def build_field_time_series(local_time_indices,
file_names,
mesh_file,
out_dir,
blocking,
all_dim_vals,
blockDimName,
variable_list,
vertices,
connectivity,
offsets,
valid_mask,
output_32bit,
combine_output,
append,
xtimeName,
topo_dim=None,
topo_cell_indices=None,
cell_to_point_map=None,
boundary_mask=None): # {{{
if len(variable_list) == 0:
return
if output_32bit:
outType = 'float32'
else:
outType = 'float64'
# Get dimension info to allocate the size of Colors
time_series_file = viz.open_netcdf(file_names[0])
if mesh_file is not None:
# blockDim may not exist in time series file
blockDim = len(mesh_file.dimensions[blockDimName])
else:
blockDim = len(time_series_file.dimensions[blockDimName])
if boundary_mask is not None:
variable_list.append('boundaryMask')
all_dim_vals['boundaryMask'] = None
pointData = True
cellData = False
else:
pointData = False
cellData = True
# Pre-compute the number of blocks
nBlocks = int(np.ceil(blockDim / blocking))
nPolygons = len(offsets)
nPoints = len(vertices[0])
nTimes = len(local_time_indices)
nVars = len(variable_list)
var_has_time_dim = np.zeros(nVars, bool)
nHyperSlabs = 0
for iVar in range(nVars):
var_name = variable_list[iVar]
if boundary_mask is not None and var_name == 'boundaryMask':
var_has_time_dim[iVar] = False
elif xtimeName is not None:
if var_name in time_series_file.variables:
var_has_time_dim[iVar] = \
'Time' in time_series_file.variables[var_name].dimensions
else:
# we can't support time dependence in the mesh file
assert ('Time' not in mesh_file.variables[var_name].dimensions)
var_has_time_dim[iVar] = False
extra_dim_vals = all_dim_vals[var_name]
if (extra_dim_vals is None) or (len(extra_dim_vals) == 0):
nHyperSlabs += 1
else:
nHyperSlabs += len(extra_dim_vals)
any_var_has_time_dim = np.any(var_has_time_dim)
if topo_dim is not None:
if (mesh_file is not None) and (topo_dim in mesh_file.dimensions):
nTopoLevels = len(mesh_file.dimensions[topo_dim])
else:
nTopoLevels = len(time_series_file.dimensions[topo_dim])
else:
nTopoLevels = None
time_series_file.close()
try:
os.makedirs(out_dir)
except OSError:
pass
if any_var_has_time_dim:
try:
os.makedirs('{}/time_series'.format(out_dir))
except OSError:
pass
else:
# there is no point in combining output if no fields have Time dim
combine_output = False
nTimes = 1
# Output time series
if use_progress_bar:
widgets = [
'Writing time series: ',
Percentage(), ' ',
Bar(), ' ',
ETA()
]
field_bar = ProgressBar(widgets=widgets,
maxval=nTimes * nHyperSlabs).start()
else:
print("Writing time series....")
suffix = blockDimName[1:]
if any_var_has_time_dim:
if combine_output or np.all(var_has_time_dim):
out_prefix = "fieldsOn{}".format(suffix)
else:
out_prefix = "timeDependentFieldsOn{}".format(suffix)
# start the pvd file
pvd_file = viz.write_pvd_header(out_dir, out_prefix)
pvd_file.write('<Collection>\n')
if not combine_output and not np.all(var_has_time_dim):
static_prefix = "staticFieldsOn{}".format(suffix)
varIndices = np.arange(nVars)[np.logical_not(var_has_time_dim)]
timeIndependentFile = viz.write_vtp_header(out_dir,
static_prefix,
varIndices[0],
varIndices,
variable_list,
all_dim_vals,
vertices,
connectivity,
offsets,
nPoints,
nPolygons,
outType,
cellData=cellData,
pointData=pointData,
xtime=None)
prev_file = ""
for time_index in range(nTimes):
if prev_file != file_names[time_index]:
if prev_file != "":
time_series_file.close()
time_series_file = viz.open_netcdf(file_names[time_index])
prev_file = file_names[time_index]
if any_var_has_time_dim:
if xtimeName is None:
xtime = None
years = float(time_index)
else:
if xtimeName == 'none':
xtime = '{}'.format(time_index)
years = float(time_index)
else:
if xtimeName not in time_series_file.variables:
raise ValueError("xtime variable name {} not found in "
"{}".format(xtimeName,
time_series_file))
var = time_series_file.variables[xtimeName]
if len(var.shape) == 2:
xtime = var[
local_time_indices[time_index], :].tostring(
).decode('utf-8').strip()
date = datetime(int(xtime[0:4]), int(xtime[5:7]),
int(xtime[8:10]), int(xtime[11:13]),
int(xtime[14:16]), int(xtime[17:19]))
years = date2num(date,
units='days since 0000-01-01',
calendar='noleap') / 365.
