Connect#

Module to Postprocess skeletonized vasculature data

addConnections(data, mask, skeleton, points, radius=20, start_points=None, remove_local_mask=True, min_quality=15.0, add_to_skeleton=True, add_to_mask=False, verbose=True, processes=12, block_size=5000, debug=False)[source]#

addDilatedPathToMask(mask, path, iterations=1)[source]#

addPathToMask(mask, path, value=True)[source]#

connectPoint(data, mask, endpoints, start_index, radius, tubeness=None, min_quality=None, remove_local_mask=True, skeleton=None, verbose=False, **trace_parameter)[source]#: Tries to connect an end point

extractNeighbourhood(data, center, radius)[source]#: Extract local neighborhood with specific radius, if to close to border pad with zeros

findEndpoints(skel, points, border=None)[source]#: Find endpoints in skeleton to try to reconnect

order(array)[source]#

plotData(data, skel, binary, ends=None, isolated=None, replot=True)[source]#

plotTracingResult(path, data_nbh, mask_nbh, center, radius, tubeness_nbh, skeleton=None, distance_nbh=None)[source]#

processSingleConnection(args)[source]#

tracePointToMask(data, mask, center, radius, points=None, plot=False, skeleton=None, tubeness=None, removeLocalMask=True, maxSteps=500, verbose=False, **trace_parameter)[source]#: Trace an endpoint to a mask

tracePointToNeighbor(data, mask, center, neighbor, radius, points=None, plot=False, skeleton=None, tubeness=None, removeLocalMask=True, maxSteps=500, verbose=False, **trace_parameter)[source]#: Trace an endpoint to a neighbour