def __init__(self, parent_window: Window.Window,
ui_widget: Declarative.UIDescription, ui_handler):
super().__init__(parent_window.ui,
app=parent_window.app,
parent_window=parent_window,
window_style="popup")
from nion.ui import Declarative # avoid circular reference
def request_close():
# this may be called in response to the user clicking a button to close.
# make sure that the button is not destructed as a side effect of closing
# the window by queueing the close. and it is not possible to use event loop
# here because the event loop limitations: not able to run both parent and child
# event loops simultaneously.
parent_window.queue_task(self.request_close)
# make and attach closer for the handler; put handler into container closer
self.__closer = Declarative.Closer()
if ui_handler and hasattr(ui_handler, "close"):
ui_handler._closer = Declarative.Closer()
self.__closer.push_closeable(ui_handler)
finishes: typing.List[typing.Callable[[], None]] = list()
self.widget = Declarative.construct(parent_window.ui, self, ui_widget,
ui_handler, finishes)
self.attach_widget(self.widget)
for finish in finishes:
finish()
if ui_handler and hasattr(ui_handler, "init_handler"):
ui_handler.init_handler()
if ui_handler and hasattr(ui_handler, "init_popup"):
ui_handler.init_popup(request_close)
self._create_menus()
self.__ui_handler = ui_handler
def show_file_param_dialog(self,
file_ext: str = None,
params_callback: callable = None):
if self.__file_param_dialog_closed_event.is_set():
document_controller = self.__api.application.document_controllers[
0]._document_controller
ui_handler = OpenFileDialogUI().get_ui_handler(
api_broker=PlugInManager.APIBroker(),
event_loop=document_controller.event_loop,
file_ext=file_ext,
title='File')
def dialog_closed():
self.__file_param_dialog_closed_event.set()
ui_handler.on_closed = dialog_closed
ui_handler.params_callback = params_callback
finishes = list()
dialog = Declarative.construct(document_controller.ui,
document_controller,
ui_handler.ui_view, ui_handler,
finishes)
for finish in finishes:
finish()
ui_handler._event_loop = document_controller.event_loop
if callable(getattr(ui_handler, 'init_handler', None)):
ui_handler.init_handler()
dialog.show()
ui_handler.request_close = dialog.request_close
self.__file_param_dialog_closed_event.clear()
self.__show_file_param_dialog_finished_event.set()
def calibrate_spectrum(api: API_1_0.API, window: API_1_0.DocumentWindow):
class UIHandler:
def __init__(self, data_item: API_1_0.DataItem, src_data_item: API_1_0.DataItem, offset_graphic: API_1_0.Graphic, second_graphic: API_1_0.Graphic, units='eV'):
self.ev_converter = Converter.PhysicalValueToStringConverter(units)
self.property_changed_event = Event.Event()
self.__data_item = data_item
self.__src_data_item = src_data_item
self.__offset_graphic = offset_graphic
self.__second_graphic = second_graphic
self.__offset_energy = 0
self.__graphic_updating = False
self.__second_point = data_item.display_xdata.dimensional_calibrations[0].convert_to_calibrated_value(second_graphic.position * len(data_item.display_xdata.data))
self.__offset_changed_listener = offset_graphic._graphic.property_changed_event.listen(self.__offset_graphic_changed)
self.__second_changed_listener = second_graphic._graphic.property_changed_event.listen(self.__second_graphic_changed)
def close(self):
self.__offset_changed_listener.close()
self.__offset_changed_listener = None
self.__second_changed_listener.close()
self.__second_changed_listener = None
self.__data_item = None
self.__src_data_item = None
self.__second_graphic = None
self.__offset_graphic = None
@property
def offset_energy(self):
return self.__offset_energy
@offset_energy.setter
def offset_energy(self, offset_energy):
self.__offset_energy = offset_energy
self.property_changed_event.fire("offset_energy")
self.__update_calibration(keep_scale=True)
@property
def second_point(self):
return self.__second_point
@second_point.setter
def second_point(self, energy):
self.__second_point = energy
self.property_changed_event.fire("second_point")
self.__update_calibration()
@contextlib.contextmanager
def __lock_graphic_updates(self):
self.__graphic_updating = True
try:
yield self.__graphic_updating
finally:
self.__graphic_updating = False
def __update_calibration(self, keep_scale=False):
dimensional_calibrations = copy.deepcopy(self.__data_item.display_xdata.dimensional_calibrations)
energy_calibration = dimensional_calibrations[0]
if keep_scale:
scale = energy_calibration.scale
else:
scale = (self.__second_point - self.__offset_energy) / ((self.__second_graphic.position - self.__offset_graphic.position) * len(self.__data_item.display_xdata.data))
offset = self.__offset_energy - self.__offset_graphic.position * len(self.__data_item.display_xdata.data) * scale
energy_calibration.scale = scale
energy_calibration.offset = offset
dimensional_calibrations = list(self.__src_data_item.xdata.dimensional_calibrations)
dimensional_calibrations[-1] = energy_calibration
