def _retrieve_label(self, node):
universe = self.retrieve(node.attrs['universe'])
data = node[...]
name = py_str(node.attrs['name'])
label_type = py_str(node.attrs['label_type'])
return mosaic.array_model.Label.from_arrays(universe, name,
data, label_type)
def _retrieve_property(self, node):
universe = self.retrieve(node.attrs['universe'])
data = node[...]
name = py_str(node.attrs['name'])
units = py_str(node.attrs['units'])
property_type = py_str(node.attrs['property_type'])
return mosaic.array_model.Property(universe, name, units,
data, property_type)
def retrieve(self, path_or_node):
"""
:param path_or_node: a HDF5 path, relative to the group used by
the HDF5Store, or an HDF5 node
:type path_or_node: str or h5py.Node
:returns: a Mosaic data item
:rtype: :class:`mosaic.api.MosaicDataItem`
"""
if isinstance(path_or_node, h5py.h5r.Reference):
path_or_node = self.root[path_or_node]
if isinstance(path_or_node, str):
path = path_or_node
else: # Group, Dataset, or classes with the same interface
path = path_or_node.name
if path[0] == '/':
if path.startswith(self.root.name):
path = path[len(self.root.name):]
if path[0] == '/':
path = path[1:]
else:
raise ValueError("path name not inside root group")
data = self._get_data(path)
if data is not None:
return data
node = self.root[path]
label = py_str(self._read_stamp(node))
if label not in self._node_types:
raise ValueError("Undefined node type %s" % label)
handler = self.storage_handler[label]
if handler is None:
raise ValueError("Retrieval of node type %s not yet implemented"
% label)
data = handler(self, node)
self._register_data_item(path, data)
return data
def _retrieve_universe(self, node):
# Work around a restriction/bug in h5py that prevents reading
# arrays of length zero.
if node['symmetry_transformations'].shape[0] == 0:
st = N.zeros((0,), dtype=node['symmetry_transformations'].dtype)
else:
st = node['symmetry_transformations'][...]
return mosaic.array_model.Universe.from_arrays(
node['atoms'][...],
node['bonds'][...],
node['fragments'][...],
node['polymers'][...]
if 'polymers' in node else None,
node['molecules'][...],
tuple(py_str(s) for s in node['symbols'][...]),
st,
py_str(node['cell_shape'][()]),
py_str(node['convention'][()]))
def strings(self):
eos = N.repeat(N.arange(self._string_array.shape[0]),
self._string_array.view(dtype=N.uint8) == 0)
strings = []
f = 0
for l in eos:
strings.append(py_str(self._string_array[f:l].tostring()))
f = l + 1
return strings
def _retrieve_selection(self, node):
universe = self.retrieve(node.attrs['universe'])
indices = node[...]
selection_type = py_str(node.attrs['selection_type'])
return mosaic.array_model.Selection(universe, indices,
selection_type)