def create_and_display_data_item(library, data_and_metadata, scan_data_list, scan_hardware_source, camera_hardware_source):
camera_hardware_source_id = camera_hardware_source._hardware_source.hardware_source_id
# data_item = library.get_data_item_for_hardware_source(scan_hardware_source, channel_id=camera_hardware_source_id, processor_id="summed", create_if_needed=True, large_format=True)
data_item = Facade.DataItem(DataItem.DataItem(large_format=True))
library._document_model.append_data_item(data_item._data_item)
data_item._data_item.session_id = library._document_model.session_id
data_item.title = _("Spectrum Image {}".format(" x ".join([str(d) for d in data_and_metadata.dimensional_shape])))
# the data item should not have any other 'clients' at this point; so setting the
# data and metadata will immediately unload the data (and write to disk). this is important,
# because the data (up to this point) can be shared data from the DLL.
data_item.set_data_and_metadata(data_and_metadata)
# assert not data_item._data_item.is_data_loaded
# now to display it will reload the data (presumably from an HDF5 or similar on-demand format).
document_window.display_data_item(data_item)
for scan_data_and_metadata in scan_data_list:
scan_channel_id = scan_data_and_metadata.metadata["hardware_source"]["channel_id"]
scan_channel_name = scan_data_and_metadata.metadata["hardware_source"]["channel_name"]
channel_id = camera_hardware_source_id + "_" + scan_channel_id
# data_item = library.get_data_item_for_hardware_source(scan_hardware_source, channel_id=channel_id, create_if_needed=True)
data_item = Facade.DataItem(DataItem.DataItem())
library._document_model.append_data_item(data_item._data_item)
data_item._data_item.session_id = library._document_model.session_id
data_item.title = "{} ({})".format(_("Spectrum Image"), scan_channel_name)
data_item.set_data_and_metadata(scan_data_and_metadata)
document_window.display_data_item(data_item)
def init():
document_controller = self.__api.application.document_controllers[
0]._document_controller
computation_data_items = document_controller.ui.get_persistent_string(
'libertem_map4d_data_items_0')
self.__computation_data_items = json.loads(
computation_data_items) if computation_data_items else dict()
self.__tool_tip_boxes = list()
document_model = self.__api.application._application.document_model
for computation in document_model.computations:
src = computation.get_input('src')
if src and self.__computation_data_items.get(str(
src.uuid)) == 'source':
target = computation.get_output('target')
if target is None:
continue
target_api = Facade.DataItem(target)
pick_graphic = None
for graphic in target_api.graphics:
if graphic.label == 'Pick':
pick_graphic = graphic
break
if pick_graphic is not None:
self.__connect_pick_graphic(Facade.DataItem(src),
target_api, pick_graphic,
computation)
self.__display_item_changed_event_listener = (
document_controller.focused_display_item_changed_event.listen(
self.__display_item_changed))
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
selected_display_item = document_controller.selected_display_item
data_item = (selected_display_item.data_items[0] if
selected_display_item and len(selected_display_item.data_items) > 0 else None)
if data_item:
api_data_item = Facade.DataItem(data_item)
if not api_data_item.xdata.is_data_4d:
self.__show_tool_tips('wrong_shape')
return
total_bin_data_item = self.__api.library.create_data_item(title='Total bin 4D of ' + data_item.title)
computation = self.__api.library.create_computation('nion.total_bin_4d_SI',
inputs={'src': api_data_item},
outputs={'target': total_bin_data_item})
computation._computation.source = total_bin_data_item._data_item
#computation._computation.mark_update()
total_bin_display_item = document_controller.document_model.get_display_item_for_data_item(
total_bin_data_item._data_item)
document_controller.show_display_item(total_bin_display_item)
dark_subtract_area_graphic = total_bin_data_item.add_rectangle_region(0.8, 0.5, 0.4, 1.0)
dark_subtract_area_graphic.label = 'Dark subtract area'
crop_region = api_data_item.add_rectangle_region(0.5, 0.5, 1.0, 1.0)
crop_region.label = 'Crop'
dark_subtract_area_graphic._graphic.is_bounds_constrained = True
crop_region._graphic.is_bounds_constrained = True
dark_corrected_data_item = Facade.DataItem(DataItem.DataItem(large_format=True))
self.__api.library._document_model.append_data_item(dark_corrected_data_item._data_item)
