# /*##########################################################################
# Copyright (C) 2016-2023 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.
#
# ############################################################################*/
"""This module provides classes and function to convert file formats supported
by *silx* into HDF5 file. Currently, SPEC file and fabio images are the
supported formats.
Read the documentation of :mod:`silx.io.spech5`, :mod:`silx.io.fioh5` and :mod:`silx.io.fabioh5` for
information on the structure of the output HDF5 files.
Text strings are written to the HDF5 datasets as variable-length utf-8.
"""
__authors__ = ["P. Knobel"]
__license__ = "MIT"
__date__ = "17/07/2018"
import logging
import h5py
import numpy
import silx.io
from .utils import is_dataset, is_group, is_softlink, visitall
from . import fabioh5
_logger = logging.getLogger(__name__)
def _create_link(h5f, link_name, target_name, link_type="soft", overwrite_data=False):
"""Create a link in a HDF5 file
If member with name ``link_name`` already exists, delete it first or
ignore link depending on global param ``overwrite_data``.
:param h5f: :class:`h5py.File` object
:param link_name: Link path
:param target_name: Handle for target group or dataset
:param str link_type: "soft" or "hard"
:param bool overwrite_data: If True, delete existing member (group,
dataset or link) with the same name. Default is False.
"""
if link_name not in h5f:
_logger.debug("Creating link " + link_name + " -> " + target_name)
elif overwrite_data:
_logger.warning("Overwriting " + link_name + " with link to " + target_name)
del h5f[link_name]
else:
_logger.warning(
link_name + " already exist. Cannot create link to " + target_name
)
return None
if link_type == "hard":
h5f[link_name] = h5f[target_name]
elif link_type == "soft":
h5f[link_name] = h5py.SoftLink(target_name)
else:
raise ValueError("link_type must be 'hard' or 'soft'")
def _attr_utf8(attr_value):
"""If attr_value is bytes, make sure we output utf-8
:param attr_value: String (possibly bytes if PY2)
:return: Attr ready to be written by h5py as utf8
"""
if isinstance(attr_value, (bytes, str)):
out_attr_value = numpy.array(attr_value, dtype=h5py.special_dtype(vlen=str))
else:
out_attr_value = attr_value
return out_attr_value
class Hdf5Writer(object):
"""Converter class to write the content of a data file to a HDF5 file."""
def __init__(
self,
h5path="/",
overwrite_data=False,
link_type="soft",
create_dataset_args=None,
min_size=500,
):
"""
:param h5path: Target path where the scan groups will be written
in the output HDF5 file.
:param bool overwrite_data:
See documentation of :func:`write_to_h5`
:param str link_type: ``"hard"`` or ``"soft"`` (default)
:param dict create_dataset_args: Dictionary of args you want to pass to
``h5py.File.create_dataset``.
See documentation of :func:`write_to_h5`
:param int min_size:
See documentation of :func:`write_to_h5`
"""
self.h5path = h5path
if not h5path.startswith("/"):
# target path must be absolute
self.h5path = "/" + h5path
if not self.h5path.endswith("/"):
self.h5path += "/"
self._h5f = None
"""h5py.File object, assigned in :meth:`write`"""
if create_dataset_args is None:
create_dataset_args = {}
self.create_dataset_args = create_dataset_args
self.min_size = min_size
self.overwrite_data = overwrite_data # boolean
self.link_type = link_type
"""'soft' or 'hard' """
self._links = []
"""List of *(link_path, target_path)* tuples."""
def write(self, infile, h5f):
"""Copy `infile` content to `h5f` file under `h5path`.
All the parameters needed for the conversion have been initialized
in the constructor.
External links in `infile` are ignored.
:param Union[commonh5.Group,h5py.Group] infile:
File/Class from which to read the content to copy from.
