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 btnComputeEvent(self):
ref_time = int(self.timeSelection.refIndex.text()) - 1
selected_variable = self.input.varBox.currentText().split('(')[0][:-1]
mad = []
try:
with Serafin.Read(self.input.ref_data.filename,
self.input.ref_data.language) as input_stream:
input_stream.header = self.input.ref_data.header
input_stream.time = self.input.ref_data.time
ref_values = input_stream.read_var_in_frame(
ref_time, selected_variable)
with Serafin.Read(self.input.test_data.filename,
self.input.test_data.language) as input_stream:
input_stream.header = self.input.test_data.header
input_stream.time = self.input.test_data.time
for i in range(len(self.input.test_data.time)):
values = input_stream.read_var_in_frame(
i, selected_variable) - ref_values
mad.append(
self.input.ref_mesh.mean_absolute_deviation(values))
except (Serafin.SerafinRequestError,
Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message,
QMessageBox.Ok, QMessageBox.Ok)
return
self.plotViewer.plot(self.input.test_data.time, mad)
def btnComputeEvent(self):
self.xlim = None
self.ylim = None
self.has_map = False
ref_time = int(self.timeSelection.refIndex.text()) - 1
test_time = int(self.timeSelection.testIndex.text()) - 1
selected_variable = self.input.varBox.currentText().split('(')[0][:-1]
try:
with Serafin.Read(self.input.ref_data.filename, self.input.ref_data.language) as input_stream:
input_stream.header = self.input.ref_data.header
input_stream.time = self.input.ref_data.time
ref_values = input_stream.read_var_in_frame(ref_time, selected_variable)
with Serafin.Read(self.input.test_data.filename, self.input.test_data.language) as input_stream:
input_stream.header = self.input.test_data.header
input_stream.time = self.input.test_data.time
test_values = input_stream.read_var_in_frame(test_time, selected_variable)
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
values = test_values - ref_values
self.ewsd = self.input.ref_mesh.element_wise_signed_deviation(values)
self.updateStats(ref_time, test_time)
self.updateHistogram()
def btnComputeEvent(self):
ref_time = int(self.timeSelection.refIndex.text()) - 1
test_time = int(self.timeSelection.testIndex.text()) - 1
init_time = int(self.initSelection.refIndex.text()) - 1
selected_variable = self.input.varBox.currentText().split('(')[0][:-1]
try:
with Serafin.Read(self.input.ref_data.filename, self.input.ref_data.language) as input_stream:
input_stream.header = self.input.ref_data.header
input_stream.time = self.input.ref_data.time
ref_values = input_stream.read_var_in_frame(ref_time, selected_variable)
with Serafin.Read(self.input.test_data.filename, self.input.test_data.language) as input_stream:
input_stream.header = self.input.test_data.header
input_stream.time = self.input.test_data.time
test_values = input_stream.read_var_in_frame(test_time, selected_variable)
init_values = input_stream.read_var_in_frame(init_time, selected_variable)
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
test_volume = self.input.ref_mesh.quadratic_volume(test_values - ref_values)
ref_volume = self.input.ref_mesh.quadratic_volume(ref_values - init_values)
if test_volume == 0 and ref_volume == 0:
bss = 1
else:
with np.errstate(divide='ignore'):
bss = 1 - test_volume / ref_volume
self.resultTextBox.appendPlainText(self.template.format(ref_time+1, test_time+1, init_time+1, bss))
def run_single(self, input_name, input_header, output_name, output_header,
pool):
i = 0
try:
with Serafin.Read(input_name,
input_header.language) as input_stream:
input_stream.header = input_header
input_stream.get_time()
inv_nb_frames = len(input_stream.time)
with Serafin.Write(output_name,
input_header.language) as output_stream:
output_stream.write_header(output_header)
for time_value, value_array in pool.evaluate_expressions(
self.augmented_path, input_stream,
self.selected_expressions):
if self.canceled:
return
i += 1
output_stream.write_entire_frame(
output_header, time_value, value_array)
self.tick.emit(100 * i * self.inv_nb_files *
inv_nb_frames)
QApplication.processEvents()
except (Serafin.SerafinRequestError,
Serafin.SerafinValidationError) as e:
QMessageBox.critical(self, 'Serafin Error', e.message,
QMessageBox.Ok)
return
def btnComputeEvent(self):
ref_time = int(self.timeSelection.refIndex.text()) - 1
test_time = int(self.timeSelection.testIndex.text()) - 1
selected_variable = self.input.varBox.currentText().split('(')[0][:-1]
try:
with Serafin.Read(self.input.ref_data.filename,
self.input.ref_data.language) as input_stream:
input_stream.header = self.input.ref_data.header
input_stream.time = self.input.ref_data.time
ref_values = input_stream.read_var_in_frame(
ref_time, selected_variable)
with Serafin.Read(self.input.test_data.filename,
self.input.test_data.language) as input_stream:
input_stream.header = self.input.test_data.header
input_stream.time = self.input.test_data.time
test_values = input_stream.read_var_in_frame(
test_time, selected_variable)
except (Serafin.SerafinRequestError,
Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message,
QMessageBox.Ok, QMessageBox.Ok)
return
values = test_values - ref_values
msd = self.input.ref_mesh.mean_signed_deviation(values)
mad = self.input.ref_mesh.mean_absolute_deviation(values)
rmsd = self.input.ref_mesh.root_mean_square_deviation(values)
self.resultTextBox.appendPlainText(
self.template.format(ref_time + 1, test_time + 1, msd, mad, rmsd))
def _run_max_min_mean(self, input_data):
"""!
