Update Remove-border-objects-plugin

.gitignore

@@ -184,6 +184,8 @@ uv.lock
 #husky
 node_modules
 
+#uv 
+transforms/images/*/uv.lock
 
 # uv lockfiles (generated; ignore in all nested projects)
 **/uv.lock

transforms/images/binary-operations-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.5.6-dev0
+current_version = 0.5.4-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

transforms/images/binary-operations-tool/README.md

@@ -1,4 +1,4 @@
-# Binary Operations Plugin (v0.5.6-dev0)
+# Binary Operations Plugin (v0.5.4-dev0)
 
 This WIPP plugin does Morphological Image Processing on binary and instance labelled images.
 The operations available are:

transforms/images/binary-operations-tool/VERSION

@@ -1 +1 @@
-0.5.6-dev0
+0.5.4-dev0

transforms/images/binary-operations-tool/plugin.json

@@ -1,7 +1,7 @@
 {
   "name": "Binary Operations Plugin",
-  "version": "0.5.6-dev0",
-  "containerId": "polusai/binary-operations-tool:0.5.6-dev0",
+  "version": "0.5.4-dev0",
+  "containerId": "polusai/binary-operations-tool:0.5.4-dev0",
   "title": "Binary Operations Plugin",
   "description": "Everything you need to start a WIPP plugin.",
   "author": "Nick Schaub (nick.schaub@nih.gov), Madhuri Vihani",

transforms/images/binary-operations-tool/pyproject.toml

@@ -5,7 +5,7 @@ requires-python = ">=3.11"
 
 [tool.poetry]
 name = "polus-images-transforms-images-binary-operations"
-version = "0.5.6-dev0"
+version = "0.5.4-dev0"
 description = ""
 authors = ["nicholas-schaub <nick.schaub@nih.gov>", "Madhuri Vihani"]
 readme = "README.md"

transforms/images/binary-operations-tool/src/polus/images/transforms/images/binary_operations/__init__.py

@@ -1,5 +1,5 @@
 """Binary operations tool."""
-__version__ = "0.5.6-dev0"
+__version__ = "0.5.4-dev0"
 
 from . import utils
 from .binops import Operation

transforms/images/image-calculator-tool/.bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 0.2.4-dev0
+current_version = 0.2.3-dev0
 commit = False
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

transforms/images/image-calculator-tool/README.md

@@ -1,4 +1,4 @@
-# Image Calculator (v0.2.4-dev0)
+# Image Calculator (v0.2.3-dev0)
 
 This plugin performs pixel-wise operations between two image collections.
 For example, images in one image collection can be subtracted from images in another collection.

transforms/images/image-calculator-tool/VERSION

@@ -1 +1 @@
-0.2.4-dev0
+0.2.3-dev0

transforms/images/image-calculator-tool/plugin.json

@@ -1,14 +1,14 @@
 {
   "name": "Image Calculator",
-  "version": "0.2.4-dev0",
+  "version": "0.2.3-dev0",
   "title": "Image Calculator",
   "description": "Perform simple mathematical operations on images.",
   "author": "Nick Schaub (nick.schaub@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/image-calculator-tool:0.2.4-dev0",
+  "containerId": "polusai/image-calculator-tool:0.2.3-dev0",
   "baseCommand": [
     "python3",
     "-m",

transforms/images/image-calculator-tool/pyproject.toml

@@ -5,7 +5,7 @@ requires-python = ">=3.11"
 
 [tool.poetry]
 name = "polus-images-transforms-images-image-calculator"
-version = "0.2.4-dev0"
+version = "0.2.3-dev0"
 description = ""
 authors = [
     "Nicholas Schaub <nick.schaub@nih.gov>",

transforms/images/image-calculator-tool/src/polus/images/transforms/images/image_calculator/__init__.py

@@ -6,4 +6,4 @@
 from .calculator import Operation
 from .calculator import process_image
 
-__version__ = "0.2.4-dev0"
+__version__ = "0.2.3-dev0"

transforms/images/polus-apply-flatfield-plugin/pyproject.toml

@@ -0,0 +1,18 @@
+[project]
+name = "polus-apply-flatfield-plugin"
+version = "1.2.0"
+requires-python = ">=3.13"
+dependencies = [
+    "bfio>=2.5.0",
+    "filepattern>=2.2.1",
+]
+
+[build-system]
+requires = ["setuptools>=61.0", "wheel"]
+build-backend = "setuptools.build_meta"
+
+[tool.setuptools.package-dir]
+"" = "src"
+
+[tool.setuptools]
+py-modules = ["main"]

transforms/images/polus-apply-flatfield-plugin/src/main.py

@@ -2,12 +2,12 @@
 import logging
 import os
 import typing
+from concurrent.futures import ProcessPoolExecutor, ThreadPoolExecutor
 from pathlib import Path
 
 from bfio import BioReader, BioWriter
 from filepattern import FilePattern
 import numpy as np
-from preadator import ProcessManager
 
