API Reference
dipy
__config__align
align._publicalign.bundleminalign.crosscorralign.expectmaxalign.imaffine
align.imwarpalign.metricsalign.parzenhistalign.reslicealign.scalespacealign.streamlinearalign.sumsqdiffalign.transformsalign.vector_fields
Bunch
floating
AffineMap
AffineRegistration
AffineTransform3D
CCMetric
DiffeomorphicMap
DiffeomorphicMap
DiffeomorphicMap.__init__()DiffeomorphicMap.allocate()DiffeomorphicMap.compute_inversion_error()DiffeomorphicMap.expand_fields()DiffeomorphicMap.get_backward_field()DiffeomorphicMap.get_forward_field()DiffeomorphicMap.get_simplified_transform()DiffeomorphicMap.interpret_matrix()DiffeomorphicMap.inverse()DiffeomorphicMap.shallow_copy()DiffeomorphicMap.transform()DiffeomorphicMap.transform_inverse()DiffeomorphicMap.transform_points()DiffeomorphicMap.transform_points_inverse()DiffeomorphicMap.warp_endomorphism()EMMetric
MutualInformationMetric
RigidIsoScalingTransform3D
RigidScalingTransform3D
RigidTransform3D
SSDMetric
StreamlineLinearRegistration
SymmetricDiffeomorphicRegistration
TranslationTransform3D
partial
AffineInvalidValuesError
AffineInversionError
AffineMap
AffineRegistration
IsotropicScaleSpace
MutualInformationMetric
Optimizer
ParzenJointHistogram
ParzenJointHistogram
ParzenJointHistogram.__init__()ParzenJointHistogram.bin_index()ParzenJointHistogram.bin_normalize_moving()ParzenJointHistogram.bin_normalize_static()ParzenJointHistogram.setup()ParzenJointHistogram.update_gradient_dense()ParzenJointHistogram.update_gradient_sparse()ParzenJointHistogram.update_pdfs_dense()ParzenJointHistogram.update_pdfs_sparse()ScaleSpace
Bunch
DiffeomorphicMap
DiffeomorphicMap
DiffeomorphicMap.__init__()DiffeomorphicMap.allocate()DiffeomorphicMap.compute_inversion_error()DiffeomorphicMap.expand_fields()DiffeomorphicMap.get_backward_field()DiffeomorphicMap.get_forward_field()DiffeomorphicMap.get_simplified_transform()DiffeomorphicMap.interpret_matrix()DiffeomorphicMap.inverse()DiffeomorphicMap.shallow_copy()DiffeomorphicMap.transform()DiffeomorphicMap.transform_inverse()DiffeomorphicMap.transform_points()DiffeomorphicMap.transform_points_inverse()DiffeomorphicMap.warp_endomorphism()DiffeomorphicRegistration
ScaleSpace
Streamlines
SymmetricDiffeomorphicRegistration
floating
CCMetric
EMMetric
SSDMetric
SimilarityMetric
SimilarityMetric
SimilarityMetric.__init__()SimilarityMetric.compute_backward()SimilarityMetric.compute_forward()SimilarityMetric.free_iteration()SimilarityMetric.get_energy()SimilarityMetric.initialize_iteration()SimilarityMetric.set_levels_above()SimilarityMetric.set_levels_below()SimilarityMetric.set_moving_image()SimilarityMetric.set_static_image()SimilarityMetric.use_moving_image_dynamics()SimilarityMetric.use_static_image_dynamics()floating
ParzenJointHistogram
ParzenJointHistogram
ParzenJointHistogram.__init__()ParzenJointHistogram.bin_index()ParzenJointHistogram.bin_normalize_moving()ParzenJointHistogram.bin_normalize_static()ParzenJointHistogram.setup()ParzenJointHistogram.update_gradient_dense()ParzenJointHistogram.update_gradient_sparse()ParzenJointHistogram.update_pdfs_dense()ParzenJointHistogram.update_pdfs_sparse()IsotropicScaleSpace
