Pass metadata (#464)

* pass plate metadata through reconstruction if it exists * simple test * bug fix * use zattrs.update Co-authored-by: Ziwen Liu <[email protected]> * add all metadata then remove `plate` Co-authored-by: Ziwen Liu <[email protected]> --------- Co-authored-by: Ziwen Liu <[email protected]>
mehta-lab · Dec 20, 2023 · 57f611e · 57f611e
1 parent b9ccc93
commit 57f611e
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diff --git a/recOrder/cli/apply_inverse_transfer_function.py b/recOrder/cli/apply_inverse_transfer_function.py
@@ -1,4 +1,5 @@
 import itertools
+import warnings
 from functools import partial
 from pathlib import Path
 
@@ -34,6 +35,19 @@ def _check_background_consistency(background_shape, data_shape):
 
 
 def get_reconstruction_output_metadata(position_path: Path, config_path: Path):
+    # Get non-OME-Zarr plate-level metadata if it's available
+    plate_metadata = {}
+    try:
+        input_plate = open_ome_zarr(
+            position_path.parent.parent.parent, mode="r"
+        )
+        plate_metadata = dict(input_plate.zattrs)
+        plate_metadata.pop("plate")
+    except RuntimeError:
+        warnings.warn(
+            "Position is not part of a plate...no plate metadata will be copied."
+        )
+
     # Load the first position to infer dataset information
     input_dataset = open_ome_zarr(str(position_path), mode="r")
     T, _, Z, Y, X = input_dataset.data.shape
@@ -76,6 +90,7 @@ def get_reconstruction_output_metadata(position_path: Path, config_path: Path):
         "scale": input_dataset.scale,
         "channel_names": channel_names,
         "dtype": np.float32,
+        "plate_metadata": plate_metadata,
     }
 
 

diff --git a/recOrder/cli/utils.py b/recOrder/cli/utils.py
@@ -17,6 +17,7 @@ def create_empty_hcs_zarr(
     scale: Tuple[float],
     channel_names: list[str],
     dtype: DTypeLike,
+    plate_metadata: dict = {},
 ) -> None:
     """If the plate does not exist, create an empty zarr plate.
 
@@ -36,13 +37,17 @@ def create_empty_hcs_zarr(
     channel_names : list[str]
         Channel names, will append if not present in metadata.
     dtype : DTypeLike
+    plate_metadata : dict
     """
 
     # Create plate
     output_plate = open_ome_zarr(
         str(store_path), layout="hcs", mode="a", channel_names=channel_names
     )
 
+    # Pass metadata
+    output_plate.zattrs.update(plate_metadata)
+
     # Create positions
     for position_key in position_keys:
         position_key_string = "/".join(position_key)

diff --git a/recOrder/tests/util_tests/test_create_empty.py b/recOrder/tests/util_tests/test_create_empty.py
@@ -17,13 +17,22 @@ def test_create_empty_hcs_zarr():
     scale = (1, 1, 1, 0.5, 0.5)
     channel_names = ["Channel1", "Channel2"]
     dtype = np.uint16
+    plate_metadata = {"test": 2}
 
     create_empty_hcs_zarr(
-        store_path, position_keys, shape, chunks, scale, channel_names, dtype
+        store_path,
+        position_keys,
+        shape,
+        chunks,
+        scale,
+        channel_names,
+        dtype,
+        plate_metadata,
     )
 
     # Verify existence of positions and channels
     with open_ome_zarr(store_path, mode="r") as plate:
+        assert plate.zattrs["test"] == 2
         for position_key in position_keys:
             position = plate["/".join(position_key)]
             assert isinstance(position, Position)