def _launch_refine_thread(self, refiner, gui_timeout_id):
@run_when_idle
def thread_completed(*args, **kwargs):
""" Called when the refinement is completed """
self.thread = None
gobject.source_remove(gui_timeout_id)
self.view.stop_spinner()
# Make some plots:
if self.model.make_psp_plots:
self.view.update_refinement_status("Processing...")
self.results_controller.generate_images()
# Set the labels:
self.results_controller.update_labels()
# Hide our shit:
self.view.hide_refinement_info()
self.view.hide()
# Show results:
self.results_view.present()
thread = CancellableThread(refiner.refine, thread_completed)
thread.start()
return thread
def refine(self, threaded=False, on_complete=None, **kwargs):
"""
This refines the selected properties using the selected algorithm.
This can be run asynchronously when threaded is set to True.
"""
refine_method = partial(self._inner_refine,
self.get_refinement_method(), self.context, **kwargs)
if not threaded:
context = refine_method()
if callable(on_complete):
on_complete(context)
else:
def thread_completed(context):
#Assuming this is GTK-thread safe (i.e. wrapped in @run_when_idle)
on_complete(context)
self.thread = None
self.thread = CancellableThread(refine_method, thread_completed)
self.thread.start()
class ProjectController(ObjectListStoreController):
treemodel_property_name = "specimens"
treemodel_class_type = Specimen
columns = []
delete_msg = "Deleting a specimen is irreversible!\nAre You sure you want to continue?"
auto_adapt = True
def register_view(self, view):
if view is not None and self.model is not None:
if self.parent is not None: # is this still needed?
tv = self.view["project_specimens"]
tv.set_model(self.treemodel)
self.view.treeview = tv
self.view.set_x_range_sensitive(self.model.axes_xlimit == 1)
self.view.set_y_range_sensitive(self.model.axes_ylimit == 1)
return
def _idle_register_view(self, *args, **kwargs):
super(ProjectController, self)._idle_register_view(*args, **kwargs)
def adapt(self, *args, **kwargs):
super(ProjectController, self).adapt(*args, **kwargs)
def setup_treeview(self, widget):
super(ProjectController, self).setup_treeview(widget)
store = self.treemodel
widget.connect('button-press-event', self.specimen_tv_button_press)
# First reset & then (re)create the columns of the treeview:
for col in widget.get_columns():
widget.remove_column(col)
# Name column:
col = new_text_column('Name',
text_col=store.c_name,
min_width=125,
xalign=0.0,
ellipsize=pango.ELLIPSIZE_END)
col.set_data("colnr", store.c_name)
widget.append_column(col)
# Check boxes:
def toggle_renderer(column, cell, model, itr, data=None):
active = False
if model.iter_is_valid(itr):
col = column.get_col_attr("active")
active = model.get_value(itr, col)
cell.set_property('active', active)
return
def setup_check_column(title, colnr):
col = new_toggle_column(title,
toggled_callback=(self.specimen_tv_toggled,
(store, colnr)),
data_func=toggle_renderer,
resizable=False,
expand=False,
activatable=True,
active_col=colnr)
col.set_data("colnr", colnr)
widget.append_column(col)
setup_check_column('Exp', store.c_display_experimental)
if self.model.layout_mode == "FULL":
setup_check_column('Cal', store.c_display_calculated)
setup_check_column('Sep', store.c_display_phases)
# Up and down arrows:
def setup_image_button(image, colnr):
col = new_pb_column("",
resizable=False,
expand=False,
stock_id=image)
col.set_data("colnr", colnr)
widget.append_column(col)
setup_image_button("213-up-arrow", 501)
setup_image_button("212-down-arrow", 502)
def edit_object(self, obj):
pass # clear this method, we're not having an 'edit' view pane...
