napari-openreadout 0.1.0__tar.gz

napari_openreadout-0.1.0/.gitignore

@@ -0,0 +1,40 @@
+/target
+/corpus/files/
+/oracle/bftools/
+/oracle/.venv/
+/oracle/.cache/
+/oracle/__pycache__/
+**/__pycache__/
+*.pyc
+/dist/
+/wheels/
+*.ome.tiff
+*.ome.tif
+!/docs/**/*.ome.tiff
+.DS_Store
+/.env
+# maturin develop drops the compiled extension next to the Python sources
+/crates/openreadout-py/python/openreadout/_native*.so
+/crates/openreadout-py/python/openreadout/_native*.pyd
+*.egg-info/
+.pytest_cache/
+# cargo-fuzz build output, crash artifacts and the growing working corpus (seeds: fuzz/corpus)
+/fuzz/target/
+/fuzz/artifacts*/
+/fuzz/work/
+/fuzz/logs/
+/fuzz/coverage/
+/book/book/
+/book/node_modules/
+/book/.astro/
+/.venv/
+/fuzz/local-seeds/
+/fuzz/found/
+# WebAssembly package build output (scripts/wasm.sh) and npm installs
+/packaging/wasm/pkg/
+/packaging/wasm/node_modules/
+/web/node_modules/
+# Claude Code worktrees and local state
+/.claude/
+# eval run output (reports, per-run records, transcripts, logs)
+/evals/results/

napari_openreadout-0.1.0/LICENSE-APACHE

@@ -0,0 +1,202 @@
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napari_openreadout-0.1.0/LICENSE-MIT

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2026 The OpenReadout Authors
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

napari_openreadout-0.1.0/PKG-INFO

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+Metadata-Version: 2.5
+Name: napari-openreadout
+Version: 0.1.0
+Summary: napari reader plugin that opens microscopy files lazily with OpenReadout
+Project-URL: Homepage, https://github.com/openreadout/openreadout
+Project-URL: Repository, https://github.com/openreadout/openreadout
+Project-URL: Documentation, https://openreadout.github.io/openreadout/guides/napari.html
+Author-email: The OpenReadout Authors <openreadout@gmail.com>
+License-Expression: MIT OR Apache-2.0
+License-File: LICENSE-APACHE
+License-File: LICENSE-MIT
+Keywords: czi,lif,microscopy,napari,nd2,ome-zarr,svs,whole-slide
+Classifier: Development Status :: 4 - Beta
+Classifier: Framework :: napari
+Classifier: Intended Audience :: Science/Research
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Topic :: Scientific/Engineering :: Image Processing
+Classifier: Typing :: Typed
+Requires-Python: >=3.10
+Requires-Dist: numpy>=1.22
+Requires-Dist: openreadout[dask]<0.2,>=0.1.0
+Provides-Extra: test
+Requires-Dist: npe2>=0.7; extra == 'test'
+Requires-Dist: pytest>=7; extra == 'test'
+Description-Content-Type: text/markdown
+
+# napari-openreadout
+
+A [napari](https://napari.org) reader plugin that opens raw microscopy and electron-microscopy files with [OpenReadout](https://github.com/openreadout/openreadout). The formats it reads are listed at <https://openreadout.github.io/openreadout/formats.html>.
+
+```bash
+pip install napari napari-openreadout
+napari slide.svs
+```
+
+- **Lazy**: layers are dask arrays; a plane (or, for large tiled planes, the tiles under the
+  view) is decoded only when displayed.
+- **Multiscale**: pyramidal files (CZI pyramids, SVS/NDPI/QPTIFF, VSI, Imaris, OME-TIFF with
+  SubIFDs, OME-Zarr multiscales) open as multiscale layers.
+- **Channels** become separate layers named after the file's channels, coloured by their
+  recorded colours; **scale** is the physical pixel size in µm (and the time step in s).
+- Every image of the file (CZI scene, ND2 position, LIF series) is its own layer.
+
+Without napari, `napari_openreadout.read(path)` returns the same `(data, kwargs, "image")` tuples.
+
+Guide: <https://openreadout.github.io/openreadout/guides/napari.html>. Licensed MIT OR Apache-2.0.

