Nyxus bug

.github/workflows/package-tests.yml

@@ -2,15 +2,9 @@ name: Package tests
 
 on:
   pull_request:
-    branches:
-      - main
-      - master
-      - dev
+    branches: [main, master, dev]
   push:
-    branches-ignore:
-      - main
-      - master
-      - dev
+    branches-ignore: [main, master, dev]
   workflow_call:
 
 permissions:
@@ -33,26 +27,30 @@ jobs:
       matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }}
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Set up Python
-        uses: actions/setup-python@v5
+      - uses: actions/checkout@v4
+        with:
+          fetch-depth: 0
+
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
-      - name: Install Poetry
-        uses: abatilo/actions-poetry@v2
-      - name: Install pre-commit
-        run: |
-          pip install pre-commit
-      - name: Run pre-commit hooks and check for changes
+
+      - uses: astral-sh/setup-uv@v4
+
+      - name: Install and run pre-commit
         run: |
           cd "${{ matrix.package_dir }}"
+          uv sync --all-extras
+          uv run pre-commit run \
+            --from-ref ${{ github.event.pull_request.base.sha || github.event.before }} \
+            --to-ref ${{ github.event.pull_request.head.sha || github.sha }}
 
-          poetry run pre-commit run --files ./**/**
-          if [[ $(git status --porcelain) ]]
-          then
-            echo "::error::pre-commit hooks failed for ${{ matrix.package_name }}" && exit 1
-          fi
+      - name: Show dirty files (if pre-commit failed)
+        if: failure()
+        run: |
+          cd "${{ matrix.package_dir }}"
+          git status --porcelain
+          git diff
 
   docker:
     name: Docker | Build ${{ matrix.package_name }}
@@ -63,92 +61,70 @@ jobs:
       matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }}
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
-      - name: Check if Dockerfile exists
-        id: check_dockerfile
+      - uses: actions/checkout@v4
+
+      - uses: docker/setup-buildx-action@v3
+
+      - name: Docker | Build Image
         run: |
-          if [ -f "${{ matrix.package_dir }}/Dockerfile" ]; then
-            echo "Dockerfile exists"
-            echo "dockerfile_exists=true" >> $GITHUB_ENV
-          else
-            echo "Dockerfile does not exist"
-            echo "dockerfile_exists=false" >> $GITHUB_ENV
+          if [ ! -f "${{ matrix.package_dir }}/Dockerfile" ]; then
+            echo "No Dockerfile found, skipping"
+            exit 0
           fi
-      - name: Docker | Tag
-        id: docker_tag
-        if: env.dockerfile_exists == 'true'
-        run: |
           version=$(cat ${{ matrix.package_dir }}/VERSION)
           tag=polusai/${{ matrix.package_name }}:${version}
-          echo "tag will be ${tag}"
-          echo "tag=${tag}" >> $GITHUB_OUTPUT
-      - name: Docker | Setup Buildx
-        uses: docker/setup-buildx-action@v3
-      - name: Docker | Check if Image exists
-        if: env.dockerfile_exists == 'true'
-        run: |
-          tag=${{ steps.docker_tag.outputs.tag }}
           docker pull ${tag} > /dev/null \
-              && $(echo "::error::${tag} already exists on DockerHub" && exit 1) \
-              || echo "success"
-      - name: Docker | Build Image
-        if: env.dockerfile_exists == 'true'
-        run: |
+            && (echo "::error::${tag} already exists on DockerHub" && exit 1) \
+            || echo "Image does not exist, safe to build"
           cp .gitignore ${{ matrix.package_dir }}/.dockerignore
           cd "${{ matrix.package_dir }}"
           if [ -f "build-docker.sh" ]; then
             bash build-docker.sh
           else
-            docker build . -t ${{ steps.docker_tag.outputs.tag }}
+            docker build . -t ${tag}
           fi
-          bash build-docker.sh
-        # docker buildx build --platform linux/amd64,linux/arm64 -t ${tag} --push .
 
