Create Tiff-File with series.

TiffWriter_series.py

import os
from tifffile import TiffWriter, imread

def create_tif_series(file, list_of_imgs, axes):
    """
    Creates a tif file that includes len(list_of_imgs) series.
    Arguments:
        file: str or File like object, where tif file is written to.
        list_of_imgs: list of numpy arrays. The imgs, that are written
        axes: list of str. The axes of the imgs, that are written
    Returns:
        None
    """
    with TiffWriter(file) as tif:
        for img, ax in zip(list_of_imgs, axes):
            if not img.ndim == len(ax):
                img = np.expand_dims(img, axis=ax.index("C"))
            tif.save(img, metadata={"axes": ax}, contiguous=False)


def create_tif_series_from_path(file, path, axes="CYX"):
    """
    Writes all tif files of a path into a single tif file. Each tif file
    into a different series.
    Arguments:
        file: str of File like object, where tif file is written to
        path: path where tif files are saved
        axes: the axes of the files in that path
    Returns:
        None
    """
    imgs = sorted(list(os.listdir(path)))
    imgs = [imread(os.path.join(path, img)) for img in imgs]
    print("imgs[0].shape: ", imgs[0].shape)
    print("using axes :", axes)
    create_tif_series(file, imgs, [axes,]*len(imgs))


def create_tifs_from_paths(path, axes="CYX", file_ending=".ome.tiff"):
    """
    Creates tif files from paths.
    Arguments:
        path: The path where more path with
        corresponding tif files reside.
    Returns:
        None
    """
    paths = list(os.listdir(path))
    paths = [
        p for p in paths if os.path.isdir(
            os.path.join(path, p)
        )
    ]
    files = [p + file_ending for p in paths]
    for f, p in zip(files, paths):
        create_tif_series_from_path(
            os.path.join(path, f),
            os.path.join(path, p),
            axes
        )