fix_worker_issue

formats/ome-converter-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.3
+current_version = 0.3.4-dev2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

formats/ome-converter-tool/Dockerfile

@@ -1,10 +1,12 @@
-FROM polusai/bfio:2.4.4
+FROM polusai/bfio:2.5.0
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
 ENV POLUS_LOG="INFO"
+ENV NUM_THREADS=2
+ENV NUM_WORKERS=4
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}

formats/ome-converter-tool/README.md

@@ -1,4 +1,4 @@
-# OME Converter (v0.3.3)
+# OME Converter (v0.3.4-dev2)
 
 This WIPP plugin converts BioFormats supported data types to the
 OME Zarr or OME TIF file format. This is not a complete implementation, rather it implements a file
@@ -35,4 +35,12 @@ This plugin takes 2 input arguments and 1 output argument:
 ## Docker Command
 
 ```bash
-docker run -e POLUS_IMG_EXT=".ome.zarr" -v /Users/username/:/Users/username/ polusai/ome-converter-tool:0.3.3 --inpDir=/Users/path/to/Images/ --filePattern=".*.tif" --outDir=/Users/path/to/outputs
+docker run \
+  -e POLUS_IMG_EXT=".ome.zarr" \
+  -e NUM_THREADS=4 \
+  -e NUM_WORKERS=2 \
+  -v /Users/username/:/Users/username/ \
+  polusai/ome-converter-tool:0.3.4-dev2 \
+  --inpDir=/Users/path/to/Images/ \
+  --filePattern=".*.tif" \
+  --outDir=/Users/path/to/outputs

formats/ome-converter-tool/VERSION

@@ -1 +1 @@
-0.3.3
+0.3.4-dev2

formats/ome-converter-tool/ict.yaml

@@ -2,13 +2,13 @@ author:
   - Nick Schaub
   - Hamdah Shafqat
 contact: nick.schaub@nih.gov
-container: polusai/ome-converter-tool:0.3.3
+container: polusai/ome-converter-tool:0.3.4-dev2
 description: Convert Bioformats supported format to OME Zarr or OME TIF
 entrypoint: python3 -m polus.images.formats.ome_converter
 inputs:
   - description: Input generic data collection to be processed by this plugin
     format:
-      - genericData
+      - string
     name: inpDir
     required: true
     type: path
@@ -38,4 +38,4 @@ ui:
     key: inputs.filePattern
     title: Filepattern
     type: text
-version: 0.3.3
+version: 0.3.4-dev2

formats/ome-converter-tool/mypy.ini

@@ -0,0 +1,16 @@
+[mypy]
+files = src/polus/images/formats/ome_converter, tests/
+exclude = \.git/
+disable_error_code = import-untyped
+
+[mypy-bfio]
+ignore_missing_imports = True
+
+[mypy-filepattern]
+ignore_missing_imports = True
+
+[mypy-tqdm]
+ignore_missing_imports = True
+
+# [mypy-polus.images.formats.ome_converter.*]
+# ignore_missing_imports = False

formats/ome-converter-tool/omeconverter.cwl

@@ -8,7 +8,7 @@ inputs:
   inpDir:
     inputBinding:
       prefix: --inpDir
-    type: Directory
+    type: string
   outDir:
     inputBinding:
       prefix: --outDir
@@ -20,7 +20,7 @@ outputs:
     type: Directory
 requirements:
   DockerRequirement:
-    dockerPull: polusai/ome-converter-tool:0.3.3
+    dockerPull: polusai/ome-converter-tool:0.3.4-dev2
   InitialWorkDirRequirement:
     listing:
     - entry: $(inputs.outDir)

formats/ome-converter-tool/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "OME Converter",
-  "version": "0.3.3",
+  "version": "0.3.4-dev2",
   "title": "OME Converter",
   "description": "Convert Bioformats supported format to OME Zarr or OME TIF",
   "author": "Nick Schaub (nick.schaub@nih.gov), Hamdah Shafqat Abbasi (hamdahshafqat.abbasi@nih.gov)",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/ome-converter-tool:0.3.3",
+  "containerId": "polusai/ome-converter-tool:0.3.4-dev2",
   "baseCommand": [
     "python3",
     "-m",
@@ -17,7 +17,7 @@
   "inputs": [
     {
       "name": "inpDir",
-      "type": "genericData",
+      "type": "string",
