* add new test for 0.5 combination of compression with sharding

* remove 0.5 commented line
* also write regions using zarr.create_array()

Author: junelsolis

test/test_to_ngff_zarr_tensorstore.py

@@ -138,7 +138,6 @@ def test_tensorstore_already_exists_failure():
             store=zarr_path,
             multiscales=multiscales,
             use_tensorstore=True,  # Enable TensorStore
-            # version="0.5",
         )
         end_time_write = time.time()
         logger.info(

test/test_to_ngff_zarr_v3_compression.py

@@ -10,7 +10,7 @@
 
 from ngff_zarr import Methods, to_multiscales, to_ngff_zarr
 
-# from ._data import verify_against_baseline
+from ._data import verify_against_baseline
 
 zarr_version = version.parse(zarr.__version__)
 
@@ -23,20 +23,17 @@
 def test_zarr_v3_compression(input_images):
     dataset_name = "cthead1"
     image = input_images[dataset_name]
-    # baseline_name = "2_4/RFC3_GAUSSIAN.zarr"
+    baseline_name = "2_4/RFC3_GAUSSIAN.zarr"
     chunks = (64, 64)
     multiscales = to_multiscales(
         image, [2, 4], chunks=chunks, method=Methods.ITKWASM_GAUSSIAN
     )
-    # store = zarr.storage.MemoryStore()
 
     compressors = zarr.codecs.BloscCodec(
         cname="zlib", clevel=5, shuffle=zarr.codecs.BloscShuffle.shuffle
     )
 
-    # chunks_per_shard = 2
-    # Test this with sharding also
-
+    # Test writing OME-Zarr 0.5 with compression
     version = "0.5"
     with tempfile.TemporaryDirectory() as tmpdir:
         to_ngff_zarr(tmpdir, multiscales, version=version, compressors=compressors)
@@ -66,3 +63,74 @@ def test_zarr_v3_compression(input_images):
         assert scale2["codecs"][1]["configuration"]["cname"] == "zlib"
         assert scale2["codecs"][1]["configuration"]["clevel"] == 5
         assert scale2["codecs"][1]["configuration"]["shuffle"] == "shuffle"
+
+        verify_against_baseline(
+            dataset_name, baseline_name, multiscales, version=version
+        )
+
+    # Test writing OME-Zarr 0.5 with compression and sharding
+    version = "0.5"
+    chunks_per_shard = 2
+
+    with tempfile.TemporaryDirectory() as tmpdir:
+        to_ngff_zarr(
+            tmpdir,
+            multiscales,
+            version=version,
+            compressors=compressors,
+            chunks_per_shard=chunks_per_shard,
+        )
+
+        with open(tmpdir + "/zarr.json") as f:
+            zarr_json = json.load(f)
+        assert zarr_json["zarr_format"] == 3
+        metadata = zarr_json["consolidated_metadata"]["metadata"]
+
+        scale0 = metadata["scale0/image"]
+        assert scale0["chunk_grid"]["configuration"]["chunk_shape"][0] == 128
+        assert scale0["chunk_grid"]["configuration"]["chunk_shape"][1] == 128
+
+        sharding_codec = scale0["codecs"][0]
+        assert sharding_codec["name"] == "sharding_indexed"
+        assert sharding_codec["configuration"]["chunk_shape"][0] == 64
+        assert sharding_codec["configuration"]["chunk_shape"][1] == 64
+
+        blosc_codec = sharding_codec["configuration"]["codecs"][1]
+        assert blosc_codec["name"] == "blosc"
+        assert blosc_codec["configuration"]["cname"] == "zlib"
+        assert blosc_codec["configuration"]["clevel"] == 5
+        assert blosc_codec["configuration"]["shuffle"] == "shuffle"
+
+        scale1 = metadata["scale1/image"]
+        sharding_codec = scale1["codecs"][0]
+        assert sharding_codec["name"] == "sharding_indexed"
+
+        blosc_codec = sharding_codec["configuration"]["codecs"][1]
+        assert blosc_codec["name"] == "blosc"
+        assert blosc_codec["configuration"]["cname"] == "zlib"
+        assert blosc_codec["configuration"]["clevel"] == 5
+        assert blosc_codec["configuration"]["shuffle"] == "shuffle"
+
+        verify_against_baseline(
+            dataset_name, baseline_name, multiscales, version=version
+        )
+
+
+def test_zarr_v3_compression_rejected_for_ome_zarr_04(input_images):
+    """Test that compressors argument is rejected for OME-Zarr version 0.4"""
+    dataset_name = "cthead1"
+    image = input_images[dataset_name]
+    chunks = (64, 64)
+    multiscales = to_multiscales(
+        image, [2, 4], chunks=chunks, method=Methods.ITKWASM_GAUSSIAN
+    )
+    store = zarr.storage.MemoryStore()
+
+    compressors = zarr.codecs.BloscCodec(
+        cname="zlib", clevel=5, shuffle=zarr.codecs.BloscShuffle.shuffle
+    )
+
+    # Setting `compressors` argument for OME-Zarr 0.4 should raise an error
+    version = "0.4"
+    with pytest.raises(ValueError, match="not supported for OME-Zarr version 0.4"):
+        to_ngff_zarr(store, multiscales, version=version, compressors=compressors)