add pixel_size testing

src/ngio/ngff_meta/fractal_image_meta.py

@@ -105,7 +105,9 @@ def __str__(self) -> str:
         return f"PixelSize(x={self.x}, y={self.y}, z={self.z}, unit={self.unit.value})"
 
     @classmethod
-    def from_list(cls, sizes: list[float], unit: SpaceUnits) -> "PixelSize":
+    def from_list(
+        cls, sizes: list[float], unit: SpaceUnits = SpaceUnits.micrometer
+    ) -> "PixelSize":
         """Build a PixelSize object from a list of sizes.
 
         Note: The order of the sizes must be z, y, x.
@@ -115,7 +117,7 @@ def from_list(cls, sizes: list[float], unit: SpaceUnits) -> "PixelSize":
             unit(SpaceUnits): The unit of the sizes.
         """
         if len(sizes) == 2:
-            return cls(y=sizes[0], x=sizes[1], unit=unit)
+            return cls(y=sizes[0], x=sizes[1], z=1, unit=unit)
         elif len(sizes) == 3:
             return cls(z=sizes[0], y=sizes[1], x=sizes[2], unit=unit)
         else:
@@ -135,10 +137,12 @@ def yx(self) -> tuple:
         """Return the xy plane pixel size in y, x order."""
         return self.y, self.x
 
+    @property
     def voxel_volume(self) -> float:
         """Return the volume of a voxel."""
-        return self.y * self.x * (self.z or 1)
+        return self.y * self.x * self.z
 
+    @property
     def xy_plane_area(self) -> float:
         """Return the area of the xy plane."""
         return self.y * self.x

tests/ngff_meta/test_pixel_size.py

@@ -0,0 +1,27 @@
+import pytest
+
+
+class TestPixelSize:
+    def test_pixel_size_from_list(self) -> None:
+        from ngio.ngff_meta import PixelSize
+
+        pix_size_2d = PixelSize.from_list([0.1625, 0.1625])
+        assert pix_size_2d.zyx == (1.0, 0.1625, 0.1625)
+
+        pix_size_3d = PixelSize.from_list([0.1625, 0.1625, 0.1625])
+        assert pix_size_3d.zyx == (0.1625, 0.1625, 0.1625)
+
+        with pytest.raises(ValueError):
+            PixelSize.from_list([0.1625, 0.1625, 0.1625, 0.1625])
+
+    def test_pixel_size(self) -> None:
+        from ngio.ngff_meta import PixelSize
+
+        pixel_size = PixelSize(x=0.1625, y=0.1625, z=0.25)
+        assert pixel_size.zyx == (0.25, 0.1625, 0.1625)
+        assert pixel_size.yx == (0.1625, 0.1625)
+        assert pixel_size.voxel_volume == 0.1625 * 0.1625 * 0.25
+        assert pixel_size.xy_plane_area == 0.1625 * 0.1625
+
+        plixel_size2 = PixelSize(x=0.1625, y=0.1625, z=0.5)
+        assert pixel_size.distance(plixel_size2) == 0.25