napari_openreadout-0.1.0/README.md

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+# napari-openreadout
+
+A [napari](https://napari.org) reader plugin that opens raw microscopy and electron-microscopy files with [OpenReadout](https://github.com/openreadout/openreadout). The formats it reads are listed at <https://openreadout.github.io/openreadout/formats.html>.
+
+```bash
+pip install napari napari-openreadout
+napari slide.svs
+```
+
+- **Lazy**: layers are dask arrays; a plane (or, for large tiled planes, the tiles under the
+  view) is decoded only when displayed.
+- **Multiscale**: pyramidal files (CZI pyramids, SVS/NDPI/QPTIFF, VSI, Imaris, OME-TIFF with
+  SubIFDs, OME-Zarr multiscales) open as multiscale layers.
+- **Channels** become separate layers named after the file's channels, coloured by their
+  recorded colours; **scale** is the physical pixel size in µm (and the time step in s).
+- Every image of the file (CZI scene, ND2 position, LIF series) is its own layer.
+
+Without napari, `napari_openreadout.read(path)` returns the same `(data, kwargs, "image")` tuples.
+
+Guide: <https://openreadout.github.io/openreadout/guides/napari.html>. Licensed MIT OR Apache-2.0.

napari_openreadout-0.1.0/napari_openreadout/__init__.py

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+"""napari reader plugin for raw microscopy files, backed by OpenReadout.
+
+Installed next to napari, it opens every image format OpenReadout reads (Zeiss CZI, Nikon ND2,
+Leica LIF, whole-slide SVS/NDPI/QPTIFF/VSI, Imaris, OME-TIFF, OME-Zarr, ...) lazily: planes and
+tiles are decoded only when napari displays them, and pyramidal files open as multiscale layers,
+so a 40 GB slide opens in about a second::
+
+    napari slide.svs   # or File > Open, or viewer.open(path, plugin="napari-openreadout")
+
+Without napari, :func:`read` returns the same layer data for scripts.
+"""
+
+from importlib.metadata import PackageNotFoundError, version
+
+from ._reader import get_reader, layer_data, read
+
+try:
+    __version__ = version("napari-openreadout")
+except PackageNotFoundError:  # pragma: no cover - running from a source checkout
+    __version__ = "uninstalled"
+
+__all__ = ["__version__", "get_reader", "layer_data", "read"]