ScaleSpace
floating
BundleMinDistanceAsymmetricMetric
BundleMinDistanceMatrixMetric
BundleMinDistanceMetric
BundleSumDistanceMatrixMetric
JointBundleMinDistanceMetric
JointStreamlineRegistrationMap
Optimizer
StreamlineDistanceMetric
StreamlineLinearRegistration
StreamlineRegistrationMap
Streamlines
combinations
AffineTransform2D
AffineTransform3D
RigidIsoScalingTransform2D
RigidIsoScalingTransform3D
RigidScalingTransform2D
RigidScalingTransform3D
RigidTransform2D
RigidTransform3D
RotationTransform2D
RotationTransform3D
ScalingTransform2D
ScalingTransform3D
Transform
TranslationTransform2D
TranslationTransform3D
bootscore
core.benchmarkscore.benchmarks.bench_spherecore.geometrycore.gradientscore.graphcore.histeqcore.interpolationcore.ndindexcore.onetime
core.optimizecore.profilecore.rngcore.spherecore.sphere_statscore.subdivide_octahedroncore.wavelet
Timer
GradientTable
HemiSphere
Graph
Interpolator
NearestNeighborInterpolator
OutsideImage
TriLinearInterpolator
OneTimeProperty
ResetMixin
NonNegativeLeastSquares
Optimizer
PositiveDefiniteLeastSquares
SKLearnLinearSolver
Version
Profiler
HemiSphere
Sphere
permutations
HemiSphere
data
data.fetcher
DataError
GradientTable
HemiSphere
Sphere
FetcherError
TripWire
tqdm
denoise
denoise.adaptive_soft_matchingdenoise.denspeeddenoise.enhancement_kerneldenoise.gibbsdenoise.localpcadenoise.nlmeansdenoise.nlmeans_blockdenoise.noise_estimatedenoise.non_local_meansdenoise.patch2selfdenoise.pca_noise_estimatedenoise.shift_twist_convolution
EnhancementKernel
HemiSphere
Sphere
Version
partial
Version
direction
direction.bootstrap_direction_getterdirection.closest_peak_direction_getterdirection.peaksdirection.pmfdirection.probabilistic_direction_getter
BootDirectionGetter
ClosestPeakDirectionGetter
DeterministicMaximumDirectionGetter
EuDXDirectionGetter
PeaksAndMetrics
ProbabilisticDirectionGetter
Sphere
repeat
BootDirectionGetter
BootPmfGen
BaseDirectionGetter
BasePmfDirectionGetter
ClosestPeakDirectionGetter
PmfGenDirectionGetter
EuDXDirectionGetter
PeaksAndMetrics
Sphere
repeat
BootPmfGen
PmfGen
SHCoeffPmfGen
SimplePmfGen
DeterministicMaximumDirectionGetter
ProbabilisticDirectionGetter
io
io.bvectxtio.dpy
io.gradientsio.imageio.peaksio.picklesio.stateful_tractogramio.streamlineio.utilsio.vtk
Dpy
Dpy
Streamlines
Version
PeaksAndMetrics
Sphere
Origin
PerArrayDict
PerArraySequenceDict
Space
StatefulTractogram
StatefulTractogram
StatefulTractogram.__init__()StatefulTractogram.affineStatefulTractogram.are_compatible()StatefulTractogram.compute_bounding_box()StatefulTractogram.data_per_pointStatefulTractogram.data_per_streamlineStatefulTractogram.dimensionsStatefulTractogram.from_sft()StatefulTractogram.get_data_per_point_keys()StatefulTractogram.get_data_per_streamline_keys()StatefulTractogram.get_streamlines_copy()StatefulTractogram.is_bbox_in_vox_valid()StatefulTractogram.originStatefulTractogram.remove_invalid_streamlines()StatefulTractogram.spaceStatefulTractogram.space_attributesStatefulTractogram.streamlinesStatefulTractogram.to_center()StatefulTractogram.to_corner()StatefulTractogram.to_origin()StatefulTractogram.to_rasmm()StatefulTractogram.to_space()StatefulTractogram.to_vox()StatefulTractogram.to_voxmm()StatefulTractogram.voxel_orderStatefulTractogram.voxel_sizesStreamlines
