4106902596

Build Type

github

Committed by GitHub

Commit Message

Merge 5de60795e into 9fb6cee18

Pull Request Pull Request #20: GitHub Actions

Run Details

294 of 306 branches covered (96.08%)

Branch coverage included in aggregate %.

1 of 1 new or added line in 1 file covered. (100.0%)

431 of 443 relevant lines covered (97.29%)

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100.0

/src/tmi/image_utils.py

import pathlib
from typing import Dict, Union

import numpy as np
import skimage.io as io


def save_image(
    fname: Union[str, pathlib.Path], data: np.ndarray, compression_level: int = 6
) -> None:
    """
    A thin wrapper around `skimage.io.imsave()`.

    Args:
        fname (str): The location to save the tiff file.
        data (np.ndarray): The Numpy array to save.
        compression_level (int, optional): The compression level for skimage.io.imsave. Increasing
            `compress` increases memory consumption, decreases compression speed and moderately
            increases compression ratio. The range of compress is `[1,9]`. Defaults to 6.
    """
    # Compression Config:
    plugin_args: Dict[str, Union[str, int, Dict]] = {
        "compression": "zlib",
        "compressionargs": {"level": compression_level},
    }

    io.imsave(fname=fname, arr=data, plugin="tifffile", check_contrast=False, **plugin_args)

1	import pathlib	1✔
2	from typing import Dict, Union	1✔
3
4	import numpy as np	1✔
5	import skimage.io as io	1✔
6
7
8	def save_image(	1✔
9	fname: Union[str, pathlib.Path], data: np.ndarray, compression_level: int = 6
10	) -> None:
11	"""
12	A thin wrapper around `skimage.io.imsave()`.
13
14	Args:
15	fname (str): The location to save the tiff file.
16	data (np.ndarray): The Numpy array to save.
17	compression_level (int, optional): The compression level for skimage.io.imsave. Increasing
18	`compress` increases memory consumption, decreases compression speed and moderately
19	increases compression ratio. The range of compress is `[1,9]`. Defaults to 6.
20	"""
21	# Compression Config:
22	plugin_args: Dict[str, Union[str, int, Dict]] = {	1✔
23	"compression": "zlib",
24	"compressionargs": {"level": compression_level},
25	}
26
27	io.imsave(fname=fname, arr=data, plugin="tifffile", check_contrast=False, **plugin_args)	1✔

angelolab / tmi / 4106902596

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