def _store_property(self, path, property):
universe = property.universe
universe_path = self._get_path(universe)
if universe_path is None:
raise IOError("universe must be stored first")
element_shape = property.data.shape[1:]
if element_shape:
dtype = N.dtype((property.data.dtype, element_shape))
else:
dtype = property.data.dtype
arr = N.ascontiguousarray(property.data)
ds = self.root.require_dataset(path,
shape=(len(arr),),
dtype=dtype)
self._stamp(ds, 'property')
ds.attrs['universe'] = self.root[universe_path].ref
ds.attrs['name'] = ascii(property.name)
ds.attrs['units'] = ascii(property.units)
ds.attrs['property_type'] = ascii(property.type)
# There doesn't seem to be any way to write this array
# using high-level operations, so we use the low-level access.
mtype = h5py.h5t.py_create(ds.id.dtype)
mspace = h5py.h5s.create_simple(ds.shape)
fspace = ds.id.get_space()
ds.id.write(mspace, fspace, arr, mtype)
def _store_label(self, path, label):
universe = label.universe
label = self._factory(label)
universe_path = self._get_path(universe)
if universe_path is None:
raise IOError("universe must be stored first")
ds = create_dataset(self.root, path, data=label._string_array)
self._stamp(ds, 'label')
ds.attrs['universe'] = self.root[universe_path].ref
ds.attrs['name'] = ascii(label.name)
ds.attrs['label_type'] = ascii(label.type)
def __iter__(self):
# First pass: universes
for name in self.root:
node = self.root[name]
if node.attrs.get('DATA_MODEL', None) == ascii('MOSAIC') \
and node.attrs['MOSAIC_DATA_TYPE'] == ascii('universe'):
yield name, self.retrieve(node)
# Second pass: anything else
for name in self.root:
node = self.root[name]
if node.attrs.get('DATA_MODEL', None) == ascii('MOSAIC') \
and node.attrs['MOSAIC_DATA_TYPE'] != ascii('universe'):
yield name, self.retrieve(node)
def _store_universe(self, path, universe):
group = self.root.require_group(path)
try:
# ActivePapers support
group.mark_as_data_item()
except AttributeError:
pass
self._stamp(group, 'universe')
# Convert the universe to an array_model
universe = self._factory(universe)
# Create HDF5 datasets
create_dataset(group, 'cell_shape',
data=universe.cell_shape)
create_dataset(group, 'symmetry_transformations',
data=N.array(universe._symmetry_transformations))
create_dataset(group, 'convention',
data=universe.convention)
create_dataset(group, 'fragments', data=universe._fragment_array)
create_dataset(group, 'atoms', data=universe._atom_array)
create_dataset(group, 'bonds', data=universe._bond_array)
create_dataset(group, 'molecules', data=universe._molecule_array)
if len(universe._polymer_array) > 0:
create_dataset(group, 'polymers', data=universe._polymer_array)
symbols = universe._symbols
symbol_table = group.require_dataset('symbols',
shape=(len(symbols),),
dtype=h5py.special_dtype(vlen=bytes))
for i, s in enumerate(symbols):
symbol_table[i] = ascii(s)
def _store_selection(self, path, selection):
universe = selection.universe
universe_path = self._get_path(universe)
if universe_path is None:
raise IOError("universe must be stored first")
ds = create_dataset(self.root, path,
N.ascontiguousarray(selection.indices))
ds.attrs['universe'] = self.root[universe_path].ref
ds.attrs['selection_type'] = ascii(selection.type)
self._stamp(ds, 'selection')
def _read_stamp(self, node):
if node.attrs['DATA_MODEL'] != ascii('MOSAIC'):
raise ValueError("Node %s not an Mosaic data item" % str(node))
version = (node.attrs['DATA_MODEL_MAJOR_VERSION'],
node.attrs['DATA_MODEL_MINOR_VERSION'])
if version[0] > api.MOSAIC_VERSION[0] \
or version[1] > api.MOSAIC_VERSION[1]:
raise ValueError("HDF5 data is for version %d.%d, "
"software is version %d.%d"
% (version + api.MOSAIC_VERSION))
return node.attrs['MOSAIC_DATA_TYPE']
def recursive_iterator(self, group=None):
if group is None:
group = self.root
# First pass: universes
for name in group:
node = group[name]
if node.attrs.get('DATA_MODEL', None) == ascii('MOSAIC') \
and node.attrs['MOSAIC_DATA_TYPE'] == ascii('universe'):
yield name, self.retrieve(node)
if isinstance(node, h5py.Group):
for gname, gnode in self.recursive_iterator(node):
yield name+'/'+gname, gnode
# Second pass: anything else
for name in group:
node = group[name]
if node.attrs.get('DATA_MODEL', None) == ascii('MOSAIC') \
and node.attrs['MOSAIC_DATA_TYPE'] != ascii('universe'):
yield name, self.retrieve(node)
if isinstance(node, h5py.Group):
for gname, gnode in self.recursive_iterator(node):
yield name+'/'+gname, gnode
def _stamp(self, node, label):
node.attrs['DATA_MODEL'] = ascii('MOSAIC')
node.attrs['DATA_MODEL_MAJOR_VERSION'] = api.MOSAIC_VERSION[0]
node.attrs['DATA_MODEL_MINOR_VERSION'] = api.MOSAIC_VERSION[1]
node.attrs['MOSAIC_DATA_TYPE'] = ascii(label)