@BaseController.status_message("Importing multiple specimens...",
"add_specimen")
def import_multiple_specimen(self):
def on_accept(dialog):
## TODO MOVE THIS (PARTIALLY?) TO THE MODEL LEVEL ##
filenames = dialog.get_filenames()
parser = dialog.get_filter().get_data("parser")
task = ThreadedTaskBox()
window = DialogFactory.get_custom_dialog(
task, parent=self.view.get_top_widget())
# Status:
status_dict = dict(total_files=len(filenames),
current_file=0,
specimens=[])
# Task:
def load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
try:
specimens = Specimen.from_experimental_data(
filename=filename,
parent=self.model,
parser=parser)
except Exception as msg:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(
filename)
message += str(msg) + "</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
logger.exception(message)
@run_when_idle
def run_dialog():
DialogFactory.get_information_dialog(
message=message,
parent=self.view.get_top_widget()).run()
return False
run_dialog()
else:
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
# Cancel & stop events:
def on_interrupted(*args, **kwargs):
window.hide()
# Status label update:
def gui_callback():
task.set_status(
"Loading file %d/%d ..." %
(status_dict["current_file"], status_dict["total_files"]))
return True
gui_timeout_id = gobject.timeout_add(250, gui_callback)
# Complete event:
@run_when_idle
def on_complete(*args, **kwargs):
last_iter = None
for specimen in status_dict["specimens"]:
last_iter = self.model.specimens.append(specimen)
if last_iter is not None:
self.view["project_specimens"].set_cursor(last_iter)
gobject.source_remove(gui_timeout_id)
window.hide()
window.destroy()
# Run task box:
task.connect("cancelrequested", on_interrupted)
task.connect("stoprequested", on_interrupted)
task.set_status("Loading ...")
task.start()
window.show_all()
# Run thread:
self.thread = CancellableThread(load_specimens, on_complete)
self.thread.start()
DialogFactory.get_load_dialog(
title="Select XRD files for import",
filters=xrd_parsers.get_import_file_filters(),
parent=self.view.get_top_widget(),
multiple=True).run(on_accept)
@BaseController.status_message("Deleting specimen...", "del_specimen")
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)
@BaseController.status_message("Removing backgrounds...",
"del_bg_specimen")
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 edit_specimen(self):
selection = self.get_selected_objects()
if selection is not None and len(selection) == 1:
# TODO move the specimen view & controller into the project level
self.parent.view.specimen.present()
@BaseController.status_message("Creating new specimen...", "add_specimen")
def add_specimen(self):
specimen = Specimen(parent=self.model, name="New Specimen")
self.model.specimens.append(specimen)
self.view.specimens_treeview.set_cursor(
self.treemodel.on_get_path(specimen))
self.edit_specimen()
return True
@contextmanager
def _multi_operation_context(self):
with self.model.hold_mixtures_data_changed():
with self.model.data_changed.hold():
yield
# ------------------------------------------------------------
# Notifications of observable properties
# ------------------------------------------------------------
@Controller.observe("name", assign=True)
def notif_change_name(self, model, prop_name, info):
self.parent.update_title()
return
@Controller.observe("axes_xlimit", assign=True)
def notif_xlimit_toggled(self, model, prop_name, info):
self.view.set_x_range_sensitive(int(self.model.axes_xlimit) == 1)
@Controller.observe("axes_ylimit", assign=True)
def notif_ylimit_toggled(self, model, prop_name, info):
self.view.set_y_range_sensitive(int(self.model.axes_ylimit) == 1)
@Controller.observe("layout_mode", assign=True)
def notif_layout_mode(self, model, prop_name, info):
self.parent.set_layout_mode(self.model.layout_mode)
if self.view is not None:
self.setup_treeview(self.view.treeview)
# ------------------------------------------------------------
# GTK Signal handlers
# ------------------------------------------------------------
def specimen_tv_toggled(self, cell, path, model, colnr):
