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]
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)
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]
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)
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_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 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]
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)
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 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 slf_to_xml(slf_name, slf_header, xml_name, scalar, time_index):
"""!
@brief Write LandXML file from a scalar variable of a Serafin file
@param slf_name <str>: path to the input Serafin file
@param slf_header <slf.Serafin.SerafinHeader>: input Serafin header
@param xml_name <str>: output LandXML filename
@param scalar <str>: variable to write
@param time_index <int>: the index of the frame (0-based)
"""
# fetch scalar variable values
with Serafin.Read(slf_name, slf_header.language) as input_stream:
input_stream.header = slf_header
scalar_values = input_stream.read_var_in_frame(time_index, scalar)
# write LandXML
with open(xml_name, 'w') as xml:
xml.write('<?xml version="1.0" ?>\n')
xml.write('<!-- Title: %s -->\n' % slf_header.title.decode('utf-8').strip())
xml.write('<!-- This file contains x and y reversed in purpose (because arcpy is buggy) -->\n')
xml.write('<LandXML version="1.2" xmlns="http://www.landxml.org/schema/LandXML-1.2" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.landxml.org/schema/LandXML-1.2 http://www.landxml.org/schema/LandXML-1.2/LandXML-1.2.xsd">\n')
xml.write(' <Surfaces>\n')
xml.write(' <Surface name="%s at frame %i/%i">\n' % (scalar, time_index+1, slf_header.nb_frames))
xml.write(' <Definition surfType="TIN">\n')
xml.write(' <Pnts>\n')
for i, (x, y, z) in enumerate(zip(slf_header.x, slf_header.y, scalar_values)):
xml.write(' <P id="%d">%.4f %.4f %.4f</P>\n' % (i+1, y, x, z))
xml.write(' </Pnts>\n')
xml.write(' <Faces>\n')
for i, (a, b, c) in enumerate(slf_header.ikle_2d):
xml.write(' <F id="%d">%d %d %d</F>\n' % (i+1, a, b, c))
xml.write(' </Faces>\n')
xml.write(' </Definition>\n')
xml.write(' </Surface>\n')
xml.write(' </Surfaces>\n')
xml.write('</LandXML>\n')
def slf_to_shp(slf_name, slf_header, shp_name, variables, time_index):
# separate vectors from scalars
coupled, non_coupled, mothers, angles = detect_vector_couples(variables, slf_header.var_IDs)
# fetch all variables values
values = {}
with Serafin.Read(slf_name, slf_header.language) as input_stream:
input_stream.header = slf_header
for var in variables:
values[var] = input_stream.read_var_in_frame(time_index, var)
# compute mothers not in the file
for mother, brother, sister in mothers:
values[mother] = np.sqrt(np.square(values[brother]) + np.square(values[sister]))
# compute angles
for brother, sister in angles:
values['Angle(%s,%s)' % (brother, sister)] = np.degrees(np.arctan2(values[sister], values[brother]))
# write shp
key_order = coupled + non_coupled + [mother for mother, _, _ in mothers] \
+ ['Angle(%s,%s)' % (brother, sister) for brother, sister in angles]
w = shapefile.Writer(shapefile.POINT)
for name in key_order:
w.field(name, 'N', decimal=4)
for i, (x, y) in enumerate(zip(slf_header.x, slf_header.y)):
w.point(x, y, shapeType=shapefile.POINT)
val = []
for var in key_order:
val.append(values[var][i])
w.record(*val)
w.save(shp_name)
def read(self):
with Serafin.Read(self.filename, self.language) as input_stream:
input_stream.read_header()
input_stream.get_time()
self.header = input_stream.header.copy()
self.time = input_stream.time[:]
if self.header.date is not None:
try:
year, month, day, hour, minute, second = self.header.date
self.start_time = datetime.datetime(year, month, day, hour,
minute, second)
except ValueError:
module_logger.warning(
'Date seems invalid, replaced by default date.')
