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) 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 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
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()
def _run_max_min_mean(self, input_data):
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.nb_var = len(scalars) + len(vectors)
output_header.var_IDs, output_header.var_names, output_header.var_units = [], [], []
for var_ID, var_name, var_unit in scalars + vectors:
output_header.var_IDs.append(var_ID)
output_header.var_names.append(var_name)
output_header.var_units.append(var_unit)
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) 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):
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
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()
progressBar.exec_()
self.parent.outDialog()
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
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()
progressBar.exec_()
self.parent.outDialog()
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.nb_var = len(selected_vars)
output_header.var_IDs, output_header.var_names, output_header.var_units = [], [], []
for var_ID in selected_vars:
var_name, var_unit = input_data.selected_vars_names[var_ID]
output_header.var_IDs.append(var_ID)
output_header.var_names.append(var_name)
output_header.var_units.append(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) 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 run_single(self, input_name, input_header, output_name, output_header, pool):
i = 0
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()
def getSelaFrame(inname, outname, overwrite, posList, timeList):
"""
Export frames from a Serafin file with a 0-based indexing list.
A negative position accesses elements from the end of the list counting backwards (-1 returns the last
frame)
"""
# Check unicity of method
if posList and timeList:
sys.exit("Precise either posList or timeList")
if not posList and not timeList:
sys.exit("Precise a posList or a timeList")
# posList = range(len(resin.time))
with Serafin.Read(inname) as resin:
resin.readHeader()
resin.get_time()
if timeList:
posList = []
for time in timeList:
posList.append(
min(range(len(resin.time)),
key=lambda i: abs(resin.time[i] - time)))
print("Position(s) found = {}".format(posList))
with Serafin.Write(outname, overwrite) as resout:
resout.copy_header(resin)
resout.write_header()
for pos in posList:
try:
time = resin.time[pos]
except IndexError:
sys.exit(
"ERROR: position n°{} is not in range [{},{}] (or in opposite interval)"
.format(pos, 1, len(resin.time)))
common_data.log("Write frame number {} (time = {})".format(
pos, time))
var = resin.read_entire_frame(time)
resout.write_entire_frame(time, var)
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) 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):
if self.secondTable.rowCount() == 0:
QMessageBox.critical(
self, 'Error',
'Choose at least one output variable before submit!',
QMessageBox.Ok)
return
canceled, filename = save_dialog('Serafin',
input_names=[
self.input.first_data.filename,
self.input.second_data.filename
])
if canceled:
return
# deduce header from selected variable IDs
output_header = self._getOutputHeader()
time_indices = self.input.common_frames
operation_type = {
0: operations.PROJECT,
1: operations.DIFF,
2: operations.REV_DIFF,
3: operations.MAX_BETWEEN,
4: operations.MIN_BETWEEN
}[self.operationBox.currentIndex()]
self.parent.inDialog()
progressBar = OutputProgressDialog()
# do some calculations
with Serafin.Read(self.input.first_data.filename,
self.input.first_data.language) as first_in:
first_in.header = self.input.first_data.header
first_in.time = self.input.first_data.time
with Serafin.Read(self.input.second_data.filename,
self.input.second_data.language) as second_in:
second_in.header = self.input.second_data.header
second_in.time = self.input.second_data.time
progressBar.setValue(5)
QApplication.processEvents()
with Serafin.Write(
filename,
self.input.first_data.language) as out_stream:
out_stream.write_header(output_header)
process = ProjectMeshThread(first_in, second_in,
out_stream, output_header,
self.input.is_inside,
self.input.point_interpolators,
time_indices, operation_type)
progressBar.connectToThread(process)
process.run()
if not process.canceled:
progressBar.outputFinished()
progressBar.exec_()
self.parent.outDialog()
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
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()
progressBar.exec_()
self.parent.outDialog()
nodes_included[j] = True
nb_nodes_included = int(np.sum(nodes_included))
print("Polyligne {} (avec {} points et une valeur à {}) contient {} noeuds".format(i, len(polyline.coords), value, nb_nodes_included))
mask = Mask(value, polyline, nodes_included)
masks.append(mask)
if args.var is not None:
var2D_list = args.var
else:
var2D_list = resin.varID
var2D_pos = [resin.varID.index(x) for x in var2D_list]
print(var2D_pos)
with Serafin.Write(args.outname, args.force) as resout:
resout.copy_header(resin)
resout.write_header()
for time in resin.time:
var = resin.read_vars_in_frame(time, resout.varID)
# Application aux zones
for pos in var2D_pos:
for mask in masks:
var[pos,:][mask.nodes_included] = mask.value
resout.write_entire_frame(time, var)
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.nb_var = len(common_vars)
output_header.var_IDs, output_header.var_names, output_header.var_units = [], [], []
for var in common_vars:
name, unit = first_input.selected_vars_names[var]
output_header.var_IDs.append(var)
output_header.var_names.append(name)
output_header.var_units.append(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) 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
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.nb_var = 2 * len(conditions)
output_header.var_IDs, output_header.var_names, output_header.var_units = [], [], []
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.var_IDs.append('')
output_header.var_names.append(bytes(name, 'utf-8').ljust(16))
output_header.var_units.append(
bytes(time_unit.upper(), 'utf-8').ljust(16))
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) 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