# This file is part of h5py, a Python interface to the HDF5 library. # # http://www.h5py.org # # Copyright 2008-2013 Andrew Collette and contributors # # License: Standard 3-clause BSD; see "license.txt" for full license terms # and contributor agreement. """ Implements high-level support for HDF5 file objects. """ from __future__ import absolute_import import sys import os from warnings import warn from .compat import filename_decode, filename_encode import six from .base import phil, with_phil from .group import Group from .. import h5, h5f, h5p, h5i, h5fd, _objects from .. import version from ..h5py_warnings import H5pyDeprecationWarning mpi = h5.get_config().mpi hdf5_version = version.hdf5_version_tuple[0:3] swmr_support = False if hdf5_version >= h5.get_config().swmr_min_hdf5_version: swmr_support = True libver_dict = {'earliest': h5f.LIBVER_EARLIEST, 'latest': h5f.LIBVER_LATEST} libver_dict_r = dict((y, x) for x, y in six.iteritems(libver_dict)) if hdf5_version >= (1, 10, 2): libver_dict.update({'v108': h5f.LIBVER_V18, 'v110': h5f.LIBVER_V110}) libver_dict_r.update({h5f.LIBVER_V18: 'v108', h5f.LIBVER_V110: 'v110'}) def _set_fapl_mpio(plist, **kwargs): import mpi4py kwargs.setdefault('info', mpi4py.MPI.Info()) plist.set_fapl_mpio(**kwargs) def _set_fapl_fileobj(plist, **kwargs): plist.set_fileobj_driver(h5fd.fileobj_driver, kwargs.get('fileobj')) _drivers = { 'sec2': lambda plist, **kwargs: plist.set_fapl_sec2(**kwargs), 'stdio': lambda plist, **kwargs: plist.set_fapl_stdio(**kwargs), 'core': lambda plist, **kwargs: plist.set_fapl_core(**kwargs), 'family': lambda plist, **kwargs: plist.set_fapl_family( memb_fapl=plist.copy(), **kwargs ), 'mpio': _set_fapl_mpio, 'fileobj': _set_fapl_fileobj, } def register_driver(name, set_fapl): """Register a custom driver. Parameters ---------- name : str The name of the driver. set_fapl : callable[PropFAID, **kwargs] -> NoneType The function to set the fapl to use your custom driver. """ _drivers[name] = set_fapl def unregister_driver(name): """Unregister a custom driver. Parameters ---------- name : str The name of the driver. """ del _drivers[name] def registered_drivers(): """Return a frozenset of the names of all of the registered drivers. """ return frozenset(_drivers) def make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, **kwds): """ Set up a file access property list """ plist = h5p.create(h5p.FILE_ACCESS) if libver is not None: if libver in libver_dict: low = libver_dict[libver] high = h5f.LIBVER_LATEST else: low, high = (libver_dict[x] for x in libver) else: # we default to earliest low, high = h5f.LIBVER_EARLIEST, h5f.LIBVER_LATEST plist.set_libver_bounds(low, high) cache_settings = list(plist.get_cache()) if rdcc_nslots is not None: cache_settings[1] = rdcc_nslots if rdcc_nbytes is not None: cache_settings[2] = rdcc_nbytes if rdcc_w0 is not None: cache_settings[3] = rdcc_w0 plist.set_cache(*cache_settings) if driver is None or (driver == 'windows' and sys.platform == 'win32'): # Prevent swallowing unused key arguments if kwds: msg = "'{key}' is an invalid keyword argument for this function" \ .format(key=next(iter(kwds))) raise TypeError(msg) return plist try: set_fapl = _drivers[driver] except KeyError: raise ValueError('Unknown driver type "%s"' % driver) else: set_fapl(plist, **kwds) return plist def make_fcpl(track_order=False): """ Set up a file creation property list """ if track_order: plist = h5p.create(h5p.FILE_CREATE) plist.set_link_creation_order( h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED) plist.set_attr_creation_order( h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED) else: plist = None return plist def make_fid(name, mode, userblock_size, fapl, fcpl=None, swmr=False): """ Get a new FileID by opening or creating a file. Also validates mode argument.""" if userblock_size is not None: if mode in ('r', 'r+'): raise ValueError("User block may only be specified " "when creating a file") try: userblock_size = int(userblock_size) except (TypeError, ValueError): raise ValueError("User block size must be an integer") if fcpl is None: fcpl = h5p.create(h5p.FILE_CREATE) fcpl.set_userblock(userblock_size) if mode == 'r': flags = h5f.ACC_RDONLY if swmr and swmr_support: flags |= h5f.ACC_SWMR_READ fid = h5f.open(name, flags, fapl=fapl) elif mode == 'r+': fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl) elif mode in ['w-', 'x']: fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) elif mode == 'w': fid = h5f.create(name, h5f.ACC_TRUNC, fapl=fapl, fcpl=fcpl) elif mode == 'a': # Open in append mode (read/write). # If that fails, create a new file only if it won't clobber an # existing one (ACC_EXCL) try: fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl) except IOError: fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) elif mode is None: warn("The default file mode will change to 'r' (read-only) in h5py 3.0. " "To suppress this warning, pass the mode you need to h5py.File(), " "or set the global default h5.get_config().default_file_mode, " "or set the environment variable H5PY_DEFAULT_READONLY=1. " "Available modes are: 'r', 'r+', 'w', 'w-'/'x', 'a'. " "See the docs for details.", H5pyDeprecationWarning, stacklevel=3) # Try to open in append mode (read/write). # If that fails, try readonly, and finally create a new file only # if it won't clobber an existing file (ACC_EXCL). try: fid = h5f.open(name, h5f.ACC_RDWR, fapl=fapl) except IOError: try: fid = h5f.open(name, h5f.ACC_RDONLY, fapl=fapl) except IOError: fid = h5f.create(name, h5f.ACC_EXCL, fapl=fapl, fcpl=fcpl) else: raise ValueError("Invalid mode; must be one of r, r+, w, w-, x, a") try: if userblock_size is not None: existing_fcpl = fid.get_create_plist() if existing_fcpl.get_userblock() != userblock_size: raise ValueError("Requested userblock size (%d) does not match that of existing file (%d)" % (userblock_size, existing_fcpl.get_userblock())) except: fid.close() raise return fid class File(Group): """ Represents an HDF5 file. """ @property def attrs(self): """ Attributes attached to this object """ # hdf5 complains that a file identifier is an invalid location for an # attribute. Instead of self, pass the root group to AttributeManager: from . import attrs with phil: return attrs.AttributeManager(self['/']) @property @with_phil def filename(self): """File name on disk""" return filename_decode(h5f.get_name(self.id)) @property @with_phil def driver(self): """Low-level HDF5 file driver used to open file""" drivers = {h5fd.SEC2: 'sec2', h5fd.STDIO: 'stdio', h5fd.CORE: 'core', h5fd.FAMILY: 'family', h5fd.WINDOWS: 'windows', h5fd.MPIO: 'mpio', h5fd.MPIPOSIX: 'mpiposix', h5fd.fileobj_driver: 'fileobj'} return drivers.get(self.id.get_access_plist().get_driver(), 'unknown') @property @with_phil def mode(self): """ Python mode used to open file """ return {h5f.ACC_RDONLY: 'r', h5f.ACC_RDWR: 'r+'}.get(self.id.get_intent()) @property @with_phil def fid(self): """File ID (backwards compatibility) """ warn("File.fid has been deprecated. " "Use File.id instead.", H5pyDeprecationWarning, stacklevel=2) return self.id @property @with_phil def libver(self): """File format version bounds (2-tuple: low, high)""" bounds = self.id.get_access_plist().get_libver_bounds() return tuple(libver_dict_r[x] for x in bounds) @property @with_phil def userblock_size(self): """ User block size (in bytes) """ fcpl = self.id.get_create_plist() return fcpl.get_userblock() if mpi and hdf5_version >= (1, 8, 9): @property @with_phil def atomic(self): """ Set/get MPI-IO atomic mode """ return self.id.get_mpi_atomicity() @atomic.setter @with_phil def atomic(self, value): # pylint: disable=missing-docstring self.id.set_mpi_atomicity(value) if swmr_support: @property def swmr_mode(self): """ Controls single-writer multiple-reader mode """ return self._swmr_mode @swmr_mode.setter @with_phil def swmr_mode(self, value): # pylint: disable=missing-docstring if value: self.id.start_swmr_write() self._swmr_mode = True else: raise ValueError("It is not possible to forcibly switch SWMR mode off.") def __init__(self, name, mode=None, driver=None, libver=None, userblock_size=None, swmr=False, rdcc_nslots=None, rdcc_nbytes=None, rdcc_w0=None, track_order=None, **kwds): """Create a new file object. See the h5py user guide for a detailed explanation of the options. name Name of the file on disk, or file-like object. Note: for files created with the 'core' driver, HDF5 still requires this be non-empty. mode r Readonly, file must exist r+ Read/write, file must exist w Create file, truncate if exists w- or x Create file, fail if exists a Read/write if exists, create otherwise (default) driver Name of the driver to use. Legal values are None (default, recommended), 'core', 'sec2', 'stdio', 'mpio'. libver Library version bounds. Supported values: 'earliest', 'v108', 'v110', and 'latest'. The 'v108' and 'v110' options can only be specified with the HDF5 1.10.2 library or later. userblock Desired size of user block. Only allowed when creating a new file (mode w, w- or x). swmr Open the file in SWMR read mode. Only used when mode = 'r'. rdcc_nbytes Total size of the raw data chunk cache in bytes. The default size is 1024**2 (1 MB) per dataset. rdcc_w0 The chunk preemption policy for all datasets. This must be between 0 and 1 inclusive and indicates the weighting according to which chunks which have been fully read or written are penalized when determining which chunks to flush from cache. A value of 0 means fully read or written chunks are treated no differently than other chunks (the preemption is strictly LRU) while a value of 1 means fully read or written chunks are always preempted before other chunks. If your application only reads or writes data once, this can be safely set to 1. Otherwise, this should be set lower depending on how often you re-read or re-write the same data. The default value is 0.75. rdcc_nslots The number of chunk slots in the raw data chunk cache for this file. Increasing this value reduces the number of cache collisions, but slightly increases the memory used. Due to the hashing strategy, this value should ideally be a prime number. As a rule of thumb, this value should be at least 10 times the number of chunks that can fit in rdcc_nbytes bytes. For maximum performance, this value should be set approximately 100 times that number of chunks. The default value is 521. track_order Track dataset/group/attribute creation order under root group if True. If None use global default h5.get_config().track_order. Additional keywords Passed on to the selected file driver. """ if swmr and not swmr_support: raise ValueError("The SWMR feature is not available in this version of the HDF5 library") if isinstance(name, _objects.ObjectID): 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 mode is None: mode = h5.get_config().default_file_mode if mode is None and os.environ.get('H5PY_DEFAULT_READONLY', ''): mode = 'r' with phil: fapl = make_fapl(driver, libver, rdcc_nslots, rdcc_nbytes, rdcc_w0, **kwds) fid = make_fid(name, mode, userblock_size, fapl, fcpl=make_fcpl(track_order=track_order), swmr=swmr) if isinstance(libver, tuple): self._libver = libver else: self._libver = (libver, 'latest') if swmr_support: self._swmr_mode = False if swmr and mode == 'r': self._swmr_mode = True Group.__init__(self, 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. id_list = h5f.get_obj_ids(self.id, ~h5f.OBJ_FILE) file_list = h5f.get_obj_ids(self.id, h5f.OBJ_FILE) id_list = [x for x in id_list if h5i.get_file_id(x).id == self.id.id] file_list = [x for x in file_list if h5i.get_file_id(x).id == self.id.id] for id_ in id_list: while id_.valid: h5i.dec_ref(id_) for id_ in file_list: while id_.valid: h5i.dec_ref(id_) 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 = u'' 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 = u'' % (os.path.basename(filename), self.mode) if six.PY2: return r.encode('utf8') return r