Fix zarr metadata writing error

pyproject.toml

@@ -5,7 +5,7 @@ requires = [
   "setuptools", 
   "wheel",
   "imagecodecs>=2021.2.26",
-  "numpy<2.0.0",
+  "numpy",
   "ome-types>=0.4.2",
   "zarr>=2.6.1",
   "scyjava",
@@ -21,7 +21,7 @@ name = "bfio"
 dynamic = ["version"]
 dependencies = [
     "imagecodecs>=2021.2.26",
-    "numpy<2.0.0",
+    "numpy",
     "ome-types>=0.4.2",
     "zarr>=2.6.1",
     "scyjava",

src/bfio/bfio.py

@@ -1042,6 +1042,17 @@ class if specified. *Defaults to None.*
             self._metadata.images[0].pixels.dimension_order = (
                 ome_types.model.Pixels_DimensionOrder.XYZCT
             )
+            # overwrite values in metadata if explicitly specified in the constructor
+            if kwargs:
+                for k, v in kwargs.items():
+                    setattr(self, k, v)
+                    if k in ("YXZCT"):
+                        setattr(
+                            self._metadata.images[0].pixels,
+                            "size_{}".format(k.lower()),
+                            v,
+                        )
+
         else:
             self._metadata = self._minimal_xml()
 

tests/test_write.py

@@ -9,6 +9,7 @@
 TEST_IMAGES = {
     "Plate1-Blue-A-12-Scene-3-P3-F2-03.czi": "https://downloads.openmicroscopy.org/images/Zeiss-CZI/idr0011/Plate1-Blue-A_TS-Stinger/Plate1-Blue-A-12-Scene-3-P3-F2-03.czi",
     "5025551.zarr": "https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0054A/5025551.zarr",
+    "0.tif": "https://osf.io/j6aer/download",
 }
 
 TEST_DIR = pathlib.Path(__file__).with_name("data")
@@ -43,12 +44,14 @@ def setUpModule():
                 shutil.rmtree(TEST_DIR.joinpath(file))
             zarr_download(url, str(TEST_DIR))
 
+
 def tearDownModule():
     """Remove test images"""
 
     logger.info("teardown - Removing test images...")
     shutil.rmtree(TEST_DIR)
 
+
 class TestOmeTiffWrite(unittest.TestCase):
     @classmethod
     def setUpClass(self):
@@ -110,25 +113,46 @@ def test_write_zarr_tensorstore(self):
 
             actual_shape = br.shape
             actual_dtype = br.dtype
-
             actual_image = br[:]
-
             actual_mdata = br.metadata
-
         with tempfile.TemporaryDirectory() as dir:
 
             # Use the temporary directory
-            test_file_path = os.path.join(dir, 'out/test.ome.zarr')
+            test_file_path = os.path.join(dir, "out/test.ome.zarr")
 
-            with bfio.BioWriter(test_file_path, metadata=actual_mdata, backend="tensorstore") as bw:
+            with bfio.BioWriter(
+                test_file_path, metadata=actual_mdata, backend="tensorstore"
+            ) as bw:
 
                 expanded = np.expand_dims(actual_image, axis=-1)
                 bw[:] = expanded
 
             with bfio.BioReader(test_file_path) as br:
 
-
                 assert br.shape == actual_shape
                 assert br.dtype == actual_dtype
 
                 assert br[:].sum() == actual_image.sum()
+
+    def test_overwrite_metadata(self):
+
+        with bfio.BioReader(str(TEST_DIR.joinpath("0.tif"))) as br:
+            with tempfile.TemporaryDirectory() as dir:
+
+                # Use the temporary directory
+                test_file_path = os.path.join(dir, "out/0.ome.zarr")
+
+                with bfio.BioWriter(
+                    test_file_path,
+                    metadata=br.metadata,
+                    backend="tensorstore",
+                    Z=br.Z * 2,
+                ) as bw:
+
+                    bw[:, :, 0, :, :] = br[:]
+                    bw[:, :, 1, :, :] = br[:]
+
+                    bw_z_dim = bw.Z
+
+                with bfio.BioReader(test_file_path) as br2:
+                    assert br2.Z == bw_z_dim