Replace preadator, update packages to pass pytest and work on cp3.11-3.13)

ruff.toml

@@ -51,6 +51,14 @@ convention = "google"
   "S101",  # Use of assert detected.
   "PLR2004",  # Use of magic values detected.
 ]
+# WIPP-style CLI names and legacy class name; keep lint noise low until refactor.
+"transforms/images/remove-border-objects-plugin/src/*.py" = [
+  "N801",
+  "N803",
+  "N816",
+  "ANN001",
+  "ANN201",
+]
 
 [isort]
 force-single-line = true

transforms/images/remove-border-objects-plugin/Dockerfile

@@ -1,8 +1,17 @@
-FROM labshare/polus-bfio-util:2.1.9-tensorflow
+FROM polusai/bfio:2.5.0
 ENV EXEC_DIR="/opt/executables"
-RUN mkdir -p ${EXEC_DIR}
-COPY VERSION ${EXEC_DIR}
-COPY src ${EXEC_DIR}/
-RUN pip3 install -r ${EXEC_DIR}/requirements.txt --no-cache-dir && \
-    pip3 install "bfio[all]"
-ENTRYPOINT ["python3", "main.py"]
+ENV POLUS_IMG_EXT=".ome.tif"
+ENV POLUS_TAB_EXT=".csv"
+ENV POLUS_LOG="INFO"
+
+WORKDIR ${EXEC_DIR}
+ENV TOOL_DIR="transforms/images/remove-border-objects-plugin"
+RUN mkdir -p image-tools
+COPY . ${EXEC_DIR}/image-tools
+RUN pip3 install -U pip setuptools wheel \
+  && python3 -c 'import sys; assert sys.version_info>=(3,11)' \
+  && R="${EXEC_DIR}/image-tools" && M="$R/$TOOL_DIR" \
+  && if [ -f "$M/pyproject.toml" ]; then pip3 install --no-cache-dir "$M"; \
+     else pip3 install --no-cache-dir "$R"; fi
+ENTRYPOINT ["python3", "-m", "main"]
+CMD ["--help"]

transforms/images/remove-border-objects-plugin/README.md

@@ -16,7 +16,7 @@ At the moment this plugin supports label images with two dimensions only. We wil
 <img src="./image.png">
 
 
-**a -** Original image contains 67 unique label objects 
+**a -** Original image contains 67 unique label objects
 **b -** Image with 16 detected border objects
 **c -** Removing Border objects and sequential relabelling
 
@@ -41,7 +41,3 @@ This plugin takes two input arguments and
 | `--inpDir`    | Input image directory                                         | Input  | collection    |
 | `--pattern`   | Filepattern to parse image files                              | Input  | string        |
 | `--outDir`    | Output collection                                             | Output | collection    |
-
-
-
-

transforms/images/remove-border-objects-plugin/VERSION

@@ -1 +1 @@
-0.1.1
+0.1.1

transforms/images/remove-border-objects-plugin/build-docker.sh

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

transforms/images/remove-border-objects-plugin/package-release.sh

@@ -13,4 +13,4 @@ bump2version --config-file bumpversion.cfg --new-version ${version} --allow-dirt
 docker push polusai/remove-border-objects-plugin:${version}
 
 # Run unittests
-python -m unittest
+python -m unittest

transforms/images/remove-border-objects-plugin/plugin.json

@@ -47,4 +47,4 @@
     }
   ],
   "validators": null
-}
+}

transforms/images/remove-border-objects-plugin/pyproject.toml

@@ -0,0 +1,46 @@
+[project]
+name = "polus-remove-border-objects-plugin"
+version = "0.1.1"
+requires-python = ">=3.11,<3.14"
+dependencies = [
+    "bfio>=2.5.0",
+    "filepattern>=2.2.4",
+    "typer>=0.24.1,<0.25.0",
+    "numpy>=2.0.0",
+    "tqdm==4.67.3",
+    "basicpy @ git+https://github.com/ndonyapour/BaSiCPy.git@chore/update-supported-python",
+]
+
+[project.optional-dependencies]
+dev = [
+    "bump2version>=1.0.1",
+    "pre-commit>=4.5.1",
+    "black>=26.3.1",
+    "flake8>=6.0.0",
+    "mypy>=1.0.0",
+    "pytest>=7.2.1",
+    "pytest-cov>=7.0.0",
+    "pytest-sugar>=1.1.1,<2.0.0",
+    "pytest-xdist>=3.8.0,<4.0.0",
+]
+
+[build-system]
+requires = ["hatchling"]
+build-backend = "hatchling.build"
+
+[tool.hatch.metadata]
+allow-direct-references = true
+
+[tool.hatch.build.targets.wheel]
+packages = ["src/polus"]
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.setuptools]
+py-modules = ["main", "functions"]

transforms/images/remove-border-objects-plugin/run-plugin.sh

@@ -19,5 +19,4 @@ docker run --mount type=bind,source=${datapath},target=/data/ \
             polusai/remove-border-objects-plugin:${version} \
             --inpDir ${inpDir} \
             --pattern ${pattern} \
-            --outDir ${outDir} 
-
+            --outDir ${outDir}

transforms/images/remove-border-objects-plugin/src/__init__.py

@@ -0,0 +1 @@
+"""Remove border objects plugin package."""

