619 lines
23 KiB
Python
619 lines
23 KiB
Python
# This file is part of h5py, a Python interface to the HDF5 library.
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#
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# http://www.h5py.org
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#
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# Copyright 2008-2013 Andrew Collette and contributors
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#
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# License: Standard 3-clause BSD; see "license.txt" for full license terms
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# and contributor agreement.
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"""
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Implements high-level support for HDF5 file objects.
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"""
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import sys
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import os
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from warnings import warn
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from .compat import filename_decode, filename_encode
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from .base import phil, with_phil
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from .group import Group
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from .. import h5, h5f, h5p, h5i, h5fd, _objects
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from .. import version
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mpi = h5.get_config().mpi
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ros3 = h5.get_config().ros3
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direct_vfd = h5.get_config().direct_vfd
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hdf5_version = version.hdf5_version_tuple[0:3]
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swmr_support = False
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if hdf5_version >= h5.get_config().swmr_min_hdf5_version:
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swmr_support = True
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libver_dict = {'earliest': h5f.LIBVER_EARLIEST, 'latest': h5f.LIBVER_LATEST}
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libver_dict_r = dict((y, x) for x, y in libver_dict.items())
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if hdf5_version >= (1, 10, 2):
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libver_dict.update({'v108': h5f.LIBVER_V18, 'v110': h5f.LIBVER_V110})
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libver_dict_r.update({h5f.LIBVER_V18: 'v108', h5f.LIBVER_V110: 'v110'})
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if hdf5_version >= (1, 11, 4):
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libver_dict.update({'v112': h5f.LIBVER_V112})
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libver_dict_r.update({h5f.LIBVER_V112: 'v112'})
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if hdf5_version >= (1, 13, 0):
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libver_dict.update({'v114': h5f.LIBVER_V114})
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libver_dict_r.update({h5f.LIBVER_V114: 'v114'})
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def _set_fapl_mpio(plist, **kwargs):
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"""Set file access property list for mpio driver"""
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if not mpi:
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raise ValueError("h5py was built without MPI support, can't use mpio driver")
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import mpi4py.MPI
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kwargs.setdefault('info', mpi4py.MPI.Info())
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plist.set_fapl_mpio(**kwargs)
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def _set_fapl_fileobj(plist, **kwargs):
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"""Set the Python file object driver in a file access property list"""
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plist.set_fileobj_driver(h5fd.fileobj_driver, kwargs.get('fileobj'))
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_drivers = {
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'sec2': lambda plist, **kwargs: plist.set_fapl_sec2(**kwargs),
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'stdio': lambda plist, **kwargs: plist.set_fapl_stdio(**kwargs),
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'core': lambda plist, **kwargs: plist.set_fapl_core(**kwargs),
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'family': lambda plist, **kwargs: plist.set_fapl_family(
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memb_fapl=plist.copy(),
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**kwargs
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),
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'mpio': _set_fapl_mpio,
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'fileobj': _set_fapl_fileobj,
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'split': lambda plist, **kwargs: plist.set_fapl_split(**kwargs),
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}
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if ros3:
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_drivers['ros3'] = lambda plist, **kwargs: plist.set_fapl_ros3(**kwargs)
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if direct_vfd:
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_drivers['direct'] = lambda plist, **kwargs: plist.set_fapl_direct(**kwargs) # noqa
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def register_driver(name, set_fapl):
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"""Register a custom driver.
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Parameters
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----------
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name : str
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The name of the driver.
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set_fapl : callable[PropFAID, **kwargs] -> NoneType
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The function to set the fapl to use your custom driver.
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"""
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_drivers[name] = set_fapl
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def unregister_driver(name):
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"""Unregister a custom driver.
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Parameters
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----------
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name : str
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The name of the driver.
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"""
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del _drivers[name]
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def registered_drivers():
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"""Return a frozenset of the names of all of the registered drivers.
