def blank_tag(dicom, field):
"""blank tag calls update_tag with value set to an
empty string. If the tag cannot be found, warns the user
and doesn't touch (in case of imaging data, or not found)
Parameters
==========
dicom: the pydicom.dataset Dataset (pydicom.read_file)
field: the name of the field to blank
"""
# Case 1: We are provided a field that is a string, retrieve data element
if isinstance(field, str):
element = dicom.data_element(field)
else:
element = dicom.get(field)
if element is not None:
# Assert we have a data element
if not isinstance(element, DataElement):
bot.warning("Issue parsing %s as a DataElement, not blanked." %
field)
return dicom
# We cannot blank VR types of US or SS
if element.VR not in ["US", "SS"]:
return update_tag(dicom, field, "")
bot.warning("Cannot determine tag for %s, skipping blank." % field)
return dicom
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 find_deid(path=None):
'''find_deid is a helper function to load_deid to find a deid file in
a folder, or return the path provided if it is the file.
Parameters
==========
path: a path on the filesystem. If not provided, will assume PWD.
'''
if path is None:
path = os.getcwd()
# The user has provided a directory
if os.path.isdir(path):
contenders = [
"%s/%s" % (path, x) for x in os.listdir(path)
if x.startswith('deid')
]
if len(contenders) == 0:
bot.error("No deid settings files found in %s, exiting." % (path))
sys.exit(1)
elif len(contenders) > 1:
bot.warning("Multiple deid files found in %s, will use first." %
(path))
path = contenders[0]
# We have a file path at this point
if not os.path.exists(path):
bot.error("Cannot find deid file %s, exiting." % (path))
sys.exit(1)
return path
def perform_action(self, field, value, action):
"""perform action takes an action (dictionary with field, action, value)
and performs the action on the loaded dicom.
Parameters
==========
fields: if provided, a filtered list of fields for expand
action: the action from the parsed deid to take
"field" (eg, PatientID) the header field to process
"action" (eg, REPLACE) what to do with the field
"value": if needed, the field from the response to replace with
"""
# Validate the action
if action not in valid_actions:
bot.warning("%s in not a valid choice. Defaulting to blanked." %
action)
action = "BLANK"
# A values list returns fields with the value (can be private tags if not removed)
if re.search("^values", field):
values = self.lookup.get(re.sub("^values:", "", field), [])
fields = self.find_by_values(values=values)
# A fields list is used vertabim
# In expand_field_expression below, the stripped_tag is being passed in to field. At this point,
# expanders for %fields lists have already been processed and each of the contenders is an
# identified, unique field. It is important to use stripped_tag at this point instead of
# element.keyword as private tags will not have a keyword and can only be identified by tag number.
elif re.search("^fields", field):
listing = {}
for uid, contender in self.lookup.get(
re.sub("^fields:", "", field), {}).items():
listing.update(
expand_field_expression(
field=contender.stripped_tag,
dicom=self.dicom,
contenders=self.fields,
))
fields = listing
else:
# If there is an expander applied to field, we iterate over
fields = expand_field_expression(field=field,
dicom=self.dicom,
contenders=self.fields)
# If it's an addition, we might not have fields
if action == "ADD":
self.add_field(field, value)
# Otherwise, these are operations on existing fields
else:
"""clone the fields dictionary. delete actions must also delete from the fields dictionary.
performing the clone and iterating on the clone allows the deletions while preventing a
runtime error - "dictionary changed size during iterations"
"""
temp_fields = deepcopy(fields)
for uid, field in temp_fields.items():
self._run_action(field=field, action=action, value=value)
def extract_fields_list(dicom, actions, fields=None):
"""Given a list of actions for a named group (a list) extract values from
the dicom based on the list of actions provided. This function
always returns a list intended to update some lookup to be used
to further process the dicom.
"""
subset = {}
if not fields:
fields = get_fields(dicom)
for action in actions:
if action["action"] == "FIELD":
subset.update(
expand_field_expression(
field=action["field"], dicom=dicom, contenders=fields
)
)
else:
bot.warning(
"Unrecognized action %s for fields list extraction." % action["action"]
)
return subset
def load_combined_deid(deids):
'''load one or more deids, either based on a path or a tag
Parameters
==========
deids: should be a custom list of deids
'''
if not isinstance(deids, list):
bot.warning("load_combined_deids expects a list.")
sys.exit(1)
found_format = None
deid = None
for single_deid in deids:
# If not a tag or path, returns None
next_deid = get_deid(tag=single_deid,
exit_on_fail=False,
quiet=True,
load=True)
if next_deid is not None:
# Formats must match
if found_format is None:
found_format = next_deid['format']
else:
if found_format != next_deid['format']:
bot.error('Mismatch in deid formats, %s and %s' %
(found_format, next_deid['format']))
sys.exit(1)
# If it's the first one, use as starter template
if deid is None:
deid = next_deid
else:
# Update filter, appending to end to give first preference
if "filter" in next_deid:
if "filter" not in deid:
deid['filter'] = next_deid['filter']
else:
for name, group in next_deid['filter'].items():
if name in deid['filter']:
deid['filter'][
name] = deid['filter'][name] + group
else:
deid['filter'][name] = group
if "header" in next_deid:
if "header" not in deid:
deid['header'] = next_deid['header']
else:
deid['header'] = deid['header'] + next_deid['header']
else:
bot.warning('Problem loading %s, skipping.' % single_deid)
return deid
def parse_value(item, value, field=None):
"""parse_value will parse the value field of an action,
either returning:
1. the string (string or from function)
2. a variable looked up (var:FieldName)
"""
# If item is passed as None
if item is None:
item = dict()
