feat: add io and cli

examples/zarr_arr.py

@@ -20,5 +20,4 @@
 except ImportError:
     raise ImportError("Please `pip install zarr aiohttp` to run this example")
 
-
-ndv.imshow(zarr_arr["s4"], current_index={1: 30}, visible_axes=(0, 2))
+ndv.imshow(zarr_arr["s4"].astype("uint16"), current_index={1: 30}, visible_axes=(0, 2))

pyproject.toml

@@ -44,6 +44,9 @@ dependencies = [
     "typing_extensions >= 4.0",
 ]
 
+[project.scripts]
+ndv = "ndv.cli:main"
+
 # https://peps.python.org/pep-0621/#dependencies-optional-dependencies
 [project.optional-dependencies]
 # Supported GUI frontends
@@ -76,10 +79,13 @@ wxpython = ["pyconify>=0.2.1", "wxpython >=4.2.2"]
 vispy = ["vispy>=0.14.3", "pyopengl >=3.1"]
 pygfx = ["pygfx>=0.8.0"]
 
+# opinionated image reading support
+io = ["imageio[tifffile] >=2.20", "zarr >2,<3", "tensorstore>=0.1.69,!=0.1.72"]
+
 # ready to go bundles with pygfx
-qt = ["ndv[pygfx,pyqt]", "imageio[tifffile] >=2.20"]
-jup = ["ndv[pygfx,jupyter]", "imageio[tifffile] >=2.20"]
-wx = ["ndv[pygfx,wxpython]", "imageio[tifffile] >=2.20"]
+qt = ["ndv[pygfx,pyqt,io]"]
+jup = ["ndv[pygfx,jupyter,io]"]
+wx = ["ndv[pygfx,wxpython,io]"]
 
 
 [project.urls]

src/ndv/cli.py

@@ -0,0 +1,20 @@
+"""command-line program."""
+
+import argparse
+
+from ndv.util import imshow
+
+
+def _parse_args() -> argparse.Namespace:
+    parser = argparse.ArgumentParser(description="ndv: ndarray viewer")
+    parser.add_argument("path", type=str, help="The filename of the numpy file to view")
+    return parser.parse_args()
+
+
+def main() -> None:
+    """Run the command-line program."""
+    from ndv import io
+
+    args = _parse_args()
+
+    imshow(io.imread(args.path))

src/ndv/io.py

@@ -0,0 +1,152 @@
+"""All the io we can think of."""
+
+from __future__ import annotations
+
+import json
+import logging
+from contextlib import suppress
+from pathlib import Path
+from textwrap import indent, wrap
+from typing import TYPE_CHECKING, Any
+
+import numpy as np
+
+if TYPE_CHECKING:
+    import zarr
+
+logger = logging.getLogger(__name__)
+
+
+class collect_errors:
+    """Store exceptions in `errors` under `key`, rather than raising."""
+
+    def __init__(self, errors: dict, key: str):
+        self.errors = errors
+        self.key = key
+
+    def __enter__(self) -> None:
+        pass
+
+    def __exit__(
+        self, exc_type: type[BaseException], exc_value: BaseException, traceback: Any
+    ) -> bool:
+        if exc_type is not None:
+            self.errors[self.key] = exc_value
+        return True
+
+
+def imread(path: str | Path) -> Any:
+    """Just read the thing already.
+
+    Try to read `path` and return something that ndv can open.
+    """
+    path_str = str(path)
+    if path_str.endswith(".npy"):
+        return np.load(path_str)
+
+    errors: dict[str, Exception] = {}
+
+    if _is_tiff_file(path):
+        with collect_errors(errors, "tifffile"):
+            return _read_tifffile(path)
+
+    if _is_zarr_folder(path):
+        with collect_errors(errors, "tensorstore-zarr"):
+            return _read_tensorstore(path)
+        with collect_errors(errors, "zarr"):
+            return _read_zarr_python(path)
+
+    if _is_n5_folder(path):
+        with collect_errors(errors, "tensorstore-n5"):
+            return _read_tensorstore(path, driver="n5")
+
+    raise ValueError(_format_error_message(errors))
+
+
+def _is_tiff_file(path: str | Path) -> bool:
+    path = Path(path)
+    if path.is_file() and path.suffix.lower() in {".tif", ".tiff"}:
+        return True
+    return False
+
+
+def _is_n5_folder(path: str | Path) -> bool:
+    path = Path(path)
+    return path.is_dir() and any(path.glob("attributes.json"))
+
+
+def _is_zarr_folder(path: str | Path) -> bool:
+    if str(path).endswith(".zarr"):
+        return True
+    path = Path(path)
+    return path.is_dir() and any(path.glob("*.zarr"))
+
+
+def _read_tifffile(path: str | Path) -> Any:
+    import tifffile
+
+    path = Path(path)
+    if not path.is_file():
+        raise ValueError(f"Path {path} is not a file.")
+    logger.info("using tifffile")
+    return tifffile.imread(path)
+
+
+def _read_tensorstore(path: str | Path, driver: str = "zarr", level: int = 0) -> Any:
+    import tensorstore as ts
+
+    sub = _array_path(path, level=level)
+    store = ts.open({"driver": driver, "kvstore": str(path) + sub}).result()
+    logger.info("using tensorstore")
+    return store
+
+
+def _format_error_message(errors: dict[str, Exception]) -> str:
+    lines = ["\nCould not read file. Here's what we tried and errors we got", ""]
+    for _key, err in errors.items():
+        lines.append(f"{_key}:")
+        wrapped = wrap(str(err), width=120)
+        indented = indent("\n".join(wrapped), "    ")
+        lines.append(indented)
+    msg = "\n".join(lines)
+
+    if "No module named" in msg:
+        msg += "\n\nPlease install ndv with io support `pip install ndv[io]`."
+    return msg
+
+
+def _read_zarr_python(path: str | Path, level: int = 0) -> zarr.Array:
+    import zarr
+
+    _subpath = _array_path(path, level=level)
+    z = zarr.open(str(path) + _subpath, mode="r")
+    logger.info("using zarr python")
+    return z
+
+
+def _array_path(path: str | Path, level: int = 0) -> str:
+    import zarr
+
+    z = zarr.open(path, mode="r")
+    if isinstance(z, zarr.Array):
+        return "/"
+    levels: list[str] = []
+    if isinstance(z, zarr.Group):
+        with suppress(TypeError):
+            zattrs = json.loads(z.store.get(".zattrs"))
+            if "multiscales" in zattrs:
+                for dset in zattrs["multiscales"][0]["datasets"]:
+                    if "path" in dset:
+                        levels.append(dset["path"])
+                if levels:
+                    return "/" + levels[level]
+
+        arrays = list(z.array_keys())
+        if arrays:
+            return f"/{arrays[0]}"
+
+    if level != 0 and levels:
+        raise ValueError(
+            f"Could not find a dataset with level {level} in the group. Found: {levels}"
+        )
+    raise ValueError("Could not find an array or multiscales information in the group.")

src/ndv/util.py

@@ -2,7 +2,7 @@
 
 from __future__ import annotations
 
-from typing import TYPE_CHECKING, overload
+from typing import TYPE_CHECKING, Any, overload
 
 from ndv.controllers import ArrayViewer
 from ndv.views._app import run_app