Update/binops (#497)

* Updated to new structure

* Fixed bumpbversion filename

* Fixed bumpversion paths and added version to README

* Bump version: 0.4.2 → 0.5.0-dev0

* Fixed JSON formatting

* Removed old binary operations plugin

* Added in memory function

* Bump version: 0.4.2 → 0.5.0-dev1

---------

Co-authored-by: nicholas-schaub <nicholas.j.schaub@gmail.com>

.pre-commit-config.yaml

@@ -23,7 +23,7 @@ repos:
       - id: detect-private-key
       - id: end-of-file-fixer
       - id: mixed-line-ending
-        args: ['--fix=lf']
+        args: ["--fix=lf"]
         description: Forces to replace line ending by the UNIX 'lf' character.
       - id: trailing-whitespace
         exclude: '.bumpversion.cfg'

transforms/images/binary-operations-plugin/.bumpversion.cfg

@@ -0,0 +1,31 @@
+[bumpversion]
+current_version = 0.5.0-dev1
+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/transforms/images/binary_operations/__init__.py]
+
+[bumpversion:file:README.md]
+search = v{current_version}
+replace = v{new_version}

transforms/images/binary-operations-plugin/Dockerfile

@@ -0,0 +1,23 @@
+FROM polusai/bfio:2.1.9
+
+# environment variables defined in polusai/bfio
+# ENV EXEC_DIR="/opt/executables"
+# ENV DATA_DIR="/data"
+# ENV POLUS_EXT=".ome.tif"
+# ENV POLUS_LOG="INFO" # Change to WARNING for fewer logs, and DEBUG for debugging
+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}
+RUN pip3 install --index-url https://test.pypi.org/simple/ filepattern==2.2.7
+COPY src ${EXEC_DIR}/src
+
+RUN pip3 install ${EXEC_DIR} --no-cache-dir
+
+ENTRYPOINT ["python3", "-m", "polus.plugins.transforms.images.binary_operations"]
+CMD ["--help"]

transforms/images/polus-binary-operations-plugin/README.md → transforms/images/binary-operations-plugin/README.md

@@ -1,57 +1,57 @@
-# Binary Operations Plugin
+# Binary Operations Plugin (v0.5.0-dev1)
 
-This WIPP plugin does Morphological Image Processing on binary and instance labelled images.  
-The operations available are: 
+This WIPP plugin does Morphological Image Processing on binary and instance labelled images.
+The operations available are:
 
-  * #### Invertion
-  
-      This operation inverts binary images.  The 0s get mapped to 1 and the 1s get mapped to 0. 
+  * #### Inversion
+
+      This operation inverts binary images.  The 0s get mapped to 1 and the 1s get mapped to 0.
       Can only be applied to binary images.
-      
+
   * #### Dilation
-  
+
       This operation increases the white region in the image, or the foreground object increases.
-      
+
   * #### Erosion
-  
+
       This operation decreases the white region in the image, or the foreground object decreases.
-      
+
   * #### Opening
-  
+
       An opening operation is similar to applying an erosion followed by a dilation.  It removes small objects/noise in the background of the images.
-      
+
   * #### Closing
-  
+
       A closing operation is similar to applying a dilation following by an erosion.  It is useful in closing small holes inside the foreground object, or small
       black points inside the image
-      
+
   * #### Morphological Gradient
-  
+
       This operation is the difference between dilation and erosion of an image.  It creates an outline of the foreground object
-      
+
   * #### Filling Holes
-  
+
       This function fills in the foreground object.  It finds countours in the object and fills it with black and inverts it back.
-      
+
   * #### Skeletonization
-  
+
       This operation reduces the foreground regions to a skeletal remnant that largely preserves the extent and connectivity of the original region while throwing away most of the original foreground pixels.
-      
+
   * #### Top Hat
-  
-      This operation is the difference between the input image and opening of the image. 
-      
+
+      This operation is the difference between the input image and opening of the image.
+
   * #### Black Hat
-  
+
       This operation is the difference between the input image and closing of the image.
-      
+
    * #### Area Filtering
-  
-      There are two types of area filtering available.  
-      1) Remove segments that are larger than an area specified. 
+
+      There are two types of area filtering available.
+      1) Remove segments that are larger than an area specified.
       2) Remove segments that are smaller than an area specified.
       A threshold needs to be defined to run this operation.
-      
+
 
 Contact [Data Scientist](mailto:Madhuri.Vihani@axleinfo.com) for more information.
 For more information on WIPP, visit the [official WIPP page](https://isg.nist.gov/deepzoomweb/software/wipp).