   tests:
     name: Test | ${{ matrix.package_name }}
     needs: package-filter
+    timeout-minutes: 30
     if: ${{ needs.package-filter.outputs.num_packages > 0 }}
     strategy:
       fail-fast: false
       matrix: ${{ fromJson(needs.package-filter.outputs.matrix) }}
     runs-on: ubuntu-latest
     steps:
-      - name: Checkout
-        uses: actions/checkout@v4
+      - uses: actions/checkout@v4
         with:
           lfs: true
-      - name: Set up Python
-        uses: actions/setup-python@v5
+
+      - uses: actions/setup-python@v5
         with:
           python-version: '3.12'
-      - name: Install Conda
+
+      - name: Run tests with conda
+        if: ${{ hashFiles(format('{0}/environment.yml', matrix.package_dir)) != '' }}
         uses: conda-incubator/setup-miniconda@v2
+
       - name: Run tests with conda
+        if: ${{ hashFiles(format('{0}/environment.yml', matrix.package_dir)) != '' }}
+        shell: bash -l {0}
         run: |
-          package_dir=${{ matrix.package_dir }}
-          cd $package_dir
-          if [ -f "environment.yml" ]; then
-            conda init bash
-            source ~/.bashrc
-            conda env create -f environment.yml
-            conda activate project_env
-            pip install -e ".[all]"
-            conda install pytest
-            python -X faulthandler -m pytest -v -p no:faulthandler
-            echo "conda_installed=true" >> $GITHUB_ENV
-          else
-            echo "conda_installed=false" >> $GITHUB_ENV
-          fi
-      - name: Install Poetry
-        uses: abatilo/actions-poetry@v2
-      - name: Run tests with poetry
-        if: env.conda_installed == 'false'
-        run: |
-          poetry config virtualenvs.create false
+          cd ${{ matrix.package_dir }}
+          conda env create -f environment.yml
+          conda activate project_env
+          pip install -e ".[all]"
+          conda install pytest -y
+          python -X faulthandler -m pytest -v -p no:faulthandler
 
-          package_dir=${{ matrix.package_dir }}
-          cd $package_dir
+      - name: Run tests with uv
+        if: ${{ hashFiles(format('{0}/environment.yml', matrix.package_dir)) == '' }}
+        uses: astral-sh/setup-uv@v4
 
-          poetry install
-          python -X faulthandler -m pytest -v -p no:faulthandler
+      - name: Run tests with uv
+        if: ${{ hashFiles(format('{0}/environment.yml', matrix.package_dir)) == '' }}
+        run: |
+          cd ${{ matrix.package_dir }}
+          uv sync --all-extras || uv pip install -e ".[all]"
+          uv pip install pytest
+          uv run python -X faulthandler -m pytest -v -p no:faulthandler

features/nyxus-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.1.8
+current_version = 0.1.8-dev2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

features/nyxus-tool/CHANGELOG.md

@@ -1,3 +1,15 @@
+# Changelog
+
+All notable changes to this project will be documented in this file.
+
+## [0.1.8-dev2] - 2026-03-06
+- Replace the nyxus `featurize_file` function with a simple `featurize` function as `single_roi` flag does not respect `ignore_mask_files`.
+- Handling of additional tuning parameter for nyxus features.
+
+## [0.1.8-dev1] - 2024-11-15
+- Fix a bug for no objects in label images.
+- Updated bfio base-container image.
+
 ## [0.1.8-dev0] - 2024-09-26
 - Renamed nyxus-plugin to nyxus-tool.
-- updated nyxus package and bfio base-container image.
+- Updated nyxus package and bfio base-container image.

features/nyxus-tool/Dockerfile

@@ -1,25 +1,33 @@
-FROM polusai/bfio:2.4.3
+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_WORKERS=4
 
-# Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# TODO: Change the tool_dir to the tool directory
-ENV TOOL_DIR="features/nyxus-tool"
+# Copy the tool
+COPY . ${EXEC_DIR}/nyxus-tool
 
-# Copy the repository into the container
-RUN mkdir image-tools
-COPY . ${EXEC_DIR}/image-tools
+# Upgrade pip/setuptools/wheel first
+RUN python3 -m pip install --upgrade pip setuptools wheel
 
-# Install the tool
-RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
+# Install build dependencies (compiler + Python headers)
+RUN apt-get update && apt-get install -y \
+    build-essential \
+    python3.11-dev \
+    && rm -rf /var/lib/apt/lists/*
 
-# Set the entrypoint
-# TODO: Change the entrypoint to the tool entrypoint
+# Install your package (Annoy will build successfully)
+RUN pip3 install "${EXEC_DIR}/nyxus-tool" --no-cache-dir
+
+# Clean up build tools to reduce image size
+RUN apt-get purge -y build-essential python3.11-dev \
+    && apt-get autoremove -y \
+    && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Entrypoint
 ENTRYPOINT ["python3", "-m", "polus.images.features.nyxus_tool"]
 CMD ["--help"]

features/nyxus-tool/README.md

@@ -1,22 +1,29 @@
-# Nyxus-Plugin(v0.1.8)
+# Nyxus-tool(v0.1.8-dev2)
 
 
-Nyxus plugin uses parallel processing of [Nyxus python package](https://pypi.org/project/nyxus/) to extract nyxus features from intensity-label image data. Especially useful when processing high throughput screens.
+Parallelized feature extraction from intensity + label image pairs using the **[Nyxus](https://pypi.org/project/nyxus/)** library.
+
+Especially useful for high-throughput microscopy screens.
 
 Contact [Hamdah Shafqat Abbasi](mailto: hamdah.abbasi@axleinfo.com) for more information.
 
