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from pathlib import Path
from typing import Callable, Optional
import imageio.v3 as iio
import npe2
import numpy as np
import pytest
import tifffile
from napari_builtins.io._write import write_csv
@pytest.fixture
def save_image(tmp_path: Path):
"""Create a temporary file."""
def _save(filename: str, data: Optional[np.ndarray] = None):
dest = tmp_path / filename
data_: np.ndarray = np.random.rand(20, 20) if data is None else data
if filename.endswith(('png', 'jpg')):
data_ = (data_ * 255).astype(np.uint8)
if dest.suffix in {'.tif', '.tiff'}:
tifffile.imwrite(str(dest), data_)
elif dest.suffix in {'.npy'}:
np.save(str(dest), data_)
else:
iio.imwrite(str(dest), data_)
return dest
return _save
@pytest.mark.parametrize('ext', ['.tif', '.npy', '.png', '.jpg'])
@pytest.mark.parametrize('stack', [False, True])
def test_reader_plugin_tif(save_image: Callable[..., Path], ext, stack):
"""Test the builtin reader plugin reads a temporary file."""
files = [
str(save_image(f'test_{i}{ext}')) for i in range(5 if stack else 1)
]
layer_data = npe2.read(files, stack=stack)
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
def test_animated_gif_reader(save_image):
threeD_data = (np.random.rand(5, 20, 20, 3) * 255).astype(np.uint8)
dest = save_image('animated.gif', threeD_data)
layer_data = npe2.read([str(dest)], stack=False)
assert len(layer_data) == 1
assert layer_data[0][0].shape == (5, 20, 20, 3)
@pytest.mark.slow
@pytest.mark.needs_network
def test_reader_plugin_url():
layer_data = npe2.read(
['https://samples.fiji.sc/FakeTracks.tif'], stack=False
)
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
def test_reader_plugin_csv(tmp_path):
"""Test the builtin reader plugin reads a temporary file."""
dest = str(tmp_path / 'test.csv')
table = np.random.random((5, 3))
write_csv(dest, table, column_names=['index', 'axis-0', 'axis-1'])
layer_data = npe2.read([dest], stack=False)
assert layer_data is not None
assert isinstance(layer_data, list)
assert len(layer_data) == 1
assert isinstance(layer_data[0], tuple)
assert layer_data[0][2] == 'points'
assert np.allclose(table[:, 1:], layer_data[0][0])
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