if model is not None:
itr = model.get_iter(path)
model.set_value(itr, colnr, not cell.get_active())
return True
return False
def specimen_tv_button_press(self, tv, event):
specimen = None
current_specimens = self.parent.model.current_specimens or []
ret = tv.get_path_at_pos(int(event.x), int(event.y))
if ret is not None:
path, col, x, y = ret
specimen = self.treemodel.get_user_data_from_path(path) # FIXME
if event.button == 3:
if specimen is not None:
# clicked a specimen which is not in the current selection,
# so clear selection and select it
if not specimen in current_specimens:
self.select_object(specimen)
else:
# clicked an empty space, so clear selection
self.select_object(None)
self.view.show_specimens_context_menu(event)
return True
elif event.type == gtk.gdk._2BUTTON_PRESS and specimen is not None and col.get_data(
"colnr") == self.treemodel.c_name: # @UndefinedVariable
self.parent.on_edit_specimen_activate(event)
return True
elif (event.button == 1 or event.type == gtk.gdk._2BUTTON_PRESS
) and specimen is not None: # @UndefinedVariable
column = col.get_data("colnr")
if column in (self.treemodel.c_display_experimental,
self.treemodel.c_display_calculated,
self.treemodel.c_display_phases):
if column == self.treemodel.c_display_experimental:
specimen.display_experimental = not specimen.display_experimental
elif column == self.treemodel.c_display_calculated:
specimen.display_calculated = not specimen.display_calculated
elif column == self.treemodel.c_display_phases:
specimen.display_phases = not specimen.display_phases
# TODO FIXME self.treemodel.on_row_changed(ret)
return True
elif column == 501:
self.model.move_specimen_down(specimen)
self.parent.model.current_specimens = self.get_selected_objects(
)
return True
elif column == 502:
self.model.move_specimen_up(specimen)
self.parent.model.current_specimens = self.get_selected_objects(
)
return True
def objects_tv_selection_changed(self, selection):
ObjectListStoreController.objects_tv_selection_changed(self, selection)
self.parent.model.current_specimens = self.get_selected_objects()
return True
pass # end of class
def on_accept(dialog):
## TODO MOVE THIS (PARTIALLY?) TO THE MODEL LEVEL ##
filenames = dialog.get_filenames()
parser = dialog.get_filter().get_data("parser")
task = ThreadedTaskBox()
window = DialogFactory.get_custom_dialog(
task, parent=self.view.get_top_widget())
# Status:
status_dict = dict(total_files=len(filenames),
current_file=0,
specimens=[])
# Task:
def load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
try:
specimens = Specimen.from_experimental_data(
filename=filename,
parent=self.model,
parser=parser)
except Exception as msg:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(
filename)
message += str(msg) + "</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
logger.exception(message)
@run_when_idle
def run_dialog():
DialogFactory.get_information_dialog(
message=message,
parent=self.view.get_top_widget()).run()
return False
run_dialog()
else:
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
# Cancel & stop events:
def on_interrupted(*args, **kwargs):
window.hide()
# Status label update:
def gui_callback():
task.set_status(
"Loading file %d/%d ..." %
(status_dict["current_file"], status_dict["total_files"]))
return True
gui_timeout_id = gobject.timeout_add(250, gui_callback)
# Complete event:
@run_when_idle
def on_complete(*args, **kwargs):
last_iter = None
for specimen in status_dict["specimens"]:
last_iter = self.model.specimens.append(specimen)
if last_iter is not None:
self.view["project_specimens"].set_cursor(last_iter)
gobject.source_remove(gui_timeout_id)
window.hide()
window.destroy()
# Run task box:
task.connect("cancelrequested", on_interrupted)
task.connect("stoprequested", on_interrupted)
task.set_status("Loading ...")
task.start()
window.show_all()
# Run thread:
self.thread = CancellableThread(load_specimens, on_complete)
self.thread.start()
class Refiner(ChildModel):
"""
A simple model that plugs onto the Mixture model. It provides
the functionality related to refinement of parameters.
