def test_picking_edge_produces_properly_configured_composite(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
model_display_item = document_model.get_display_item_for_data_item(
model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].pick_action()
self.__run_until_complete(document_controller)
self.assertEqual(2, len(document_model.data_items))
eels_data_item = document_model.data_items[1]
self.assertEqual(model_display_item.graphics[0],
eels_data_item.source)
self.assertEqual(eels_data_item,
document_model.data_structures[1].source)
self.assertEqual("elemental_mapping_edge_ref",
document_model.data_structures[1].structure_type)
self.assertEqual(
document_model.data_structures[0],
document_model.data_structures[1].get_referenced_object(
"edge"))
def test_multiprofile_of_two_maps_builds_two_line_profiles(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].map_action()
self.__run_until_complete(document_controller)
edge_bundle[1].map_action()
self.__run_until_complete(document_controller)
self.assertEqual(3, len(document_model.data_items))
elemental_mapping_controller.build_multiprofile(
document_controller)
self.assertEqual(5, len(document_model.data_items))
self.assertEqual(6, len(document_model.display_items))
composite_display_item = document_model.display_items[3]
line_profile1_data_item = document_model.data_items[3]
line_profile2_data_item = document_model.data_items[4]
self.assertIn(line_profile1_data_item,
composite_display_item.data_items)
self.assertIn(line_profile2_data_item,
composite_display_item.data_items)
def test_deleting_pick_region_also_deletes_pick_composition(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
model_display_item = document_model.get_display_item_for_data_item(
model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].pick_action()
self.__run_until_complete(document_controller)
pick_region = model_display_item.graphics[0]
eels_data_item = document_model.data_items[1]
self.assertEqual(1, len(document_model.computations))
self.assertEqual(2, len(document_model.data_items))
self.assertEqual(2, len(document_model.data_structures))
model_display_item.remove_graphic(pick_region)
self.assertEqual(0, len(document_model.computations))
self.assertEqual(1, len(document_model.data_items))
self.assertEqual(1, len(document_model.data_structures))
def test_deleting_pick_region_also_deletes_pick_composition(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
model_display_item = document_model.get_display_item_for_data_item(
model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].pick_action()
self.__run_until_complete(document_controller)
pick_region = model_display_item.graphics[0]
eels_data_item = document_model.data_items[1]
self.assertEqual(1, len(document_model.computations))
self.assertEqual(2, len(document_model.data_items))
self.assertEqual(2, len(document_model.data_structures))
model_display_item.remove_graphic(pick_region)
self.assertEqual(0, len(document_model.computations))
self.assertEqual(1, len(document_model.data_items))
self.assertEqual(1, len(document_model.data_structures))
def test_multiprofile_of_two_maps_builds_two_line_profiles(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].map_action()
self.__run_until_complete(document_controller)
edge_bundle[1].map_action()
self.__run_until_complete(document_controller)
self.assertEqual(3, len(document_model.data_items))
elemental_mapping_controller.build_multiprofile(
document_controller)
self.assertEqual(5, len(document_model.data_items))
self.assertEqual(6, len(document_model.display_items))
composite_display_item = document_model.display_items[3]
line_profile1_data_item = document_model.data_items[3]
line_profile2_data_item = document_model.data_items[4]
self.assertIn(line_profile1_data_item,
composite_display_item.data_items)
self.assertIn(line_profile2_data_item,
composite_display_item.data_items)
def test_multiprofile_of_two_maps_connects_line_profiles(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].map_action()
self.__run_until_complete(document_controller)
edge_bundle[1].map_action()
self.__run_until_complete(document_controller)
elemental_mapping_controller.build_multiprofile(
document_controller)
map1_display_item = document_model.get_display_item_for_data_item(
document_model.data_items[1])
map2_display_item = document_model.get_display_item_for_data_item(
document_model.data_items[2])
# composite_data_item = document_model.data_items[3]
# line_profile1_data_item = document_model.data_items[4]
# line_profile2_data_item = document_model.data_items[5]
line_region1 = map1_display_item.graphics[0]
line_region2 = map2_display_item.graphics[0]
self.assertEqual(line_region1.vector, line_region2.vector)
