integrated filepattern in filerenaming

formats/file-renaming-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.4
+current_version = 0.2.5-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
@@ -22,6 +22,12 @@ replace = version = "{new_version}"
 
 [bumpversion:file:plugin.json]
 
+[bumpversion:file:FileRenaming.cwl]
+
+[bumpversion:file:ict.yaml]
+
 [bumpversion:file:VERSION]
 
+[bumpversion:file:README.md]
+
 [bumpversion:file:src/polus/images/formats/file_renaming/__init__.py]

formats/file-renaming-tool/CHANGELOG.md

@@ -2,3 +2,8 @@
 ### Added
 - Pytests to test this plugin
 - Added a support for recursively searching for files within a directory and its subdirectories of specified pattern by passing value either raw or map for `mapDirectory` input argument.
+
+## [0.2.4-dev2] - 2024-12-17
+### Added
+- Integrated filepattern in this tool
+- Modified the sorting dictionary letters key with respect to length

formats/file-renaming-tool/Dockerfile

@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.3.6
+FROM polusai/bfio:2.4.5
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

formats/file-renaming-tool/README.md

@@ -1,4 +1,4 @@
-# File Renaming(0.2.4-dev0)
+# File Renaming(v0.2.5-dev0)
 This WIPP plugin uses supplied file naming patterns to dynamically
 rename and save files in an image collection to a new image collection.
 
@@ -16,10 +16,10 @@ naming conventions.
 `newdata_x001_y001_c002.tif`
 `newdata_x001_y001_c003.tif`
 
- * **User input pattern:**
+ * **filePattern:**
 `img_x{row:dd}_y{col:dd}_{channel:c+}.ome.tif`
 
- * **User output pattern:**
+ * **outFilePattern:**
 `newdata_x{row:ddd}_y{col:ddd}_c{channel:ddd}.ome.tif`
 
 * The user can format the output digit using the number of digits
@@ -38,7 +38,41 @@ exception:
 then the script sorts the strings that match the character pattern and
 assigns numbers 0+ to them.
 
-* New optional feature `mapDirectory` implemented to include directory name in renamed files. This plugin also handles nested directories and one level up directory name is added  to renamed files if `raw` value passed, `map` for mapped subdirectories `d0, d1, d2, ... dn` and if not passed then no directory name is added in renamed files.
+* Implemented a new optional boolean feature `mapDirectory` to append mapped directory names in renamed files.
+
+
+## Renaming files within a complex nested directory structure:
+In specific scenarios where users need to rename files within nested subdirectories, this functionality can be leveraged by providing an appropriate pattern
+
+For Example
+
+```
+└── BBBC001
+    └── raw
+        ├── Ground_Truth
+        │   └── groundtruth_images
+        │       ├── AS_09125_050118150001_A03f00d0.tif
+        │       ├── AS_09125_050118150001_A03f01d0.tif
+        │       ├── AS_09125_050118150001_A03f02d0.tif
+        │       ├── AS_09125_050118150001_A03f03d0.tif
+        │       ├── AS_09125_050118150001_A03f04d0.tif
+        │       └── AS_09125_050118150001_A03f05d0.tif
+        └── Images
+            └── human_ht29_colon_cancer_1_images
+                ├── AS_09125_050118150001_A03f00d0.tif
+                ├── AS_09125_050118150001_A03f01d0.tif
+                ├── AS_09125_050118150001_A03f02d0.tif
+                ├── AS_09125_050118150001_A03f03d0.tif
+                ├── AS_09125_050118150001_A03f04d0.tif
+                └── AS_09125_050118150001_A03f05d0.tif
+
+```
+
+Now, renaming files within the `human_ht29_colon_cancer_1_images` is achievable by providing a `filepattern` such as `/.*/.*/.*/Images/(?P<directory>.*)/.*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif`, and specifying `outFilePattern` as `x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}.tif`. If the mapDirectory option is not utilized, the raw directory name will be appended in the renamed files. To handle directory names containing both letters and digits, employ `(?P<directory>.*)`; use `{directory:c+}` or `{directory:d+}` if it contains solely letters or digits, respectively.
+
+#### Note:
+To extract directory names, the pattern should start with a backslash
+
 
