def format_exception(self, e) -> List[dict]:
from markdown import markdown
if e.__cause__ is not None:
result = self.format_exception(e.__cause__)
result[-1]["tail"] = traceback._cause_message
elif e.__context__ is not None and not e.__suppress_context__:
result = self.format_exception(e.__context__)
result[-1]["tail"] = traceback._context_message
else:
result = []
result.append(
dict(
frames=self.format_stack(e.__traceback__),
exception=dict(
type=type(e).__name__,
message=traceback._some_str(e),
),
tail="",
didyoumean=didyoumean_suggestions(e),
friendly=markdown(friendly_message(e, double_newline=True)),
)
)
return result
def GetExpectedTracebackMessage(self, actual_exception):
# Getting the type of the "actual exception" because its type might be different than self.exception_type
reraised_exception_name = type(actual_exception).__name__
exception_message = self.GetExpectedExceptionMessage()
if self.expected_traceback_message is not None:
exception_message = self.expected_traceback_message
else:
exception_message = reraised_exception_name + ": " + exception_message + "\n"
# HACK [muenz]: the 'traceback' module does this, so in order to be able to compare strings we need this workaround
# notice that if the exception "leaks" the Python console handles the unicode symbols properly
exception_message = traceback._some_str(exception_message)
assert type(exception_message) == bytes
return exception_message
def GetExpectedTracebackMessage(self,
actual_exception,
use_utf_8_encoding=True):
# Getting the type of the "actual exception" because its type might be different than self.exception_type
reraised_exception_name = type(actual_exception).__name__
exception_message = self.GetExpectedExceptionMessage()
if self.expected_traceback_message is not None:
exception_message = self.expected_traceback_message
else:
exception_message = (reraised_exception_name + ": " +
exception_message + "\n")
# HACK [muenz]: the 'traceback' module does this, so in order to be able to compare strings we
# need this workaround notice that if the exception "leaks" the Python console handles the
# unicode symbols properly
if use_utf_8_encoding:
exception_message = exception_message.encode("utf-8")
else:
exception_message = traceback._some_str(exception_message)
assert isinstance(exception_message, bytes)
return exception_message
def get_expected_traceback_message(self, actual_exception):
# Getting the type of the "actual exception" because its type might be
# different than self.exception_type
reraised_exception_name = type(actual_exception).__name__
if six.PY3 and reraised_exception_name.startswith('Reraised'):
reraised_exception_name = 'zerotk.reraiseit._reraiseit.' + \
reraised_exception_name
exception_message = self.get_expected_exception_message()
if self.expected_traceback_message is not None:
exception_message = self.expected_traceback_message
else:
exception_message = reraised_exception_name + ": " + \
exception_message + "\n"
# HACK [muenz]: the 'traceback' module does this, so in order to be
# able to compare strings we need this workaround notice that if the
# exception "leaks" the Python console handles the unicode symbols
# properly
exception_message = traceback._some_str(exception_message)
assert type(exception_message) == MESSAGE_TYPE
return exception_message
def format_exception(self, e) -> List[dict]:
if e.__cause__ is not None:
result = self.format_exception(e.__cause__)
result[-1]["tail"] = traceback._cause_message
elif e.__context__ is not None and not e.__suppress_context__:
result = self.format_exception(e.__context__)
result[-1]["tail"] = traceback._context_message
else:
result = []
result.append(
dict(
frames=self.format_stack(e.__traceback__),
exception=dict(
type=type(e).__name__,
message=traceback._some_str(e),
),
tail="",
didyoumean=didyoumean_suggestions(e),
friendly=markdown(
friendly_generic(e) + "\n\n" + friendly_runtime_cause(e)),
))
return result
def __init__(self, parent, output_dir, use_cuts, elements, x_units,
line_zero, line_scale, systematic_error):
'''Inits widget.
Args:
parent: A MeasurementTabWidget.
output_dir: A string representing directory in which the depth files
are located.
use_cuts: A string list representing Cut files.
elements: A list of Element objects that are used in depth profile.
x_units: Units to be used for x-axis of depth profile.
line_zero: A boolean representing if vertical line is drawn at zero.
line_scale: A boolean representing if horizontal line is drawn at
the defined depth scale.
systematic_error: A double representing systematic error.
'''
try:
super().__init__()
self.parent = parent
self.icon_manager = parent.icon_manager
self.measurement = parent.measurement
self.output_dir = output_dir
self.elements = elements
self.x_units = x_units
self.__use_cuts = use_cuts;
self.__line_zero = line_zero
self.__line_scale = line_scale
self.__systerr = systematic_error
self.ui = uic.loadUi(os.path.join("ui_files",
"ui_depth_profile.ui"),
self)
# Make the directory for depth files
if not os.path.exists(self.output_dir):
os.makedirs(self.output_dir)
output_files = os.path.join(self.output_dir, 'depth')
dp = DepthFiles(self.__use_cuts, output_files)
dp.create_depth_files()
# Check for RBS selections.
rbs_list = {}
for cut in self.__use_cuts:
filename = os.path.basename(cut)
split = filename.split('.')
element = Element(split[1])
if is_rbs(cut):
# This should work for regular cut and split.
key = "{0}.{1}.{2}".format(split[1], split[2], split[3])
scatter_element = get_scatter_element(cut)
rbs_list[key] = scatter_element
index = 0
found_scatter = False
for elm in elements: # Makeshift
if elm == element:
found_scatter = True
break
index += 1
# When loading project, the scatter element is already
# replaced. This is essentially done only when creating
# a new Depth Profile graph.
if found_scatter:
elements[index] = scatter_element
self.measurement.generate_tof_in()
settings = self.measurement.measurement_settings.\
get_measurement_settings()
ds = settings.depth_profile_settings
depth_scale_from = ds.depths_for_concentration_from
depth_scale_to = ds.depths_for_concentration_to
self.matplotlib = MatplotlibDepthProfileWidget(self,
self.output_dir,
self.elements,
rbs_list,
(depth_scale_from, depth_scale_to),
self.x_units,
True, # legend
self.__line_zero,
self.__line_scale,
self.__systerr)
except:
import traceback
msg = "Could not create Depth Profile graph. "
err_file = sys.exc_info()[2].tb_frame.f_code.co_filename
str_err = ", ".join([sys.exc_info()[0].__name__ + ": " + \
traceback._some_str(sys.exc_info()[1]),
err_file,
str(sys.exc_info()[2].tb_lineno)])
msg += str_err
logging.getLogger(self.measurement.measurement_name).error(msg)
if hasattr(self, "matplotlib"):
self.matplotlib.delete()
def update_event(self, inp=-1):
self.set_output_val(0, traceback._some_str(self.input(0)))
def tof_list(cut_file, directory, save_output=False):
'''ToF_list
Arstila's tof_list executables interface for Python.
Args:
cut_file: A string representing cut file to be ran through tof_list.
directory: A string representing measurement's energy spectrum directory.
save_output: A boolean representing whether tof_list output is saved.
Returns:
Returns cut file as list transformed through Arstila's tof_list program.
'''
bin_dir = join(realpath(curdir), "external", "Potku-bin")
tof_list_array = []
if not cut_file:
return []
stdout = None
try:
if platform.system() == 'Windows':
startupinfo = subprocess.STARTUPINFO()
startupinfo.dwFlags |= subprocess.STARTF_USESHOWWINDOW
command = (str(join(bin_dir, "tof_list.exe")),
cut_file)
stdout = subprocess.check_output(command,
cwd=bin_dir,
shell=True,
startupinfo=startupinfo)
else:
command = "{0} {1}".format(join(".", "tof_list"), cut_file, bin_dir)
p = subprocess.Popen(command.split(' ', 1), cwd=bin_dir,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
stdout, unused_stderr = p.communicate()
lines = stdout.decode().strip().replace("\r", "").split("\n")
for line in lines:
if not line: # Can still result in empty lines at the end, skip.
continue
line_split = re.split("\s+", line.strip())
tupled = (float(line_split[0]),
float(line_split[1]),
float(line_split[2]),
int(line_split[3]),
float(line_split[4]),
line_split[5],
float(line_split[6]),
int(line_split[7]))
tof_list_array.append(tupled)
if save_output:
if not directory:
directory = join(realpath(curdir), "energy_spectrum_output")
if not exists(directory):
makedirs(directory)
unused_dir, file = split(cut_file)
directory_es_file = join(directory,
"{0}.tof_list".format(splitext(file)[0]))
numpy_array = numpy.array(tof_list_array,
dtype=[('float1', float),
('float2', float),
('float3', float),
('int1', int),
('float4', float),
('string', numpy.str_, 3),
('float5', float),
('int2', int)])
numpy.savetxt(directory_es_file, numpy_array,
delimiter=" ",
fmt="%5.1f %5.1f %10.5f %3d %8.4f %s %6.3f %d")
except:
import traceback
msg = "Error in tof_list: "
err_file = sys.exc_info()[2].tb_frame.f_code.co_filename
str_err = ", ".join([sys.exc_info()[0].__name__ + ": " + \
traceback._some_str(sys.exc_info()[1]),
err_file,
str(sys.exc_info()[2].tb_lineno)])
msg += str_err
print(msg)
finally:
return tof_list_array
def generate_tof_in(self):
"""Generate tof.in file for external programs.
Generates tof.in file for measurement to be used in external programs
(tof_list, erd_depth).