       "description": "Input generic data collection to be processed by this plugin",
       "required": true
     },

formats/ome-converter-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-formats-ome-converter"
-version = "0.3.3"
+version = "0.3.4-dev2"
 description = "Convert BioFormats datatypes to ome.tif or ome.zarr file format"
 authors = [
     "Nick Schaub <nick.schaub@nih.gov>",
@@ -11,21 +11,31 @@ readme = "README.md"
 packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.12"
-bfio = {version = "^2.4.4", extras = ["all"]}
-filepattern = "^2.0.4"
-typer = "^0.7.0"
+python = ">=3.11,<3.13"
+bfio =  "2.5.0"
+filepattern = "2.1.4"
+typer = "0.24.1"
 tqdm = "^4.64.1"
-preadator = "0.4.0-dev2"
-numpy = "<2.0.0"
+numpy = ">2.0.0"
+scikit-image = "^0.26.0"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"
 pre-commit = "^3.0.4"
 pytest = "^7.2.1"
 ipykernel = "^6.21.2"
 requests = "^2.28.2"
-scikit-image = "^0.19.3"
+scikit-image = ">=0.26.0"
+matplotlib = "3.9.4"
+
+[tool.mypy]
+files = "."
+
+# Use strict defaults
+strict = true
+warn_unreachable = true
+warn_no_return = true
+
 
 [build-system]
 requires = ["poetry-core"]

formats/ome-converter-tool/run-plugin.sh

@@ -15,8 +15,12 @@ outDir=/data/output
 # docker run polusai/ome-converter-plugin:${version}
 
 # Run the plugin
-docker run -e POLUS_IMG_EXT=${fileExtension} --mount type=bind,source=${datapath},target=/data/ \
-            polusai/ome-converter-tool:${version} \
-            --inpDir ${inpDir} \
-            --filePattern ${filePattern} \
-            --outDir ${outDir}
+docker run \
+    -e POLUS_IMG_EXT=${fileExtension} \
+    -e NUM_THREADS=2 \
+    -e NUM_WORKERS=4 \
+    --mount type=bind,source=${datapath},target=/data/ \
+    polusai/ome-converter-tool:${version} \
+    --inpDir ${inpDir} \
+    --filePattern ${filePattern} \
+    --outDir ${outDir}

formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py

@@ -1,6 +1,6 @@
 """Ome Converter."""
 
-__version__ = "0.3.3"
+__version__ = "0.3.4-dev2"
 
 from .image_converter import batch_convert
 from .image_converter import convert_image

formats/ome-converter-tool/src/polus/images/formats/ome_converter/__main__.py

@@ -3,16 +3,13 @@
 import logging
 import os
 import pathlib
-from concurrent.futures import as_completed
 from typing import Any
 from typing import Optional
 
 import filepattern as fp
-import preadator
 import typer
-from polus.images.formats.ome_converter.image_converter import NUM_THREADS
-from polus.images.formats.ome_converter.image_converter import convert_image
-from tqdm import tqdm
+from polus.images.formats.ome_converter.image_converter import POLUS_IMG_EXT
+from polus.images.formats.ome_converter.image_converter import batch_convert
 
 app = typer.Typer()
 
@@ -23,22 +20,71 @@
 )
 logger = logging.getLogger("polus.images.formats.ome_converter")
 logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO))
-POLUS_IMG_EXT = os.environ.get("POLUS_IMG_EXT", ".ome.tif")
+
+
+def parse_input_dir(value: str) -> pathlib.Path | list[pathlib.Path]:
+    """Parse a directory or comma-separated file paths."""
+    if "," in value:
+        files = [
+            pathlib.Path(f.strip()).expanduser().resolve()
+            for f in value.split(",")
+            if f.strip()
+        ]
+        if not files:
+            msg = "Empty file list provided"
+            raise typer.BadParameter(msg)
+        return files
+    path = pathlib.Path(value).expanduser().resolve()
+    if not path.is_dir():
+        msg = f"Directory {path} does not exist"
+        raise typer.BadParameter(msg)
+    return path
+
+
+def _collect_files(