 
 Contact [Melanie Parham](mailto:[email protected]), [Hamdah Shafqat abbasi](mailto:[email protected]) for more
@@ -67,5 +101,5 @@ This plugin takes three input argument and one output argument:
 | `--filePattern`    | Input filename pattern            | Input    | string     |
 | `--outDir`         | Output collection                 | Output   | collection |
 | `--outFilePattern` | Output filename pattern           | Input    | string     |
-| `--mapDirectory`   | Directory name (`raw`, `map`)     | Input    | enum       |
+| `--mapDirectory`   | Extract mapped directory name     | Input    | boolean    |
 | `--preview`        | Generate a JSON file with outputs | Output   | JSON       |

formats/file-renaming-tool/VERSION

@@ -1 +1 @@
-0.2.4
+0.2.5-dev0

formats/file-renaming-tool/filerenaming.cwl

@@ -12,7 +12,7 @@ inputs:
   mapDirectory:
     inputBinding:
       prefix: --mapDirectory
-    type: string?
+    type: boolean?
   outDir:
     inputBinding:
       prefix: --outDir
@@ -28,7 +28,7 @@ outputs:
     type: Directory
 requirements:
   DockerRequirement:
-    dockerPull: polusai/file-renaming-tool:0.2.4-dev0
+    dockerPull: polusai/file-renaming-tool:0.2.5-dev0
   InitialWorkDirRequirement:
     listing:
     - entry: $(inputs.outDir)

formats/file-renaming-tool/ict.yaml

@@ -1,65 +1,61 @@
 author:
-- Melanie Parham
-- Hamdah Shafqat
-contact: [email protected]
-container: polusai/file-renaming-tool:0.2.4-dev0
+  - Hamdah Shafqat
+  - Melanie Parham
+contact: [email protected]
+container: polusai/file-renaming-tool:0.2.5-dev0
 description: Rename and store image collection files in a new image collection
 entrypoint: python3 -m polus.images.formats.file_renaming
 inputs:
-- description: Filename pattern used to separate data
-  format:
-  - string
-  name: filePattern
-  required: true
-  type: string
-- description: Input image collection to be processed by this plugin
-  format:
-  - collection
-  name: inpDir
-  required: true
-  type: path
-- description: Desired filename pattern used to rename and separate data
-  format:
-  - string
-  name: outFilePattern
-  required: true
-  type: string
-- description: Get directory name incorporated in renamed files
-  format:
-  - enum
-  name: mapDirectory
-  required: false
-  type: string
+  - description: Input image collection to be processed by this plugin
+    format:
+      - collection
+    name: inpDir
+    required: true
+    type: path
+  - description: Filename pattern used to separate data
+    format:
+      - string
+    name: filePattern
+    required: true
+    type: string
+  - description: Desired filename pattern used to rename and separate data
+    format:
+      - string
+    name: outFilePattern
+    required: true
+    type: string
+  - description: Incorporate mapped directory names into renamed files
+    format:
+      - boolean
+    name: mapDirectory
+    required: false
+    type: boolean
 name: polusai/FileRenaming
 outputs:
-- description: Output collection
-  format:
-  - collection
-  name: outDir
-  required: true
-  type: path
-repository: https://github.com/PolusAI/polus-plugins
+  - description: Output collection
+    format:
+      - collection
+    name: outDir
+    required: true
+    type: path
+repository: https://github.com/PolusAI/image-tools
 specVersion: 1.0.0
 title: File Renaming
 ui:
-- description: Filename pattern used to separate data
-  key: inputs.filePattern
-  title: Filename pattern
-  type: text
-- description: Input image collection to be processed by this plugin
-  key: inputs.inpDir
-  title: Input collection
-  type: path
-- description: Desired filename pattern used to rename and separate data
-  key: inputs.outFilePattern
-  title: Output filename pattern
-  type: text
-- description: Get directory name incorporated in renamed files
-  fields:
-  - raw
-  - map
-  - default
-  key: inputs.mapDirectory
-  title: mapDirectory
-  type: select
-version: 0.2.4-dev0
+  - description: Input image collection to be processed by this plugin
+    key: inputs.inpDir
+    title: Input collection
+    type: path
+  - description: Filename pattern used to separate data
+    key: inputs.filePattern
+    title: Filename pattern
+    type: text
+  - description: Desired filename pattern used to rename and separate data
+    key: inputs.outFilePattern
+    title: Output filename pattern
+    type: text
+  - description: Incorporate mapped directory names into renamed files
+    key: inputs.mapDirectory
+    title: mapDirectory
+    type: checkbox
+version: 0.2.5-dev0