@brief Write Serafin with `Temporal Min/Max/Mean` operator
@param input_data <slf.datatypes.SerafinData>: input SerafinData stream
"""
selected = [(var, input_data.selected_vars_names[var][0],
input_data.selected_vars_names[var][1])
for var in input_data.selected_vars]
scalars, vectors, additional_equations = operations.scalars_vectors(
input_data.header.var_IDs, selected, input_data.us_equation)
output_header = input_data.header.copy()
output_header.set_variables(scalars + vectors)
if input_data.to_single:
output_header.to_single_precision()
with Serafin.Read(input_data.filename,
input_data.language) as input_stream:
input_stream.header = input_data.header
input_stream.time = input_data.time
has_scalar, has_vector = False, False
scalar_calculator, vector_calculator = None, None
if scalars:
has_scalar = True
scalar_calculator = operations.ScalarMaxMinMeanCalculator(
input_data.operator, input_stream, scalars,
input_data.selected_time_indices, additional_equations)
if vectors:
has_vector = True
vector_calculator = operations.VectorMaxMinMeanCalculator(
input_data.operator, input_stream, vectors,
input_data.selected_time_indices, additional_equations)
for i, time_index in enumerate(input_data.selected_time_indices):
if has_scalar:
scalar_calculator.max_min_mean_in_frame(time_index)
if has_vector:
vector_calculator.max_min_mean_in_frame(time_index)
self.progress_bar.setValue(
100 * (i + 1) / len(input_data.selected_time_indices))
QApplication.processEvents()
if has_scalar and not has_vector:
values = scalar_calculator.finishing_up()
elif not has_scalar and has_vector:
values = vector_calculator.finishing_up()
else:
values = np.vstack((scalar_calculator.finishing_up(),
vector_calculator.finishing_up()))
with Serafin.Write(self.filename, input_data.language,
True) as output_stream:
output_stream.write_header(output_header)
output_stream.write_entire_frame(output_header,
input_data.time[0], values)
self.success('Output saved to {}.'.format(self.filename))
return True
def btnSubmitEvent(self):
canceled, filename = save_dialog('Serafin', self.data.filename)
if canceled:
return
# fetch the list of selected variables
selected_vars = self.inputTab.getSelectedVariables()
# deduce header from selected variable IDs and write header
output_header = self.getOutputHeader(selected_vars)
# fetch the list of selected frames
if self.timeSelection.manualSelection.hasData:
output_time_indices = self.timeSelection.getManualTime()
output_message = 'Writing the output with variables %s for %d frame%s between frame %d and %d.' \
% (str(output_header.var_IDs), len(output_time_indices),
['', 's'][len(output_time_indices) > 1], output_time_indices[0]+1, output_time_indices[-1]+1)
else:
start_index, end_index, sampling_frequency, output_time_indices = self.timeSelection.getTime()
output_message = 'Writing the output with variables %s between frame %d and %d with sampling frequency %d.' \
% (str(output_header.var_IDs), start_index, end_index, sampling_frequency)
self.parent.inDialog()
progressBar = OutputProgressDialog()
# do some calculations
try:
with Serafin.Read(self.data.filename, self.data.language) as input_stream:
# instead of re-reading the header and the time, just do a copy
input_stream.header = self.data.header
input_stream.time = self.data.time
progressBar.setValue(5)
QApplication.processEvents()
with Serafin.Write(filename, self.data.language) as output_stream:
logging.info(output_message)
output_stream.write_header(output_header)
# do some additional computations
necessary_equations = get_necessary_equations(self.data.header.var_IDs, output_header.var_IDs,
is_2d=output_header.is_2d,
us_equation=self.data.us_equation)
process = ExtractVariablesThread(necessary_equations, self.data.us_equation, input_stream,
output_stream, output_header, output_time_indices)
progressBar.connectToThread(process)
process.run()
if not process.canceled:
progressBar.outputFinished()
progressBar.exec_()
self.parent.outDialog()
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
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 btnSubmitEvent(self):
if not self.conditions:
QMessageBox.critical(self, 'Error', 'Add at least one condition.',
QMessageBox.Ok)
return
start_index = int(self.timeSelection.startIndex.text()) - 1
end_index = int(self.timeSelection.endIndex.text())
time_indices = list(range(start_index, end_index))
if len(time_indices) == 1:
QMessageBox.critical(self, 'Error', 'Start and end frame cannot be the same.',
QMessageBox.Ok)
return
canceled, filename = save_dialog('Serafin', self.data.filename)
if canceled:
return
# deduce header from selected variable IDs and write header
output_header = self.getOutputHeader()
output_message = 'Computing Arrival / Duration between frame %d and %d.' \
% (start_index+1, end_index)
self.parent.inDialog()
logging.info(output_message)
progressBar = OutputProgressDialog()
# do some calculations
try:
with Serafin.Read(self.data.filename, self.data.language) as input_stream:
input_stream.header = self.data.header
input_stream.time = self.data.time
progressBar.setValue(5)
QApplication.processEvents()
with Serafin.Write(filename, self.data.language) as output_stream:
process = ArrivalDurationThread(input_stream, self.conditions, time_indices)
progressBar.connectToThread(process)
values = process.run()
if not process.canceled:
values = self._convertTimeUnit(time_indices, values)
output_stream.write_header(output_header)
output_stream.write_entire_frame(output_header, self.data.time[0], values)
progressBar.outputFinished()
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
progressBar.exec_()
self.parent.outDialog()
def landxml_to_slf(args):
root = ET.parse(args.in_xml).getroot()
PREFIX = '{http://www.landxml.org/schema/LandXML-1.2}'
nodes = [] # list of (x, y) coordinates
ikle = [] # list of triangle triplet (1-indexed)
output_header = None
with Serafin.Write(args.out_slf, args.lang,
overwrite=args.force) as resout:
for i, surface in enumerate(root.find(PREFIX + 'Surfaces')):
surface_name = surface.get('name')
if ' ' in surface_name:
varname = surface_name.split(' ')[0]
else:
varname = surface_name
# time_duration = surface_name.split(' ')[-1]
tin = surface.find(PREFIX + 'Definition')
