Enable remote image reading

.github/workflows/test_and_deploy.yml

@@ -49,7 +49,7 @@ jobs:
           wm: herbstluftwm
 
       - name: Run tests
-        run: uv run --dev pytest -v --color=yes -m "not network" --cov=ndevio --cov-report=xml
+        run: uv run --dev pytest -v --color=yes --cov=ndevio --cov-report=xml
 
       - name: Coverage
         uses: codecov/codecov-action@v5

src/ndevio/nimage.py

@@ -99,8 +99,12 @@ class nImage(BioImage):
 
     Attributes
     ----------
-    path : Path | None
-        Path to the source file, or None if created from array data.
+    path : str | None
+        Path or URI to the source file, or None if created from array data.
+        Always a plain string — local paths are stored as-is, ``file://`` URIs
+        are normalised to their path component, and remote URIs (``s3://``,
+        ``https://``, …) are kept verbatim.  Use ``_is_remote`` to distinguish
+        local from remote.
 
     Examples
     --------
@@ -120,7 +124,8 @@ class nImage(BioImage):
     """
 
     # Class-level type hints for instance attributes
-    path: Path | None
+    path: str | None
+    _is_remote: bool
     _layer_data: xr.DataArray | None
 
     def __init__(
@@ -156,7 +161,24 @@ def __init__(
 
         # Instance state
         self._layer_data = None
-        self.path = Path(image) if isinstance(image, str | Path) else None
+        if isinstance(image, str | Path):
+            import fsspec
+            from fsspec.implementations.local import LocalFileSystem
+
+            s = str(image)
+            fs, resolved = fsspec.url_to_fs(s)
+            if isinstance(fs, LocalFileSystem):
+                # Normalise file:// URIs and any platform variations to an
+                # OS-native path string so Path(self.path) always round-trips.
+                self.path = str(Path(resolved))
+                self._is_remote = False
+            else:
+                # Remote URI (s3://, https://, gc://, …) — keep verbatim.
+                self.path = s
+                self._is_remote = True
+        else:
+            self.path = None
+            self._is_remote = False
 
     @property
     def layer_data(self) -> xr.DataArray:
@@ -179,13 +201,39 @@ def layer_data(self) -> xr.DataArray:
 
         """
         if self._layer_data is None:
-            in_memory = determine_in_memory(self.path)
-            if in_memory:
-                self._layer_data = self.xarray_data.squeeze()
-            else:
+            if self._is_remote or not determine_in_memory(self.path):
                 self._layer_data = self.xarray_dask_data.squeeze()
+            else:
+                self._layer_data = self.xarray_data.squeeze()
         return self._layer_data
 
+    @property
+    def path_stem(self) -> str:
+        """Filename stem derived from path or URI, used in layer names.
+
+        Returns
+        -------
+        str
+            The stem of the filename (no extension, no parent path), or
+            ``'unknown'`` when the image was created from array data.
+
+        Examples
+        --------
+        >>> nImage("/data/cells.ome.tiff").path_stem
+        'cells.ome'
+        >>> nImage("s3://bucket/experiment/image.zarr").path_stem
+        'image'
+
+        """
+        if self.path is None:
+            return 'unknown'
+        if self._is_remote:
+            from pathlib import PurePosixPath
+            from urllib.parse import urlparse
+
+            return PurePosixPath(urlparse(self.path).path).stem
+        return Path(self.path).stem
+
     @property
     def layer_scale(self) -> tuple[float, ...]:
         """Physical scale for dimensions in layer data.
@@ -334,8 +382,7 @@ def _build_layer_name(self, channel_name: str | None = None) -> str:
         if len(self.scenes) > 1 or self.current_scene != 'Image:0':
             parts.extend([str(self.current_scene_index), self.current_scene])
 
-        path_stem = self.path.stem if self.path is not None else 'unknown path'
-        parts.append(path_stem)
+        parts.append(self.path_stem)
 
         return delim.join(parts)
 

src/ndevio/utils/_layer_utils.py

@@ -3,7 +3,6 @@
 from __future__ import annotations
 
 import logging
-from pathlib import Path
 from typing import TYPE_CHECKING
 
 if TYPE_CHECKING:
@@ -109,16 +108,16 @@ def resolve_layer_type(
 
 
 def determine_in_memory(
-    path: Path | None,
+    path: str | None,
     max_in_mem_bytes: float = 4e9,
     max_in_mem_percent: float = 0.3,
 ) -> bool:
     """Determine whether to load image data in memory or as dask array.
 
