updated czi-extract-plugin

formats/czi-extract-plugin/.dockerignore

@@ -0,0 +1,4 @@
+.venv
+out
+tests
+__pycache__

formats/czi-extract-plugin/.gitignore

@@ -0,0 +1,23 @@
+# Jupyter Notebook
+.ipynb_checkpoints
+poetry.lock
+../../poetry.lock
+# Environments
+.env
+.myenv
+.venv
+env/
+venv/
+# test data directory
+data
+# yaml file
+.pre-commit-config.yaml
+# hidden files
+.DS_Store
+.ds_store
+# flake8
+.flake8
+../../.flake8
+__pycache__
+.mypy_cache
+requirements.txt

formats/czi-extract-plugin/CHANGELOG.md

@@ -0,0 +1,10 @@
+## [1.1.2-dev] - 2024-01-10
+### Added
+- Pytests to test this plugin
+- This plugin is now installable with pip.
+
+### Changed
+- Updated dependencies (bfio, filepattern, preadator) to latest
+- Argparse package is replaced with Typer package for command line arguments
+- Replaced docker base image with latest container image with pre-installed bfio 
+

formats/czi-extract-plugin/Dockerfile

@@ -0,0 +1,19 @@
+FROM polusai/bfio:2.3.3
+
+# environment variables defined in polusai/bfio
+ENV EXEC_DIR="/opt/executables"
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+
+# Work directory defined in the base container
+WORKDIR ${EXEC_DIR}
+
+COPY pyproject.toml ${EXEC_DIR}
+COPY VERSION ${EXEC_DIR}
+COPY README.md ${EXEC_DIR}
+COPY src ${EXEC_DIR}/src
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+ENTRYPOINT ["python3", "-m", "polus.plugins.formats.czi_extract"]
+CMD ["--help"]

formats/polus-czi-extract-plugin/README.md → formats/czi-extract-plugin/README.md

@@ -1,4 +1,4 @@
-# Polus CZI Extraction Plugin (v1.1.0)
+# Polus CZI Extraction Plugin (v1.1.2-dev)
 
 This WIPP plugin will import individual fields of view from a CZI file (will
 only import one scene or collection of images). Images are exported as tiled
@@ -39,19 +39,22 @@ the contents of `plugin.json` into the pop-up window and submit.
 
 ## Options
 
-This plugin takes one input argument and one output argument:
+This plugin takes two input arguments and one output argument:
 
 | Name     | Description             | I/O    | Type |
 | -------- | ----------------------- | ------ | ---- |
-| `inpDir` | Input image collection  | Input  | Path |
-| `outDir` | Output image collection | Output | List |
+| `--inpDir` | Input image collection  | Input  | genericData |
+| `--filePattern` | Pattern to parse image files  | Input  | string |
+| `--outDir` | Output image collection | Output | collection |
+| `--preview`        | Generate a JSON file with outputs                                  | Output | JSON          |
 
 ## Run the plugin
 
 ### Run the Docker Container
 
 ```bash
-docker run -v /path/to/data:/data polus-czi-extract-plugin \
+docker run -v /path/to/data:/data polusai/czi-extract-plugin:1.1.2-dev \
   --inpDir /data/input \
+  --filePattern ".*.czi" \
   --outDir /data/output
 ```

formats/czi-extract-plugin/VERSION

@@ -0,0 +1 @@
+1.1.2-dev

formats/czi-extract-plugin/build-docker.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+
+version=$(<VERSION)
+docker build . -t polusai/czi-extract-plugin:${version}

formats/czi-extract-plugin/bumpversion.cfg

@@ -0,0 +1,27 @@
+[bumpversion]
+current_version = 1.1.2-dev
+commit = True
+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:plugin.json]
+
+[bumpversion:file:VERSION]
+
+[bumpversion:file:src/polus/plugins/formats/czi_extract/__init__.py]

formats/czi-extract-plugin/plugin.json

@@ -0,0 +1,63 @@
+{
+  "name": "Czi Extraction",
+  "version": "1.1.2-dev",
+  "title": "Extract TIFFs From CZI",
+  "description": "Extracts individual fields of view from a CZI file. Saves as OME TIFF.",
+  "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/polus-plugins",
+  "website": "https://ncats.nih.gov/preclinical/core/informatics",
+  "containerId": "polusai/czi-extract-plugin:1.1.2-dev",
+  "baseCommand": [
+    "python3",
+    "-m",
+    "polus.plugins.formats.czi_extract"
+  ],
+  "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"
+    },
+    "preview": {
+      "type": "boolean",
+      "title": "Preview",
+      "description": "Generate an output preview.",
+      "required": "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": ".*.czi"
+    },
+    "preview": {
+      "type": "boolean",
+      "title": "Preview example output of this plugin",
+      "description": "Generate an output preview.",
+      "required": "False"
+    }
+  }
+}