values = []
for j, pnts in enumerate(tin.find(PREFIX + 'Pnts')):
assert int(pnts.get('id')) == j + 1
y, x, z = (float(n) for n in pnts.text.split())
values.append(z)
if i == 0:
nodes.append((x, y))
else:
if (x, y) != nodes[j]:
raise RuntimeError(
"Coordinates are not strictly identical")
for j, face in enumerate(tin.find(PREFIX + 'Faces')):
if 'id' in face.attrib:
assert int(face.get('id')) == j + 1
n1, n2, n3 = (int(n) for n in face.text.split())
if i == 0:
ikle.append((n1, n2, n3))
else:
if (n1, n2, n3) != ikle[j]:
raise RuntimeError("Mesh is not strictly identical")
if i == 0:
output_header = Serafin.SerafinHeader(
title='Converted from LandXML (written by PyTelTools)')
output_header.from_triangulation(
np.array(nodes, dtype=np.int64),
np.array(ikle, dtype=np.int64))
output_header.add_variable_str(varname, varname, '')
resout.write_header(output_header)
time = i * 3600.0 # FIXME: should convert time_duration to float
resout.write_entire_frame(output_header, time,
np.expand_dims(np.array(values), axis=0))
def btnSubmitEvent(self):
# fetch the list of selected variables
selected_vars = self._getSelectedVariables()
if not selected_vars:
QMessageBox.critical(self, 'Error', 'Select at least one variable.',
QMessageBox.Ok)
return
canceled, filename = save_dialog('Serafin', self.data.filename)
if canceled:
return
# deduce header from selected variable IDs and write header
output_header = self.getOutputHeader(selected_vars)
start_index = int(self.timeSelection.startIndex.text()) - 1
end_index = int(self.timeSelection.endIndex.text())
time_indices = list(range(start_index, end_index))
var = self.varBox.currentText().split(' (')[0]
output_message = 'Computing SynchMax of variables %s between frame %d and %d.' \
% (str(list(map(lambda x: x[0], selected_vars[1:]))), start_index+1, end_index)
self.parent.inDialog()
logging.info(output_message)
progressBar = OutputProgressDialog()
# do some calculations
try:
with Serafin.Read(self.data.filename, self.data.language) as input_stream:
input_stream.header = self.data.header
input_stream.time = self.data.time
progressBar.setValue(5)
QApplication.processEvents()
with Serafin.Write(filename, self.data.language) as output_stream:
process = SynchMaxThread(input_stream, selected_vars[1:], time_indices, var)
progressBar.connectToThread(process)
values = process.run()
if not process.canceled:
output_stream.write_header(output_header)
output_stream.write_entire_frame(output_header, self.data.time[0], values)
progressBar.outputFinished()
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
progressBar.exec_()
self.parent.outDialog()
def bottom(inname, outname, i3s_names, overwrite, threshold):
# global prev_line, zones, np_coord, Xt, Z, ref_rows, polyline
with Serafin.Read(inname, 'fr') as resin:
resin.read_header()
if not resin.header.is_2d:
sys.exit("The current script is working only with 2D meshes !")
resin.get_time()
# Define zones from polylines
zones = []
for i3s_name in i3s_names:
zones += Zone.get_zones_from_i3s_file(i3s_name, threshold)
with Serafin.Write(outname, 'fr', overwrite) as resout:
output_header = resin.header
resout.write_header(output_header)
posB = output_header.var_IDs.index('B')
for time_index, time in enumerate(resin.time):
var = np.empty((output_header.nb_var, output_header.nb_nodes),
dtype=output_header.np_float_type)
for i, var_ID in enumerate(output_header.var_IDs):
var[i, :] = resin.read_var_in_frame(time_index, var_ID)
# Replace bottom locally
nmodif = 0
for i in range(
output_header.nb_nodes): # iterate over all nodes
x, y = output_header.x[i], output_header.y[i]
pt = geo.Point(x, y)
for j, zone in enumerate(zones):
if zone.contains(pt):
# Current point is inside zone number j
# and is between polylines a and b
print("node {} is in zone n°{}".format(i + 1, j))
# Replace value by a linear interpolation
z_int = zone.interpolate(pt)
print(z_int)
var[posB, i] = min(var[posB, i], z_int)
nmodif += 1
break
resout.write_entire_frame(output_header, time, var)
print("{} nodes were overwritten".format(nmodif))
def btnEvolutionEvent(self):
if not self.has_figure:
all_bss = []
ref_time = int(self.timeSelection.refIndex.text()) - 1
init_time = int(self.initSelection.refIndex.text()) - 1
selected_variable = self.input.varBox.currentText().split(
'(')[0][:-1]
try:
with Serafin.Read(
self.input.ref_data.filename,
self.input.ref_data.language) as input_stream:
input_stream.header = self.input.ref_data.header
input_stream.time = self.input.ref_data.time
ref_values = input_stream.read_var_in_frame(
ref_time, selected_variable)
with Serafin.Read(
self.input.test_data.filename,
self.input.test_data.language) as input_stream:
input_stream.header = self.input.test_data.header
input_stream.time = self.input.test_data.time
init_values = input_stream.read_var_in_frame(
init_time, selected_variable)
ref_volume = self.input.ref_mesh.quadratic_volume(
ref_values - init_values)
for index in range(len(self.input.test_data.time)):
test_values = input_stream.read_var_in_frame(
index, selected_variable)
test_volume = self.input.ref_mesh.quadratic_volume(
test_values - ref_values)
if test_volume == 0 and ref_volume == 0:
bss = 1
else:
with np.errstate(divide='ignore'):
bss = 1 - test_volume / ref_volume
all_bss.append(bss)
except (Serafin.SerafinRequestError,
Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message,
QMessageBox.Ok, QMessageBox.Ok)
return
self.plotViewer.plot(self.input.test_data.time, all_bss)
self.plotViewer.show()
def update_culverts_file(args):
with Serafin.Read(args.in_slf_ori, args.lang) as mesh_ori:
mesh_ori.read_header()
with Serafin.Read(args.in_slf_new, args.lang) as mesh_new:
mesh_new.read_header()
with open(args.in_txt, 'r') as in_txt:
with open(args.out_txt, 'w', newline='') as out_txt:
for i, line in enumerate(in_txt):
if i < 3:
out_txt.write(line)
else:
n1_ori, n2_ori, txt = line.split(maxsplit=2)
n1_new = mesh_new.header.nearest_node(
mesh_ori.header.x[int(n1_ori) - 1],
mesh_ori.header.y[int(n1_ori) - 1])
n2_new = mesh_new.header.nearest_node(
mesh_ori.header.x[int(n2_ori) - 1],
mesh_ori.header.y[int(n2_ori) - 1])
out_txt.write('%i %i %s' % (n1_new, n2_new, txt))
def _run_synch_max(self, input_data):
"""!
