.. AUTO-GENERATED FILE -- DO NOT EDIT! :mod:`align` ============ .. automodule:: dipy.align .. currentmodule:: dipy.align .. autosummary:: Bunch floating .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`align.imaffine` ----------------------------- .. automodule:: dipy.align.imaffine .. currentmodule:: dipy.align.imaffine .. autosummary:: AffineInvalidValuesError AffineInversionError AffineMap AffineRegistration IsotropicScaleSpace MutualInformationMetric Optimizer ParzenJointHistogram ScaleSpace compute_parzen_mi get_direction_and_spacings interpolate_scalar_2d interpolate_scalar_3d sample_domain_regular transform_centers_of_mass transform_geometric_centers transform_origins warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`align.imwarp` --------------------------- .. automodule:: dipy.align.imwarp .. currentmodule:: dipy.align.imwarp .. autosummary:: Bunch DiffeomorphicMap DiffeomorphicRegistration ScaleSpace SymmetricDiffeomorphicRegistration floating get_direction_and_spacings mult_aff .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`align.metrics` ---------------------------- .. automodule:: dipy.align.metrics .. currentmodule:: dipy.align.metrics .. autosummary:: CCMetric EMMetric SSDMetric SimilarityMetric floating gradient v_cycle_2d v_cycle_3d .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`align.reslice` ---------------------------- .. automodule:: dipy.align.reslice .. currentmodule:: dipy.align.reslice .. autosummary:: Pool affine_transform cpu_count reslice .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`align.scalespace` ------------------------------- .. automodule:: dipy.align.scalespace .. currentmodule:: dipy.align.scalespace .. autosummary:: IsotropicScaleSpace ScaleSpace floating .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`align.streamlinear` --------------------------------- .. automodule:: dipy.align.streamlinear .. currentmodule:: dipy.align.streamlinear .. autosummary:: BundleMinDistanceAsymmetricMetric BundleMinDistanceMatrixMetric BundleMinDistanceMetric BundleSumDistanceMatrixMetric Optimizer StreamlineDistanceMetric StreamlineLinearRegistration StreamlineRegistrationMap Streamlines bundle_min_distance bundle_min_distance_asymmetric_fast bundle_min_distance_fast bundle_sum_distance center_streamlines compose_matrix compose_matrix44 compose_transformations decompose_matrix decompose_matrix44 distance_matrix_mdf length progressive_slr qbx_and_merge remove_clusters_by_size select_random_set_of_streamlines set_number_of_points slr_with_qbx time transform_streamlines unlist_streamlines whole_brain_slr .. currentmodule:: dipy.align :class:`Bunch` ~~~~~~~~~~~~~~ .. autoclass:: Bunch :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`floating` ~~~~~~~~~~~~~~~~~ .. autoclass:: floating :members: :undoc-members: :show-inheritance: .. automethod:: __init__ .. currentmodule:: dipy.align.imaffine :class:`AffineInvalidValuesError` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: AffineInvalidValuesError :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`AffineInversionError` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: AffineInversionError :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`AffineMap` ~~~~~~~~~~~~~~~~~~ .. autoclass:: AffineMap :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`AffineRegistration` ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: AffineRegistration :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`IsotropicScaleSpace` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IsotropicScaleSpace :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MutualInformationMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MutualInformationMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Optimizer` ~~~~~~~~~~~~~~~~~~ .. autoclass:: Optimizer :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ParzenJointHistogram` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ParzenJointHistogram :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ScaleSpace` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ScaleSpace :members: :undoc-members: :show-inheritance: .. automethod:: __init__ compute_parzen_mi ~~~~~~~~~~~~~~~~~ .. autofunction:: compute_parzen_mi get_direction_and_spacings ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: get_direction_and_spacings interpolate_scalar_2d ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: interpolate_scalar_2d interpolate_scalar_3d ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: interpolate_scalar_3d sample_domain_regular ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: sample_domain_regular transform_centers_of_mass ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: transform_centers_of_mass transform_geometric_centers ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: transform_geometric_centers transform_origins ~~~~~~~~~~~~~~~~~ .. autofunction:: transform_origins warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.align.imwarp :class:`Bunch` ~~~~~~~~~~~~~~ .. autoclass:: Bunch :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffeomorphicMap` ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffeomorphicMap :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`DiffeomorphicRegistration` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: DiffeomorphicRegistration :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ScaleSpace` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ScaleSpace :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SymmetricDiffeomorphicRegistration` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: SymmetricDiffeomorphicRegistration :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`floating` ~~~~~~~~~~~~~~~~~ .. autoclass:: floating :members: :undoc-members: :show-inheritance: .. automethod:: __init__ get_direction_and_spacings ~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: get_direction_and_spacings mult_aff ~~~~~~~~ .. autofunction:: mult_aff .. currentmodule:: dipy.align.metrics :class:`CCMetric` ~~~~~~~~~~~~~~~~~ .. autoclass:: CCMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`EMMetric` ~~~~~~~~~~~~~~~~~ .. autoclass:: EMMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SSDMetric` ~~~~~~~~~~~~~~~~~~ .. autoclass:: SSDMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SimilarityMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: SimilarityMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`floating` ~~~~~~~~~~~~~~~~~ .. autoclass:: floating :members: :undoc-members: :show-inheritance: .. automethod:: __init__ gradient ~~~~~~~~ .. autofunction:: gradient v_cycle_2d ~~~~~~~~~~ .. autofunction:: v_cycle_2d v_cycle_3d ~~~~~~~~~~ .. autofunction:: v_cycle_3d .. currentmodule:: dipy.align.reslice Pool ~~~~ .. autofunction:: Pool affine_transform ~~~~~~~~~~~~~~~~ .. autofunction:: affine_transform cpu_count ~~~~~~~~~ .. autofunction:: cpu_count reslice ~~~~~~~ .. autofunction:: reslice .. currentmodule:: dipy.align.scalespace :class:`IsotropicScaleSpace` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IsotropicScaleSpace :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ScaleSpace` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ScaleSpace :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`floating` ~~~~~~~~~~~~~~~~~ .. autoclass:: floating :members: :undoc-members: :show-inheritance: .. automethod:: __init__ .. currentmodule:: dipy.align.streamlinear :class:`BundleMinDistanceAsymmetricMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: BundleMinDistanceAsymmetricMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`BundleMinDistanceMatrixMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: BundleMinDistanceMatrixMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`BundleMinDistanceMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: BundleMinDistanceMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`BundleSumDistanceMatrixMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: BundleSumDistanceMatrixMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Optimizer` ~~~~~~~~~~~~~~~~~~ .. autoclass:: Optimizer :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`StreamlineDistanceMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: StreamlineDistanceMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`StreamlineLinearRegistration` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: StreamlineLinearRegistration :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`StreamlineRegistrationMap` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: StreamlineRegistrationMap :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Streamlines` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: Streamlines :members: :undoc-members: :show-inheritance: .. automethod:: __init__ bundle_min_distance ~~~~~~~~~~~~~~~~~~~ .. autofunction:: bundle_min_distance bundle_min_distance_asymmetric_fast ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bundle_min_distance_asymmetric_fast bundle_min_distance_fast ~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bundle_min_distance_fast bundle_sum_distance ~~~~~~~~~~~~~~~~~~~ .. autofunction:: bundle_sum_distance center_streamlines ~~~~~~~~~~~~~~~~~~ .. autofunction:: center_streamlines compose_matrix ~~~~~~~~~~~~~~ .. autofunction:: compose_matrix compose_matrix44 ~~~~~~~~~~~~~~~~ .. autofunction:: compose_matrix44 compose_transformations ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: compose_transformations decompose_matrix ~~~~~~~~~~~~~~~~ .. autofunction:: decompose_matrix decompose_matrix44 ~~~~~~~~~~~~~~~~~~ .. autofunction:: decompose_matrix44 distance_matrix_mdf ~~~~~~~~~~~~~~~~~~~ .. autofunction:: distance_matrix_mdf length ~~~~~~ .. autofunction:: length progressive_slr ~~~~~~~~~~~~~~~ .. autofunction:: progressive_slr qbx_and_merge ~~~~~~~~~~~~~ .. autofunction:: qbx_and_merge remove_clusters_by_size ~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: remove_clusters_by_size select_random_set_of_streamlines ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: select_random_set_of_streamlines set_number_of_points ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: set_number_of_points slr_with_qbx ~~~~~~~~~~~~ .. autofunction:: slr_with_qbx time ~~~~ .. autofunction:: time transform_streamlines ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: transform_streamlines unlist_streamlines ~~~~~~~~~~~~~~~~~~ .. autofunction:: unlist_streamlines whole_brain_slr ~~~~~~~~~~~~~~~ .. autofunction:: whole_brain_slr