:param h5py.File h5f: File where to write the copied content to
"""
# Recurse through all groups and datasets to add them to the HDF5
self._h5f = h5f
for name, item in visitall(infile):
self.append_member_to_h5(name, item)
# Handle the attributes of the root group
root_grp = h5f[self.h5path]
for key in infile.attrs:
if self.overwrite_data or key not in root_grp.attrs:
root_grp.attrs.create(key, _attr_utf8(infile.attrs[key]))
# Handle links at the end, when their targets are created
for link_name, target_name in self._links:
_create_link(
self._h5f,
link_name,
target_name,
link_type=self.link_type,
overwrite_data=self.overwrite_data,
)
self._links = []
def append_member_to_h5(self, h5like_name, obj):
"""Add one group or one dataset to :attr:`h5f`"""
h5_name = self.h5path + h5like_name.lstrip("/")
if is_softlink(obj):
# links to be created after all groups and datasets
h5_target = self.h5path + obj.path.lstrip("/")
self._links.append((h5_name, h5_target))
elif is_dataset(obj):
_logger.debug("Saving dataset: " + h5_name)
member_initially_exists = h5_name in self._h5f
if self.overwrite_data and member_initially_exists:
_logger.warning("Overwriting dataset: " + h5_name)
del self._h5f[h5_name]
if self.overwrite_data or not member_initially_exists:
if isinstance(obj, fabioh5.FrameData) and len(obj.shape) > 2:
# special case of multiframe data
# write frame by frame to save memory usage low
ds = self._h5f.create_dataset(
h5_name,
shape=obj.shape,
dtype=obj.dtype,
**self.create_dataset_args,
)
for i, frame in enumerate(obj):
ds[i] = frame
else:
# fancy arguments don't apply to small dataset
if obj.size < self.min_size:
ds = self._h5f.create_dataset(h5_name, data=obj[()])
else:
ds = self._h5f.create_dataset(
h5_name, data=obj[()], **self.create_dataset_args
)
else:
ds = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in ds.attrs:
ds.attrs.create(key, _attr_utf8(obj.attrs[key]))
if not self.overwrite_data and member_initially_exists:
_logger.warning("Not overwriting existing dataset: " + h5_name)
elif is_group(obj):
if h5_name not in self._h5f:
_logger.debug("Creating group: " + h5_name)
grp = self._h5f.create_group(h5_name)
else:
grp = self._h5f[h5_name]
# add HDF5 attributes
for key in obj.attrs:
if self.overwrite_data or key not in grp.attrs:
grp.attrs.create(key, _attr_utf8(obj.attrs[key]))
else:
_logger.warning("Unsuppored entity, ignoring: %s", h5_name)
[docs]
def write_to_h5(
infile,
h5file,
h5path="/",
mode="a",
overwrite_data=False,
link_type="soft",
create_dataset_args=None,
min_size=500,
):
"""Write content of a h5py-like object into a HDF5 file.
Warning: External links in `infile` are ignored.
:param infile: Path of input file, :class:`commonh5.File`,
:class:`commonh5.Group`, :class:`h5py.File` or :class:`h5py.Group`
:param h5file: Path of output HDF5 file or HDF5 file handle
(`h5py.File` object)
:param str h5path: Target path in HDF5 file in which scan groups are created.
Default is root (``"/"``)
:param str mode: Can be ``"r+"`` (read/write, file must exist),
``"w"`` (write, existing file is lost), ``"w-"`` (write, fail
if exists) or ``"a"`` (read/write if exists, create otherwise).
This parameter is ignored if ``h5file`` is a file handle.
:param bool overwrite_data: If ``True``, existing groups and datasets can be
overwritten, if ``False`` they are skipped. This parameter is only
relevant if ``file_mode`` is ``"r+"`` or ``"a"``.
:param str link_type: *"soft"* (default) or *"hard"*
:param dict create_dataset_args: Dictionary of args you want to pass to
``h5py.File.create_dataset``. This allows you to specify filters and
compression parameters. Don't specify ``name`` and ``data``.
These arguments are only applied to datasets larger than 1MB.
:param int min_size: Minimum number of elements in a dataset to apply
chunking and compression. Default is 500.
The structure of the spec data in an HDF5 file is described in the
documentation of :mod:`silx.io.spech5`.
"""
writer = Hdf5Writer(
h5path=h5path,
overwrite_data=overwrite_data,
link_type=link_type,
create_dataset_args=create_dataset_args,
min_size=min_size,
)
# both infile and h5file can be either file handle or a file name: 4 cases
if not isinstance(h5file, h5py.File) and not is_group(infile):
with silx.io.open(infile) as h5pylike:
with h5py.File(h5file, mode) as h5f:
writer.write(h5pylike, h5f)
elif isinstance(h5file, h5py.File) and not is_group(infile):
with silx.io.open(infile) as h5pylike:
writer.write(h5pylike, h5file)
elif is_group(infile) and not isinstance(h5file, h5py.File):
with h5py.File(h5file, mode) as h5f:
writer.write(infile, h5f)
else:
writer.write(infile, h5file)
[docs]
def convert(infile, h5file, mode="w-", create_dataset_args=None):
"""Convert a supported file into an HDF5 file, write scans into the
root group (``/``).
This is a convenience shortcut to call::
write_to_h5(h5like, h5file, h5path='/',
mode="w-", link_type="soft")
:param infile: Path of input file or :class:`commonh5.File` object
or :class:`commonh5.Group` object
:param h5file: Path of output HDF5 file, or h5py.File object
:param mode: Can be ``"w"`` (write, existing file is
lost), ``"w-"`` (write, fail if exists). This is ignored
if ``h5file`` is a file handle.
:param create_dataset_args: Dictionary of args you want to pass to
``h5py.File.create_dataset``. This allows you to specify filters and
compression parameters. Don't specify ``name`` and ``data``.
"""
if mode not in ["w", "w-"]:
raise IOError(
"File mode must be 'w' or 'w-'. Use write_to_h5"
+ " to append data to an existing HDF5 file."
)
write_to_h5(
infile, h5file, h5path="/", mode=mode, create_dataset_args=create_dataset_args
)