@brief Write Serafin with `SynchMax` operator
@param input_data <slf.datatypes.SerafinData>: input SerafinData stream
"""
selected_vars = [
var for var in input_data.selected_vars
if var in input_data.header.var_IDs
]
output_header = input_data.header.copy()
output_header.empty_variables()
for var_ID in selected_vars:
var_name, var_unit = input_data.selected_vars_names[var_ID]
output_header.add_variable(var_ID, var_name, var_unit)
if input_data.to_single:
output_header.to_single_precision()
nb_frames = len(input_data.selected_time_indicies)
with Serafin.Read(input_data.filename,
input_data.language) as input_stream:
input_stream.header = input_data.header
input_stream.time = input_data.time
calculator = operations.SynchMaxCalculator(
input_stream, selected_vars, input_data.selected_time_indicies,
input_data.metadata['var'])
for i, time_index in enumerate(
input_data.selected_time_indicies[1:]):
calculator.synch_max_in_frame(time_index)
self.progress_bar.setValue(100 * (i + 1) / nb_frames)
QApplication.processEvents()
values = calculator.finishing_up()
with Serafin.Write(self.filename, input_data.language,
True) as output_stream:
output_stream.write_header(output_header)
output_stream.write_entire_frame(output_header,
input_data.time[0], values)
self.success('Output saved to {}.'.format(self.filename))
return True
def btnSubmitEvent(self):
selected_var_IDs = self.getSelectedVariables()
if not selected_var_IDs:
QMessageBox.critical(self, 'Error', 'Choose at least one output variable before submit!',
QMessageBox.Ok)
return
canceled, filename = save_dialog('CSV')
if canceled:
return
self.csvNameBox.setText(filename)
logging.info('Writing the output to %s' % filename)
self.parent.inDialog()
sampling_frequency = int(self.timeSampling.text())
selected_time = self.data.time[::sampling_frequency]
indices_inside = [i for i in range(len(self.points)) if self.point_interpolators[i] is not None]
# initialize the progress bar
process = WriteCSVProcess(self.parent.csv_separator, self.parent.fmt_float, self.mesh)
progressBar = OutputProgressDialog()
try:
with Serafin.Read(self.data.filename, self.data.language) as input_stream:
input_stream.header = self.data.header
input_stream.time = self.data.time
progressBar.setValue(1)
QApplication.processEvents()
with open(filename, 'w') as output_stream:
progressBar.connectToThread(process)
process.write_csv(input_stream, selected_time, selected_var_IDs, output_stream,
indices_inside,
[self.points[i] for i in indices_inside],
[self.point_interpolators[i] for i in indices_inside])
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
if not process.canceled:
progressBar.outputFinished()
progressBar.exec_()
self.parent.outDialog()
if process.canceled:
self.csvNameBox.clear()
return
self.parent.imageTab.getData(selected_var_IDs, indices_inside)
self.parent.tab.setTabEnabled(1, True)
def btnSubmitEvent(self):
canceled, filename = save_dialog('CSV')
if canceled:
return
self.csvNameBox.setText(filename)
sampling_frequency = int(self.timeSampling.text())
flux_type, self.var_IDs, flux_title = self._getFluxSection()
self.parent.tab.setTabEnabled(1, False)
logging.info('Writing the output to %s' % filename)
self.parent.inDialog()
# initialize the progress bar
progressBar = OutputProgressDialog()
# do the calculations
names = ['Section %d' % (i + 1) for i in range(len(self.polylines))]
try:
with Serafin.Read(self.data.filename,
self.data.language) as input_stream:
input_stream.header = self.data.header
input_stream.time = self.data.time
calculator = FluxCalculatorThread(
flux_type, self.var_IDs, input_stream, names,
self.polylines, sampling_frequency, self.mesh,
self.parent.csv_separator, self.parent.fmt_float)
progressBar.setValue(5)
QApplication.processEvents()
with open(filename, 'w') as f2:
progressBar.connectToThread(calculator)
calculator.write_csv(f2)
except (Serafin.SerafinRequestError,
Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message,
QMessageBox.Ok, QMessageBox.Ok)
return
if not calculator.canceled:
progressBar.outputFinished()
progressBar.exec_()
self.parent.outDialog()
if calculator.canceled:
self.csvNameBox.clear()
return
# unlock the image viewer
self.parent.imageTab.getData(flux_title)
self.parent.tab.setTabEnabled(1, True)
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 btnSubmitEvent(self):
selected_var_IDs = self.getSelectedVariables()
if not selected_var_IDs:
QMessageBox.critical(self, 'Error', 'Choose at least one output variable before submit!',
QMessageBox.Ok)
return
canceled, filename = save_dialog('CSV')
if canceled:
return
self.csvNameBox.setText(filename)
logging.info('Writing the output to %s' % filename)
self.parent.inDialog()
indices_nonempty = [i for i in range(len(self.input.lines)) if self.input.line_interpolators[i][0]]
# initialize the progress bar
process = WriteCSVProcess(self.parent.csv_separator, self.parent.fmt_float, self.input.mesh)
progressBar = OutputProgressDialog()
try:
with Serafin.Read(self.input.data.filename, self.input.data.language) as input_stream:
input_stream.header = self.input.data.header
input_stream.time = self.input.data.time
progressBar.setValue(1)
QApplication.processEvents()
with open(filename, 'w') as output_stream:
progressBar.connectToThread(process)
if self.intersect.isChecked():
process.write_csv(input_stream, selected_var_IDs, output_stream,
self.input.line_interpolators, indices_nonempty)
else:
process.write_csv(input_stream, selected_var_IDs, output_stream,
self.input.line_interpolators_internal, indices_nonempty)
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
if not process.canceled:
progressBar.outputFinished()
progressBar.exec_()
self.parent.outDialog()
if process.canceled:
self.csvNameBox.clear()
return
def slf_last(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)])
# 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'
)
values = np.empty((output_header.nb_var, output_header.nb_nodes),
dtype=output_header.np_float_type)
with Serafin.Write(args.out_slf, args.lang,
overwrite=args.force) as resout:
resout.write_header(output_header)
time_index = len(resin.time) - 1
time = resin.time[-1] if args.time is None else args.time
for i, var_ID in enumerate(output_header.var_IDs):
values[i, :] = resin.read_var_in_frame(time_index, var_ID)
resout.write_entire_frame(output_header, time, values)
def slf_to_raster(args):
with Serafin.Read(args.in_slf, args.lang) as resin:
resin.read_header()
header = resin.header
logger.info(header.summary())
resin.get_time()
if args.vars is None:
var_names = [
var_name.decode('utf-8') for var_name in header.var_names
]
var_IDs = header.var_IDs
else:
var_names = []
var_IDs = []
for var_ID, var_name in zip(header.var_IDs, header.var_names):
if var_ID in args.vars:
var_names.append(var_name.decode('utf-8'))
var_IDs.append(var_ID)
# Shift mesh coordinates if necessary
if args.shift:
header.transform_mesh(
[Transformation(0, 1, 1, args.shift[0], args.shift[1], 0)])
# Build output regular grid and matplotlib triangulation of the mesh
m_xi, m_yi = np.meshgrid(
np.arange(header.x.min(), header.x.max(), args.resolution),
np.arange(header.y.min(), header.y.max(), args.resolution))
triang = mtri.Triangulation(header.x,
header.y,
triangles=header.ikle_2d - 1)
# Build list containing all interpolated variables on the regular grid
array_list = []
for i, (var_ID, var_name) in enumerate(zip(var_IDs, var_names)):
values = resin.read_var_in_frame(args.frame_index, var_ID)
interp = mtri.LinearTriInterpolator(triang, values)
data = interp(
m_xi,
m_yi)[::-1] # reverse array so the tif looks like the array
array_list.append((var_name, data))
logger.info(
"Min and max values for interpolated %s variable: [%f, %f]" %
(var_name, data.min(), data.max()))
# Write data in the raster output file
arrays2raster(args.out_tif, (header.x.min(), header.y.max()),
args.resolution, -args.resolution, array_list)
def _run_arrival_duration(self, input_data):
"""!
