NEW Update in Apply flatfield tool

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

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 2.0.1
+current_version = 2.0.2-dev0
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

transforms/images/apply-flatfield-tool/Dockerfile

@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.3.3
+FROM python:3.13-slim
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"
@@ -9,7 +9,7 @@ ENV POLUS_LOG="INFO"
 # Work directory defined in the base container
 WORKDIR ${EXEC_DIR}
 
-# TODO: Change the tool_dir to the tool directory
+
 ENV TOOL_DIR="transforms/images/apply-flatfield-tool"
 
 # Copy the repository into the container
@@ -19,7 +19,6 @@ COPY . ${EXEC_DIR}/image-tools
 # Install the tool
 RUN pip3 install "${EXEC_DIR}/image-tools/${TOOL_DIR}" --no-cache-dir
 
-# Set the entrypoint
-# TODO: Change the entrypoint to the tool entrypoint
+
 ENTRYPOINT ["python3", "-m", "polus.images.transforms.images.apply_flatfield"]
 CMD ["--help"]

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

@@ -1,4 +1,4 @@
-# Apply Flatfield Plugin (v2.0.1)
+# Apply Flatfield Plugin (v2.0.2-dev0)
 
 This WIPP plugin applies a flatfield operation on every image in a collection.
 The algorithm used to apply the flatfield is as follows:

transforms/images/apply-flatfield-tool/VERSION

@@ -1 +1 @@
-2.0.1
+2.0.2-dev0

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

@@ -1,14 +1,14 @@
 {
   "name": "Apply Flatfield",
-  "version": "2.0.1",
+  "version": "2.0.2-dev0",
   "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-tool:2.0.1",
+  "containerId": "polusai/apply-flatfield-tool:2.0.2-dev0",
   "baseCommand": [
     "python3",
     "-m",

transforms/images/apply-flatfield-tool/pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-transforms-images-apply-flatfield"
-version = "2.0.1"
+version = "2.0.2-dev0"
 description = ""
 authors = [
     "Nick Schaub <nicholas.schaub@nih.gov>",
@@ -10,13 +10,12 @@ readme = "README.md"
 packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
-python = ">=3.9,<3.12"
-bfio = { version = "^2.3.3", extras = ["all"] }
-filepattern = "2.0.4"
-typer = { version = "^0.7.0", extras = ["all"] }
-numpy = "^1.24.3"
+python = ">=3.12"
+bfio = ">=2.5.0"
+filepattern = ">=2.1.4"
+typer = ">=0.24.0"
+numpy = ">=2.4.3"
 tqdm = "^4.65.0"
-preadator = "0.4.0-dev2"
 
 [tool.poetry.group.dev.dependencies]
 bump2version = "^1.0.1"

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

@@ -3,4 +3,4 @@
 from . import utils
 from .apply_flatfield import apply
 
-__version__ = "2.0.1"
+__version__ = "2.0.2-dev0"

transforms/images/apply-flatfield-tool/src/polus/images/transforms/images/apply_flatfield/apply_flatfield.py

@@ -4,10 +4,10 @@
 import operator
 import pathlib
 import typing
+from concurrent.futures import ProcessPoolExecutor
 
 import bfio
 import numpy
-import preadator
 import tqdm
 from filepattern import FilePattern
 
@@ -145,18 +145,14 @@ def _unshade_batch(
         df_image: component to be used for flatfield correction
     """
     # Load images
-    with preadator.ProcessManager(
-        name="unshade_batch::load",
-        num_processes=utils.MAX_WORKERS,
-        threads_per_process=2,
-    ) as load_executor:
+    with ProcessPoolExecutor(max_workers=utils.MAX_WORKERS) as load_executor:
         load_futures = []
         for i, inp_path in enumerate(batch_paths):
             load_futures.append(
-                load_executor.submit_process(utils.load_img, inp_path, i),
+                load_executor.submit(utils.load_img, inp_path, i),
             )
 
-        load_executor.join_processes()
+        [f.result() for f in load_futures]
         images = [f.result() for f in load_futures]
 
     images = [img for _, img in sorted(images, key=operator.itemgetter(0))]
@@ -169,11 +165,10 @@ def _unshade_batch(
     img_stack /= ff_image + 1e-8
 
     # Save outputs
-    with preadator.ProcessManager(
-        name="unshade_batch::save",
-        num_processes=utils.MAX_WORKERS,
-        threads_per_process=2,
-    ) as save_executor:
+    with ProcessPoolExecutor(max_workers=utils.MAX_WORKERS) as save_executor:
         for inp_path, img in zip(batch_paths, img_stack):
-            save_executor.submit_process(utils.save_img, inp_path, img, out_dir)
-        save_executor.join_processes()
+            save_futures = [
+                save_executor.submit(utils.save_img, inp_path, img, out_dir),
+            ]
+        for f in save_futures:
+            f.result()