Tractogram
product
Dpy
Origin
Space
StatefulTractogram
StatefulTractogram
StatefulTractogram.__init__()StatefulTractogram.affineStatefulTractogram.are_compatible()StatefulTractogram.compute_bounding_box()StatefulTractogram.data_per_pointStatefulTractogram.data_per_streamlineStatefulTractogram.dimensionsStatefulTractogram.from_sft()StatefulTractogram.get_data_per_point_keys()StatefulTractogram.get_data_per_streamline_keys()StatefulTractogram.get_streamlines_copy()StatefulTractogram.is_bbox_in_vox_valid()StatefulTractogram.originStatefulTractogram.remove_invalid_streamlines()StatefulTractogram.spaceStatefulTractogram.space_attributesStatefulTractogram.streamlinesStatefulTractogram.to_center()StatefulTractogram.to_corner()StatefulTractogram.to_origin()StatefulTractogram.to_rasmm()StatefulTractogram.to_space()StatefulTractogram.to_vox()StatefulTractogram.to_voxmm()StatefulTractogram.voxel_orderStatefulTractogram.voxel_sizesTractogram
Nifti1Image
nn
nn.histo_resdnnnn.model
reconst
reconst.basereconst.benchmarksreconst.benchmarks.bench_bounding_boxreconst.benchmarks.bench_csdreconst.benchmarks.bench_peaksreconst.benchmarks.bench_squashreconst.benchmarks.bench_vec_val_sumreconst.cachereconst.cross_validationreconst.csdeconvreconst.dkireconst.dki_microreconst.dsireconst.dtireconst.eudx_direction_getterreconst.forecastreconst.fwdtireconst.gqireconst.ivimreconst.mapmrireconst.mcsdreconst.msdkireconst.multi_voxelreconst.odfreconst.qtdmrireconst.qtireconst.quick_squashreconst.recspeedreconst.rumbareconst.sfmreconst.shm
reconst.shorereconst.utilsreconst.vec_val_sum
ReconstFit
ReconstModel
ConstrainedSphericalDeconvModel
GradientTable
Cache
AxSymShResponse
ConstrainedSDTModel
ConstrainedSphericalDeconvModel
SphHarmFit
SphHarmModel
TensorModel
DiffusionKurtosisFit
DiffusionKurtosisModel
ReconstModel
TensorFit
TensorFit
TensorFit.__init__()TensorFit.S0_hatTensorFit.ad()TensorFit.adc()TensorFit.color_fa()TensorFit.directionsTensorFit.evalsTensorFit.evecsTensorFit.fa()TensorFit.ga()TensorFit.linearity()TensorFit.lower_triangular()TensorFit.md()TensorFit.mode()TensorFit.odf()TensorFit.planarity()TensorFit.predict()TensorFit.quadratic_formTensorFit.rd()TensorFit.shapeTensorFit.sphericity()TensorFit.trace()DiffusionKurtosisFit
DiffusionKurtosisModel
KurtosisMicrostructuralFit
KurtosisMicrostructuralFit
KurtosisMicrostructuralFit.__init__()KurtosisMicrostructuralFit.awfKurtosisMicrostructuralFit.axonal_diffusivityKurtosisMicrostructuralFit.hindered_adKurtosisMicrostructuralFit.hindered_evalsKurtosisMicrostructuralFit.hindered_rdKurtosisMicrostructuralFit.predict()KurtosisMicrostructuralFit.restricted_evalsKurtosisMicrostructuralFit.tortuosityKurtosisMicrostructureModel
