image2image-io 0.1.10__py3-none-any.whl

image2image_io/__init__.py

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+"""Various image readers."""
+
+from importlib.metadata import PackageNotFoundError, version
+
+try:
+    __version__ = version("image2image-io")
+except PackageNotFoundError:
+    __version__ = "uninstalled"
+
+__author__ = "Lukasz G. Migas"
+__email__ = "lukas.migas@yahoo.com"

image2image_io/_version.py

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+# file generated by setuptools-scm
+# don't change, don't track in version control
+
+__all__ = ["__version__", "__version_tuple__", "version", "version_tuple"]
+
+TYPE_CHECKING = False
+if TYPE_CHECKING:
+    from typing import Tuple
+    from typing import Union
+
+    VERSION_TUPLE = Tuple[Union[int, str], ...]
+else:
+    VERSION_TUPLE = object
+
+version: str
+__version__: str
+__version_tuple__: VERSION_TUPLE
+version_tuple: VERSION_TUPLE
+
+__version__ = version = '0.1.10'
+__version_tuple__ = version_tuple = (0, 1, 10)

image2image_io/cli/__init__.py

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+"""Main CLI."""
+
+import click
+import koyo.compat
+from loguru import logger
+
+from image2image_io import __version__
+from image2image_io.cli.convert import convert
+from image2image_io.cli.czi2tiff import czi2tiff
+from image2image_io.cli.merge import merge
+from image2image_io.cli.thumbnail import thumbnail
+from image2image_io.cli.transform import transform
+
+LOG_FMT = "[<level>{level: <8}</level>][{time:YYYY-MM-DD HH:mm:ss:SSS}][{extra[src]}] {message}"
+COLOR_LOG_FMT = (
+    "<green>[<level>{level: <8}</level>]</green>"
+    "<cyan>[{time:YYYY-MM-DD HH:mm:ss:SSS}]</cyan>"
+    "<red>[{process}]</red>"
+    "<blue>[{extra[src]}]</blue>"
+    " {message}"
+)
+
+
+@click.group(
+    context_settings={
+        "help_option_names": ["-h", "--help"],
+        "max_content_width": 120,
+        "ignore_unknown_options": True,
+    }
+)
+@click.option(
+    "--dev",
+    help="Flat to indicate that CLI should run in development mode and catch all errors.",
+    default=False,
+    is_flag=True,
+    show_default=True,
+)
+@click.option(
+    "--no_color",
+    help="Flag to enable colored while doing tasks.",
+    default=False,
+    is_flag=True,
+    show_default=True,
+)
+@click.version_option(__version__)
+@click.option(
+    "--verbose",
+    "-v",
+    "verbosity",
+    default=1,
+    count=True,
+    help="Verbose output. This is additive flag so `-vvv` will print `INFO` messages and -vvvv will print `DEBUG`"
+    " information.",
+)
+@click.option("--quiet", "-q", "verbosity", flag_value=0, help="Minimal output")
+@click.option("--debug", "verbosity", flag_value=0.5, help="Maximum output")
+def cli(verbosity: int, no_color: bool, dev: bool) -> None:
+    """image2image-io CLI."""
+    from koyo.hooks import install_debugger_hook, uninstall_debugger_hook
+    from koyo.logging import get_loguru_config, set_loguru_env, set_loguru_log
+
+    verbosity = 2 - int(verbosity)  # default is INFO
+    if verbosity < 0:
+        verbosity = 0
+    if dev:
+        install_debugger_hook()
+        verbosity = 0
+    elif dev:
+        uninstall_debugger_hook()
+    level = verbosity * 10
+    level, fmt, colorize, enqueue = get_loguru_config(level, no_color=no_color)
+    set_loguru_env(fmt, level, colorize, enqueue)
+    set_loguru_log(
+        level=level.upper(),
+        no_color=no_color,
+        logger=logger,
+        fmt=LOG_FMT if no_color else COLOR_LOG_FMT,
+    )
+    logger.configure(extra={"src": "CLI"})
+    logger.enable("image2image_io")
+    logger.enable("koyo")
+    logger.debug(f"Activated logger with level '{level}'.")
+
+
+# register commands
+cli.add_command(czi2tiff)
+cli.add_command(thumbnail)
+cli.add_command(merge)
+cli.add_command(convert)
+if transform:
+    cli.add_command(transform)
+
+
+def main():
+    """Execute the "imimspy" command line program."""
+    cli.main(windows_expand_args=False)
+
+
+if __name__ == "__main__":
+    cli.main(windows_expand_args=False)

