"""
This module contains tools to read and write ome-tiff files.
"""
# Copyright (c) 2020 Idiap Research Institute, http://www.idiap.ch/
# Written by François Marelli <francois.marelli@idiap.ch>
#
# This file is part of CBI Toolbox.
#
# CBI Toolbox is free software: you can redistribute it and/or modify
# it under the terms of the 3-Clause BSD License.
#
# CBI Toolbox is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# 3-Clause BSD License for more details.
#
# You should have received a copy of the 3-Clause BSD License along
# with CBI Toolbox. If not, see https://opensource.org/licenses/BSD-3-Clause.
#
# SPDX-License-Identifier: BSD-3-Clause
import numpy as np
import apeer_ometiff_library.io as omeio
[docs]def load_ome_tiff(file_path):
"""
Load an OME tiff file as a numpy array [ZXY].
Parameters
----------
file_path : string
The file to load.
Returns
-------
tuple (array [ZXY], str)
The loaded array, and its xml metadata.
"""
array, xmlstring = omeio.read_ometiff(file_path)
array = array.squeeze()
array = np.ascontiguousarray(array.transpose((0, 2, 1)))
return array, xmlstring
[docs]def save_ome_tiff(file_path, image, xmlstring=None):
"""
Save numpy array to OME tiff format.
Parameters
----------
file_path : string
Where to save the data.
image : array[ZXY]
The array to save.
xmlstring : str, optional
Xml metadata, by default None.
"""
image = image.transpose((0, 2, 1))
image = image[None, :, None, ...]
omeio.write_ometiff(file_path, image, xmlstring)