def update_data_item_from_data_element(data_item: DataItem.DataItem, data_element, data_file_path=None):
data_item.ensure_data_source()
version = data_element["version"] if "version" in data_element else 1
if version == 1:
update_data_item_from_data_element_1(data_item, data_element, data_file_path)
else:
raise NotImplementedError("Data element version {:d} not supported.".format(version))
def update_data_item_from_data_element(
data_item: DataItem.DataItem,
data_element: DataElementType,
data_file_path: typing.Optional[pathlib.Path] = None) -> None:
data_item.ensure_data_source()
version = data_element["version"] if "version" in data_element else 1
if version == 1:
update_data_item_from_data_element_1(data_item, data_element,
data_file_path)
else:
raise NotImplementedError(
"Data element version {:d} not supported.".format(version))
def __get_storage_for_item(
self, item: DataItem.DataItem) -> DataItemStorageAdapter:
if not item.uuid in self.__data_item_storage:
storage_handler = self.make_storage_handler(item)
self.register_data_item(item, item.uuid, storage_handler,
item.write_to_dict())
return self.__data_item_storage.get(item.uuid)
def append_data_item(self, data_item: DataItem.DataItem) -> None:
assert not self.get_item_by_uuid("data_items", data_item.uuid)
self.append_item("data_items", data_item)
data_item.write_data_if_not_delayed() # initially write to disk
def update_data_item_from_data_element_1(data_item: DataItem.DataItem, data_element: typing.Dict, data_file_path=None):
assert data_item
with data_item.data_item_changes(), data_item.data_source_changes():
# file path
# master data
if data_file_path is not None:
data_item.source_file_path = data_file_path
data_and_metadata = convert_data_element_to_data_and_metadata(data_element)
data = data_and_metadata.data
dimensional_calibrations = data_and_metadata.dimensional_calibrations
intensity_calibration = data_and_metadata.intensity_calibration
is_sequence = data_and_metadata.is_sequence
collection_dimension_count = data_and_metadata.collection_dimension_count
datum_dimension_count = data_and_metadata.datum_dimension_count
data_shape_data_dtype = data_and_metadata.data_shape_and_dtype
is_same_shape = data_item.data_shape == data_shape_data_dtype[0] and data_item.data_dtype == data_shape_data_dtype[1] and data_item.is_sequence == is_sequence and data_item.collection_dimension_count == collection_dimension_count and data_item.datum_dimension_count == datum_dimension_count
if is_same_shape:
with data_item.data_ref() as data_ref:
sub_area = data_element.get("sub_area")
if sub_area is not None:
top = sub_area[0][0]
bottom = sub_area[0][0] + sub_area[1][0]
left = sub_area[0][1]
right = sub_area[0][1] + sub_area[1][1]
data_ref.master_data[top:bottom, left:right] = data[top:bottom, left:right]
else:
data_ref.master_data[:] = data[:]
data_ref.data_updated() # trigger change notifications
if dimensional_calibrations is not None:
for dimension, dimensional_calibration in enumerate(dimensional_calibrations):
data_item.set_dimensional_calibration(dimension, dimensional_calibration)
if intensity_calibration:
data_item.set_intensity_calibration(intensity_calibration)
data_item.metadata = data_and_metadata.metadata
else:
data_item.set_xdata(data_and_metadata)
# title
if "title" in data_element:
data_item.title = data_element["title"]
# description
# dates are _local_ time and must use this specific ISO 8601 format. 2013-11-17T08:43:21.389391
# time zones are offsets (east of UTC) in the following format "+HHMM" or "-HHMM"
# daylight savings times are time offset (east of UTC) in format "+MM" or "-MM"
# timezone is for conversion and is the Olson timezone string.
# datetime.datetime.strptime(datetime.datetime.isoformat(datetime.datetime.now()), "%Y-%m-%dT%H:%M:%S.%f" )
# datetime_modified, datetime_modified_tz, datetime_modified_dst, datetime_modified_tzname is the time at which this image was modified.
# datetime_original, datetime_original_tz, datetime_original_dst, datetime_original_tzname is the time at which this image was created.
utc_datetime = data_and_metadata.timestamp
data_item.created = utc_datetime
if "time_zone" in data_and_metadata.metadata.get("description", dict()):
timezone_dict = copy.deepcopy(data_and_metadata.metadata["description"]["time_zone"])
timezone = timezone_dict.get("timezone")
if timezone is not None:
data_item.timezone = timezone
timezone_offset = timezone_dict.get("tz")
if timezone_offset is not None:
data_item.timezone_offset = timezone_offset
async def change_edge(document_controller: DocumentController.DocumentController, model_data_item: DataItem.DataItem, eels_data_item: DataItem.DataItem, edge: "ElementalMappingEdge") -> None:
"""Change the eels data item and associated items to display new edge.
The library will be changed in the following way:
- the pick region will be renamed
- the pick data item will connect fit/signal regions to new edge data structure
- the background subtraction computation will use edge intervals from new edge
- the pick, background, subtracted, and eels line plot data items will be renamed
- the eels line plot will connect fit/signal regions to new edge data structure
- the edge reference will reference the new edge
"""
document_model = document_controller.document_model
computation = None # type: Symbolic.Computation
for computation_ in document_model.computations:
if computation_.source == eels_data_item and computation_.processing_id == "eels.background_subtraction11":
computation = computation_
break
edge_ref_data_structure = None
old_edge_data_structure = None
for data_structure in document_model.data_structures:
if data_structure.source == eels_data_item and data_structure.structure_type == "elemental_mapping_edge_ref":
edge_ref_data_structure = data_structure
old_edge_data_structure = data_structure.get_referenced_object("edge")
break
if not computation or not edge_ref_data_structure or not old_edge_data_structure:
return
pick_region = edge_ref_data_structure.get_referenced_object("pick_region")
if not eels_data_item or not pick_region:
return
pick_region.label = "{} {}".format(_("Pick"), str(edge.electron_shell))
for connection in copy.copy(document_model.connections):
if connection.parent == eels_data_item and connection.source_property in ("fit_interval", "signal_interval"):
source_property = connection.source_property
target_property = connection.target_property
target = connection._target
document_model.remove_connection(connection)
new_connection = Connection.PropertyConnection(edge.data_structure, source_property, target, target_property, parent=eels_data_item)
document_model.append_connection(new_connection)
for computation_variable in computation.variables:
if computation_variable.name in ("fit_interval", "signal_interval"):
computation_variable.specifier = document_model.get_object_specifier(edge.data_structure)
eels_data_item.title = "{} EELS Data of {}".format(pick_region.label, model_data_item.title)
for connection in copy.copy(document_model.connections):
if connection.parent == eels_data_item and connection.source_property in ("fit_interval", "signal_interval"):
source_property = connection.source_property
target_property = connection.target_property
target = connection._target
document_model.remove_connection(connection)
new_connection = Connection.PropertyConnection(edge.data_structure, source_property, target, target_property, parent=eels_data_item)
document_model.append_connection(new_connection)
edge_ref_data_structure.remove_referenced_object("edge")
edge_ref_data_structure.set_referenced_object("edge", edge.data_structure)
# the eels item will need the initial computation results to display properly (view to intervals)
await document_model.compute_immediate(document_controller.event_loop, computation)
eels_display_item = document_model.get_display_item_for_data_item(eels_data_item)
eels_display_item.view_to_intervals(eels_data_item.xdata, [edge.fit_interval, edge.signal_interval])