Feature/nd2reader-xarray-ome-metadata (#533)

* include parsed ome metadata as attrs of returned xarray DataArray * update tests to reflect change in type of metadata returned by reader
AllenCellModeling · Oct 18, 2023 · 942cc53 · 942cc53
1 parent e12198a
commit 942cc53
Show file tree

Hide file tree

Showing 2 changed files with 24 additions and 3 deletions.
diff --git a/aicsimageio/readers/nd2_reader.py b/aicsimageio/readers/nd2_reader.py
@@ -85,6 +85,14 @@ def _xarr_reformat(self, delayed: bool) -> xr.DataArray:
                 xarr.attrs[constants.METADATA_UNPROCESSED][
                     "frame"
                 ] = rdr.frame_metadata(self.current_scene_index)
+
+            # include OME metadata as attrs of returned xarray.DataArray if possible
+            # (not possible with `nd2` version < 0.7.0; see PR #521)
+            try:
+                xarr.attrs[constants.METADATA_PROCESSED] = self.ome_metadata
+            except NotImplementedError:
+                pass
+
         return xarr.isel({nd2.AXIS.POSITION: 0}, missing_dims="ignore")
 
     @property

diff --git a/aicsimageio/tests/readers/extra_readers/test_nd2_reader.py b/aicsimageio/tests/readers/extra_readers/test_nd2_reader.py
@@ -31,7 +31,8 @@
     "expected_dtype, "
     "expected_dims_order, "
     "expected_channel_names, "
-    "expected_physical_pixel_sizes",
+    "expected_physical_pixel_sizes, "
+    "expected_metadata_type",
     [
         pytest.param(
             "example.txt",
@@ -42,6 +43,7 @@
             None,
             None,
             None,
+            None,
             marks=pytest.mark.xfail(raises=exceptions.UnsupportedFileFormatError),
         ),
         pytest.param(
@@ -53,6 +55,7 @@
             "TCYX",
             ["20phase", "20xDiO"],
             (1, 50, 50),
+            dict,
         ),
         (
             "ND2_jonas_header_test2.nd2",
@@ -63,6 +66,7 @@
             "CTZYX",
             ["Jonas_DIC"],
             (0.5, 0.12863494437945, 0.12863494437945),
+            OME,
         ),
         (
             "ND2_maxime_BF007.nd2",
@@ -73,6 +77,7 @@
             "CYX",
             ["405/488/561/633nm"],
             (1.0, 0.158389678930686, 0.158389678930686),
+            OME,
         ),
         (
             "ND2_dims_p4z5t3c2y32x32.nd2",
@@ -83,6 +88,7 @@
             "TZCYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_c2y32x32.nd2",
@@ -93,6 +99,7 @@
             "CYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_p1z5t3c2y32x32.nd2",
@@ -103,6 +110,7 @@
             "TZCYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_p2z5t3-2c4y32x32.nd2",
@@ -113,6 +121,7 @@
             "TZCYX",
             ["Widefield Green", "Widefield Red", "Widefield Far-Red", "Brightfield"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_t3c2y32x32.nd2",
@@ -123,6 +132,7 @@
             "TCYX",
             ["Widefield Green", "Widefield Red"],
             (1.0, 0.652452890023035, 0.652452890023035),
+            OME,
         ),
         (
             "ND2_dims_rgb_t3p2c2z3x64y64.nd2",
@@ -133,6 +143,7 @@
             "TZCYXS",
             ["Brightfield", "Brightfield"],
             (0.01, 0.34285714285714286, 0.34285714285714286),
+            OME,
         ),
         (
             "ND2_dims_rgb.nd2",
@@ -143,6 +154,7 @@
             "CYXS",
             ["Brightfield"],
             (1.0, 0.34285714285714286, 0.34285714285714286),
+            OME,
         ),
     ],
 )
@@ -156,6 +168,7 @@ def test_nd2_reader(
     expected_dims_order: str,
     expected_channel_names: List[str],
     expected_physical_pixel_sizes: Tuple[float, float, float],
+    expected_metadata_type: Union[type, Tuple[Union[type, Tuple[Any, ...]], ...]],
 ) -> None:
     # Construct full filepath
     uri = get_resource_full_path(filename, host)
@@ -172,7 +185,7 @@ def test_nd2_reader(
         expected_dims_order=expected_dims_order,
         expected_channel_names=expected_channel_names,
         expected_physical_pixel_sizes=expected_physical_pixel_sizes,
-        expected_metadata_type=dict,
+        expected_metadata_type=expected_metadata_type,
     )
 
 
@@ -196,7 +209,7 @@ def test_nd2_reader(
             dimensions.DEFAULT_DIMENSION_ORDER,
             ["Jonas_DIC"],
             (0.5, 0.12863494437945, 0.12863494437945),
-            dict,
+            OME,
         ),
     ],
 )