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"""
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return frozenset(_drivers)
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def make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, locking,
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page_buf_size, min_meta_keep, min_raw_keep,
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alignment_threshold, alignment_interval, meta_block_size,
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**kwds):
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""" Set up a file access property list """
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plist = h5p.create(h5p.FILE_ACCESS)
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if libver is not None:
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if libver in libver_dict:
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low = libver_dict[libver]
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high = h5f.LIBVER_LATEST
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else:
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low, high = (libver_dict[x] for x in libver)
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else:
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# we default to earliest
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low, high = h5f.LIBVER_EARLIEST, h5f.LIBVER_LATEST
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plist.set_libver_bounds(low, high)
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plist.set_alignment(alignment_threshold, alignment_interval)
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cache_settings = list(plist.get_cache())
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if rdcc_nslots is not None:
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cache_settings[1] = rdcc_nslots
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if rdcc_nbytes is not None:
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cache_settings[2] = rdcc_nbytes
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if rdcc_w0 is not None:
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cache_settings[3] = rdcc_w0
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plist.set_cache(*cache_settings)
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if page_buf_size:
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plist.set_page_buffer_size(int(page_buf_size), int(min_meta_keep),
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int(min_raw_keep))
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if meta_block_size is not None:
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plist.set_meta_block_size(int(meta_block_size))
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if locking is not None:
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if hdf5_version < (1, 12, 1) and (hdf5_version[:2] != (1, 10) or hdf5_version[2] < 7):
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raise ValueError(
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"HDF5 version >= 1.12.1 or 1.10.x >= 1.10.7 required for file locking.")
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if locking in ("false", False):
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plist.set_file_locking(False, ignore_when_disabled=False)
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elif locking in ("true", True):
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plist.set_file_locking(True, ignore_when_disabled=False)
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elif locking == "best-effort":
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plist.set_file_locking(True, ignore_when_disabled=True)
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else:
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raise ValueError(f"Unsupported locking value: {locking}")
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if driver is None or (driver == 'windows' and sys.platform == 'win32'):
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# Prevent swallowing unused key arguments
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if kwds:
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msg = "'{key}' is an invalid keyword argument for this function" \
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.format(key=next(iter(kwds)))
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raise TypeError(msg)
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return plist
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try:
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set_fapl = _drivers[driver]
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except KeyError:
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raise ValueError('Unknown driver type "%s"' % driver)
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else:
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set_fapl(plist, **kwds)
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return plist
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def make_fcpl(track_order=False, fs_strategy=None, fs_persist=False,
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fs_threshold=1, fs_page_size=None):
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""" Set up a file creation property list """
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if track_order or fs_strategy:
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plist = h5p.create(h5p.FILE_CREATE)
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if track_order:
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plist.set_link_creation_order(
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h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
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plist.set_attr_creation_order(
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h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
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if fs_strategy:
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strategies = {
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'fsm': h5f.FSPACE_STRATEGY_FSM_AGGR,
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'page': h5f.FSPACE_STRATEGY_PAGE,
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'aggregate': h5f.FSPACE_STRATEGY_AGGR,
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'none': h5f.FSPACE_STRATEGY_NONE
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}
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fs_strat_num = strategies.get(fs_strategy, -1)
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if fs_strat_num == -1:
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raise ValueError("Invalid file space strategy type")
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plist.set_file_space_strategy(fs_strat_num, fs_persist, fs_threshold)
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if fs_page_size and fs_strategy == 'page':
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plist.set_file_space_page_size(int(fs_page_size))
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else:
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plist = None
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return plist
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def make_fid(name, mode, userblock_size, fapl, fcpl=None, swmr=False):
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""" Get a new FileID by opening or creating a file.
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Also validates mode argument."""
