.. AUTO-GENERATED FILE -- DO NOT EDIT! :mod:`segment` ============== .. automodule:: dipy.segment .. currentmodule:: dipy.segment .. autosummary:: .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.benchmarks` --------------------------------- .. automodule:: dipy.segment.benchmarks .. currentmodule:: dipy.segment.benchmarks .. autosummary:: .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.benchmarks.bench_quickbundles` ---------------------------------------------------- .. automodule:: dipy.segment.benchmarks.bench_quickbundles .. currentmodule:: dipy.segment.benchmarks.bench_quickbundles .. autosummary:: MDFpy Metric QB_New Streamlines assert_array_equal assert_arrays_equal assert_equal bench_quickbundles get_fnames load_tractogram measure set_number_of_points .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.bundles` ------------------------------ .. automodule:: dipy.segment.bundles .. currentmodule:: dipy.segment.bundles .. autosummary:: BundleMinDistanceAsymmetricMetric BundleMinDistanceMetric BundleSumDistanceMatrixMetric RecoBundles StreamlineLinearRegistration Streamlines chain apply_affine bundle_adjacency bundles_distances_mam bundles_distances_mdf check_range length nbytes qbx_and_merge select_random_set_of_streamlines set_number_of_points time .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.clustering` --------------------------------- .. automodule:: dipy.segment.clustering .. currentmodule:: dipy.segment.clustering .. autosummary:: ABCMeta AveragePointwiseEuclideanMetric Cluster ClusterCentroid ClusterMap ClusterMapCentroid Clustering Identity Metric MinimumAverageDirectFlipMetric QuickBundles QuickBundlesX ResampleFeature TreeCluster TreeClusterMap abstractmethod nbytes qbx_and_merge set_number_of_points time .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.mask` --------------------------- .. automodule:: dipy.segment.mask .. currentmodule:: dipy.segment.mask .. autosummary:: applymask binary_dilation bounding_box clean_cc_mask color_fa crop fractional_anisotropy generate_binary_structure median_filter median_otsu multi_median otsu segment_from_cfa warn .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.metric` ----------------------------- .. automodule:: dipy.segment.metric .. currentmodule:: dipy.segment.metric .. autosummary:: ArcLengthFeature AveragePointwiseEuclideanMetric CenterOfMassFeature CosineMetric EuclideanMetric Feature IdentityFeature Metric MidpointFeature MinimumAverageDirectFlipMetric ResampleFeature SumPointwiseEuclideanMetric VectorOfEndpointsFeature dist distance_matrix mdf .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.threshold` -------------------------------- .. automodule:: dipy.segment.threshold .. currentmodule:: dipy.segment.threshold .. autosummary:: otsu upper_bound_by_percent upper_bound_by_rate .. AUTO-GENERATED FILE -- DO NOT EDIT! Module: :mod:`segment.tissue` ----------------------------- .. automodule:: dipy.segment.tissue .. currentmodule:: dipy.segment.tissue .. autosummary:: ConstantObservationModel IteratedConditionalModes TissueClassifierHMRF add_noise .. currentmodule:: dipy.segment .. currentmodule:: dipy.segment.benchmarks .. currentmodule:: dipy.segment.benchmarks.bench_quickbundles :class:`MDFpy` ~~~~~~~~~~~~~~ .. autoclass:: MDFpy :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Metric` ~~~~~~~~~~~~~~~ .. autoclass:: Metric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QB_New` ~~~~~~~~~~~~~~~ .. autoclass:: QB_New :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Streamlines` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: Streamlines :members: :undoc-members: :show-inheritance: .. automethod:: __init__ assert_array_equal ~~~~~~~~~~~~~~~~~~ .. autofunction:: assert_array_equal assert_arrays_equal ~~~~~~~~~~~~~~~~~~~ .. autofunction:: assert_arrays_equal assert_equal ~~~~~~~~~~~~ .. autofunction:: assert_equal bench_quickbundles ~~~~~~~~~~~~~~~~~~ .. autofunction:: bench_quickbundles get_fnames ~~~~~~~~~~ .. autofunction:: get_fnames load_tractogram ~~~~~~~~~~~~~~~ .. autofunction:: load_tractogram measure ~~~~~~~ .. autofunction:: measure set_number_of_points ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: set_number_of_points .. currentmodule:: dipy.segment.bundles :class:`BundleMinDistanceAsymmetricMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: BundleMinDistanceAsymmetricMetric :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:`RecoBundles` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: RecoBundles :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`StreamlineLinearRegistration` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: StreamlineLinearRegistration :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Streamlines` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: Streamlines :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`chain` ~~~~~~~~~~~~~~ .. autoclass:: chain :members: :undoc-members: :show-inheritance: .. automethod:: __init__ apply_affine ~~~~~~~~~~~~ .. autofunction:: apply_affine bundle_adjacency ~~~~~~~~~~~~~~~~ .. autofunction:: bundle_adjacency bundles_distances_mam ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bundles_distances_mam bundles_distances_mdf ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: bundles_distances_mdf check_range ~~~~~~~~~~~ .. autofunction:: check_range length ~~~~~~ .. autofunction:: length nbytes ~~~~~~ .. autofunction:: nbytes qbx_and_merge ~~~~~~~~~~~~~ .. autofunction:: qbx_and_merge select_random_set_of_streamlines ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: select_random_set_of_streamlines set_number_of_points ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: set_number_of_points time ~~~~ .. autofunction:: time .. currentmodule:: dipy.segment.clustering :class:`ABCMeta` ~~~~~~~~~~~~~~~~ .. autoclass:: ABCMeta :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`AveragePointwiseEuclideanMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: AveragePointwiseEuclideanMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Cluster` ~~~~~~~~~~~~~~~~ .. autoclass:: Cluster :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ClusterCentroid` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ClusterCentroid :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ClusterMap` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: ClusterMap :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ClusterMapCentroid` ~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ClusterMapCentroid :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Clustering` ~~~~~~~~~~~~~~~~~~~ .. autoclass:: Clustering :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Identity` ~~~~~~~~~~~~~~~~~ .. autoclass:: Identity :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Metric` ~~~~~~~~~~~~~~~ .. autoclass:: Metric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MinimumAverageDirectFlipMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MinimumAverageDirectFlipMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QuickBundles` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: QuickBundles :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`QuickBundlesX` ~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: QuickBundlesX :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ResampleFeature` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ResampleFeature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TreeCluster` ~~~~~~~~~~~~~~~~~~~~ .. autoclass:: TreeCluster :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TreeClusterMap` ~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: TreeClusterMap :members: :undoc-members: :show-inheritance: .. automethod:: __init__ abstractmethod ~~~~~~~~~~~~~~ .. autofunction:: abstractmethod nbytes ~~~~~~ .. autofunction:: nbytes qbx_and_merge ~~~~~~~~~~~~~ .. autofunction:: qbx_and_merge set_number_of_points ~~~~~~~~~~~~~~~~~~~~ .. autofunction:: set_number_of_points time ~~~~ .. autofunction:: time .. currentmodule:: dipy.segment.mask applymask ~~~~~~~~~ .. autofunction:: applymask binary_dilation ~~~~~~~~~~~~~~~ .. autofunction:: binary_dilation bounding_box ~~~~~~~~~~~~ .. autofunction:: bounding_box clean_cc_mask ~~~~~~~~~~~~~ .. autofunction:: clean_cc_mask color_fa ~~~~~~~~ .. autofunction:: color_fa crop ~~~~ .. autofunction:: crop fractional_anisotropy ~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: fractional_anisotropy generate_binary_structure ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: generate_binary_structure median_filter ~~~~~~~~~~~~~ .. autofunction:: median_filter median_otsu ~~~~~~~~~~~ .. autofunction:: median_otsu multi_median ~~~~~~~~~~~~ .. autofunction:: multi_median otsu ~~~~ .. autofunction:: otsu segment_from_cfa ~~~~~~~~~~~~~~~~ .. autofunction:: segment_from_cfa warn ~~~~ .. autofunction:: warn .. currentmodule:: dipy.segment.metric :class:`ArcLengthFeature` ~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ArcLengthFeature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`AveragePointwiseEuclideanMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: AveragePointwiseEuclideanMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`CenterOfMassFeature` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: CenterOfMassFeature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`CosineMetric` ~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: CosineMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`EuclideanMetric` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: EuclideanMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Feature` ~~~~~~~~~~~~~~~~ .. autoclass:: Feature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`IdentityFeature` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IdentityFeature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`Metric` ~~~~~~~~~~~~~~~ .. autoclass:: Metric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MidpointFeature` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MidpointFeature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`MinimumAverageDirectFlipMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: MinimumAverageDirectFlipMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`ResampleFeature` ~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ResampleFeature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`SumPointwiseEuclideanMetric` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: SumPointwiseEuclideanMetric :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`VectorOfEndpointsFeature` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: VectorOfEndpointsFeature :members: :undoc-members: :show-inheritance: .. automethod:: __init__ dist ~~~~ .. autofunction:: dist distance_matrix ~~~~~~~~~~~~~~~ .. autofunction:: distance_matrix mdf ~~~ .. autofunction:: mdf .. currentmodule:: dipy.segment.threshold otsu ~~~~ .. autofunction:: otsu upper_bound_by_percent ~~~~~~~~~~~~~~~~~~~~~~ .. autofunction:: upper_bound_by_percent upper_bound_by_rate ~~~~~~~~~~~~~~~~~~~ .. autofunction:: upper_bound_by_rate .. currentmodule:: dipy.segment.tissue :class:`ConstantObservationModel` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: ConstantObservationModel :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`IteratedConditionalModes` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: IteratedConditionalModes :members: :undoc-members: :show-inheritance: .. automethod:: __init__ :class:`TissueClassifierHMRF` ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ .. autoclass:: TissueClassifierHMRF :members: :undoc-members: :show-inheritance: .. automethod:: __init__ add_noise ~~~~~~~~~ .. autofunction:: add_noise