updated bfio dependency and tests

PolusAI · Sep 30, 2024 · dc3f634 · dc3f634
1 parent dcdb6b1
commit dc3f634
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Showing 4 changed files with 19 additions and 12 deletions.
diff --git a/formats/ome-converter-tool/Dockerfile b/formats/ome-converter-tool/Dockerfile
@@ -1,4 +1,4 @@
-FROM polusai/bfio:2.4.3
+FROM polusai/bfio:2.4.4
 
 # environment variables defined in polusai/bfio
 ENV EXEC_DIR="/opt/executables"

diff --git a/formats/ome-converter-tool/pyproject.toml b/formats/ome-converter-tool/pyproject.toml
@@ -12,7 +12,7 @@ packages = [{include = "polus", from = "src"}]
 
 [tool.poetry.dependencies]
 python = ">=3.9,<3.12"
-bfio = {version = "^2.4.3", 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/src/polus/images/formats/ome_converter/image_converter.py b/formats/ome-converter-tool/src/polus/images/formats/ome_converter/image_converter.py
@@ -28,6 +28,8 @@
 
 
 def write_image(
+    br: BioReader,
+    c: int,
     image: np.ndarray,
     out_path: pathlib.Path,
     max_workers: int,
@@ -40,8 +42,8 @@ def write_image(
     and manages channel names based on the provided BioReader.
 
     Args:
-        c: The index of the channel in the image.
         br:  An instance of BioReader containing metadata for the image.
+        c: The index of the channel in the image.
         image: The image data to be written.
         out_path: Path to an output image.
         max_workers: The maximum number of worker threads to use for writing.
@@ -54,7 +56,8 @@ def write_image(
         max_workers,
     ) as bw:
         # Handling of parsing channels when channels names are not provided.
-        # if bw.channel_names != [None]:
+        if bw.channel_names != [None]:
+            bw.channel_names = [br.channel_names[c]]
         bw.C = 1
         bw.T = 1
         bw.Z = 1
@@ -126,6 +129,8 @@ def convert_image(
                     t,
                 ]
                 write_image(
+                    br=br,
+                    c=c,
                     image=image,
                     out_path=out_path,
                     max_workers=NUM_THREADS,

diff --git a/formats/ome-converter-tool/tests/conftest.py b/formats/ome-converter-tool/tests/conftest.py
@@ -10,7 +10,6 @@
 import pytest
 import requests
 import skimage.data
-import skimage.io
 import skimage.measure
 
 
@@ -52,15 +51,18 @@ def synthetic_images(
     size, extension = get_params
 
     syn_dir = pathlib.Path(tempfile.mkdtemp(suffix="_syn_data"))
+
     images: list[numpy.ndarray] = []
-    for i in range(5):
-        # Create images
-        blobs: numpy.ndarray = skimage.data.binary_blobs(
-            length=size,
-            volume_fraction=0.05,
-            blob_size_fraction=0.05,
+    # Create a random number generator
+    rng = numpy.random.default_rng()
+
+    for i in range(3):
+        syn_img: numpy.ndarray = rng.integers(
+            low=0,
+            high=256,
+            size=(size, size),
+            dtype=numpy.uint8,
         )
-        syn_img: numpy.ndarray = skimage.measure.label(blobs)
         outname = f"syn_image_{i}{extension}"
 
         # Save image