Merge remote-tracking branch 'origin/master' into scaler_preserve_dtype

Author: will-moore

.pre-commit-config.yaml

@@ -19,18 +19,18 @@ repos:
           - --autofix
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.12.11
+    rev: v0.13.2
     hooks:
     - id: ruff-check
       args: ["--fix", "--show-fixes"]
 
   - repo: https://github.com/psf/black
-    rev: 25.1.0
+    rev: 25.9.0
     hooks:
       - id: black
 
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: v1.17.1
+    rev: v1.18.2
     hooks:
       - id: mypy
         args: [--config-file=mypy.ini]

docs/source/cli.rst

@@ -28,10 +28,13 @@ Local data::
 view
 ====
 
-Use the `ome_zarr` command to view Zarr data in the https://ome.github.io/ome-ngff-validator::
+Use the `ome_zarr` command to serve local Zarr data and view in the https://ome.github.io/ome-ngff-validator::
 
     ome_zarr view 6001240.zarr/
 
+    # Use -f or --force to open in browser even if no valid data is found
+    ome_zarr view 6001240.zarr/ -f
+
 finder
 ======
 

ome_zarr/cli.py

@@ -35,7 +35,7 @@ def info(args: argparse.Namespace) -> None:
 def view(args: argparse.Namespace) -> None:
     """Wrap the :func:`~ome_zarr.utils.view` method."""
     config_logging(logging.WARNING, args)
-    zarr_view(args.path, args.port)
+    zarr_view(args.path, args.port, force=args.force)
 
 
 def finder(args: argparse.Namespace) -> None:
@@ -133,6 +133,12 @@ def main(args: list[str] | None = None) -> None:
     parser_view.add_argument(
         "--port", type=int, default=8000, help="Port to serve the data (default: 8000)"
     )
+    parser_view.add_argument(
+        "--force",
+        "-f",
+        action="store_true",
+        help="Force open in browser. Don't check for OME-Zarr data first.",
+    )
     parser_view.set_defaults(func=view)
 
     # finder (open a dir of images in BioFile Finder in a browser)

ome_zarr/data.py

@@ -67,7 +67,7 @@ def astronaut() -> tuple[list, list]:
     pyramid = scaler.nearest(pixels)
 
     shape = list(pyramid[0].shape)
-    c, y, x = shape
+    _c, y, x = shape
     label = np.zeros((y, x), dtype=np.int8)
     make_circle(100, 100, 1, label[200:300, 200:300])
     make_circle(150, 150, 2, label[250:400, 250:400])

ome_zarr/scale.py

@@ -74,6 +74,10 @@ class Scaler:
     max_layer: int = 4
     method: str = "nearest"
 
+    # 0: Nearest-neighbor
+    # 1: Bi-linear (default)
+    order: int = 1  # only used for resize
+
     @staticmethod
     def methods() -> Iterator[str]:
         """Return the name of all methods which define a downsampling.
@@ -172,7 +176,11 @@ def _resize(image: ArrayLike, out_shape: tuple, **kwargs: Any) -> ArrayLike:
 
         dtype = image.dtype
         image = _resize(
-            image.astype(float), out_shape, order=1, mode="reflect", anti_aliasing=False
+            image.astype(float),
+            out_shape,
+            order=self.order,
+            mode="reflect",
+            anti_aliasing=False,
         )
         return image.astype(dtype)
 

ome_zarr/utils.py

@@ -73,21 +73,24 @@ def info(path: str, stats: bool = False) -> Iterator[Node]:
         yield node
 
 
-def view(input_path: str, port: int = 8000, dry_run: bool = False) -> None:
+def view(
+    input_path: str, port: int = 8000, dry_run: bool = False, force: bool = False
+) -> None:
     # serve the parent directory in a simple server with CORS. Open browser
     # dry_run is for testing, so we don't open the browser or start the server
 