     Parameters
     ----------
-    path : Path | None
-        Path to the image file. If None (array data), returns True.
+    path : str | None
+        Path to the image file as a string. If None (array data), returns True.
     max_in_mem_bytes : float
         Maximum file size in bytes for in-memory loading.
         Default is 4 GB (4e9 bytes).

tests/test_napari_reader.py

@@ -14,6 +14,7 @@
 PNG_FILE = 'nDev-logo-small.png'
 ND2_FILE = 'ND2_dims_rgb.nd2'
 OME_TIFF = 'cells3d2ch_legacy.tiff'
+REMOTE_ZARR = 'https://uk1s3.embassy.ebi.ac.uk/ebi-ngff-challenge-2024/4ffaeed2-fa70-4907-820f-8a96ef683095.zarr'  # from https://github.com/bioio-devs/bioio-ome-zarr/blob/main/bioio_ome_zarr/tests/test_remote_read_zarrV3.py
 
 ###############################################################################
 
@@ -48,6 +49,15 @@ def test_napari_viewer_open_directory(
     assert viewer.layers[0].data.shape == (2, 4, 4)
 
 
+@pytest.mark.network
+def test_napari_viewer_open_remote(make_napari_viewer) -> None:
+    viewer = make_napari_viewer()
+    viewer.open(REMOTE_ZARR, plugin='ndevio')
+
+    assert len(viewer.layers) == 2
+    assert viewer.layers[0].data.shape == (512, 512)
+
+
 @pytest.mark.parametrize(
     (
         'filename',

tests/test_nimage.py

@@ -24,7 +24,7 @@
 def test_nImage_init(resources_dir: Path):
     """Test nImage initialization with a file that should work."""
     img = nImage(resources_dir / CELLS3D2CH_OME_TIFF)
-    assert img.path == resources_dir / CELLS3D2CH_OME_TIFF
+    assert img.path == str(resources_dir / CELLS3D2CH_OME_TIFF)
     assert img.reader is not None
     # Shape is (T, C, Z, Y, X) = (1, 2, 60, 66, 85)
     assert img.data.shape == (1, 2, 60, 66, 85)
@@ -38,10 +38,21 @@ def test_nImage_zarr(resources_dir: Path):
     """Test that nImage can read a Zarr file."""
     img = nImage(resources_dir / ZARR)
     assert img.data is not None
-    assert img.path == resources_dir / ZARR
+    assert img.path == str(resources_dir / ZARR)
     assert img.data.shape == (1, 1, 2, 4, 4)
 
 
+@pytest.mark.network
+def test_nImage_remote_zarr():
+    """Test that nImage can read a remote Zarr file."""
+    remote_zarr = 'https://uk1s3.embassy.ebi.ac.uk/ebi-ngff-challenge-2024/4ffaeed2-fa70-4907-820f-8a96ef683095.zarr'  # from https://github.com/bioio-devs/bioio-ome-zarr/blob/main/bioio_ome_zarr/tests/test_remote_read_zarrV3.py
+    img = nImage(remote_zarr)
+    assert img.path == remote_zarr
+    assert img._is_remote
+    # original shape is (1, 2, 1, 512, 512) but layer_data is squeezed
+    assert img.layer_data.shape == (2, 512, 512)
+
+
 def test_nImage_ome_reader(resources_dir: Path):
     """
     Test that the OME-TIFF reader is used for OME-TIFF files.
@@ -224,7 +235,7 @@ def test_nimage_init_with_various_formats(
         # Must successfully initialize
         img = nImage(resources_dir / filename)
         assert img.data is not None
-        assert img.path == resources_dir / filename
+        assert img.path == str(resources_dir / filename)
     elif should_work is False:
         # Must fail with helpful error
         with pytest.raises(UnsupportedFileFormatError) as exc_info: