def slf_max_over_files(args):
if args.vars is None:
with Serafin.Read(args.in_slfs[0], args.lang) as resin:
resin.read_header()
var_IDs = resin.header.var_IDs if args.vars is None else args.vars
else:
var_IDs = args.vars
if args.operation == 'max':
fun = np.maximum
elif args.operation == 'min':
fun = np.minimum
else:
raise NotImplementedError
# Read polygons
if args.in_polygons is not None:
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.info('The file contains {} polygon{}.'.format(len(polygons), 's' if len(polygons) > 1 else ''))
else:
polygons = None
output_header = None
out_values = None # min or max values
mask_nodes = None
for i, in_slf in enumerate(args.in_slfs):
with Serafin.Read(in_slf, args.lang) as resin:
resin.read_header()
logger.info(resin.header.summary())
if not resin.header.is_2d:
logger.critical('The file has to be a 2D Serafin!')
sys.exit(3)
resin.get_time()
for var_ID in var_IDs:
if var_ID not in resin.header.var_IDs:
logger.critical('The variable %s is missing in %s' % (var_ID, in_slf))
sys.exit(3)
if i == 0:
output_header = resin.header.copy()
output_header.empty_variables()
for var_ID in var_IDs:
output_header.add_variable_from_ID(var_ID)
out_values = np.empty((output_header.nb_var, output_header.nb_nodes),
dtype=output_header.np_float_type)
if polygons is not None:
mask_nodes = np.zeros(output_header.nb_nodes, dtype=bool)
for idx_node, (x, y) in enumerate(zip(output_header.x, output_header.y)):
point = Point(x, y)
for polygon in polygons:
if polygon.contains(point):
mask_nodes[idx_node] = True
break
logger.info('Number of nodes inside polygon(s): %i (over %i)'
% (mask_nodes.sum(), output_header.nb_nodes))
else:
mask_nodes = np.ones(output_header.nb_nodes, dtype=bool)
else:
if not resin.header.same_2d_mesh(output_header):
logger.critical('The mesh of %s is different from the first one' % in_slf)
sys.exit(1)
for time_index, time in enumerate(resin.time):
for j, var_ID in enumerate(var_IDs):
values = resin.read_var_in_frame(time_index, var_ID)
if time_index == 0 and i == 0:
out_values[j, :] = values
else:
out_values[j, mask_nodes] = fun(out_values[j, mask_nodes], values[mask_nodes])
with Serafin.Write(args.out_slf, args.lang, overwrite=args.force) as resout:
resout.write_header(output_header)
resout.write_entire_frame(output_header, 0.0, out_values)
help='upper variable',
metavar='VA',
required=True)
parser.add_argument('--lower_var',
help='lower variable',
metavar='VB',
default=None)
parser.add_argument('--detailed',
help='add positive and negative volumes',
action='store_true')
parser.add_known_argument('out_csv')
parser.add_group_general(['force', 'verbose'])
if __name__ == '__main__':
args = parser.parse_args()
try:
slf_volume(args)
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError):
# Message is already reported by slf logger
sys.exit(1)
except FileNotFoundError as e:
logger.error('Input file %s not found.' % e.filename)
sys.exit(3)
except FileExistsError as e:
logger.error(
'Output file %s already exists. Remove it or add `--force` argument'
% e.filename)
sys.exit(3)
def slf_volume(args):
# Read set of lines from input file
polygons = []
if args.in_polygons.endswith('.i2s'):
with BlueKenue.Read(args.in_polygons) as f:
f.read_header()
for poly in f.get_polygons():
polygons.append(poly)
elif args.in_polygons.endswith('.shp'):
try:
for polygon in Shapefile.get_polygons(args.in_polygons):
polygons.append(polygon)
except ShapefileException as e:
logger.error(e)
sys.exit(3)
else:
logger.error('File "%s" is not a i2s or shp file.' % args.in_polygons)
sys.exit(2)
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))]
# Read Serafin file
with Serafin.Read(args.in_slf, args.lang) as resin:
resin.read_header()
logger.info(resin.header.summary())
resin.get_time()
if not resin.header.is_2d:
logger.error('The file has to be a 2D Serafin!')
sys.exit(3)
# Check variables consistency
if args.upper_var not in resin.header.var_IDs:
logger.error('Upper variable "%s" is not in Serafin file' %
args.upper_var)
sys.exit(1)
upper_var = args.upper_var
lower_var = args.lower_var
if args.lower_var is not None:
if args.lower_var == 'init':
lower_var = VolumeCalculator.INIT_VALUE
else:
if lower_var not in resin.header.var_IDs:
logger.error('Lower variable "%s" is not in Serafin file' %
lower_var)
sys.exit(1)
if args.detailed:
volume_type = VolumeCalculator.POSITIVE
else:
volume_type = VolumeCalculator.NET
calculator = VolumeCalculator(volume_type, upper_var, lower_var, resin,
names, polygons, args.ech)
calculator.construct_triangles(tqdm)
calculator.construct_weights(tqdm)
result = []
for time_index in tqdm(calculator.time_indices, unit='frame'):
i_result = [str(resin.time[time_index])]
values = calculator.read_values_in_frame(time_index)
for j in range(len(calculator.polygons)):
weight = calculator.weights[j]
volume = calculator.volume_in_frame_in_polygon(
weight, values, calculator.polygons[j])
if calculator.volume_type == VolumeCalculator.POSITIVE:
for v in volume:
i_result.append(settings.FMT_FLOAT.format(v))
else:
i_result.append(settings.FMT_FLOAT.format(volume))
result.append(i_result)
# Write CSV
mode = 'w' if args.force else 'x'
with open(args.out_csv, mode) as out_csv:
calculator.write_csv(result, out_csv, args.sep)
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)