def _run_simple(self, input_data):
"""!
@brief Write Serafin without any operator
@param input_data <slf.datatypes.SerafinData>: input SerafinData stream
"""
output_header = input_data.default_output_header()
with Serafin.Read(input_data.filename,
input_data.language) as input_stream:
input_stream.header = input_data.header
input_stream.time = input_data.time
with Serafin.Write(self.filename, input_data.language,
True) as output_stream:
output_stream.write_header(output_header)
for i, time_index in enumerate(
input_data.selected_time_indices):
values = do_calculations_in_frame(
input_data.equations,
input_stream,
time_index,
input_data.selected_vars,
output_header.np_float_type,
is_2d=output_header.is_2d,
us_equation=input_data.us_equation)
output_stream.write_entire_frame(
output_header, input_data.time[time_index], values)
self.progress_bar.setValue(
100 * (i + 1) / len(input_data.selected_time_indices))
QApplication.processEvents()
self.success('Output saved to {}.'.format(self.filename))
return True
def run(self):
iter_pbar = ProgressBarIterator.prepare(self.tick.emit, (5, 100))
for time_index in iter_pbar(self.time_indices):
if self.canceled:
return
values = do_calculations_in_frame(self.necessary_equations, self.input_stream, time_index,
self.output_header.var_IDs, self.output_header.np_float_type,
is_2d=self.output_header.is_2d, us_equation=self.us_equation)
self.output_stream.write_entire_frame(self.output_header, self.input_stream.time[time_index], values)
def slf_base(args):
with Serafin.Read(args.in_slf, args.lang) as resin:
resin.read_header()
logger.info(resin.header.summary())
resin.get_time()
output_header = resin.header.copy()
# Shift mesh coordinates if necessary
if args.shift:
output_header.transform_mesh([Transformation(0, 1, 1, args.shift[0], args.shift[1], 0)])
# Set mesh origin coordinates
if args.set_mesh_origin:
output_header.set_mesh_origin(args.set_mesh_origin[0], args.set_mesh_origin[1])
# Toggle output file endianness if necessary
if args.toggle_endianness:
output_header.toggle_endianness()
# Convert to single precision
if args.to_single_precision:
if resin.header.is_double_precision():
output_header.to_single_precision()
else:
logger.warn('Input file is already single precision! Argument `--to_single_precision` is ignored')
# Remove variables if necessary
if args.var2del:
output_header.empty_variables()
for var_ID, var_name, var_unit in zip(resin.header.var_IDs, resin.header.var_names, resin.header.var_units):
if var_ID not in args.var2del:
output_header.add_variable(var_ID, var_name, var_unit)
# Add new derived variables
if args.var2add is not None:
for var_ID in args.var2add:
if var_ID in output_header.var_IDs:
logger.warn('Variable %s is already present (or asked)' % var_ID)
else:
output_header.add_variable_from_ID(var_ID)
us_equation = get_US_equation(args.friction_law)
necessary_equations = get_necessary_equations(resin.header.var_IDs, output_header.var_IDs,
is_2d=resin.header.is_2d, us_equation=us_equation)
with Serafin.Write(args.out_slf, args.lang, overwrite=args.force) as resout:
resout.write_header(output_header)
for time_index, time in tqdm(resin.subset_time(args.start, args.end, args.ech), unit='frame'):
values = do_calculations_in_frame(necessary_equations, resin, time_index, output_header.var_IDs,
output_header.np_float_type, is_2d=output_header.is_2d,
us_equation=us_equation, ori_values={})
resout.write_entire_frame(output_header, time, values)
def _run_layer_selection(self, input_data):
"""!