dark_corrected_data_item._data_item.session_id = self.__api.library._document_model.session_id
dark_corrected_data_item.title = '4D dark correction of ' + data_item.title
computation = self.__api.library.create_computation('nion.dark_correction_4d',
inputs={'src1': api_data_item,
'src2': total_bin_data_item,
'dark_area_region': dark_subtract_area_graphic,
'crop_region': crop_region,
'bin_spectrum': True,
'gain_image': [],
'gain_mode': 'custom'},
outputs={'target': dark_corrected_data_item})
computation._computation.source = dark_corrected_data_item._data_item
dark_corrected_display_item = document_controller.document_model.get_display_item_for_data_item(
dark_corrected_data_item._data_item)
document_controller.show_display_item(dark_corrected_display_item)
self.__computation_data_items.update({data_item: 'source',
total_bin_data_item._data_item: 'total bin',
dark_corrected_data_item._data_item: 'corrected'})
self.__show_tool_tips()
self.__display_item_changed_event_listener = (
document_controller.focused_display_item_changed_event.listen(self.__display_item_changed))
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
display_item = document_controller.selected_display_item
data_item = display_item.data_items[0] if display_item and len(
display_item.data_items) > 0 else None
if not data_item:
return
api_data_item = Facade.DataItem(data_item)
if api_data_item.xdata.is_sequence and api_data_item.xdata.datum_dimension_count == 2:
result_data_item = {
"output":
self.__api.library.create_data_item(
title="Color COM image of " + data_item.title)
}
self.__api.library.create_computation("nion.make_color_com",
inputs={
"src": api_data_item,
"com_x_index": 0,
"com_y_index": 1,
"magnitude_min": 0,
"magnitude_max": 100,
"rotation": "None"
},
outputs=result_data_item)
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
selected_display_items = document_controller.selected_display_items
data_items = list()
# Check if it makes sense to copy display properties from the source to the result display item.
# For line plots with multiple display layers we want to copy the display properties so that the joined item
# look like the original display items. We copy the display properties of the first display item, but only
# if the number of display layers is the same for all input display items.
display_layers = None
legend_position = None
display_type = None
copy_display_properties = False
for i, display_item in enumerate(selected_display_items):
data_item = display_item.data_items[0] if display_item and len(
display_item.data_items) > 0 else None
if data_item:
data_items.append(data_item)
if (len(display_item.data_items) == 1
and len(data_item.data_shape) > 1
and (data_item.xdata.datum_dimension_count == 1
or display_item.display_type == 'line_plot')):
if i == 0:
display_layers = copy.deepcopy(
display_item.display_layers)
legend_position = display_item.get_display_property(
'legend_position')
display_type = display_item.display_type
copy_display_properties = True
elif display_layers is not None:
copy_display_properties &= len(display_layers) == len(
display_item.display_layers)
if not data_items:
return
api_data_items = [
Facade.DataItem(data_item) for data_item in data_items
]
result_data_item = self.__api.library.create_data_item(
title="Joined " + data_items[0].title)
computation = self.__api.library.create_computation(
"nion.join_sequence",
inputs={"src_list": api_data_items},
outputs={"target": result_data_item})
computation._computation.source = result_data_item._data_item
result_display_item = document_controller.document_model.get_display_item_for_data_item(
result_data_item._data_item)
document_controller.show_display_item(result_display_item)
if copy_display_properties:
if display_layers is not None:
result_display_item.display_layers = display_layers
if legend_position is not None:
result_display_item.set_display_property(
'legend_position', legend_position)
if display_type is not None:
result_display_item.display_type = display_type
def menu_item_execute(self, window: API.DocumentWindow) -> None:
try:
document_controller = window._document_controller
display_specifier = document_controller.selected_display_specifier
if display_specifier.data_item:
average_data_item = document_controller.document_model.make_data_item_with_computation(
"nion.calculate_4d_average", [(display_specifier.data_item, None)],
{'src': []})