transforms/images/remove-border-objects-plugin/src/functions.py

@@ -1,37 +1,43 @@
-import os
-from bfio import BioReader, BioWriter
+"""Label image border cleanup and sequential relabelling."""
+
 from pathlib import Path
+
 import numpy as np
+from bfio import BioReader
+from bfio import BioWriter
 from skimage.segmentation import relabel_sequential
 
 
 class Discard_borderobjects:
-
     """Discard objects which touches image borders and relabelling of objects.
+
     Args:
         inpDir (Path) : Path to label image directory
         outDir (Path) : Path to relabel image directory
         filename (str): Name of a label image
     Returns:
         label_image : ndarray of dtype int
-        label_image, with discarded objects touching border
-    """ 
-    def __init__(self, inpDir, outDir, filename):
+        label_image, with discarded objects touching border.
+    """
+
+    def __init__(self, inpDir, outDir, filename) -> None:
+        """Load label image from ``inpDir`` / ``filename``."""
         self.inpDir = inpDir
-        self.outDir=  outDir
+        self.outDir = outDir
         self.filename = filename
-        self.imagepath = os.path.join(self.inpDir, self.filename)
-        self.br_image = BioReader(self.imagepath)
+        self.imagepath = Path(self.inpDir) / self.filename
+        self.br_image = BioReader(str(self.imagepath))
         self.label_img = self.br_image.read().squeeze()
 
     def discard_borderobjects(self):
-        """ This functions identifies which label pixels touches image borders and 
-        setting the values of those label pixels to background pixels values which is 0
+        """Clear labels that touch the image border.
+
+        Sets border-touching label pixels to background (0).
         """
         borderobj = list(self.label_img[0, :])
         borderobj.extend(self.label_img[:, 0])
-        borderobj.extend(self.label_img[- 1, :])
-        borderobj.extend(self.label_img[:, - 1])
+        borderobj.extend(self.label_img[-1, :])
+        borderobj.extend(self.label_img[:, -1])
         borderobj = np.unique(borderobj).tolist()
 
         for obj in borderobj:
@@ -40,21 +46,19 @@ def discard_borderobjects(self):
         return self.label_img
 
     def relabel_sequential(self):
-        """ Sequential relabelling of objects in a label image
-        """
-        relabel_img, _, inverse_map  = relabel_sequential(self.label_img)
+        """Sequential relabelling of objects in a label image."""
+        relabel_img, _, inverse_map = relabel_sequential(self.label_img)
         return relabel_img, inverse_map
 
-
     def save_relabel_image(self, x):
-        """ Writing images with relabelled and cleared border touching objects
-        """
-        with BioWriter(file_path = Path(self.outDir, self.filename),
-                    backend='python',
-                    metadata  = self.br_image.metadata, 
-                    X=self.label_img.shape[0],  
-                    Y=self.label_img.shape[0], 
-                    dtype=self.label_img.dtype) as bw:
+        """Writing images with relabelled and cleared border touching objects."""
+        with BioWriter(
+            file_path=Path(self.outDir, self.filename),
+            backend="python",
+            metadata=self.br_image.metadata,
+            X=self.label_img.shape[0],
+            Y=self.label_img.shape[0],
+            dtype=self.label_img.dtype,
+        ) as bw:
             bw[:] = x
-            bw.close() 
-        return       
+            bw.close()

transforms/images/remove-border-objects-plugin/src/main.py

@@ -1,89 +1,105 @@
-import argparse, logging, os, time, filepattern
+"""CLI entrypoint for the remove-border-objects plugin."""
+
+import argparse
+import logging
+import os
+import sys
+import time
 from pathlib import Path
-from functions import *
 
+import filepattern
+from functions import Discard_borderobjects
 
-#Import environment variables
-POLUS_LOG = getattr(logging,os.environ.get('POLUS_LOG','INFO'))
-POLUS_EXT = os.environ.get('POLUS_EXT','.ome.tif')
+# Import environment variables
+POLUS_LOG = getattr(logging, os.environ.get("POLUS_LOG", "INFO"))
+POLUS_EXT = os.environ.get("POLUS_EXT", ".ome.tif")
 
