Add a copy of silx h5py_read_dataset to xsocs

xsocs/util/silx_io_utils.py

+# coding: utf-8
+# /*##########################################################################
+# Copyright (C) 2016-2020 European Synchrotron Radiation Facility
+#
+# 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.
+#
+# ############################################################################*/
+""" I/O utility functions"""
+
+__authors__ = ["P. Knobel", "V. Valls"]
+__license__ = "MIT"
+__date__ = "25/09/2020"
+
+import logging
+
+import numpy
+
+import h5py
+import h5py.h5t
+
+
+logger = logging.getLogger(__name__)
+
+
+def h5py_decode_value(value, encoding="utf-8", errors="surrogateescape"):
+    """Keep bytes when value cannot be decoded
+
+    :param value: bytes or array of bytes
+    :param encoding str:
+    :param errors str:
+    """
+    try:
+        if numpy.isscalar(value):
+            return value.decode(encoding, errors=errors)
+        str_item = [b.decode(encoding, errors=errors) for b in value.flat]
+        return numpy.array(str_item, dtype=object).reshape(value.shape)
+    except UnicodeDecodeError:
+        return value
+
+
+def h5py_encode_value(value, encoding="utf-8", errors="surrogateescape"):
+    """Keep string when value cannot be encoding
+
+    :param value: string or array of strings
+    :param encoding str:
+    :param errors str:
+    """
+    try:
+        if numpy.isscalar(value):
+            return value.encode(encoding, errors=errors)
+        bytes_item = [s.encode(encoding, errors=errors) for s in value.flat]
+        return numpy.array(bytes_item, dtype=object).reshape(value.shape)
+    except UnicodeEncodeError:
+        return value
+
+
+class H5pyDatasetReadWrapper:
+    """Wrapper to handle H5T_STRING decoding on-the-fly when reading
+    a dataset. Uniform behaviour for h5py 2.x and h5py 3.x
+
+    h5py abuses H5T_STRING with ASCII character set
+    to store `bytes`: dset[()] = b"..."
+    Therefore an H5T_STRING with ASCII encoding is not decoded by default.
+    """
+
+    H5PY_AUTODECODE_NONASCII = int(h5py.version.version.split(".")[0]) < 3
+
+    def __init__(self, dset, decode_ascii=False):
+        """
+        :param h5py.Dataset dset:
+        :param bool decode_ascii:
+        """
+        try:
+            string_info = h5py.h5t.check_string_dtype(dset.dtype)
+        except AttributeError:
+            # h5py < 2.10
+            try:
+                idx = dset.id.get_type().get_cset()
+            except AttributeError:
+                # Not an H5T_STRING
+                encoding = None
+            else:
+                encoding = ["ascii", "utf-8"][idx]
+        else:
+            # h5py >= 2.10
+            try:
+                encoding = string_info.encoding
+            except AttributeError:
+                # Not an H5T_STRING
+                encoding = None
+        if encoding == "ascii" and not decode_ascii:
+            encoding = None
+        if encoding != "ascii" and self.H5PY_AUTODECODE_NONASCII:
+            # Decoding is already done by the h5py library
+            encoding = None
+        if encoding == "ascii":
+            # ASCII can be decoded as UTF-8
+            encoding = "utf-8"
+        self._encoding = encoding
+        self._dset = dset
+
+    def __getitem__(self, args):
+        value = self._dset[args]
+        if self._encoding:
+            return h5py_decode_value(value, encoding=self._encoding)
+        else:
+            return value
+
+
+def h5py_read_dataset(dset, index=tuple(), decode_ascii=False):
+    """Read data from dataset object. UTF-8 strings will be
+    decoded while ASCII strings will only be decoded when
+    `decode_ascii=True`.
+
+    :param h5py.Dataset dset:
+    :param index: slicing (all by default)
+    :param bool decode_ascii:
+    """
+    return H5pyDatasetReadWrapper(dset, decode_ascii=decode_ascii)[index]