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if userblock_size is not None:
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if mode in ('r', 'r+'):
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raise ValueError("User block may only be specified "
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"when creating a file")
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try:
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userblock_size = int(userblock_size)
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except (TypeError, ValueError):
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raise ValueError("User block size must be an integer")
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if fcpl is None:
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fcpl = h5p.create(h5p.FILE_CREATE)
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fcpl.set_userblock(userblock_size)
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if mode == 'r':
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flags = h5f.ACC_RDONLY
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if swmr and swmr_support:
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flags |= h5f.ACC_SWMR_READ
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fid = h5f.open(name, flags, fapl=fapl)
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elif mode == 'r+':
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fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
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elif mode in ['w-', 'x']:
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fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl)
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elif mode == 'w':
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fid = h5f.create(name, h5f.ACC_TRUNC, fapl=fapl, fcpl=fcpl)
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elif mode == 'a':
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# Open in append mode (read/write).
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# If that fails, create a new file only if it won't clobber an
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# existing one (ACC_EXCL)
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try:
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fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl)
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# Not all drivers raise FileNotFoundError (commented those that do not)
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except FileNotFoundError if fapl.get_driver() in (
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h5fd.SEC2,
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h5fd.DIRECT if direct_vfd else -1,
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# h5fd.STDIO,
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# h5fd.CORE,
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h5fd.FAMILY,
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h5fd.WINDOWS,
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# h5fd.MPIO,
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# h5fd.MPIPOSIX,
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h5fd.fileobj_driver,
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h5fd.ROS3D if ros3 else -1,
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) else OSError:
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fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl)
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else:
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raise ValueError("Invalid mode; must be one of r, r+, w, w-, x, a")
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try:
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if userblock_size is not None:
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existing_fcpl = fid.get_create_plist()
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if existing_fcpl.get_userblock() != userblock_size:
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raise ValueError("Requested userblock size (%d) does not match that of existing file (%d)" % (userblock_size, existing_fcpl.get_userblock()))
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except Exception as e:
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fid.close()
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raise e
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return fid
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class File(Group):
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"""
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Represents an HDF5 file.
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"""
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@property
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def attrs(self):
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""" Attributes attached to this object """
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# hdf5 complains that a file identifier is an invalid location for an
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# attribute. Instead of self, pass the root group to AttributeManager:
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from . import attrs
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with phil:
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return attrs.AttributeManager(self['/'])
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@property
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@with_phil
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def filename(self):
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"""File name on disk"""
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return filename_decode(h5f.get_name(self.id))
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@property
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@with_phil
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def driver(self):
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"""Low-level HDF5 file driver used to open file"""
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drivers = {h5fd.SEC2: 'sec2',
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h5fd.STDIO: 'stdio',
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h5fd.CORE: 'core',
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h5fd.FAMILY: 'family',
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h5fd.WINDOWS: 'windows',
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h5fd.MPIO: 'mpio',
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h5fd.MPIPOSIX: 'mpiposix',
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h5fd.fileobj_driver: 'fileobj'}
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if ros3:
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drivers[h5fd.ROS3D] = 'ros3'
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if direct_vfd:
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drivers[h5fd.DIRECT] = 'direct'
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return drivers.get(self.id.get_access_plist().get_driver(), 'unknown')
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@property
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@with_phil
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def mode(self):
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""" Python mode used to open file """
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write_intent = h5f.ACC_RDWR
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if swmr_support:
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write_intent |= h5f.ACC_SWMR_WRITE
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return 'r+' if self.id.get_intent() & write_intent else 'r'
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@property
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@with_phil
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def libver(self):
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"""File format version bounds (2-tuple: low, high)"""
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bounds = self.id.get_access_plist().get_libver_bounds()
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return tuple(libver_dict_r[x] for x in bounds)
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@property
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@with_phil
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def userblock_size(self):
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""" User block size (in bytes) """
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fcpl = self.id.get_create_plist()
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return fcpl.get_userblock()
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@property
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@with_phil
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def meta_block_size(self):
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""" Meta block size (in bytes) """
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fapl = self.id.get_access_plist()
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return fapl.get_meta_block_size()
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if mpi and hdf5_version >= (1, 8, 9):
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@property
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@with_phil
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def atomic(self):
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""" Set/get MPI-IO atomic mode
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"""
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return self.id.get_mpi_atomicity()
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@atomic.setter
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@with_phil
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def atomic(self, value):
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# pylint: disable=missing-docstring
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self.id.set_mpi_atomicity(value)
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@property
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@with_phil
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def swmr_mode(self):
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""" Controls single-writer multiple-reader mode """
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return swmr_support and bool(self.id.get_intent() & (h5f.ACC_SWMR_READ | h5f.ACC_SWMR_WRITE))
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@swmr_mode.setter
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@with_phil
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def swmr_mode(self, value):
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# pylint: disable=missing-docstring
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if swmr_support:
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if value:
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self.id.start_swmr_write()
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else:
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raise ValueError("It is not possible to forcibly switch SWMR mode off.")