self.assertEqual(line_region1.width, line_region2.width)
line_region1.vector = (0.11, 0.12), (0.21, 0.22)
self.assertEqual(line_region1.vector, line_region2.vector)
self.assertEqual(line_region1.width, line_region2.width)
def test_mapping_edge_produces_properly_configured_map(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].map_action()
self.__run_until_complete(document_controller)
self.assertEqual(2, len(document_model.data_items))
mapped_data_item = document_model.data_items[1]
self.assertEqual(model_data_item, mapped_data_item.source)
self.assertEqual(1, len(document_model.computations))
self.assertEqual("eels.mapping",
document_model.computations[0].processing_id)
self.assertEqual(mapped_data_item.dimensional_calibrations,
model_data_item.dimensional_calibrations[0:2])
def __create_edge(self, model_data_item: DataItem.DataItem,
electron_shell: PeriodicTable.ElectronShell):
binding_energy_eV = PeriodicTable.PeriodicTable(
).nominal_binding_energy_ev(electron_shell)
signal_interval_eV = binding_energy_eV, binding_energy_eV * 1.10
fit_interval_eV = binding_energy_eV * 0.93, binding_energy_eV * 0.98
dimensional_shape = model_data_item.dimensional_shape
dimensional_calibrations = model_data_item.dimensional_calibrations
if dimensional_shape is not None and dimensional_calibrations is not None and len(
dimensional_calibrations) > 0:
calibration = dimensional_calibrations[-1]
if calibration.units == "eV":
fit_region_start = calibration.convert_from_calibrated_value(
fit_interval_eV[0]) / dimensional_shape[-1]
fit_region_end = calibration.convert_from_calibrated_value(
fit_interval_eV[1]) / dimensional_shape[-1]
signal_region_start = calibration.convert_from_calibrated_value(
signal_interval_eV[0]) / dimensional_shape[-1]
signal_region_end = calibration.convert_from_calibrated_value(
signal_interval_eV[1]) / dimensional_shape[-1]
fit_interval = fit_region_start, fit_region_end
signal_interval = signal_region_start, signal_region_end
return ElementalMappingController.ElementalMappingEdge(
electron_shell=electron_shell,
fit_interval=fit_interval,
signal_interval=signal_interval)
return None
def test_adding_multiple_edges(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
self.assertEqual(2, len(document_model.data_structures))
def test_explore_adds_edge(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
document_controller.event_loop.create_task(
elemental_mapping_controller.explore_edges(
document_controller))
document_controller.periodic() # start tasks
document_model.recompute_all()
document_controller.periodic() # finish tasks
explorer_data_item = document_model.data_items[1]
explorer_display_item = document_model.get_display_item_for_data_item(
explorer_data_item)
elemental_mapping_controller.set_current_data_item(
explorer_data_item)
self.assertIsNotNone(elemental_mapping_controller.model_data_item)
energy_calibration = explorer_data_item.dimensional_calibrations[
-1]
explorer_display_item.graphics[
-1].interval = energy_calibration.convert_from_calibrated_value(
1200
) / 1024, energy_calibration.convert_from_calibrated_value(
1226) / 1024
for _ in range(3):
# there is something funny about how async works; recent versions of Swift are faster
# and have revealed some race condition about how items get added to the async queue.
# to avoid that problem, do periodic over a period of a few ms.
document_controller.periodic() # update explorer interval
time.sleep(0.01)
edges = PeriodicTable.PeriodicTable(
).find_edges_in_energy_interval(
elemental_mapping_controller.explorer_interval)
elemental_mapping_controller.add_edge(edges[0])
self.assertEqual(1, len(document_model.data_structures))
edge_data_struct = document_model.data_structures[0]
self.assertEqual("elemental_mapping_edge",
edge_data_struct.structure_type)
self.assertEqual(model_data_item, edge_data_struct.source)
self.assertEqual(
32, edge_data_struct.get_property_value("atomic_number"))
self.assertEqual(
2, edge_data_struct.get_property_value("shell_number"))
self.assertEqual(
3, edge_data_struct.get_property_value("subshell_index"))
def test_adding_multiple_edges(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
self.assertEqual(2, len(document_model.data_structures))
def test_explore_adds_edge(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
document_controller.event_loop.create_task(
elemental_mapping_controller.explore_edges(
document_controller))
document_controller.periodic() # start tasks
document_model.recompute_all()
document_controller.periodic() # finish tasks
explorer_data_item = document_model.data_items[1]
explorer_display_item = document_model.get_display_item_for_data_item(