self.__src_data_item.set_dimensional_calibrations(dimensional_calibrations)
offset_graphic_position = (self.offset_energy - offset) / scale / len(self.__data_item.display_xdata.data)
second_graphic_position = (self.second_point - offset) / scale / len(self.__data_item.display_xdata.data)
with self.__lock_graphic_updates():
self.__offset_graphic.position = min(max(0, offset_graphic_position), 0.99)
self.__second_graphic.position = min(max(0, second_graphic_position), 0.99)
def __offset_graphic_changed(self, property_name):
if not self.__graphic_updating:
self.__update_calibration(keep_scale=True)
def __second_graphic_changed(self, property_name):
if not self.__graphic_updating:
self.__update_calibration()
ui = Declarative.DeclarativeUI()
row_1 = ui.create_row(ui.create_label(text="Move the graphics in the spectrum and/or change the numbers\nin the fields below to change the calibration.\n"
"The offset graphic will be positioned on the ZLP if possible."),
margin=5, spacing=5)
row_2 = ui.create_row(ui.create_label(text="Offset Point energy"),
ui.create_line_edit(text="@binding(offset_energy, converter=ev_converter)"),
ui.create_stretch(),
margin=5, spacing=5)
row_3 = ui.create_row(ui.create_label(text="Scale Point energy"),
ui.create_line_edit(text="@binding(second_point, converter=ev_converter)"),
ui.create_stretch(),
margin=5, spacing=5)
column = ui.create_column(row_1, row_2, row_3, ui.create_stretch(), margin=5, spacing=5)
data_item: API_1_0.DataItem = window.target_data_item
class DummyHandler:
...
if data_item is None or data_item.xdata is None or not data_item.display_xdata.is_data_1d:
window.show_modeless_dialog(ui.create_modeless_dialog(ui.create_label(text=("This tool cannot be used for the selected type of data.\n"
"To use it you have to select a data item containing 1-D data or a sequence of 1-D data.")),
title="Calibrate Spectrum", margin=10),
handler=DummyHandler)
return
if data_item._data_item.is_live:
window.show_modeless_dialog(ui.create_modeless_dialog(ui.create_label(text=("This tool cannot be used on live data.\n"
"To use it you have to select a data item containing 1-D data or a sequence of 1-D data.")),
title="Calibrate Spectrum", margin=10),
handler=DummyHandler)
return
# This is the data item we will update the calibrations on. If the selected data item is the result of a pick
# computation we will update the source SI. Otherwise we just update the spectrum itself.
src_data_item = data_item
for computation in api.library._document_model.computations:
if computation.processing_id in {"pick-point", "pick-mask-average", "pick-mask-sum"}:
if computation.get_output("target") == data_item._data_item:
input_ = computation.get_input("src")
# If input_ is a "DataSource" we need to get the actual data item
if hasattr(input_, "data_item"):
input_ = input_.data_item
src_data_item = api._new_api_object(input_)
mx_pos = numpy.nan
try:
mx_pos = ZLP_Analysis.estimate_zlp_amplitude_position_width_fit_spline(data_item.display_xdata.data)[1]
except TypeError:
pass
# fallback to com if fit failed
if mx_pos is numpy.nan:
mx_pos = ZLP_Analysis.estimate_zlp_amplitude_position_width_com(data_item.display_xdata.data)[1]
# fallback to simple max if everything else failed
if mx_pos is numpy.nan:
mx_pos = float(numpy.argmax(data_item.display_xdata.data))
# We need to move the detected maximum by half a pixel because we want to center the calibration and the graphic
# on the pixel center but the maximum is calculated for the left edge.
mx_pos += 0.5
dimensional_calibrations = list(data_item.display_xdata.dimensional_calibrations)
energy_calibration = dimensional_calibrations[0]
energy_calibration.offset = -mx_pos * energy_calibration.scale
dimensional_calibrations = list(src_data_item.xdata.dimensional_calibrations)
dimensional_calibrations[-1] = energy_calibration
src_data_item.set_dimensional_calibrations(dimensional_calibrations)
offset_graphic = data_item.add_channel_region(mx_pos / len(data_item.display_xdata.data))
offset_graphic.label = "Offset Point"
offset_graphic._graphic.color = "#CE00AC"
second_graphic = data_item.add_channel_region((offset_graphic.position + 1.0) * 0.5)
second_graphic.label = "Scale Point"
second_graphic._graphic.color = "#CE00AC"
handler = UIHandler(data_item, src_data_item, offset_graphic, second_graphic, units=energy_calibration.units)
dialog = typing.cast(Dialog.ActionDialog,
Declarative.construct(window._document_controller.ui, window._document_controller,
ui.create_modeless_dialog(column, title="Calibrate Spectrum"), handler))
def wc(w):
data_item.remove_region(offset_graphic)
data_item.remove_region(second_graphic)
getattr(handler, "configuration_dialog_close_listener").close()
delattr(handler, "configuration_dialog_close_listener")
# use set handler to pass type checking.
setattr(handler, "configuration_dialog_close_listener", dialog._window_close_event.listen(wc))
dialog.show()
# Return the dialog which is useful for testing
return dialog