image2image_io/cli/_common.py

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+import click
+
+
+# noinspection PyUnusedLocal
+def arg_split_bbox(ctx, param, value):
+    """Split arguments."""
+    if value is None:
+        return None
+    args = [int(arg.strip()) for arg in value.split(",")]
+    assert len(args) == 4, "Bounding box must have 4 values"
+    return args
+
+
+ALLOW_EXTRA_ARGS = {"help_option_names": ["-h", "--help"], "ignore_unknown_options": True, "allow_extra_args": True}
+overwrite_ = click.option(
+    "-W",
+    "--overwrite",
+    help="Overwrite existing data.",
+    is_flag=True,
+    default=False,
+    show_default=True,
+)
+as_uint8_ = click.option(
+    "-u/-U",
+    "--as_uint8/--no_as_uint8",
+    help="Downcast the image data format to uint8 which will substantially reduce the size of the files (unless it's"
+    " already in uint8...).",
+    is_flag=True,
+    default=None,
+    show_default=True,
+)
+fmt_ = click.option(
+    "-f",
+    "--fmt",
+    help="Output format.",
+    type=click.Choice(["ome-tiff"], case_sensitive=False),
+    default="ome-tiff",
+    show_default=True,
+    required=False,
+)

image2image_io/cli/convert.py

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+"""Utilities."""
+
+from __future__ import annotations
+
+import click
+from koyo.click import Parameter, cli_parse_paths_sort, print_parameters
+
+from image2image_io.cli._common import ALLOW_EXTRA_ARGS
+
+
+@click.option(
+    "-W",
+    "--overwrite",
+    help="Overwrite existing data.",
+    is_flag=True,
+    default=None,
+    show_default=True,
+)
+@click.option(
+    "-u/-U",
+    "--as_uint8/--no_as_uint8",
+    help="Downcast the image data format to uint8 which will substantially reduce the size of the files (unless it's"
+    " already in uint8...).",
+    is_flag=True,
+    default=None,
+    show_default=True,
+)
+@click.option(
+    "-t",
+    "--tile_size",
+    help="Tile size.",
+    type=click.Choice(["256", "512", "1024", "2048"], case_sensitive=False),
+    default="512",
+    show_default=True,
+    required=False,
+)
+@click.option(
+    "-f",
+    "--fmt",
+    help="Output format.",
+    type=click.Choice(["ome-tiff"], case_sensitive=False),
+    default="ome-tiff",
+    show_default=True,
+    required=False,
+)
+@click.option(
+    "-o",
+    "--output_dir",
+    help="Path to the output directory where images should be saved to.",
+    type=click.Path(file_okay=False, dir_okay=True, resolve_path=True),
+    show_default=True,
+    required=True,
+)
+@click.option(
+    "-i",
+    "--image",
+    help="Path(s) of images to be converted.",
+    type=click.UNPROCESSED,
+    show_default=True,
+    required=True,
+    multiple=True,
+    callback=cli_parse_paths_sort,
+)
+@click.command("convert", context_settings=ALLOW_EXTRA_ARGS)
+def convert(image: list[str], output_dir: str, fmt: str, tile_size: str, as_uint8: bool, overwrite: bool) -> None:
+    """Convert images to pyramidal OME-TIFF."""
+    convert_runner(image, output_dir, fmt, tile_size, as_uint8, overwrite)
+
+
+def convert_runner(
+    paths: list[str],
+    output_dir: str,
+    fmt: str = "ome-tiff",
+    tile_size: int | str = 512,
+    as_uint8: bool | None = None,
+    overwrite: bool = False,
+) -> None:
+    """Convert images to pyramidal OME-TIFF."""
+    from image2image_io.writers import images_to_ome_tiff
+
+    print_parameters(
+        Parameter("Images", "-i/--image", paths),
+        Parameter("Output directory", "-o/--output_dir", output_dir),
+        Parameter("Output format", "-f/--fmt", fmt),
+        Parameter("Tile size", "-t/--tile_size", tile_size),
+        Parameter("Downcast to uint8", "-u/--as_uint8", as_uint8),
+        Parameter("Overwrite", "-W/--overwrite", overwrite),
+    )
+    for _ in images_to_ome_tiff(paths, output_dir, tile_size=int(tile_size), as_uint8=as_uint8, overwrite=overwrite):
+        pass