"""
tof_in_directory = os.path.join(os.path.realpath(os.path.curdir), "external", "Potku-bin")
tof_in_file = os.path.join(tof_in_directory, "tof.in")
# Get settings
use_settings = self.measurement_settings.get_measurement_settings()
global_settings = self.project.global_settings
# Measurement settings
str_beam = "Beam: {0}\n".format(use_settings.measuring_unit_settings.element)
str_energy = "Energy: {0}\n".format(use_settings.measuring_unit_settings.energy)
str_detector = "Detector angle: {0}\n".format(use_settings.measuring_unit_settings.detector_angle)
str_target = "Target angle: {0}\n".format(use_settings.measuring_unit_settings.target_angle)
str_toflen = "Toflen: {0}\n".format(use_settings.measuring_unit_settings.time_of_flight_length)
str_carbon = "Carbon foil thickness: {0}\n".format(use_settings.measuring_unit_settings.carbon_foil_thickness)
str_density = "Target density: {0}\n".format(use_settings.measuring_unit_settings.target_density)
# Depth Profile settings
str_depthnumber = "Number of depth steps: {0}\n".format(
use_settings.depth_profile_settings.number_of_depth_steps
)
str_depthstop = "Depth step for stopping: {0}\n".format(
use_settings.depth_profile_settings.depth_step_for_stopping
)
str_depthout = "Depth step for output: {0}\n".format(use_settings.depth_profile_settings.depth_step_for_output)
str_depthscale = "Depths for concentration scaling: {0} {1}\n".format(
use_settings.depth_profile_settings.depths_for_concentration_from,
use_settings.depth_profile_settings.depths_for_concentration_to,
)
# Cross section
flag_cross = global_settings.get_cross_sections()
str_cross = "Cross section: {0}\n".format(flag_cross)
# Cross Sections: 1=Rutherford, 2=L'Ecuyer, 3=Andersen
str_num_iterations = "Number of iterations: {0}\n".format(global_settings.get_num_iterations())
# Efficiency directory
eff_directory = global_settings.get_efficiency_directory()
str_eff_dir = "Efficiency directory: {0}".format(eff_directory)
# Combine strings
measurement = str_beam + str_energy + str_detector + str_target + str_toflen + str_carbon + str_density
calibration = "TOF calibration: {0} {1}\n".format(
use_settings.calibration_settings.slope, use_settings.calibration_settings.offset
)
anglecalibration = "Angle calibration: {0} {1}\n".format(
use_settings.calibration_settings.angleslope, use_settings.calibration_settings.angleoffset
)
depthprofile = str_depthnumber + str_depthstop + str_depthout + str_depthscale
tof_in = (
measurement + calibration + anglecalibration + depthprofile + str_cross + str_num_iterations + str_eff_dir
)
# Get md5 of file and new settings
md5 = hashlib.md5()
md5.update(tof_in.encode("utf8"))
digest = md5.digest()
digest_file = None
if os.path.isfile(tof_in_file):
f = open(tof_in_file, "r")
digest_file = md5_for_file(f)
f.close()
# If different back up old tof.in and generate a new one.
if digest_file != digest:
# Try to back up old file.
try:
new_file = "{0}_{1}.bak".format(tof_in_file, time.strftime("%Y-%m-%d_%H.%M.%S"))
shutil.copyfile(tof_in_file, new_file)
back_up_msg = "Backed up old tof.in file to {0}".format(os.path.realpath(new_file))
logging.getLogger(self.measurement_name).info(back_up_msg)
except:
import traceback
err_file = sys.exc_info()[2].tb_frame.f_code.co_filename
str_err = ", ".join(
[
sys.exc_info()[0].__name__ + ": " + traceback._some_str(sys.exc_info()[1]),
err_file,
str(sys.exc_info()[2].tb_lineno),
]
)
error_msg = "Unexpected error when generating tof.in: {0}".format(str_err)
logging.getLogger(self.measurement_name).error(error_msg)
# Write new settings to the file.
with open(tof_in_file, "wt+") as fp:
fp.write(tof_in)
str_logmsg = "Generated tof.in with params> {0}".format(tof_in.replace("\n", "; "))
logging.getLogger(self.measurement_name).info(str_logmsg)
def __init__(self, parent, reference_cut_file, checked_cuts, partition_count, y_scale):
"""Inits widget.
Args:
parent: MeasurementTabWidget
reference_cut_file: String representing reference cut file.
checked_cuts: String list representing cut files.
partition_count: Integer representing how many splits cut files
are divided to.
y_scale: Integer flag representing how Y axis is scaled.
