[WIP] OME ZARR Autosegmentation plugin

segmentation/ome-zarr-autosegmentation-plugin/.bumpversion.cfg

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+[bumpversion]
+current_version = 0.1.0
+commit = False
+tag = False
+parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
+serialize = 
+	{major}.{minor}.{patch}-{release}{dev}
+	{major}.{minor}.{patch}
+
+[bumpversion:part:release]
+optional_value = _
+first_value = dev
+values = 
+	dev
+	_
+
+[bumpversion:part:dev]
+
+[bumpversion:file:pyproject.toml]
+search = version = "{current_version}"
+replace = version = "{new_version}"
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:README.md]
+
+[bumpversion:file:plugin.json]
+
+[bumpversion:file:src/polus/plugins/images/segmentation/ome_zarr_autosegmentation/__init__.py]

segmentation/ome-zarr-autosegmentation-plugin/.dockerignore

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+.venv
+out
+tests
+__pycache__

segmentation/ome-zarr-autosegmentation-plugin/.gitignore

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+poetry.lock
+uv.lock
+test_datasets/**
+**/models/**
+autogenerated/**
+cachedir/**
+provenance/**
+output_job.json

segmentation/ome-zarr-autosegmentation-plugin/.python-version

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+3.11

segmentation/ome-zarr-autosegmentation-plugin/CHANGELOG.md

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+# CHANGELOG
+
+## 0.1.0
+
+Initial release.

segmentation/ome-zarr-autosegmentation-plugin/Dockerfile

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+# Build stage
+FROM python:3.11-slim AS builder
+
+RUN apt-get update && apt-get install -y \
+    gcc \
+    g++ \
+    python3-dev \
+    && apt-get autoremove -y \
+    && apt-get clean \
+    && rm -rf /var/lib/apt/lists/*
+
+# Install uv
+COPY --from=ghcr.io/astral-sh/uv:latest /uv /uvx /bin/
+
+WORKDIR /app
+
+COPY pyproject.toml ./
+
+RUN uv pip install --system -e .
+
+COPY . .
+
+# Final stage
+FROM python:3.11-slim
+
+WORKDIR /app
+
+COPY --from=builder /app /app
+
+COPY --from=builder /usr/local/lib/python3.11/site-packages /usr/local/lib/python3.11/site-packages
+
+WORKDIR /app/src
+
+ENTRYPOINT ["python3", "-m", "polus.images.segmentation.ome_zarr_autosegmentation"]
+CMD ["--help"]

segmentation/ome-zarr-autosegmentation-plugin/README.md

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+# ome_zarr_autosegmentation (0.1.0)
+
+description goes here
+
+## Building
+
+To build the Docker image for the conversion plugin, run `./build-docker.sh`.
+Download the model you want to use for SAM from `https://github.com/facebookresearch/sam2?tab=readme-ov-file#download-checkpoints`
+
+## Install WIPP Plugin
+
+If WIPP is running, navigate to the plugins page and add a new plugin. Paste the
+contents of `plugin.json` into the pop-up window and submit.
+
+## Options
+
+This plugin takes 1 input arguments and 1 output argument:
+
+| Name          | Description             | I/O    | Type   | Default
+|---------------|-------------------------|--------|--------|
+| inpDir        | Input dataset to be processed by this plugin | Input | collection
+| preview   | Generate an output preview | Input | boolean | False
+| outDir        | Output collection | Output | collection

segmentation/ome-zarr-autosegmentation-plugin/VERSION

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+0.1.0

segmentation/ome-zarr-autosegmentation-plugin/build-docker.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/ome-zarr-autosegmentation-plugin:${version}

segmentation/ome-zarr-autosegmentation-plugin/job.wic

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+steps:
+  ome-zarr-autosegmentation:
+    in:
+      inpDir: !ii input_directory
+      outDir: !ii output_directory
+    out:
+    - outDir: !& output_directory

segmentation/ome-zarr-autosegmentation-plugin/plugin.json

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+{
+    "name": "ome_zarr_autosegmentation",
+    "version": "0.1.0",
+    "title": "ome_zarr_autosegmentation",
+    "description": "description goes here",
+    "author": "Zhiyuan Liu (zhiyuan.liu@axleinfo.com)",
+    "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
+    "repository": "https://github.com/labshare/polus-plugins",
+    "website": "https://ncats.nih.gov/preclinical/core/informatics",
+    "citation": "",
+    "containerId": "polusai/ome-zarr-autosegmentation-plugin:0.1.0",
+    "baseCommand": ["python3", "-m", "polus.plugins.images.segmentation.ome_zarr_autosegmentation"],
+    "inputs": {
+      "inpDir": {
+          "type": "collection",
+          "title": "Input collection",
+          "description": "Input image collection to be processed by this plugin.",
+          "required": "True"
+      },
+      "filePattern": {
+          "type": "string",
+          "title": "Filename pattern",
+          "description": "Filename pattern used to separate data.",
+          "required": "False",
+          "default": ".*"
+      },
+      "preview": {
+        "type": "boolean",
+        "title": "Preview",
+        "description": "Generate an output preview.",
+        "required": "False",
+        "default": "False"
+    }
+  },
+  "outputs": {
+      "outDir": {
+          "type": "collection",
+          "description": "Output collection."
+      }
+  },
+    "ui": {
+      "inpDir": {
+        "type": "collection",
+        "title": "Input collection",
+        "description": "Input image collection to be processed by this plugin.",
+        "required": "True"
+      },
+      "filePattern": {
+        "type": "string",
+        "title": "Filename pattern",
+        "description": "Filename pattern used to separate data.",
+        "required": "False",
+        "default": "False"
+      },
+      "preview": {
+        "type": "boolean",
+        "title": "Filename pattern",
+        "description": "Generate an output preview.",
+        "required": "False",
+        "default": "False"
+      }
+  }
+}