@brief Write Serafin with `Compute Arrival Duration` operator
@param input_data <slf.datatypes.SerafinData>: input SerafinData stream
"""
conditions, table, time_unit = input_data.metadata['conditions'], \
input_data.metadata['table'], input_data.metadata['time unit']
output_header = input_data.header.copy()
output_header.empty_variables()
for row in range(len(table)):
a_name = table[row][1]
d_name = table[row][2]
for name in [a_name, d_name]:
output_header.add_variable_str('', name, time_unit.upper())
if input_data.to_single:
output_header.to_single_precision()
with Serafin.Read(input_data.filename,
input_data.language) as input_stream:
input_stream.header = input_data.header
input_stream.time = input_data.time
calculators = []
for i, condition in enumerate(conditions):
calculators.append(
operations.ArrivalDurationCalculator(
input_stream, input_data.selected_time_indices,
condition))
for i, index in enumerate(input_data.selected_time_indices[1:]):
for calculator in calculators:
calculator.arrival_duration_in_frame(index)
self.progress_bar.setValue(
100 * (i + 1) / len(input_data.selected_time_indices))
QApplication.processEvents()
values = np.empty(
(2 * len(conditions), input_data.header.nb_nodes))
for i, calculator in enumerate(calculators):
values[2 * i, :] = calculator.arrival
values[2 * i + 1, :] = calculator.duration
if time_unit == 'minute':
values /= 60
elif time_unit == 'hour':
values /= 3600
elif time_unit == 'day':
values /= 86400
elif time_unit == 'percentage':
values *= 100 / (
input_data.time[input_data.selected_time_indices[-1]] -
input_data.time[input_data.selected_time_indices[0]])
with Serafin.Write(self.filename, input_data.language,
True) as output_stream:
output_stream.write_header(output_header)
output_stream.write_entire_frame(output_header,
input_data.time[0], values)
self.success('Output saved to {}.'.format(self.filename))
return True
def mesh_crue10_run(args):
set_logger_level(args.verbose)
t1 = perf_counter()
# Read the model and its submodels from xml/shp files
etude = Etude(args.infile_etu)
modele = etude.get_modele(args.model_name)
modele.read_all()
logger.info(modele)
for sous_modele in modele.liste_sous_modeles:
sous_modele.remove_sectioninterpolee()
sous_modele.normalize_geometry()
logger.info(sous_modele.summary())
# sous_modele.write_shp_limites_lits_numerotes('limites_lits.shp') # DEBUG
logger.info(modele)
global_mesh_constr = MeshConstructor()
# Handle branches in minor bed
for i, branche in enumerate(modele.get_liste_branches()):
# Ignore branch if branch_patterns is set and do not match with current branch name
if args.branch_patterns is not None:
ignore = True
for pattern in args.branch_patterns:
if pattern in branche.id:
ignore = False
break
else:
ignore = False
if branche.type not in args.branch_types_filter or not branche.is_active:
ignore = True
if not ignore:
logger.info("===== TRAITEMENT DE LA BRANCHE %s =====" % branche.id)
axe = branche.geom
try:
section_seq = CrossSectionSequence()
for crue_section in branche.liste_sections_dans_branche:
if isinstance(crue_section, SectionProfil):
coords = list(crue_section.get_coord(add_z=True))
section = CrossSection(crue_section.id,
[(coord[0], coord[1])
for coord in coords],
'Section')
# Determine some variables (constant over the simulation) from the geometry
z = np.array([coord[2] for coord in coords])
is_bed_active = crue_section.get_is_bed_active_array()
mean_strickler = crue_section.get_friction_coeff_array(
)
section.coord.values = np.core.records.fromarrays(
np.column_stack(
(z, is_bed_active, mean_strickler)).T,
names=VARIABLES_FROM_GEOMETRY)
section_seq.add_section(section)
section_seq.compute_dist_proj_axe(axe, args.dist_max)
if len(section_seq) >= 2:
section_seq.check_intersections()
# section_seq.sort_by_dist() is useless because profiles are already sorted
constraint_lines = ConstraintLine.get_lines_and_set_limits_from_sections(
section_seq, args.interp_constraint_lines)
mesh_constr = MeshConstructor(
section_seq=section_seq,
lat_step=args.lat_step,
nb_pts_lat=args.nb_pts_lat,
interp_values=args.interp_values)
mesh_constr.build_interp(constraint_lines, args.long_step,
args.constant_long_disc)
mesh_constr.build_mesh(in_floworiented_crs=True)
global_mesh_constr.append_mesh_constr(mesh_constr)
else:
logger.warning("Branche ignorée par manque de sections")
except TatooineException as e:
logger.error(
"/!\\ Branche ignorée à cause d'une erreur bloquante :")
logger.error(e.message)
logger.info("\n")
# Handle casiers in floodplain
nb_casiers = len(modele.get_liste_casiers())
if args.infile_dem and nb_casiers > 0:
logger.info("===== TRAITEMENT DES CASIERS =====")
if not os.path.exists(args.infile_dem):
raise TatooineException("File not found: %s" % args.infile_dem)
from gdal import Open
raster = Open(args.infile_dem)
dem_interp = interp_raster(raster)
floodplain_step = args.floodplain_step if not None else args.long_step
max_elem_area = floodplain_step * floodplain_step / 2.0
simplify_dist = floodplain_step / 2.0
for i, casier in enumerate(modele.get_liste_casiers()):
if casier.is_active:
if casier.geom is None:
raise TatooineException(
"Geometry of %s could not be found" % casier)
line = casier.geom.simplify(simplify_dist)
if not line.is_closed:
raise RuntimeError
coords = resample_2d_line(
line.coords,
floodplain_step)[1:] # Ignore last duplicated node
hard_nodes_xy = np.array(coords, dtype=np.float)
hard_nodes_idx = np.arange(0, len(hard_nodes_xy), dtype=np.int)
hard_segments = np.column_stack(
(hard_nodes_idx, np.roll(hard_nodes_idx, 1)))
tri = {
'vertices':
np.array(
