KummerIntegrandMethod | ( | const double & | x, |
| const double & | a, | ||
| const double & | b | ||
| ) |
According to Muller, K. E. (2001) ‘Computing the confluent hypergeometric function, M (a, b, x)’, Numerische Mathematik, pp. 179–196. Method with integral if b > a > 0.
Definition at line 99 of file animaKummerFunctions.cxx.
References anima::KummerIntegrand::SetAValue(), anima::KummerIntegrand::SetBValue(), and anima::KummerIntegrand::SetXValue().
Referenced by GetKummerFunctionValue(), and GetScaledKummerFunctionValue().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::KummerMethod1 | ( | const double & | x, |
| const double & | a, | ||
| const double & | b, | ||
| const unsigned int | maxIter, | ||
| const double | tol | ||
| ) |
According to Muller, K. E. (2001) ‘Computing the confluent hypergeometric function, M (a, b, x)’, Numerische Mathematik, pp. 179–196. Method 1.C, p.5.
Definition at line 21 of file animaKummerFunctions.cxx.
Referenced by GetKummerFunctionValue(), and GetScaledKummerFunctionValue().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::KummerMethod2 | ( | const double & | x, |
| const double & | a, | ||
| const double & | b, | ||
| const unsigned int | maxIter, | ||
| const double | tol | ||
| ) |
According to Muller, K. E. (2001) ‘Computing the confluent hypergeometric function, M (a, b, x)’, Numerische Mathematik, pp. 179–196. Method 2, p.6.
Definition at line 54 of file animaKummerFunctions.cxx.
References PochHammer().
Referenced by GetKummerFunctionValue(), and GetScaledKummerFunctionValue().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::legendre_first_derivative | ( | int | L, |
| int | M, | ||
| double | value | ||
| ) |
Definition at line 9 of file animaLegendreDerivatives.cxx.
Referenced by anima::SphericalHarmonic::getThetaFirstDerivative(), anima::SphericalHarmonic::getThetaPhiDerivative(), and anima::SphericalHarmonic::getThetaSecondDerivative().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::legendre_second_derivative | ( | int | L, |
| int | M, | ||
| double | value | ||
| ) |
Definition at line 45 of file animaLegendreDerivatives.cxx.
Referenced by anima::SphericalHarmonic::getThetaSecondDerivative().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::log_bessel_i | ( | unsigned int | N, |
| double | x | ||
| ) |
Computes the log of modified Bessel function of the first kind: I_{N} (N >= 0)
Definition at line 12 of file animaBesselFunctions.cxx.
References bessel_ratio_i().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::log_bessel_i_lower_bound | ( | unsigned int | N, |
| double | x | ||
| ) |
Computes a lower bound of the log of modified Bessel function of the first kind: I_{N} (N >= 0)
Definition at line 63 of file animaBesselFunctions.cxx.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::log_bessel_order_derivative_i | ( | double | x, |
| unsigned int | order, | ||
| double | emc, | ||
| unsigned int | approx_order | ||
| ) |
Computes the derivative of the log of modified Bessel function of the first kind w.r.t. its order (emc is the Euler-Mascheroni constant)
Definition at line 130 of file animaBesselFunctions.cxx.
References psi_function().
| void anima::LowerTriangularSolver | ( | vnl_matrix< ScalarType > & | matrix, |
| VectorType & | rhs, | ||
| VectorType & | result, | ||
| unsigned int | rank = 0 |
||
| ) |
Solves lower triangular system matrix * result = rhs using Gauss elimination. Matrix is a square matrix. Can be used with rhs and result pointing to the same address in which case, result will be erased. result has to be the same size as rhs If the matrix is not of full rank, rank can be set to something different than zero, in which case the solver will take only the first rank rows and columns
Definition at line 76 of file animaMatrixOperations.hxx.
Referenced by anima::BLMLambdaCostFunction::GetDerivative().
| void anima::Normalize | ( | const VectorType & | v, |
| const unsigned int | NDimension, | ||
| VectorType & | resVec | ||
| ) |
Definition at line 326 of file animaVectorOperations.hxx.
References ComputeNorm().
Referenced by ExtractPPDRotationFromJacobianMatrix(), anima::dtiTractographyImageFilter::GetNextDirection(), Normalize(), ProjectOnOrthogonalPlane(), SampleFromWatsonDistribution(), anima::ODFEstimatorImageFilter< TInputPixelType, TOutputPixelType >::SetBValuesList(), TransformCartesianToSphericalCoordinates(), and anima::GradientFileReader< GradientType, BValueScalarType >::Update().
| void anima::Normalize | ( | const itk::Vector< ScalarType, NDimension > & | v, |
| itk::Vector< ScalarType, NDimension > & | resVec | ||
| ) |
Definition at line 339 of file animaVectorOperations.hxx.
References Normalize().
| void anima::Normalize | ( | const itk::VariableLengthVector< ScalarType > & | v, |
| itk::VariableLengthVector< ScalarType > & | resVec | ||
| ) |
Definition at line 344 of file animaVectorOperations.hxx.