Cache
DiffusionSpectrumDeconvFit
DiffusionSpectrumDeconvModel
DiffusionSpectrumFit
DiffusionSpectrumModel
OdfFit
OdfModel
ReconstModel
TensorFit
TensorFit
TensorFit.__init__()TensorFit.S0_hatTensorFit.ad()TensorFit.adc()TensorFit.color_fa()TensorFit.directionsTensorFit.evalsTensorFit.evecsTensorFit.fa()TensorFit.ga()TensorFit.linearity()TensorFit.lower_triangular()TensorFit.md()TensorFit.mode()TensorFit.odf()TensorFit.planarity()TensorFit.predict()TensorFit.quadratic_formTensorFit.rd()TensorFit.shapeTensorFit.sphericity()TensorFit.trace()TensorModel
Version
EuDXDirectionGetter
Cache
ForecastFit
ForecastModel
OdfFit
OdfModel
Version
FreeWaterTensorFit
FreeWaterTensorModel
ReconstModel
TensorFit
TensorFit
TensorFit.__init__()TensorFit.S0_hatTensorFit.ad()TensorFit.adc()TensorFit.color_fa()TensorFit.directionsTensorFit.evalsTensorFit.evecsTensorFit.fa()TensorFit.ga()TensorFit.linearity()TensorFit.lower_triangular()TensorFit.md()TensorFit.mode()TensorFit.odf()TensorFit.planarity()TensorFit.predict()TensorFit.quadratic_formTensorFit.rd()TensorFit.shapeTensorFit.sphericity()TensorFit.trace()Cache
GeneralizedQSamplingFit
GeneralizedQSamplingModel
OdfFit
OdfModel
IvimFit
IvimModelTRR
IvimModelVP
ReconstModel
Version
Cache
MapmriFit
MapmriFit
MapmriFit.__init__()MapmriFit.fitted_signal()MapmriFit.mapmri_RMapmriFit.mapmri_coeffMapmriFit.mapmri_muMapmriFit.msd()MapmriFit.ng()MapmriFit.ng_parallel()MapmriFit.ng_perpendicular()MapmriFit.norm_of_laplacian_signal()MapmriFit.odf()MapmriFit.odf_sh()MapmriFit.pdf()MapmriFit.predict()MapmriFit.qiv()MapmriFit.rtap()MapmriFit.rtop()MapmriFit.rtpp()MapmriModel
Optimizer
PositiveDefiniteLeastSquares
ReconstFit
ReconstModel
Version
GradientTable
MSDeconvFit
MultiShellDeconvModel
MultiShellResponse
QpFitter
TensorModel
Version
MeanDiffusionKurtosisFit
MeanDiffusionKurtosisModel
ReconstModel
CallableArray
MultiVoxelFit
ReconstFit
tqdm
tqdm
tqdm.__init__()tqdm.clear()tqdm.close()tqdm.display()tqdm.external_write_mode()tqdm.format_dicttqdm.format_interval()tqdm.format_meter()tqdm.format_num()tqdm.format_sizeof()tqdm.get_lock()tqdm.monitortqdm.monitor_intervaltqdm.moveto()tqdm.pandas()tqdm.refresh()tqdm.reset()tqdm.set_description()tqdm.set_description_str()tqdm.set_lock()tqdm.set_postfix()tqdm.set_postfix_str()tqdm.status_printer()tqdm.unpause()tqdm.update()tqdm.wrapattr()tqdm.write()OdfFit
OdfModel
ReconstFit
ReconstModel
Cache
QtdmriFit
QtdmriFit
QtdmriFit.__init__()QtdmriFit.fitted_signal()QtdmriFit.msd()QtdmriFit.norm_of_laplacian_signal()QtdmriFit.odf()QtdmriFit.odf_sh()QtdmriFit.pdf()QtdmriFit.predict()QtdmriFit.qiv()QtdmriFit.qtdmri_to_mapmri_coef()QtdmriFit.rtap()QtdmriFit.rtop()QtdmriFit.rtpp()QtdmriFit.sparsity_abs()QtdmriFit.sparsity_density()QtdmriModel
Version
QtiFit
QtiModel
ReconstModel
Version
AxSymShResponse
OdfFit
OdfModel
RumbaFit
RumbaSDModel
Sphere
Cache
ExponentialIsotropicFit
ExponentialIsotropicModel
IsotropicFit
IsotropicModel
OrderedDict
ReconstFit
ReconstModel
SparseFascicleFit
SparseFascicleModel
Cache
CsaOdfModel
OdfFit
OdfModel