napari_openreadout-0.1.0/napari_openreadout/_reader.py

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+"""The napari reader: every image of a file as a lazy (dask) image layer, multiscale when the file
+stores a pyramid, one layer per channel with the channel's name and colour, physical scale in µm
+(and seconds for time)."""
+
+from __future__ import annotations
+
+import os
+from typing import Any, Callable, Dict, List, Optional, Sequence, Tuple, Union
+
+import openreadout
+
+__all__ = ["get_reader", "layer_data", "read"]
+
+PathOrPaths = Union[str, Sequence[str]]
+LayerData = Tuple[Any, Dict[str, Any], str]
+ReaderFunction = Callable[[PathOrPaths], List[LayerData]]
+
+#: napari colormap names the channel colours are mapped to (nearest in RGB).
+_COLORMAPS: Dict[str, Tuple[int, int, int]] = {
+    "red": (255, 0, 0),
+    "green": (0, 255, 0),
+    "blue": (0, 0, 255),
+    "cyan": (0, 255, 255),
+    "magenta": (255, 0, 255),
+    "yellow": (255, 255, 0),
+    "gray": (255, 255, 255),
+}
+_DEFAULT_ORDER = ["green", "magenta", "cyan", "red", "blue", "yellow", "gray"]
+
+
+def _one_path(path: PathOrPaths) -> Optional[str]:
+    if isinstance(path, (list, tuple)):
+        return os.fspath(path[0]) if len(path) == 1 else None
+    return os.fspath(path)
+
+
+def get_reader(path: PathOrPaths) -> Optional[ReaderFunction]:
+    """napari hook: a reader for ``path`` when OpenReadout recognises it by its signature and it
+    holds images; ``None`` otherwise (napari then asks other plugins)."""
+    p = _one_path(path)
+    if p is None:
+        return None
+    try:
+        det = openreadout.info(p, view="format")
+    except (openreadout.OpenReadoutError, OSError):
+        return None
+    if det.get("confidence") == "extension-only":
+        return None
+    return read
+
+
+def _colormap(color: Optional[str], position: int) -> str:
+    if color and len(color.lstrip("#")) == 6:
+        h = color.lstrip("#")
+        try:
+            rgb = tuple(int(h[i : i + 2], 16) for i in (0, 2, 4))
+        except ValueError:
+            rgb = None
+        if rgb is not None:
+            return min(
+                _COLORMAPS,
+                key=lambda n: sum((a - b) ** 2 for a, b in zip(_COLORMAPS[n], rgb, strict=True)),
+            )
+    return _DEFAULT_ORDER[position % len(_DEFAULT_ORDER)]
+
+
+def layer_data(f: openreadout.File, image: int) -> LayerData:
+    """One image of an open file as napari layer data ``(data, kwargs, "image")``.
+
+    ``data`` is a list of dask arrays (full resolution first) for pyramidal images, else one
+    dask array, dims ``T, C, Z, Y, X`` (plus ``S`` for RGB). Channels are split into layers
+    (``channel_axis=1``) named after the file's channels; ``scale`` is ``(T s, Z µm, Y µm, X µm)``
+    where the file records them (1 otherwise).
+    """
+    im = f.images[image]
+    levels = f.levels(image)
+    multiscale = len(levels) > 1
+    data: Any = f.pyramid(image) if multiscale else f.to_dask(image)
+    rgb = im["samples_per_pixel"] == 3
+    ps = im.get("physical_size") or {}
+    dt = im.get("time_increment_s") or 1.0
+    tzyx = (
+        float(dt),
+        float(ps.get("z") or 1.0),
+        float(ps.get("y") or 1.0),
+        float(ps.get("x") or 1.0),
+    )
+    base = im.get("name") or os.path.basename(f.path)
+    kwargs: Dict[str, Any] = {
+        "multiscale": multiscale,
+        "rgb": rgb,
+        "metadata": {
+            "openreadout": {
+                "path": f.path,
+                "format": f.format,
+                "image": image,
+                "dims": f.dims(image),
+                "levels": levels,
+            }
+        },
+    }
+    size_c = im["size_c"]
+    if size_c > 1:
+        by_index = {ch["index"]: ch for ch in im.get("channels", [])}
+        names = []
+        cmaps = []
+        for c in range(size_c):
+            ch = by_index.get(c, {})
+            names.append(f"{base} {ch.get('name') or f'channel {c}'}")
+            cmaps.append(_colormap(ch.get("color"), c))
+        kwargs.update(channel_axis=1, name=names, scale=tzyx, blending="additive")
+        if not rgb:
+            kwargs["colormap"] = cmaps
+    else:
+        kwargs.update(name=base, scale=(tzyx[0], 1.0, *tzyx[1:]))
+    return (data, kwargs, "image")
+
+
+def read(path: PathOrPaths) -> List[LayerData]:
+    """Open ``path`` and return one layer (or one per channel) per image in the file. The file
+    stays open while the lazy arrays reference it."""
+    p = _one_path(path)
+    if p is None:
+        return []
+    f = openreadout.File(p)
+    return [layer_data(f, i) for i in range(len(f.images))]

napari_openreadout-0.1.0/napari_openreadout/napari.yaml

@@ -0,0 +1,44 @@
+name: napari-openreadout
+display_name: OpenReadout
+visibility: public
+categories: ["IO"]
+contributions:
+  commands:
+    - id: napari-openreadout.get_reader
+      python_name: napari_openreadout._reader:get_reader
+      title: Open a microscopy file with OpenReadout
+  readers:
+    - command: napari-openreadout.get_reader
+      accepts_directories: true
+      filename_patterns:
+        - "*.czi"
+        - "*.nd2"
+        - "*.lif"
+        - "*.lof"
+        - "*.xlef"
+        - "*.oir"
+        - "*.vsi"
+        - "*.ets"
+        - "*.zvi"
+        - "*.oib"
+        - "*.oif"
+        - "*.dcimg"
+        - "*.tif"
+        - "*.tiff"
+        - "*.ome.tif"
+        - "*.ome.tiff"
+        - "*.btf"
+        - "*.svs"
+        - "*.ndpi"
+        - "*.qptiff"
+        - "*.lsm"
+        - "*.stk"
+        - "*.nd"
+        - "*.ims"
+        - "*.zarr"
+        - "*.mrc"
+        - "*.map"
+        - "*.dm3"
+        - "*.dm4"
+        - "*.ser"
+        - "*.emd"

