def on_pattern_file_set(self, button, dialog):
# TODO
# This should allow more flexibility:
# Patterns should be allowed to not have the exact same shape,
# add an x-shift variable to align them
filename = dialog.filename
parser = dialog.parser
data_objects = None
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(filename)
message += "{}</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
with DialogFactory.error_dialog_handler(message, parent=self.view.get_toplevel(), reraise=settings.DEBUG):
# Parse the pattern file
data_objects = parser.parse(filename)
pattern = data_objects[0].data
bg_pattern_x = pattern[:, 0].copy()
bg_pattern_y = pattern[:, 1].copy()
del pattern
# Interpolate/Extrapolate where needed to match data shape and range
from scipy.interpolate import interp1d
f = interp1d(
bg_pattern_x, bg_pattern_y,
bounds_error=False, fill_value=0
)
bg_xnew = self.model.data_x
bg_ynew = f(bg_xnew)
self.model.bg_pattern = bg_ynew
def on_pattern_file_set(self, dialog):
# TODO
# This should allow more flexibility:
# Patterns should be allowed to not have the exact same shape,
# add an x-shift variable to align them
filename = dialog.filename
parser = dialog.parser
data_objects = None
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(
filename)
message += "{}</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
with DialogFactory.error_dialog_handler(
message, parent=self.view.get_toplevel(), reraise=False):
# Parse the pattern file
data_objects = parser.parse(filename)
pattern = data_objects[0].data
bg_pattern_x = pattern[:, 0].copy()
bg_pattern_y = pattern[:, 1].copy()
del pattern
# Interpolate/Extrapolate where needed to match data shape and range
from scipy.interpolate import interp1d
f = interp1d(bg_pattern_x,
bg_pattern_y,
bounds_error=False,
fill_value=0)
bg_xnew = self.model.data_x
bg_ynew = f(bg_xnew)
self.model.bg_pattern = bg_ynew
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occurred when trying to parse '%s'.\n" % os.path.basename(filename)
message += "This is most likely caused by an invalid or unsupported file format."
with DialogFactory.error_dialog_handler(message, parent=self.view.get_toplevel(), reraise=False):
self.model.experimental_pattern.load_data(parser, filename, clear=True)
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occurred when trying to save '%s'.\n" % os.path.basename(filename)
message += "Contact the developer about this!"
with DialogFactory.error_dialog_handler(message, parent=self.view.get_toplevel(), reraise=False):
header = "%s %s" % (self.model.name, self.model.sample_name)
self.model.exclusion_ranges.save_data(parser, filename, header=header)
def on_accept(dialog):
# Try to load the project:
with DialogFactory.error_dialog_handler(
"An error has occurred:\n<i>{0}</i>\n Your project was not loaded!",
parent=self.view.get_toplevel(), reraise=False):
self.model.current_project = dialog.parser.parse(dialog.filename)
self.model.current_project.parent = self.model
# Update the title
self.update_title()
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occurred when trying to save to '%s'." % os.path.basename(
filename)
with DialogFactory.error_dialog_handler(
message, parent=self.view.get_toplevel(), reraise=False):
line.save_data(parser, filename,
**self.model.get_export_meta_data())
def on_accept(dialog):
# Try to load the project:
with DialogFactory.error_dialog_handler(
"An error has occurred:\n<i>{0}</i>\n Your project was not loaded!",
parent=self.view.get_toplevel(), title="Parsing error", reraise=False):
self.model.current_project = dialog.parser.parse(dialog.filename)
self.model.current_project.parent = self.model
self.model.update_project_last_save_hash()
# Update the title
self.update_title()
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occurred when trying to parse '%s'.\n" % os.path.basename(
filename)
message += "This is most likely caused by an invalid or unsupported file format."
with DialogFactory.error_dialog_handler(
message, parent=self.view.get_toplevel(), reraise=False):
self.model.experimental_pattern.load_data(parser,
filename,
clear=True)
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occurred when trying to save '%s'.\n" % os.path.basename(
filename)
message += "Contact the developer about this!"
