laywerrobot/lib/python3.6/site-packages/h5py/_hl/group.py
2020-08-27 21:55:39 +02:00

548 lines
19 KiB
Python

# 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 support for high-level access to HDF5 groups.
"""
from __future__ import absolute_import
import posixpath as pp
import six
import numpy
from .compat import filename_decode, filename_encode
from .. import h5g, h5i, h5o, h5r, h5t, h5l, h5p
from . import base
from .base import HLObject, MutableMappingHDF5, phil, with_phil
from . import dataset
from . import datatype
class Group(HLObject, MutableMappingHDF5):
""" Represents an HDF5 group.
"""
def __init__(self, bind):
""" Create a new Group object by binding to a low-level GroupID.
"""
with phil:
if not isinstance(bind, h5g.GroupID):
raise ValueError("%s is not a GroupID" % bind)
HLObject.__init__(self, bind)
_gcpl_crt_order = h5p.create(h5p.GROUP_CREATE)
_gcpl_crt_order.set_link_creation_order(
h5p.CRT_ORDER_TRACKED | h5p.CRT_ORDER_INDEXED)
def create_group(self, name, track_order=False):
""" Create and return a new subgroup.
Name may be absolute or relative. Fails if the target name already
exists.
track_order
Track dataset/group creation order under this group if True.
"""
with phil:
name, lcpl = self._e(name, lcpl=True)
gcpl = Group._gcpl_crt_order if track_order else None
gid = h5g.create(self.id, name, lcpl=lcpl, gcpl=gcpl)
return Group(gid)
def create_dataset(self, name, shape=None, dtype=None, data=None, **kwds):
""" Create a new HDF5 dataset
name
Name of the dataset (absolute or relative). Provide None to make
an anonymous dataset.
shape
Dataset shape. Use "()" for scalar datasets. Required if "data"
isn't provided.
dtype
Numpy dtype or string. If omitted, dtype('f') will be used.
Required if "data" isn't provided; otherwise, overrides data
array's dtype.
data
Provide data to initialize the dataset. If used, you can omit
shape and dtype arguments.
Keyword-only arguments:
chunks
(Tuple) Chunk shape, or True to enable auto-chunking.
maxshape
(Tuple) Make the dataset resizable up to this shape. Use None for
axes you want to be unlimited.
compression
(String or int) Compression strategy. Legal values are 'gzip',
'szip', 'lzf'. If an integer in range(10), this indicates gzip
compression level. Otherwise, an integer indicates the number of a
dynamically loaded compression filter.
compression_opts
Compression settings. This is an integer for gzip, 2-tuple for
szip, etc. If specifying a dynamically loaded compression filter
number, this must be a tuple of values.
scaleoffset
(Integer) Enable scale/offset filter for (usually) lossy
compression of integer or floating-point data. For integer
data, the value of scaleoffset is the number of bits to
retain (pass 0 to let HDF5 determine the minimum number of
bits necessary for lossless compression). For floating point
data, scaleoffset is the number of digits after the decimal
place to retain; stored values thus have absolute error
less than 0.5*10**(-scaleoffset).
shuffle
(T/F) Enable shuffle filter.
fletcher32
(T/F) Enable fletcher32 error detection. Not permitted in
conjunction with the scale/offset filter.
fillvalue
(Scalar) Use this value for uninitialized parts of the dataset.
track_times
(T/F) Enable dataset creation timestamps.
"""
with phil:
dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)
dset = dataset.Dataset(dsid)
if name is not None:
self[name] = dset
return dset
def require_dataset(self, name, shape, dtype, exact=False, **kwds):
""" Open a dataset, creating it if it doesn't exist.
If keyword "exact" is False (default), an existing dataset must have
the same shape and a conversion-compatible dtype to be returned. If
True, the shape and dtype must match exactly.
Other dataset keywords (see create_dataset) may be provided, but are
only used if a new dataset is to be created.
Raises TypeError if an incompatible object already exists, or if the
shape or dtype don't match according to the above rules.
"""
with phil:
if not name in self:
return self.create_dataset(name, *(shape, dtype), **kwds)
dset = self[name]
if not isinstance(dset, dataset.Dataset):
raise TypeError("Incompatible object (%s) already exists" % dset.__class__.__name__)
if not shape == dset.shape:
raise TypeError("Shapes do not match (existing %s vs new %s)" % (dset.shape, shape))
if exact:
if not dtype == dset.dtype:
raise TypeError("Datatypes do not exactly match (existing %s vs new %s)" % (dset.dtype, dtype))
elif not numpy.can_cast(dtype, dset.dtype):
raise TypeError("Datatypes cannot be safely cast (existing %s vs new %s)" % (dset.dtype, dtype))
return dset
def require_group(self, name):
""" Return a group, creating it if it doesn't exist.
TypeError is raised if something with that name already exists that
isn't a group.
