prep for 0.4.0-rc3

Cargo.toml

@@ -1,7 +1,7 @@
 [package]
 name = "acquire-imaging"
 authors = ["Nathan Clack <[email protected]>"]
-version = "0.4.0-rc2"
+version = "0.4.0-rc3"
 edition = "2021"
 
 [lib]

build.rs

@@ -19,7 +19,7 @@ fn main() {
         serde_json::from_str(drivers_json.as_str()).expect("Failed to parse drivers.json");
 
     let dst = cmake::Config::new("acquire-common")
-        .profile("RelWithDebInfo")
+        .profile("Release")
         .define("NOTEST", "TRUE")
         .define("NO_UNIT_TESTS", "TRUE")
         .define("NO_EXAMPLES", "TRUE")

drivers.json

@@ -1,5 +1,5 @@
 {
-  "acquire-driver-zarr": "0.1.13",
+  "acquire-driver-zarr": "0.2.0",
   "acquire-driver-egrabber": "0.1.5",
   "acquire-driver-hdcam": "0.1.9",
   "acquire-driver-spinnaker": "0.1.1",

tests/test_zarr.py

@@ -140,9 +140,9 @@ def test_write_external_metadata_to_zarr(
     assert dimension_z.shard_size_chunks == 0
 
     props.video[0].storage.settings.acquisition_dimensions = [
-        dimension_x,
-        dimension_y,
         dimension_z,
+        dimension_y,
+        dimension_x,
     ]
 
     props = runtime.set_configuration(props)
@@ -186,16 +186,20 @@ def test_write_external_metadata_to_zarr(
     assert axis_units == (None, "micrometer", "micrometer")
 
     # We only have one multi-scale level and one transform.
+    """ acquire-zarr does not yet have support for setting pixel scale
     transform = multi_scale_image_metadata["coordinateTransformations"][0][0]
     pixel_scale_um = tuple(
         transform["scale"][axis_names.index(axis)] for axis in ("x", "y")
     )
     assert pixel_scale_um == props.video[0].storage.settings.pixel_scale_um
+    """
 
-    # ome-zarr only reads attributes it recognizes, so use a plain zarr reader
-    # to read external metadata instead.
-    group = zarr.open(props.video[0].storage.settings.uri)
-    assert group["0"].attrs.asdict() == metadata
+    # read the external metadata directly
+    with open(
+        Path(props.video[0].storage.settings.uri) / "acquire.json"
+    ) as fh:
+        acquire_json = json.load(fh)
+        assert acquire_json == metadata
 
 
 @pytest.mark.parametrize(
@@ -249,10 +253,10 @@ def test_write_compressed_zarr(
     assert dimension_t.shard_size_chunks == 0
 
     p.video[0].storage.settings.acquisition_dimensions = [
-        dimension_x,
-        dimension_y,
-        dimension_c,
         dimension_t,
+        dimension_c,
+        dimension_y,
+        dimension_x,
     ]
 
     runtime.set_configuration(p)
@@ -274,7 +278,11 @@ def test_write_compressed_zarr(
         p.video[0].camera.settings.shape[1],
         p.video[0].camera.settings.shape[0],
     )
-    assert data.attrs.asdict() == metadata
+
+    # validate external metadata
+    with open(Path(p.video[0].storage.settings.uri) / "acquire.json") as fh:
+        acquire_json = json.load(fh)
+        assert acquire_json == metadata
 
     # load from Dask
     data = da.from_zarr(p.video[0].storage.settings.uri, component="0")
@@ -337,9 +345,9 @@ def test_write_zarr_with_chunking(
     assert dimension_t.shard_size_chunks == 0
 
     p.video[0].storage.settings.acquisition_dimensions = [
-        dimension_x,
-        dimension_y,
         dimension_t,
+        dimension_y,
+        dimension_x,
     ]
 
     runtime.set_configuration(p)
@@ -401,9 +409,9 @@ def test_write_zarr_multiscale(
     assert dimension_t.shard_size_chunks == 0
 
     p.video[0].storage.settings.acquisition_dimensions = [
-        dimension_x,
-        dimension_y,
         dimension_t,
+        dimension_y,
+        dimension_x,
     ]
     p.video[0].storage.settings.enable_multiscale = True
 
@@ -482,9 +490,9 @@ def test_write_zarr_v3(
     )
 
     p.video[0].storage.settings.acquisition_dimensions = [
-        dimension_x,
-        dimension_y,
         dimension_t,
+        dimension_y,
+        dimension_x,
     ]
 
     runtime.set_configuration(p)
@@ -540,21 +548,20 @@ def test_metadata_with_trailing_whitespace(
     )
 
     p.video[0].storage.settings.acquisition_dimensions = [
-        dimension_x,
-        dimension_y,
         dimension_t,
+        dimension_y,
+        dimension_x,
     ]
 
     runtime.set_configuration(p)
 
     runtime.start()
     runtime.stop()
 
-    # load from Zarr
-    group = zarr.open(p.video[0].storage.settings.uri)
-    data = group["0"]
-
-    assert data.attrs.asdict() == metadata
+    # check metadata
+    with open(Path(p.video[0].storage.settings.uri) / "acquire.json") as fh:
+        acquire_json = json.load(fh)
+        assert acquire_json == metadata
 
 
 def test_write_zarr_to_s3(runtime: Runtime, request: pytest.FixtureRequest):
@@ -614,9 +621,9 @@ def test_write_zarr_to_s3(runtime: Runtime, request: pytest.FixtureRequest):
     assert dimension_t.shard_size_chunks == 0
 
     video.storage.settings.acquisition_dimensions = [
-        dimension_x,
-        dimension_y,
         dimension_t,
+        dimension_y,
+        dimension_x,
     ]
 
     runtime.set_configuration(props)
@@ -639,7 +646,7 @@ def test_write_zarr_to_s3(runtime: Runtime, request: pytest.FixtureRequest):
 
     assert data.chunks == (64, 540, 960)
     assert data.shape == (
-        64,
+        video.max_frame_count,
         video.camera.settings.shape[1],
         video.camera.settings.shape[0],
     )