References Normalize().
| void anima::Normalize | ( | const itk::Point< ScalarType, NDimension > & | v, |
| itk::Point< ScalarType, NDimension > & | resVec | ||
| ) |
Definition at line 350 of file animaVectorOperations.hxx.
References Normalize().
| void anima::Normalize | ( | const vnl_vector< ScalarType > & | v, |
| vnl_vector< ScalarType > & | resVec | ||
| ) |
Definition at line 355 of file animaVectorOperations.hxx.
References Normalize().
| void anima::Normalize | ( | const vnl_vector_fixed< ScalarType, NDimension > & | v, |
| vnl_vector_fixed< ScalarType, NDimension > & | resVec | ||
| ) |
Definition at line 361 of file animaVectorOperations.hxx.
References Normalize().
| void anima::Normalize | ( | const std::vector< ScalarType > & | v, |
| std::vector< ScalarType > & | resVec | ||
| ) |
Definition at line 366 of file animaVectorOperations.hxx.
References Normalize().
| double anima::ovlScore | ( | vnl_diag_matrix< T1 > & | eigsX, |
| vnl_matrix< T1 > & | eigVecsX, | ||
| vnl_diag_matrix< T1 > & | eigsY, | ||
| vnl_matrix< T1 > & | eigVecsY | ||
| ) |
Definition at line 317 of file animaBaseTensorTools.hxx.
Referenced by anima::TensorGeneralizedCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue().
| void anima::pairingToQuaternion | ( | const vnl_vector_fixed< TInput, NDimensions > & | inputPoint, |
| const vnl_vector_fixed< TInput, NDimensions > & | inputTransformedPoint, | ||
| vnl_matrix< TOutput > & | outputMatrix | ||
| ) |
Definition at line 388 of file animaLinearTransformEstimationTools.hxx.
Referenced by computeAnisotropSimLSWFromTranslations(), computeRigidLSWFromTranslations(), GetRotationMatrixFromVectors(), and pairingToQuaternion().
| void anima::pairingToQuaternion | ( | const itk::Vector< TInput, NDimensions > & | inputPoint, |
| const itk::Vector< TInput, NDimensions > & | inputTransformedPoint, | ||
| vnl_matrix< TOutput > & | outputMatrix | ||
| ) |
Definition at line 395 of file animaLinearTransformEstimationTools.hxx.
References pairingToQuaternion().
| void anima::pairingToQuaternion | ( | const PointType & | inputPoint, |
| const PointType & | inputTransformedPoint, | ||
| vnl_matrix< TOutput > & | outputMatrix, | ||
| unsigned int | ndim | ||
| ) |
Definition at line 402 of file animaLinearTransformEstimationTools.hxx.
| void anima::pairingToQuaternionScalingsDerivative | ( | const vnl_vector_fixed< TInput, NDimensions > & | inputPoint, |
| const vnl_vector_fixed< TInput, NDimensions > & | inputTransformedPoint, | ||
| vnl_matrix< TOutput > & | outputMatrix, | ||
| const int & | dimScal | ||
| ) |
Definition at line 439 of file animaLinearTransformEstimationTools.hxx.
Referenced by computeAnisotropSimLSWFromTranslations(), and pairingToQuaternionScalingsDerivative().
| void anima::pairingToQuaternionScalingsDerivative | ( | const itk::Vector< TInput, NDimensions > & | inputPoint, |
| const itk::Vector< TInput, NDimensions > & | inputTransformedPoint, | ||
| vnl_matrix< TOutput > & | outputMatrix, | ||
| const int & | dimScal | ||
| ) |
Definition at line 446 of file animaLinearTransformEstimationTools.hxx.
References pairingToQuaternionScalingsDerivative().
| void anima::pairingToQuaternionScalingsDerivative | ( | const PointType & | inputPoint, |
| const PointType & | inputTransformedPoint, | ||
| vnl_matrix< TOutput > & | outputMatrix, | ||
| unsigned int | ndim, | ||
| const int & | dimScal | ||
| ) |
Definition at line 453 of file animaLinearTransformEstimationTools.hxx.
| ANIMASPECIALFUNCTIONS_EXPORT double anima::PochHammer | ( | const double & | x, |
| const unsigned int | n | ||
| ) |
Definition at line 9 of file animaKummerFunctions.cxx.
Referenced by KummerMethod2().
| void anima::ProjectOnOrthogonalPlane | ( | const std::vector< T1 > & | v, |
| const std::vector< T2 > & | normalVec, | ||
| std::vector< T3 > & | resVec | ||
| ) |
Definition at line 529 of file animaVectorOperations.hxx.
References ComputeScalarProduct(), and Normalize().
| void anima::ProjectOnTensorSpace | ( | const vnl_matrix< T > & | matrix, |
| vnl_matrix< T > & | tensor | ||
| ) |
Definition at line 135 of file animaBaseTensorTools.hxx.