image2image_io/cli/czi2tiff.py

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+"""Convert images from one format to OME-TIFF format."""
+
+from __future__ import annotations
+
+import click
+from koyo.click import arg_split_int, arg_split_str
+from loguru import logger
+
+
+@click.option(
+    "-N",
+    "--channel_names",
+    type=click.STRING,
+    default=None,
+    help="Specify a list of channel names to be used by the task. Names should be separated by commas. "
+    "e.g. 'DAPI,CD3,CD20'",
+    callback=arg_split_str,
+    show_default=True,
+    required=False,
+)
+@click.option(
+    "-I",
+    "--channel_ids",
+    type=click.STRING,
+    default=None,
+    help="Specify a list of channel indices to be used by the task. Channel IDs should be separated by comma."
+    "e.g. '1,2,4'.",
+    callback=arg_split_int,
+    show_default=True,
+    required=False,
+)
+@click.option(
+    "-u",
+    "--as_uint8",
+    is_flag=True,
+    help="Convert to uint8. If not specified, the original data type will be used.",
+    show_default=True,
+    required=False,
+)
+@click.option(
+    "-t",
+    "--tile_size",
+    help="Tile size.",
+    type=click.Choice(["256", "512", "1024", "2048"], case_sensitive=False),
+    default="512",
+    show_default=True,
+    required=False,
+)
+@click.option(
+    "-s",
+    "--scene",
+    "scene_index",
+    type=click.INT,
+    help="Specify the scene to be processed. If not specified, all scenes will be processed.",
+    default=None,
+    show_default=True,
+    required=True,
+)
+@click.option(
+    "-o",
+    "--output_dir",
+    help="Path to directory where OME-TIFF files will be saved.",
+    default=".",  # cwd
+    type=click.Path(exists=False, resolve_path=True, file_okay=False, dir_okay=True),
+    show_default=True,
+    required=True,
+)
+@click.option(
+    "-i",
+    "--input",
+    "input_",
+    help="Path to the CZI file that should be converted.",
+    type=click.Path(exists=False, resolve_path=False, file_okay=True, dir_okay=False),
+    show_default=True,
+    required=True,
+)
+@click.command()
+def czi2tiff(
+    input_: str,
+    output_dir: str,
+    scene_index: int,
+    tile_size: str,
+    as_uint8: bool,
+    channel_ids: list[int] | None,
+    channel_names: list[str | None],
+) -> None:
+    """Convert CZI to OME-TIFF."""
+    from image2image_io.writers import czi_to_ome_tiff
+
+    metadata = None
+    if channel_ids and channel_names:
+        if len(channel_ids) != len(channel_names):
+            raise ValueError("Number of channel IDs and channel names must be equal.")
+        metadata = {scene_index: {"channel_ids": channel_ids, "channel_names": channel_names}}
+
+    for key, scene_index, total, _ in czi_to_ome_tiff(
+        input_, output_dir, as_uint8=as_uint8, tile_size=int(tile_size), metadata=metadata, scenes=[scene_index]
+    ):
+        logger.info(f"Converted {key} scene {scene_index}/{total}")