-    zarrs = []
-    if (Path(input_path) / ".zattrs").exists() or (
-        Path(input_path) / "zarr.json"
-    ).exists():
-        zarrs = find_multiscales(Path(input_path))
-    if len(zarrs) == 0:
-        print(
-            f"No OME-Zarr images found in {input_path}. "
-            f"Try $ ome_zarr finder {input_path}"
-        )
-        return
+    if not force:
+        zarrs = []
+        if (Path(input_path) / ".zattrs").exists() or (
+            Path(input_path) / "zarr.json"
+        ).exists():
+            zarrs = find_multiscales(Path(input_path))
+        if len(zarrs) == 0:
+            print(
+                f"No OME-Zarr images found in {input_path}. "
+                f"Try $ ome_zarr finder {input_path} or use -f to force open in browser."
+            )
+            return
 
     parent_dir, image_name = os.path.split(input_path)
     if len(image_name) == 0:

ome_zarr/writer.py

@@ -927,7 +927,7 @@ def write_labels(
     labels: np.ndarray | da.Array,
     group: zarr.Group,
     name: str,
-    scaler: Scaler = Scaler(),
+    scaler: Scaler = Scaler(order=0),
     chunks: tuple[Any, ...] | int | None = None,
     fmt: Format | None = None,
     axes: AxesType = None,
@@ -955,8 +955,11 @@ def write_labels(
     :param name: The name of this labels data.
     :type scaler: :class:`ome_zarr.scale.Scaler`
     :param scaler:
-      Scaler implementation for downsampling the image argument. If None,
-      no downsampling will be performed.
+      Scaler implementation for downsampling the image argument.
+      NB: Labels downsampling should avoid interpolation.
+      If no scaler is provided, the default scaler with nearest neighbour
+      interpolation will be used.
+      If scaler=None, no downsampling will be performed.
     :type chunks: int or tuple of ints, optional
     :param chunks:
         The size of the saved chunks to store the image.

tests/test_cli.py

@@ -54,7 +54,7 @@ def test_coins_info(self, capsys, fmt):
             args += ["--format", fmt.version]
         main(args)
         main(["info", filename])
-        out, err = capsys.readouterr()
+        out, _err = capsys.readouterr()
         print("Captured output:", out)
         assert os.path.join("labels", "coins") in out
         version = fmt.version if fmt else CurrentFormat().version
@@ -153,6 +153,10 @@ def _rotate_and_test(self, *hierarchy: Path, reverse: bool = True):
             self._rotate_and_test(*list(secondpass), reverse=False)
 
     def test_view(self):
+        # view empty dir for code coverage
+        view(str(self.path), 8000, True)
+        view(str(self.path), 8000, True, force=True)
+
         filename = f"{self.path}-4"
         main(["create", "--method=astronaut", filename])
         # CLI doesn't support the dry_run option yet

tests/test_writer.py

@@ -1,6 +1,7 @@
 import filecmp
 import json
 import pathlib
+import re
 from typing import Any
 
 import dask.array as da
@@ -16,6 +17,7 @@
 from ome_zarr_models.v05.hcs import HCS as Models05HCS
 from ome_zarr_models.v05.image import Image as Models05Image
 from ome_zarr_models.v05.well import Well as Models05Well
+from skimage.data import binary_blobs
 from zarr.abc.codec import BytesBytesCodec
 from zarr.codecs import BloscCodec
 
@@ -664,7 +666,9 @@ def test_multi_levels_transformations(self, fmt):
         # No arrays, so this is expected:
         with pytest.raises(
             ValueError,
-            match="Expected to find an array at /0, but no array was found there.",
+            match=re.escape(
+                "Expected to find an array at 0, but no array was found there."
+            ),
         ):
             if fmt.version == "0.4":
                 Models04Image.from_zarr(group)
@@ -756,7 +760,9 @@ def test_valid_transformations(self, coordinateTransformations):
         # No arrays, so this is expected:
         with pytest.raises(
             ValueError,
-            match="Expected to find an array at /0, but no array was found there.",
+            match=re.escape(
+                "Expected to find an array at 0, but no array was found there."
+            ),
         ):
             Models04Image.from_zarr(self.root)
 
