added sensospot_rename command for batch renaming images

README.md

@@ -3,6 +3,7 @@ work-helpers
 
 Some helper scripts for the day to day work with Ubuntu in WSL2
 
+ - **sensospot_rename**: rename sensospot images in a batch
  - **sg_mbp_new_version**: creates a new version folder, new excel changes files and modifies the overall changelog
  - **sg_mbp_release**: collect and annotate all files used for a safeguard workbook release
  - **sg_list_frms**: collect gitea issues and related frm filenames

pyproject.toml

@@ -27,3 +27,4 @@ sg_mbp_release = "work_helpers.sg_mbp_release:sg_mbp_release"
 sg_mbp_new_version = "work_helpers.sg_mbp_release:sg_mbp_new_version"
 sg_list_frms = "work_helpers.sg_frm_list:cli"
 random_password = "work_helpers.password:get_random_password"
+sensospot_rename = "work_helpers.sensospot_rename:sensospot_rename"

work_helpers/sensospot_rename.py

@@ -0,0 +1,92 @@
+""" rename sensospot images """
+
+import click
+import pathlib
+import shutil
+
+
+RENAME_MAP_NAME = "rename_map.txt"
+IMAGE_SUFFIXES = {".tif", ".jpg"}
+
+
+def get_map_file_path(directory:str) -> pathlib.Path:
+    return pathlib.Path(directory) / RENAME_MAP_NAME
+
+
+def list_images(directory:str) -> list[pathlib.Path]:
+    parent = pathlib.Path(directory)
+    non_hidden = (i for i in parent.iterdir() if not i.name.startswith("."))
+    return [i for i in non_hidden if i.suffix.lower() in IMAGE_SUFFIXES]
+
+
+def get_image_parts(image_path:pathlib.Path) -> tuple[str, str, str]:
+    return image_path.stem.rsplit("_", maxsplit=2)
+
+
+def get_unique_parts(images:list[pathlib.Path]) -> list[list[str], list[str], list[str]]: 
+    parts = [get_image_parts(p) for p in images]
+    return [sorted(set(items)) for items in zip(*parts)]
+
+
+def write_rename_map(map_file:pathlib.Path) -> None:
+    images = list_images(directory)
+    parts = get_unique_parts(images)
+    headers = ["stems", "wells", "exposures"]
+    
+    lines = []
+    for header, items in zip(headers, parts):
+        lines.append(f"# {header}")
+        lines.extend([f"{i}\t" for i in items])
+        lines.append("")
+    lines.append("")
+    
+    map_file.write_text("\n".join(lines))
+
+
+def _parse_rename_map(content:str) -> tuple[str, str]:
+    lines = [line.strip() for line in content.splitlines()]
+    for i, line in enumerate(lines, start=1):
+        if not line or line.startswith("#"):
+            continue
+        if not "\t" in line:
+            raise ValueError(f"No tab in line {i}: '{line}'")
+        yield line.split("\t", maxsplit=1)
+
+
+def read_rename_map(map_file:pathlib.Path) -> dict[str, str]:
+    content = map_file.read_text()
+    return {k: v for k, v in _parse_rename_map(content)}
+
+
+def prepare_rename(images:list[pathlib.Path], rename_map:dict[str, str], sep="_") -> list[tuple[pathlib.Path, pathlib.Path]]:
+    for path in images:
+        renamed_parts = [rename_map[p] for p in get_image_parts(path)]
+        yield path, path.with_stem(sep.join(renamed_parts))
+
+
+@click.command()
+@click.argument("directory", type=click.Path(exists=True, file_okay=False, dir_okay=True))
+def sensospot_rename(directory):
+    images = list_images(directory)
+    if not images:
+        raise click.UsageError(f"No images found in '{directory}'")
+
+    map_file = get_map_file_path(directory)
+    if not map_file.is_file():
+        write_rename_map(map_file)
+        click.echo(f"Prepared rename map at '{map_file!s}'")
+        click.echo(f"Rerun the command after editing the file.")
+    else:
+        click.echo(f"Reading rename map at '{map_file!s}'")
+        try:
+            rename_map = read_rename_map(map_file)
+        except ValueError as e:
+            raise click.UsageError(str(e))
+        try:
+            prepared = list(prepare_rename(images, rename_map))
+        except Exception:
+            raise click.UsageError("Could not rename images. Please check the image directory and rename map file.")
+
+        for src, dst in prepared:
+            click.echo(f"renaming: {src} -> {dst}")
+            shutil.move(src, dst)