Update polus-apply-flatfield-plugin

transforms/images/polus-apply-flatfield-plugin/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.2.0
+current_version = 1.2.1
 commit = False
 tag = False
 

transforms/images/polus-apply-flatfield-plugin/Dockerfile

@@ -1,18 +1,14 @@
-
-FROM labshare/polus-bfio-util:2.1.9
-
-# COPY VERSION /
-
-# ARG EXEC_DIR="/opt/executables"
-# ARG DATA_DIR="/data"
-
-# RUN mkdir -p ${EXEC_DIR} \
-#     && mkdir -p ${DATA_DIR}/inputs \
-#     && mkdir ${DATA_DIR}/outputs
-
-COPY src ${EXEC_DIR}/
+# Build from repo root (monorepo) or from this tool directory — both work.
+FROM polusai/bfio:2.5.0
+ENV EXEC_DIR="/opt/executables" POLUS_IMG_EXT=".ome.tif" POLUS_TAB_EXT=".csv" POLUS_LOG="INFO"
 WORKDIR ${EXEC_DIR}
-
-RUN pip3 install -r ${EXEC_DIR}/requirements.txt --no-cache-dir
-
-ENTRYPOINT ["python3", "main.py"]
+ENV TOOL_DIR="transforms/images/polus-apply-flatfield-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/polus-apply-flatfield-plugin/VERSION

@@ -1 +1 @@
-1.2.0
+1.2.1

transforms/images/polus-apply-flatfield-plugin/build-docker.sh

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

transforms/images/polus-apply-flatfield-plugin/plugin.json

@@ -1,89 +1,89 @@
 {
-    "name": "Apply Flatfield",
-    "version": "1.2.0",
-    "title": "Apply Flatfield",
-    "description": "Apply a flatfield algorithm to a collection of images.",
-    "author": "Nick Schaub (Nick.Schaub@nih.gov)",
-    "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/apply-flatfield-plugin:1.2.0",
-    "inputs": [
-      {
-        "name": "darkPattern",
-        "type": "string",
-        "description": "Filename pattern used to match darkfield files to image files",
-        "required": false
-      },
-      {
-        "name": "ffDir",
-        "type": "collection",
-        "description": "Image collection containing flatfield and/or darkfield images",
-        "required": true
-      },
-      {
-        "name": "brightPattern",
-        "type": "string",
-        "description": "Filename pattern used to match brightfield files to image files",
-        "required": true
-      },
-      {
-        "name": "imgDir",
-        "type": "collection",
-        "description": "Input image collection to be processed by this plugin",
-        "required": true
-      },
-      {
-        "name": "imgPattern",
-        "type": "string",
-        "description": "Filename pattern used to separate data and match with flatfied files",
-        "required": true
-      },
-      {
-        "name": "photoPattern",
-        "type": "string",
-        "description": "Filename pattern used to match photobleach files to image files",
-        "required": true
-      }
-    ],
-    "outputs": [
-      {
-        "name": "outDir",
-        "type": "collection",
-        "description": "Output collection"
-      }
-    ],
-    "ui": [
-      {
-        "key": "inputs.imgDir",
-        "title": "Images to correct",
-        "description": "Input image collection to be processed by this plugin"
-      },
-      {
-        "key": "inputs.imgPattern",
-        "title": "Image pattern",
-        "description": "Filename pattern used to separate data and match with flatfied files"
-      },
-      {
-        "key": "inputs.ffDir",
-        "title": "Background images (flatfield/darkfield)",
-        "description": "Image collection containing flatfield and/or darkfield images"
-      },
-      {
-        "key": "inputs.brightPattern",
-        "title": "Brightfield file pattern",
-        "description": "Filename pattern used to match brightfield files to image files"
-      },
-      {
-        "key": "inputs.darkPattern",
-        "title": "Darkfield file pattern",
-        "description": "Filename pattern used to match darkfield files to image files"
-      },
-      {
-        "key": "inputs.photoPattern",
-        "title": "Photobleach file pattern",
-        "description": "Filename pattern used to match photobleach files to image files"
-      }
-    ]
-  }
+  "name": "Apply Flatfield",
+  "version": "1.2.1",
+  "title": "Apply Flatfield",
+  "description": "Apply a flatfield algorithm to a collection of images.",
+  "author": "Nick Schaub (Nick.Schaub@nih.gov)",
+  "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/apply-flatfield-plugin:1.2.1",
+  "inputs": [
+    {
+      "name": "darkPattern",
+      "type": "string",
+      "description": "Filename pattern used to match darkfield files to image files",
+      "required": false
+    },
+    {
+      "name": "ffDir",
+      "type": "collection",
+      "description": "Image collection containing flatfield and/or darkfield images",
+      "required": true
+    },
+    {
+      "name": "brightPattern",
+      "type": "string",
+      "description": "Filename pattern used to match brightfield files to image files",
+      "required": true
+    },
+    {
+      "name": "imgDir",
+      "type": "collection",
+      "description": "Input image collection to be processed by this plugin",
+      "required": true
+    },
+    {
+      "name": "imgPattern",
+      "type": "string",
+      "description": "Filename pattern used to separate data and match with flatfied files",
+      "required": true
+    },
+    {
+      "name": "photoPattern",
+      "type": "string",
+      "description": "Filename pattern used to match photobleach files to image files",
+      "required": true
+    }
+  ],
+  "outputs": [
+    {
+      "name": "outDir",
+      "type": "collection",
+      "description": "Output collection"
+    }
+  ],
+  "ui": [
+    {
+      "key": "inputs.imgDir",
+      "title": "Images to correct",
+      "description": "Input image collection to be processed by this plugin"
+    },
+    {
+      "key": "inputs.imgPattern",
+      "title": "Image pattern",
+      "description": "Filename pattern used to separate data and match with flatfied files"
+    },
+    {
+      "key": "inputs.ffDir",
+      "title": "Background images (flatfield/darkfield)",
+      "description": "Image collection containing flatfield and/or darkfield images"
+    },
+    {
+      "key": "inputs.brightPattern",
+      "title": "Brightfield file pattern",
+      "description": "Filename pattern used to match brightfield files to image files"
+    },
+    {
+      "key": "inputs.darkPattern",
+      "title": "Darkfield file pattern",
+      "description": "Filename pattern used to match darkfield files to image files"
+    },
+    {
+      "key": "inputs.photoPattern",
+      "title": "Photobleach file pattern",
+      "description": "Filename pattern used to match photobleach files to image files"
+    }
+  ]
+}

transforms/images/polus-apply-flatfield-plugin/pyproject.toml

@@ -0,0 +1,18 @@
+[project]
+name = "polus-apply-flatfield-plugin"
+version = "1.2.0"
+requires-python = ">=3.11"
+dependencies = [
+    "bfio>=2.5.0",
+    "filepattern>=2.2.1",
+]
+
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.setuptools]
+py-modules = ["main"]

transforms/images/polus-apply-flatfield-plugin/src/__init__.py

@@ -0,0 +1 @@
+"""Polus apply flatfield plugin."""