PolusAI · nishaq503 · Sep 18, 2024
@@ -1,6 +1,6 @@
 [bumpversion]
-current_version = 2.0.1
-commit = False
+current_version = 2.1.0-dev0
+commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
 serialize = 

@@ -1,4 +1,4 @@
-# Apply Flatfield Plugin (v2.0.1)
+# Apply Flatfield Plugin (v2.1.0-dev0)
 
 This WIPP plugin applies a flatfield operation on every image in a collection.
 The algorithm used to apply the flatfield is as follows:

@@ -1 +1 @@
-2.0.1
+2.1.0-dev0
@@ -1,14 +1,14 @@
 {
   "name": "Apply Flatfield",
-  "version": "2.0.1",
+  "version": "2.1.0-dev0",
   "title": "Apply Flatfield",
   "description": "Apply a flatfield algorithm to a collection of images.",
   "author": "Nick Schaub ([email protected]), Najib Ishaq ([email protected])",
   "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:2.1.0-dev0",
   "baseCommand": [
     "python3",
     "-m",

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-transforms-images-apply-flatfield"
-version = "2.0.1"
+version = "2.1.0-dev0"
 description = ""
 authors = [
     "Nick Schaub <[email protected]>",
@@ -11,10 +11,10 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bfio = { version = "^2.3.3", extras = ["all"] }
+bfio = { version = "^2.4.3", extras = ["all"] }
 filepattern = "2.0.4"
 typer = { version = "^0.7.0", extras = ["all"] }
-numpy = "^1.24.3"
+numpy = "^2.0.0"
 tqdm = "^4.65.0"
 preadator = "0.4.0-dev2"
 

@@ -3,4 +3,4 @@
 from . import utils
 from .apply_flatfield import apply
 
-__version__ = "2.0.1"
+__version__ = "2.1.0-dev0"
@@ -134,7 +134,8 @@ def _unshade_batch(
     batch_paths: list[pathlib.Path],
     out_dir: pathlib.Path,
     ff_image: numpy.ndarray,
-    df_image: typing.Optional[numpy.ndarray] = None,
+    df_image: typing.Optional[numpy.ndarray],
+    dtype: numpy.dtype = numpy.float32,
 ) -> None:
     """Apply flatfield correction to a batch of images.
 
@@ -143,6 +144,7 @@ def _unshade_batch(
         out_dir: directory to save the corrected images
         ff_image: component to be used for flatfield correction
         df_image: component to be used for flatfield correction
+        dtype: data type to use for the corrected images
     """
     # Load images
     with preadator.ProcessManager(
@@ -160,11 +162,11 @@ def _unshade_batch(
         images = [f.result() for f in load_futures]
 
     images = [img for _, img in sorted(images, key=operator.itemgetter(0))]
-    img_stack = numpy.stack(images, axis=0).astype(numpy.float32)
+    img_stack = numpy.stack(images, axis=0).astype(dtype)
 
     # Apply flatfield correction
     if df_image is not None:
-        img_stack -= df_image
+        img_stack -= df_image.astype(dtype)
 
     img_stack /= ff_image + 1e-8
 

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.4.2
+current_version = 1.5.0-dev0
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?

@@ -1,4 +1,4 @@
-# Image Assembler (1.4.2)
+# Image Assembler (1.5.0-dev0)
 
 This WIPP plugin assembles images into a stitched image using an image stitching
 vector. It can assemble 2d and z-stacked images. When assembling z-stacked images,

@@ -1 +1 @@
-1.4.2
+1.5.0-dev0
@@ -1,14 +1,14 @@
 {
   "name": "Image Assembler",
-  "version": "1.4.2",
+  "version": "1.5.0-dev0",
   "title": "Image Assembler",
   "description": "A scalable image assembling plugin.",
   "author": "Nick Schaub ([email protected]), Antoine Gerardin ([email protected])",
   "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-assembler-tool:1.4.2",
+  "containerId": "polusai/image-assembler-tool:1.5.0-dev0",
   "baseCommand": [
     "python3",
     "-m",

@@ -1,18 +1,18 @@
 [tool.poetry]
 name = "polus-images-transforms-images-image-assembler"
-version = "1.4.2"
+version = "1.5.0-dev0"
 description = "A scalable image assembler plugin."
 authors = ["Nick Schaub <[email protected]>", "Antoine Gerardin <[email protected]>"]
 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"
+bfio = {version = "^2.4.3", extras = ["all"]}
+filepattern = "^2.0.4"
 preadator = "0.4.0.dev2"
 typer = "^0.7.0"
-numpy = "<2.0.0"
+numpy = "^2.0.0"
 
 
 [tool.poetry.group.dev.dependencies]

@@ -1,6 +1,6 @@
 """Image Assembler Plugin."""
 