References RecomposeTensor().
| ANIMASPECIALFUNCTIONS_EXPORT double anima::psi_function | ( | unsigned int | n, |
| double | emc | ||
| ) |
Definition at line 11 of file animaGammaFunctions.cxx.
Referenced by log_bessel_order_derivative_i().
| void anima::QRGivensDecomposition | ( | vnl_matrix< ScalarType > & | aMatrix, |
| vnl_vector< ScalarType > & | bVector | ||
| ) |
Computes QR decomposition following Golub et al. Matrix computations. 1996 (algorithm 5.2.2) Computes aMatrix = Q * R Only the R matrix gets stored back into aMatrix. If bVector is not empty, it is replaced by Q^t bVector
Definition at line 9 of file animaQRDecomposition.hxx.
Referenced by anima::BLMLambdaCostFunction::GetValue().
| void anima::QRPivotDecomposition | ( | vnl_matrix< ScalarType > & | aMatrix, |
| std::vector< unsigned int > & | pivotVector, | ||
| std::vector< ScalarType > & | houseBetaValues, | ||
| unsigned int & | rank | ||
| ) |
Computes QR decomposition with pivoting following Golub et al. Matrix computations. 1996 (algorithm 5.4.1) Computes aMatrix * pivot = Q * R Everything gets stored back into aMatrix and housBetaValues (R is the upper triangular part of aMatrix) Pivot is stored as pivotVector allowing to construct pivot by setting pivot(pivotVector(i),i) = 1, the rest being null
Definition at line 57 of file animaQRDecomposition.hxx.
References ComputeHouseholderVector().
Referenced by main(), and anima::BoundedLevenbergMarquardtOptimizer::StartOptimization().
| itk::SmartPointer<ImageType> anima::readImage | ( | std::string | filename | ) |
Definition at line 12 of file animaReadWriteFunctions.h.
Referenced by main().
| void anima::RecomposeTensor | ( | vnl_diag_matrix< T1 > & | eigs, |
| vnl_matrix< T1 > & | eigVecs, | ||
| vnl_matrix< T2 > & | resMatrix | ||
| ) |
Recompose tensor from values extracted using SymmetricEigenAnalysis (vnl_symmetric_eigensystem transposes all this)
Definition at line 254 of file animaBaseTensorTools.hxx.
Referenced by anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::ComputeCostAtPosition(), anima::MCMWeightedAverager::ComputeOutputTensorCompatibleModel(), anima::DTIEstimationImageFilter< InputPixelScalarType, OutputPixelScalarType >::DynamicThreadedGenerateData(), ExtractRotationFromJacobianMatrix(), anima::dtiTractographyImageFilter::GetNextDirection(), anima::LogEuclideanTensorCalculator< TScalarType >::GetTensorExponential(), anima::LogEuclideanTensorCalculator< TScalarType >::GetTensorLogarithm(), anima::LogEuclideanTensorCalculator< TScalarType >::GetTensorPower(), ProjectOnTensorSpace(), and SampleFromMultivariateGaussianDistribution().
| itk::SmartPointer<ImageType> anima::reorient3DImage | ( | typename itk::SmartPointer< ImageType > | input, |
| itk::SpatialOrientation::ValidCoordinateOrientationFlags | orientation | ||
| ) |
Definition at line 12 of file animaReorientation.h.
| void anima::reorientGradients | ( | typename itk::SmartPointer< ImageType > | input, |
| std::vector< GradientType > & | gradients | ||
| ) |
Definition at line 139 of file animaReorientation.h.
Referenced by convert().
| itk::SmartPointer<ImageType> anima::reorientImage | ( | typename itk::SmartPointer< ImageType > | input, |
| itk::SpatialOrientation::ValidCoordinateOrientationFlags | orientation | ||
| ) |
Definition at line 31 of file animaReorientation.h.
Referenced by convert().
| void anima::Revert | ( | const VectorType & | v, |
| const unsigned int | vSize, | ||
| VectorType & | resVec | ||
| ) |
Definition at line 450 of file animaVectorOperations.hxx.
Referenced by anima::BaseTractographyImageFilter::ComputeFiber(), anima::dtiTractographyImageFilter::GetNextDirection(), and Revert().
| void anima::Revert | ( | const std::vector< ScalarType > & | v, |
| std::vector< ScalarType > & | resVec | ||
| ) |
Definition at line 456 of file animaVectorOperations.hxx.
References Revert().
| void anima::Revert | ( | const itk::Point< ScalarType > & | v, |
| itk::Point< ScalarType > & | resVec | ||
| ) |
Definition at line 462 of file animaVectorOperations.hxx.
References Revert().
| void anima::Revert | ( | const vnl_vector_fixed< ScalarType, NDimension > & | v, |
| vnl_vector_fixed< ScalarType, NDimension > & | resVec | ||
| ) |
Definition at line 469 of file animaVectorOperations.hxx.
