Network / Fiber / Segment

class Qiber3D.Network(data)

Class representing the complete network

Parameters

data (dict) – metadata and segment data collection

Variables

  • segment – directory of Segment forming the Network

  • fiber – directory of Fiber forming the Network

  • average_radius (float) – average radius

  • cylinder_radius (float) – radius if segment is interpreted as single cylinder

  • average_diameter (float) – average diameters

  • length (float) – overall length

  • volume (int) – overall volume modeled as truncated cones

  • number_of_fibers – fiber count

  • vector (ndarray) – vectors between points

  • direction (ndarray) – vector pointing from start to end

  • bbox (float) – bounding box corners

  • bbox_volume – bounding box volume

  • center (ndarray) – bounding box center

  • bbox_size (ndarray) – bounding box size

export(out_path='.', overwrite=False, mode=None, **kwargs)

Export the network data. Available file types: .json, .qiber, .swc, .xlsx, .csv, .static, .tif or .mv3d. For more details see Qiber3D.io.IO.

Parameters

  • out_path (str, Path) – file or folder path where to save the network

  • overwrite –

  • mode –

  • kwargs –

Returns

static load(path, **kwargs)

Load a Network. Available file types: .tif, .nd2, .json, .qiber, .swc, .ntr, .csv, or .mv3d. For more details see Qiber3D.io.IO.

Parameters

path (str, Path) – file path to input file

Returns

Qiber3D.Network

save(out_path='.', overwrite=False, save_steps=False)

Save network to file.

Parameters

  • out_path (str, Path) – file or folder path where to save the network

  • overwrite (bool) – allow file overwrite

  • save_steps (bool) – add extraction steps to the saved file

Returns

path to saved file

Return type

Path

class Qiber3D.Fiber(network, fiber_id, segment_ids)

Class representing the large elements in a network

Parameters

  • network (Network) – overarching network

  • fiber_id (int) – unique fiber identifier

  • segment_ids (list) – list of segment identifier forming the Fiber

Variables

  • fid – unique fiber identifier

  • segment – directory of Segment forming the Fiber

  • average_radius (float) – average radius

  • cylinder_radius (float) – radius if segment is interpreted as single cylinder

  • average_diameter (float) – average diameters

  • length (float) – overall length

  • volume (float) – overall volume modeled as truncated cones

  • graph (nx.Graph) – Fiber represented as networkx graph

class Qiber3D.Segment(point, radius, segment_index)

Class representing the small element in a network

Parameters

  • point (ndarray) – ordered list of points forming the Segment

  • radius (ndarray) – radii (same order as point)

  • segment_index (int) – unique identifier

Variables

  • sid – unique segment identifier

  • point (ndarray) – ordered points forming the Segment

  • x (ndarray) – ordered list of x coordinates

  • y (ndarray) – ordered list of y coordinates

  • z (ndarray) – ordered list of z coordinates

  • radius (ndarray) – radii in same order as point (also available as r)

  • average_radius (float) – average radius

  • cylinder_radius (float) – radius if segment is interpreted as single cylinder

  • diameter (ndarray) – diameters in same order as point (also available as d)

  • average_diameter (float) – average diameters

  • start (tuple) – start point coordinates

  • end (tuple) – end point coordinates

  • vector (ndarray) – vectors between points

  • direction (ndarray) – vector pointing from start to end

  • length (float) – length from start to end

  • volume (float) – Segment volume modeled as truncated cones