explorer_data_item)
elemental_mapping_controller.set_current_data_item(
explorer_data_item)
self.assertIsNotNone(elemental_mapping_controller.model_data_item)
energy_calibration = explorer_data_item.dimensional_calibrations[
-1]
explorer_display_item.graphics[
-1].interval = energy_calibration.convert_from_calibrated_value(
1200
) / 1024, energy_calibration.convert_from_calibrated_value(
1226) / 1024
document_controller.periodic() # update explorer interval
edges = PeriodicTable.PeriodicTable(
).find_edges_in_energy_interval(
elemental_mapping_controller.explorer_interval)
elemental_mapping_controller.add_edge(edges[0])
self.assertEqual(1, len(document_model.data_structures))
edge_data_struct = document_model.data_structures[0]
self.assertEqual("elemental_mapping_edge",
edge_data_struct.structure_type)
self.assertEqual(model_data_item, edge_data_struct.source)
self.assertEqual(
32, edge_data_struct.get_property_value("atomic_number"))
self.assertEqual(
2, edge_data_struct.get_property_value("shell_number"))
self.assertEqual(
3, edge_data_struct.get_property_value("subshell_index"))
def test_removing_edges(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
ge_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
si_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
self.assertEqual(2, len(document_model.data_structures))
elemental_mapping_controller.remove_edge(ge_edge)
self.assertEqual(1, len(document_model.data_structures))
self.assertEqual(
14, document_model.data_structures[0].get_property_value(
"atomic_number"))
elemental_mapping_controller.remove_edge(si_edge)
self.assertEqual(0, len(document_model.data_structures))
def test_selecting_composite_updates_edge_value(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
si_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].pick_action()
self.__run_until_complete(document_controller)
self.assertIsNone(elemental_mapping_controller.edge)
eels_data_item = document_model.data_items[1]
elemental_mapping_controller.set_current_data_item(eels_data_item)
self.assertEqual(model_data_item,
elemental_mapping_controller.model_data_item)
self.assertEqual(si_edge.data_structure,
elemental_mapping_controller.edge.data_structure)
def test_controller_has_proper_edge_bundles_when_explorer_selected(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
document_controller.event_loop.create_task(
elemental_mapping_controller.explore_edges(
document_controller))
self.__run_until_complete(document_controller)
explorer_data_item = document_model.data_items[1]
elemental_mapping_controller.set_current_data_item(
explorer_data_item)
self.assertIsNotNone(elemental_mapping_controller.model_data_item)
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
self.assertEqual(1, len(edge_bundle))
def test_explore_creates_initial_line_plot(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
data_item = self.__create_spectrum_image()
document_model.append_data_item(data_item)
elemental_mapping_controller.set_current_data_item(data_item)
document_controller.event_loop.create_task(
elemental_mapping_controller.explore_edges(
document_controller))
document_controller.periodic() # start tasks
document_model.recompute_all()
document_controller.periodic() # finish tasks
self.assertEqual(2, len(document_model.data_items))
explorer_data_item = document_model.data_items[1]
explorer_display_item = document_model.get_display_item_for_data_item(
explorer_data_item)
self.assertEqual(1, len(explorer_data_item.dimensional_shape))
self.assertEqual("explore",
explorer_display_item.graphics[-1].graphic_id)
def test_background_subtraction_computation_functions_reasonably(self):
document_model = DocumentModel.DocumentModel()
self.app._set_document_model(
document_model) # required to allow API to find document model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
si_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
spectrum_data_item = self.__create_spectrum()
document_model.append_data_item(spectrum_data_item)
spectrum_display_item = document_model.get_display_item_for_data_item(
spectrum_data_item)
spectrum_display_data_channel = spectrum_display_item.get_display_data_channel_for_data_item(
spectrum_data_item)
computation = document_model.create_computation()
computation.create_object(
"eels_spectrum_xdata",
document_model.get_object_specifier(
spectrum_display_data_channel, "display_xdata"))
computation.create_input(
"fit_interval",
document_model.get_object_specifier(si_edge.data_structure),
"fit_interval")
computation.create_input(
"signal_interval",
document_model.get_object_specifier(si_edge.data_structure),
"signal_interval")
computation.processing_id = "eels.background_subtraction"
