+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+from typing import Any, Dict, Tuple
+
+import nd2
+import xarray as xr
+from bioio_base import constants, exceptions, io, reader, types
+from fsspec.implementations.local import LocalFileSystem
+from fsspec.spec import AbstractFileSystem
+
+###############################################################################
+
+
+
+
[docs]
+
class Reader(reader.Reader):
+
"""Read NIS-Elements files using the Nikon nd2 SDK.
+
+
This reader requires `nd2` to be installed in the environment.
+
+
Parameters
+
----------
+
image : Path or str
+
path to file
+
fs_kwargs: Dict[str, Any]
+
Any specific keyword arguments to pass down to the fsspec created filesystem.
+
Default: {}
+
+
Raises
+
------
+
exceptions.UnsupportedFileFormatError
+
If the file is not supported by ND2.
+
"""
+
+
@staticmethod
+
def _is_supported_image(fs: AbstractFileSystem, path: str, **kwargs: Any) -> bool:
+
return nd2.is_supported_file(path, fs.open)
+
+
def __init__(self, image: types.PathLike, fs_kwargs: Dict[str, Any] = {}):
+
self._fs, self._path = io.pathlike_to_fs(
+
image,
+
enforce_exists=True,
+
fs_kwargs=fs_kwargs,
+
)
+
# Catch non-local file system
+
if not isinstance(self._fs, LocalFileSystem):
+
raise ValueError(
+
f"Cannot read ND2 from non-local file system. "
+
f"Received URI: {self._path}, which points to {type(self._fs)}."
+
)
+
+
if not self._is_supported_image(self._fs, self._path):
+
raise exceptions.UnsupportedFileFormatError(
+
self.__class__.__name__, self._path
+
)
+
+
@property
+
def scenes(self) -> Tuple[str, ...]:
+
with nd2.ND2File(self._path) as rdr:
+
return tuple(rdr._position_names())
+
+
def _read_delayed(self) -> xr.DataArray:
+
return self._xarr_reformat(delayed=True)
+
+
def _read_immediate(self) -> xr.DataArray:
+
return self._xarr_reformat(delayed=False)
+
+
def _xarr_reformat(self, delayed: bool) -> xr.DataArray:
+
with nd2.ND2File(self._path) as rdr:
+
xarr = rdr.to_xarray(
+
delayed=delayed, squeeze=False, position=self.current_scene_index
+
)
+
xarr.attrs[constants.METADATA_UNPROCESSED] = xarr.attrs.pop("metadata")
+
if self.current_scene_index is not None:
+
xarr.attrs[constants.METADATA_UNPROCESSED][
+
"frame"
+
] = rdr.frame_metadata(self.current_scene_index)
+
return xarr.isel({nd2.AXIS.POSITION: 0}, missing_dims="ignore")
+
+
@property
+
def physical_pixel_sizes(self) -> types.PhysicalPixelSizes:
+
"""
+
Returns
+
-------
+
sizes: PhysicalPixelSizes
+
Using available metadata, the floats representing physical pixel sizes for
+
dimensions Z, Y, and X.
+
+
Notes
+
-----
+
We currently do not handle unit attachment to these values. Please see the file
+
metadata for unit information.
+
"""
+
with nd2.ND2File(self._path) as rdr:
+
return types.PhysicalPixelSizes(*rdr.voxel_size()[::-1])