IO¶

class Qiber3D.IO.load(path, **kwargs)¶

Bases: object

Returns a new Qiber3D.Network from file.

Supports: .qiber, .json, .mv3d, .tif, .nd2, .swc, .ntr

Parameters

path (str, Path) – file path to load
kwargs – key-word arguments are passed down to the individual IO functions

static binary(path)¶

Create a Qiber3D.Network from a .qiber file, created by Qiber3D.Network.save()

Parameters: path (str, Path) – file path to load
Returns: Qiber3D.Network

static image(path, channel=None, voxel_size=None)¶

Create a Qiber3D.Network from a image file.

Parameters

path (str, Path) – file path to load
channel (int, str) – either index or name of image channel
voxel_size (tuple(float)) – physical size of voxel in (x,y,z)

Returns

Qiber3D.Network

static json(path, data=None)¶

Create a Qiber3D.Network from a .json file.

Parameters

path (str, Path) – file path to load
data (dict) – load network from a dict representation of the .json file directly

Returns

Qiber3D.Network

static mv3d(path)¶

Create a Qiber3D.Network from a .mv3d file.

Parameters: path (str, Path) – file path to load
Returns: Qiber3D.Network

static nd2(path, channel=None)¶

Create a Qiber3D.Network from a .nd2 file.

Parameters

path (str, Path) – file path to load
channel (int, str) – either index or name of image channel

Returns

Qiber3D.Network

static network(net, scale=1, input_path=None, segment_list=None)¶

Create a new Qiber3D.Network from a Qiber3D.Network.

Parameters

net (Qiber3D.Network) – original network
scale (float) – scale all points and radii by this value
input_path (str, Path) – set this path as new imput path of the returning network
segment_list (tuple) – limit the new network to this list of segments (sid)

Returns

Qiber3D.Network

static ntr(path)¶

Create a Qiber3D.Network from a .ntr file.

Parameters: path (str, Path) – file path to load
Returns: Qiber3D.Network

static swc(path, allowed_types=None)¶

Create a Qiber3D.Network from a .swc file.

Parameters

path (str, Path) – file path to load
allowed_types (tuple) – limit the returned network to these SEGMENT_TYPEs

Returns

Qiber3D.Network

classmethod synthetic_network()¶

Create the synthetic test network.

Returns: Qiber3D.Network

class Qiber3D.IO.export(net, out_path='.', overwrite=False, mode=None, **kwargs)¶

Bases: object

Export a Qiber3D.Network to file. Selecting the appropriate format based on the file suffix.

Supports: .qiber, .json, .mv3d, .tif, .nd2, .swc, .csv, .tsv, .xlsx, .x3d

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite
mode (str) – select the file format ignoring the file suffix. Choose from [‘binary’, ‘json’, ‘mv3d’, ‘x3d’, ‘swc’, ‘xlsx’, ‘csv’, ‘tsv’, ‘tif’]
kwargs – key-word arguments are passed down to the individual IO functions

Returns

path to saved file

Return type

Path

static binary(net, out_path='.', overwrite=False, save_steps=False)¶

Export Qiber3D.Network as binary file (.qiber).

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite
save_steps (bool) – save extraction steps image stacks

Returns

path to saved file

Return type

Path

static csv(net, out_path='.', overwrite=False, separator=';')¶

Export Qiber3D.Network as .csv file.

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite
separator (str) – char to separate values

Returns

path to saved file

Return type

Path

static json(net, out_path='.', overwrite=False)¶

Export Qiber3D.Network as .json file.

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite

Returns

path to saved file

Return type

Path

static mv3d(net, out_path='.', overwrite=False)¶

Export Qiber3D.Network as .mv3d file.

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite

Returns

path to saved file

Return type

Path

static swc(net, out_path='.', overwrite=False, multiple_files=False)¶

Export Qiber3D.Network as .swc file.

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite
multiple_files (bool) – save each fiber as separate swc file

Returns

path to saved file

Return type

Path

static tif(net, out_path='.', overwrite=False, voxel_resolution=None, segment_list=None)¶

Export Qiber3D.Network as .tif image stack.

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network, if None show the plot.
overwrite (bool) – allow file overwrite
voxel_resolution (float) – number of voxels per unit length
segment_list (tuple) – limit the visualisation to certain segment (use sid)

Returns

path to saved file

Return type

Path

static x3d(net, out_path='.', overwrite=False, color_mode='flat', color_map='jet', color=None, object_type=None, segment_list=None, azimuth=None, elevation=None, roll=None)¶

Export Qiber3D.Network as .x3d file.

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite
color_mode (str) – sets the way to color the network choose one of [‘flat’, ‘fiber’, ‘fiber_length’, ‘fiber_volume’, ‘segment’, ‘segment_length’, ‘segment_volume’, ‘fiber_segment_ratio’]
color_map (str) – name of a matplotlib colormap
color (tuple(float)) – color if color_mode is ‘flat’
object_type (str) – when set to ‘line’ render center line
segment_list (tuple) – limit the visualisation to certain segment (use sid)
azimuth (float) – change camera azimuth
elevation (float) – change camera elevation
roll (float) – roll camera

Returns

path to saved file

Return type

Path

static xlsx(net, out_path='.', overwrite=False)¶

Export Qiber3D.Network as Excel file (.xlsx).

Parameters

net (Qiber3D.Network) – network to export
out_path (str, Path) – file or folder path where to save the network
overwrite (bool) – allow file overwrite

Returns

path to saved file

Return type

Path