OpdtModel
QballBaseModel
QballModel
ResidualBootstrapWrapper
SphHarmFit
SphHarmModel
Cache
ShoreFit
ShoreModel
Version
segment
segment.benchmarkssegment.benchmarks.bench_quickbundlessegment.bundlessegment.clusteringsegment.clustering_algorithmssegment.clusteringspeedsegment.cythonutilssegment.featurespeedsegment.masksegment.metricsegment.metricspeedsegment.mrfsegment.thresholdsegment.tissue
MDFpy
Metric
QB_New
Streamlines
BundleMinDistanceAsymmetricMetric
BundleMinDistanceMetric
BundleSumDistanceMatrixMetric
RecoBundles
StreamlineLinearRegistration
Streamlines
chain
ABCMeta
AveragePointwiseEuclideanMetric
Cluster
ClusterCentroid
ClusterMap
ClusterMapCentroid
Clustering
Identity
Metric
MinimumAverageDirectFlipMetric
QuickBundles
QuickBundlesX
ResampleFeature
TreeCluster
TreeClusterMap
ClusterCentroid
ClusterMapCentroid
DTYPE
ClusterCentroid
ClusterMapCentroid
Clusters
ClustersCentroid
DTYPE
QuickBundles
QuickBundlesX
TreeCluster
TreeClusterMap
ArcLengthFeature
CenterOfMassFeature
CythonFeature
Feature
IdentityFeature
MidpointFeature
ResampleFeature
VectorOfEndpointsFeature
AveragePointwiseEuclideanMetric
CosineMetric
EuclideanMetric
Metric
MinimumAverageDirectFlipMetric
SumPointwiseEuclideanMetric
AveragePointwiseEuclideanMetric
CosineMetric
CythonMetric
Metric
MinimumAverageDirectFlipMetric
SumPointwiseEuclideanMetric
ConstantObservationModel
IteratedConditionalModes
ConstantObservationModel
IteratedConditionalModes
TissueClassifierHMRF
sims
sims.phantomsims.voxel
GradientTable
stats
stats.analysis
AveragePointwiseEuclideanMetric
QuickBundles
Streamlines
cKDTree
cKDTree
cKDTree.__init__()cKDTree.boxsizecKDTree.count_neighbors()cKDTree.datacKDTree.indicescKDTree.leafsizecKDTree.mcKDTree.maxescKDTree.minscKDTree.ncKDTree.query()cKDTree.query_ball_point()cKDTree.query_ball_tree()cKDTree.query_pairs()cKDTree.sizecKDTree.sparse_distance_matrix()cKDTree.treetracking
tracking._utilstracking.benchmarkstracking.benchmarks.bench_streamlinetracking.direction_gettertracking.distancestracking.fbcmeasurestracking.learningtracking.lifetracking.local_trackingtracking.localtracktracking.meshtracking.metricstracking.propspeedtracking.stopping_criteriontracking.streamlinetracking.streamlinespeedtracking.utils
tracking.vox2track
Streamlines
Streamlines
DirectionGetter
FBCMeasures
KDTree
interp1d
FiberFit
FiberModel
LifeSignalMaker
ReconstFit
ReconstModel
AnatomicalStoppingCriterion
Iterable
LocalTracking
ParticleFilteringTracking
StreamlineStatus
ActStoppingCriterion
AnatomicalStoppingCriterion
BinaryStoppingCriterion
CmcStoppingCriterion
StoppingCriterion
StreamlineStatus
ThresholdStoppingCriterion
Streamlines
Streamlines
OrderedDict
combinations
defaultdict
groupby
viz
viz.appviz.gmemviz.panelviz.plottingviz.projectionsviz.regtoolsviz.streamline
GlobalHorizon
Horizon
Space
StatefulTractogram
StatefulTractogram