segmentation/ome-zarr-autosegmentation-plugin/pyproject.toml

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+[project]
+name = "ome_zarr_autosegmentation_plugin"
+version = "0.1.0"
+description = "Add your description here"
+readme = "README.md"
+requires-python = ">=3.11"
+dependencies = [
+    "torch>=2.1.0",
+    "torchvision>=0.16.0",
+    "greenlet>=3.1.1",
+    "ome-zarr>=0.9.0",
+    "bfio>=2.3.6",
+    "sam2>=1.1.0",
+    "ngff-zarr[dask-image,tensorstore]>=0.12.2",
+    "argolid>=0.0.6",
+    "typer>=0.15.1",  
+]
+
+[dependency-groups]
+dev = [
+    "ruff>=0.8.0",
+]
+
+[tool.ruff.lint]
+extend-select = ["I"]

segmentation/ome-zarr-autosegmentation-plugin/run-plugin.sh

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+#!/bin/bash
+
+version=$(<VERSION)
+
+# Update with your data
+inpDir=/tmp/path/to/input
+outDir=/tmp/path/to/output
+
+container_input_dir="/inpDir"
+container_output_dir="/outDir"
+
+docker run -v $inpDir:/${container_input_dir} \
+           -v $outDir:/${container_output_dir} \
+            --user $(id -u):$(id -g) \
+            polusai/ome-zarr-autosegmentation-plugin:${version} \
+            --inpDir ${container_input_dir} \
+            --outDir ${container_output_dir}

segmentation/ome-zarr-autosegmentation-plugin/src/polus/images/segmentation/ome_zarr_autosegmentation/__init__.py

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+"""ome_zarr_autosegmentation."""
+
+__version__ = "0.1.0"
+
+from polus.images.segmentation import (  # noqa # pylint: disable=unused-import
+    ome_zarr_autosegmentation,
+)

segmentation/ome-zarr-autosegmentation-plugin/src/polus/images/segmentation/ome_zarr_autosegmentation/__main__.py

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+"""Package entrypoint for the ome_zarr_autosegmentation package."""
+
+# Base packages
+import json
+import logging
+from os import environ
+from pathlib import Path
+
+import typer
+from polus.images.segmentation.ome_zarr_autosegmentation.autosegmentation import autosegmentation
+
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+POLUS_LOG = getattr(logging, environ.get("POLUS_LOG", "INFO"))
+logger = logging.getLogger("polus.images.segmentation.ome_zarr_autosemgentation")
+logger.setLevel(POLUS_LOG)
+
+app = typer.Typer(help="ome_zarr_autosegmentation.")
+
+def generate_preview(
+    in_dir: Path,
+    out_dir: Path,
+) -> None:
+    """Generate preview of the plugin outputs."""
+
+    preview = {}
+
+    with Path.open(out_dir / "preview.json", "w") as fw:
+        json.dump(preview, fw, indent=2)
+
+@app.command()
+def main(
+    inp_dir: Path = typer.Option(
+        ...,
+        "--inpDir",
+        "-i",
+        help="Input directory to be processed.",
+        exists=True,
+        readable=True,
+        file_okay=False,
+        resolve_path=True,
+    ),
+    out_dir: Path = typer.Option(
+        ...,
+        "--outDir",
+        "-o",
+        help="Output directory.",
+        exists=False,
+        writable=True,
+        file_okay=False,
+        resolve_path=True,
+    ),
+    preview: bool = typer.Option(
+        False,
+        "--preview",
+        "-v",
+        help="Preview of expected outputs (dry-run)",
+        show_default=False,
+    ),
+):
+    """ome_zarr_autosegmentation."""
+    logger.info(f"inpDir: {inp_dir}")
+    logger.info(f"outDir: {out_dir}")
+
+    if preview:
+        generate_preview(inp_dir, out_dir)
+        logger.info(f"generating preview data in : {out_dir}.")
+        return
+
+    autosegmentation(inp_dir, out_dir)
+
+
+if __name__ == "__main__":
+    app()