"""
try:
super().__init__()
self.parent = parent
self.icon_manager = parent.icon_manager
self.measurement = self.parent.measurement
self.reference_cut_file = reference_cut_file
self.checked_cuts = checked_cuts
self.partition_count = partition_count
self.y_scale = y_scale
# TODO: Use Null with GUI ProgresBar.
if self.measurement.statusbar:
self.progress_bar = QtGui.QProgressBar()
self.measurement.statusbar.addWidget(self.progress_bar, 1)
self.progress_bar.show()
QtCore.QCoreApplication.processEvents(QtCore.QEventLoop.AllEvents)
# Mac requires event processing to show progress bar and its
# process.
else:
self.progress_bar = None
self.ui = uic.loadUi(os.path.join("ui_files", "ui_element_losses.ui"), self)
title = "{0} - Reference cut: {1}".format(self.ui.windowTitle(), os.path.basename(self.reference_cut_file))
self.ui.setWindowTitle(title)
# Calculate elemental losses
self.losses = ElementLosses(
self.measurement.directory_cuts,
self.measurement.directory_elemloss,
self.reference_cut_file,
self.checked_cuts,
self.partition_count,
progress_bar=self.progress_bar,
)
self.split_counts = self.losses.count_element_cuts()
# Check for RBS selections.
rbs_list = {}
for cut in self.checked_cuts:
filename = os.path.basename(cut)
split = filename.split(".")
if is_rbs(cut):
# This should work for regular cut and split.
key = "{0}.{1}.{2}".format(split[1], split[2], split[3])
rbs_list[key] = get_scatter_element(cut)
# Connect buttons
self.ui.splitSaveButton.clicked.connect(self.__save_splits)
self.matplotlib = MatplotlibElementLossesWidget(
self, self.split_counts, legend=True, y_scale=y_scale, rbs_list=rbs_list
)
except:
import traceback
msg = "Could not create Elemental Losses graph. "
err_file = sys.exc_info()[2].tb_frame.f_code.co_filename
str_err = ", ".join(
[
sys.exc_info()[0].__name__ + ": " + traceback._some_str(sys.exc_info()[1]),
err_file,
str(sys.exc_info()[2].tb_lineno),
]
)
msg += str_err
logging.getLogger(self.measurement.measurement_name).error(msg)
if hasattr(self, "matplotlib"):
self.matplotlib.delete()
finally:
if self.progress_bar:
self.measurement.statusbar.removeWidget(self.progress_bar)
self.progress_bar.hide()
def __init__(self, parent, use_cuts, width):
'''Inits widget.
Args:
parent: A MeasurementTabWidget.
use_cuts: A string list representing Cut files.
width: A float representing Energy Spectrum histogram's bin width.
'''
try:
super().__init__()
self.parent = parent
self.icon_manager = parent.icon_manager
self.measurement = self.parent.measurement
self.use_cuts = use_cuts
self.width = width
if self.measurement.statusbar:
self.progress_bar = QtGui.QProgressBar()
self.measurement.statusbar.addWidget(self.progress_bar, 1)
self.progress_bar.show()
QtCore.QCoreApplication.processEvents(QtCore.QEventLoop.AllEvents)
# Mac requires event processing to show progress bar and its
# process.
else:
self.progress_bar = None
self.ui = uic.loadUi(os.path.join("ui_files",
"ui_energy_spectrum.ui"),
self)
title = "{0} - Bin Width: {1}".format(self.ui.windowTitle(), width)
self.ui.setWindowTitle(title)
# Generate new tof.in file for external programs
self.measurement.generate_tof_in()
# Do energy spectrum stuff on this
self.energy_spectrum = EnergySpectrum(self.measurement,
use_cuts,
width,
progress_bar=self.progress_bar)
self.energy_spectrum_data = self.energy_spectrum.calculate_spectrum()
# Check for RBS selections.
rbs_list = {}
for cut in self.use_cuts:
filename = os.path.basename(cut)
split = filename.split('.')
if is_rbs(cut):
# This should work for regular cut and split.
key = "{0}.{1}.{2}".format(split[1], split[2], split[3])
rbs_list[key] = get_scatter_element(cut)
# Graph in matplotlib widget and add to window
self.matplotlib = MatplotlibEnergySpectrumWidget(
self,
self.energy_spectrum_data,
rbs_list)
except:
import traceback
msg = "Could not create Energy Spectrum graph. "
err_file = sys.exc_info()[2].tb_frame.f_code.co_filename
str_err = ", ".join([sys.exc_info()[0].__name__ + ": " + \
traceback._some_str(sys.exc_info()[1]),
err_file,
str(sys.exc_info()[2].tb_lineno)])
msg += str_err
logging.getLogger(self.measurement.measurement_name).error(msg)
if hasattr(self, "matplotlib"):
self.matplotlib.delete()
finally:
if self.progress_bar:
self.measurement.statusbar.removeWidget(self.progress_bar)
self.progress_bar.hide()