new_display_specifier = DataItem.DisplaySpecifier.from_data_item(average_data_item)
document_controller.display_data_item(new_display_specifier)
api_average_data_item = Facade.DataItem(average_data_item)
spectrum_graphic = api_average_data_item.add_rectangle_region(0.5, 0.5, 0.1, 1.0)
spectrum_graphic.label = 'Spectrum'
bottom_dark_graphic = api_average_data_item.add_rectangle_region(0.7, 0.5, 0.1, 1.0)
bottom_dark_graphic.label = 'Bottom dark area'
top_dark_graphic = api_average_data_item.add_rectangle_region(0.3, 0.5, 0.1, 1.0)
top_dark_graphic.label = 'Top dark area'
dark_corrected_data_item = document_controller.document_model.make_data_item_with_computation(
"nion.framewise_dark_correction", [(display_specifier.data_item, None), (average_data_item, None)],
{"src1": [], "src2": [spectrum_graphic._graphic, top_dark_graphic._graphic, bottom_dark_graphic._graphic]})
new_display_specifier2 = DataItem.DisplaySpecifier.from_data_item(dark_corrected_data_item)
document_controller.display_data_item(new_display_specifier2)
spectrum_graphic._graphic.is_bounds_constrained = True
bottom_dark_graphic._graphic.is_bounds_constrained = True
top_dark_graphic._graphic.is_bounds_constrained = True
except Exception as e:
print(e)
raise
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
selected_display_item = document_controller.selected_display_item
data_item = (selected_display_item.data_items[0]
if selected_display_item
and len(selected_display_item.data_items) > 0 else None)
if data_item:
api_data_item = Facade.DataItem(data_item)
if not api_data_item.xdata.metadata.get('libertem-io'):
self.__show_tool_tips('wrong_shape')
return
map_data_item = self.__api.library.create_data_item(
title='Map 4D of ' + data_item.title)
display_item = document_controller.document_model.get_display_item_for_data_item(
map_data_item._data_item)
show_display_item(window, display_item)
map_regions = list()
for graphic in api_data_item.graphics:
if graphic._graphic.role == 'mask':
map_regions.append(graphic)
computation = self.__api.library.create_computation(
'nion.libertem.map_4d',
inputs={
'src': api_data_item,
'map_regions': map_regions
},
outputs={'target': map_data_item})
computation._computation.source = data_item
map_display_item = document_controller.document_model.get_display_item_for_data_item(
map_data_item)
document_controller.show_display_item(map_display_item)
pick_graphic = map_data_item.add_point_region(0.5, 0.5)
pick_graphic.label = 'Pick'
self.__connect_pick_graphic(api_data_item, map_data_item,
pick_graphic, computation._computation)
# def collection_index_changed(key):
# if key == 'collection_index':
# collection_index = selected_display_item.display_data_channel.collection_index
# if int(pick_graphic.position[0]*data_item.data.shape[0]) != collection_index[0]:
# computation.pick_graphic_binding_0.update_source(collection_index)
# if int(pick_graphic.position[1]*data_item.data.shape[1]) != collection_index[1]:
# computation.pick_graphic_binding_1.update_source(collection_index)
#computation.collection_index_changed_event_listener = selected_display_item.display_data_channel.property_changed_event.listen(collection_index_changed)
self.__computation_data_items.update({
str(data_item.uuid):
'source',
str(map_data_item._data_item.uuid):
'map_4d'
})
self.__api.application.document_controllers[
0]._document_controller.ui.set_persistent_string(
'libertem_map4d_data_items_0',
json.dumps(self.__computation_data_items))
self.__show_tool_tips()
def map_thickness(api, window):
target_display = window.target_display
target_data_item_ = target_display._display_item.data_items[0] if target_display and len(target_display._display_item.data_items) > 0 else None
if target_data_item_ and target_display:
spectrum_image = Facade.DataItem(target_data_item_)
map = api.library.create_data_item_from_data(numpy.zeros_like(spectrum_image.display_xdata.data), title="{} Thickness Map".format(spectrum_image.title))
computation = api.library.create_computation("eels.thickness_mapping", inputs={"spectrum_image_data_item": spectrum_image}, outputs={"map": map})
computation._computation.source = spectrum_image._data_item
window.display_data_item(map)
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
display_item = document_controller.selected_display_item
data_item = display_item.data_items[0] if display_item and len(
display_item.data_items) > 0 else None
if not data_item:
return
# Check if it makes sense to copy display properties from the source to the result display item.
# For line plots with multiple display layers we want to copy the display properties so that the split items
# look like the original display item. Exclude case where the display layers are generated from the sequence
# dimension because in this case the display layers are not valid anymore.
display_layers = None
legend_position = None
display_type = None
if (len(display_item.data_items) == 1 and len(data_item.data_shape) > 2
and (data_item.xdata.datum_dimension_count == 1
or display_item.display_type == 'line_plot')):
display_layers = copy.deepcopy(display_item.display_layers)
legend_position = display_item.get_display_property(
'legend_position')
display_type = display_item.display_type
api_data_item = Facade.DataItem(data_item)
if api_data_item.xdata.is_sequence:
if api_data_item.xdata.data_shape[0] > 100:
logging.error(
"Splitting sequences of more than 100 items is disabled for performance reasons."
)
return
result_data_items = {
f"target_{i}":
self.__api.library.create_data_item(title=f"Split ({i}) of " +
data_item.title)
for i in range(api_data_item.xdata.data_shape[0])
}
computation = self.__api.library.create_computation(
"nion.split_sequence",
inputs={"src": api_data_item},
outputs=result_data_items)
computation._computation.source = result_data_items[
"target_0"]._data_item
for result_data_item in result_data_items.values():
result_display_item = document_controller.document_model.get_display_item_for_data_item(
result_data_item._data_item)
document_controller.show_display_item(result_display_item)
if display_layers is not None:
result_display_item.display_layers = display_layers
if legend_position is not None:
result_display_item.set_display_property(
'legend_position', legend_position)
if display_type is not None:
result_display_item.display_type = display_type
def menu_item_execute(self, window: API.DocumentWindow) -> None:
try:
document_controller = window._document_controller
display_specifier = document_controller.selected_display_specifier
if display_specifier.data_item:
total_bin_data_item = document_controller.document_model.make_data_item_with_computation(
"nion.total_bin_4d_SI",
[(display_specifier.data_item, None)], {'src': []})
new_display_specifier = DataItem.DisplaySpecifier.from_data_item(
total_bin_data_item)
document_controller.display_data_item(new_display_specifier)
api_total_bin_data_item = Facade.DataItem(total_bin_data_item)
api_data_item = Facade.DataItem(display_specifier.data_item)
dark_subtract_area_graphic = api_total_bin_data_item.add_rectangle_region(
0.8, 0.5, 0.4, 1.0)
dark_subtract_area_graphic.label = 'Dark subtract area'
crop_region = api_data_item.add_rectangle_region(
0.5, 0.5, 1.0, 1.0)
crop_region.label = 'Crop'
dark_corrected_data_item = document_controller.document_model.make_data_item_with_computation(
"nion.4d_dark_correction",
[(display_specifier.data_item, None),
(total_bin_data_item, None)], {
"src1": [crop_region._graphic],
"src2": [dark_subtract_area_graphic._graphic]
})
new_display_specifier2 = DataItem.DisplaySpecifier.from_data_item(
dark_corrected_data_item)
document_controller.display_data_item(new_display_specifier2)
dark_subtract_area_graphic._graphic.is_bounds_constrained = True
crop_region._graphic.is_bounds_constrained = True
except Exception as e:
print(e)
raise
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
selected_display_item = document_controller.selected_display_item
data_item = (selected_display_item.data_items[0]
if selected_display_item
and len(selected_display_item.data_items) > 0 else None)
if data_item:
api_data_item = Facade.DataItem(data_item)
if not api_data_item.xdata.is_data_4d:
self.__show_tool_tips('wrong_shape')
return
map_data_item = self.__api.library.create_data_item(
title='Map 4D of ' + data_item.title)