napari_openreadout-0.1.0/pyproject.toml

@@ -0,0 +1,49 @@
+[build-system]
+requires = ["hatchling>=1.26"]
+build-backend = "hatchling.build"
+
+[project]
+name = "napari-openreadout"
+version = "0.1.0"
+description = "napari reader plugin that opens microscopy files lazily with OpenReadout"
+readme = "README.md"
+license = "MIT OR Apache-2.0"
+license-files = ["LICENSE-MIT", "LICENSE-APACHE"]
+requires-python = ">=3.10"
+authors = [{ name = "The OpenReadout Authors", email = "openreadout@gmail.com" }]
+keywords = ["napari", "microscopy", "czi", "nd2", "lif", "svs", "whole-slide", "ome-zarr"]
+classifiers = [
+  "Development Status :: 4 - Beta",
+  "Framework :: napari",
+  "Intended Audience :: Science/Research",
+  "Programming Language :: Python :: 3",
+  "Programming Language :: Python :: 3 :: Only",
+  "Topic :: Scientific/Engineering :: Image Processing",
+  "Typing :: Typed",
+]
+# napari itself is not a dependency: the plugin is loaded by napari, and its tests run without
+# a GUI (npe2 reads the manifest; the reader returns plain layer data).
+dependencies = [
+  "openreadout[dask]>=0.1.0,<0.2",
+  "numpy>=1.22",
+]
+
+[project.optional-dependencies]
+test = ["pytest>=7", "npe2>=0.7"]
+
+[project.entry-points."napari.manifest"]
+napari-openreadout = "napari_openreadout:napari.yaml"
+
+[project.urls]
+Homepage = "https://github.com/openreadout/openreadout"
+Repository = "https://github.com/openreadout/openreadout"
+Documentation = "https://openreadout.github.io/openreadout/guides/napari.html"
+
+[tool.hatch.build.targets.wheel]
+packages = ["napari_openreadout"]
+
+[tool.hatch.build.targets.sdist]
+include = ["napari_openreadout", "tests", "README.md", "LICENSE-MIT", "LICENSE-APACHE"]
+
+[tool.pytest.ini_options]
+addopts = "--import-mode=importlib"

napari_openreadout-0.1.0/tests/conftest.py

@@ -0,0 +1,25 @@
+"""Fixtures: locate corpus files (``OPENREADOUT_CORPUS_DIR`` or ``<repo>/corpus/files``)."""
+
+from __future__ import annotations
+
+import os
+from pathlib import Path
+from typing import Callable
+
+import pytest
+
+REPO = Path(__file__).resolve().parents[3]
+
+
+@pytest.fixture(scope="session")
+def corpus() -> Callable[[str], Path]:
+    """``corpus("name.czi")`` → path, or skip the test if the file is absent."""
+    root = Path(os.environ.get("OPENREADOUT_CORPUS_DIR") or REPO / "corpus" / "files")
+
+    def get(name: str) -> Path:
+        p = root / name
+        if not p.is_file():
+            pytest.skip(f"corpus file {name} not present (cargo xtask corpus fetch --tier smoke)")
+        return p
+
+    return get