document_model.append_computation(computation)
document_model.recompute_all()
document_controller.periodic()
self.assertEqual(2, len(document_model.data_items))
def test_mapping_edge_produces_properly_configured_map(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].map_action()
self.__run_until_complete(document_controller)
self.assertEqual(2, len(document_model.data_items))
mapped_data_item = document_model.data_items[1]
self.assertEqual(model_data_item, mapped_data_item.source)
self.assertEqual(1, len(document_model.computations))
self.assertEqual("eels.mapping",
document_model.computations[0].processing_id)
self.assertEqual(mapped_data_item.dimensional_calibrations,
model_data_item.dimensional_calibrations[0:2])
def test_removing_edges(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
ge_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
si_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
self.assertEqual(2, len(document_model.data_structures))
elemental_mapping_controller.remove_edge(ge_edge)
self.assertEqual(1, len(document_model.data_structures))
self.assertEqual(
14, document_model.data_structures[0].get_property_value(
"atomic_number"))
elemental_mapping_controller.remove_edge(si_edge)
self.assertEqual(0, len(document_model.data_structures))
def test_background_subtraction_computation_functions_reasonably(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller_with_application(
)
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
si_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
spectrum_data_item = self.__create_spectrum()
document_model.append_data_item(spectrum_data_item)
spectrum_display_item = document_model.get_display_item_for_data_item(
spectrum_data_item)
spectrum_display_data_channel = spectrum_display_item.get_display_data_channel_for_data_item(
spectrum_data_item)
computation = document_model.create_computation()
computation.create_input_item(
"eels_spectrum_xdata",
Symbolic.make_item(spectrum_display_data_channel,
type="display_xdata"))
computation.create_input_item("fit_interval",
Symbolic.make_item(
si_edge.data_structure),
property_name="fit_interval")
computation.create_input_item("signal_interval",
Symbolic.make_item(
si_edge.data_structure),
property_name="signal_interval")
computation.processing_id = "eels.background_subtraction"
document_model.append_computation(computation)
document_model.recompute_all()
document_controller.periodic()
self.assertEqual(2, len(document_model.data_items))
def test_controller_has_proper_edge_bundles_when_explorer_selected(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
document_controller.event_loop.create_task(
elemental_mapping_controller.explore_edges(
document_controller))
self.__run_until_complete(document_controller)
explorer_data_item = document_model.data_items[1]
elemental_mapping_controller.set_current_data_item(
explorer_data_item)
self.assertIsNotNone(elemental_mapping_controller.model_data_item)
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
self.assertEqual(1, len(edge_bundle))
def test_selecting_composite_updates_edge_value(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
si_edge = elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].pick_action()
self.__run_until_complete(document_controller)
self.assertIsNone(elemental_mapping_controller.edge)
eels_data_item = document_model.data_items[1]
elemental_mapping_controller.set_current_data_item(eels_data_item)
self.assertEqual(model_data_item,
elemental_mapping_controller.model_data_item)
self.assertEqual(si_edge.data_structure,
elemental_mapping_controller.edge.data_structure)
def test_explore_creates_initial_line_plot(self):
document_model = DocumentModel.DocumentModel()
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
document_controller = DocumentController.DocumentController(
self.app.ui, document_model, workspace_id="library")
with contextlib.closing(document_controller), contextlib.closing(
elemental_mapping_controller):
data_item = self.__create_spectrum_image()
document_model.append_data_item(data_item)
elemental_mapping_controller.set_current_data_item(data_item)
document_controller.event_loop.create_task(
elemental_mapping_controller.explore_edges(
document_controller))
document_controller.periodic() # start tasks
document_model.recompute_all()
document_controller.periodic() # finish tasks
self.assertEqual(2, len(document_model.data_items))
explorer_data_item = document_model.data_items[1]
explorer_display_item = document_model.get_display_item_for_data_item(
explorer_data_item)
self.assertEqual(1, len(explorer_data_item.dimensional_shape))
self.assertEqual("explore",
explorer_display_item.graphics[-1].graphic_id)