np.column_stack(
(hard_nodes_xy[:, 0], hard_nodes_xy[:, 1]))),
'segments':
hard_segments,
}
triangulation = triangle.triangulate(tri,
opts='qpa%f' %
max_elem_area)
nodes_xy = np.array(triangulation['vertices'], dtype=np.float)
bottom = dem_interp(nodes_xy)
points = unstructured_to_structured(np.column_stack(
(nodes_xy, bottom)),
names=['X', 'Y', 'Z'])
global_mesh_constr.add_floodplain_mesh(triangulation, points)
if len(global_mesh_constr.points) == 0:
raise ExceptionCrue10(
"Aucun point à traiter, adaptez l'option `--branch_patterns` et/ou `--branch_types_filter`"
)
logger.info(global_mesh_constr.summary()
) # General information about the merged mesh
if args.infile_rcal:
# Read rcal result file
results = RunResults(args.infile_rcal)
logger.info(results.summary())
# Check result consistency
missing_sections = modele.get_missing_active_sections(
results.emh['Section'])
if missing_sections:
raise ExceptionCrue10("Sections manquantes :\n%s" %
missing_sections)
# Subset results to get requested variables at active sections
varnames_1d = results.variables['Section']
logger.info("Variables 1D disponibles aux sections: %s" % varnames_1d)
try:
pos_z = varnames_1d.index('Z')
except ValueError:
raise TatooineException(
"La variable Z doit être présente dans les résultats aux sections"
)
if global_mesh_constr.has_floodplain:
try:
pos_z_fp = results.variables['Casier'].index('Z')
except ValueError:
raise TatooineException(
"La variable Z doit être présente dans les résultats aux casiers"
)
else:
pos_z_fp = None
pos_variables = [
results.variables['Section'].index(var) for var in varnames_1d
]
pos_sections_list = [
results.emh['Section'].index(profil.id)
for profil in global_mesh_constr.section_seq
]
if global_mesh_constr.has_floodplain:
pos_casiers_list = [
results.emh['Casier'].index(casier.id)
for casier in modele.get_liste_casiers() if casier.is_active
]
else:
pos_casiers_list = []
additional_variables_id = ['H']
if 'Vact' in varnames_1d:
additional_variables_id.append('M')
values_geom = global_mesh_constr.interp_values_from_geom()
z_bottom = values_geom[0, :]
with Serafin.Write(args.outfile_mesh, args.lang,
overwrite=True) as resout:
title = '%s (written by TatooineMesher)' % os.path.basename(
args.outfile_mesh)
output_header = Serafin.SerafinHeader(title=title, lang=args.lang)
output_header.from_triangulation(
global_mesh_constr.triangle['vertices'],
global_mesh_constr.triangle['triangles'] + 1)
for var_name in VARIABLES_FROM_GEOMETRY:
if var_name in ['B', 'W']:
output_header.add_variable_from_ID(var_name)
else:
output_header.add_variable_str(var_name, var_name, '')
for var_id in additional_variables_id:
output_header.add_variable_from_ID(var_id)
for var_name in varnames_1d:
output_header.add_variable_str(var_name, var_name, '')
resout.write_header(output_header)
if args.calc_unsteady is None:
for i, calc_name in enumerate(results.calc_steady_dict.keys()):
logger.info("~> Calcul permanent %s" % calc_name)
# Read a single *steady* calculation
res_steady = results.get_res_steady(calc_name)
variables_at_profiles = res_steady['Section'][
pos_sections_list, :][:, pos_variables]
if global_mesh_constr.has_floodplain:
z_at_casiers = res_steady['Casier'][pos_casiers_list,
pos_z_fp]
else:
z_at_casiers = None
# Interpolate between sections and set in casiers
values_res = global_mesh_constr.interp_values_from_res(
variables_at_profiles, z_at_casiers, pos_z)
# Compute water depth: H = Z - Zf and clip below 0m (avoid negative values)
depth = np.clip(values_res[pos_z, :] - z_bottom,
a_min=0.0,
a_max=None)
# Merge and write values
if 'Vact' in varnames_1d:
# Compute velocity magnitude from Vact and apply mask "is active bed"
velocity = values_res[
varnames_1d.index('Vact'), :] * values_geom[1, :]
values = np.vstack(
(values_geom, depth, velocity, values_res))
else:
values = np.vstack((values_geom, depth, values_res))
resout.write_entire_frame(output_header, 3600.0 * i,
values)
else:
calc_unsteady = results.get_calc_unsteady(args.calc_unsteady)
logger.info("Calcul transitoire %s" % args.calc_unsteady)
res_unsteady = results.get_res_unsteady(args.calc_unsteady)
for i, (time, _) in enumerate(calc_unsteady.frame_list):
logger.info("~> %fs" % time)
res_at_sections = res_unsteady['Section'][i, :, :]
variables_at_profiles = res_at_sections[
pos_sections_list, :][:, pos_variables]
if global_mesh_constr.has_floodplain:
z_at_casiers = res_unsteady['Casier'][i,
pos_casiers_list,
pos_z_fp]
else:
z_at_casiers = None
# Interpolate between sections
values_res = global_mesh_constr.interp_values_from_res(
variables_at_profiles, z_at_casiers, pos_z)
# Compute water depth: H = Z - Zf and clip below 0m (avoid negative values)
depth = np.clip(values_res[pos_z, :] - z_bottom,
a_min=0.0,
a_max=None)
# Merge and write values
if 'Vact' in varnames_1d:
# Compute velocity magnitude from Vact and apply mask "is active bed"
velocity = values_res[
varnames_1d.index('Vact'), :] * values_geom[1, :]
values = np.vstack(
(values_geom, depth, velocity, values_res))
else:
values = np.vstack((values_geom, depth, values_res))
resout.write_entire_frame(output_header, time, values)
else:
# Write a single frame with only variables from geometry
global_mesh_constr.export_mesh(args.outfile_mesh, lang=args.lang)
t2 = perf_counter()
logger.info("=> Execution time: {}s".format(t2 - t1))
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_3d_to_2d(args):
with Serafin.Read(args.in_slf, args.lang) as resin:
resin.read_header()
logger.info(resin.header.summary())
resin.get_time()
if resin.header.is_2d:
logger.critical('The input file is not 3D.')