"""
with phil:
if not name in self:
return self.create_group(name)
grp = self[name]
if not isinstance(grp, Group):
raise TypeError("Incompatible object (%s) already exists" % grp.__class__.__name__)
return grp
@with_phil
def __getitem__(self, name):
""" Open an object in the file """
if isinstance(name, h5r.Reference):
oid = h5r.dereference(name, self.id)
if oid is None:
raise ValueError("Invalid HDF5 object reference")
else:
oid = h5o.open(self.id, self._e(name), lapl=self._lapl)
otype = h5i.get_type(oid)
if otype == h5i.GROUP:
return Group(oid)
elif otype == h5i.DATASET:
return dataset.Dataset(oid)
elif otype == h5i.DATATYPE:
return datatype.Datatype(oid)
else:
raise TypeError("Unknown object type")
def get(self, name, default=None, getclass=False, getlink=False):
""" Retrieve an item or other information.
"name" given only:
Return the item, or "default" if it doesn't exist
"getclass" is True:
Return the class of object (Group, Dataset, etc.), or "default"
if nothing with that name exists
"getlink" is True:
Return HardLink, SoftLink or ExternalLink instances. Return
"default" if nothing with that name exists.
"getlink" and "getclass" are True:
Return HardLink, SoftLink and ExternalLink classes. Return
"default" if nothing with that name exists.
Example:
>>> cls = group.get('foo', getclass=True)
>>> if cls == SoftLink:
... print '"foo" is a soft link!'
"""
# pylint: disable=arguments-differ
with phil:
if not (getclass or getlink):
try:
return self[name]
except KeyError:
return default
if not name in self:
return default
elif getclass and not getlink:
typecode = h5o.get_info(self.id, self._e(name)).type
try:
return {h5o.TYPE_GROUP: Group,
h5o.TYPE_DATASET: dataset.Dataset,
h5o.TYPE_NAMED_DATATYPE: datatype.Datatype}[typecode]
except KeyError:
raise TypeError("Unknown object type")
elif getlink:
typecode = self.id.links.get_info(self._e(name)).type
if typecode == h5l.TYPE_SOFT:
if getclass:
return SoftLink
linkbytes = self.id.links.get_val(self._e(name))
return SoftLink(self._d(linkbytes))
elif typecode == h5l.TYPE_EXTERNAL:
if getclass:
return ExternalLink
filebytes, linkbytes = self.id.links.get_val(self._e(name))
return ExternalLink(
filename_decode(filebytes), self._d(linkbytes)
)
elif typecode == h5l.TYPE_HARD:
return HardLink if getclass else HardLink()
else:
raise TypeError("Unknown link type")
def __setitem__(self, name, obj):
""" Add an object to the group. The name must not already be in use.
The action taken depends on the type of object assigned:
Named HDF5 object (Dataset, Group, Datatype)
A hard link is created at "name" which points to the
given object.
SoftLink or ExternalLink
Create the corresponding link.
Numpy ndarray
The array is converted to a dataset object, with default
settings (contiguous storage, etc.).
Numpy dtype
Commit a copy of the datatype as a named datatype in the file.
Anything else
Attempt to convert it to an ndarray and store it. Scalar
values are stored as scalar datasets. Raise ValueError if we
can't understand the resulting array dtype.
"""
do_link = False
with phil:
name, lcpl = self._e(name, lcpl=True)
if isinstance(obj, HLObject):
h5o.link(obj.id, self.id, name, lcpl=lcpl, lapl=self._lapl)
elif isinstance(obj, SoftLink):
self.id.links.create_soft(name, self._e(obj.path),
lcpl=lcpl, lapl=self._lapl)
elif isinstance(obj, ExternalLink):
do_link = True
elif isinstance(obj, numpy.dtype):
htype = h5t.py_create(obj, logical=True)
htype.commit(self.id, name, lcpl=lcpl)
else:
ds = self.create_dataset(None, data=obj, dtype=base.guess_dtype(obj))
h5o.link(ds.id, self.id, name, lcpl=lcpl)
if do_link:
fn = filename_encode(obj.filename)
with phil:
self.id.links.create_external(name, fn, self._e(obj.path),
lcpl=lcpl, lapl=self._lapl)
@with_phil
def __delitem__(self, name):
""" Delete (unlink) an item from this group. """
self.id.unlink(self._e(name))
@with_phil
def __len__(self):
""" Number of members attached to this group """
return self.id.get_num_objs()
@with_phil
def __iter__(self):
""" Iterate over member names """
for x in self.id.__iter__():
yield self._d(x)
@with_phil
def __contains__(self, name):
""" Test if a member name exists """
return self._e(name) in self.id
def copy(self, source, dest, name=None,
shallow=False, expand_soft=False, expand_external=False,
expand_refs=False, without_attrs=False):
"""Copy an object or group.
The source can be a path, Group, Dataset, or Datatype object. The
destination can be either a path or a Group object. The source and
destinations need not be in the same file.
If the source is a Group object, all objects contained in that group
will be copied recursively.
When the destination is a Group object, by default the target will
be created in that group with its current name (basename of obj.name).
You can override that by setting "name" to a string.