@@ -835,7 +841,8 @@ def test_omero_metadata(self, metadata: dict[str, Any] | None):
             datasets.append({"path": str(level), "coordinateTransformations": transf})
         if metadata is None:
             with pytest.raises(
-                KeyError, match="If `'omero'` is present, value cannot be `None`."
+                KeyError,
+                match=re.escape("If `'omero'` is present, value cannot be `None`."),
             ):
                 write_multiscales_metadata(
                     self.root,
@@ -856,7 +863,7 @@ def test_omero_metadata(self, metadata: dict[str, Any] | None):
             )
             if window_metadata is not None and len(window_metadata) < 4:
                 if isinstance(window_metadata, dict):
-                    with pytest.raises(KeyError, match=".*`'window'`.*"):
+                    with pytest.raises(KeyError, match="window"):
                         write_multiscales_metadata(
                             self.root,
                             datasets,
@@ -865,7 +872,7 @@ def test_omero_metadata(self, metadata: dict[str, Any] | None):
                             fmt=FormatV04(),
                         )
                 elif isinstance(window_metadata, list):
-                    with pytest.raises(TypeError, match=".*`'window'`.*"):
+                    with pytest.raises(TypeError, match="window"):
                         write_multiscales_metadata(
                             self.root,
                             datasets,
@@ -874,7 +881,7 @@ def test_omero_metadata(self, metadata: dict[str, Any] | None):
                             fmt=FormatV04(),
                         )
             elif color_metadata is not None and len(color_metadata) != 6:
-                with pytest.raises(TypeError, match=".*`'color'`.*"):
+                with pytest.raises(TypeError, match="color"):
                     write_multiscales_metadata(
                         self.root,
                         datasets,
@@ -891,7 +898,9 @@ def test_omero_metadata(self, metadata: dict[str, Any] | None):
                 # no arrays, so this is expected
                 with pytest.raises(
                     ValueError,
-                    match="Expected to find an array at /0, but no array was found there.",
+                    match=re.escape(
+                        "Expected to find an array at 0, but no array was found there."
+                    ),
                 ):
                     Models04Image.from_zarr(self.root)
 
@@ -1457,6 +1466,12 @@ def verify_label_data(
         name = imglabel_attrs["multiscales"][0].get("name", "")
         assert label_name == name
 
+        labels_paths = [
+            ds["path"] for ds in imglabel_attrs["multiscales"][0]["datasets"]
+        ]
+        label_data = [da.from_zarr(label_group[path]) for path in labels_paths]
+        return label_data
+
     @pytest.mark.parametrize(
         "format_version",
         (
@@ -1468,7 +1483,9 @@ def verify_label_data(
         ),
     )
     @pytest.mark.parametrize("array_constructor", [np.array, da.from_array])
-    def test_write_labels(self, shape, scaler, format_version, array_constructor):
+    @pytest.mark.parametrize("scale_type", ["custom", "noop", "default"])
+    def test_write_labels(self, shape, format_version, array_constructor, scale_type):
+
         fmt = format_version()
         if fmt.version == "0.5":
             img_path = self.path_v3
@@ -1485,11 +1502,23 @@ def test_write_labels(self, shape, scaler, format_version, array_constructor):
             transformations.append(
                 [{"type": "scale", "scale": transf["scale"][-len(shape) :]}]
             )
-            if scaler is None:
+            if scale_type == "noop":
                 break
 
-        # create the actual label data
-        label_data = np.random.randint(0, 1000, size=shape)
+        # create the actual label data: zeros with blobs
+        label_data = np.zeros(shape, dtype=np.uint8)
+        # add some blobs, corresponding to shape
+        blobs = binary_blobs(length=256, volume_fraction=0.1, n_dim=2).astype("int8")
+        # we only apply blobs to the last two dimensions of label_data
+        slices = [slice(None)] * (len(shape) - blobs.ndim)
+        slices += [slice(0, 256), slice(0, 256)]
+        label_data[tuple(slices)] = 2 * blobs
+
+        print("label_data.shape:", label_data.shape, shape)
+        assert label_data.max() == 2
+        assert label_data.min() == 0
+        assert np.unique(label_data).tolist() == [0, 2]
+
         if fmt.version in ("0.1", "0.2"):
             # v0.1 and v0.2 require 5d
             expand_dims = (np.s_[None],) * (5 - len(shape))
@@ -1498,21 +1527,33 @@ def test_write_labels(self, shape, scaler, format_version, array_constructor):
         label_name = "my-labels"
         label_data = array_constructor(label_data)
 
+        scaler = Scaler()
+        if scale_type == "noop":
+            scaler = None
+        kwargs = {"scaler": scaler}
+        if scale_type == "default":
+            del kwargs["scaler"]
+
         # create the root level image data
         self.create_image_data(group, shape, scaler, fmt, axes, transformations)
 
         write_labels(
             label_data,
             group,
-            scaler=scaler,
             name=label_name,
             fmt=fmt,
             axes=axes,
             coordinate_transformations=transformations,
+            **kwargs,
         )
-        self.verify_label_data(
+        label_data = self.verify_label_data(
             img_path, label_name, label_data, fmt, shape, transformations
         )
+
+        for level in label_data:
+            if scale_type == "default":
+                assert np.unique(level.compute()).tolist() == [0, 2]
+
         if fmt.version == "0.4":
             test_root = zarr.open(self.path)
             Models04Labels.from_zarr(test_root["labels"])