.. AUTO-GENERATED FILE -- DO NOT EDIT! :mod:`tracking` =============== .. automodule:: dipy.tracking .. currentmodule:: dipy.tracking .. autosummary:: Streamlines bench test .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking._utils` ------------------------------ .. automodule:: dipy.tracking._utils .. currentmodule:: dipy.tracking._utils .. autosummary:: warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.benchmarks` ---------------------------------- .. automodule:: dipy.tracking.benchmarks .. currentmodule:: dipy.tracking.benchmarks .. autosummary:: .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.benchmarks.bench_streamline` --------------------------------------------------- .. automodule:: dipy.tracking.benchmarks.bench_streamline .. currentmodule:: dipy.tracking.benchmarks.bench_streamline .. autosummary:: Streamlines assert_array_almost_equal assert_array_equal bench_compress_streamlines bench_length bench_set_number_of_points compress_streamlines compress_streamlines_python generate_streamlines get_fnames length length_python load_tractogram measure set_number_of_points set_number_of_points_python setup .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.learning` -------------------------------- .. automodule:: dipy.tracking.learning .. currentmodule:: dipy.tracking.learning .. autosummary:: detect_corresponding_tracks detect_corresponding_tracks_plus .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.life` ---------------------------- .. automodule:: dipy.tracking.life .. currentmodule:: dipy.tracking.life .. autosummary:: FiberFit FiberModel LifeSignalMaker ReconstFit ReconstModel grad_tensor gradient streamline_gradients streamline_signal streamline_tensors transform_streamlines unique_rows voxel2streamline .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.local_tracking` -------------------------------------- .. automodule:: dipy.tracking.local_tracking .. currentmodule:: dipy.tracking.local_tracking .. autosummary:: AnatomicalStoppingCriterion LocalTracking ParticleFilteringTracking StreamlineStatus local_tracker pft_tracker .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.metrics` ------------------------------- .. automodule:: dipy.tracking.metrics .. currentmodule:: dipy.tracking.metrics .. autosummary:: arbitrarypoint bytes center_of_mass downsample endpoint frenet_serret generate_combinations inside_sphere inside_sphere_points intersect_sphere length longest_track_bundle magn mean_curvature mean_orientation midpoint midpoint2point principal_components splev spline splprep startpoint winding .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.streamline` ---------------------------------- .. automodule:: dipy.tracking.streamline .. currentmodule:: dipy.tracking.streamline .. autosummary:: Streamlines apply_affine bundles_distances_mdf cdist center_streamlines cluster_confidence compress_streamlines deepcopy deform_streamlines dist_to_corner interpolate_scalar_3d interpolate_vector_3d length nbytes orient_by_rois orient_by_streamline relist_streamlines select_by_rois select_random_set_of_streamlines set_number_of_points transform_streamlines unlist_streamlines values_from_volume warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`tracking.utils` ----------------------------- .. automodule:: dipy.tracking.utils .. currentmodule:: dipy.tracking.utils .. autosummary:: defaultdict apply_affine asarray cdist connectivity_matrix density_map dist_to_corner empty length minimum_at ndbincount near_roi path_length random_seeds_from_mask ravel_multi_index reduce_labels reduce_rois seeds_from_mask streamline_near_roi subsegment target target_line_based transform_tracking_output unique_rows warn wraps .. currentmodule:: dipy.tracking :class:`Streamlines` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: Streamlines :members: :undoc-members: :show-inheritance: .. automethod:: __init__ bench ~~~~~ .. autofunction:: bench test ~~~~ .. autofunction:: test .. currentmodule:: dipy.tracking._utils warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.tracking.benchmarks .. currentmodule:: dipy.tracking.benchmarks.bench_streamline :class:`Streamlines` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: Streamlines :members: :undoc-members: :show-inheritance: .. automethod:: __init__ assert_array_almost_equal ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: assert_array_almost_equal assert_array_equal ~~~~~~~~~~~~~~~~~~ .. autofunction:: assert_array_equal bench_compress_streamlines ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bench_compress_streamlines bench_length ~~~~~~~~~~~~ .. autofunction:: bench_length bench_set_number_of_points ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bench_set_number_of_points compress_streamlines ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: compress_streamlines compress_streamlines_python ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: compress_streamlines_python generate_streamlines ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: generate_streamlines get_fnames ~~~~~~~~~~ .. autofunction:: get_fnames length ~~~~~~ .. autofunction:: length length_python ~~~~~~~~~~~~~ .. autofunction:: length_python load_tractogram ~~~~~~~~~~~~~~~ .. autofunction:: load_tractogram measure ~~~~~~~ .. autofunction:: measure set_number_of_points ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: set_number_of_points set_number_of_points_python ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: set_number_of_points_python setup ~~~~~ .. autofunction:: setup .. currentmodule:: dipy.tracking.learning detect_corresponding_tracks ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: detect_corresponding_tracks detect_corresponding_tracks_plus ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: detect_corresponding_tracks_plus .. currentmodule:: dipy.tracking.life :class:`FiberFit` ~~~~~~~~~~~~~~~~~ .. autoclass:: FiberFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`FiberModel` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: FiberModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`LifeSignalMaker` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: LifeSignalMaker :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstFit` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstFit :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ReconstModel` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ReconstModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ grad_tensor ~~~~~~~~~~~ .. autofunction:: grad_tensor gradient ~~~~~~~~ .. autofunction:: gradient streamline_gradients ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: streamline_gradients streamline_signal ~~~~~~~~~~~~~~~~~ .. autofunction:: streamline_signal streamline_tensors ~~~~~~~~~~~~~~~~~~ .. autofunction:: streamline_tensors transform_streamlines ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: transform_streamlines unique_rows ~~~~~~~~~~~ .. autofunction:: unique_rows voxel2streamline ~~~~~~~~~~~~~~~~ .. autofunction:: voxel2streamline .. currentmodule:: dipy.tracking.local_tracking :class:`AnatomicalStoppingCriterion` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: AnatomicalStoppingCriterion :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`LocalTracking` ~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: LocalTracking :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ParticleFilteringTracking` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ParticleFilteringTracking :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`StreamlineStatus` ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: StreamlineStatus :members: :undoc-members: :show-inheritance: .. automethod:: __init__ local_tracker ~~~~~~~~~~~~~ .. autofunction:: local_tracker pft_tracker ~~~~~~~~~~~ .. autofunction:: pft_tracker .. currentmodule:: dipy.tracking.metrics arbitrarypoint ~~~~~~~~~~~~~~ .. autofunction:: arbitrarypoint bytes ~~~~~ .. autofunction:: bytes center_of_mass ~~~~~~~~~~~~~~ .. autofunction:: center_of_mass downsample ~~~~~~~~~~ .. autofunction:: downsample endpoint ~~~~~~~~ .. autofunction:: endpoint frenet_serret ~~~~~~~~~~~~~ .. autofunction:: frenet_serret generate_combinations ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: generate_combinations inside_sphere ~~~~~~~~~~~~~ .. autofunction:: inside_sphere inside_sphere_points ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: inside_sphere_points intersect_sphere ~~~~~~~~~~~~~~~~ .. autofunction:: intersect_sphere length ~~~~~~ .. autofunction:: length longest_track_bundle ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: longest_track_bundle magn ~~~~ .. autofunction:: magn mean_curvature ~~~~~~~~~~~~~~ .. autofunction:: mean_curvature mean_orientation ~~~~~~~~~~~~~~~~ .. autofunction:: mean_orientation midpoint ~~~~~~~~ .. autofunction:: midpoint midpoint2point ~~~~~~~~~~~~~~ .. autofunction:: midpoint2point principal_components ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: principal_components splev ~~~~~ .. autofunction:: splev spline ~~~~~~ .. autofunction:: spline splprep ~~~~~~~ .. autofunction:: splprep startpoint ~~~~~~~~~~ .. autofunction:: startpoint winding ~~~~~~~ .. autofunction:: winding .. currentmodule:: dipy.tracking.streamline :class:`Streamlines` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: Streamlines :members: :undoc-members: :show-inheritance: .. automethod:: __init__ apply_affine ~~~~~~~~~~~~ .. autofunction:: apply_affine bundles_distances_mdf ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bundles_distances_mdf cdist ~~~~~ .. autofunction:: cdist center_streamlines ~~~~~~~~~~~~~~~~~~ .. autofunction:: center_streamlines cluster_confidence ~~~~~~~~~~~~~~~~~~ .. autofunction:: cluster_confidence compress_streamlines ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: compress_streamlines deepcopy ~~~~~~~~ .. autofunction:: deepcopy deform_streamlines ~~~~~~~~~~~~~~~~~~ .. autofunction:: deform_streamlines dist_to_corner ~~~~~~~~~~~~~~ .. autofunction:: dist_to_corner interpolate_scalar_3d ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: interpolate_scalar_3d interpolate_vector_3d ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: interpolate_vector_3d length ~~~~~~ .. autofunction:: length nbytes ~~~~~~ .. autofunction:: nbytes orient_by_rois ~~~~~~~~~~~~~~ .. autofunction:: orient_by_rois orient_by_streamline ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: orient_by_streamline relist_streamlines ~~~~~~~~~~~~~~~~~~ .. autofunction:: relist_streamlines select_by_rois ~~~~~~~~~~~~~~ .. autofunction:: select_by_rois select_random_set_of_streamlines ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: select_random_set_of_streamlines set_number_of_points ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: set_number_of_points transform_streamlines ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: transform_streamlines unlist_streamlines ~~~~~~~~~~~~~~~~~~ .. autofunction:: unlist_streamlines values_from_volume ~~~~~~~~~~~~~~~~~~ .. autofunction:: values_from_volume warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.tracking.utils :class:`defaultdict` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: defaultdict :members: :undoc-members: :show-inheritance: .. automethod:: __init__ apply_affine ~~~~~~~~~~~~ .. autofunction:: apply_affine asarray ~~~~~~~ .. autofunction:: asarray cdist ~~~~~ .. autofunction:: cdist connectivity_matrix ~~~~~~~~~~~~~~~~~~~ .. autofunction:: connectivity_matrix density_map ~~~~~~~~~~~ .. autofunction:: density_map dist_to_corner ~~~~~~~~~~~~~~ .. autofunction:: dist_to_corner empty ~~~~~ .. autofunction:: empty length ~~~~~~ .. autofunction:: length minimum_at ~~~~~~~~~~ .. autofunction:: minimum_at ndbincount ~~~~~~~~~~ .. autofunction:: ndbincount near_roi ~~~~~~~~ .. autofunction:: near_roi path_length ~~~~~~~~~~~ .. autofunction:: path_length random_seeds_from_mask ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: random_seeds_from_mask ravel_multi_index ~~~~~~~~~~~~~~~~~ .. autofunction:: ravel_multi_index reduce_labels ~~~~~~~~~~~~~ .. autofunction:: reduce_labels reduce_rois ~~~~~~~~~~~ .. autofunction:: reduce_rois seeds_from_mask ~~~~~~~~~~~~~~~ .. autofunction:: seeds_from_mask streamline_near_roi ~~~~~~~~~~~~~~~~~~~ .. autofunction:: streamline_near_roi subsegment ~~~~~~~~~~ .. autofunction:: subsegment target ~~~~~~ .. autofunction:: target target_line_based ~~~~~~~~~~~~~~~~~ .. autofunction:: target_line_based transform_tracking_output ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: transform_tracking_output unique_rows ~~~~~~~~~~~ .. autofunction:: unique_rows warn ~~~~ .. autofunction:: warn wraps ~~~~~ .. autofunction:: wraps