There are various options which all default to "False":
- shallow: copy only immediate members of a group.
- expand_soft: expand soft links into new objects.
- expand_external: expand external links into new objects.
- expand_refs: copy objects that are pointed to by references.
- without_attrs: copy object without copying attributes.
Example:
>>> f = File('myfile.hdf5')
>>> f.listnames()
['MyGroup']
>>> f.copy('MyGroup', 'MyCopy')
>>> f.listnames()
['MyGroup', 'MyCopy']
"""
with phil:
if isinstance(source, HLObject):
source_path = '.'
else:
# Interpret source as a path relative to this group
source_path = source
source = self
if isinstance(dest, Group):
if name is not None:
dest_path = name
else:
# copy source into dest group: dest_name/source_name
dest_path = pp.basename(h5i.get_name(source[source_path].id))
elif isinstance(dest, HLObject):
raise TypeError("Destination must be path or Group object")
else:
# Interpret destination as a path relative to this group
dest_path = dest
dest = self
flags = 0
if shallow:
flags |= h5o.COPY_SHALLOW_HIERARCHY_FLAG
if expand_soft:
flags |= h5o.COPY_EXPAND_SOFT_LINK_FLAG
if expand_external:
flags |= h5o.COPY_EXPAND_EXT_LINK_FLAG
if expand_refs:
flags |= h5o.COPY_EXPAND_REFERENCE_FLAG
if without_attrs:
flags |= h5o.COPY_WITHOUT_ATTR_FLAG
if flags:
copypl = h5p.create(h5p.OBJECT_COPY)
copypl.set_copy_object(flags)
else:
copypl = None
h5o.copy(source.id, self._e(source_path), dest.id, self._e(dest_path),
copypl, base.dlcpl)
def move(self, source, dest):
""" Move a link to a new location in the file.
If "source" is a hard link, this effectively renames the object. If
"source" is a soft or external link, the link itself is moved, with its
value unmodified.
"""
with phil:
if source == dest:
return
self.id.links.move(self._e(source), self.id, self._e(dest),
lapl=self._lapl, lcpl=self._lcpl)
def visit(self, func):
""" Recursively visit all names in this group and subgroups (HDF5 1.8).
You supply a callable (function, method or callable object); it
will be called exactly once for each link in this group and every
group below it. Your callable must conform to the signature:
func(<member name>) => <None or return value>
Returning None continues iteration, returning anything else stops
and immediately returns that value from the visit method. No
particular order of iteration within groups is guaranteed.
Example:
>>> # List the entire contents of the file
>>> f = File("foo.hdf5")
>>> list_of_names = []
>>> f.visit(list_of_names.append)
"""
with phil:
def proxy(name):
""" Call the function with the text name, not bytes """
return func(self._d(name))
return h5o.visit(self.id, proxy)
def visititems(self, func):
""" Recursively visit names and objects in this group (HDF5 1.8).
You supply a callable (function, method or callable object); it
will be called exactly once for each link in this group and every
group below it. Your callable must conform to the signature:
func(<member name>, <object>) => <None or return value>
Returning None continues iteration, returning anything else stops
and immediately returns that value from the visit method. No
particular order of iteration within groups is guaranteed.
Example:
# Get a list of all datasets in the file
>>> mylist = []
>>> def func(name, obj):
... if isinstance(obj, Dataset):
... mylist.append(name)
...
>>> f = File('foo.hdf5')
>>> f.visititems(func)
"""
with phil:
def proxy(name):
""" Use the text name of the object, not bytes """
name = self._d(name)
return func(name, self[name])
return h5o.visit(self.id, proxy)
@with_phil
def __repr__(self):
if not self:
r = u"<Closed HDF5 group>"
else:
namestr = (
u'"%s"' % self.name
) if self.name is not None else u"(anonymous)"
r = u'<HDF5 group %s (%d members)>' % (namestr, len(self))
if six.PY2:
return r.encode('utf8')
return r
class HardLink(object):
"""
Represents a hard link in an HDF5 file. Provided only so that
Group.get works in a sensible way. Has no other function.
"""
pass
class SoftLink(object):
"""
Represents a symbolic ("soft") link in an HDF5 file. The path
may be absolute or relative. No checking is performed to ensure
that the target actually exists.
"""
@property
def path(self):
""" Soft link value. Not guaranteed to be a valid path. """
return self._path
def __init__(self, path):
self._path = str(path)
def __repr__(self):
return '<SoftLink to "%s">' % self.path
class ExternalLink(object):
"""
Represents an HDF5 external link. Paths may be absolute or relative.
No checking is performed to ensure either the target or file exists.
"""
@property
def path(self):
""" Soft link path, i.e. the part inside the HDF5 file. """
return self._path
@property
def filename(self):
""" Path to the external HDF5 file in the filesystem. """
return self._filename
def __init__(self, filename, path):
self._filename = filename_decode(filename_encode(filename))
self._path = path
def __repr__(self):
return '<ExternalLink to "%s" in file "%s"' % (self.path, self.filename)