Lambda: Update arcadia-microscopy-tools to 0.4.1

lambda/pyproject.toml

@@ -4,7 +4,7 @@ version = "0.2.0"
 requires-python = ">=3.12"
 dependencies = [
     "data-hub-shared",
-    "arcadia-microscopy-tools>=0.3.2",
+    "arcadia-microscopy-tools>=0.4.1",
     "aws-lambda-typing>=2.20.0",
     "click>=8.1",
     "matplotlib>=3.8",

lambda/src/data_hub_lambda/hina_microscope/image_processing.py

@@ -64,7 +64,7 @@ def _render_rgb(self) -> NDArray[np.float64]:
         """Produce the RGB overlay for the loaded image."""
         per_channel_2d: dict[Channel, NDArray[np.float64]] = {}
         for channel in self.image.channels:
-            intensities = self.image.get_intensities_from_channel(channel)
+            intensities = self.image.get_channel_intensities(channel)
             reduced = self._reduce_to_2d(intensities, self._non_channel_axes())
             per_channel_2d[channel] = _rescale_percentile(reduced, CONTRAST_PERCENTILES)
 

lambda/src/data_hub_lambda/hina_microscope/parse_metadata.py

@@ -26,7 +26,7 @@ def parse_metadata(image: MicroscopyImage) -> dict[str, Any]:
 
 
 def _channel_to_dict(channel: Channel) -> dict[str, Any]:
-    color = channel.color.hex_code if channel.color is not None else None
+    color = channel.color.lower()
     return {
         "name": channel.name,
         "excitation_nm": channel.excitation_nm,

lambda/tests/hina_microscope/test_parse_metadata.py

@@ -121,18 +121,18 @@ def test_channel_without_wavelengths(self) -> None:
         assert result["emission_nm"] is None
         assert result["color"] == "#ffffff"
 
-    def test_channel_with_none_color(self) -> None:
+    def test_channel_color_normalized_to_lowercase(self) -> None:
         from arcadia_microscopy_tools.channels import Channel
 
-        bare = Channel(name="CUSTOM", excitation_nm=500, emission_nm=520, color=None)
+        custom = Channel(name="CUSTOM", excitation_nm=500, emission_nm=520, color="#AABBCC")
 
-        result = _channel_to_dict(bare)
+        result = _channel_to_dict(custom)
 
         assert result == {
             "name": "CUSTOM",
             "excitation_nm": 500,
             "emission_nm": 520,
-            "color": None,
+            "color": "#aabbcc",
         }