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92 lines
3.0 KiB
92 lines
3.0 KiB
""" 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(map_file.parent) |
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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) |