formats/file-renaming-tool/plugin.json

@@ -1,32 +1,32 @@
 {
   "name": "File Renaming",
-  "version": "0.2.4",
+  "version": "0.2.5-dev0",
   "title": "File Renaming",
   "description": "Rename and store image collection files in a new image collection",
-  "author": "Melanie Parham ([email protected]), Hamdah Shafqat Abbasi ([email protected])",
+  "author": "Hamdah Shafqat Abbasi ([email protected]), Melanie Parham ([email protected])",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
   "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/file-renaming-tool:0.2.4",
+  "containerId": "polusai/file-renaming-tool:0.2.5-dev0",
   "baseCommand": [
     "python3",
     "-m",
     "polus.images.formats.file_renaming"
   ],
   "inputs": [
-    {
-      "name": "filePattern",
-      "type": "string",
-      "description": "Filename pattern used to separate data",
-      "required": true
-    },
     {
       "name": "inpDir",
       "type": "collection",
       "description": "Input image collection to be processed by this plugin",
       "required": true
     },
+    {
+      "name": "filePattern",
+      "type": "string",
+      "description": "Filename pattern used to separate data",
+      "required": true
+    },
     {
       "name": "outFilePattern",
       "type": "string",
@@ -35,16 +35,8 @@
     },
     {
       "name": "mapDirectory",
-      "type": "enum",
-      "description": "Get directory name incorporated in renamed files",
-      "default": "default",
-      "options": {
-        "values": [
-          "raw",
-          "map",
-          "default"
-        ]
-      },
+      "type": "boolean",
+      "description": "Incorporate mapped directory names into renamed files",
       "required": false
     }
   ],
@@ -56,16 +48,16 @@
     }
   ],
   "ui": [
-    {
-      "key": "inputs.filePattern",
-      "title": "Filename pattern",
-      "description": "Filename pattern used to separate data"
-    },
     {
       "key": "inputs.inpDir",
       "title": "Input collection",
       "description": "Input image collection to be processed by this plugin"
     },
+    {
+      "key": "inputs.filePattern",
+      "title": "Filename pattern",
+      "description": "Filename pattern used to separate data"
+    },
     {
       "key": "inputs.outFilePattern",
       "title": "Output filename pattern",
@@ -74,8 +66,7 @@
     {
       "key": "inputs.mapDirectory",
       "title": "mapDirectory",
-      "description": "Get directory name incorporated in renamed files",
-      "default": ""
+      "description": "Incorporate mapped directory names into renamed files"
     }
   ]
 }

formats/file-renaming-tool/pyproject.toml

@@ -1,10 +1,10 @@
 [tool.poetry]
 name = "polus-images-formats-file-renaming"
-version = "0.2.4"
-description = "Rename and store image collection files in a new image collection"
+version = "0.2.5-dev0"
+description = "Convert BioFormats datatypes to ome.tif or ome.zarr file format"
 authors = [
-"Melanie Parham <[email protected]>",
-"Hamdah Shafqat abbasi <[email protected]>"
+    "Hamdah Shafqat abbasi <[email protected]>",
+    "Melanie Parham <[email protected]>",
 ]
 readme = "README.md"
 packages = [{include = "polus", from = "src"}]
@@ -14,6 +14,7 @@ python = ">=3.9,<3.12"
 typer = "^0.7.0"
 tqdm = "^4.64.1"
 numpy = "^1.26.3"
+filepattern = "^2.0.5"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"
@@ -26,3 +27,8 @@ pytest = "^7.2.1"
 [build-system]
 requires = ["poetry-core"]
 build-backend = "poetry.core.masonry.api"
+
+[tool.pytest.ini_options]
+pythonpath = [
+  "."
+]

formats/file-renaming-tool/run-plugin.sh

@@ -1,23 +1,25 @@
-#!/bin/bash
+!/bin/bash
+
+
 version=$(<VERSION)
 datapath=$(readlink --canonicalize data)
 
 # Inputs
 inpDir=/data/inputs
 filePattern=".*_{row:c}{col:dd}_s{s:d}_w{channel:d}.*.tif"
 outFilePattern="r01_x{row:c}_y{col:dd}_p{s:d}_c{channel:d}.ome.tif"
-mapDirectory="raw"
+mapDirectory=true
 # Output paths
 outDir=/data/output
 
 # Show the help options
-docker run polusai/file-renaming-plugin:${version}
+docker run polusai/file-renaming-tool:${version}
 
 # Run the plugin
 docker run --mount type=bind,source=${datapath},target=/data/ \
-            polusai/file-renaming-plugin:${version} \
+            polusai/file-renaming-tool:${version} \
             --inpDir ${inpDir} \
             --filePattern ${filePattern} \
             --outFilePattern ${outFilePattern} \
-            --mapDirectory ${outFilePattern} \
+            --mapDirectory
             --outDir ${outDir}