AFQ.recognition.utils

Attributes

axes_dict

Classes

SlsBeingRecognized

Functions

manual_orient_sls(fgarray)	Helper function to manually orient streamlines by their endpoints,
tolerance_mm_to_vox(img, dist_to_waypoint, ...)
flip_sls(select_sl, idx_to_flip[, in_place])	Helper function to flip streamlines
cut_sls_by_closest(select_sl, roi_closest, roi_idxs[, ...])	Helper function to cut streamlines according to which points
orient_by_streamline(sls, template_sl)
resample_tg(tg, n_points)

Module Contents

AFQ.recognition.utils.axes_dict

AFQ.recognition.utils.manual_orient_sls(fgarray)

Helper function to manually orient streamlines by their endpoints, according to LPI+ pyAFQ standard assuming streamlines are in RASMM

AFQ.recognition.utils.tolerance_mm_to_vox(img, dist_to_waypoint, input_dist_to_atlas)

AFQ.recognition.utils.flip_sls(select_sl, idx_to_flip, in_place=False)

Helper function to flip streamlines

AFQ.recognition.utils.cut_sls_by_closest(select_sl, roi_closest, roi_idxs, in_place=False)

Helper function to cut streamlines according to which points are closest to certain rois.

Parameters:

select_sl

streamlines to cut

roi_closest

indices into given streamline of points nearest to inclusion rois

roi_idxs

two indices into the list of inclusion rois to use for the cut

in_place

whether to modify select_sl

AFQ.recognition.utils.orient_by_streamline(sls, template_sl)

AFQ.recognition.utils.resample_tg(tg, n_points)

class AFQ.recognition.utils.SlsBeingRecognized(sls, save_intermediates, b_name, ref, n_roi)

oriented_yet = False

selected_fiber_idxs

sls_flipped

start_time = -1

save_intermediates

b_name

ref_sls

ref

n_roi

initiate_selection(clean_name)

select(idx, clean_name, cut=False)

get_selected_sls(cut=False, flip=False)

reorient(idx)

__bool__()

__len__()

copy(new_name, n_roi)

export_selected(chunk_offset)

classmethod from_selected(survivor_dicts, full_streamlines, save_intermediates, b_name, ref, n_roi)