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 +2,13 @@
 ### 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
+
+## [0.2.5-dev0] - 2026-03-04
+### Added
+- Updated dependencies and base container image
+- refactored code

formats/file-renaming-tool/Dockerfile

@@ -1,10 +1,11 @@
-FROM polusai/bfio:2.3.6
+FROM polusai/bfio:2.5.0
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
 ENV POLUS_IMG_EXT=".ome.tif"
 ENV POLUS_TAB_EXT=".csv"
 ENV POLUS_LOG="INFO"
+ENV NUM_THREADS=8
 
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}

formats/file-renaming-tool/README.md

@@ -1,6 +1,12 @@
-# File Renaming(0.2.4-dev0)
-This WIPP plugin uses supplied file naming patterns to dynamically
-rename and save files in an image collection to a new image collection.
+# File Renaming(v0.2.5-dev0)
+This WIPP plugin renames files in an image collection (typically microscopy images) using powerful, user-defined filename patterns for both input matching and output naming.
+
+It is particularly useful for:
+- Standardizing file names across experiments
+- Converting channel names (GFP, DAPI, TXRED…) to numeric indices
+- Adding zero-padding consistently
+- Reorganizing naming schemes
+- Working with nested directory structures
 
 ## Example Usage
 * The user can upload an image collection where all files contain similar
@@ -16,12 +22,14 @@ 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`
 
+**Important rules:**
+
 * The user can format the output digit using the number of digits
 specified in the output format.
  * `d` represents *digit*
@@ -38,7 +46,41 @@ 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:melanie.parham@axleinfo.com), [Hamdah Shafqat abbasi](mailto:hamdahshafqat.abbasi@nih.gov) for more
@@ -57,6 +99,38 @@ To build the Docker image for the conversion plugin, run
 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.
 
+## Docker / CLI Examples
+
+Basic
+
+```
+docker run --rm \
+  -v "/path/to/input/images:/data/input" \
+  -v "/path/to/output:/data/output" \
+  polusai/file-renaming-tool:0.2.5-dev0 \
+    --inpDir         /data/input \
+    --outDir         /data/output \
+    --filePattern    'img_x{row:dd}_y{col:dd}_{channel:c+}.tif' \
+    --outFilePattern 'r{row:03d}_c{col:03d}_ch{channel:03d}.ome.tif'
+
+
+```
+Directory mapping
+
+```
+docker run --rm \
+  -v "/path/to/dataset:/data" \
+  polusai/file-renaming-tool:0.2.5-dev0 \
+    --inpDir         /data/input \
+    --outDir         /data/output \
+    --filePattern    '/.*/Images/(?P<directory>.*)/.*_{row:c}{col:dd}f{f:dd}d{channel:d}.tif' \
+    --outFilePattern 'x{row:dd}_y{col:dd}_p{f:dd}_c{channel:d}_dir{directory}.tif' \
+    --mapDirectory
+
+
+```
+
+
 ## Options
 
 This plugin takes three input argument and one output argument:
@@ -67,5 +141,5 @@ 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: melanie.parham@axleinfo.com
-container: polusai/file-renaming-tool:0.2.4-dev0
+  - Hamdah Shafqat
+  - Melanie Parham
+contact: hamdahshafqat.abbasi@nih.gov
+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