sys.exit(1)
if 'Z' not in resin.header.var_IDs:
logger.critical('The elevation variable Z is not found in the Serafin file.')
sys.exit(1)
if args.layer is not None:
upper_plane = resin.header.nb_planes
if args.layer < 1 or args.layer > upper_plane:
logger.critical('Layer has to be in [1, %i]' % upper_plane)
sys.exit(1)
output_header = resin.header.copy_as_2d()
# 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')
if args.aggregation is not None:
if args.aggregation == 'max':
operation_type = operations.MAX
elif args.aggregation == 'min':
operation_type = operations.MIN
else: # args.aggregation == 'mean'
operation_type = operations.MEAN
selected_vars = [var for var in output_header.iter_on_all_variables()]
vertical_calculator = operations.VerticalMaxMinMeanCalculator(operation_type, resin, output_header,
selected_vars, args.vars)
output_header.set_variables(vertical_calculator.get_variables()) # sort variables
# Add some elevation variables
for var_ID in args.vars:
output_header.add_variable_from_ID(var_ID)
with Serafin.Write(args.out_slf, args.lang, overwrite=args.force) as resout:
resout.write_header(output_header)
vars_2d = np.empty((output_header.nb_var, output_header.nb_nodes_2d), dtype=output_header.np_float_type)
for time_index, time in enumerate(tqdm(resin.time, unit='frame')):
if args.aggregation is not None:
vars_2d = vertical_calculator.max_min_mean_in_frame(time_index)
else:
for i, var in enumerate(output_header.var_IDs):
vars_2d[i, :] = resin.read_var_in_frame_as_3d(time_index, var)[args.layer - 1, :]
resout.write_entire_frame(output_header, time, vars_2d)
def export_mesh(self, path, lang='en'):
"""
Export generated mesh in slf, t3s or LandXML
TODO: export multiple variables in t3s and LandXML
"""
logger.info("~> Write generated mesh")
nnode, nelem = len(self.triangle['vertices']), len(
self.triangle['triangles'])
if path.endswith('.t3s'):
with open(path, 'w', newline='') as fileout:
# Write header
date = time.strftime("%Y-%m-%d %H:%M:%S", time.gmtime())
fileout.write(
"""#########################################################################
:FileType t3s ASCII EnSim 1.0
# Canadian Hydraulics Centre/National Research Council (c) 1998-2012
# DataType 2D T3 Scalar Mesh
#
:Application BlueKenue
:Version 3.3.4
:WrittenBy TatooineMesher
:CreationDate {}
#
#------------------------------------------------------------------------
#
:NodeCount {}
:ElementCount {}
:ElementType T3
#
:EndHeader
""".format(date, nnode, nelem))
with open(path, mode='ab') as fileout:
# Table with x, y, z coordinates
np.savetxt(fileout,
np.column_stack(
(self.triangle['vertices'],
self.interp_values_from_geom()[0, :])),
delimiter=' ',
fmt='%.{}f'.format(DIGITS))
# Table with elements (connectivity)
np.savetxt(fileout,
self.triangle['triangles'] + 1,
delimiter=' ',
fmt='%i')
elif path.endswith('.xml'):
env = Environment(loader=FileSystemLoader(
os.path.join(os.path.dirname(os.path.realpath(__file__)),
'data')))
template = env.get_template("LandXML_template.xml")
template_render = template.render(nodes=np.round(
np.column_stack((self.triangle['vertices'],
self.interp_values_from_geom()[0, :])),
DIGITS),
ikle=self.triangle['triangles'] +
1)
# Write XML file
with open(path, 'w') as fileout:
fileout.write(template_render)
elif path.endswith('.slf'):
with Serafin.Write(path, lang, overwrite=True) as resout:
output_header = Serafin.SerafinHeader(
title='%s (Written by TatooineMesher)' %
os.path.basename(path),
lang=lang)
output_header.from_triangulation(
self.triangle['vertices'], self.triangle['triangles'] + 1)
for var in self.var_names():
if var in basic_2D_vars_IDs:
output_header.add_variable_from_ID(var)
else:
output_header.add_variable_str(var, var, '')
resout.write_header(output_header)
resout.write_entire_frame(output_header, 0.0,
self.interp_values_from_geom())
else:
raise NotImplementedError(
"Only slf, t3s and xml formats are supported for the output mesh"
)
def btnSubmitEvent(self):
# fetch the list of selected variables
selected_vars = self._getSelectedVariables()
if not selected_vars:
QMessageBox.critical(self, 'Error', 'Select at least one variable.',
QMessageBox.Ok)
return
canceled, filename = save_dialog('Serafin', self.data.filename)
if canceled:
return
# separate scalars and vectors
scalars, vectors, additional_equations = operations.scalars_vectors(self.data.header.var_IDs, selected_vars)
# get the operation type
if self.maxButton.isChecked():
max_min_type = operations.MAX
elif self.minButton.isChecked():
max_min_type = operations.MIN
else:
max_min_type = operations.MEAN
# deduce header from selected variable IDs and write header
output_header = self.getOutputHeader(scalars, vectors)
start_index = int(self.timeSelection.startIndex.text()) - 1
end_index = int(self.timeSelection.endIndex.text())
time_indices = list(range(start_index, end_index))
output_message = 'Computing %s of variables %s between frame %d and %d.' \
% ('Max' if self.maxButton.isChecked() else ('Min' if self.minButton.isChecked() else 'Mean'),
str(output_header.var_IDs), start_index+1, end_index)
self.parent.inDialog()
logging.info(output_message)
progressBar = OutputProgressDialog()
# do some calculations
try:
with Serafin.Read(self.data.filename, self.data.language) as input_stream:
input_stream.header = self.data.header
input_stream.time = self.data.time
progressBar.setValue(5)
QApplication.processEvents()
with Serafin.Write(filename, self.data.language) as output_stream:
process = MaxMinMeanThread(max_min_type, input_stream, scalars, vectors, time_indices,
additional_equations)
progressBar.connectToThread(process)
values = process.run()
if not process.canceled:
output_stream.write_header(output_header)
output_stream.write_entire_frame(output_header, self.data.time[0], values)
progressBar.outputFinished()
except (Serafin.SerafinRequestError, Serafin.SerafinValidationError) as e:
QMessageBox.critical(None, 'Serafin Error', e.message, QMessageBox.Ok, QMessageBox.Ok)
return
progressBar.exec_()
self.parent.outDialog()
def slf_int2d(args):
# Read set of points file
fields, indices = Shapefile.get_attribute_names(args.in_points)
points = []
attributes = []
for point, attribute in Shapefile.get_points(args.in_points, indices):
points.append(point)
attributes.append(attribute)
if not points:
logger.critical('The Shapefile does not contain any point.')