# the following uses internal API and should not be used as example code.
computation = document_controller.document_model.create_computation(
)
computation.create_input_item(
"src",
Symbolic.make_item(
selected_display_item.
get_display_data_channel_for_data_item(data_item)))
computation.create_input_item("map_regions",
Symbolic.make_item_list([]))
computation.processing_id = "nion.map_4d.2"
document_controller.document_model.set_data_item_computation(
map_data_item._data_item, computation)
map_display_item = document_controller.document_model.get_display_item_for_data_item(
map_data_item._data_item)
document_controller.show_display_item(map_display_item)
graphic = Graphics.PointGraphic()
graphic.label = "Pick"
graphic.role = "collection_index"
map_display_item.add_graphic(graphic)
# see note above.
self.__computation_data_items.update({
str(data_item.uuid):
'source',
str(map_data_item._data_item.uuid):
'map_4d'
})
self.__show_tool_tips()
self.__display_item_changed_event_listener = (
document_controller.focused_display_item_changed_event.listen(
self.__display_item_changed))
def select_button_clicked():
graphics = Facade.DataItem(
self.computation._computation.source).graphics
if not graphics:
return
graphics_variable = self.computation._computation._get_variable(
'map_regions')
graphics_variable.disconnect_items()
if graphics_variable.bound_items_model is None:
return
num_items = len(graphics_variable.bound_items_model.items)
for _ in range(num_items):
self.computation._computation.remove_item_from_objects(
'map_regions', 0)
for graphic in graphics:
if graphic._graphic.role == 'mask':
self.computation._computation.insert_item_into_objects(
'map_regions', 0,
Symbolic.make_item(graphic._graphic,
type='graphic'))
def create_and_display_data_item(document_window, data_and_metadata: DataAndMetadata.DataAndMetadata) -> None:
# create the data item; large format if it's a collection
data_item = Facade.DataItem(DataItem.DataItem(large_format=data_and_metadata.is_collection))
document_window.library._document_model.append_data_item(data_item._data_item)
# update the session id
data_item._data_item.session_id = document_window.library._document_model.session_id
# set the title
channel_name = data_and_metadata.metadata.get("hardware_source", dict()).get("channel_name", data_and_metadata.metadata.get("hardware_source", dict()).get("hardware_source_name", "Data"))
dimension_str = (" " + " x ".join([str(d) for d in data_and_metadata.collection_dimension_shape])) if data_and_metadata.is_collection else str()
data_item.title = f"{title_base}{dimension_str} ({channel_name})"
# if the last dimension is 1, squeeze the data (1D SI)
if data_and_metadata.data_shape[0] == 1:
data_and_metadata = xd.squeeze(data_and_metadata)
# the data item should not have any other 'clients' at this point; so setting the
# data and metadata will immediately unload the data (and write to disk). this is important,
# because the data (up to this point) can be shared data from the DLL.
data_item.set_data_and_metadata(data_and_metadata)