 # Initialize the logger
-logging.basicConfig(format='%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s',
-                    datefmt='%d-%b-%y %H:%M:%S')
+logging.basicConfig(
+    format="%(asctime)s - %(name)-8s - %(levelname)-8s - %(message)s",
+    datefmt="%d-%b-%y %H:%M:%S",
+)
 logger = logging.getLogger("main")
 logger.setLevel(POLUS_LOG)
 
 
-def main(inpDir:Path, 
-         pattern:str,
-         outDir:Path,         
-         ):       
-        starttime= time.time()
-        if pattern is None:
-            logger.info(
-                    "No filepattern was provided so filepattern uses all input files"
-                )
+def main(
+    inpDir: Path,
+    pattern: str,
+    outDir: Path,
+) -> None:
+    """Run border discard and relabel for all matching images in ``inpDir``."""
+    starttime = time.time()
+    if pattern is None:
+        logger.info("No filepattern was provided so filepattern uses all input files")
 
-        assert inpDir.exists(), logger.info("Input directory does not exist")
-        count=0
-        fp = filepattern.FilePattern(inpDir,pattern)
-        imagelist = len([f for f in fp])
+    if not inpDir.exists():
+        logger.error("Input directory does not exist")
+        sys.exit(1)
+    count = 0
+    fp = filepattern.FilePattern(inpDir, pattern)
+    imagelist = len(list(fp))
 
-        for f in fp():
-            count += 1
-            file = f[0]['file'].name
-            logger.info(f'Label image: {file}')
-            db = Discard_borderobjects(inpDir, outDir, file)
-            db.discard_borderobjects()
-            relabel_img, _ = db.relabel_sequential()
-            db.save_relabel_image(relabel_img)
-            logger.info(f'Saving {count}/{imagelist} Relabelled image with discarded objects: {file}') 
-        logger.info('Finished all processes')
-        endtime = (time.time() - starttime)/60
-        logger.info(f'Total time taken to process all images: {endtime}')
+    for f in fp():
+        count += 1
+        file = f[0]["file"].name
+        logger.info(f"Label image: {file}")
+        db = Discard_borderobjects(inpDir, outDir, file)
+        db.discard_borderobjects()
+        relabel_img, _ = db.relabel_sequential()
+        db.save_relabel_image(relabel_img)
+        msg = (
+            f"Saving {count}/{imagelist} Relabelled image "
+            f"with discarded objects: {file}"
+        )
+        logger.info(msg)
+    logger.info("Finished all processes")
+    endtime = (time.time() - starttime) / 60
+    logger.info(f"Total time taken to process all images: {endtime}")
 
 
 # ''' Argument parsing '''
 logger.info("Parsing arguments...")
-parser = argparse.ArgumentParser(prog='main', description='Discard Border Objects Plugin')    
+parser = argparse.ArgumentParser(
+    prog="main",
+    description="Discard Border Objects Plugin",
+)
 #   # Input arguments
 
 parser.add_argument(
-        "--inpDir",
-        dest="inpDir",
-        type=str,
-        help="Input image collection to be processed by this plugin",
-        required=True
-    )
+    "--inpDir",
+    dest="inpDir",
+    type=str,
+    help="Input image collection to be processed by this plugin",
+    required=True,
+)
 parser.add_argument(
-        "--pattern",
-        dest="pattern",
-        type=str,
-        default=".+",
-        help="Filepattern regex used to parse image files",
-        required=False
-    )                   
+    "--pattern",
+    dest="pattern",
+    type=str,
+    default=".+",
+    help="Filepattern regex used to parse image files",
+    required=False,
+)
 #  # Output arguments
-parser.add_argument('--outDir',
-    dest='outDir',
+parser.add_argument(
+    "--outDir",
+    dest="outDir",
     type=str,
-    help='Output directory',
-    required=True
-    )   
+    help="Output directory",
+    required=True,
+)
 # # Parse the arguments
 args = parser.parse_args()
 inpDir = Path(args.inpDir)
 
-if (inpDir.joinpath('images').is_dir()):
-    inputDir = inpDir.joinpath('images').absolute()
-logger.info('inpDir = {}'.format(inpDir))
+if inpDir.joinpath("images").is_dir():
+    inputDir = inpDir.joinpath("images").absolute()
+logger.info(f"inpDir = {inpDir}")
 pattern = args.pattern
-logger.info("pattern = {}".format(pattern))
+logger.info(f"pattern = {pattern}")
 outDir = Path(args.outDir)
-logger.info('outDir = {}'.format(outDir))
+logger.info(f"outDir = {outDir}")
 
-if __name__=="__main__":
-    main(inpDir=inpDir,
-         pattern=pattern,
-         outDir=outDir
-         )
+if __name__ == "__main__":
+    main(inpDir=inpDir, pattern=pattern, outDir=outDir)