def observable(self, obs_name, shape=None, dtype=None, data=None, time=True, unit=None, time_unit=None, **kwargs):
"""Returns observable data as a TimeData object."""
if "observables" in self.f.keys():
group = self.f["observables"]
else:
group = self.f.create_group("observables")
if obs_name in self.f["observables"].keys():
item = group[obs_name]
if type(item) == h5py.Group:
assert is_h5md(item)
return TimeData(group, obs_name)
elif type(item) == h5py.Dataset:
assert shape == dtype == data == None
return FixedData(group, obs_name)
else:
raise Exception("obs_name does not provide H5MD data")
else:
if time:
return TimeData(
self.f["observables"],
obs_name,
shape=shape,
dtype=dtype,
data=data,
unit=unit,
time_unit=time_unit,
**kwargs
)
else:
return FixedData(
self.f["observables"], obs_name, shape=shape, dtype=dtype, data=data, unit=unit, **kwargs
)
def walk(self, g=None):
if g == None:
g = self.f['/']
if type(g) == h5py.Group:
if is_h5md(g): self.walk_list.append(g)
for k in g.keys():
self.walk(g[k])
def walk(self, g=None):
if g == None:
g = self.f["/"]
if type(g) == h5py.Group:
if is_h5md(g):
self.walk_list.append(g)
for k in g.keys():
self.walk(g[k])
def box(self, dimension=None, boundary=None, edges=None, time=False, unit=None, time_unit=None):
"""Creates a box in the particles group. Returns the box group."""
if dimension is None or boundary is None:
item = self["box/edges"]
if type(item) == h5py.Group:
assert is_h5md(item)
return TimeData(self["box"], "edges")
elif type(item) == h5py.Dataset:
return FixedData(self["box"], "edges")
return Box(self, dimension, boundary, edges, time, unit, time_unit)
def box(self,
dimension=None,
boundary=None,
edges=None,
time=False,
unit=None,
time_unit=None):
"""Creates a box in the particles group. Returns the box group."""
if dimension is None or boundary is None:
item = self['box/edges']
if type(item) == h5py.Group:
assert is_h5md(item)
return TimeData(self['box'], 'edges')
elif type(item) == h5py.Dataset:
return FixedData(self['box'], 'edges')
return Box(self, dimension, boundary, edges, time, unit, time_unit)
def particle_data(group, name=None, shape=None, dtype=None, data=None, time=True, unit=None, time_unit=None, **kwargs):
"""Returns particles data as a FixedData or TimeData."""
if name is None:
raise Exception("No name provided")
if name in group.keys():
item = group[name]
if type(item) == h5py.Group:
assert is_h5md(item)
return TimeData(group, name)
elif type(item) == h5py.Dataset:
assert shape == dtype == data == None
return FixedData(group, name)
else:
raise Exception("name does not provide H5MD data")
else:
if time:
return TimeData(group, name, shape, dtype, data, unit=unit, time_unit=time_unit, **kwargs)
else:
return FixedData(group, name, shape, dtype, data, unit=unit, **kwargs)
def observable(self,
obs_name,
shape=None,
dtype=None,
data=None,
time=True,
unit=None,
time_unit=None,
**kwargs):
"""Returns observable data as a TimeData object."""
if 'observables' in self.f.keys():
group = self.f['observables']
else:
group = self.f.create_group('observables')
if obs_name in self.f['observables'].keys():
item = group[obs_name]
if type(item) == h5py.Group:
assert is_h5md(item)
return TimeData(group, obs_name)
elif type(item) == h5py.Dataset:
assert shape == dtype == data == None
return FixedData(group, obs_name)
else:
raise Exception('obs_name does not provide H5MD data')
else:
if time:
return TimeData(self.f['observables'],
obs_name,
shape=shape,
dtype=dtype,
data=data,
unit=unit,
time_unit=time_unit,
**kwargs)
else:
return FixedData(self.f['observables'],
obs_name,
shape=shape,
dtype=dtype,
data=data,
unit=unit,
**kwargs)
def particle_data(group,
name=None,
shape=None,
dtype=None,
data=None,
time=True,
unit=None,
time_unit=None,
**kwargs):
"""Returns particles data as a FixedData or TimeData."""
if name is None:
raise Exception('No name provided')
if name in group.keys():
item = group[name]
if type(item) == h5py.Group:
assert is_h5md(item)
return TimeData(group, name)
elif type(item) == h5py.Dataset:
assert shape == dtype == data == None
return FixedData(group, name)
else:
raise Exception('name does not provide H5MD data')
else:
if time:
return TimeData(group,
name,
shape,
dtype,
data,
unit=unit,
time_unit=time_unit,
**kwargs)
else:
return FixedData(group,
name,
shape,
dtype,
data,
unit=unit,
**kwargs)
def check(self):
if len(self.walk_list) == 0:
raise Exception("Nothing to check")
for g in self.walk_list:
assert is_h5md(g)
def check(self):
if len(self.walk_list) == 0:
raise Exception('Nothing to check')
for g in self.walk_list:
assert (is_h5md(g))