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else:
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raise RuntimeError('SWMR support is not available in HDF5 version {}.{}.{}.'.format(*hdf5_version))
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def __init__(self, name, mode='r', driver=None, libver=None, userblock_size=None, swmr=False,
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rdcc_nslots=None, rdcc_nbytes=None, rdcc_w0=None, track_order=None,
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fs_strategy=None, fs_persist=False, fs_threshold=1, fs_page_size=None,
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page_buf_size=None, min_meta_keep=0, min_raw_keep=0, locking=None,
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alignment_threshold=1, alignment_interval=1, meta_block_size=None, **kwds):
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"""Create a new file object.
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See the h5py user guide for a detailed explanation of the options.
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name
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Name of the file on disk, or file-like object. Note: for files
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created with the 'core' driver, HDF5 still requires this be
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non-empty.
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mode
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r Readonly, file must exist (default)
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r+ Read/write, file must exist
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w Create file, truncate if exists
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w- or x Create file, fail if exists
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a Read/write if exists, create otherwise
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driver
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Name of the driver to use. Legal values are None (default,
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recommended), 'core', 'sec2', 'direct', 'stdio', 'mpio', 'ros3'.
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libver
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Library version bounds. Supported values: 'earliest', 'v108',
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'v110', 'v112' and 'latest'. The 'v108', 'v110' and 'v112'
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options can only be specified with the HDF5 1.10.2 library or later.
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userblock_size
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Desired size of user block. Only allowed when creating a new
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file (mode w, w- or x).
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swmr
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Open the file in SWMR read mode. Only used when mode = 'r'.
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rdcc_nbytes
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Total size of the dataset chunk cache in bytes. The default size
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is 1024**2 (1 MiB) per dataset. Applies to all datasets unless individually changed.
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rdcc_w0
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The chunk preemption policy for all datasets. This must be
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between 0 and 1 inclusive and indicates the weighting according to
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which chunks which have been fully read or written are penalized
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when determining which chunks to flush from cache. A value of 0
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means fully read or written chunks are treated no differently than
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other chunks (the preemption is strictly LRU) while a value of 1
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means fully read or written chunks are always preempted before
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other chunks. If your application only reads or writes data once,
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this can be safely set to 1. Otherwise, this should be set lower
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depending on how often you re-read or re-write the same data. The
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default value is 0.75. Applies to all datasets unless individually changed.
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rdcc_nslots
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The number of chunk slots in the raw data chunk cache for this
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file. Increasing this value reduces the number of cache collisions,
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but slightly increases the memory used. Due to the hashing
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strategy, this value should ideally be a prime number. As a rule of
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thumb, this value should be at least 10 times the number of chunks
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that can fit in rdcc_nbytes bytes. For maximum performance, this
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value should be set approximately 100 times that number of
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chunks. The default value is 521. Applies to all datasets unless individually changed.
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track_order
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Track dataset/group/attribute creation order under root group
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if True. If None use global default h5.get_config().track_order.