transforms/images/binary-operations-plugin/VERSION

@@ -0,0 +1 @@
+0.5.0-dev1

transforms/images/binary-operations-plugin/plugin.json

@@ -0,0 +1,136 @@
+{
+  "name": "Binary Operations Plugin",
+  "version": "0.5.0-dev1",
+  "containerId": "polusai/binary-operations-plugin:0.5.0-dev1",
+  "title": "Binary Operations Plugin",
+  "description": "Everything you need to start a WIPP plugin.",
+  "authors": "nicholas-schaub (nick.schaub@nih.gov), Madhuri Vihani",
+  "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",
+  "citation": "",
+  "runCommand": [
+    "python3",
+    "-m",
+    "polus.plugins.transforms.images.binary_operations"
+  ],
+  "inputs": [
+    {
+      "name": "inpDir",
+      "description": "Input image collection to be processed by this plugin",
+      "type": "collection",
+      "options": null,
+      "required": true
+    },
+    {
+      "name": "filePattern",
+      "description": "Pattern of the images in Input",
+      "type": "string",
+      "options": null,
+      "required": false
+    },
+    {
+      "name": "kernel",
+      "description": "Kernel size that should be used for transformation",
+      "type": "number",
+      "options": null,
+      "required": false
+    },
+    {
+      "name": "operation",
+      "description": "The Binary Operations that will be done on the image",
+      "type": "enum",
+      "options": {
+        "values": [
+          "blackhat",
+          "close",
+          "dilate",
+          "erode",
+          "fillHoles",
+          "invert",
+          "morphologicalGradient",
+          "open",
+          "removeLarge",
+          "removeSmall",
+          "skeleton",
+          "tophat"
+        ]
+      },
+      "required": true
+    },
+    {
+      "name": "shape",
+      "description": "Structuring Shape (Default is Elliptical)",
+      "type": "enum",
+      "options": {
+        "values": [
+          "ellipse",
+          "rect",
+          "cross"
+        ]
+      },
+      "required": false
+    },
+    {
+      "name": "threshold",
+      "description": "Minimum Area of objects to keep.",
+      "type": "number",
+      "options": null,
+      "required": false
+    },
+    {
+      "name": "iterations",
+      "description": "Number of times to perform an operation (when applicable).",
+      "type": "number",
+      "options": null,
+      "required": false
+    }
+  ],
+  "outputs": [
+    {
+      "name": "outDir",
+      "description": "Output collection",
+      "type": "collection",
+      "options": null,
+      "required": true
+    }
+  ],
+  "ui": [
+    {
+      "key": "inputs.operation",
+      "title": "Operations",
+      "description": "Operations that will be used on image"
+    },
+    {
+      "key": "inputs.filePattern",
+      "title": "Image Pattern: ",
+      "description": "Pattern of images in input collection (image_r{rrr}_c{ccc}_z{zzz}.ome.tif). "
+    },
+    {
+      "key": "inputs.inpDir",
+      "title": "Input collection",
+      "description": "Input image collection to be processed by this plugin"
+    },
+    {
+      "key": "inputs.kernel",
+      "title": "Kernel Size",
+      "description": "Kernel size to use for operations"
+    },
+    {
+      "key": "inputs.shape",
+      "title": "Structuring Shape (Default is Elliptical)",
+      "description": "Kernel shape to use for operations"
+    },
+    {
+      "key": "inputs.threshold",
+      "title": "Threshold of area for objects in images",
+      "description": "Threshold to use for operations"
+    },
+    {
+      "key": "inputs.iterations",
+      "title": "Iterations",
+      "description": "Number of iterations to perform"
+    }
+  ],
+  "validators": null
+}

transforms/images/binary-operations-plugin/pyproject.toml

@@ -0,0 +1,34 @@
+[tool.poetry]
+name = "polus-plugins-transforms-images-binary-operations"
+version = "0.5.0-dev1"
+description = ""
+authors = ["nicholas-schaub <nick.schaub@nih.gov>", "Madhuri Vihani"]
+readme = "README.md"
+packages = [{include = "polus", from = "src"}]
+
+[tool.poetry.dependencies]
+python = "^3.9"
+bfio = {version = "2.1.9", extras = ["all"]}
+typer = "^0.7.0"
+filepattern = "^2.2.7"
+opencv-python = "^4.7.0.72"
+preadator = "^0.2.0"
+
+
+[tool.poetry.group.dev.dependencies]
+pytest = "^7.2.1"
+mypy = "^1.0.1"
+black = "^23.1.0"
+flake8 = "^6.0.0"
+pre-commit = "^3.1.0"
+bump2version = "^1.0.1"
+flake8-docstrings = "^1.7.0"
+
+[[tool.poetry.source]]
+name = "test"
+url = "https://test.pypi.org/simple/"
+secondary = true
+
+[build-system]
+requires = ["poetry-core"]
+build-backend = "poetry.core.masonry.api"

transforms/images/binary-operations-plugin/run-plugin.sh

@@ -0,0 +1,31 @@
+version=$(<VERSION)
+datapath=$(readlink --canonicalize ../../../data/)
+
+# Inputs: these parameters can be changed
+inpDir=/data/input/ # relative directory for where the input data is saved
+shape=ellipse #image or segmentation
+operation=removeLarge #boolean
+filePattern=None #the kinds of images/labels you want to use in the input directory
+
+# Depending on what operation is chosen, need to give values to certain arguments
+kernel=5 # necessary for dilation
+threshold=1 # Threshold for object sizes, only used for removeLarge and removeSmall
+iterations=1 # Number of iterations for an operation, only used by some operations
+
+# Outputs
+outDir=/data/output/
+
+# Show the help message
+sudo docker run polusai/binary-operations-plugin:${version}
+
+# Run Docker
+sudo docker run --mount type=bind,source=${datapath},target=/data/ \
+    polusai/binary-operations-plugin:${version} \
+    --inpDir ${inpDir} \
+    --outDir ${outDir} \
+    --shape ${shape} \
+    --operation ${operation} \
+    --filePattern ${filePattern} \
+    --kernel ${kernel} \
+    --threshold ${threshold} \
+    --iterations ${iterations}

transforms/images/binary-operations-plugin/src/polus/plugins/transforms/images/binary_operations/__init__.py

@@ -0,0 +1,25 @@
+"""Binary operations tool."""
+__version__ = "0.5.0-dev1"
+
+from polus.plugins.transforms.images.binary_operations.binops import (  # noqa
+    Operation,
+    StructuringShape,
+    batch_binary_ops,
+    binary_op,
+    scalable_binary_op,
+)
+from polus.plugins.transforms.images.binary_operations.utils import (  # noqa
+    blackhat,
+    close_,
+    dilate,
+    erode,
+    fill_holes,
+    invert,
+    iterate_tiles,
+    morphgradient,
+    open_,
+    remove_large,
+    remove_small,
+    skeletonize,
+    tophat,
+)