test

brainlit/utils/tests/test_write.py

@@ -1,7 +1,12 @@
 import pytest
 import zarr
 import numpy as np
-from brainlit.utils.write import zarr_to_omezarr, czi_to_zarr, write_trace_layer
+from brainlit.utils.write import (
+    zarr_to_omezarr,
+    zarr_to_omezarr_single,
+    czi_to_zarr,
+    write_trace_layer,
+)
 import os
 import shutil
 import zipfile
@@ -87,6 +92,27 @@ def test_writeome_baddim(init_3dzarr, init_4dzarr):
     shutil.rmtree(out_path)
 
 
+def test_writeome_single_baddim(init_3dzarr, init_4dzarr):
+    # error for 4d zarrs
+    zarr_path, data_dir = init_4dzarr
+    out_path = data_dir / "fg_ome.zarr"
+    with pytest.raises(ValueError, match=r"Conversion only supported for 3D arrays"):
+        zarr_to_omezarr_single(zarr_path=zarr_path, out_path=out_path, res=[1, 1, 1])
+
+    # error if ome already exists
+    zarr_path, data_dir = init_3dzarr
+    out_path = data_dir / "fg_ome.zarr"
+    zarr_to_omezarr_single(zarr_path=zarr_path, out_path=out_path, res=[1, 1, 1])
+
+    with pytest.raises(
+        ValueError,
+        match=f"{out_path} already exists, please delete the existing file or change the name of the ome-zarr to be created.",
+    ):
+        zarr_to_omezarr_single(zarr_path=zarr_path, out_path=out_path, res=[1, 1, 1])
+
+    shutil.rmtree(out_path)
+
+
 def test_writezarr_badpar(init_4dczi):
     czi_path, data_dir = init_4dczi
     with pytest.raises(ValueError, match="parallel must be positive integer, not 1"):
@@ -159,6 +185,39 @@ def test_writeome(init_3dzarr):
         )
 
 
+def test_writeome_single(init_3dzarr):
+    res = [1, 1, 2]  # in nm
+    dimension_map = {"x": 0, "y": 1, "z": 2}
+    zarr_path, data_dir = init_3dzarr
+    out_path = data_dir / "fg_ome_single.zarr"
+
+    assert not os.path.exists(out_path)
+    zarr_to_omezarr_single(zarr_path=zarr_path, out_path=out_path, res=res)
+    assert os.path.exists(out_path)
+
+    # check units are micrometers
+    ome_zarr = zarr.open(out_path)
+    metadata = ome_zarr.attrs["multiscales"][0]
+
+    dimension_names = []
+    for dimension in metadata["axes"]:
+        assert dimension["unit"] == "micrometer"
+        assert dimension["type"] == "space"
+        dimension_names.append(dimension["name"])
+
+    # check resolutions are multiples of 2 scaled in xy
+    for resolution in metadata["datasets"]:
+        lvl = int(resolution["path"])
+        true_res = np.multiply(res, [2**lvl, 2**lvl, 1]) / 1000  # in microns
+        true_res = [
+            true_res[dimension_map[dimension_name]]
+            for dimension_name in dimension_names
+        ]
+        np.testing.assert_almost_equal(
+            true_res, resolution["coordinateTransformations"][0]["scale"], decimal=3
+        )
+
+
 def test_write_trace_layer(init_omezarr):
     data_dir, res = init_omezarr
 

brainlit/utils/write.py

@@ -220,7 +220,11 @@ def zarr_to_omezarr_single(zarr_path: str, out_path: str, res: list, parallel: i
                 "coordinateTransformations": [
                     {
                         "type": "scale",
-                        "scale": [res[2], res[0] * 2**lvl, res[1] * 2**lvl],
+                        "scale": [
+                            res[2] / 1000,
+                            res[0] * 2**lvl / 1000,
+                            res[1] * 2**lvl / 1000,
+                        ],
                     }
                 ],
             }