def remove_backgrounds(self, specimens):
"""
Opens the 'remove background' dialog for the given specimens,
raises a ValueError error if (one of) the specimens is not part of
this project.
"""
def on_automated(dialog):
for specimen in specimens:
if not specimen in self.model.specimens:
raise ValueError("Specimen `%s` is not part of this Project!" % specimen)
else:
specimen.experimental_pattern.bg_type = 0 # Linear see settings
specimen.experimental_pattern.find_bg_position()
specimen.experimental_pattern.remove_background()
specimen.experimental_pattern.clear_bg_variables()
def on_not_automated(dialog):
for specimen in specimens:
if not specimen in self.model.specimens:
raise ValueError("Specimen `%s` is not part of this Project!" % specimen)
else:
bg_view = BackgroundView(parent=self.parent.view)
BackgroundController(model=specimen.experimental_pattern, view=bg_view, parent=self)
bg_view.present()
# Ask user if he/she wants automation:
DialogFactory.get_confirmation_dialog(
"Do you want to perform an automated linear background subtraction?",
parent=self.parent.view.get_top_widget()
).run(on_automated, on_not_automated)
def remove_backgrounds(self, specimens):
"""
Opens the 'remove background' dialog for the given specimens,
raises a ValueError error if (one of) the specimens is not part of
this project.
"""
def on_automated(dialog):
for specimen in specimens:
if not specimen in self.model.specimens:
raise ValueError, "Specimen `%s` is not part of this Project!" % specimen
else:
specimen.experimental_pattern.bg_type = 0 # Linear see settings
specimen.experimental_pattern.find_bg_position()
specimen.experimental_pattern.remove_background()
specimen.experimental_pattern.clear_bg_variables()
def on_not_automated(dialog):
for specimen in specimens:
if not specimen in self.model.specimens:
raise ValueError, "Specimen `%s` is not part of this Project!" % specimen
else:
bg_view = BackgroundView(parent=self.parent.view)
BackgroundController(model=specimen.experimental_pattern,
view=bg_view,
parent=self)
bg_view.present()
# Ask user if he/she wants automation:
DialogFactory.get_confirmation_dialog(
"Do you want to perform an automated linear background subtraction?",
parent=self.parent.view.get_top_widget()).run(
on_automated, on_not_automated)
def on_find_peaks_clicked(self, widget):
def after_cb(threshold):
self.model.auto_add_peaks(threshold)
sel_model = ThresholdSelector(parent=self.model)
sel_view = DetectPeaksView(parent=self.view)
sel_ctrl = ThresholdController(model=sel_model, view=sel_view, parent=self, callback=after_cb) #@UnusedVariable
show_threshold_plot = DialogFactory.get_progress_dialog(
action=sel_model.update_threshold_plot_data,
complete_callback=lambda *a, **k: sel_view.present(),
gui_message="Finding peaks {progress:.0f}%...",
toplevel=self.view.get_top_widget()
)
if len(self.model.markers) > 0:
def on_accept(dialog):
self.model.clear_markers()
show_threshold_plot()
def on_reject(dialog):
show_threshold_plot()
DialogFactory.get_confirmation_dialog(
"Do you want to clear the current markers for this pattern?",
parent=self.view.get_top_widget()
).run(on_accept, on_reject)
else:
show_threshold_plot()
def on_import_wavelength_distribution_clicked(self, widget, data=None):
def on_confirm(dialog):
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
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):
self.model.wavelength_distribution.load_data(parser,
filename,
clear=True)
DialogFactory.get_load_dialog(
title="Import wavelength distribution",
parent=self.view.get_top_widget(),
filters=wld_parsers.get_import_file_filters(),
current_folder=settings.DATA_REG.get_directory_path(
"DEFAULT_WL_DISTR")).run(on_accept)
DialogFactory.get_confirmation_dialog(
"Importing a wavelength distribution will erase all current data.\nAre you sure you want to continue?",
parent=self.view.get_top_widget()).run(on_confirm)
def on_find_peaks_clicked(self, widget):
def after_cb(threshold):
self.model.auto_add_peaks(threshold)
sel_model = ThresholdSelector(parent=self.model)
sel_view = DetectPeaksView(parent=self.view)
sel_ctrl = ThresholdController(model=sel_model,
view=sel_view,
parent=self,
callback=after_cb) #@UnusedVariable
sel_model.update_threshold_plot_data()
if len(self.model.markers) > 0:
def on_accept(dialog):
self.model.clear_markers()
sel_view.present()
def on_reject(dialog):
sel_view.present()
DialogFactory.get_confirmation_dialog(
"Do you want to clear the current markers for this pattern?",
parent=self.view.get_top_widget()).run(on_accept, on_reject)
else:
sel_view.present()
def on_find_peaks_clicked(self, widget):
def after_cb(threshold):
self.model.auto_add_peaks(threshold)
sel_model = ThresholdSelector(parent=self.model)
sel_view = DetectPeaksView(parent=self.view)
sel_ctrl = ThresholdController(model=sel_model,
view=sel_view,
parent=self,
callback=after_cb) #@UnusedVariable
show_threshold_plot = DialogFactory.get_progress_dialog(
action=sel_model.update_threshold_plot_data,
complete_callback=lambda *a, **k: sel_view.present(),
gui_message="Finding peaks {progress:.0f}%...",
toplevel=self.view.get_top_widget())
