Merge pull request #142 from fmi-faim/channel_metadata

Add test for ImageXpress transmitted light

pyproject.toml

@@ -27,7 +27,7 @@ classifiers = [
 dependencies = [
   "pydantic",
   "distributed",
-  "numpy",
+  "numpy<2",
   "matplotlib",
   "scikit-image",
   "pandas",

src/faim_ipa/io/ChannelMetadata.py

@@ -1,17 +1,17 @@
-from typing import Optional, Union
+from typing import Optional
 
-from pydantic import BaseModel, NonNegativeInt, PositiveFloat, PositiveInt
+from pydantic import BaseModel, NonNegativeInt, PositiveFloat
 
 
 class ChannelMetadata(BaseModel):
     channel_index: NonNegativeInt
     channel_name: str
     display_color: str
-    spatial_calibration_x: float
-    spatial_calibration_y: float
+    spatial_calibration_x: PositiveFloat
+    spatial_calibration_y: PositiveFloat
     spatial_calibration_units: str
-    z_spacing: Optional[PositiveFloat]
-    wavelength: Union[PositiveInt, str]
-    exposure_time: Optional[PositiveFloat]
-    exposure_time_unit: Optional[str]
+    z_spacing: Optional[PositiveFloat] = None
+    wavelength: NonNegativeInt
+    exposure_time: Optional[PositiveFloat] = None
+    exposure_time_unit: Optional[str] = None
     objective: str

src/faim_ipa/io/MetaSeriesTiff.py

@@ -4,7 +4,7 @@
 from tifffile import tifffile
 
 
-def load_metaseries_tiff_metadata(path: Path) -> tuple[ArrayLike, dict]:
+def load_metaseries_tiff_metadata(path: Path) -> dict:
     """Load parts of the metadata of a metaseries tiff file.
 
     The following metadata is collected:

tests/io/test_ChannelMetadata.py

@@ -0,0 +1,32 @@
+from faim_ipa.io.MetaSeriesTiff import load_metaseries_tiff_metadata
+from faim_ipa.io.ChannelMetadata import ChannelMetadata
+
+from pathlib import Path
+import pytest
+
+
+@pytest.fixture
+def transmission_sample_image_path():
+    return (
+        Path(__file__).parent.parent.parent
+        / "resources"
+        / "ImageXpress"
+        / "exp126-d0_C03_thumbA6B0784C-19ED-4F35-9E6A-0A306794BB11.tif"
+    )
+
+
+def test_transmission_metadata(transmission_sample_image_path):
+    metadata = load_metaseries_tiff_metadata(transmission_sample_image_path)
+    channel_metadata = ChannelMetadata(
+        channel_index=0,
+        channel_name="test_channel",
+        display_color="FFFFFF",
+        spatial_calibration_x=metadata["spatial-calibration-x"],
+        spatial_calibration_y=metadata["spatial-calibration-y"],
+        spatial_calibration_units=metadata["spatial-calibration-units"],
+        objective="4x",
+        **metadata,
+    )
+    assert channel_metadata.spatial_calibration_x == 43.3613
+    assert channel_metadata.spatial_calibration_y == 54.2016
+    assert channel_metadata.wavelength == 0