"""
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
[docs]
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)]