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92 lines
3.0 KiB
92 lines
3.0 KiB
2 years ago
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""" rename sensospot images """
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import click
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import pathlib
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import shutil
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RENAME_MAP_NAME = "rename_map.txt"
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IMAGE_SUFFIXES = {".tif", ".jpg"}
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def get_map_file_path(directory:str) -> pathlib.Path:
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return pathlib.Path(directory) / RENAME_MAP_NAME
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def list_images(directory:str) -> list[pathlib.Path]:
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parent = pathlib.Path(directory)
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non_hidden = (i for i in parent.iterdir() if not i.name.startswith("."))
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return [i for i in non_hidden if i.suffix.lower() in IMAGE_SUFFIXES]
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def get_image_parts(image_path:pathlib.Path) -> tuple[str, str, str]:
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return image_path.stem.rsplit("_", maxsplit=2)
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def get_unique_parts(images:list[pathlib.Path]) -> list[list[str], list[str], list[str]]:
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parts = [get_image_parts(p) for p in images]
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return [sorted(set(items)) for items in zip(*parts)]
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def write_rename_map(map_file:pathlib.Path) -> None:
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images = list_images(directory)
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parts = get_unique_parts(images)
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headers = ["stems", "wells", "exposures"]
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lines = []
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for header, items in zip(headers, parts):
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lines.append(f"# {header}")
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lines.extend([f"{i}\t" for i in items])
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lines.append("")
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lines.append("")
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map_file.write_text("\n".join(lines))
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def _parse_rename_map(content:str) -> tuple[str, str]:
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lines = [line.strip() for line in content.splitlines()]
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for i, line in enumerate(lines, start=1):
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if not line or line.startswith("#"):
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continue
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if not "\t" in line:
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raise ValueError(f"No tab in line {i}: '{line}'")
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yield line.split("\t", maxsplit=1)
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def read_rename_map(map_file:pathlib.Path) -> dict[str, str]:
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content = map_file.read_text()
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return {k: v for k, v in _parse_rename_map(content)}
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def prepare_rename(images:list[pathlib.Path], rename_map:dict[str, str], sep="_") -> list[tuple[pathlib.Path, pathlib.Path]]:
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for path in images:
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renamed_parts = [rename_map[p] for p in get_image_parts(path)]
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yield path, path.with_stem(sep.join(renamed_parts))
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@click.command()
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@click.argument("directory", type=click.Path(exists=True, file_okay=False, dir_okay=True))
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def sensospot_rename(directory):
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images = list_images(directory)
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if not images:
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raise click.UsageError(f"No images found in '{directory}'")
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map_file = get_map_file_path(directory)
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if not map_file.is_file():
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write_rename_map(map_file)
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click.echo(f"Prepared rename map at '{map_file!s}'")
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click.echo(f"Rerun the command after editing the file.")
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else:
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click.echo(f"Reading rename map at '{map_file!s}'")
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try:
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rename_map = read_rename_map(map_file)
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except ValueError as e:
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raise click.UsageError(str(e))
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try:
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prepared = list(prepare_rename(images, rename_map))
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except Exception:
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raise click.UsageError("Could not rename images. Please check the image directory and rename map file.")
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for src, dst in prepared:
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click.echo(f"renaming: {src} -> {dst}")
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shutil.move(src, dst)
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