Source code for satpy.readers.hdf5_utils

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# Copyright (c) 2016-2017, 2019 Satpy developers
# This file is part of satpy.
# satpy is free software: you can redistribute it and/or modify it under the
# terms of the GNU General Public License as published by the Free Software
# Foundation, either version 3 of the License, or (at your option) any later
# version.
# satpy is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE.  See the GNU General Public License for more details.
# You should have received a copy of the GNU General Public License along with
# satpy.  If not, see <>.
"""Helpers for reading hdf5-based files."""

import logging

import dask.array as da
import h5py
import numpy as np
import xarray as xr

from satpy import CHUNK_SIZE
from satpy.readers.file_handlers import BaseFileHandler
from satpy.readers.utils import np2str

LOG = logging.getLogger(__name__)

[docs]class HDF5FileHandler(BaseFileHandler): """Small class for inspecting a HDF5 file and retrieve its metadata/header data.""" def __init__(self, filename, filename_info, filetype_info): """Initialize file handler.""" super(HDF5FileHandler, self).__init__( filename, filename_info, filetype_info) self.file_content = {} self._attrs_cache = {} try: file_handle = h5py.File(self.filename, 'r') except IOError: LOG.exception( 'Failed reading file %s. Possibly corrupted file', self.filename) raise file_handle.visititems(self.collect_metadata) self._collect_attrs('', file_handle.attrs) file_handle.close() def _collect_attrs(self, name, attrs): attrs_cache = self._attrs_cache.setdefault(name, {}) for key, value in attrs.items(): value = np.squeeze(value) fc_key = "{}/attr/{}".format(name, key) try: value = np2str(value) except ValueError: # use the original value pass except AttributeError: # A HDF5 reference ? value = self.get_reference(name, key) if value is None: LOG.warning("Value cannot be converted - skip setting attribute %s", fc_key) continue self.file_content[fc_key] = attrs_cache[key] = value
[docs] def get_reference(self, name, key): """Get reference.""" with h5py.File(self.filename, 'r') as hf: return self._get_reference(hf, hf[name].attrs[key])
def _get_reference(self, hf, ref): try: return [self._get_reference(hf, elt) for elt in ref] except TypeError: if isinstance(ref, h5py.h5r.Reference): ref_name = h5py.h5r.get_name(ref, return hf[ref_name][()]
[docs] def collect_metadata(self, name, obj): """Collect metadata.""" if isinstance(obj, h5py.Dataset): self.file_content[name] = obj self.file_content[name + "/dtype"] = obj.dtype self.file_content[name + "/shape"] = obj.shape self._collect_attrs(name, obj.attrs)
def __getitem__(self, key): """Get item for given key.""" val = self.file_content[key] if isinstance(val, h5py.Dataset): # these datasets are closed and inaccessible when the file is closed, need to reopen dset = h5py.File(self.filename, 'r')[key] dset_data = da.from_array(dset, chunks=CHUNK_SIZE) attrs = self._attrs_cache.get(key, dset.attrs) if dset.ndim == 2: return xr.DataArray(dset_data, dims=['y', 'x'], attrs=attrs) return xr.DataArray(dset_data, attrs=attrs) return val def __contains__(self, item): """Get item from file content.""" return item in self.file_content
[docs] def get(self, item, default=None): """Get item.""" if item in self: return self[item] else: return default