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fs_strategy
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The file space handling strategy to be used. Only allowed when
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creating a new file (mode w, w- or x). Defined as:
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"fsm" FSM, Aggregators, VFD
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"page" Paged FSM, VFD
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"aggregate" Aggregators, VFD
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"none" VFD
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If None use HDF5 defaults.
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fs_page_size
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File space page size in bytes. Only used when fs_strategy="page". If
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None use the HDF5 default (4096 bytes).
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fs_persist
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A boolean value to indicate whether free space should be persistent
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or not. Only allowed when creating a new file. The default value
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is False.
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fs_threshold
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The smallest free-space section size that the free space manager
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will track. Only allowed when creating a new file. The default
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value is 1.
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page_buf_size
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Page buffer size in bytes. Only allowed for HDF5 files created with
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fs_strategy="page". Must be a power of two value and greater or
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equal than the file space page size when creating the file. It is
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not used by default.
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min_meta_keep
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Minimum percentage of metadata to keep in the page buffer before
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allowing pages containing metadata to be evicted. Applicable only if
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page_buf_size is set. Default value is zero.
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min_raw_keep
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Minimum percentage of raw data to keep in the page buffer before
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allowing pages containing raw data to be evicted. Applicable only if
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page_buf_size is set. Default value is zero.
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locking
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The file locking behavior. Defined as:
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|
|
- False (or "false") -- Disable file locking
|
|
- True (or "true") -- Enable file locking
|
|
- "best-effort" -- Enable file locking but ignore some errors
|
|
- None -- Use HDF5 defaults
|
|
|
|
.. warning::
|
|
|
|
The HDF5_USE_FILE_LOCKING environment variable can override
|
|
this parameter.
|
|
|
|
Only available with HDF5 >= 1.12.1 or 1.10.x >= 1.10.7.
|
|
|
|
alignment_threshold
|
|
Together with ``alignment_interval``, this property ensures that
|
|
any file object greater than or equal in size to the alignement
|
|
threshold (in bytes) will be aligned on an address which is a
|
|
multiple of alignment interval.
|
|
|
|
alignment_interval
|
|
This property should be used in conjunction with
|
|
``alignment_threshold``. See the description above. For more
|
|
details, see
|
|
https://portal.hdfgroup.org/display/HDF5/H5P_SET_ALIGNMENT
|
|
|
|
meta_block_size
|
|
Set the current minimum size, in bytes, of new metadata block allocations.
|
|
See https://portal.hdfgroup.org/display/HDF5/H5P_SET_META_BLOCK_SIZE
|
|
|
|
Additional keywords
|
|
Passed on to the selected file driver.
|
|
"""
|
|
if (fs_strategy or page_buf_size) and hdf5_version < (1, 10, 1):
|
|
raise ValueError("HDF5 version 1.10.1 or greater required for file space strategy or page buffering support.")
|
|
|
|
if swmr and not swmr_support:
|
|
raise ValueError("The SWMR feature is not available in this version of the HDF5 library")
|
|
|
|
if driver == 'ros3':
|
|
if ros3:
|
|
from urllib.parse import urlparse
|
|
url = urlparse(name)
|
|
if url.scheme == 's3':
|
|
aws_region = kwds.get('aws_region', b'').decode('ascii')
|
|
if len(aws_region) == 0:
|
|
raise ValueError('AWS region required for s3:// location')
|
|
name = f'https://s3.{aws_region}.amazonaws.com/{url.netloc}{url.path}'
|
|
elif url.scheme not in ('https', 'http'):
|
|
raise ValueError(f'{name}: S3 location must begin with '
|
|
'either "https://", "http://", or "s3://"')
|
|
else:
|
|
raise ValueError(
|
|
"h5py was built without ROS3 support, can't use ros3 driver")
|
|
|
|
if locking is not None and hdf5_version < (1, 12, 1) and (
|
|
hdf5_version[:2] != (1, 10) or hdf5_version[2] < 7):
|
|
raise ValueError("HDF5 version >= 1.12.1 or 1.10.x >= 1.10.7 required for file locking options.")
