API Reference
dipy
__config__
align
align._public
align.bundlemin
align.crosscorr
align.expectmax
align.imaffine
align.imwarp
align.metrics
align.parzenhist
align.reslice
align.scalespace
align.streamlinear
align.sumsqdiff
align.transforms
align.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
boots
core
core.benchmarks
core.benchmarks.bench_sphere
core.geometry
core.gradients
core.graph
core.histeq
core.interpolation
core.ndindex
core.onetime
core.optimize
core.profile
core.rng
core.sphere
core.sphere_stats
core.subdivide_octahedron
core.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_matching
denoise.denspeed
denoise.enhancement_kernel
denoise.gibbs
denoise.localpca
denoise.nlmeans
denoise.nlmeans_block
denoise.noise_estimate
denoise.non_local_means
denoise.patch2self
denoise.pca_noise_estimate
denoise.shift_twist_convolution
EnhancementKernel
HemiSphere
Sphere
Version
partial
Version
direction
direction.bootstrap_direction_getter
direction.closest_peak_direction_getter
direction.peaks
direction.pmf
direction.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.bvectxt
io.dpy
io.gradients
io.image
io.peaks
io.pickles
io.stateful_tractogram
io.streamline
io.utils
io.vtk
Dpy
Dpy
Streamlines
Version
PeaksAndMetrics
Sphere
Origin
PerArrayDict
PerArraySequenceDict
Space
StatefulTractogram
StatefulTractogram
StatefulTractogram.__init__()
StatefulTractogram.affine
StatefulTractogram.are_compatible()
StatefulTractogram.compute_bounding_box()
StatefulTractogram.data_per_point
StatefulTractogram.data_per_streamline
StatefulTractogram.dimensions
StatefulTractogram.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.origin
StatefulTractogram.remove_invalid_streamlines()
StatefulTractogram.space
StatefulTractogram.space_attributes
StatefulTractogram.streamlines
StatefulTractogram.to_center()
StatefulTractogram.to_corner()
StatefulTractogram.to_origin()
StatefulTractogram.to_rasmm()
StatefulTractogram.to_space()
StatefulTractogram.to_vox()
StatefulTractogram.to_voxmm()
StatefulTractogram.voxel_order
StatefulTractogram.voxel_sizes
Streamlines
Tractogram
product
Dpy
Origin
Space
StatefulTractogram
StatefulTractogram
StatefulTractogram.__init__()
StatefulTractogram.affine
StatefulTractogram.are_compatible()
StatefulTractogram.compute_bounding_box()
StatefulTractogram.data_per_point
StatefulTractogram.data_per_streamline
StatefulTractogram.dimensions
StatefulTractogram.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.origin
StatefulTractogram.remove_invalid_streamlines()
StatefulTractogram.space
StatefulTractogram.space_attributes
StatefulTractogram.streamlines
StatefulTractogram.to_center()
StatefulTractogram.to_corner()
StatefulTractogram.to_origin()
StatefulTractogram.to_rasmm()
StatefulTractogram.to_space()
StatefulTractogram.to_vox()
StatefulTractogram.to_voxmm()
StatefulTractogram.voxel_order
StatefulTractogram.voxel_sizes
Tractogram
Nifti1Image
nn
nn.histo_resdnn
nn.model
reconst
reconst.base
reconst.benchmarks
reconst.benchmarks.bench_bounding_box
reconst.benchmarks.bench_csd
reconst.benchmarks.bench_peaks
reconst.benchmarks.bench_squash
reconst.benchmarks.bench_vec_val_sum
reconst.cache
reconst.cross_validation
reconst.csdeconv
reconst.dki
reconst.dki_micro
reconst.dsi
reconst.dti
reconst.eudx_direction_getter
reconst.forecast
reconst.fwdti
reconst.gqi
reconst.ivim
reconst.mapmri
reconst.mcsd
reconst.msdki
reconst.multi_voxel
reconst.odf
reconst.qtdmri
reconst.qti
reconst.quick_squash
reconst.recspeed
reconst.rumba
reconst.sfm
reconst.shm
reconst.shore
reconst.utils
reconst.vec_val_sum
ReconstFit
ReconstModel
ConstrainedSphericalDeconvModel
GradientTable
Cache
AxSymShResponse
ConstrainedSDTModel
ConstrainedSphericalDeconvModel
SphHarmFit
SphHarmModel
TensorModel
DiffusionKurtosisFit
DiffusionKurtosisModel
ReconstModel
TensorFit
TensorFit
TensorFit.__init__()
TensorFit.S0_hat
TensorFit.ad()
TensorFit.adc()
TensorFit.color_fa()
TensorFit.directions
TensorFit.evals
TensorFit.evecs
TensorFit.fa()
TensorFit.ga()
TensorFit.linearity()
TensorFit.lower_triangular()
TensorFit.md()
TensorFit.mode()
TensorFit.odf()
TensorFit.planarity()
TensorFit.predict()
TensorFit.quadratic_form
TensorFit.rd()
TensorFit.shape
TensorFit.sphericity()
TensorFit.trace()
DiffusionKurtosisFit
DiffusionKurtosisModel
KurtosisMicrostructuralFit
KurtosisMicrostructuralFit
KurtosisMicrostructuralFit.__init__()
KurtosisMicrostructuralFit.awf
KurtosisMicrostructuralFit.axonal_diffusivity
KurtosisMicrostructuralFit.hindered_ad
KurtosisMicrostructuralFit.hindered_evals
KurtosisMicrostructuralFit.hindered_rd
KurtosisMicrostructuralFit.predict()
KurtosisMicrostructuralFit.restricted_evals