 FILE_EXT = os.environ.get("POLUS_EXT", None)
 FILE_EXT = FILE_EXT if FILE_EXT is not None else ".ome.tif"
@@ -21,61 +21,57 @@ def unshade_images(
     flatfield: np.ndarray,
     darkfield: np.ndarray = None,
 ):
-    with ProcessManager.process():
-
-        # Initialize the output
-        X = flatfield.shape[1]
-        Y = flatfield.shape[0]
-        N = len(flist)
-
-        img_stack = np.zeros((N, Y, X), dtype=np.float32)
-
-        # Load the images
-        def load_and_store(fname, ind):
-            with ProcessManager.thread() as active_threads:
-                with BioReader(fname["file"], max_workers=active_threads.count) as br:
-                    img_stack[ind, ...] = np.squeeze(br[:, :, 0, 0, 0])
-
-        for ind, fname in enumerate(flist):
-            ProcessManager.submit_thread(load_and_store, fname, ind)
-
-        ProcessManager.join_threads(5)
-
-        # Apply flatfield correction
-        if darkfield is not None:
-            img_stack -= darkfield
-
-        img_stack /= flatfield
-
-        # Save outputs
-        def save_output(fname, ind):
-            with ProcessManager.thread() as active_threads:
-                with BioReader(fname["file"], max_workers=active_threads.count) as br:
-
-                    # replace the file name extension if needed
-                    inp_image = fname["file"]
-                    extension = "".join(
-                        [
-                            suffix
-                            for suffix in inp_image.suffixes[-2:]
-                            if len(suffix) < 6
-                        ]
-                    )
-                    out_path = out_dir.joinpath(
-                        inp_image.name.replace(extension, FILE_EXT)
-                    )
-
-                    with BioWriter(
-                        out_path,
-                        metadata=br.metadata,
-                        max_workers=active_threads.count,
-                    ) as bw:
-                        bw[:] = img_stack[ind].astype(bw.dtype)
-
-        for ind, fname in enumerate(flist):
-            ProcessManager.submit_thread(save_output, fname, ind)
-
-        ProcessManager.join_threads(5)
+    max_workers = 5
+    # Initialize the output
+    X = flatfield.shape[1]
+    Y = flatfield.shape[0]
+    N = len(flist)
+
+    img_stack = np.zeros((N, Y, X), dtype=np.float32)
+
+    # Load the images
+    def load_and_store(fname, ind):
+        with BioReader(fname["file"], max_workers=max_workers) as br:
+            img_stack[ind, ...] = np.squeeze(br[:, :, 0, 0, 0])
+
+    with ThreadPoolExecutor(max_workers=max_workers) as executor:
+        futures = [
+            executor.submit(load_and_store, fname, ind)
+            for ind, fname in enumerate(flist)
+        ]
+        for f in futures:
+            f.result()
+
+    # Apply flatfield correction
+    if darkfield is not None:
+        img_stack -= darkfield
+
+    img_stack /= flatfield
+
+    # Save outputs
+    def save_output(fname, ind):
+        with BioReader(fname["file"], max_workers=max_workers) as br:
+            inp_image = fname["file"]
+            extension = "".join(
+                [suffix for suffix in inp_image.suffixes[-2:] if len(suffix) < 6]
+            )
+            out_path = out_dir.joinpath(
+                inp_image.name.replace(extension, FILE_EXT)
+            )
+            with BioWriter(
+                out_path,
+                metadata=br.metadata,
+                max_workers=max_workers,
+            ) as bw:
+                bw[:] = img_stack[ind].astype(bw.dtype)
+
+    with ThreadPoolExecutor(max_workers=max_workers) as executor:
+        futures = [
+            executor.submit(save_output, fname, ind)
+            for ind, fname in enumerate(flist)
+        ]
+        for f in futures:
+            f.result()
 
 
 def unshade_batch(
@@ -97,17 +93,19 @@ def unshade_batch(
     if batches[-1] != len(files):
         batches.append(len(files))
 
-    for i_start, i_end in zip(batches[:-1], batches[1:]):
-
-        ProcessManager.submit_process(
-            unshade_images,
-            files[i_start:i_end],
-            out_dir,
-            brightfield_image,
-            darkfield_image,
-        )
-
-    ProcessManager.join_processes()
+    with ProcessPoolExecutor() as executor:
+        futures = [
+            executor.submit(
+                unshade_images,
+                files[i_start:i_end],
+                out_dir,
+                brightfield_image,
+                darkfield_image,
+            )
+            for i_start, i_end in zip(batches[:-1], batches[1:])
+        ]
+        for f in futures:
+            f.result()
 
 
 def main(
@@ -134,9 +132,6 @@ def main(
     group_by = [v for v in fp.variables if v not in ff_files.variables]
     GROUPED = group_by + ["file"]
 
-    ProcessManager.init_processes("main", "unshade")
-    logger.info(f"Running with {ProcessManager.num_processes()} processes.")
-
     for files in fp(group_by=group_by):
 
         flat_path = ff_files.get_matching(
@@ -168,8 +163,6 @@ def main(
 
         unshade_batch(files, outDir, flat_path, dark_path, photo_path)
 
-    # ProcessManager.join_processes()
-
 
 if __name__ == "__main__":
     """Initialize the logger"""

transforms/images/polus-apply-flatfield-plugin/src/requirements.txt

@@ -1,3 +1,2 @@
-bfio==2.1.9
-filepattern==1.4.7
-preadator==0.2.0
+bfio>=2.5.0
+filepattern>=2.2.1

transforms/images/polus-autocropping-plugin/src/autocrop_utils/helpers.py

@@ -1,4 +1,3 @@
-"""Helpers for tiles, strips, distograms, gradients, and bounding boxes."""
 from collections.abc import Generator
 from pathlib import Path
 from typing import Optional

transforms/images/polus-ftl-label-plugin/pyproject.toml

@@ -0,0 +1,12 @@
+[project]
+name = "polus-ftl-label-plugin"
+version = "0.3.10"
+requires-python = ">=3.13"
+dependencies = [
+    "numpy>=2.4.3",
+    "bfio>=2.5.0",
+]
+
+[build-system]
+requires = ["setuptools>=41.0.0", "wheel", "setuptools_rust>=0.10.2"]
+build-backend = "setuptools.build_meta"