if self.start_time is None:
self.start_time = datetime.datetime(1900, 1, 1, 0, 0, 0)
self.time_second = list(
map(lambda x: datetime.timedelta(seconds=x), self.time))
self.selected_vars = self.header.var_IDs[:]
self.selected_vars_names = {
var_id: (var_name, var_unit)
for (var_id, var_name,
var_unit) in zip(self.header.var_IDs, self.header.var_names,
self.header.var_units)
}
self.selected_time_indices = list(range(len(self.time)))
return self.header.is_2d
def btnSubmitEvent(self):
canceled, filename = save_dialog('CSV')
if canceled:
return
self.csvNameBox.setText(filename)
logging.info('Writing the output to %s' % filename)
self.parent.inDialog()
# initialize the progress bar
progressBar = OutputProgressDialog()
# do the calculations
sampling_frequency = int(self.timeSampling.text())
self.var_ID = self.firstVarBox.currentText().split('(')[0][:-1]
self.second_var_ID = self.secondVarBox.currentText()
if self.second_var_ID == '0':
self.second_var_ID = None
elif '(' in self.second_var_ID:
self.second_var_ID = self.second_var_ID.split('(')[0][:-1]
else:
self.second_var_ID = VolumeCalculator.INIT_VALUE
names = ['Polygon %d' % (i + 1) for i in range(len(self.polygons))]
with Serafin.Read(self.data.filename,
self.data.language) as input_stream:
input_stream.header = self.data.header
input_stream.time = self.data.time
if self.supVolumeBox.isChecked():
calculator = VolumeCalculatorThread(
VolumeCalculator.POSITIVE, self.var_ID, self.second_var_ID,
input_stream, names, self.polygons, sampling_frequency,
self.mesh, self.parent.csv_separator, self.parent.digits)
else:
calculator = VolumeCalculatorThread(
VolumeCalculator.NET, self.var_ID, self.second_var_ID,
input_stream, names, self.polygons, sampling_frequency,
self.mesh, self.parent.csv_separator, self.parent.digits)
progressBar.setValue(5)
QApplication.processEvents()
with open(filename, 'w') as f2:
progressBar.connectToThread(calculator)
calculator.write_csv(f2)
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()
self.parent.tab.setTabEnabled(1, 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]
]
reference = self.input.lines[
int(self.referenceLine.currentText().split()[1]) - 1]
time_index = int(self.timeSelection.index.text()) - 1
# initialize the progress bar
process = WriteCSVProcess(self.parent.csv_separator,
self.parent.digits, self.input.mesh)
progressBar = OutputProgressDialog()
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, reference, time_index)
else:
process.write_csv(input_stream, selected_var_IDs,
output_stream,
self.input.line_interpolators_internal,
indices_nonempty, reference, time_index)
if not process.canceled:
progressBar.outputFinished()
progressBar.exec_()
self.parent.outDialog()
if process.canceled:
self.csvNameBox.clear()
return
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 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.digits, self.mesh)
progressBar = OutputProgressDialog()
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])
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 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 slf_to_vtk_2d(slf_name, slf_header, vtk_name, scalars, vectors,
variable_names, time_index):
with Serafin.Read(slf_name, slf_header.language) as input_stream:
input_stream.header = slf_header
with open(vtk_name, 'w') as output_stream:
# write header
header = '# vtk DataFile Version 2.0\nMesh export\nASCII\nDATASET UNSTRUCTURED_GRID\n\n'
output_stream.write(header)
# write vertices
output_stream.write('POINTS %d float\n' % slf_header.nb_nodes)
for ix, iy in zip(slf_header.x, slf_header.y):
output_stream.write('%.6f %.6f 0.\n' % (ix, iy))
output_stream.write('\n')
# write cells
output_stream.write(
'CELLS %d %d\n' %
(slf_header.nb_elements, slf_header.nb_elements * 4))
ikle = slf_header.ikle_2d - 1
for k1, k2, k3 in ikle:
output_stream.write('3 %d %d %d\n' % (k1, k2, k3))
output_stream.write('\n')
output_stream.write('CELL_TYPES %d\n' % slf_header.nb_elements)
for _ in range(slf_header.nb_elements):
output_stream.write('5\n')
output_stream.write('\n')
# write scalar and vector data
output_stream.write('POINT_DATA %d\n' % slf_header.nb_nodes)
for scalar in scalars:
values = input_stream.read_var_in_frame(time_index, scalar)
name = variable_names[scalar]
output_stream.write(
'SCALARS %s float\nLOOKUP_TABLE default\n' % name)
for v in values:
output_stream.write('%.6f\n' % v)
output_stream.write('\n')
for triple in vectors:
u_values = input_stream.read_var_in_frame(
time_index, triple[0])
v_values = input_stream.read_var_in_frame(
time_index, triple[1])
name = variable_names[triple]
output_stream.write('VECTORS %s float\n' % name)
for u, v in zip(u_values, v_values):
output_stream.write('%.6f %.6f 0.\n' % (u, v))
output_stream.write('\n')
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 btnComputeEvent(self):
ref_time = int(self.timeSelection.refIndex.text()) - 1
selected_variable = self.input.varBox.currentText().split('(')[0][:-1]
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)
mad = []
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))
self.plotViewer.plot(self.input.test_data.time, mad)