else:
xtime = var[local_time_indices[time_index]]
years = xtime / 365.
xtime = str(xtime)
# write the header for the vtp file
vtp_file_prefix = "time_series/{}.{:d}".format(
out_prefix, time_index)
file_name = '{}/{}.vtp'.format(out_dir, vtp_file_prefix)
if append and os.path.exists(file_name):
pvd_file.write('<DataSet timestep="{:.16f}" group="" '
'part="0"\n'.format(years))
pvd_file.write('\tfile="{}.vtp"/>\n'.format(vtp_file_prefix))
continue
if combine_output:
varIndices = np.arange(nVars)
else:
varIndices = np.arange(nVars)[var_has_time_dim]
timeDependentFile = viz.write_vtp_header(out_dir,
vtp_file_prefix,
varIndices[0],
varIndices,
variable_list,
all_dim_vals,
vertices,
connectivity,
offsets,
nPoints,
nPolygons,
outType,
cellData=cellData,
pointData=pointData,
xtime=xtime)
# add time step to pdv file
pvd_file.write('<DataSet timestep="{:.16f}" group="" '
'part="0"\n'.format(years))
pvd_file.write('\tfile="{}.vtp"/>\n'.format(vtp_file_prefix))
if time_index == 0 or combine_output:
varIndices = np.arange(nVars)
else:
# only the time-dependent variables
varIndices = np.arange(nVars)[var_has_time_dim]
iHyperSlabProgress = 0
for iVar in varIndices:
has_time = var_has_time_dim[iVar]
var_name = variable_list[iVar]
(out_var_names, dim_list) = \
viz.get_hyperslab_name_and_dims(var_name,
all_dim_vals[var_name])
if has_time or combine_output:
vtkFile = timeDependentFile
else:
vtkFile = timeIndependentFile
for iHyperSlab in range(len(out_var_names)):
if dim_list is not None:
dim_vals = dim_list[iHyperSlab]
else:
dim_vals = None
if boundary_mask is not None and var_name == 'boundaryMask':
field = np.array(boundary_mask, dtype=outType)
else:
field = np.zeros(blockDim, dtype=outType)
for iBlock in np.arange(0, nBlocks):
blockStart = iBlock * blocking
blockEnd = min((iBlock + 1) * blocking, blockDim)
block_indices = np.arange(blockStart, blockEnd)
if topo_cell_indices is None:
block_topo_cell_indices = None
else:
block_topo_cell_indices = \
topo_cell_indices[block_indices]
field_block = viz.read_field(
var_name,
mesh_file,
time_series_file,
dim_vals,
local_time_indices[time_index],
block_indices,
outType,
topo_dim=topo_dim,
topo_cell_indices=block_topo_cell_indices,
nTopoLevels=nTopoLevels)
field[blockStart:blockEnd] = field_block
field = field[valid_mask]
if cell_to_point_map is not None:
# map field from cells to points
field = field[cell_to_point_map]
vtkFile.appendData(field)
if use_progress_bar:
field_bar.update(time_index * nHyperSlabs +
iHyperSlabProgress)
iHyperSlabProgress += 1
del field
if any_var_has_time_dim:
timeDependentFile.save()
del timeDependentFile
if time_index == 0 and not combine_output and not \
np.all(var_has_time_dim):
timeIndependentFile.save()
del timeIndependentFile
time_series_file.close()
if use_progress_bar:
field_bar.finish()
if any_var_has_time_dim:
# finish the pdv file
pvd_file.write('</Collection>\n')
pvd_file.write('</VTKFile>\n')
pvd_file.close() # }}}
(time_indices,
time_file_names) = viz.setup_time_indices(args.filename_pattern,
args.xtime)
if args.time:
time_indices, time_file_names = \
viz.parse_time_indices(args.time, time_indices, time_file_names)
separate_mesh_file = True
if not args.mesh_filename:
args.mesh_filename = time_file_names[0]
separate_mesh_file = False
# Setting dimension values:
time_series_file = viz.open_netcdf(time_file_names[0])
if separate_mesh_file:
mesh_file = viz.open_netcdf(args.mesh_filename)
else:
mesh_file = None
extra_dims, topo_cell_indices = \
viz.parse_extra_dims(args.dimension_list, time_series_file,
mesh_file, topo_dim=args.topo_dim,
topo_cell_index_name=args.topo_cell_index)
basic_dims = ['nCells', 'nEdges', 'nVertices', 'Time']
include_dims = ['nCells', 'nEdges', 'nVertices']
if args.topo_dim is not None:
basic_dims.append(args.topo_dim)
include_dims = ['nCells']
(all_dim_vals, cellVars, vertexVars, edgeVars) = \