Source code for ewokscore.persistence.nexus

from pathlib import Path
from typing import Any
from typing import List
from typing import Mapping

import h5py
from silx.io import h5py_utils
from silx.io.dictdump import dicttonx
from silx.io.dictdump import nxtodict
from silx.utils.proxy import docstring

from . import atomic
from .file import FileProxy


# @h5py_utils.retry(retry_period=1)


def h5_item_exists(path, item):
    try:
        with h5py_utils.File(path) as f:
            return item in f
    except Exception:
        return False





class NexusProxy(FileProxy):
    SCHEME = "nexus"
    EXTENSIONS = [".nx", "nxs", ".h5", ".hdf5", ".nexus"]
    ALLOW_PATH_IN_FILE = True



    @docstring(FileProxy)
    def exists(self) -> bool:
        if not super().exists():
            return False
        return h5_item_exists(self.path, self.path_in_file)


    def _dump(self, path: Path, data: Any, update_mode: str = "add", **_) -> None:
        if isinstance(data, Mapping):
            h5group = self.path_in_file
        else:
            h5group = self.path_in_file_parent
            h5name = self.path_in_file_name
            if h5name:
                data = {h5name: data}
            elif not isinstance(data, Mapping):
                raise TypeError("'data' must be a dictionary")
        with atomic.atomic_write_hdf5(path, h5group) as (h5file, h5group):
            dicttonx(
                treedict=data,
                h5file=h5file,
                h5path=h5group,
                update_mode=update_mode,
                add_nx_class=True,
            )
            self._set_nx_classes(h5file, self.path_in_file_parts())

    @staticmethod
    def _set_nx_classes(h5file, parts: List[str]):
        h5file.attrs["NX_class"] = "NXroot"
        h5group = h5file
        for i, name in enumerate(parts):
            h5group = h5group[name]
            if not isinstance(h5group, h5py.Group):
                break
            if i == 0:
                NX_class = "NXentry"
            elif i == 1:
                NX_class = "NXprocess"
            else:
                NX_class = "NXcollection"
            h5group.attrs["NX_class"] = NX_class

    def _load(self, path: Path, **kw) -> Any:
        h5group = self.path_in_file_parent
        h5name = self.path_in_file_name
        adict = nxtodict(h5file=str(path), path=h5group, **kw)
        if h5name:
            return adict[h5name]
        return adict