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]
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)
self.plotViewer.plot(self.input.test_data.time, all_bss)
self.plotViewer.show()
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):
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))]
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.digits)
progressBar.setValue(5)
QApplication.processEvents()
with open(filename, 'w') as f2:
progressBar.connectToThread(calculator)
calculator.write_csv(f2)
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_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 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()
from slf import Serafin, common_data
parser = myargparse(description=__doc__, add_args=['force', 'verbose'])
parser.add_argument("inname1", help="reference Serafin input filename")
parser.add_argument("inname2", help="Serafin input filename to subtract")
parser.add_argument("outname", help="Serafin output filename")
parser.add_argument(
"--velMag",
help=
"compute velocity 2D (or 3D) difference instead of a simple difference for U, V (and W)",
action="store_true")
args = parser.parse_args()
common_data.verbose = args.verbose
with Serafin.Read(args.inname1) as res1, Serafin.Read(args.inname2) as res2:
res1.readHeader()
res2.readHeader()
res1.get_time()
res2.get_time()
# Check coherence between input files
if not res1.sameMesh(res2):
sys.exit("mesh {} and {} are different".format(inname1, inname2))
with Serafin.Write(args.outname, args.force) as resout:
resout.copy_header(res1)
# Find common variables
varID_list = res1.commonVarID(res2)
#!/usr/bin/python3
"""
@brief:
Vérifier que les extrêmes des variables d'unu résultat 2D
"""
import numpy as np
import os
from common.arg_command_line import myargparse
from slf import common_data, Serafin
parser = myargparse(description=__doc__, add_args=['verbose'])
parser.add_argument("resname", help="Serafin input filename")
args = parser.parse_args()
common_data.verbose = args.verbose
with open('arf.csv', 'w') as fileout:
with Serafin.Read(args.resname) as res:
res.readHeader()
res.get_time()
fileout.write(';'.join(['time', 'H_min', 'Vmax']) + '\n')
for time in res.time:
H = res.read_var_in_frame(time, 'H')
M = res.read_var_in_frame(time, 'M')
fileout.write(';'.join(
str(x) for x in [time, H.min(), M.max()]) + '\n')
fileout.flush()
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()
def int2d(resname,
xyzname,
varID_list,
outCSV,
overwrite=False,
sep=',',
digits=4):
with Serafin.Read(resname) as res:
res.readHeader()
res.get_time()
# Read points coord and id from CSV file
points = pd.read_csv(xyzname, sep=sep, header=0, index_col=0)
common_data.log("{} points found in {}".format(len(points.index),
xyzname))
# Compute ponderation for each target points
res.compute_element_barycenters()
ponderation = {}
for ptID, coord in points.iterrows():
common_data.log("Search position of point {}".format(ptID))
ponderation[ptID] = res.ponderation_in_element(
coord['x'], coord['y'])
common_data.log("Ponderation coefficients: {}".format(ponderation))
# Read results
first = True
for time in res.time:
var = res.read_vars_in_frame(time, varID_list)
df_var = pd.DataFrame(index=None, columns=None, dtype='float64')
for ptID in points.index:
result = np.zeros((res.nplan, len(varID_list)))
for node, coeff in ponderation[ptID].items():
nodes = [(node - 1) + x * res.nnode2d
for x in range(res.nplan)] # 3D nodes -1
result = result + coeff * (var[:, nodes].transpose())
df_append = pd.DataFrame(result,
columns=varID_list,
dtype='float64')
# Add columns
df_append['time'] = str(time)
df_append['iplan'] = list(
[str(x + 1) for x in df_append.index]
) # Bricolage pour retrouver le numero du plan et passer en str pour eviter le float
df_append['id'] = ptID
df_append['x'] = list(
str(x) for x in points['x'][
df_append['id']]) # list pour effacer index
df_append['y'] = list(
str(x) for x in points['y'][
df_append['id']]) # list pour effacer index
df_var = df_var.append(df_append)
if first:
mode = 'w' if overwrite else 'x'
df_var.to_csv(outCSV,
mode=mode,
sep=sep,
index=False,
float_format='%1.' + str(digits - 1) + 'e')
first = False
else:
df_var.to_csv(outCSV,
mode='a',
sep=sep,
index=False,
float_format='%1.' + str(digits - 1) + 'e',
header=None)
class Mask:
"""
Mask: definir une zone pour laquelle, les noeuds inclus dedans sont traités différement
Attributs:
* value = valeur
TODO
"""
def __init__(self, value, geom, nodes_included):
self.value = value
self.geom = geom
self.nodes_included = nodes_included
with Serafin.Read(args.inname) as resin:
resin.readHeader()
if resin.type != '2D':
sys.exit("The current script is working only with 2D meshes !")
resin.get_time()
# Define zones from polylines
print("~> Lecture des polylignes et recherche des noeuds inclus dedans")
masks = []
with BlueKenueRead_i2s(args.i2s_name) as in_i2s:
in_i2s.read_header()
for i, (value, polyline) in enumerate(in_i2s.iter_on_polylines()):
if not polyline.is_valid:
sys.exit("ERROR: polyline {} is not valid (probably because it intersects itself) !".format(i))
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