# now to display it will reload the data (presumably from an HDF5 or similar on-demand format).
document_window.display_data_item(data_item)
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
display_item = document_controller.selected_display_item
data_item = display_item.data_items[0] if display_item and len(
display_item.data_items) > 0 else None
if not data_item:
return
api_data_item = Facade.DataItem(data_item)
if api_data_item.xdata.is_sequence and api_data_item.xdata.datum_dimension_count == 2:
result_data_item = {
"output":
self.__api.library.create_data_item(title="iDPC of " +
data_item.title)
}
self.__api.library.create_computation("nion.make_idpc",
inputs={
"src": api_data_item,
"gradient_x_index": 0,
"gradient_y_index": 1
},
outputs=result_data_item)
def start(self, processing: ScanAcquisitionProcessing) -> None:
document_window = self.__document_controller
scan_hardware_source = typing.cast(scan_base.ScanHardwareSource, self.__scan_hardware_source._hardware_source)
scan_frame_parameters = scan_hardware_source.get_frame_parameters(2)
scan_hardware_source.apply_scan_context_subscan(scan_frame_parameters, self.__scan_specifier.size)
scan_frame_parameters["scan_id"] = str(uuid.uuid4())
# useful code for testing to exit cleanly at this point.
# self.acquisition_state_changed_event.fire(SequenceState.scanning)
# self.acquisition_state_changed_event.fire(SequenceState.idle)
# return
camera_hardware_source = typing.cast(camera_base.CameraHardwareSource, self.__camera_hardware_source._hardware_source)
camera_frame_parameters = camera_hardware_source.get_frame_parameters(0)
camera_frame_parameters["processing"] = processing.value.processing_id
grab_sync_info = scan_hardware_source.grab_synchronized_get_info(
scan_frame_parameters=scan_frame_parameters,
camera=camera_hardware_source,
camera_frame_parameters=camera_frame_parameters)
camera_data_channel = CameraDataChannel(self.__document_controller.library._document_model, camera_hardware_source.display_name, grab_sync_info)
self.__document_controller.display_data_item(Facade.DataItem(camera_data_channel.data_item))
camera_data_channel.start()
drift_correction_behavior : typing.Optional[DriftCorrectionBehavior] = None
section_height = None
if self.__scan_specifier.drift_interval_lines > 0:
drift_correction_behavior = DriftCorrectionBehavior(document_window.library._document_model, scan_hardware_source, scan_frame_parameters)
section_height = self.__scan_specifier.drift_interval_lines
def grab_synchronized():
self.acquisition_state_changed_event.fire(SequenceState.scanning)
try:
combined_data = scan_hardware_source.grab_synchronized(scan_frame_parameters=scan_frame_parameters,
camera=camera_hardware_source,
camera_frame_parameters=camera_frame_parameters,
camera_data_channel=camera_data_channel,
scan_behavior=drift_correction_behavior,
section_height=section_height)
if combined_data is not None:
scan_data_list, camera_data_list = combined_data
def create_and_display_data_item_task():
# this will be executed in UI thread
for data_and_metadata in scan_data_list:
create_and_display_data_item(document_window, data_and_metadata)
# queue the task to be executed in UI thread
document_window.queue_task(create_and_display_data_item_task)
finally:
def stop_channel():
camera_data_channel.stop()
document_window.queue_task(stop_channel)
self.acquisition_state_changed_event.fire(SequenceState.idle)
self.__thread = threading.Thread(target=grab_synchronized)
self.__thread.start()
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
selected_display_item = document_controller.selected_display_item
data_item = (selected_display_item.data_items[0]
if selected_display_item
and len(selected_display_item.data_items) > 0 else None)
if data_item:
api_data_item = Facade.DataItem(data_item)
if not api_data_item.xdata.is_data_4d:
self.__show_tool_tips('wrong_shape')
return
average_data_item = self.__api.library.create_data_item(
title='Frame average of ' + data_item.title)
computation = self.__api.library.create_computation(
'nion.calculate_4d_average',
inputs={'src': api_data_item},
outputs={'target': average_data_item})
computation._computation.source = average_data_item._data_item