def __init__(self, document_controller, panel_id, properties):
super().__init__(document_controller, panel_id,
_("Elemental Mappings"))
document_model = document_controller.document_model
self.__elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
ui = document_controller.ui
self.__button_group = None
column = ui.create_column_widget()
edge_column = ui.create_column_widget()
explore_column = ui.create_column_widget()
add_edge_column = ui.create_column_widget()
auto_edge_column = ui.create_column_widget()
column.add(edge_column)
column.add_spacing(12)
column.add(explore_column)
column.add_spacing(12)
column.add(add_edge_column)
column.add_spacing(12)
column.add(auto_edge_column)
column.add_spacing(12)
column.add_stretch()
self.widget = column
explore_row = ui.create_row_widget()
explore_button_widget = ui.create_push_button_widget(_("Explore"))
multiprofile_button_widget = ui.create_push_button_widget(
_("Multiprofile"))
explore_row.add(explore_button_widget)
explore_row.add_spacing(8)
explore_row.add(multiprofile_button_widget)
explore_row.add_stretch()
explore_column.add(explore_row)
def data_item_changed(data_item) -> None:
self.__elemental_mapping_controller.set_current_data_item(
data_item)
current_data_item = data_item
model_data_item = self.__elemental_mapping_controller.model_data_item
edge = self.__elemental_mapping_controller.edge
edge_column.remove_all()
add_edge_column.remove_all()
if self.__button_group:
self.__button_group.close()
self.__button_group = None
if model_data_item:
def explore_pressed():
document_controller.event_loop.create_task(
self.__elemental_mapping_controller.explore_edges(
document_controller))
explore_button_widget.on_clicked = explore_pressed
multiprofile_button_widget.on_clicked = functools.partial(
self.__elemental_mapping_controller.build_multiprofile,
document_controller)
self.__button_group = ui.create_button_group()
for index, edge_bundle in enumerate(
self.__elemental_mapping_controller.build_edge_bundles(
document_controller)):
def delete_pressed():
edge_bundle.delete_action()
data_item_changed(current_data_item
) # TODO: this should be automatic
row = ui.create_row_widget()
radio_button = None
label = None
if edge:
radio_button = ui.create_radio_button_widget(
edge_bundle.electron_shell_str)
self.__button_group.add_button(radio_button, index)
radio_button.checked = edge_bundle.selected
radio_button.on_clicked = edge_bundle.select_action
else:
label = ui.create_label_widget(
edge_bundle.electron_shell_str)
delete_button = ui.create_push_button_widget(_("Delete"))
pick_button = ui.create_push_button_widget(_("Pick"))
map_button = ui.create_push_button_widget(_("Map"))
delete_button.on_clicked = delete_pressed
pick_button.on_clicked = edge_bundle.pick_action
map_button.on_clicked = edge_bundle.map_action
row.add_spacing(20)
if radio_button:
row.add(radio_button)
row.add_spacing(4)
elif label:
row.add(label)
row.add_spacing(12)
row.add(pick_button)
row.add_spacing(12)
row.add(map_button)
row.add_stretch()
row.add(delete_button)
row.add_spacing(12)
edge_column.add(row)
atomic_number_widget = ui.create_combo_box_widget(
items=PeriodicTable.PeriodicTable().get_elements_list(),
item_getter=operator.itemgetter(1))
edge_widget = ui.create_combo_box_widget(
items=PeriodicTable.PeriodicTable().get_edges_list(1),
item_getter=operator.itemgetter(1))
add_button_widget = ui.create_push_button_widget(_("Add Edge"))
atomic_number_row = ui.create_row_widget()
atomic_number_row.add_spacing(20)
atomic_number_row.add(ui.create_label_widget(_("Element")))
atomic_number_row.add_spacing(8)
atomic_number_row.add(atomic_number_widget)
atomic_number_row.add_spacing(8)
atomic_number_row.add_stretch()
edge_row = ui.create_row_widget()
edge_row.add_spacing(20)
edge_row.add(ui.create_label_widget(_("Edge")))
edge_row.add_spacing(8)
edge_row.add(edge_widget)
edge_row.add_spacing(8)
edge_row.add_stretch()
add_button_row = ui.create_row_widget()
add_button_row.add_spacing(20)
add_button_row.add(add_button_widget)
add_button_row.add_spacing(8)
add_button_row.add_stretch()
add_edge_column.add(atomic_number_row)
add_edge_column.add(edge_row)
add_edge_column.add(add_button_row)
def add_edge_current():
self.__elemental_mapping_controller.add_edge(
edge_widget.current_item[0])
data_item_changed(model_data_item)
data_item_changed(data_item)
add_button_widget.on_clicked = add_edge_current
def atomic_number_changed(item):
edge_widget.items = PeriodicTable.PeriodicTable(
).get_edges_list(item[0])
atomic_number_widget.on_current_item_changed = atomic_number_changed
add_row = ui.create_row_widget()
add_column = ui.create_column_widget()
refresh_row = ui.create_row_widget()
add_grid = ui.create_row_widget()
