Fix endian bug and replace fileExtension with environmental variable …

…omeconverter (#565) * Bump version: 0.3.2 → 0.3.3-dev1 * fix endian and remove fileExtension input argument * updated bfio dependency and tests * Bump version: 0.3.3-dev1 → 0.3.3-dev2 * Bump version: 0.3.3-dev2 → 0.3.3-dev3 * fix writing tiled large images * updated doc
PolusAI · Oct 23, 2024 · 29d3dcb · 29d3dcb
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diff --git a/formats/ome-converter-tool/.bumpversion.cfg b/formats/ome-converter-tool/.bumpversion.cfg
@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.3.2
+current_version = 0.3.3-dev3
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
@@ -24,6 +24,10 @@ replace = version = "{new_version}"
 
 [bumpversion:file:VERSION]
 
+[bumpversion:file:ict.yaml]
+
+[bumpversion:file:omeconverter.cwl]
+
 [bumpversion:file:README.md]
 
 [bumpversion:file:src/polus/images/formats/ome_converter/__init__.py]
diff --git a/formats/ome-converter-tool/Dockerfile b/formats/ome-converter-tool/Dockerfile
@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.3.3
+FROM polusai/bfio:2.4.4
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

diff --git a/formats/ome-converter-tool/README.md b/formats/ome-converter-tool/README.md
@@ -1,4 +1,4 @@
-# OME Converter (v0.3.2)
+# OME Converter (v0.3.3-dev3)
 
 This WIPP plugin converts BioFormats supported data types to the
 OME Zarr or OME TIF file format. This is not a complete implementation, rather it implements a file
@@ -23,12 +23,16 @@ contents of `plugin.json` into the pop-up window and submit.
 
 ## Options
 
-This plugin takes 3 input arguments and 1 output argument:
+This plugin takes 2 input arguments and 1 output argument:
 
 | Name             | Description                                                  | I/O    | Type        |
 |------------------|--------------------------------------------------------------|--------|-------------|
 | `--inpDir`       | Input generic data collection to be processed by this plugin | Input  | genericData |
 | `--filePattern`  | A filepattern, used to select data for conversion            | Input  | string      |
-| `--fileExtension`| A desired file format for conversion                         | Input  | enum        |
 | `--outDir`       | Output collection                                            | Output | genericData |
 | `--preview`      | Generate a JSON file with outputs                            | Output | JSON        |
+
+## Docker Command
+
+```bash
+docker run -e POLUS_IMG_EXT=".ome.zarr" -v /Users/username/:/Users/username/ polusai/ome-converter-tool:0.3.3-dev3 --inpDir=/Users/path/to/Images/ --filePattern=".*.tif" --outDir=/Users/path/to/outputs
diff --git a/formats/ome-converter-tool/VERSION b/formats/ome-converter-tool/VERSION
@@ -1 +1 @@
-0.3.2
+0.3.3-dev3
diff --git a/formats/ome-converter-tool/ict.yaml b/formats/ome-converter-tool/ict.yaml
@@ -1,55 +1,41 @@
 author:
-- Nick Schaub
-- Hamdah Shafqat
+  - Nick Schaub
+  - Hamdah Shafqat
 contact: [email protected]
-container: polusai/ome-converter-tool:0.3.2-dev0
+container: polusai/ome-converter-tool:0.3.3-dev3
 description: Convert Bioformats supported format to OME Zarr or OME TIF
 entrypoint: python3 -m polus.images.formats.ome_converter
 inputs:
-- description: Input generic data collection to be processed by this plugin
-  format:
-  - genericData
-  name: inpDir
-  required: true
-  type: path
-- description: A filepattern, used to select data to be converted
-  format:
-  - string
-  name: filePattern
-  required: true
-  type: string
-- description: Type of data conversion
-  format:
-  - enum
-  name: fileExtension
-  required: true
-  type: string
+  - description: Input generic data collection to be processed by this plugin
+    format:
+      - genericData
+    name: inpDir
+    required: true
+    type: path
+  - description: A filepattern, used to select data to be converted
+    format:
+      - string
+    name: filePattern
+    required: true
+    type: string
 name: polusai/OMEConverter
 outputs:
-- description: Output collection
-  format:
-  - genericData
-  name: outDir
-  required: true
-  type: path
-repository: https://github.com/PolusAI/polus-plugins
+  - description: Output collection
+    format:
+      - genericData
+    name: outDir
+    required: true
+    type: path
+repository: https://github.com/PolusAI/image-tools
 specVersion: 1.0.0
 title: OME Converter
 ui:
-- description: Input generic data collection to be processed by this plugin
-  key: inputs.inpDir
-  title: Input generic collection
-  type: path
-- description: A filepattern, used to select data for conversion
-  key: inputs.filePattern
-  title: Filepattern
-  type: text
-- description: Type of data conversion
-  fields:
-  - .ome.tif
-  - .ome.zarr
-  - default
-  key: inputs.fileExtension
-  title: fileExtension
-  type: select
-version: 0.3.2-dev0
+  - description: Input generic data collection to be processed by this plugin
+    key: inputs.inpDir
+    title: Input generic collection
+    type: path
+  - description: A filepattern, used to select data for conversion
+    key: inputs.filePattern
+    title: Filepattern
+    type: text
+version: 0.3.3-dev3
diff --git a/formats/ome-converter-tool/omeconverter.cwl b/formats/ome-converter-tool/omeconverter.cwl
@@ -1,10 +1,6 @@
 class: CommandLineTool
 cwlVersion: v1.2
 inputs:
-  fileExtension:
-    inputBinding:
-      prefix: --fileExtension
-    type: string
   filePattern:
     inputBinding:
       prefix: --filePattern
@@ -24,7 +20,7 @@ outputs:
     type: Directory
 requirements:
   DockerRequirement:
-    dockerPull: polusai/ome-converter-tool:0.3.2-dev0
+    dockerPull: polusai/ome-converter-tool:0.3.3-dev3
   InitialWorkDirRequirement:
     listing:
     - entry: $(inputs.outDir)