with DialogFactory.error_dialog_handler(
message, parent=self.view.get_toplevel(), reraise=False):
header = "%s, %s" % ("Wavelength", "Factor")
self.model.wavelength_distribution.save_data(parser,
filename,
header=header)
def _save_project(self, filename=None):
# Set the filename to the current location if None or "" was given:
filename = filename or self.model.current_filename
# Try to save the project:
with DialogFactory.error_dialog_handler(
"An error has occurred while saving!\n<i>{0}</i>",
parent=self.view.get_toplevel(), reraise=False):
JSONProjectParser.write(self.model.current_project, filename, zipped=True)
self.model.current_project.filename = filename
# Update the title
self.update_title()
def _save_project(self, filename=None):
# Set the filename to the current location if None or "" was given:
filename = filename or self.model.current_filename
# Try to save the project:
with DialogFactory.error_dialog_handler(
"An error has occurred while saving!\n<i>{0}</i>",
parent=self.view.get_toplevel(), reraise=False):
JSONProjectParser.write(self.model.current_project, filename, zipped=True)
self.model.current_project.filename = filename
self.model.update_project_last_save_hash()
# Update the title
self.update_title()
def load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
# Error message is case parsing fails:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(filename)
message += "%s</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
# Run & report any errors:
with DialogFactory.error_dialog_handler(
message, self.view.get_top_widget(),
title="Failed to load file", reraise=False):
specimens = Specimen.from_experimental_data(filename=filename, parent=self.model, parser=parser)
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
def on_refine_clicked(self, event):
with self.model.mixture.needs_update.hold():
with self.model.mixture.data_changed.hold():
if len(self.model.mixture.specimens) > 0:
# Create the refiner object
with DialogFactory.error_dialog_handler(
"There was an error when creating the refinement setup:\n{}",
parent=self.view.get_toplevel(),
reraise=False):
refiner = self.model.get_refiner()
# Setup results controller
self.results_view = RefinerView(
parent=self.view.parent)
self.results_controller = RefinerController(
refiner=refiner,
model=self.model,
view=self.results_view,
parent=self)
# Gtk timeout loop for our GUI updating:
gui_timeout_id = self._launch_gui_updater(refiner)
# This creates a thread that will run the refiner.refine method:
thread = self._launch_refine_thread(
refiner, gui_timeout_id)
# Connect the cancel button:
self._connect_cancel_button(refiner, gui_timeout_id,
thread)
# Show the context updates in the gui:
self.view.show_refinement_info()
self.view.start_spinner()
else:
DialogFactory.get_information_dialog(
"Cannot refine an empty mixture!",
parent=self.view.get_toplevel()).run()
def on_refine_clicked(self, event):
with self.model.mixture.needs_update.hold():
with self.model.mixture.data_changed.hold():
if len(self.model.mixture.specimens) > 0:
# Create the refiner object
with DialogFactory.error_dialog_handler(
"There was an error when creating the refinement setup:\n{}",
parent=self.view.get_toplevel(), reraise=False):
refiner = self.model.get_refiner()
# Setup results controller
self.results_view = RefinerView(parent=self.view.parent)
self.results_controller = RefinerController(
refiner=refiner,
model=self.model,
view=self.results_view,
parent=self
)
# Gtk timeout loop for our GUI updating:
gui_timeout_id = self._launch_gui_updater(refiner)
# This creates a thread that will run the refiner.refine method:
thread = self._launch_refine_thread(refiner, gui_timeout_id)
# Connect the cancel button:
self._connect_cancel_button(refiner, gui_timeout_id, thread)
# Show the context updates in the gui:
self.view.show_refinement_info()
self.view.start_spinner()
else:
DialogFactory.get_information_dialog(
"Cannot refine an empty mixture!", parent=self.view.get_toplevel()
).run()
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occurred when trying to save to '%s'." % os.path.basename(filename)
with DialogFactory.error_dialog_handler(message, parent=self.view.get_toplevel(), reraise=False):
line.save_data(parser, filename, **self.model.get_export_meta_data())
