def _perform_action(dicom, field, action, value=None, item=None):
'''_perform_action is the base function for performing an action.
perform_action (above) typically is called using a loaded deid,
and perform_addition is typically done via an addition in a config
Both result in a call to this function. If an action fails or is not
done, None is returned, and the calling function should handle this.
'''
if action not in valid_actions:
bot.warning('''%s in not a valid choice [%s].
Defaulting to blanked.''' %
(action, ".".join(valid_actions)))
action = "BLANK"
if field in dicom and action != "ADD":
# Blank the value
if action == "BLANK":
dicom = blank_tag(dicom, field)
# Code the value with something in the response
elif action == "REPLACE":
newvalue = parse_value(item, value, field)
if newvalue is not None:
# If we make it here, do the replacement
dicom = update_tag(dicom, field=field, value=newvalue)
else:
bot.warning("REPLACE %s unsuccessful" % field)
elif action == "SCREEN":
newvalue = parse_value(item, value, field)
if newvalue is not None:
# If we make it here, do the replacement
dicom = update_tag(dicom, field=field, value=newvalue)
bot.warning("SCREEN identified a hit in %s" % field)
# Code the value with something in the response
elif action == "JITTER":
value = parse_value(item, value, field)
if value is not None:
# Jitter the field by the supplied value
dicom = jitter_timestamp(dicom=dicom, field=field, value=value)
else:
bot.warning("JITTER %s unsuccessful" % field)
# elif "KEEP" --> Do nothing. Keep the original
# Remove the field entirely
elif action == "REMOVE":
dicom = remove_tag(dicom, field)
elif action == "ADD":
value = parse_value(item, value, field)
if value is not None:
dicom = add_tag(dicom, field, value, quiet=True)
return dicom
def _run_action(self, field, action, value=None):
"""perform_action (above) typically is called using a loaded deid,
and _run_addition is typically done via an addition in a config
Both result in a call to this function. If an action fails or is not
done, None is returned, and the calling function should handle this.
"""
# Blank the value
if action == "BLANK":
self.blank_field(field)
# Unlikely to be called from perform_action
elif action == "ADD":
self.add_field(field, value)
# Code the value with something in the response
elif action == "REPLACE":
self.replace_field(field, value)
# Code the value with something in the response
elif action == "JITTER":
value = parse_value(item=self.lookup,
dicom=self.dicom,
value=value,
field=field)
if value is not None:
# Jitter the field by the supplied value
jitter_timestamp(dicom=self.dicom,
field=field.element.keyword,
value=value)
else:
bot.warning("JITTER %s unsuccessful" % field)
# elif "KEEP" --> Do nothing. Keep the original
# Remove the field entirely
elif action == "REMOVE":
# If a value is defined, parse it (could be filter)
do_removal = True
if value != None:
do_removal = parse_value(item=self.lookup,
dicom=self.dicom,
value=value,
field=field)
if do_removal == True:
self.delete_field(field)
def add_field(self, field, value):
"""add a field to the dicom. If it's already present, update the value.
"""
value = parse_value(item=self.lookup,
value=value,
field=field,
dicom=self.dicom)
# Assume we don't want to add an empty value
if value is not None:
# If provided a field object, create based on keyword or tag identifer
name = field
if isinstance(field, DicomField):
name = field.element.keyword or field.stripped_tag
# Generate a tag item, add if it's a name found in the dicom dictionary
tag = get_tag(name)
# Second try, it might be a private (or other numerical) string identifier
if not tag:
tag = add_tag(name)
if tag:
uid = str(tag["tag"])
element = DataElement(tag["tag"], tag["VR"], value)
self.dicom.add(element)
self.fields[uid] = DicomField(element, name, uid)
bot.warning("Cannot find tag for field %s, skipping." % name)
def _perform_expanded_action(dicom,
expanded_field,
action,
value=None,
item=None):
"""akin to _perform_action, but we expect to be dealing with an expanded
sequence, and need to step into the Dicom data structure.
Add, jitter, and delete are currently not supported.
The field is expected to have the format FieldA__FieldB where the
last one is where we want to do the replacement.
"""
field = expanded_field.split("__")[-1]
while field != expanded_field:
next_field, expanded_field = expanded_field.split("__", 1)
# Case 1: we have a Dataset
if isinstance(dicom, Dataset):
dicom = dicom.get(next_field)
elif isinstance(dicom, Sequence):
for sequence in dicom:
for subitem in sequence:
if subitem.keyword == next_field:
dicom = subitem
break
# Field should be equal to expanded_field, and in dicom
if isinstance(dicom, Dataset):
return _perform_action(dicom=dicom,
field=field,
item=item,
action=action,
value=value)
elif isinstance(dicom, Sequence):
for sequence in dicom:
for subitem in sequence:
if subitem.keyword == field:
dicom = subitem
break
if not dicom:
return
# Not sure if this is possible
if dicom.keyword != field:
bot.warning("Early return, looking for %s, found %s" %
(field, dicom.keyword))
return
# Blank the value
if action == "BLANK":
if dicom.VR not in ["US", "SS"]:
dicom.value = ""
# Code the value with something in the response
elif action == "REPLACE":
value = parse_value(item, value, field)
if value is not None:
dicom.value = value