average_display_item = document_controller.document_model.get_display_item_for_data_item(
average_data_item._data_item)
document_controller.show_display_item(average_display_item)
spectrum_graphic = average_data_item.add_rectangle_region(
0.5, 0.5, 0.1, 1.0)
spectrum_graphic.label = 'Spectrum'
bottom_dark_graphic = average_data_item.add_rectangle_region(
0.7, 0.5, 0.1, 1.0)
bottom_dark_graphic.label = 'Bottom dark area'
top_dark_graphic = average_data_item.add_rectangle_region(
0.3, 0.5, 0.1, 1.0)
top_dark_graphic.label = 'Top dark area'
spectrum_graphic._graphic.is_bounds_constrained = True
bottom_dark_graphic._graphic.is_bounds_constrained = True
top_dark_graphic._graphic.is_bounds_constrained = True
dark_corrected_data_item = Facade.DataItem(
DataItem.DataItem(large_format=True))
self.__api.library._document_model.append_data_item(
dark_corrected_data_item._data_item)
dark_corrected_data_item._data_item.session_id = self.__api.library._document_model.session_id
dark_corrected_data_item.title = 'Framewise dark correction of ' + data_item.title
computation = self.__api.library.create_computation(
'nion.framewise_dark_correction',
inputs={
'src1': api_data_item,
'src2': average_data_item,
'spectrum_region': spectrum_graphic,
'top_dark_region': top_dark_graphic,
'bottom_dark_region': bottom_dark_graphic,
'bin_spectrum': True,
'gain_image': [],
'gain_mode': 'custom'
},
outputs={'target': dark_corrected_data_item})
computation._computation.source = dark_corrected_data_item._data_item
dark_corrected_display_item = document_controller.document_model.get_display_item_for_data_item(
dark_corrected_data_item._data_item)
document_controller.show_display_item(dark_corrected_display_item)
self.__computation_data_items.update({
data_item:
'source',
average_data_item._data_item:
'average',
dark_corrected_data_item._data_item:
'corrected'
})
self.__show_tool_tips()
self.__display_item_changed_event_listener = (
document_controller.focused_display_item_changed_event.listen(
self.__display_item_changed))
def menu_item_execute(self, window: API.DocumentWindow) -> None:
document_controller = window._document_controller
selected_display_item = document_controller.selected_display_item
data_item = (selected_display_item.data_items[0]
if selected_display_item
and len(selected_display_item.data_items) > 0 else None)
if data_item:
api_data_item = Facade.DataItem(data_item)
ds = None
if not api_data_item.xdata.metadata.get('libertem-io'):
executor = Registry.get_component('libertem_executor')
if not executor:
return
ds = LiberTEMAdapter(
self.__api,
executor).niondata_to_libertemdata(api_data_item)
if not api_data_item.xdata.metadata.get('libertem-io'):
self.__show_tool_tips('wrong_shape')
return
map_data_item = self.__api.library.create_data_item(
title='Map 4D of ' + data_item.title)
display_item = document_controller.document_model.get_display_item_for_data_item(
map_data_item._data_item)
show_display_item(window, display_item)
map_regions = list()
for graphic in api_data_item.graphics:
if graphic._graphic.role == 'mask':
map_regions.append(graphic)
computation = self.__api.library.create_computation(
'nion.libertem.map_4d',
inputs={
'src': api_data_item,
'map_regions': map_regions
},
outputs={'target': map_data_item})
computation._computation.source = data_item
if ds is not None:
computation._computation.ds = ds
map_display_item = document_controller.document_model.get_display_item_for_data_item(
map_data_item)
document_controller.show_display_item(map_display_item)
pick_graphic = map_data_item.add_point_region(0.5, 0.5)
pick_graphic.label = 'Pick'
threading.Thread(target=self.__connect_pick_graphic,
args=(api_data_item, map_data_item, pick_graphic,
computation._computation, 30),
daemon=True).start()
self.__computation_data_items.update({
str(data_item.uuid):
'source',
str(map_data_item._data_item.uuid):
'map_4d'
})
self.__api.application.document_controllers[
0]._document_controller.ui.set_persistent_string(
'libertem_map4d_data_items_0',
json.dumps(self.__computation_data_items))
self.__show_tool_tips()
def display_data_item(
document_controller: DocumentController.DocumentController,
data_item: DataItem.DataItem) -> None:
Facade.DocumentWindow(document_controller).display_data_item(
Facade.DataItem(data_item))
