def copy(self, source, dest, name=None):
""" 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.
Example:
>>> f = File('myfile.hdf5')
>>> f.listnames()
['MyGroup']
>>> f.copy('MyGroup', 'MyCopy')
>>> f.listnames()
['MyGroup', 'MyCopy']
"""
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
h5o.copy(source.id, self._e(source_path), dest.id, self._e(dest_path))
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']
"""
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 name(self):
""" Return the full name of this object. None if anonymous. """
return self._d(h5i.get_name(self.id))
def name(self):
""" Return the full name of this object. None if anonymous. """
return self._d(h5i.get_name(self.id))
def swap(old, new):
"""
Swap every dataset in old with the corresponding one in new
Datasets in old that aren't in new are ignored.
"""
move_names = []
def _move(name, object):
if isinstance(object, Dataset):
if name in new:
move_names.append(name)
old.visititems(_move)
for name in move_names:
if new[name].is_virtual:
# We cannot simply move virtual datasets, because they will still
# point to the old raw_data location. So instead, we have to
# recreate them, pointing to the new raw_data.
oldd = old[name]
newd = new[name]
def _normalize(path):
return path if path.endswith('/') else path + '/'
def _replace_prefix(path, name1, name2):
"""Replace the prefix name1 with name2 in path"""
name1 = _normalize(name1)
name2 = _normalize(name2)
return name2 + path[len(name1):]
def _new_vds_layout(d, name1, name2):
"""Recreate a VirtualLayout for d, replacing name1 with name2 in the source dset name"""
virtual_sources = d.virtual_sources()
layout = VirtualLayout(d.shape, dtype=d.dtype)
for vmap in virtual_sources:
vspace, fname, dset_name, src_space = vmap
assert dset_name.startswith(name1)
dset_name = _replace_prefix(dset_name, name1, name2)
fname = fname.encode('utf-8')
new_vmap = VDSmap(vspace, fname, dset_name, src_space)
# h5py 3.3 changed the VirtualLayout code. See
# https://github.com/h5py/h5py/pull/1905.
if hasattr(layout, 'sources'):
layout.sources.append(new_vmap)
else:
layout.dcpl.set_virtual(vspace, fname,
dset_name.encode('utf-8'),
src_space)
return layout
old_layout = _new_vds_layout(oldd, old.name, new.name)
new_layout = _new_vds_layout(newd, new.name, old.name)
old_fillvalue = old[name].fillvalue
new_fillvalue = new[name].fillvalue
old_attrs = dict(old[name].attrs)
new_attrs = dict(new[name].attrs)
del old[name]
old.create_virtual_dataset(name,
new_layout,
fillvalue=new_fillvalue)
for k, v in new_attrs.items():
if isinstance(v, str) and v.startswith(new.name):
v = _replace_prefix(v, new.name, old.name)
old[name].attrs[k] = v
del new[name]
new.create_virtual_dataset(name,
old_layout,
fillvalue=old_fillvalue)
for k, v in old_attrs.items():
if isinstance(v, str) and v.startswith(old.name):
v = _replace_prefix(v, old.name, new.name)
new[name].attrs[k] = v
else:
# Invalidate any InMemoryGroups that point to these groups
delete = []
for bind in _groups:
if get_name(bind) and (
get_name(bind).startswith(get_name(old.id))
or get_name(bind).startswith(get_name(new.id))):
delete.append(bind)
for d in delete:
del _groups[d]
old.move(name, pp.join(new.name, name + '__tmp'))
new.move(name, pp.join(old.name, name))
new.move(name + '__tmp', name)