if len(self.model.markers) > 0:
def on_accept(dialog):
self.model.clear_markers()
show_threshold_plot()
def on_reject(dialog):
show_threshold_plot()
DialogFactory.get_confirmation_dialog(
"Do you want to clear the current markers for this pattern?",
parent=self.view.get_top_widget()).run(on_accept, on_reject)
else:
show_threshold_plot()
def on_import_exclusion_ranges_clicked(self, widget, data=None):
def on_confirm(dialog):
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occured 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):
self.model.exclusion_ranges.load_data(parser,
filename,
clear=True)
DialogFactory.get_load_dialog(
title="Import exclusion ranges",
parent=self.view.get_top_widget(),
filters=exc_parsers.get_import_file_filters()).run(on_accept)
DialogFactory.get_confirmation_dialog(
"Importing exclusion ranges will erase all current data.\nAre you sure you want to continue?",
parent=self.view.get_top_widget()).run(on_confirm)
def on_btn_import_raw_pattern_clicked(self, widget, data=None):
def on_confirm(dialog):
self.on_replace_raw_pattern()
DialogFactory.get_confirmation_dialog(
"Importing a new experimental file will erase all current data.\nAre you sure you want to continue?",
parent=self.view.get_toplevel()).run(on_confirm)
return True
def on_btn_import_experimental_data_clicked(self, widget, data=None):
def on_confirm(dialog):
self.on_replace_experimental_data()
DialogFactory.get_confirmation_dialog(
"Importing a new experimental file will erase all current data.\nAre you sure you want to continue?",
parent=self.view.get_top_widget()
).run(on_confirm)
return True
def on_load_object_clicked(self, widget, user_data=None):
def import_layer(dialog):
def on_accept(dialog):
del self.treemodel_data[:] # clears the list
Atom.get_from_csv(dialog.filename, self.treemodel_data.append, self.model)
DialogFactory.get_load_dialog(
"Import atoms", parent=self.view.get_toplevel(),
filters=self.file_filters
).run(on_accept)
DialogFactory.get_confirmation_dialog(
message="Are you sure?\nImporting a layer file will clear the current list of atoms!",
parent=self.view.get_toplevel()
).run(import_layer)
def delete_selected_specimens(self):
"""
Asks the user for confirmation and if positive deletes all the
selected specimens. Does nothing when no specimens are selected.
"""
selection = self.get_selected_objects()
if selection is not None and len(selection) >= 1:
def delete_objects(dialog):
for obj in selection:
if obj is not None:
self.model.specimens.remove(obj)
DialogFactory.get_confirmation_dialog(
message='Deleting a specimen is irreversible!\nAre You sure you want to continue?',
parent=self.view.get_top_widget()
).run(delete_objects)
def on_cmb_import_gonio_changed(self, combobox, *args):
model = combobox.get_model()
itr = combobox.get_active_iter()
if itr:
# first column is the name, second column the path and third column
# a flag indicating if this can be selected
path = model.get_value(itr, 1)
if path:
def on_accept(dialog):
self.model.reset_from_file(path)
DialogFactory.get_confirmation_dialog(
"Are you sure?\nYou will loose the current settings!",
parent=self.view.get_toplevel()).run(on_accept)
combobox.set_active(-1) # deselect
def accept_wrapper(self, *args, **kwargs):
if self.model.check_for_changes():
return DialogFactory.get_confirmation_dialog(
confirm_msg, parent=self.view.get_top_widget()
).run(lambda d: on_accept(self, *args, **kwargs), on_reject)
else:
return on_accept(self, *args, **kwargs)
def accept_wrapper(self, *args, **kwargs):
if self.model.current_project and self.model.current_project.needs_saving:
return DialogFactory.get_confirmation_dialog(
confirm_msg, parent=self.view.get_top_widget()
).run(lambda d: on_accept(self, *args, **kwargs), on_reject)
else:
return on_accept(self, *args, **kwargs)
def on_del_object_clicked(self, event, del_callback=None, callback=None):
tv = self.view.treeview
selection = tv.get_selection()
if selection.count_selected_rows() >= 1:
def delete_objects(dialog):
with self._multi_operation_context():
for obj in self.get_selected_objects():
if callable(del_callback):
del_callback(obj)
else:
self.treemodel_data.remove(obj)
if callable(callback): callback(obj)
self.edit_object(None)
parent = self.view.get_top_widget()
if not isinstance(parent, Gtk.Window): # @UndefinedVariable
parent = None
DialogFactory.get_confirmation_dialog(
message=self.delete_msg, parent=parent
).run(delete_objects)
def on_import_exclusion_ranges_clicked(self, widget, data=None):
def on_confirm(dialog):
def on_accept(dialog):
filename = dialog.filename
parser = dialog.parser
message = "An unexpected error has occured 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):
self.model.exclusion_ranges.load_data(parser, filename, clear=True)
DialogFactory.get_load_dialog(
title="Import exclusion ranges", parent=self.view.get_top_widget(),
filters=exc_parsers.get_import_file_filters()
).run(on_accept)
DialogFactory.get_confirmation_dialog(
"Importing exclusion ranges will erase all current data.\nAre you sure you want to continue?",
parent=self.view.get_top_widget()
).run(on_confirm)