 For more information on WIPP, visit the [official WIPP page](https://isg.nist.gov/deepzoomweb/software/wipp).
 
 
-## Note
-Use two separate [filepatterns](https://filepattern.readthedocs.io/en/latest/) for intensity and label images.
-For example if you have label images of one channel `c1`\
-`segPattern='p00{z}_x{x+}_y{y+}_wx{t}_wy{p}_c1.ome.tif'`\
-Use filepattern if you require to extract features from intensity images of all other channels\
-`intPattern=p00{z}_x{x+}_y{y+}_wx{t}_wy{p}_c{c}.ome.tif`
+## Important notes
+
+- Use two separate **[filepattern](https://filepattern.readthedocs.io/en/latest/)** for intensity and label images.
+- Example naming scheme:
+
+    Intensity (multi-channel):
+    `intPattern=p00{z}_x{x+}_y{y+}_wx{t}_wy{p}_c{c}.ome.tif`
 
-## Output Format
-Computed features outputs can be saved in either of formats `.csv`, `.arrow`, `.parquet` by passing values `pandas`, `arrowipc`, `parquet` to `fileExtension`. By default plugin saves outputs in `.csv`
+    Segmentation :
+    `segPattern='p00{z}_x{x+}_y{y+}_wx{t}_wy{p}_c1.ome.tif'`
+
+- `--singleRoi` mode treats each intensity image as one whole-object ROI (ignores segmentation mask)
+- Nyxus parameters (e.g., `neighbor_distance`, `pixels_per_micron`) are passed via repeatable `--kwargs KEY=VALUE`
+- Output file extension (format) is controlled via environment variable `POLUS_TAB_EXT` (default: `pandas`; options: `pandas`, `arrowipc`, `parquet`)
 
 
 ## Building
@@ -29,20 +36,40 @@ To build the Docker image for the conversion plugin, run
 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.
 
+## Quick run example (Docker)
+
+See `run-plugin.sh` for a template.
+
+
+```bash
+docker run --rm -v /path/to/data:/data \
+  -e POLUS_TAB_EXT=pandas \
+  polusai/nyxus-tool:0.1.8-dev2 \
+  --inpDir      /data/intensity \
+  --segDir      /data/segmentation \
+  --intPattern  'p00{z}_x{x+}_y{y+}_wx{t}_wy{p}_c{c}.ome.tif' \
+  --segPattern  'p00{z}_x{x+}_y{y+}_wx{t}_wy{p}_c1.ome.tif' \
+  --features    "BASIC_MORPHOLOGY,ALL_INTENSITY" \
+  --kwargs      neighbor_distance=5 \
+  --kwargs      pixels_per_micron=1.0 \
+  --singleRoi   false \
+  --outDir      /data/features
+```
+
+
 ## Options
 
-This plugin takes nine input arguments and one output argument:
+This plugin takes seven input arguments and one output argument:
 
 | Name               | Description                                                        | I/O    | Type          |
 |--------------------|--------------------------------------------------------------------|--------|---------------|
-| `--inpDir`         | Input image directory                                              | Input  | collection    |
-| `--segDir`         | Input label image directory                                        | Input  | collection    |
+| `--inpDir`         | Intensity images folder                                            | Input  | collection    |
+| `--segDir`         | Label / segmentation images folder directory                                        | Input  | collection    |
 | `--intPattern`     | Filepattern to parse intensity images                              | Input  | string        |
 | `--segPattern`     | Filepattern to parse label images                                  | Input  | string        |
-| `--features`       | [nyxus features](https://pypi.org/project/nyxus/)                  | Input  | string        |
-| `--fileExtension`  | A desired file format for nyxus features output                    | Input  | enum          |
-| `--neighborDist`   | Distance between two neighbor objects                              | Input  | integer       |
-| `--pixelPerMicron` | Pixel Size in micrometer                                           | Input  | float         |
-| `--singleRoi`      | Treat intensity image as single roi and ignoring segmentation mask | Input  | bool          |
+| `--features`       | [Feature groups or individual nyxus features (comma-separated or repeated)](https://pypi.org/project/nyxus/)                  | Input  | string        |      |
+| `--singleRoi`      | Treat each intensity image as single ROI (whole-image features, no mask) | Input  | bool
+| `--kwargs`      | Nyxus params as KEY=VALUE (repeatable; e.g., neighbor_distance=5) | Input  | list[str]         |
 | `--outDir`         | Output collection                                                  | Output | collection    |
-| `--preview`        | Generate a JSON file with outputs                                  | Output | JSON          |
+| `--preview`        | Generate a JSON file with outputs                                  | Output |
+ JSON          |

features/nyxus-tool/VERSION

@@ -1 +1 @@
-0.1.8
+0.1.8-dev2