"""
# MODEL INTEL:
class Meta(ChildModel.Meta):
properties = [ # TODO add labels
PropIntel(name="refinables", label="", has_widget=True, data_type=object, is_column=True, widget_type="object_tree_view", class_type=RefinableWrapper),
PropIntel(name="refine_options", label="", data_type=dict, is_column=False),
OptionPropIntel(name="refine_method", label="Refinement method", has_widget=True, data_type=int, options={ key: method.name for key, method in get_all_refine_methods().iteritems() }),
PropIntel(name="make_psp_plots", label="", data_type=bool, is_colum=False, has_widget=True, storable=False),
]
store_id = "Refiner"
mixture = property(ChildModel.parent.fget, ChildModel.parent.fset)
#: Refinement context
context = None
#: Refinement thread (or None if not running)
thread = None
#: Flag, True if after refinement plots should be generated of the parameter space
make_psp_plots = False
#: TreeNode containing the refinable properties
refinables = None
#: A dict containing an instance of each refinement method
refine_methods = None
_refine_method = 0
@property
def refine_method(self):
""" An integer describing which method to use for the refinement (see
refinement.methods.get_all_refine_methods) """
return self._refine_method
@refine_method.setter
def refine_method(self, value): self._refine_method = int(value)
#: A dict containing the current refinement options
@property
def refine_options(self):
method = self.get_refinement_method()
return { name: getattr(method, name) for name in method.options }
#: A dict containing all refinement options
@property
def all_refine_options(self):
return {
method.index : { name: getattr(method, name) for name in method.options }
for method in self.refine_methods.values()
}
def __init__(self, *args, **kwargs):
my_kwargs = self.pop_kwargs(kwargs,
"refine_method", "refine_options"
)
super(Refiner, self).__init__(*args, **kwargs)
kwargs = my_kwargs
# Setup the refinables treestore
self.refinables = TreeNode()
# Setup the refine methods
try:
self.refine_method = int(self.get_kwarg(kwargs, None, "refine_method"))
except ValueError:
self.refine_method = self.refine_method
pass # ignore faulty values, these indices change from time to time.
self.refine_methods = self.create_refine_methods(self.get_kwarg(kwargs, None, "refine_options"))
self.update_refinement_treestore()
# ------------------------------------------------------------
# Methods & Functions
# ------------------------------------------------------------
def setup_context(self, store=False):
"""
Creates a RefineContext object filled with parameters based on the
current state of the Mixture object.
"""
self.context = RefineContext(
parent=self.parent,
options=self.parent.refine_options,
store=store
)
def delete_context(self):
"""
Clears the RefineContext from this model
"""
self.context = None
def _inner_refine(self, refine_method, context, stop=None, **kwargs):
# Suppress updates:
with self.mixture.needs_update.hold():
with self.mixture.data_changed.hold():
# If something has been selected: continue...
if len(context.ref_props) > 0:
# Make sure the stop signal is not set from a previous run:
if stop is not None:
stop.clear()
# Log some information:
logger.info("-"*80)
logger.info("Starting refinement with this setup:")
msg_frm = "%22s: %s"
logger.info(msg_frm % ("refinement method", refine_method))
logger.info(msg_frm % ("number of parameters", len(context.ref_props)))
logger.info(msg_frm % ("GUI mode", settings.GUI_MODE))
# Record start time
t1 = time.time()
try: # Run until it ends or it raises an exception:
refine_method(context, stop=stop)
except any as error:
logger.exception("Unhandled run-time error when refining: %s" % error)
context.status = "error"
context.status_message = "Error occurred..."
else: # No errors occurred:
if stop is not None and stop.is_set():
context.status = "stopped"
context.status_message = "Stopped ..."
logger.info("Refinement was stopped prematurely")
else:
context.status = "finished"
context.status_message = "Finished"
logger.info("Refinement ended successfully")
# Record end time
t2 = time.time()
# Log some more information:
logger.info('%s took %0.3f ms' % ("Total refinement", (t2 - t1) * 1000.0))
logger.info('Best solution found was:')
for line in context.best_solution_to_string().split('\n'):
logger.info(line)
logger.info("-"*80)
else: # nothing selected for refinement
context.status = "error"
context.status_message = "No parameters selected!"