|
|
|
|
if isinstance(name, _objects.ObjectID):
|
|
if fs_strategy:
|
|
raise ValueError("Unable to set file space strategy of an existing file")
|
|
|
|
with phil:
|
|
fid = h5i.get_file_id(name)
|
|
else:
|
|
if hasattr(name, 'read') and hasattr(name, 'seek'):
|
|
if driver not in (None, 'fileobj'):
|
|
raise ValueError("Driver must be 'fileobj' for file-like object if specified.")
|
|
driver = 'fileobj'
|
|
if kwds.get('fileobj', name) != name:
|
|
raise ValueError("Invalid value of 'fileobj' argument; "
|
|
"must equal to file-like object if specified.")
|
|
kwds.update(fileobj=name)
|
|
name = repr(name).encode('ASCII', 'replace')
|
|
else:
|
|
name = filename_encode(name)
|
|
|
|
if track_order is None:
|
|
track_order = h5.get_config().track_order
|
|
|
|
if fs_strategy and mode not in ('w', 'w-', 'x'):
|
|
raise ValueError("Unable to set file space strategy of an existing file")
|
|
|
|
if swmr and mode != 'r':
|
|
warn(
|
|
"swmr=True only affects read ('r') mode. For swmr write "
|
|
"mode, set f.swmr_mode = True after opening the file.",
|
|
stacklevel=2,
|
|
)
|
|
|
|
with phil:
|
|
fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0,
|
|
locking, page_buf_size, min_meta_keep, min_raw_keep,
|
|
alignment_threshold=alignment_threshold,
|
|
alignment_interval=alignment_interval,
|
|
meta_block_size=meta_block_size,
|
|
**kwds)
|
|
fcpl = make_fcpl(track_order=track_order, fs_strategy=fs_strategy,
|
|
fs_persist=fs_persist, fs_threshold=fs_threshold,
|
|
fs_page_size=fs_page_size)
|
|
fid = make_fid(name, mode, userblock_size, fapl, fcpl, swmr=swmr)
|
|
|
|
if isinstance(libver, tuple):
|
|
self._libver = libver
|
|
else:
|
|
self._libver = (libver, 'latest')
|
|
|
|
super().__init__(fid)
|
|
|
|
def close(self):
|
|
""" Close the file. All open objects become invalid """
|
|
with phil:
|
|
# Check that the file is still open, otherwise skip
|
|
if self.id.valid:
|
|
# We have to explicitly murder all open objects related to the file
|
|
|
|
# Close file-resident objects first, then the files.
|
|
# Otherwise we get errors in MPI mode.
|
|
self.id._close_open_objects(h5f.OBJ_LOCAL | ~h5f.OBJ_FILE)
|
|
self.id._close_open_objects(h5f.OBJ_LOCAL | h5f.OBJ_FILE)
|
|
|
|
self.id.close()
|
|
_objects.nonlocal_close()
|
|
|
|
def flush(self):
|
|
""" Tell the HDF5 library to flush its buffers.
|
|
"""
|
|
with phil:
|
|
h5f.flush(self.id)
|
|
|
|
@with_phil
|
|
def __enter__(self):
|
|
return self
|
|
|
|
@with_phil
|
|
def __exit__(self, *args):
|
|
if self.id:
|
|
self.close()
|
|
|
|
@with_phil
|
|
def __repr__(self):
|
|
if not self.id:
|
|
r = '<Closed HDF5 file>'
|
|
else:
|
|
# Filename has to be forced to Unicode if it comes back bytes
|
|
# Mode is always a "native" string
|
|
filename = self.filename
|
|
if isinstance(filename, bytes): # Can't decode fname
|
|
filename = filename.decode('utf8', 'replace')
|
|
r = f'<HDF5 file "{os.path.basename(filename)}" (mode {self.mode})>'
|
|
|
|
return r
|