formats/czi-extract-plugin/pyproject.toml

@@ -0,0 +1,34 @@
+[tool.poetry]
+name = "polus-plugins-formats-czi-extract"
+version = "1.1.2-dev"
+description = "Extracts individual fields of view from a CZI file. Saves as OME TIFF."
+authors = [
+           "Nick Schaub <nick.schaub@nih.gov>",
+           "Hamdah Shafqat abbasi <hamdahshafqat.abbasi@nih.gov>"
+           ]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = ">=3.9,<3.12"
+filepattern = "^2.0.4"
+typer = "^0.7.0"
+tqdm = "^4.64.1"
+bfio = {version = "2.3.3", extras = ["all"]}
+preadator="0.4.0.dev2"
+czifile="^2019.7.2"
+
+[tool.poetry.group.dev.dependencies]
+bump2version = "^1.0.1"
+pre-commit = "^3.0.4"
+black = "^23.1.0"
+flake8 = "^6.0.0"
+mypy = "^1.0.0"
+pytest = "^7.2.1"
+ipykernel = "^6.21.2"
+requests = "^2.28.2"
+scikit-image = "^0.22.0"
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

formats/polus-czi-extract-plugin/run-plugin.sh → formats/czi-extract-plugin/run-plugin.sh

@@ -6,6 +6,8 @@ datapath=$(readlink --canonicalize ../data)
 # Inputs
 inpDir=/data/path_to_files
 
+filePattern=".*.czi"
+
 # Output paths
 outDir=/data/path_to_output
 
@@ -15,7 +17,7 @@ LOGLEVEL=INFO
 docker run --mount type=bind,source=${datapath},target=/data/ \
             --user $(id -u):$(id -g) \
             --env POLUS_LOG=${LOGLEVEL} \
-            labshare/polus-polus-czi-extract-plugin:${version} \
+            polusai/czi-extract-plugin:${version} \
             --inpDir ${inpDir} \
-            --outDir ${outDir} 
-
+            --filePattern ${filePattern} \
+            --outDir ${outDir}

formats/czi-extract-plugin/src/polus/plugins/formats/czi_extract/__init__.py

@@ -0,0 +1,2 @@
+"""Czi Extract Plugin."""
+__version__ = "1.1.2-dev"

formats/czi-extract-plugin/src/polus/plugins/formats/czi_extract/__main__.py

@@ -0,0 +1,91 @@
+"""Czi Extract Plugin."""
+import json
+import logging
+import os
+from multiprocessing import cpu_count
+from pathlib import Path
+from typing import Any
+from typing import Optional
+
+import filepattern as fp
+import polus.plugins.formats.czi_extract.czi as cz
+import typer
+
+# Import environment variables
+POLUS_EXT = os.environ.get("POLUS_EXT", ".ome.tif")
+
+app = typer.Typer()
+
+# Initialize the logger
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
+logger = logging.getLogger("polus.plugins.formats.czi_extract")
+
+
+@app.command()
+def main(
+    inp_dir: Path = typer.Option(
+        ...,
+        "--inpDir",
+        "-i",
+        help="Path to folder with CZI files",
+    ),
+    file_pattern: str = typer.Option(
+        ".*.czi",
+        "--filePattern",
+        "-f",
+        help="Pattern use to parse filenames",
+    ),
+    out_dir: Path = typer.Option(
+        ...,
+        "--outDir",
+        "-o",
+        help="Output directory",
+    ),
+    preview: Optional[bool] = typer.Option(
+        False,
+        "--preview",
+        help="Output a JSON preview of files",
+    ),
+) -> None:
+    """Extracts individual fields of view from a CZI file and saves as OME TIFF."""
+    logger.info(f"--inpDir = {inp_dir}")
+    logger.info(f"--filePattern = {file_pattern}")
+    logger.info(f"--outDir = {out_dir}")
+
+    inp_dir = inp_dir.resolve()
+    out_dir = out_dir.resolve()
+
+    assert inp_dir.exists(), f"{inp_dir} does not exist!! Please check input path again"
+    assert (
+        out_dir.exists()
+    ), f"{out_dir} does not exist!! Please check output path again"
+
+    files = fp.FilePattern(inp_dir, file_pattern)
+
+    file_ext = all(Path(f[1][0].name).suffix for f in files())
+    assert (
+        file_ext is True
+    ), f"{inp_dir} does not contain all czi files!! Please check input directory again"
+
+    if preview:
+        with Path.open(Path(out_dir, "preview.json"), "w") as jfile:
+            out_json: dict[str, Any] = {
+                "filepattern": file_pattern,
+                "outDir": [],
+            }
+            for file in files():
+                out_name = file[1][0].name.replace(
+                    "".join(file[1][0].suffixes),
+                    ".ome.tif",
+                )
+                out_json["outDir"].append(out_name)
+            json.dump(out_json, jfile, indent=2)
+    else:
+        for file in files():
+            cz.extract_fovs(file[1][0], out_dir)
+
+if __name__ == "__main__":
+    app()