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 byQiber3D.Network.save()
- Parameters
path (str, Path) – file path to load
- Returns
- 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
- 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
- static mv3d(path)¶
Create a
Qiber3D.Network
from a.mv3d
file.- Parameters
path (str, Path) – file path to load
- Returns
- 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
- static network(net, scale=1, input_path=None, segment_list=None)¶
Create a new
Qiber3D.Network
from aQiber3D.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
- static ntr(path)¶
Create a
Qiber3D.Network
from a.ntr
file.- Parameters
path (str, Path) – file path to load
- Returns
- 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
- classmethod synthetic_network()¶
Create the synthetic test network.
- Returns
- 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