@brief Write Serafin with `Select Single Layer` operator
@param input_data <slf.datatypes.SerafinData>: input SerafinData stream
"""
output_header = input_data.build_2d_output_header()
with Serafin.Read(input_data.filename,
input_data.language) as input_stream:
input_stream.header = input_data.header
input_stream.time = input_data.time
with Serafin.Write(self.filename, input_data.language,
True) as output_stream:
output_stream.write_header(output_header)
for i, time_index in enumerate(
input_data.selected_time_indices):
# FIXME Optimization: Do calculations only on target layer and avoid reshaping afterwards
values = do_calculations_in_frame(
input_data.equations,
input_stream,
time_index,
input_data.selected_vars,
output_header.np_float_type,
is_2d=output_header.is_2d,
us_equation=input_data.us_equation)
new_shape = (values.shape[0],
input_stream.header.nb_planes,
values.shape[1] //
input_stream.header.nb_planes)
values_at_layer = values.reshape(
new_shape)[:, input_data.metadata['layer_selection'] -
1, :]
output_stream.write_entire_frame(
output_header, input_data.time[time_index],
values_at_layer)
self.progress_bar.setValue(
100 * (i + 1) / len(input_data.selected_time_indices))
QApplication.processEvents()
self.success('Output saved to {}.'.format(self.filename))
return True
def slf_sedi_chain(args):
# Check that float parameters are positive (especially ws!)
for arg in ('Cmud', 'ws', 'C', 'M'):
if getattr(args, arg) < 0:
logger.critical('The argument %s has to be positive' % args)
sys.exit(1)
with Serafin.Read(args.in_slf, args.lang) as resin:
resin.read_header()
logger.info(resin.header.summary())
resin.get_time()
us_equation = get_US_equation(args.friction_law)
necessary_equations = get_necessary_equations(resin.header.var_IDs,
['TAU'],
is_2d=True,
us_equation=us_equation)
if resin.header.nb_frames < 1:
logger.critical('The input file must have at least one frame!')
sys.exit(1)
output_header = resin.header.copy()
# Shift mesh coordinates if necessary
if args.shift:
output_header.transform_mesh(
[Transformation(0, 1, 1, args.shift[0], args.shift[1], 0)])
# Toggle output file endianness if necessary
if args.toggle_endianness:
output_header.toggle_endianness()
# Convert to single precision
if args.to_single_precision:
if resin.header.is_double_precision():
output_header.to_single_precision()
else:
logger.warn(
'Input file is already single precision! Argument `--to_single_precision` is ignored'
)
output_header.empty_variables()
output_header.add_variable_from_ID('B')
output_header.add_variable_from_ID('EV')
with Serafin.Write(args.out_slf, args.lang,
overwrite=args.force) as resout:
resout.write_header(output_header)
prev_time = None
prev_tau = None
initial_bottom = resin.read_var_in_frame(0, 'B')
bottom = copy(initial_bottom)
for time_index, time in enumerate(resin.time):
tau = do_calculations_in_frame(necessary_equations,
resin,
time_index, ['TAU'],
output_header.np_float_type,
is_2d=True,
us_equation=us_equation,
ori_values={})[0]
if prev_time is not None:
dt = time - prev_time
mean_tau = (prev_tau + tau) / 2
if args.Tcd > 0:
bottom += args.Cmud * args.ws * args.C * \
(1 - np.clip(mean_tau/args.Tcd, a_min=None, a_max=1.)) * dt
if args.Tce > 0:
bottom -= args.Cmud * args.M * (np.clip(
mean_tau / args.Tce, a_min=1., a_max=None) -
1.) * dt
evol_bottom = bottom - initial_bottom
resout.write_entire_frame(output_header, time,
np.vstack((bottom, evol_bottom)))
prev_time = time
prev_tau = tau
def slf_bottom_friction(args):
# Check argument consistency
if args.in_strickler_zones is not None or args.in_strickler_attr is not None:
if args.in_strickler_zones is None or args.in_strickler_attr is None:
logger.critical(
'Both arguments `--in_strickler_zones` and `--in_strickler_attr` have to be defined.'