diff --git a/formats/ome-converter-tool/plugin.json b/formats/ome-converter-tool/plugin.json
@@ -1,14 +1,14 @@
 {
   "name": "OME Converter",
-  "version": "0.3.2",
+  "version": "0.3.3-dev3",
   "title": "OME Converter",
   "description": "Convert Bioformats supported format to OME Zarr or OME TIF",
   "author": "Nick Schaub ([email protected]), Hamdah Shafqat Abbasi ([email protected])",
   "institution": "National Center for Advancing Translational Sciences, National Institutes of Health",
-  "repository": "https://github.com/PolusAI/polus-plugins",
+  "repository": "https://github.com/PolusAI/image-tools",
   "website": "https://ncats.nih.gov/preclinical/core/informatics",
   "citation": "",
-  "containerId": "polusai/ome-converter-tool:0.3.2",
+  "containerId": "polusai/ome-converter-tool:0.3.3-dev3",
   "baseCommand": [
     "python3",
     "-m",
@@ -26,20 +26,6 @@
       "type": "string",
       "description": "A filepattern, used to select data to be converted",
       "required": true
-    },
-    {
-      "name": "fileExtension",
-      "type": "enum",
-      "description": "Type of data conversion",
-      "default": "default",
-      "options": {
-        "values": [
-          ".ome.tif",
-          ".ome.zarr",
-          "default"
-        ]
-      },
-      "required": true
     }
   ],
   "outputs": [
@@ -59,12 +45,6 @@
       "key": "inputs.filePattern",
       "title": "Filepattern",
       "description": "A filepattern, used to select data for conversion"
-    },
-    {
-      "key": "inputs.fileExtension",
-      "title": "fileExtension",
-      "description": "Type of data conversion",
-      "default": ".ome.tif"
     }
   ]
 }
diff --git a/formats/ome-converter-tool/pyproject.toml b/formats/ome-converter-tool/pyproject.toml
@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-formats-ome-converter"
-version = "0.3.2"
+version = "0.3.3-dev3"
 description = "Convert BioFormats datatypes to ome.tif or ome.zarr file format"
 authors = [
     "Nick Schaub <[email protected]>",
@@ -12,7 +12,7 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bfio = {version = "^2.3.3", extras = ["all"]}
+bfio = {version = "^2.4.4", extras = ["all"]}
 filepattern = "^2.0.4"
 typer = "^0.7.0"
 tqdm = "^4.64.1"

