def _parse_parameter_file(self):
fh = h5py.File(self.filename, "r")
for attr in ["hubble_constant", "omega_matter", "omega_lambda"]:
setattr(self, attr, fh.attrs[attr])
if "unit_registry_json" in fh.attrs:
self.unit_registry = \
UnitRegistry.from_json(
fh.attrs["unit_registry_json"].astype(str))
self.unit_registry.modify("h", self.hubble_constant)
self.box_size = _hdf5_yt_attr(fh,
"box_size",
unit_registry=self.unit_registry)
field_list = []
fi = {}
for field in fh["data"]:
d = fh["data"][field]
units = _hdf5_yt_attr(d, "units")
if isinstance(units, bytes):
units = units.decode("utf")
if len(d.shape) > 1:
for ax in "xyz":
my_field = "%s_%s" % (field, ax)
field_list.append(my_field)
fi[my_field] = {"vector": True, "units": units}
else:
field_list.append(field)
fi[field] = {"units": units}
fh.close()
self.field_list = field_list
self.field_info.update(fi)
def _parse_parameter_file(self):
self.refine_by = 2
with h5py.File(self.parameter_filename, mode="r") as f:
for key in f.attrs.keys():
v = parse_h5_attr(f, key)
if key == "con_args":
try:
v = eval(v)
except ValueError:
# support older ytdata outputs
v = v.astype('str')
self.parameters[key] = v
self._with_parameter_file_open(f)
# if saved, restore unit registry from the json string
if "unit_registry_json" in self.parameters:
self.unit_registry = UnitRegistry.from_json(
self.parameters["unit_registry_json"])
# reset self.arr and self.quan to use new unit_registry
self._arr = None
self._quan = None
for dim in [
"length", "mass", "pressure", "temperature", "time",
"velocity"
]:
cu = "code_" + dim
if cu not in self.unit_registry:
self.unit_registry.add(cu, 1.0, getattr(dimensions, dim))
if "code_magnetic" not in self.unit_registry:
self.unit_registry.add("code_magnetic", 1.0,
dimensions.magnetic_field)
# if saved, set unit system
if "unit_system_name" in self.parameters:
unit_system = self.parameters["unit_system_name"]
del self.parameters["unit_system_name"]
else:
unit_system = "cgs"
# reset unit system since we may have a new unit registry
self._assign_unit_system(unit_system)
# assign units to parameters that have associated unit string
del_pars = []
for par in self.parameters:
ustr = "%s_units" % par
if ustr in self.parameters:
if isinstance(self.parameters[par], np.ndarray):
to_u = self.arr
else:
to_u = self.quan
self.parameters[par] = to_u(self.parameters[par],
self.parameters[ustr])
del_pars.append(ustr)
for par in del_pars:
del self.parameters[par]
for attr in self._con_attrs:
setattr(self, attr, self.parameters.get(attr))
def _parse_parameter_file(self):
fh = h5py.File(self.filename, "r")
for attr in ["hubble_constant", "omega_matter", "omega_lambda"]:
setattr(self, attr, fh.attrs[attr])
my_ur = UnitRegistry.from_json(parse_h5_attr(fh, "unit_registry_json"))
right = _hdf5_yt_attr(fh, "domain_right_edge", unit_registry=my_ur)
left = _hdf5_yt_attr(fh, "domain_left_edge", unit_registry=my_ur)
# Drop the "cm" suffix because all lengths will
# be in comoving units.
self.box_size = self.quan((right - left)[0].to("Mpccm/h"), "Mpc/h")
fh.close()
def _parse_parameter_file(self):
self._prefix = \
self.filename[:self.filename.rfind(self._suffix)]
fh = h5py.File(self.filename, "r")
for attr in ["hubble_constant", "omega_matter", "omega_lambda"]:
setattr(self, attr, fh.attrs[attr])
if "unit_registry_json" in fh.attrs:
self.unit_registry = \
UnitRegistry.from_json(
parse_h5_attr(fh, "unit_registry_json"))
self.box_size = _hdf5_yt_attr(fh,
"box_size",
unit_registry=self.unit_registry)
self.field_info.update(json.loads(parse_h5_attr(fh, "field_info")))
self.field_list = list(self.field_info.keys())
fh.close()
def _parse_parameter_file(self):
self.refine_by = 2
with h5py.File(self.parameter_filename, mode="r") as f:
for key in f.attrs.keys():
v = parse_h5_attr(f, key)
if key == "con_args":
try:
v = eval(v)
except ValueError:
# support older ytdata outputs
v = v.astype("str")
except NameError:
# This is the most common error we expect, and it
# results from having the eval do a concatenated decoded
# set of the values.
v = [_.decode("utf8") for _ in v]
self.parameters[key] = v
self._with_parameter_file_open(f)
# if saved, restore unit registry from the json string
if "unit_registry_json" in self.parameters:
self.unit_registry = UnitRegistry.from_json(
self.parameters["unit_registry_json"])
# reset self.arr and self.quan to use new unit_registry
self._arr = None
self._quan = None
for dim in [
"length",
"mass",
"pressure",
"temperature",
"time",
"velocity",
]:
cu = "code_" + dim
if cu not in self.unit_registry:
self.unit_registry.add(cu, 1.0, getattr(dimensions, dim))
if "code_magnetic" not in self.unit_registry:
self.unit_registry.add("code_magnetic", 1.0,
dimensions.magnetic_field)
# if saved, set unit system
if "unit_system_name" in self.parameters:
unit_system = self.parameters["unit_system_name"]
del self.parameters["unit_system_name"]
else:
unit_system = "cgs"
# reset unit system since we may have a new unit registry
self._assign_unit_system(unit_system)
# assign units to parameters that have associated unit string
del_pars = []
for par in self.parameters:
ustr = f"{par}_units"
if ustr in self.parameters:
if isinstance(self.parameters[par], np.ndarray):
to_u = self.arr
else:
to_u = self.quan
self.parameters[par] = to_u(self.parameters[par],
self.parameters[ustr])
del_pars.append(ustr)
for par in del_pars:
del self.parameters[par]
for attr in self._con_attrs:
try:
sattr = _set_attrs.get(attr, attr)
setattr(self, sattr, self.parameters.get(attr))
except TypeError:
# some Dataset attributes are properties with setters
# which may not accept None as an input
pass
if self.geometry is None:
self.geometry = "cartesian"
def hubble_constant(self, value):
self._hubble_constant = value
# reset the unit registry lut while preserving other changes
self.unit_registry = UnitRegistry.from_json(
self.unit_registry.to_json())
self.unit_registry.modify("h", self.hubble_constant)
def test_registry_json():
reg = UnitRegistry()
json_reg = reg.to_json()
unserialized_reg = UnitRegistry.from_json(json_reg)
assert_equal(reg.lut, unserialized_reg.lut)
