def write_time(base, cycle, time):
if cycle is not None:
time_group = safe_create_group(base, "time")
kv.set_attrs(time_group.name, "vsType", "time");
# time_group.attrs["vsType"] = np.string_("time")
if cycle is not None:
kv.set_attrs(time_group.name, "vsStep", cycle);
# time_group.attrs["vsStep"] = cycle
if time is not None:
kv.set_attrs(time_group.name, "vsTime", time);
# time_group.attrs["vsTime"] = time
del time_group
def write(self, base, base_name=""):
mesh_groups = dict()
datasets = dict()
if self.__local_only:
keys = self.__data.keys()
else:
keys = self.__meta_data.keys()
for key in keys:
md = self.__meta_data[key]
dom_string = ""
for i in key:
dom_string += "_"
dom_string += str(i)
base_name = self.__name+dom_string
var_group = safe_create_group(base, base_name)
mesh_group = safe_create_group(var_group, "mesh")
# Add mesh attributes.
# mesh_group.attrs["vsType"] = np.string_("mesh")
kv.set_attrs(mesh_group.name, "vsType", "mesh");
#mesh_group.attrs["vsKind"] = np.string_("rectilinear")
kv.set_attrs(mesh_group.name, "vsKind", "rectilinear");
#mesh_group.attrs["vsMD"] = np.string_(self.__name + "mesh")
kv.set_attrs(mesh_group.name, "vsMD", self.__name + "mesh");
data_shape = []
if self.__type > 0:
for i in range(self.__type):
data_shape.append(len(md))
for i in range(len(md)):
#mesh_group.attrs["vsAxis"+str(i)] = np.string_("axis"+str(i))
kv.set_attrs(mesh_group.name, "vsAxis"+str(i), "axis"+str(i));
ds = safe_create_dataset(mesh_group, "axis"+str(i), shape=(md[i].stop-md[i].start,), dtype='float64')
data_shape.append(md[i].stop-md[i].start)
# Compute shape for mesh datasets
mesh_groups[key] = mesh_group
test = safe_create_dataset(var_group, self.__name, shape=tuple(data_shape), dtype='float64')
#test.attrs["vsType"] = np.string_('variable')
kv.set_attrs(test.name, "vsType", "variable");
#test.attrs["vsMesh"] = np.string_('/'+base_name+'/mesh')
kv.set_attrs(test.name, "vsMesh", '/'+base_name+'/mesh')
if self.__var_unit is not None:
#test.attrs["vsUnits"] = np.string_(self.__var_unit)
kv.set_attrs(test.name, "vsUnits", self.__var_unit);
if self.__type > 0:
#test.attrs["vsIndexOrder"] = np.string_("compMajorC")
kv.set_attrs(test.name, "vsIndexOrder", "compMajorC");
if self.__type < 2:
derived_vars = safe_create_group(base, "derived_vars")
#derived_vars.attrs["vsType"] = np.string_("vsVars")
kv.set_attrs(derived_vars.name, "vsType", "vsVars");
tmp = "{"
for i in range(len(md)):
tmp += self.__name+"_"+str(i)
if i < len(md)**self.__type-1:
tmp += ", "
tmp += "}"
#derived_vars.attrs[self.__name] = np.string_(tmp)
kv.set_attrs(derived_vars.name, self.__name, tmp)
if 'time' in base:
#test.attrs["vsTimeGroup"] = np.string_("/time")
kv.set_attrs(test.name, "vsTimeGroup", "/time");
#test.attrs["vsMD"] = np.string_(self.__name)
kv.set_attrs(test.name, "vsMD", self.__name);
datasets[key] = test
# Create Mesh Groups/Datasets
# Create Variable Datasets
# This is done from data and domain.mesh for the corresponding process:
# Write mesh and data
for key in self.__data.keys():
data_shape = []
for i in range(len(key)):
if H5P_COLLECTIVE:
with mesh_groups[key]["axis"+str(i)].collective:
mesh_groups[key]["axis"+str(i)][:] = self.__domains[key].mesh.axes[i][:]
else:
mesh_groups[key]["axis"+str(i)][:] = self.__domains[key].mesh.axes[i][:]
if H5P_COLLECTIVE:
with datasets[key].collective:
datasets[key][:] = self.__data[key][:]
else:
datasets[key][:] = self.__data[key][:]
if hasattr(context, 'comm'):
context.comm.Barrier()
# delete groups and datasets before closing the file!
for d in datasets.values():
try:
del d
except UnboundLocalError:
pass
try:
del datasets
except UnboundLocalError:
pass
try:
del var_group
except UnboundLocalError:
pass
try:
del mesh_group
except UnboundLocalError:
pass
for g in mesh_groups.values():
try:
del g
except UnboundLocalError:
pass
try:
del mesh_groups
except UnboundLocalError:
pass
def write_provenance_data(h5file):
run_info = safe_create_group(h5file, "runinfo")
#run_info.attrs["vsType"] = np.string_("runInfo")
kv.set_attrs(run_info.name, "vsType", "runInfo");
#run_info.attrs["vsSoftware"] = np.string_("maui")
kv.set_attrs(run_info.name, "vsSoftware", "maui");
#run_info.attrs["vsSwVersion"] = np.string_(maui.__version__)
kv.set_attrs(run_info.name, "vsSwVersion", maui.__version__);
#run_info.attrs["vsVsVersion"] = np.string_("4.0.0")
kv.set_attrs(run_info.name, "vsVsVersion", "4.0.0");
#run_info.attrs["vsUser"] = np.string_(getpass.getuser())
kv.set_attrs(run_info.name, "vsUser", getpass.getuser());
#run_info.attrs["vsRunDate"] = np.string_(str(datetime.datetime.now()))
kv.set_attrs(run_info.name, "vsRunDate", str(datetime.datetime.now()))
tmp = str(sys.executable) + " "
for arg in sys.argv:
tmp = tmp + str(arg) + " "
#run_info.attrs["vsCommandLine"] = np.string_(tmp.strip())
kv.set_attrs(run_info.name, "vsCommandLine", tmp.strip())
#run_info.attrs["vsRunHost"] = np.string_(socket.gethostname())
kv.set_attrs(run_info.name, "vsRunHost", socket.gethostname())
del run_info
# -*- coding: utf-8 -*-
import kv
import h5py as h5
base = h5.File("file"+'.vsh5', 'w', driver='sec2')
a_group = h5.Group.create_group(base, "time")
kv.set_attrs(a_group.name, "aa", str.encode("utf8"))
kv.set_attrs(a_group.name, "vsType1", str.encode("utf8"))
a_group = h5.Group.create_group(base, "time1")
kv.set_attrs(a_group.name, "vsType", str.encode("utf8"))
kv.set_attrs(a_group.name, "vsType1", str.encode("utf8"))
a_group = h5.Group.create_group(base, "abc")
kv.set_attrs(a_group.name, "vsType1", str.encode("utf8"))
a_group = h5.Group.create_group(base, "qabc")
kv.set_attrs(a_group.name, "vsType1", str.encode("utf8"))
base.close
kv.finalize("file")