)
sys.exit(2)
# Read polygons to compute volume
if not args.in_polygons.endswith('.shp'):
logger.critical('File "%s" is not a shp file.' % args.in_polygons)
sys.exit(3)
polygons = []
try:
for polygon in Shapefile.get_polygons(args.in_polygons):
polygons.append(polygon)
except ShapefileException as e:
logger.error(e)
sys.exit(3)
if not polygons:
logger.error('The file does not contain any polygon.')
sys.exit(1)
logger.debug('The file contains {} polygon{}.'.format(
len(polygons), 's' if len(polygons) > 1 else ''))
names = ['Polygon %d' % (i + 1) for i in range(len(polygons))]
varIDs = ['US', 'TAU']
out_varIDs = ['W'] + varIDs
pos_TAU = out_varIDs.index('TAU')
with Serafin.Read(args.in_slf, args.lang) as resin:
resin.read_header()
if not resin.header.is_2d:
logger.critical('The file has to be a 2D Serafin!')
sys.exit(3)
in_varIDs = resin.header.var_IDs
# Compute Strickler values if necessary
ori_values = {}
if args.in_strickler_zones is not None:
if not args.in_strickler_zones.endswith('.shp'):
logger.critical('File "%s" is not a shp file.' %
args.in_strickler_zones)
sys.exit(3)
attributes = Shapefile.get_numeric_attribute_names(
args.in_strickler_zones)
try:
index_attr = [attr for _, attr in attributes
].index(args.in_strickler_attr)
except ValueError:
logger.critical('Attribute "%s" is not found.' %
args.in_strickler_attr)
sys.exit(1)
strickler_zones = []
try:
for zone in Shapefile.get_polygons(args.in_strickler_zones):
strickler_zones.append(zone)
except ShapefileException as e:
logger.error(e)
sys.exit(3)
if not strickler_zones:
logger.error('The file does not contain any friction zone.')
sys.exit(1)
logger.debug('Recomputing friction coefficient values from zones')
friction_coeff = np.full(
resin.header.nb_nodes_2d,
0.0) # default value for nodes not included in any zone
for i, (x, y) in enumerate(
zip(tqdm(resin.header.x), tqdm(resin.header.y))):
point = Point(x, y)
for zone in strickler_zones:
if zone.contains(point):
friction_coeff[i] = zone.attributes()[index_attr]
exit
in_varIDs.append('W')
ori_values['W'] = friction_coeff
else:
if 'W' not in resin.header.varIDs:
logger.critical('The variable W is missing.')
sys.exit(1)
us_equation = None
if args.friction_law:
us_equation = get_US_equation(args.friction_law)
resin.get_time()
necessary_equations = get_necessary_equations(in_varIDs,
out_varIDs,
is_2d=True,
us_equation=us_equation)
calculator = VolumeCalculator(VolumeCalculator.NET, 'TAU', None, resin,
names, polygons, 1)
calculator.construct_triangles(tqdm)
calculator.construct_weights(tqdm)
output_header = resin.header.copy()
output_header.empty_variables()
for var_ID in out_varIDs:
output_header.add_variable_from_ID(var_ID)
with Serafin.Write(args.out_slf, args.lang, args.force) as resout:
resout.write_header(output_header)
mode = 'w' if args.force else 'x'
with open(args.out_csv, mode, newline='') as csvfile:
csvwriter = csv.writer(csvfile, delimiter=args.sep)
csvwriter.writerow(['time'] + names)
for time_index, time in enumerate(tqdm(resin.time)):
values = do_calculations_in_frame(
necessary_equations,
resin,
time_index,
out_varIDs,
resin.header.np_float_type,
is_2d=True,
us_equation=STRICKLER_EQUATION,
ori_values=ori_values)
resout.write_entire_frame(output_header, time, values)
row = [time]
for j in range(len(calculator.polygons)):
weight = calculator.weights[j]
volume = calculator.volume_in_frame_in_polygon(
weight, values[pos_TAU], calculator.polygons[j])
row.append(volume)
csvwriter.writerow(row)