napari_openreadout-0.1.0/tests/test_napari_openreadout.py

@@ -0,0 +1,98 @@
+"""napari-openreadout without a GUI: the npe2 manifest validates and routes files to the
+reader, and the reader returns lazy (multiscale) layer data whose pixels equal the oracles'."""
+
+from __future__ import annotations
+
+import itertools
+import json
+from importlib.metadata import entry_points
+from pathlib import Path
+from typing import Callable
+
+import napari_openreadout
+import numpy as np
+import pytest
+from napari_openreadout import get_reader, read
+
+Corpus = Callable[[str], Path]
+REPO = Path(__file__).resolve().parents[3]
+
+CZI = "aics-s-3-t-1-c-3-z-5.czi"  # 3 scenes, C=3, Z=5
+SVS = "openslide-aperio-CMU-1-Small-Region.svs"  # RGB, one level
+PYRAMID_CZI = "zenodo10577621-Kidney-RAC-3color.czi"  # 5 levels, C=4
+ND2_RGB = "aics-ND2-dims-rgb.nd2"
+
+
+def test_manifest_validates_and_is_registered() -> None:
+    npe2 = pytest.importorskip("npe2")
+    eps = {ep.name: ep for ep in entry_points(group="napari.manifest")}
+    assert "napari-openreadout" in eps
+    mf = npe2.PluginManifest.from_distribution("napari-openreadout")
+    assert mf.name == "napari-openreadout"
+    patterns = mf.contributions.readers[0].filename_patterns
+    for ext in ("*.czi", "*.nd2", "*.lif", "*.svs", "*.vsi", "*.ims", "*.zarr"):
+        assert ext in patterns
+
+
+def test_npe2_routes_files_to_the_reader(corpus: Corpus) -> None:
+    npe2 = pytest.importorskip("npe2")
+    path = str(corpus(CZI))
+    pm = npe2.PluginManager.instance()
+    pm.discover()
+    readers = [r.plugin_name for r in pm.iter_compatible_readers([path])]
+    assert "napari-openreadout" in readers
+    layers = npe2.read([path], plugin_name="napari-openreadout", stack=False)
+    assert len(layers) == 3  # one per scene
+
+
+def test_unknown_files_are_declined(tmp_path: Path) -> None:
+    junk = tmp_path / "notes.czi"
+    junk.write_bytes(b"not an image at all" * 10)
+    assert get_reader(str(junk)) is None
+    assert get_reader([str(junk), str(junk)]) is None
+
+
+def test_channels_become_named_layers_with_scale(corpus: Corpus) -> None:
+    path = corpus(CZI)
+    reader = get_reader(str(path))
+    assert reader is read
+    layers = read(str(path))
+    assert len(layers) == 3
+    data, kw, kind = layers[1]
+    assert kind == "image" and kw["channel_axis"] == 1 and not kw["multiscale"]
+    assert len(kw["name"]) == 3 and kw["name"][0].endswith("EGFP")
+    assert len(kw["scale"]) == 4 and kw["scale"][2] == pytest.approx(kw["scale"][3])
+    assert data.shape == (1, 3, 5, 325, 475)
+    # Lazy: nothing decoded until computed; values equal the File's own read.
+    import openreadout
+
+    with openreadout.File(path) as f:
+        np.testing.assert_array_equal(np.asarray(data[0, 2, 4]), f.read_plane(1, c=2, z=4))
+    assert kw["metadata"]["openreadout"]["format"] == "czi"
+
+
+def test_rgb_single_channel(corpus: Corpus) -> None:
+    data, kw, _ = read(str(corpus(SVS)))[0]
+    assert kw["rgb"] and "channel_axis" not in kw
+    assert data.shape[-1] == 3 and len(kw["scale"]) == 5
+
+
+def test_pyramid_is_multiscale_and_matches_levels(corpus: Corpus) -> None:
+    data, kw, _ = read(str(corpus(PYRAMID_CZI)))[0]
+    assert kw["multiscale"] and isinstance(data, list) and len(data) == 5
+    shapes = [d.shape[-2:] for d in data]
+    assert shapes[0] == (5718, 10128)
+    assert all(a[0] > b[0] for a, b in itertools.pairwise(shapes))
+    # A coarse level equals the committed czifile oracle for that level.
+    oracle = json.loads(
+        (REPO / "corpus" / "oracle" / "zenodo10577621-Kidney-RAC-3color.json").read_text()
+    )
+    lv = next(x for x in oracle["images"][0]["levels"] if x["level"] == 4 and x["planes"])
+    xxhash = pytest.importorskip("xxhash")
+    for p in lv["planes"][:2]:
+        plane = np.ascontiguousarray(np.asarray(data[4][0, p["c"], p["z"]]))
+        assert xxhash.xxh3_128_hexdigest(plane.tobytes()) == p["xxh3"]
+
+
+def test_version() -> None:
+    assert napari_openreadout.__version__