# Return the context to whatever called this
return context
def refine(self, threaded=False, on_complete=None, **kwargs):
"""
This refines the selected properties using the selected algorithm.
This can be run asynchronously when threaded is set to True.
"""
refine_method = partial(self._inner_refine,
self.get_refinement_method(), self.context, **kwargs)
if not threaded:
context = refine_method()
if callable(on_complete):
on_complete(context)
else:
def thread_completed(context):
#Assuming this is GTK-thread safe (i.e. wrapped in @run_when_idle)
on_complete(context)
self.thread = None
self.thread = CancellableThread(refine_method, thread_completed)
self.thread.start()
def cancel(self):
"""
Cancels a threaded refinement,
and will call the on_complete callback passed to `refine`
"""
if self.thread is not None:
logger.info("Refinement cancelled")
self.thread.cancel()
else:
logger.info("Cannot cancel, no refinement running")
self.thread = None
def stop(self):
""" Stops a threaded refinement, not returning any result """
if self.thread is not None:
logger.info("Refinement stopped")
self.thread.stop()
else:
logger.info("Cannot stop, no refinement running")
self.thread = None
# ------------------------------------------------------------
# Refinement Methods Management
# ------------------------------------------------------------
@staticmethod
def get_all_refine_methods():
return get_all_refine_methods()
@staticmethod
def create_refine_methods(refine_options):
"""
Returns a dict of refine methods as values and their index as key
with the passed refine_options dict applied.
"""
# 1. Create a list of refinement instances:
refine_methods = {}
for index, method in get_all_refine_methods().iteritems():
refine_methods[index] = method()
# 2. Create dict of default options
default_options = {}
for method in refine_methods.values():
default_options[method.index] = {
name: getattr(type(method), name).default for name in method.options
}
# 3. Apply the refine options to the methods
if not refine_options == None:
for index, options in zip(refine_options.keys(), refine_options.values()):
index = int(index)
if index in refine_methods:
method = refine_methods[index]
for arg, value in zip(options.keys(), options.values()):
if hasattr(method, arg):
setattr(method, arg, value)
return refine_methods
def get_refinement_method(self):
"""
Returns the actual refinement method by translating the
`refine_method` attribute
"""
return self.refine_methods[self.refine_method]
def get_refinement_option(self, option):
return getattr(type(self.get_refinement_method()), option)
def get_refinement_option_value(self, option):
return getattr(self.get_refinement_method(), option)
def set_refinement_option_value(self, option, value):
return setattr(self.get_refinement_method(), option, value)
# ------------------------------------------------------------
# Refinables Management
# ------------------------------------------------------------
# TODO set a restrict range attribute on the PropIntels, so we can use custom ranges for each property
def auto_restrict(self):
"""
Convenience function that restricts the selected properties
automatically by setting their minimum and maximum values.
"""
with self.mixture.needs_update.hold():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value_min = ref_prop.value * 0.8
ref_prop.value_max = ref_prop.value * 1.2
def randomize(self):
"""
Convenience function that randomize the selected properties.
Respects the current minimum and maximum values.
Executes an optimization after the randomization.
"""
with self.mixture.data_changed.hold_and_emit():
with self.mixture.needs_update.hold_and_emit():
for node in self.refinables.iter_children():
ref_prop = node.object
if ref_prop.refine and ref_prop.refinable:
ref_prop.value = random.uniform(ref_prop.value_min, ref_prop.value_max)
def update_refinement_treestore(self):
"""
This creates a tree store with all refinable properties and their
minimum, maximum and current value.
