def time(self, val):
if viscid.is_datetime_like(val):
val = viscid.as_timedelta(self.basetime - viscid.as_datetime64(val))
val = val.total_seconds()
elif viscid.is_timedelta_like(val, conservative=True):
val = viscid.as_timedelta(val).total_seconds()
elif val is not None:
self.set_info('time', float(val))
def time(self, val):
if viscid.is_datetime_like(val):
val = viscid.as_timedelta(self.basetime -
viscid.as_datetime64(val))
val = val.total_seconds()
elif viscid.is_timedelta_like(val, conservative=True):
val = viscid.as_timedelta(val).total_seconds()
elif val is not None:
self.set_info('time', float(val))
def as_floating_t(self, t, none_passthrough=False):
t_as_s = None
try:
t = vutil.str_to_value(t)
if viscid.is_timedelta_like(t, conservative=True):
t_as_s = viscid.as_timedelta(t).total_seconds()
elif viscid.is_datetime_like(t, conservative=True):
delta_t = viscid.as_datetime64(t) - self.basetime
t_as_s = viscid.as_timedelta(delta_t).total_seconds()
elif not isinstance(t, (int, np.integer, type(None))):
t_as_s = float(t)
except AttributeError:
if t is None:
if none_passthrough:
pass
else:
t = 0.0
else:
t_as_s = float(t)
return t_as_s
def as_floating_t(self, t, none_passthrough=False):
t_as_s = None
try:
t = vutil.str_to_value(t)
if viscid.is_timedelta_like(t, conservative=True):
t_as_s = viscid.as_timedelta(t).total_seconds()
elif viscid.is_datetime_like(t, conservative=True):
delta_t = viscid.as_datetime64(t) - self.basetime
t_as_s = viscid.as_timedelta(delta_t).total_seconds()
elif not isinstance(t, (int, np.integer, type(None))):
t_as_s = float(t)
except AttributeError:
if t is None:
if none_passthrough:
pass
else:
t = 0.0
else:
t_as_s = float(t)
return t_as_s
def time_as_timedelta(self):
return viscid.as_timedelta(self.time, unit='s')
def save_fields(cls, fname, flds, complevel=0, compression='gzip',
compression_opts=None, **kwargs):
""" save some fields using the format given by the class """
# FIXME: this is only good for writing cartesian rectilnear flds
# FIXME: axes are renamed if flds[0] is 1D or 2D
assert len(flds) > 0
fname = os.path.expanduser(os.path.expandvars(fname))
if complevel and compression == 'gzip' and compression_opts is None:
compression_opts = complevel
# TODO: what if compression != 'gzip'
do_compression = compression_opts is not None
if isinstance(flds, list):
if isinstance(flds[0], (list, tuple)):
flds = OrderedDict(flds)
else:
flds = OrderedDict([(fld.name, fld) for fld in flds])
# FIXME: all coordinates are saved as non-uniform, the proper
# way to do this is to have let coordinate format its own
# hdf5 / xdmf / numpy binary output
fld0 = next(iter(flds.values()))
clist = fld0.crds.get_clist(full_arrays=True)
crd_arrs = [np.array([0.0])] * 3
crd_names = ["x", "y", "z"]
for i, c in enumerate(clist):
crd_arrs[i] = c[1]
crd_shape = [len(arr) for arr in crd_arrs]
time = fld0.time
# write arrays to the hdf5 file
with h5py.File(fname, 'w') as f:
for axis_name, arr in zip(crd_names, crd_arrs):
loc = cls._CRDS_GROUP + '/' + axis_name
if do_compression:
f.create_dataset(loc, data=arr, compression=compression,
compression_opts=compression_opts)
else:
f[loc] = arr
for name, fld in flds.items():
loc = cls._FLD_GROUPS[fld.center.lower()] + '/' + name
# xdmf files use kji ordering
if do_compression:
f.create_dataset(loc, data=fld.data.T, compression=compression,
compression_opts=compression_opts)
else:
f[loc] = fld.data.T
# big bad openggcm time_str hack to put basetime into hdf5 file
for fld in flds.values():
try:
tfmt = "%Y:%m:%d:%H:%M:%S.%f"
sec_td = viscid.as_timedelta64(fld.time, 's')
dtime = viscid.as_datetime(fld.basetime + sec_td).strftime(tfmt)
epoch = viscid.readers.openggcm.GGCM_EPOCH
ts = viscid.as_timedelta(fld.basetime - epoch).total_seconds()
ts += fld.time
timestr = "time= {0} {1:.16e} {2} 300c".format(fld.time, ts, dtime)
f.create_group('openggcm')
f['openggcm'].attrs['time_str'] = np.string_(timestr)
break
except viscid.NoBasetimeError:
pass
# now write an xdmf file
xdmf_fname = os.path.splitext(fname)[0] + ".xdmf"
relh5fname = "./" + os.path.basename(fname)
