tube_map#

This module contains the classes to generate annotated graphs from vasculature lightsheet data [Kirst2020].

class BinaryVesselProcessor(preprocessor=None)[source]#

Bases: TabProcessor

binarize()[source]#

binarize_channel(channel)[source]#

combine_binary()[source]#

deep_fill_channel(channel)[source]#

fill(channel)[source]#

fill_channel(channel)[source]#

get_n_blocks(dim_size)[source]#

plot_binarization_result(parent=None, postfix='', arrange=False)[source]#

postfix str:: empty for raw

plot_combined(parent=None, arrange=False)[source]#

plot_results(steps, channels=('raw',), side_by_side=True, arrange=True, parent=None)[source]#

plot_vessel_filling_results(parent=None, postfix_base='', arrange=False)[source]#

run()[source]#

setup(preprocessor)[source]#

smooth(channel)[source]#

smooth_channel(channel)[source]#

class BinaryVesselProcessorSteps(workspace, postfix='')[source]#

Bases: ProcessorSteps

path_from_step_name(step)[source]#

property steps#

class VesselGraphProcessor(preprocessor=None)[source]#

Bases: TabProcessor

The graph contains the following edge properties:

artery_raw
artery_binary
artery
vein
radii
distance_to_surface

clean_graph()[source]#

get_structure_sub_graph(structure_id)[source]#

plot_graph_chunk(graph_chunk, plot_type='mesh', title='sub graph', region_color=None, show=True, n_max_vertices=300000)[source]#

plot_graph_structure(structure_id, plot_type)[source]#

plot_voxelization(parent)[source]#

post_process()[source]#

Iteratively refine arteries and veins based on one another

Returns

pre_process()[source]#

reduce_graph(vertex_to_edge_mapping=None, edge_to_edge_mappings=None)[source]#

register()[source]#

run()[source]#

save_graph(base_name)[source]#

setup(preprocessor)[source]#

skeletonize(**kwargs)#

skeletonize_and_build_graph()[source]#

unload_temporary_graphs()[source]#

To free up memory

Returns

visualize_graph_annotations(chunk_range, plot_type='mesh', graph_step='reduced', show=True)[source]#

voxelize(weight_by_radius=False, vertex_degrees=None)[source]#

write_vertex_table()[source]#: Write a table with vertex coordinates and properties

property graph_annotated#

property graph_cleaned#

property graph_raw#

property graph_reduced#

property graph_traced#

property use_arteries_for_graph#

class VesselGraphProcessorSteps(workspace, postfix='')[source]#

Bases: ProcessorSteps

path_from_step_name(step)[source]#

property steps#