StatefulTractogram.__init__()StatefulTractogram.affineStatefulTractogram.are_compatible()StatefulTractogram.compute_bounding_box()StatefulTractogram.data_per_pointStatefulTractogram.data_per_streamlineStatefulTractogram.dimensionsStatefulTractogram.from_sft()StatefulTractogram.get_data_per_point_keys()StatefulTractogram.get_data_per_streamline_keys()StatefulTractogram.get_streamlines_copy()StatefulTractogram.is_bbox_in_vox_valid()StatefulTractogram.originStatefulTractogram.remove_invalid_streamlines()StatefulTractogram.spaceStatefulTractogram.space_attributesStatefulTractogram.streamlinesStatefulTractogram.to_center()StatefulTractogram.to_corner()StatefulTractogram.to_origin()StatefulTractogram.to_rasmm()StatefulTractogram.to_space()StatefulTractogram.to_vox()StatefulTractogram.to_voxmm()StatefulTractogram.voxel_orderStatefulTractogram.voxel_sizesStreamlines
GlobalHorizon
GlobalHorizon
workflows
workflows.alignworkflows.baseworkflows.combined_workflowworkflows.denoiseworkflows.docstring_parserworkflows.flow_runnerworkflows.ioworkflows.maskworkflows.multi_ioworkflows.reconstworkflows.segmentworkflows.statsworkflows.trackingworkflows.vizworkflows.workflow
AffineMap
ApplyTransformFlow
CCMetric
DiffeomorphicMap
DiffeomorphicMap
DiffeomorphicMap.__init__()DiffeomorphicMap.allocate()DiffeomorphicMap.compute_inversion_error()DiffeomorphicMap.expand_fields()DiffeomorphicMap.get_backward_field()DiffeomorphicMap.get_forward_field()DiffeomorphicMap.get_simplified_transform()DiffeomorphicMap.interpret_matrix()DiffeomorphicMap.inverse()DiffeomorphicMap.shallow_copy()DiffeomorphicMap.transform()DiffeomorphicMap.transform_inverse()DiffeomorphicMap.transform_points()DiffeomorphicMap.transform_points_inverse()DiffeomorphicMap.warp_endomorphism()EMMetric
ImageRegistrationFlow
MotionCorrectionFlow
ResliceFlow
SSDMetric
SlrWithQbxFlow
SymmetricDiffeomorphicRegistration
SynRegistrationFlow
Workflow
IntrospectiveArgumentParser
IntrospectiveArgumentParser
IntrospectiveArgumentParser.__init__()IntrospectiveArgumentParser.add_description()IntrospectiveArgumentParser.add_epilogue()IntrospectiveArgumentParser.add_sub_flow_args()IntrospectiveArgumentParser.add_workflow()IntrospectiveArgumentParser.get_flow_args()IntrospectiveArgumentParser.optional_parametersIntrospectiveArgumentParser.output_parametersIntrospectiveArgumentParser.positional_parametersIntrospectiveArgumentParser.show_argument()IntrospectiveArgumentParser.update_argument()NumpyDocString
CombinedWorkflow
Workflow
GibbsRingingFlow
LPCAFlow
MPPCAFlow
NLMeansFlow
Patch2SelfFlow
Workflow
NumpyDocString
Reader
IntrospectiveArgumentParser
IntrospectiveArgumentParser
IntrospectiveArgumentParser.__init__()IntrospectiveArgumentParser.add_description()IntrospectiveArgumentParser.add_epilogue()IntrospectiveArgumentParser.add_sub_flow_args()IntrospectiveArgumentParser.add_workflow()IntrospectiveArgumentParser.get_flow_args()IntrospectiveArgumentParser.optional_parametersIntrospectiveArgumentParser.output_parametersIntrospectiveArgumentParser.positional_parametersIntrospectiveArgumentParser.show_argument()IntrospectiveArgumentParser.update_argument()FetchFlow
IoInfoFlow
SplitFlow
Workflow
MaskFlow
Workflow
IOIterator
ConstrainedSphericalDeconvModel