References Revert().
| void anima::RotateAroundAxis | ( | const std::vector< T1 > & | v, |
| const T2 & | phi, | ||
| const std::vector< T3 > & | normalVec, | ||
| std::vector< T4 > & | resVec | ||
| ) |
Definition at line 546 of file animaVectorOperations.hxx.
Referenced by SampleFromWatsonDistribution().
| void anima::RotateAroundAxis | ( | const Vector3DType & | v, |
| const ScalarType & | phi, | ||
| const Vector3DType & | normalVec, | ||
| Vector3DType & | resVec | ||
| ) |
Definition at line 582 of file animaVectorOperations.hxx.
| void anima::RotateSymmetricMatrix | ( | T1 & | tensor, |
| T2 & | rotationMatrix, | ||
| T3 & | rotated_tensor, | ||
| unsigned int | tensorDim | ||
| ) |
Rotates a symmetric matrix by performing R^T D R where R is a rotation matrix and D the symmetric matrix.
Definition at line 276 of file animaBaseTensorTools.hxx.
Referenced by anima::TensorMeanSquaresImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorGeneralizedCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::GetValue(), anima::TensorCompartment::Reorient(), anima::TensorResampleImageFilter< TImageType, TInterpolatorPrecisionType >::ReorientInterpolatedModel(), and RotateSymmetricMatrix().
| void anima::RotateSymmetricMatrix | ( | vnl_matrix< T1 > & | tensor, |
| vnl_matrix< T2 > & | rotationMatrix, | ||
| vnl_matrix< T2 > & | rotated_tensor | ||
| ) |
Definition at line 300 of file animaBaseTensorTools.hxx.
References RotateSymmetricMatrix().
| void anima::RotateSymmetricMatrix | ( | itk::Matrix< T1, NDim, NDim > & | tensor, |
| itk::Matrix< T2, NDim, NDim > & | rotationMatrix, | ||
| itk::Matrix< T2, NDim, NDim > & | rotated_tensor | ||
| ) |
Definition at line 309 of file animaBaseTensorTools.hxx.
References RotateSymmetricMatrix().
| double anima::safe_log | ( | const ScalarType | x | ) |
Definition at line 7 of file animaLogarithmFunctions.hxx.
Referenced by anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::ComputeFiber(), anima::DTIProbabilisticTractographyImageFilter::ProposeNewDirection(), anima::ODFProbabilisticTractographyImageFilter::ProposeNewDirection(), SampleFromVMFDistribution(), SampleFromVMFDistributionNumericallyStable(), anima::BaseProbabilisticTractographyImageFilter< itk::VectorImage< double, 3 > >::UpdateClassesMemberships(), and VMFDistance().
| unsigned int anima::SampleFromBernoulliDistribution | ( | const T & | p, |
| std::mt19937 & | generator | ||
| ) |
Definition at line 45 of file animaDistributionSampling.hxx.
| double anima::SampleFromGaussianDistribution | ( | const T & | mean, |
| const T & | std, | ||
| std::mt19937 & | generator | ||
| ) |
Definition at line 52 of file animaDistributionSampling.hxx.
Referenced by anima::NoiseGeneratorImageFilter< ImageType >::DynamicThreadedGenerateData(), and SampleFromMultivariateGaussianDistribution().
| void anima::SampleFromMultivariateGaussianDistribution | ( | const VectorType & | mean, |
| const vnl_matrix< ScalarType > & | mat, | ||
| VectorType & | resVec, | ||
| std::mt19937 & | generator, | ||
| bool | isMatCovariance = true |
||
| ) |
Definition at line 59 of file animaDistributionSampling.hxx.
References RecomposeTensor(), and SampleFromGaussianDistribution().
| double anima::SampleFromUniformDistribution | ( | const T & | a, |
| const T & | b, | ||
| std::mt19937 & | generator | ||
| ) |
Definition at line 18 of file animaDistributionSampling.hxx.
Referenced by main(), SampleFromVMFDistribution(), SampleFromVMFDistributionNumericallyStable(), and SampleFromWatsonDistribution().
| void anima::SampleFromUniformDistributionOn2Sphere | ( | std::mt19937 & | generator, |
| VectorType & | resVec | ||
| ) |
Definition at line 26 of file animaDistributionSampling.hxx.
Referenced by main().
| void anima::SampleFromVMFDistribution | ( | const ScalarType & | kappa, |
| const VectorType & | meanDirection, | ||
| VectorType & | resVec, | ||
| std::mt19937 & | generator | ||
| ) |
Definition at line 93 of file animaDistributionSampling.hxx.
References GetRotationMatrixFromVectors(), safe_log(), SampleFromUniformDistribution(), and TransformCartesianToSphericalCoordinates().
| void anima::SampleFromVMFDistributionNumericallyStable | ( | const ScalarType & | kappa, |
| const VectorType & | meanDirection, | ||
| VectorType & | resVec, | ||
| std::mt19937 & | generator | ||
| ) |
Definition at line 143 of file animaDistributionSampling.hxx.