col1 = ui.create_column_widget()
col2 = ui.create_column_widget()
add_grid.add(col1)
add_grid.add(col2)
add_grid.add_stretch()
def update_add_buttons():
col1.remove_all()
col2.remove_all()
explore_interval = self.__elemental_mapping_controller.explorer_interval
if explore_interval is not None:
edges = PeriodicTable.PeriodicTable(
).find_edges_in_energy_interval(explore_interval)
for i, edge in enumerate(edges[0:4]):
button = ui.create_push_button_widget(
edge.to_long_str())
def add_edge(model_data_item, edge, data_item):
self.__elemental_mapping_controller.add_edge(
edge)
data_item_changed(model_data_item)
data_item_changed(data_item)
button.on_clicked = functools.partial(
add_edge, model_data_item, edge, data_item)
col = col1 if i % 2 == 0 else col2
col.add(button)
col1.add_stretch()
col2.add_stretch()
refresh_widget = ui.create_push_button_widget("\u21BB")
refresh_widget.on_clicked = lambda: data_item_changed(
current_data_item) # TODO: re-layout in Qt is awful
update_add_buttons()
refresh_row.add(refresh_widget)
refresh_row.add_stretch()
add_column.add(refresh_row)
add_column.add(add_grid)
add_row.add_spacing(20)
add_row.add(add_column)
add_row.add_stretch()
add_edge_column.add(add_row)
def display_item_changed(display_item):
data_item = display_item.data_item if display_item else None
data_item_changed(data_item)
self.__focused_display_item_changed_event_listener = document_controller.focused_display_item_changed_event.listen(
display_item_changed)
selected_data_item = document_controller.selected_data_item
data_item_changed(selected_data_item)
def test_changing_edge_configures_other_items_correctly(self):
with TestContext.create_memory_context() as test_context:
document_controller = test_context.create_document_controller()
document_model = document_controller.document_model
elemental_mapping_controller = ElementalMappingController.ElementalMappingController(
document_model)
model_data_item = self.__create_spectrum_image()
document_model.append_data_item(model_data_item)
model_display_item = document_model.get_display_item_for_data_item(
model_data_item)
elemental_mapping_controller.set_current_data_item(model_data_item)
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(14, 1, 1)) # Si-K
elemental_mapping_controller.add_edge(
PeriodicTable.ElectronShell(32, 2, 3)) # Ge-L
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
edge_bundle[0].pick_action()
self.__run_until_complete(document_controller)
eels_data_item = document_model.data_items[1]
eels_display_item = document_model.get_display_item_for_data_item(
eels_data_item)
elemental_mapping_controller.set_current_data_item(eels_data_item)
edge_bundle = elemental_mapping_controller.build_edge_bundles(
document_controller)
# apply the change to the other edge
edge_bundle[1].select_action()
self.__run_until_complete(document_controller)
computation = document_model.computations[0]
old_edge_data_structure = document_model.data_structures[0]
new_edge_data_structure = document_model.data_structures[1]
edge_ref_data_structure = document_model.data_structures[2]
pick_region = model_display_item.graphics[0]
# check the titles
self.assertEqual("Pick Ge-L3", pick_region.label)
self.assertEqual("Pick Ge-L3 EELS Data of Untitled",
eels_data_item.title)
# check the old intervals are disconnected and the new are connected
old_fit_interval = eels_display_item.graphics[0].interval
old_signal_interval = eels_display_item.graphics[1].interval
new_fit_interval = (0.6, 0.7)
new_signal_interval = (0.7, 0.8)
# ensure changing old edge doesn't affect any connections
old_edge_data_structure.set_property_value("fit_interval",
new_fit_interval)
old_edge_data_structure.set_property_value("signal_interval",
new_signal_interval)
self.assertEqual(old_fit_interval,
eels_display_item.graphics[0].interval)
self.assertEqual(old_signal_interval,
eels_display_item.graphics[1].interval)
self.assertEqual(old_fit_interval,
computation.get_input("fit_interval"))
self.assertEqual(old_signal_interval,
computation.get_input("signal_interval"))
# ensure changing new edge affects all connections
new_edge_data_structure.set_property_value("fit_interval",
new_fit_interval)
new_edge_data_structure.set_property_value("signal_interval",
new_signal_interval)
self.assertEqual(new_fit_interval,
eels_display_item.graphics[0].interval)
self.assertEqual(new_signal_interval,
eels_display_item.graphics[1].interval)
self.assertEqual(new_fit_interval,
computation.get_input("fit_interval"))
self.assertEqual(new_signal_interval,
computation.get_input("signal_interval"))
# and the edge reference
self.assertEqual(
new_edge_data_structure,
edge_ref_data_structure.get_referenced_object("edge"))