"""
if self.parent is not None: # not linked so no valid phases!
self.refinables.clear()
def add_property(parent_node, obj, prop, is_grouper):
rp = RefinableWrapper(obj=obj, prop=prop, parent=self.mixture, is_grouper=is_grouper)
return parent_node.append(TreeNode(rp))
def parse_attribute(obj, prop, root_node):
"""
obj: the object
attr: the attribute of obj or None if obj contains attributes
root_node: the root TreeNode new iters should be put under
"""
if prop is not None:
if hasattr(obj, "get_uninherited_property_value"):
value = obj.get_uninherited_property_value(prop)
else:
value = getattr(obj, prop.name)
else:
value = obj
if isinstance(value, RefinementValue): # AtomRelation and UnitCellProperty
new_node = add_property(root_node, value, prop, False)
elif hasattr(value, "__iter__"): # List or similar
for new_obj in value:
parse_attribute(new_obj, None, root_node)
elif isinstance(value, RefinementGroup): # Phase, Component, Probability
if len(value.refinables) > 0:
new_node = add_property(root_node, value, prop, True)
for prop in value.refinables:
parse_attribute(value, prop, new_node)
else: # regular values
new_node = add_property(root_node, obj, prop, False)
for phase in self.mixture.project.phases:
if phase in self.mixture.phase_matrix:
parse_attribute(phase, None, self.refinables)
pass # end of class
class ProjectController(ObjectListStoreController):
treemodel_property_name = "specimens"
treemodel_class_type = Specimen
columns = [ ]
delete_msg = "Deleting a specimen is irreversible!\nAre You sure you want to continue?"
auto_adapt = True
file_filters = Specimen.Meta.file_filters
def register_view(self, view):
if view is not None and self.model is not None:
if self.parent is not None: # is this still needed?
tv = self.view["project_specimens"]
tv.set_model(self.treemodel)
self.view.treeview = tv
self.view.set_x_range_sensitive(self.model.axes_xlimit == 1)
self.view.set_y_range_sensitive(self.model.axes_ylimit == 1)
return
def _idle_register_view(self, *args, **kwargs):
super(ProjectController, self)._idle_register_view(*args, **kwargs)
def adapt(self, *args, **kwargs):
super(ProjectController, self).adapt(*args, **kwargs)
def setup_treeview(self, widget):
super(ProjectController, self).setup_treeview(widget)
store = self.treemodel
widget.connect('button-press-event', self.specimen_tv_button_press)
# First reset & then (re)create the columns of the treeview:
for col in widget.get_columns():
widget.remove_column(col)
# Name column:
col = new_text_column('Name',
text_col=store.c_name,
min_width=125,
xalign=0.0,
ellipsize=pango.ELLIPSIZE_END)
col.set_data("colnr", store.c_name)
widget.append_column(col)
# Check boxes:
def toggle_renderer(column, cell, model, itr, data=None):
active = False
if model.iter_is_valid(itr):
col = column.get_col_attr("active")
active = model.get_value(itr, col)
cell.set_property('active', active)
return
def setup_check_column(title, colnr):
col = new_toggle_column(title,
toggled_callback=(self.specimen_tv_toggled, (store, colnr)),
data_func=toggle_renderer,
resizable=False,
expand=False,
activatable=True,
active_col=colnr)
col.set_data("colnr", colnr)
widget.append_column(col)
setup_check_column('Exp', store.c_display_experimental)
if self.model.layout_mode == "FULL":
setup_check_column('Cal', store.c_display_calculated)
setup_check_column('Sep', store.c_display_phases)
# Up and down arrows:
def setup_image_button(image, colnr):
col = new_pb_column("", resizable=False, expand=False, stock_id=image)
col.set_data("colnr", colnr)
widget.append_column(col)
setup_image_button("213-up-arrow", 501)
setup_image_button("212-down-arrow", 502)
def edit_object(self, obj):
pass # clear this method, we're not having an 'edit' view pane...
