# -*- coding: utf-8 -*-
"""
Files
=====
Module defining test data files.
"""
__author__ = 'Christoph Kirst <christoph.kirst.ck@gmail.com>'
__license__ = 'GPLv3 - GNU General Pulic License v3 (see LICENSE)'
__copyright__ = 'Copyright © 2020 by Christoph Kirst'
__webpage__ = 'http://idisco.info'
__download__ = 'http://www.github.com/ChristophKirst/ClearMap2'
import ClearMap.IO.IO as io
###############################################################################
### Files
###############################################################################
base_directory = io.split(io.abspath(__file__))[0];
"""The base directory for test data."""
data_directory = io.join(base_directory, 'Data');
"""The base directory for test data."""
vasculature_directory = io.join(data_directory, 'Vasculature');
"""Directory for vasculature sample data."""
vasculature_raw = io.join(vasculature_directory, 'vasculature_raw.npy');
"""Vasculature sample data."""
vasculature_pre = io.join(vasculature_directory, 'vasculature_pre.npy');
"""Vasculature sample data."""
vasculature_surface_raw = io.join(vasculature_directory, 'vasculature_surface_raw.npy');
"""Vasculature sample data."""
vasculature_surface_pre = io.join(vasculature_directory, 'vasculature_surface_pre.npy');
"""Vasculature sample data."""
vasculature_arteries_raw = io.join(vasculature_directory, 'vasculature_arteries_raw.npy');
"""Vasculature sample data."""
vasculature_arteries_pre = io.join(vasculature_directory, 'vasculature_arteries_pre.npy');
"""Vasculature sample data."""
vasculature_surface_arteries_raw = io.join(vasculature_directory, 'vasculature_surface_arteries_raw.npy');
"""Vasculature sample data."""
vasculature_surface_arteries_pre = io.join(vasculature_directory, 'vasculature_surface_arteries_pre.npy');
"""Vasculature sample data."""
vasculature_weak_raw = io.join(vasculature_directory, 'vasculature_weak_raw.npy');
"""Vasculature sample data."""
vasculature_weak_pre = io.join(vasculature_directory, 'vasculature_weak_pre.npy');
"""Vasculature sample data."""
vasculature_weak_high_raw = io.join(vasculature_directory, 'vasculature_weak_high_raw.npy');
"""Vasculature sample data."""
vasculature_lightsheet_raw = io.join(vasculature_directory, 'vasculature_lightsheet_raw.npy');
"""Vasculature sample data."""
vasculature_low_contrast_raw = io.join(vasculature_directory, 'vasculature_low_contrast_raw.npy');
"""Vasculature sample data."""
vasculature_low_contrast_surface_raw = io.join(vasculature_directory, 'vasculature_low_contrast_surface_raw.npy');
"""Vasculature sample data."""
tif_directory = io.join(data_directory, 'Tif');
"""Directory for tif sample data."""
tif_2d = io.join(tif_directory, '2d.tif');
"""2d tif file."""
tif_2d_color = io.join(tif_directory, '2d_color.tif');
"""2d color tif file."""
tif_3d = io.join(tif_directory, '3d.tif');
"""3d tif file."""
tif_sequence = io.join(tif_directory, 'sequence');
"""tif file sequence."""
skeleton_directory = io.join(data_directory, 'Skeletonization');
"""Directory for smaple data to test skeletonization."""
skeleton = io.join(skeleton_directory, 'skeleton.npy');
"""Skeleton sample file."""
skeleton_binary = io.join(skeleton_directory, 'binary.npy');
"""Binary sample data for skeleton generation."""
temp = io.join(data_directory, 'temp.npy');
"""Temporary file"""
###############################################################################
### Filenames and sources
###############################################################################
[docs]def filename(data, postfix = None):
"""Returns a test data file name.
Arguments
---------
data : str
The type of the sample data to initialize.
{'vasculature'}
Returns
-------
source : Source
A data source of the sample data.
"""
if data in ['v', 'vasculature_raw']:
return vasculature_raw;
elif data in ['vp', 'vasculature_pre']:
return vasculature_pre;
elif data in ['vs', 'vasculature_surface_raw']:
return vasculature_surface_raw;
elif data in ['vsp', 'vasculature_surfaace_pre']:
return vasculature_surface_pre;
elif data in ['va', 'vasculature_arteries_raw']:
return vasculature_arteries_raw;
elif data in ['vap', 'vasculature_arteries_pre']:
return vasculature_arteries_pre;
elif data in ['vsa', 'vasculature_surface_arteries_raw']:
return vasculature_surface_arteries_raw;
elif data in ['vsap', 'vasculature_surfaace_arteries_pre']:
return vasculature_surface_arteries_pre;
elif data in ['vw', 'vasculature_weak_raw']:
return vasculature_weak_raw;
elif data in ['vwp', 'vasculature_weak_pre']:
return vasculature_weak_pre;
elif data in ['vwh']:
return vasculature_weak_high_raw;
elif data in ['vls', 'vasculature_lightsheet_raw']:
return vasculature_lightsheet_raw;
elif data in ['vlc']:
return vasculature_low_contrast_raw;
elif data in ['vlcs']:
return vasculature_low_contrast_surface_raw;
elif data in ['tif_2d', 't2d']:
return tif_2d;
elif data in ['tif_2d_color', 't2dc']:
return tif_2d_color;
elif data in ['tif_3d', 't3d']:
return tif_3d;
elif data in ['tif_sequence', 'ts']:
return tif_sequence
elif data in ['skeleton', 'sk']:
return skeleton
elif data in ['skeleton_binary', 'skb']:
return skeleton_binary
elif data in ['temp', 'tmp', 't']:
if postfix is not None:
return temp[:-4] + '_' + postfix + '.npy';
else:
return temp;
else:
raise ValueError('Data sample type %r not found' % data);
[docs]def source(*args, **kwargs):
"""Initializes a test data source.
Arguments
---------
As in :func:`filename`
Returns
-------
source : Source
A data source of the sample data.
"""
return io.source(filename(*args, **kwargs));
Source