References GetRotationMatrixFromVectors(), safe_log(), SampleFromUniformDistribution(), TransformCartesianToSphericalCoordinates(), and xi().
| void anima::SampleFromWatsonDistribution | ( | const ScalarType & | kappa, |
| const VectorType & | meanDirection, | ||
| VectorType & | resVec, | ||
| unsigned int | DataDimension, | ||
| std::mt19937 & | generator | ||
| ) |
void
SampleFromWatsonDistribution(const ScalarType &kappa,
const VectorType &meanDirection,
VectorType &resVec,
unsigned int DataDimension,
std::mt19937 &generator)
Sample from the Watson distribution using the procedure described in Fisher et al., Statistical Analysis of Spherical Data, 1993, p.59.
| kappa | Concentration parameter of the Watson distribution. |
| meanDirection | Mean direction of the Watson distribution. |
| resVec | Resulting sample. |
| DataDimension | Dimension of the sphere + 1. |
| generator | Pseudo-random number generator. |
Definition at line 177 of file animaDistributionSampling.hxx.
References ComputeCrossProduct(), ComputeNorm(), Normalize(), RotateAroundAxis(), SampleFromUniformDistribution(), and TransformCartesianToSphericalCoordinates().
Referenced by anima::DTIProbabilisticTractographyImageFilter::ProposeNewDirection(), anima::ODFProbabilisticTractographyImageFilter::ProposeNewDirection(), and SampleFromWatsonDistribution().
| void anima::SampleFromWatsonDistribution | ( | const ScalarType & | kappa, |
| const vnl_vector_fixed< ScalarType, DataDimension > & | meanDirection, | ||
| vnl_vector_fixed< ScalarType, DataDimension > & | resVec, | ||
| std::mt19937 & | generator | ||
| ) |
void
SampleFromWatsonDistribution(const ScalarType &kappa,
const vnl_vector_fixed < ScalarType, DataDimension > &meanDirection,
vnl_vector_fixed < ScalarType, DataDimension > &resVec,
std::mt19937 &generator)
Sample from the Watson distribution using the procedure described in Fisher et al., Statistical Analysis of Spherical Data, 1993, p.59.
| kappa | Concentration parameter of the Watson distribution. |
| meanDirection | Mean direction of the Watson distribution. |
| resVec | Resulting sample. |
| generator | Pseudo-random number generator. |
Definition at line 292 of file animaDistributionSampling.hxx.
References SampleFromWatsonDistribution().
| void anima::SampleFromWatsonDistribution | ( | const ScalarType & | kappa, |
| const itk::Point< ScalarType, DataDimension > & | meanDirection, | ||
| itk::Point< ScalarType, DataDimension > & | resVec, | ||
| std::mt19937 & | generator | ||
| ) |
void
SampleFromWatsonDistribution(const ScalarType &kappa,
const itk::Point < ScalarType, DataDimension > &meanDirection,
itk::Point < ScalarType, DataDimension > &resVec,
std::mt19937 &generator)
Sample from the Watson distribution using the procedure described in Fisher et al., Statistical Analysis of Spherical Data, 1993, p.59.
| kappa | Concentration parameter of the Watson distribution. |
| meanDirection | Mean direction of the Watson distribution. |
| resVec | Resulting sample. |
| generator | Pseudo-random number generator. |
Definition at line 320 of file animaDistributionSampling.hxx.
References SampleFromWatsonDistribution().
| void anima::SampleFromWatsonDistribution | ( | const ScalarType & | kappa, |
| const itk::Vector< ScalarType, DataDimension > & | meanDirection, | ||
| itk::Vector< ScalarType, DataDimension > & | resVec, | ||
| std::mt19937 & | generator | ||
| ) |
void
SampleFromWatsonDistribution(const ScalarType &kappa,
const itk::Vector < ScalarType, DataDimension > &meanDirection,
itk::Vector < ScalarType, DataDimension > &resVec,
std::mt19937 &generator)
Sample from the Watson distribution using the procedure described in Fisher et al., Statistical Analysis of Spherical Data, 1993, p.59.
| kappa | Concentration parameter of the Watson distribution. |
| meanDirection | Mean direction of the Watson distribution. |
| resVec | Resulting sample. |
| generator | Pseudo-random number generator. |
Definition at line 348 of file animaDistributionSampling.hxx.
References SampleFromWatsonDistribution().
| unsigned int anima::setMultipleImageFilterInputsFromFileName | ( | std::string & | fileName, |
| ImageFilterType * | filter | ||
| ) |
Set inputs of an image to image filter from a file name containing either a list of files or a higher dimensional image.