@BaseController.status_message("Importing multiple specimens...", "add_specimen")
def import_multiple_specimen(self):
def on_accept(dialog):
## TODO MOVE THIS (PARTIALLY?) TO THE MODEL LEVEL ##
filenames = dialog.get_filenames()
parser = dialog.get_filter().get_data("parser")
task = ThreadedTaskBox()
window = self.get_custom_dialog(task, parent=self.view.get_top_widget())
# Status:
status_dict = dict(
total_files=len(filenames),
current_file=0,
specimens=[]
)
# Task:
def load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
try:
specimens = Specimen.from_experimental_data(filename=filename, parent=self.model, parser=parser)
except Exception as msg:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(filename)
message += str(msg) + "</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
logger.exception(message)
@run_when_idle
def run_dialog():
self.run_information_dialog(
message=message,
parent=self.view.get_top_widget()
)
return False
run_dialog()
else:
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
# Cancel & stop events:
def on_interrupted(*args, **kwargs):
window.hide()
# Status label update:
def gui_callback():
task.set_status("Loading file %d/%d ..." % (
status_dict["current_file"],
status_dict["total_files"]
))
return True
gui_timeout_id = gobject.timeout_add(250, gui_callback)
# Complete event:
@run_when_idle
def on_complete(*args, **kwargs):
last_iter = None
for specimen in status_dict["specimens"]:
last_iter = self.model.specimens.append(specimen)
if last_iter is not None:
self.view["project_specimens"].set_cursor(last_iter)
gobject.source_remove(gui_timeout_id)
window.hide()
window.destroy()
# Run task box:
task.connect("cancelrequested", on_interrupted)
task.connect("stoprequested", on_interrupted)
task.set_status("Loading ...")
task.start()
window.show_all()
# Run thread:
self.thread = CancellableThread(load_specimens, on_complete)
self.thread.start()
self.run_load_dialog(title="Select XRD files for import",
on_accept_callback=on_accept,
parent=self.view.get_top_widget(),
multiple=True)
@BaseController.status_message("Deleting specimen...", "del_specimen")
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)
self.run_confirmation_dialog(
message='Deleting a specimen is irreversible!\nAre You sure you want to continue?',
on_accept_callback=delete_objects,
parent=self.view.get_top_widget())
@BaseController.status_message("Removing backgrounds...", "del_bg_specimen")
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:
self.run_confirmation_dialog(
"Do you want to perform an automated linear background subtraction?",
on_automated, on_not_automated, parent=self.parent.view.get_top_widget()
)
def edit_specimen(self):
selection = self.get_selected_objects()
if selection is not None and len(selection) == 1:
# TODO move the specimen view & controller into the project level
self.parent.view.specimen.present()
@BaseController.status_message("Creating new specimen...", "add_specimen")
def add_specimen(self):
specimen = Specimen(parent=self.model, name="New Specimen")
self.model.specimens.append(specimen)
self.view.specimens_treeview.set_cursor(self.treemodel.on_get_path(specimen))
self.edit_specimen()
return True
@contextmanager
def _multi_operation_context(self):
with self.model.hold_mixtures_data_changed():
with self.model.data_changed.hold():
yield
# ------------------------------------------------------------
# Notifications of observable properties
# ------------------------------------------------------------
@Controller.observe("name", assign=True)
def notif_change_name(self, model, prop_name, info):
self.parent.update_title()
return
@Controller.observe("axes_xlimit", assign=True)
def notif_xlimit_toggled(self, model, prop_name, info):
self.view.set_x_range_sensitive(int(self.model.axes_xlimit) == 1)
@Controller.observe("axes_ylimit", assign=True)
def notif_ylimit_toggled(self, model, prop_name, info):
self.view.set_y_range_sensitive(int(self.model.axes_ylimit) == 1)
@Controller.observe("layout_mode", assign=True)
def notif_layout_mode(self, model, prop_name, info):
self.parent.set_layout_mode(self.model.layout_mode)
if self.view is not None:
self.setup_treeview(self.view.treeview)