KurtosisMicrostructuralFit.tortuosity
KurtosisMicrostructureModel
Cache
DiffusionSpectrumDeconvFit
DiffusionSpectrumDeconvModel
DiffusionSpectrumFit
DiffusionSpectrumModel
OdfFit
OdfModel
ReconstModel
TensorFit
TensorFit
TensorFit.__init__()
TensorFit.S0_hat
TensorFit.ad()
TensorFit.adc()
TensorFit.color_fa()
TensorFit.directions
TensorFit.evals
TensorFit.evecs
TensorFit.fa()
TensorFit.ga()
TensorFit.linearity()
TensorFit.lower_triangular()
TensorFit.md()
TensorFit.mode()
TensorFit.odf()
TensorFit.planarity()
TensorFit.predict()
TensorFit.quadratic_form
TensorFit.rd()
TensorFit.shape
TensorFit.sphericity()
TensorFit.trace()
TensorModel
Version
EuDXDirectionGetter
Cache
ForecastFit
ForecastModel
OdfFit
OdfModel
Version
FreeWaterTensorFit
FreeWaterTensorModel
ReconstModel
TensorFit
TensorFit
TensorFit.__init__()
TensorFit.S0_hat
TensorFit.ad()
TensorFit.adc()
TensorFit.color_fa()
TensorFit.directions
TensorFit.evals
TensorFit.evecs
TensorFit.fa()
TensorFit.ga()
TensorFit.linearity()
TensorFit.lower_triangular()
TensorFit.md()
TensorFit.mode()
TensorFit.odf()
TensorFit.planarity()
TensorFit.predict()
TensorFit.quadratic_form
TensorFit.rd()
TensorFit.shape
TensorFit.sphericity()
TensorFit.trace()
Cache
GeneralizedQSamplingFit
GeneralizedQSamplingModel
OdfFit
OdfModel
IvimFit
IvimModelTRR
IvimModelVP
ReconstModel
Version
Cache
MapmriFit
MapmriFit
MapmriFit.__init__()
MapmriFit.fitted_signal()
MapmriFit.mapmri_R
MapmriFit.mapmri_coeff
MapmriFit.mapmri_mu
MapmriFit.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_dict
tqdm.format_interval()
tqdm.format_meter()
tqdm.format_num()
tqdm.format_sizeof()
tqdm.get_lock()
tqdm.monitor
tqdm.monitor_interval
tqdm.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.benchmarks
segment.benchmarks.bench_quickbundles
segment.bundles
segment.clustering
segment.clustering_algorithms
segment.clusteringspeed
segment.cythonutils
segment.featurespeed
segment.mask
segment.metric
segment.metricspeed
segment.mrf
segment.threshold
segment.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.phantom
sims.voxel
GradientTable
stats
stats.analysis
AveragePointwiseEuclideanMetric
QuickBundles
Streamlines
cKDTree
cKDTree
cKDTree.__init__()
cKDTree.boxsize
cKDTree.count_neighbors()
cKDTree.data
cKDTree.indices
cKDTree.leafsize
cKDTree.m
cKDTree.maxes
cKDTree.mins
cKDTree.n
cKDTree.query()
cKDTree.query_ball_point()
cKDTree.query_ball_tree()
cKDTree.query_pairs()
cKDTree.size
cKDTree.sparse_distance_matrix()
cKDTree.tree
tracking
tracking._utils
tracking.benchmarks
tracking.benchmarks.bench_streamline
tracking.direction_getter
tracking.distances
tracking.fbcmeasures
tracking.learning
tracking.life
tracking.local_tracking
tracking.localtrack
tracking.mesh
tracking.metrics
tracking.propspeed
tracking.stopping_criterion
tracking.streamline
tracking.streamlinespeed
tracking.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.app
viz.gmem
viz.panel
viz.plotting
viz.projections
viz.regtools
viz.streamline
GlobalHorizon
Horizon
Space
StatefulTractogram
StatefulTractogram
StatefulTractogram.__init__()
StatefulTractogram.affine
StatefulTractogram.are_compatible()
StatefulTractogram.compute_bounding_box()
StatefulTractogram.data_per_point
StatefulTractogram.data_per_streamline
StatefulTractogram.dimensions
StatefulTractogram.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.origin
StatefulTractogram.remove_invalid_streamlines()
StatefulTractogram.space
StatefulTractogram.space_attributes
StatefulTractogram.streamlines
StatefulTractogram.to_center()
StatefulTractogram.to_corner()
StatefulTractogram.to_origin()
StatefulTractogram.to_rasmm()
StatefulTractogram.to_space()
StatefulTractogram.to_vox()
StatefulTractogram.to_voxmm()
StatefulTractogram.voxel_order
StatefulTractogram.voxel_sizes
Streamlines
GlobalHorizon
GlobalHorizon
workflows
workflows.align
workflows.base
workflows.combined_workflow
workflows.denoise
workflows.docstring_parser
workflows.flow_runner
workflows.io
workflows.mask
workflows.multi_io
workflows.reconst
workflows.segment
workflows.stats
workflows.tracking
workflows.viz
workflows.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_parameters
IntrospectiveArgumentParser.output_parameters
IntrospectiveArgumentParser.positional_parameters
IntrospectiveArgumentParser.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_parameters
IntrospectiveArgumentParser.output_parameters
IntrospectiveArgumentParser.positional_parameters
IntrospectiveArgumentParser.show_argument()
IntrospectiveArgumentParser.update_argument()
FetchFlow
IoInfoFlow
SplitFlow
Workflow
MaskFlow
Workflow
IOIterator
ConstrainedSphericalDeconvModel