image2image_io/cli/merge.py

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+"""Merge command."""
+
+from __future__ import annotations
+
+import typing as ty
+
+import click
+from koyo.click import Parameter, arg_parse_framelist_multi, cli_parse_paths_sort, print_parameters
+from koyo.timer import MeasureTimer
+from loguru import logger
+
+from image2image_io.cli._common import as_uint8_, fmt_, overwrite_
+from image2image_io.enums import WriterMode
+
+
+@overwrite_
+@as_uint8_
+@fmt_
+@click.option(
+    "-C",
+    "--channel_ids",
+    type=click.STRING,
+    default=None,
+    help="Specify channel ids in the format: 1,2,4-6. You can provide multiple. If you are providing any, make sure to"
+    " provide one for each file you are trying to merge.",
+    callback=arg_parse_framelist_multi,
+    show_default=True,
+    multiple=True,
+    required=False,
+)
+@click.option(
+    "-o",
+    "--output_dir",
+    help="Path to images to be merged.",
+    type=click.Path(file_okay=False, dir_okay=True, resolve_path=True),
+    show_default=True,
+    required=True,
+)
+@click.option(
+    "-p",
+    "--path",
+    help="Path to images to be merged.",
+    type=click.UNPROCESSED,
+    show_default=True,
+    required=True,
+    multiple=True,
+    callback=cli_parse_paths_sort,
+)
+@click.option(
+    "-n",
+    "--name",
+    help="Name of the merged image.",
+    type=click.STRING,
+    show_default=True,
+    required=True,
+)
+@click.command("merge")
+def merge(
+    name: str,
+    path: ty.Sequence[str],
+    output_dir: str,
+    channel_ids: ty.Sequence[tuple] | None,
+    fmt: WriterMode,
+    as_uint8: bool | None,
+    overwrite: bool,
+) -> None:
+    """Export images."""
+    merge_runner(name, path, output_dir, channel_ids, fmt, as_uint8, overwrite)
+
+
+def merge_runner(
+    name: str,
+    paths: ty.Sequence[str],
+    output_dir: str,
+    channel_ids: ty.Sequence[tuple] | None,
+    fmt: WriterMode = "ome-tiff",
+    as_uint8: bool | None = False,
+    overwrite: bool = False,
+) -> None:
+    """Register images."""
+    from image2image_io.workflows.merge import merge as merge_images
+
+    print_parameters(
+        Parameter("Name", "-n/--name", name),
+        Parameter("Image paths", "-p/--path", paths),
+        Parameter("Output directory", "-o/--output_dir", output_dir),
+        Parameter("Channel ids", "-C/--channel_ids", channel_ids),
+        Parameter("Output format", "-f/--fmt", fmt),
+        Parameter("Write images as uint8", "--as_uint8/--no_as_uint8", as_uint8),
+        Parameter("Overwrite", "-W/--overwrite", overwrite),
+    )
+
+    if channel_ids:
+        if len(channel_ids) != len(paths):
+            raise ValueError("Number of channel ids must match number of images.")
+
+    with MeasureTimer() as timer:
+        merge_images(name, list(paths), output_dir, fmt, as_uint8, channel_ids=channel_ids, overwrite=overwrite)
+    logger.info(f"Finished processing project in {timer()}.")

image2image_io/cli/thumbnail.py

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+"""Create thumbnail for image(s)."""
+
+from __future__ import annotations
+
+import click
+from koyo.click import cli_parse_paths_sort
+from loguru import logger
+from tqdm import tqdm
+
+
+@click.option(
+    "-f/-F",
+    "--first_only/--no_first_only",
+    help="Export only the first channel from the stack.",
+    is_flag=True,
+    default=False,
+    show_default=True,
+)
+@click.option(
+    "-t/-T",
+    "--with_title/--no_with_title",
+    help="Export image with title.",
+    is_flag=True,
+    default=True,
+    show_default=True,
+)
+@click.option(
+    "-o",
+    "--output_dir",
+    help="Path to directory where OME-TIFF files will be saved.",
+    default=".",  # cwd
+    type=click.Path(exists=False, resolve_path=True, file_okay=False, dir_okay=True),
+    show_default=True,
+    required=True,
+)
+@click.option(
+    "-i",
+    "--input",
+    "input_",
+    help="Path to supported file(s).",
+    type=click.UNPROCESSED,
+    show_default=True,
+    required=True,
+    multiple=True,
+    callback=cli_parse_paths_sort,
+)
+@click.command()
+def thumbnail(input_: str, output_dir: str, with_title: bool, first_only: bool) -> None:
+    """Create a thumbnail for image(s)."""
+    from image2image_io.utils.utilities import write_thumbnail
+
+    for path in tqdm(input_, desc="Creating thumbnails..."):
+        write_thumbnail(path, output_dir, with_title=with_title, first_only=first_only)
+        logger.info(f"Created thumbnail for '{path}'.")