AFQ.recognition.criteria

Attributes

criteria_order_chunk_local
criteria_order_pre_other_bundles
criteria_order_post_other_bundles
valid_noncriterion
logger

Functions

prob_map(b_sls, bundle_def, preproc_plan, ...)
cross_midline(b_sls, bundle_def, preproc_plan, **kwargs)
start(b_sls, bundle_def, preproc_plan, **kwargs)
end(b_sls, bundle_def, preproc_plan, **kwargs)
length(b_sls, bundle_def, preproc_plan, **kwargs)
endpoint_dists(b_sls, bundle_def, preproc_plan, **kwargs)
primary_axis(b_sls, bundle_def, **kwargs)
include(b_sls, bundle_def, **kwargs)
curvature(b_sls, bundle_def, mapping, img, ...)	Filters streamlines by how well they match
exclude(b_sls, bundle_def, **kwargs)
recobundles(b_sls, mapping, bundle_def, reg_template, ...)
qb_thresh(b_sls, bundle_def, clip_edges, **kwargs)
clean_by_other_bundle(b_sls, bundle_def, img, ...)
orient_mahal(b_sls, bundle_def, **kwargs)
isolation_forest(b_sls, bundle_def, rng, **kwargs)
mahalanobis(b_sls, bundle_def, clip_edges, ...)
_prepare_bundle_def(bundle_dict, bundle_name, mapping, img)	Warp ROIs and apply distance-transform conversion
_validate_criteria(bundle_def, bundle_name, ...)
_run_chunk_local(bundle_def, chunk_streamlines, ...)
_run_global_phase(bundle_def, bundle_name, b_sls, ...)
recognize_bundles(tg, bundle_dict, mapping, img, ...)

Module Contents

AFQ.recognition.criteria.criteria_order_chunk_local = ['length', 'endpoint_dists', 'cross_midline', 'start', 'end', 'prob_map', 'primary_axis',...

AFQ.recognition.criteria.criteria_order_pre_other_bundles = ['length', 'endpoint_dists', 'cross_midline', 'start', 'end', 'prob_map', 'primary_axis',...

AFQ.recognition.criteria.criteria_order_post_other_bundles = ['orient_mahal', 'isolation_forest', 'qb_thresh']

AFQ.recognition.criteria.valid_noncriterion = ['space', 'mahal', 'inc_addtol', 'exc_addtol', 'exact_endpoints', 'ORG_spectral_subbundles',...

AFQ.recognition.criteria.logger

AFQ.recognition.criteria.prob_map(b_sls, bundle_def, preproc_plan, prob_threshold, img, **kwargs)

AFQ.recognition.criteria.cross_midline(b_sls, bundle_def, preproc_plan, **kwargs)

AFQ.recognition.criteria.start(b_sls, bundle_def, preproc_plan, **kwargs)

AFQ.recognition.criteria.end(b_sls, bundle_def, preproc_plan, **kwargs)

AFQ.recognition.criteria.length(b_sls, bundle_def, preproc_plan, **kwargs)

AFQ.recognition.criteria.endpoint_dists(b_sls, bundle_def, preproc_plan, **kwargs)

AFQ.recognition.criteria.primary_axis(b_sls, bundle_def, **kwargs)

AFQ.recognition.criteria.include(b_sls, bundle_def, **kwargs)

AFQ.recognition.criteria.curvature(b_sls, bundle_def, mapping, img, save_intermediates, **kwargs)

Filters streamlines by how well they match a curve in orientation and shape but not scale

AFQ.recognition.criteria.exclude(b_sls, bundle_def, **kwargs)

AFQ.recognition.criteria.recobundles(b_sls, mapping, bundle_def, reg_template, img, refine_reco, save_intermediates, rng, rb_recognize_params, **kwargs)

AFQ.recognition.criteria.qb_thresh(b_sls, bundle_def, clip_edges, **kwargs)

AFQ.recognition.criteria.clean_by_other_bundle(b_sls, bundle_def, img, other_bundle_name, other_bundle_sls, **kwargs)

AFQ.recognition.criteria.orient_mahal(b_sls, bundle_def, **kwargs)

AFQ.recognition.criteria.isolation_forest(b_sls, bundle_def, rng, **kwargs)

AFQ.recognition.criteria.mahalanobis(b_sls, bundle_def, clip_edges, cleaning_params, **kwargs)

AFQ.recognition.criteria._prepare_bundle_def(bundle_dict, bundle_name, mapping, img)

Warp ROIs and apply distance-transform conversion

AFQ.recognition.criteria._validate_criteria(bundle_def, bundle_name, bundle_dict, recognized_bundles_dict)

AFQ.recognition.criteria._run_chunk_local(bundle_def, chunk_streamlines, bundle_name, img, preproc_plan, save_intermediates, vox_dim, tol, dist_to_atlas, **segmentation_params)

AFQ.recognition.criteria._run_global_phase(bundle_def, bundle_name, b_sls, fgarray_for_candidates, candidate_global_idx, mapping, img, reg_template, preproc_scalars, recognized_bundles_dict, vox_dim, tol, dist_to_atlas, is_subbundle=False, **segmentation_params)

AFQ.recognition.criteria.recognize_bundles(tg, bundle_dict, mapping, img, reg_template, chunk_size, dist_to_waypoint, dist_to_atlas, save_intermediates, **segmentation_params)