diff --git a/formats/ome-converter-tool/run-plugin.sh b/formats/ome-converter-tool/run-plugin.sh
@@ -12,12 +12,11 @@ fileExtension=".ome.zarr"
 outDir=/data/output
 
 # Show the help options
-docker run polusai/ome-converter-plugin:${version}
+# docker run polusai/ome-converter-plugin:${version}
 
 # Run the plugin
-docker run --mount type=bind,source=${datapath},target=/data/ \
-            polusai/ome-converter-plugin:${version} \
+docker run -e POLUS_IMG_EXT=${fileExtension} --mount type=bind,source=${datapath},target=/data/ \
+            polusai/ome-converter-tool:${version} \
             --inpDir ${inpDir} \
             --filePattern ${filePattern} \
-            --fileExtension ${fileExtension} \
             --outDir ${outDir}
diff --git a/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__init__.py
@@ -1,6 +1,6 @@
 """Ome Converter."""
 
-__version__ = "0.3.2"
+__version__ = "0.3.3-dev3"
 
 from .image_converter import batch_convert
 from .image_converter import convert_image
diff --git a/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__main__.py b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/__main__.py
@@ -11,7 +11,6 @@
 import preadator
 import typer
 from polus.images.formats.ome_converter.image_converter import NUM_THREADS
-from polus.images.formats.ome_converter.image_converter import Extension
 from polus.images.formats.ome_converter.image_converter import convert_image
 from tqdm import tqdm
 
@@ -24,6 +23,7 @@
 )
 logger = logging.getLogger("polus.images.formats.ome_converter")
 logger.setLevel(os.environ.get("POLUS_LOG", logging.INFO))
+POLUS_IMG_EXT = os.environ.get("POLUS_IMG_EXT", ".ome.tif")
 
 
 @app.command()
@@ -43,11 +43,6 @@ def main(
         "--filePattern",
         help="A filepattern defining the images to be converted",
     ),
-    file_extension: Extension = typer.Option(
-        Extension,
-        "--fileExtension",
-        help="Type of data conversion",
-    ),
     out_dir: pathlib.Path = typer.Option(
         ...,
         "--outDir",
@@ -68,7 +63,6 @@ def main(
     logger.info(f"inpDir = {inp_dir}")
     logger.info(f"outDir = {out_dir}")
     logger.info(f"filePattern = {pattern}")
-    logger.info(f"fileExtension = {file_extension}")
 
     fps = fp.FilePattern(inp_dir, pattern)
 
@@ -79,7 +73,7 @@ def main(
                 "outDir": [],
             }
             for file in fps():
-                out_name = str(file[1][0].name.split(".")[0]) + file_extension
+                out_name = str(file[1][0].name.split(".")[0]) + POLUS_IMG_EXT
                 out_json["outDir"].append(out_name)
             json.dump(out_json, jfile, indent=2)
         return
@@ -93,14 +87,14 @@ def main(
         for files in fps():
             file = files[1][0]
             threads.append(
-                executor.submit_process(convert_image, file, file_extension, out_dir),
+                executor.submit_process(convert_image, file, POLUS_IMG_EXT, out_dir),
             )
 
         for f in tqdm(
             as_completed(threads),
             total=len(threads),
             mininterval=5,
-            desc=f"converting images to {file_extension}",
+            desc=f"converting images to {POLUS_IMG_EXT}",
             initial=0,
             unit_scale=True,
             colour="cyan",