sys.exit(1)
# Read Serafin file
with Serafin.Read(args.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()
output_header = resin.header.copy()
mesh = MeshInterpolator(output_header, True)
is_inside, point_interpolators = mesh.get_point_interpolators(points)
nb_inside = sum(map(int, is_inside))
if nb_inside == 0:
logger.critical('No point inside the mesh.')
sys.exit(3)
logger.debug(
'The file contains {} point{}. {} point{} inside the mesh'.format(
len(points), 's' if len(points) > 1 else '', nb_inside,
's are' if nb_inside > 1 else ' is'))
var_IDs = output_header.var_IDs if args.vars is None else args.vars
mode = 'w' if args.force else 'x'
with open(args.out_csv, mode, newline='') as csvfile:
csvwriter = csv.writer(csvfile, delimiter=args.sep)
header = ['time_id', 'time']
if args.long:
header = header + [
'point_id', 'point_x', 'point_y', 'variable', 'value'
]
else:
for pt_id, (x, y) in enumerate(points):
for var in var_IDs:
header.append(
'Point %d %s (%s|%s)' %
(pt_id + 1, var, settings.FMT_COORD.format(x),
settings.FMT_COORD.format(y)))
csvwriter.writerow(header)
for time_index, time in enumerate(tqdm(resin.time, unit='frame')):
values = [time_index, time]
for var_ID in var_IDs:
var = resin.read_var_in_frame(time_index, var_ID)
for pt_id, (point, point_interpolator) in enumerate(
zip(points, point_interpolators)):
if args.long:
values_long = values + [str(pt_id + 1)] + [
settings.FMT_COORD.format(x) for x in point
]
if point_interpolator is None:
if args.long:
csvwriter.writerow(values_long +
[var_ID, settings.NAN_STR])
else:
values.append(settings.NAN_STR)
else:
(i, j, k), interpolator = point_interpolator
int_value = settings.FMT_FLOAT.format(
interpolator.dot(var[[i, j, k]]))
if args.long:
csvwriter.writerow(values_long +
[var_ID, int_value])
else:
values.append(int_value)
if not args.long: csvwriter.writerow(values)
def _run_project_mesh(self, first_input):
"""!
@brief Write Serafin with `Projet Mesh` operator
@param input_data <slf.datatypes.SerafinData>: input SerafinData stream
"""
operation_type = first_input.operator
second_input = first_input.metadata['operand']
if second_input.filename == self.filename:
self.fail('cannot overwrite to the input file.')
return
# common vars
first_vars = [
var for var in first_input.header.var_IDs
if var in first_input.selected_vars
]
second_vars = [
var for var in second_input.header.var_IDs
if var in second_input.selected_vars
]
common_vars = []
for var in first_vars:
if var in second_vars:
common_vars.append(var)
if not common_vars:
self.fail('the two input files do not share common variables.')
return False
# common frames
first_frames = [
first_input.start_time + first_input.time_second[i]
for i in first_input.selected_time_indices
]
second_frames = [
second_input.start_time + second_input.time_second[i]
for i in second_input.selected_time_indices
]
common_frames = []
for first_index, first_frame in zip(first_input.selected_time_indices,
first_frames):
for second_index, second_frame in zip(
second_input.selected_time_indices, second_frames):
if first_frame == second_frame:
common_frames.append((first_index, second_index))
if not common_frames:
self.fail('the two input files do not share common time frames.')
return False
# construct output header
output_header = first_input.header.copy()
output_header.empty_variables()
for var in common_vars:
name, unit = first_input.selected_vars_names[var]
output_header.add_variable(var, name, unit)
if first_input.to_single:
output_header.to_single_precision()
# map points of A onto mesh B
mesh = MeshInterpolator(second_input.header, False)
if second_input.triangles:
mesh.index = second_input.index
mesh.triangles = second_input.triangles
else:
self.construct_mesh(mesh)
second_input.index = mesh.index
second_input.triangles = mesh.triangles
is_inside, point_interpolators = mesh.get_point_interpolators(
list(zip(first_input.header.x, first_input.header.y)))
# run the calculator
with Serafin.Read(first_input.filename,
first_input.language) as first_in:
first_in.header = first_input.header
first_in.time = first_input.time
with Serafin.Read(second_input.filename,
second_input.language) as second_in:
second_in.header = second_input.header
second_in.time = second_input.time
calculator = operations.ProjectMeshCalculator(
first_in, second_in, common_vars, is_inside,
point_interpolators, common_frames, operation_type)
with Serafin.Write(self.filename, first_input.language,
True) as out_stream:
out_stream.write_header(output_header)
for i, (first_time_index, second_time_index) in enumerate(
calculator.time_indices):
values = calculator.operation_in_frame(
first_time_index, second_time_index)
out_stream.write_entire_frame(
output_header,
calculator.first_in.time[first_time_index], values)
self.progress_bar.setValue(100 * (i + 1) /
len(common_frames))
QApplication.processEvents()
self.success(
'Output saved to {}.\nThe two files has {} common variables and {} common frames.\n'
'The mesh A has {} / {} nodes inside the mesh B.'.format(
self.filename, len(common_vars), len(common_frames),
sum(is_inside), first_input.header.nb_nodes))
return True