+    inp: str | pathlib.Path | list[pathlib.Path],
+    pattern: str,
+) -> list[pathlib.Path]:
+    """Normalize input into a list of files."""
+    if isinstance(inp, (str, pathlib.Path)):
+        dir_path = pathlib.Path(inp) if isinstance(inp, str) else inp
+        if not dir_path.is_dir():
+            msg = f"Input path is not a directory: {dir_path}"
+            raise ValueError(msg)
+        fps = fp.FilePattern(dir_path, pattern)
+        return [files[1][0] for files in fps()]
+
+    if isinstance(inp, list):
+        return [pathlib.Path(p) if isinstance(p, str) else p for p in inp]
+    msg = "Expected str, Path, or list[Path/str]"
+    raise TypeError(msg)
+
+
+def write_preview(
+    out_dir: pathlib.Path,
+    file_pattern: str,
+    files: list[pathlib.Path],
+) -> None:
+    """Write a JSON preview of the files that would be converted."""
+    preview: dict[str, Any] = {
+        "filePattern": file_pattern,
+        "outDir": [f.stem + POLUS_IMG_EXT for f in files],
+    }
+    preview_path = out_dir / "preview.json"
+    with preview_path.open("w") as f:
+        json.dump(preview, f, indent=2)
+    logger.info(f"Preview written to {preview_path}")
 
 
 @app.command()
 def main(
-    inp_dir: pathlib.Path = typer.Option(
+    inp_dir: str = typer.Option(
         ...,
         "--inpDir",
         help="Input generic data collection to be processed by this plugin",
-        exists=True,
-        resolve_path=True,
-        readable=True,
-        file_okay=False,
-        dir_okay=True,
+        callback=parse_input_dir,
     ),
-    pattern: str = typer.Option(
+    file_pattern: str = typer.Option(
         ".+",
         "--filePattern",
         help="A filepattern defining the images to be converted",
@@ -62,44 +108,22 @@ def main(
     """Convert bioformat supported image datatypes conversion to ome.tif or ome.zarr."""
     logger.info(f"inpDir = {inp_dir}")
     logger.info(f"outDir = {out_dir}")
-    logger.info(f"filePattern = {pattern}")
+    logger.info(f"filePattern = {file_pattern}")
+    logger.info(f"preview     = {preview}")
 
-    fps = fp.FilePattern(inp_dir, pattern)
+    files = _collect_files(inp_dir, file_pattern)  # type: ignore
+    logger.info(f"Found {len(files)} file(s) to process.")
 
     if preview:
-        with out_dir.joinpath("preview.json").open("w") as jfile:
-            out_json: dict[str, Any] = {
-                "filepattern": pattern,
-                "outDir": [],
-            }
-            for file in fps():
-                out_name = str(file[1][0].name.split(".")[0]) + POLUS_IMG_EXT
-                out_json["outDir"].append(out_name)
-            json.dump(out_json, jfile, indent=2)
+        write_preview(out_dir, file_pattern, files)
         return
 
-    with preadator.ProcessManager(
-        name="ome_converter",
-        num_processes=NUM_THREADS,
-        threads_per_process=2,
-    ) as executor:
-        threads = []
-        for files in fps():
-            file = files[1][0]
-            threads.append(
-                executor.submit_process(convert_image, file, POLUS_IMG_EXT, out_dir),
-            )
-
-        for f in tqdm(
-            as_completed(threads),
-            total=len(threads),
-            mininterval=5,
-            desc=f"converting images to {POLUS_IMG_EXT}",
-            initial=0,
-            unit_scale=True,
-            colour="cyan",
-        ):
-            f.result()
+    batch_convert(
+        inp_dir=inp_dir,
+        out_dir=out_dir,
+        file_pattern=file_pattern,
+        file_extension=POLUS_IMG_EXT,
+    )
 
 
 if __name__ == "__main__":