build: bump version 2.0.0-dev7 -> 2.0.0-dev8

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

@@ -0,0 +1,29 @@
+[bumpversion]
+current_version = 2.0.0-dev8
+commit = False
+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:README.md]
+
+[bumpversion:file:src/polus/plugins/transforms/images/apply_flatfield/__init__.py]

transforms/images/apply-flatfield-plugin/README.md

@@ -0,0 +1,49 @@
+# Apply Flatfield Plugin (v2.0.0-dev8)
+
+This WIPP plugin applies a flatfield operation on every image in a collection.
+The algorithm used to apply the flatfield is as follows:
+
+![Corrected = \frac{Original - Darkfield}{Brightfield} - Photobleach + Offset](https://render.githubusercontent.com/render/math?math=Corrected%20%3D%20%5Cfrac%7BOriginal%20-%20Darkfield%7D%7BBrightfield%7D%20-%20Photobleach%20%2B%20Offset)
+
+A brief description of the variables:
+1. ![Corrected](https://render.githubusercontent.com/render/math?math=Corrected) is the flatfield corrected image.
+2. ![Darkfield](https://render.githubusercontent.com/render/math?math=Darkfield) is the darkfield image (sometimes referred to as offset, dark current, or dark  noise). This is an image collected by the camera when the shutter is closed.
+3. ![Brightfield](https://render.githubusercontent.com/render/math?math=Brightfield) is the normalized brightfield image. This is an image collected when the shutter  is open and illumination is on. The image should contain single precision  floating point values, where ![mean(Brightfield)=1](https://render.githubusercontent.com/render/math?math=mean(Brightfield)%3D1).
+4. ![Photobleach](https://render.githubusercontent.com/render/math?math=Photobleach) is a scalar indicating how much the image has been photobleached. This is a per-image scalar offset.
+5. ![Offset](https://render.githubusercontent.com/render/math?math=Offset) is a  scalar applied to all images in the collection. If ![Photobleach](https://render.githubusercontent.com/render/math?math=Photobleach) is specified, then this plugin uses ![Offset=mean(Photobleach)](https://render.githubusercontent.com/render/math?math=Offset%3Dmean(Photobleach)).
+
+For more information on flatfielding, see the paper by [Young](https://currentprotocols.onlinelibrary.wiley.com/doi/full/10.1002/0471142956.cy0211s14).
+This plugin specifically uses the formulation from [Peng et al](https://www.nature.com/articles/ncomms14836).
+
+For more information on WIPP, visit the
+[official WIPP page](https://isg.nist.gov/deepzoomweb/software/wipp).
+
+## To Do
+
+Implement additional formulations of flatfield correction. Specifically, the formula specified by Young:
+
+![Corrected = \frac{Original - Darkfield}{Brightfield - Darkfield} ](https://render.githubusercontent.com/render/math?math=Corrected%20%3D%20%5Cfrac%7BOriginal%20-%20Darkfield%7D%7BBrightfield%20-%20Darkfield%7D%20)
+
+Additional formulations may also include reference image free algorithms for  flatfield correction, such as the [rolling ball algorithm](https://www.computer.org/csdl/magazine/co/1983/01/01654163/13rRUwwJWBB).
+
+## Building
+
+To build the Docker image for the conversion plugin, run `./build-docker.sh`.
+
+## Install WIPP Plugin
+
+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.
+
+## Options
+
+Command line options:
+
+| Name             | Description                                                           | I/O    | Type       |
+|------------------|-----------------------------------------------------------------------|--------|------------|
+| `--darkPattern`  | Filename pattern used to match darkfield files to image files         | Input  | string     |
+| `--ffDir`        | Image collection containing flatfield and/or darkfield images         | Input  | collection |
+| `--flatPattern`  | Filename pattern used to match flatfield files to image files         | Input  | string     |
+| `--imgDir`       | Input image collection to be processed by this plugin                 | Input  | collection |
+| `--imgPattern`   | Filename pattern used to separate data and match with flatfield files | Input  | string     |
+| `--outDir`       | Output collection                                                     | Output | collection |

transforms/images/apply-flatfield-plugin/VERSION

@@ -0,0 +1 @@
+2.0.0-dev8

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

@@ -0,0 +1,94 @@
+{
+  "name": "Apply Flatfield",
+  "version": "2.0.0-dev8",
+  "title": "Apply Flatfield",
+  "description": "Apply a flatfield algorithm to a collection of images.",
+  "author": "Nick Schaub (Nick.Schaub@nih.gov), Najib Ishaq (najib.ishaq@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:2.0.0-dev8",
+  "baseCommand": [
+    "python3",
+    "-m",
+    "polus.plugins.transforms.images.apply_flatfield"
+  ],
+  "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/apply-flatfield-plugin/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-plugins-transforms-images-apply-flatfield"
-version = "2.0.0-dev7"
+version = "2.0.0-dev8"
 description = ""
 authors = [
     "Nick Schaub <nicholas.schaub@nih.gov>",

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

@@ -14,6 +14,8 @@
 
 from . import utils
 
+__version__ = "2.0.0-dev8"
+
 logger = logging.getLogger(__name__)
 logger.setLevel(utils.POLUS_LOG)