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https://github.com/turleyjm/cell-division-dl-plugin
24 August 2024, 11:55:15 UTC
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  • cell_division_dl_plugin
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  • _reader.py
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Tip revision: f6c3290670f23524d47ccddc873ef5673eda4b3c authored by turleyjm on 11 July 2024, 02:09:47 UTC
Update README.md
Tip revision: f6c3290
_reader.py
"""
This module is an example of a barebones numpy reader plugin for napari.

It implements the Reader specification, but your plugin may choose to
implement multiple readers or even other plugin contributions. see:
https://napari.org/stable/plugins/guides.html?#readers
"""
import numpy as np


def napari_get_reader(path):
    """A basic implementation of a Reader contribution.

    Parameters
    ----------
    path : str or list of str
        Path to file, or list of paths.

    Returns
    -------
    function or None
        If the path is a recognized format, return a function that accepts the
        same path or list of paths, and returns a list of layer data tuples.
    """
    if isinstance(path, list):
        # reader plugins may be handed single path, or a list of paths.
        # if it is a list, it is assumed to be an image stack...
        # so we are only going to look at the first file.
        path = path[0]

    # if we know we cannot read the file, we immediately return None.
    if not path.endswith(".npy"):
        return None

    # otherwise we return the *function* that can read ``path``.
    return reader_function


def reader_function(path):
    """Take a path or list of paths and return a list of LayerData tuples.

    Readers are expected to return data as a list of tuples, where each tuple
    is (data, [add_kwargs, [layer_type]]), "add_kwargs" and "layer_type" are
    both optional.

    Parameters
    ----------
    path : str or list of str
        Path to file, or list of paths.

    Returns
    -------
    layer_data : list of tuples
        A list of LayerData tuples where each tuple in the list contains
        (data, metadata, layer_type), where data is a numpy array, metadata is
        a dict of keyword arguments for the corresponding viewer.add_* method
        in napari, and layer_type is a lower-case string naming the type of
        layer. Both "meta", and "layer_type" are optional. napari will
        default to layer_type=="image" if not provided
    """
    # handle both a string and a list of strings
    paths = [path] if isinstance(path, str) else path
    # load all files into array
    arrays = [np.load(_path) for _path in paths]
    # stack arrays into single array
    data = np.squeeze(np.stack(arrays))

    # optional kwargs for the corresponding viewer.add_* method
    add_kwargs = {}

    layer_type = "image"  # optional, default is "image"
    return [(data, add_kwargs, layer_type)]

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