# ------------------------------------------------------------
# GTK Signal handlers
# ------------------------------------------------------------
def specimen_tv_toggled(self, cell, path, model, colnr):
if model is not None:
itr = model.get_iter(path)
model.set_value(itr, colnr, not cell.get_active())
return True
return False
def specimen_tv_button_press(self, tv, event):
specimen = None
current_specimens = self.parent.model.current_specimens or []
ret = tv.get_path_at_pos(int(event.x), int(event.y))
if ret is not None:
path, col, x, y = ret
specimen = self.treemodel.get_user_data_from_path(path) # FIXME
if event.button == 3:
if specimen is not None:
# clicked a specimen which is not in the current selection,
# so clear selection and select it
if not specimen in current_specimens:
self.select_object(specimen)
else:
# clicked an empty space, so clear selection
self.select_object(None)
self.view.show_specimens_context_menu(event)
return True
elif event.type == gtk.gdk._2BUTTON_PRESS and specimen is not None and col.get_data("colnr") == self.treemodel.c_name:
self.parent.on_edit_specimen_activate(event)
return True
elif (event.button == 1 or event.type == gtk.gdk._2BUTTON_PRESS) and specimen is not None:
column = col.get_data("colnr")
if column in (self.treemodel.c_display_experimental,
self.treemodel.c_display_calculated,
self.treemodel.c_display_phases):
if column == self.treemodel.c_display_experimental:
specimen.display_experimental = not specimen.display_experimental
elif column == self.treemodel.c_display_calculated:
specimen.display_calculated = not specimen.display_calculated
elif column == self.treemodel.c_display_phases:
specimen.display_phases = not specimen.display_phases
# TODO FIXME self.treemodel.on_row_changed(ret)
return True
elif column == 501:
self.model.move_specimen_down(specimen)
self.parent.model.current_specimens = self.get_selected_objects()
return True
elif column == 502:
self.model.move_specimen_up(specimen)
self.parent.model.current_specimens = self.get_selected_objects()
return True
def objects_tv_selection_changed(self, selection):
ObjectListStoreController.objects_tv_selection_changed(self, selection)
self.parent.model.current_specimens = self.get_selected_objects()
return True
pass # end of class
def on_accept(dialog):
## TODO MOVE THIS (PARTIALLY?) TO THE MODEL LEVEL ##
filenames = dialog.get_filenames()
parser = dialog.get_filter().get_data("parser")
task = ThreadedTaskBox()
window = self.get_custom_dialog(task, parent=self.view.get_top_widget())
# Status:
status_dict = dict(
total_files=len(filenames),
current_file=0,
specimens=[]
)
# Task:
def load_specimens(stop=None):
for filename in filenames:
if stop is not None and stop.is_set():
return
try:
specimens = Specimen.from_experimental_data(filename=filename, parent=self.model, parser=parser)
except Exception as msg:
message = "An unexpected error has occurred when trying to parse %s:\n\n<i>" % os.path.basename(filename)
message += str(msg) + "</i>\n\n"
message += "This is most likely caused by an invalid or unsupported file format."
logger.exception(message)
@run_when_idle
def run_dialog():
self.run_information_dialog(
message=message,
parent=self.view.get_top_widget()
)
return False
run_dialog()
else:
status_dict["specimens"] += specimens
status_dict["current_file"] += 1
# Cancel & stop events:
def on_interrupted(*args, **kwargs):
window.hide()
# Status label update:
def gui_callback():
task.set_status("Loading file %d/%d ..." % (
status_dict["current_file"],
status_dict["total_files"]
))
return True
gui_timeout_id = gobject.timeout_add(250, gui_callback)
# Complete event:
@run_when_idle
def on_complete(*args, **kwargs):
last_iter = None
for specimen in status_dict["specimens"]:
last_iter = self.model.specimens.append(specimen)
if last_iter is not None:
self.view["project_specimens"].set_cursor(last_iter)
gobject.source_remove(gui_timeout_id)
window.hide()
window.destroy()
# Run task box:
task.connect("cancelrequested", on_interrupted)
task.connect("stoprequested", on_interrupted)
task.set_status("Loading ...")
task.start()
window.show_all()
# Run thread:
self.thread = CancellableThread(load_specimens, on_complete)
self.thread.start()
