pymaid.get_nodes_in_volume¶
- pymaid.get_nodes_in_volume(*x, coord_format='NM', resolution=(4, 4, 50), remote_instance=None)[source]¶
Retrieve nodes and connectors in given bounding box.
Please note that there is a cap on the number of nodes returned that is hard wired into the CATMAID server’s settings.
- Parameters
*x –
Coordinates defining the bounding box. Can be either:
1d list of coordinates: left, right, top, bottom, z1, z2
2d list of coordinates: [[left, right], [top, bottom], [z1, z2]]
pymaid.Volume
Can be given in nm or pixels.
coord_format (str, optional) – Define whether provided coordinates are in nanometer (‘NM’) or in pixels/slices (‘PIXEL’).
resolution (tuple of floats, optional) – x/y/z resolution in nm [default = (4, 4, 50)] Used to transform to nm if limits are given in pixels.
remote_instance (CatmaidInstance, optional) – If not passed directly, will try using global.
- Returns
nodes (pandas.DataFrame) –
DataFrame in which each row is a node:
node_id parent_id x y z confidence radius skeleton_id edition_time user_id 0 1 2
connectors (pandas.DataFrame) –
DataFrame in which each row is a connector:
connector_id x y z confidence edition_time user_id partners 0 1 2 ``partners`` are lists of:: [node_id, relation_id, link_confidence, link_edition_time, link_id]
truncated (bool) – If True, lists are truncated due to node limit reached.
relation_map (dict) – Map for
relation_id
in connector’spartner
column.
Examples
Get (truncated) lists of nodes and connectors in the bounding box of the AL:
>>> al = pymaid.get_volume('AL_R') >>> nodes, connectors, truncated, relation_map = pymaid.get_nodes_in_volume(al) >>> truncated True