-__version__ = "1.4.2"
+__version__ = "1.5.0-dev0"
 
 from .image_assembler import (  # noqa
     assemble_images,

@@ -1,7 +1,6 @@
 """Package entrypoint for Image Assembler."""
 import json
 import logging
-import typing
 from os import environ
 from pathlib import Path
 
@@ -38,7 +37,7 @@ def generate_preview(
         timeslice_naming,
     )
 
-    preview: dict[str, typing.Union[list, str]] = {
+    preview: dict[str, list[str]] = {
         "outputDir": [],
     }
 
@@ -57,18 +56,33 @@ def main(
         "-i",
         help="""Absolute path to the input image collection
         directory to be processed by this plugin.""",
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+        resolve_path=True,
     ),
     stitch_path: Path = typer.Option(
         ...,
         "--stitchPath",
         "-s",
         help="Absolute path to a stitching vector directory.",
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        readable=True,
+        resolve_path=True,
     ),
     out_dir: Path = typer.Option(
         ...,
         "--outDir",
         "-o",
         help="Absolute path to the output collection directory.",
+        exists=True,
+        file_okay=False,
+        dir_okay=True,
+        writable=True,
+        resolve_path=True,
     ),
     timeslice_naming: bool = typer.Option(
         False,
@@ -89,18 +103,6 @@ def main(
     logger.info(f"outDir: {out_dir}")
     logger.info(f"timesliceNaming: {timeslice_naming}")
 
-    if not img_path.exists():
-        msg = "imgPath does not exist"
-        raise ValueError(msg, img_path)
-
-    if not out_dir.exists():
-        msg = "outDir does not exist"
-        raise ValueError(msg, out_dir)
-
-    if not stitch_path.exists():
-        msg = "stitchPath does not exist"
-        raise ValueError(msg, stitch_path)
-
     # if the input image collection contains a images subdirectory, we use that
     # TODO this is an artifact from WIPP integration.
     # This should eventually be removed from the implementation.

@@ -335,7 +335,7 @@ def assemble_chunk(
             chunk[
                 chunk_start_y : chunk_start_y + region_height,
                 chunk_start_x : chunk_start_x + region_width,
-            ] = data
+            ] = data.astype(bw.dtype)
 
     # completed chunk is written to disk
     # we only write what fits in the image since that the behavior bfio expects

@@ -82,4 +82,4 @@ def test_cli_bad_input(local_data: tuple[Path, Path, Path, Path]):
         ],
     )
 
-    assert result.exc_info[0] is ValueError
+    assert result.exc_info[0] is SystemExit
@@ -1,6 +1,6 @@
 [bumpversion]
-current_version = 0.2.2
-commit = False
+current_version = 0.3.0-dev0
+commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<dev>\d+))?
 serialize = 

@@ -1,4 +1,4 @@
-# Image Calculator (v0.2.2)
+# Image Calculator (v0.3.0-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.

@@ -1 +1 @@
-0.2.2
+0.3.0-dev0
@@ -1,14 +1,14 @@
 {
   "name": "Image Calculator",
-  "version": "0.2.2",
+  "version": "0.3.0-dev0",
   "title": "Image Calculator",
   "description": "Perform simple mathematical operations on images.",
   "author": "Nick Schaub ([email protected])",
   "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:0.2.2",
+  "containerId": "polusai/image-calculator-tool:0.3.0-dev0",
   "baseCommand": [
     "python3",
     "-m",

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "polus-images-transforms-images-image-calculator"
-version = "0.2.2"
+version = "0.3.0-dev0"
 description = ""
 authors = [
     "Nicholas Schaub <[email protected]>",
@@ -11,11 +11,12 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bfio = {version = "2.3.3", extras = ["all"]}
-filepattern = "2.0.4"
+bfio = {version = "^2.4.3", extras = ["all"]}
+filepattern = "^2.0.7"
 typer = "^0.7.0"
 tqdm = "^4.65.0"
 preadator = "0.4.0.dev2"
+numpy = "^2.0"
 
 [tool.poetry.group.dev.dependencies]
 pre-commit = "^3.3.3"

@@ -6,4 +6,4 @@
 from .calculator import Operation
 from .calculator import process_image
 
-__version__ = "0.2.2"
+__version__ = "0.3.0-dev0"
@@ -89,9 +89,11 @@ def _process_chunk(  # noqa: PLR0913
     operation: Operation,
 ) -> None:
     """Process on chunk of the images in a thread/process."""
+    left = primary_reader[y:y_max, x:x_max, z]
+    right = secondary_reader[y:y_max, x:x_max, z]
     writer[y:y_max, x:x_max, z] = operation.func()(
-        primary_reader[y:y_max, x:x_max, z],
-        secondary_reader[y:y_max, x:x_max, z],
+        left,
+        right.astype(primary_reader.dtype),
     )
 
 
@@ -121,6 +123,8 @@ def process_image(
 
         # Initialize the output image
         with bfio.BioWriter(out_path, metadata=primary_reader.metadata) as writer:
+            writer.dtype = primary_reader.dtype
+
             for z in range(primary_reader.Z):
                 for x in range(0, primary_reader.X, CHUNK_SIZE):
                     x_max = min(x + CHUNK_SIZE, primary_reader.X)
-Original file line number
+Diff line change
@@ Expand Up @@
             ],
         )
-        assert result.exc_info[0] is ValueError
+        assert result.exc_info[0] is SystemExit