Definition at line 79 of file animaReadWriteFunctions.h.
| double anima::ShOverId | ( | const T & | x | ) |
Definition at line 8 of file animaHyperbolicFunctions.hxx.
| double anima::ShRatio | ( | const T1 & | k, |
| const T2 & | alpha, | ||
| const T3 & | beta | ||
| ) |
Definition at line 33 of file animaHyperbolicFunctions.hxx.
| double anima::SinOverId | ( | const T & | x | ) |
Definition at line 8 of file animaTrigonometricFunctions.hxx.
| void anima::sphere_exp_map | ( | const std::vector< ScalarType > & | p, |
| const std::vector< ScalarType > & | x, | ||
| std::vector< ScalarType > & | expValue | ||
| ) |
Computes the exponential map on the hyper-sphere.
| p | log-point to exponentiate |
| x | reference point of the exponential |
| expValue | exponential value (result) |
Definition at line 32 of file animaLogExpMapsUnitSphere.hxx.
Referenced by ComputeSphericalCentroid().
| void anima::sphere_log_map | ( | const std::vector< ScalarType > & | p, |
| const std::vector< ScalarType > & | x, | ||
| std::vector< ScalarType > & | logValue | ||
| ) |
Computes the logarithm map on the hyper-sphere.
| p | point to compute the logarithm from |
| x | reference point on the sphere (unfolding happens from that point) |
| logValue | Logarithm value (result) |
Definition at line 8 of file animaLogExpMapsUnitSphere.hxx.
Referenced by ComputeSphericalCentroid().
| void anima::TransformCartesianToSphericalCoordinates | ( | const VectorType & | v, |
| VectorType & | resVec | ||
| ) |
Definition at line 474 of file animaVectorOperations.hxx.
References ComputeNorm(), and Normalize().
Referenced by anima::ODFEstimatorImageFilter< TInputPixelType, TOutputPixelType >::AddGradientDirection(), anima::ODFEstimatorImageFilter< TInputPixelType, TOutputPixelType >::BeforeThreadedGenerateData(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData(), anima::ODFProbabilisticTractographyImageFilter::FindODFMaxima(), InitializeSampleDirections(), anima::ODFProbabilisticTractographyImageFilter::ProposeNewDirection(), anima::BaseCompartment::Reorient(), SampleFromVMFDistribution(), SampleFromVMFDistributionNumericallyStable(), SampleFromWatsonDistribution(), anima::StickCompartment::SetCompartmentVector(), anima::ZeppelinCompartment::SetCompartmentVector(), anima::NODDICompartment::SetCompartmentVector(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::SparseInitializeSticks(), anima::PyramidalSymmetryBridge< PixelType, ScalarType >::Update(), and anima::TensorCompartment::UpdateParametersFromTensor().
| void anima::TransformSphericalToCartesianCoordinates | ( | const VectorType & | v, |
| VectorType & | resVec | ||
| ) |
Definition at line 504 of file animaVectorOperations.hxx.
Referenced by anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::BeforeThreadedGenerateData(), anima::ODFProbabilisticTractographyImageFilter::FindODFMaxima(), anima::StickCompartment::GetCompartmentVector(), anima::ZeppelinCompartment::GetCompartmentVector(), anima::NODDICompartment::GetCompartmentVector(), anima::StickCompartment::GetDiffusionTensor(), anima::ZeppelinCompartment::GetDiffusionTensor(), anima::NODDICompartment::GetDiffusionTensor(), anima::NODDICompartment::GetLogDiffusionProfile(), anima::StickCompartment::GetLogDiffusionProfile(), anima::ZeppelinCompartment::GetLogDiffusionProfile(), anima::NODDICompartment::GetSignalAttenuationJacobian(), anima::BaseCompartment::IsEqual(), anima::BaseCompartment::Reorient(), and anima::NODDICompartment::UpdateSignals().
| void anima::TransformSphericalToCartesianCoordinates | ( | double | theta, |
| double | phi, | ||
| double | vectorNorm, | ||
| VectorType & | resVec | ||
| ) |
Definition at line 509 of file animaVectorOperations.hxx.
| void anima::UpperTriangularSolver | ( | const vnl_matrix< ScalarType > & | matrix, |
| const VectorType & | rhs, | ||
| VectorType & | result, | ||
| unsigned int | rank = 0 |
||
| ) |
Solves upper triangular system matrix * result = rhs using Gauss elimination. Matrix is a square matrix. Can be used with rhs and result pointing to the same address in which case, result will be erased. result has to be the same size as rhs If the matrix is not of full rank, rank can be set to something different than zero, in which case the solver will take only the first rank rows and columns
Definition at line 94 of file animaMatrixOperations.hxx.
Referenced by anima::BLMLambdaCostFunction::GetValue().
| double anima::VectorCovarianceTest | ( | vnl_matrix< T > & | logRefPatchCov, |
| vnl_matrix< T > & | movingPatchCov | ||
| ) |
Test if covariance matrices are different (returns distance)
Definition at line 147 of file animaVectorImagePatchStatistics.hxx.