with open(xdmf_fname, 'w') as f:
xloc = cls._CRDS_GROUP + '/' + crd_names[0]
yloc = cls._CRDS_GROUP + '/' + crd_names[1]
zloc = cls._CRDS_GROUP + '/' + crd_names[2]
dim_str = " ".join([str(l) for l in crd_shape][::-1])
f.write(cls._XDMF_TEMPLATE_BEGIN.format(time=time))
s = cls._XDMF_TEMPLATE_RECTILINEAR_GRID_BEGIN.format(
grid_name="vgrid", crd_dims=dim_str, h5fname=relh5fname,
xdim=crd_shape[0], ydim=crd_shape[1], zdim=crd_shape[2],
xloc=xloc, yloc=yloc, zloc=zloc)
f.write(s)
for fld in flds.values():
_crd_system = viscid.as_crd_system(fld, None)
if _crd_system:
f.write(cls._XDMF_INFO_TEMPLATE.format(name="crd_system",
value=_crd_system))
break
for name, fld in flds.items():
fld = fld.as_flat().T
dt = fld.dtype.name.rstrip("0123456789").title()
precision = fld.dtype.itemsize
fld_dim_str = " ".join([str(l) for l in fld.shape])
loc = cls._FLD_GROUPS[fld.center.lower()] + '/' + name
s = cls._XDMF_TEMPLATE_ATTRIBUTE.format(
fld_name=name,
fld_type=fld.fldtype, center=fld.center.title(),
dtype=dt, precision=precision, fld_dims=fld_dim_str,
h5fname=relh5fname, fld_loc=loc)
f.write(s)
f.write(cls._XDMF_TEMPLATE_GRID_END)
f.write(cls._XDMF_TEMPLATE_END)
def save_fields(cls, fname, flds, **kwargs):
""" save some fields using the format given by the class """
# FIXME: this is only good for writing cartesian rectilnear flds
# FIXME: axes are renamed if flds[0] is 1D or 2D
assert len(flds) > 0
fname = os.path.expanduser(os.path.expandvars(fname))
# FIXME: all coordinates are saved as non-uniform, the proper
# way to do this is to have let coordinate format its own
# hdf5 / xdmf / numpy binary output
clist = flds[0].crds.get_clist(full_arrays=True)
crd_arrs = [np.array([0.0])] * 3
crd_names = ["x", "y", "z"]
for i, c in enumerate(clist):
crd_arrs[i] = c[1]
crd_shape = [len(arr) for arr in crd_arrs]
time = flds[0].time
# write arrays to the hdf5 file
with h5py.File(fname, 'w') as f:
for axis_name, arr in zip(crd_names, crd_arrs):
loc = cls._CRDS_GROUP + '/' + axis_name
f[loc] = arr
for fld in flds:
loc = cls._FLD_GROUPS[fld.center.lower()] + '/' + fld.name
# xdmf files use kji ordering
f[loc] = fld.data.T
# big bad openggcm time_str hack to put basetime into hdf5 file
for fld in flds:
try:
tfmt = "%Y:%m:%d:%H:%M:%S.%f"
sec_td = viscid.as_timedelta64(fld.time, 's')
dtime = viscid.as_datetime(fld.basetime + sec_td).strftime(tfmt)
epoch = viscid.readers.openggcm.GGCM_EPOCH
ts = viscid.as_timedelta(fld.basetime - epoch).total_seconds()
ts += fld.time
timestr = "time= {0} {1:.16e} {2} 300c".format(fld.time, ts, dtime)
f.create_group('openggcm')
f['openggcm'].attrs['time_str'] = np.string_(timestr)
break
except viscid.NoBasetimeError:
pass
# now write an xdmf file
xdmf_fname = os.path.splitext(fname)[0] + ".xdmf"
relh5fname = "./" + os.path.basename(fname)
with open(xdmf_fname, 'w') as f:
xloc = cls._CRDS_GROUP + '/' + crd_names[0]
yloc = cls._CRDS_GROUP + '/' + crd_names[1]
zloc = cls._CRDS_GROUP + '/' + crd_names[2]
dim_str = " ".join([str(l) for l in crd_shape][::-1])
f.write(cls._XDMF_TEMPLATE_BEGIN.format(time=time))
s = cls._XDMF_TEMPLATE_RECTILINEAR_GRID_BEGIN.format(
grid_name="vgrid", crd_dims=dim_str, h5fname=relh5fname,
xdim=crd_shape[0], ydim=crd_shape[1], zdim=crd_shape[2],
xloc=xloc, yloc=yloc, zloc=zloc)
f.write(s)
for fld in flds:
_crd_system = viscid.get_crd_system(fld, None)
if _crd_system:
f.write(cls._XDMF_INFO_TEMPLATE.format(name="crd_system",
value=_crd_system))
break
for fld in flds:
fld = fld.as_flat().T
dt = fld.dtype.name.rstrip("0123456789").title()
precision = fld.dtype.itemsize
fld_dim_str = " ".join([str(l) for l in fld.shape])
loc = cls._FLD_GROUPS[fld.center.lower()] + '/' + fld.name
s = cls._XDMF_TEMPLATE_ATTRIBUTE.format(
fld_name=fld.name,
fld_type=fld.fldtype, center=fld.center.title(),
dtype=dt, precision=precision, fld_dims=fld_dim_str,
h5fname=relh5fname, fld_loc=loc)
f.write(s)
f.write(cls._XDMF_TEMPLATE_GRID_END)
f.write(cls._XDMF_TEMPLATE_END)
def time_as_timedelta(self):
return viscid.as_timedelta(self.time, unit='s')
def time_as_timedelta(self):
return viscid.as_timedelta(self.time_as_timedelta64())