Referenced by anima::LocalPatchCovarianceDistanceImageFilter< PixelScalarType >::DynamicThreadedGenerateData(), and anima::NLMeansVectorPatchSearcher< ImageScalarType, DataImageType >::TestPatchConformity().
| double anima::VectorMeansTest | ( | itk::VariableLengthVector< T > & | refPatchMean, |
| itk::VariableLengthVector< T > & | movingPatchMean, | ||
| const unsigned int & | refPatchNumElts, | ||
| const unsigned int & | movingPatchNumElts, | ||
| vnl_matrix< T > & | refPatchCov, | ||
| vnl_matrix< T > & | movingPatchCov | ||
| ) |
Test if vector means are different (returns distance)
Definition at line 179 of file animaVectorImagePatchStatistics.hxx.
Referenced by anima::LocalPatchMeanDistanceImageFilter< PixelScalarType >::DynamicThreadedGenerateData(), and anima::NLMeansVectorPatchSearcher< ImageScalarType, DataImageType >::TestPatchConformity().
| double anima::VMFDistance | ( | const itk::Point< ScalarType, Dimension > & | muFirst, |
| const double & | kappaFirst, | ||
| const itk::Point< ScalarType, Dimension > & | muSec, | ||
| const double & | kappaSec | ||
| ) |
Definition at line 46 of file animaVMFDistribution.hxx.
References safe_log().
| void anima::writeImage | ( | std::string | filename, |
| OutputImageType * | img | ||
| ) |
Definition at line 28 of file animaReadWriteFunctions.h.
Referenced by main().
| double anima::xi | ( | const T & | k | ) |
| const double anima::DiffusionBigDelta = 40.0e-3 |
Default big delta value (classical values)
Definition at line 30 of file animaMCMConstants.h.
Referenced by anima::ApproximateMCMSmoothingCostFunction::ApproximateMCMSmoothingCostFunction(), anima::BaseMCMCost::BaseMCMCost(), anima::StaniszCompartment::GetLogDiffusionProfile(), anima::GradientFileReader< GradientType, BValueScalarType >::GradientFileReader(), main(), anima::MCMBlockMatcher< TInputImageType >::MCMBlockMatcher(), anima::MCMCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::MCMCorrelationImageToImageMetric(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMEstimatorImageFilter(), anima::MCML2DistanceComputer::MCML2DistanceComputer(), and anima::PyramidalDenseMCMSVFMatchingBridge< ImageDimension >::PyramidalDenseMCMSVFMatchingBridge().
| const double anima::DiffusionGyromagneticRatio = 267.513e6 |
Gyromagnetic ratio (in rad/s/T), from Nelson, J., Nuclear Magnetic Resonance Spectroscopy, Prentice Hall, Londres, 2003.
Definition at line 10 of file animaMCMConstants.h.
Referenced by anima::StaniszCompartment::GetFourierTransformedDiffusionProfile(), anima::StaniszCompartment::GetLogDiffusionProfile(), anima::StaniszCompartment::GetSignalAttenuationJacobian(), and anima::StaniszCompartment::UpdateSignals().
| const double anima::DiffusionSmallDelta = 10.0e-3 |
Default small delta value (classical values)
Definition at line 27 of file animaMCMConstants.h.
Referenced by anima::ApproximateMCMSmoothingCostFunction::ApproximateMCMSmoothingCostFunction(), anima::BaseMCMCost::BaseMCMCost(), anima::StaniszCompartment::GetLogDiffusionProfile(), anima::GradientFileReader< GradientType, BValueScalarType >::GradientFileReader(), main(), anima::MCMBlockMatcher< TInputImageType >::MCMBlockMatcher(), anima::MCMCorrelationImageToImageMetric< TFixedImagePixelType, TMovingImagePixelType, ImageDimension >::MCMCorrelationImageToImageMetric(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::MCMEstimatorImageFilter(), anima::MCML2DistanceComputer::MCML2DistanceComputer(), and anima::PyramidalDenseMCMSVFMatchingBridge< ImageDimension >::PyramidalDenseMCMSVFMatchingBridge().
| const double anima::MCMAxialDiffusivityAddonLowerBound = 5.0e-4 |
Axial diffusivity add on to lower bound (used to ensure a minimal anisotropy to the anisotropic compartments)
Definition at line 42 of file animaMCMConstants.h.
Referenced by anima::StickCompartment::GetParameterLowerBounds(), anima::ZeppelinCompartment::GetParameterLowerBounds(), anima::TensorCompartment::GetParameterLowerBounds(), and anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TensorCoarseGridInitialization().
| const double anima::MCMAzimuthAngleUpperBound = 2.0 * M_PI |
Azimuth angle upper bound.
Definition at line 69 of file animaMCMConstants.h.
Referenced by anima::BaseCompartment::BaseCompartment(), anima::NODDICompartment::GetParameterUpperBounds(), anima::StickCompartment::GetParameterUpperBounds(), anima::ZeppelinCompartment::GetParameterUpperBounds(), and anima::TensorCompartment::GetParameterUpperBounds().
| const double anima::MCMCompartmentsFractionUpperBound = 1.0e7 |
Compartment fractions upper bound (B0 times weight)
Definition at line 39 of file animaMCMConstants.h.
Referenced by anima::MultiCompartmentModel::GetParameterUpperBounds().
| const double anima::MCMConcentrationUpperBound = 128.0 |
Concentration upper bound (used in NODDI and DDI)
Definition at line 72 of file animaMCMConstants.h.
Referenced by anima::NODDICompartment::GetParameterUpperBounds().
| const double anima::MCMDiffusivityLowerBound = 1.0e-6 |
Diffusivity lower bound for estimation.
Definition at line 45 of file animaMCMConstants.h.
Referenced by anima::NODDICompartment::GetParameterLowerBounds(), anima::StaniszCompartment::GetParameterLowerBounds(), anima::ZeppelinCompartment::GetParameterLowerBounds(), anima::TensorCompartment::GetParameterLowerBounds(), anima::MCMEstimatorImageFilter< InputPixelType, OutputPixelType >::TensorCoarseGridInitialization(), and anima::TensorCompartment::UpdateParametersFromTensor().
| const double anima::MCMDiffusivityUpperBound = 3.0e-3 |
Diffusivity upper bound.
Definition at line 48 of file animaMCMConstants.h.
Referenced by anima::NODDICompartment::GetParameterUpperBounds(), anima::StaniszCompartment::GetParameterUpperBounds(), anima::StickCompartment::GetParameterUpperBounds(), anima::ZeppelinCompartment::GetParameterUpperBounds(), anima::TensorCompartment::GetParameterUpperBounds(), and anima::TensorCompartment::UpdateParametersFromTensor().
| const double anima::MCMEpsilon = 1.0e-2 |
Epsilon value in case we do not want to have parameters reaching their true bounds (used for now in DDI)
Definition at line 36 of file animaMCMConstants.h.
| const double anima::MCMFractionUpperBound = 1.0 |
Fraction upper bound (intra/extra axonal)
Definition at line 75 of file animaMCMConstants.h.
Referenced by anima::MultiCompartmentModel::GetParameterLowerBounds(), and anima::NODDICompartment::GetParameterUpperBounds().
| const double anima::MCMFreeWaterDiffusivityLowerBound = 2.0e-3 |
Free water diffusivity lower bound.
Definition at line 54 of file animaMCMConstants.h.
Referenced by anima::FreeWaterCompartment::GetParameterLowerBounds().
| const double anima::MCMFreeWaterDiffusivityUpperBound = 4.0e-3 |
Free water diffusivity upper bound.
Definition at line 57 of file animaMCMConstants.h.
Referenced by anima::FreeWaterCompartment::GetParameterUpperBounds().
| const double anima::MCMIsotropicRestrictedWaterDiffusivityLowerBound = 0.25e-4 |
Isotropic restricted water diffusivity lower bound.
Definition at line 60 of file animaMCMConstants.h.
Referenced by anima::IsotropicRestrictedWaterCompartment::GetParameterLowerBounds().
| const double anima::MCMIsotropicRestrictedWaterDiffusivityUpperBound = 2.0e-3 |
Isotropic restricted water diffusivity upper bound.
Definition at line 63 of file animaMCMConstants.h.
Referenced by anima::IsotropicRestrictedWaterCompartment::GetParameterUpperBounds().
| const double anima::MCMPolarAngleUpperBound = M_PI |
Polar angle upper bound (used in tensor for now)
Definition at line 66 of file animaMCMConstants.h.
Referenced by anima::NODDICompartment::GetParameterUpperBounds(), anima::StickCompartment::GetParameterUpperBounds(), anima::ZeppelinCompartment::GetParameterUpperBounds(), and anima::TensorCompartment::GetParameterUpperBounds().
| const double anima::MCMRadialDiffusivityUpperBound = 1.0e-3 |
Radial diffusivity upper bound.
Definition at line 51 of file animaMCMConstants.h.
Referenced by anima::ZeppelinCompartment::GetParameterUpperBounds(), and anima::TensorCompartment::GetParameterUpperBounds().
| const double anima::MCMTissueRadiusLowerBound = 1.0e-4 |
Tissue radius lower bound (in Stanisz for now)
Definition at line 78 of file animaMCMConstants.h.
Referenced by anima::StaniszCompartment::GetParameterLowerBounds().
| const double anima::MCMTissueRadiusUpperBound = 4.01e-2 |
Tissue radius upper bound (in Stanisz for now)
Definition at line 81 of file animaMCMConstants.h.
Referenced by anima::StaniszCompartment::GetParameterUpperBounds().
| const double anima::MCMZeroLowerBound = 0.0 |
Default zero lower bound (in case we want something else than zero one day)
Definition at line 33 of file animaMCMConstants.h.
Referenced by anima::NODDICompartment::GetParameterLowerBounds(), anima::StickCompartment::GetParameterLowerBounds(), anima::ZeppelinCompartment::GetParameterLowerBounds(), anima::TensorCompartment::GetParameterLowerBounds(), anima::MultiCompartmentModel::GetParameterLowerBounds(), and anima::MultiCompartmentModel::GetParameterUpperBounds().
1.8.13