# Does the user want a custom value?
if re.search("[:]", value):
value_type, value_option = value.split(":", 1)
if value_type.lower() == "var":
# If selected variable not provided, skip
if value_option not in item:
return None
return item[value_option]
# The user is providing a specific function
elif value_type.lower() == "func":
if value_option not in item:
bot.warning("%s not found in item lookup %s" % (value_option))
return None
# item is the lookup, value from the recipe, and field
# If the user writes a custom function for private, will need
# to convert field to str() in the function.
return item[value_option](item, value, field)
bot.warning("%s is not a valid value type, skipping." % (value_type))
return None
return value
def extract_sequence(sequence, prefix=None):
"""return a pydicom.sequence.Sequence recursively
as a flattened list of items. For example, a nested FieldA and FieldB
would return as:
{'FieldA__FieldB': '111111'}
Parameters
==========
sequence: the sequence to extract, should be pydicom.sequence.Sequence
prefix: the parent name
"""
items = {}
for item in sequence:
# If it's a Dataset, we need to further unwrap it
if isinstance(item, Dataset):
for subitem in item:
items.update(extract_item(subitem, prefix=prefix))
# Private tags are DataElements
elif isinstance(item, DataElement):
items[item.tag] = extract_item(item, prefix=prefix)
else:
bot.warning(
"Unrecognized type %s in extract sequences, skipping." %
type(item))
return items
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.
'''
done = False
result = None
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":
result = blank_tag(dicom, field)
done = True
# Code the value with something in the response
elif action == "REPLACE":
value = parse_value(item, value)
if value is not None:
# If we make it here, do the replacement
done = True
result = update_tag(dicom, field=field, value=value)
# Code the value with something in the response
elif action == "JITTER":
value = parse_value(item, value)
if value is not None:
# Jitter the field by the supplied value
done = True
result = jitter_timestamp(dicom, field=field, value=value)
# Do nothing. Keep the original
elif action == "KEEP":
done = True
result = dicom
# Remove the field entirely
elif action == "REMOVE":
result = remove_tag(dicom, field)
done = True
if not done:
bot.warning("%s %s not done" % (action, field))
elif action == "ADD":
value = parse_value(item, value)
if value is not None:
result = add_tag(dicom, field, value)
return result
def parse_value(item, value, field=None):
'''parse_value will parse the value field of an action,
either returning:
1. the string (string or from function)
2. a variable looked up (var:FieldName)
'''
# If item is passed as None
if item is None:
item = dict()
# Does the user want a custom value?
if re.search('[:]', value):
value_type, value_option = value.split(':')
if value_type.lower() == "var":
# If selected variable not provided, skip
if value_option not in item:
return None
return item[value_option]
# The user is providing a specific function
elif value_type.lower() == "func":
if value_option not in item:
bot.warning('%s not found in item lookup %s' % (value_option))
return None
return item[value_option](item, value, field)
bot.warning('%s is not a valid value type, skipping.' % (value_type))
return None
return value
def get_figure(self, show=False, image_type="cleaned", title=None):
"""get a figure for an original or cleaned image. If the image
was already clean, it is simply a copy of the original.
If show is True, plot the image. If a 4d image is discovered, we use
randomly choose a slice.
"""
if hasattr(self, image_type):
_, ax = plt.subplots(figsize=(10, 6))
# Retrieve full image
image = getattr(self, image_type)
# Handle 4d data by choosing one dimension
if len(image.shape) == 4:
channel = random.choice(range(image.shape[3]))
bot.warning(
"Image detected as 4d, will sample channel %s and middle slice"
% channel
)
image = image[math.floor(image.shape[0] / 2), :, :, channel]
ax.imshow(image, cmap=self.cmap)
if title is not None:
plt.title(title, fontdict=self.font)
if show is True:
plt.show()
return plt
def apply_filter(dicom,field,filter_name,value):
'''essentially a switch statement to apply a filter to
a dicom file.
'''
filter_name = filter_name.lower().strip()
if filter_name == "contains":
return dicom.contains(field,value)
if filter_name == "notcontains":
return dicom.notContains(field,value)
elif filter_name == "equals":
return dicom.equals(field,value)
elif filter_name == "missing":
return dicom.missing(field)
elif filter_name == "present":
return not dicom.missing(field)
elif filter_name == "empty":
return dicom.empty(field)
elif filter_name == "notequals":
return dicom.notEquals(field,value)
bot.warning("%s is not a valid filter name, returning False" %filter_name)
return False
def validate_dicoms(dcm_files, force=False):
"""validate dicoms will test opening one or more dicom files,
and return a list of valid files.
Parameters
==========
dcm_files: one or more dicom files to test
"""
if not isinstance(dcm_files, list):
dcm_files = [dcm_files]
valids = []
bot.debug("Checking %s dicom files for validation." % (len(dcm_files)))
for dcm_file in dcm_files:
try:
with open(dcm_file, "rb") as filey:
read_file(filey, force=force)
valids.append(dcm_file)
except:
bot.warning(
"Cannot read input file {0!s}, skipping.".format(dcm_file))
bot.debug("Found %s valid dicom files" % (len(valids)))
return valids
def perform_action(dicom, action, item=None, fields=None, return_seen=False):
'''perform action takes
Parameters
==========
dicom: a loaded dicom file (pydicom read_file)
item: a dictionary with keys as fields, values as values
fields: if provided, a filtered list of fields for expand
action: the action from the parsed deid to take
"deid" (eg, PatientID) the header field to process
"action" (eg, REPLACE) what to do with the field
"value": if needed, the field from the response to replace with
'''
field = action.get('field') # e.g: PatientID, endswith:ID
value = action.get('value') # "suid" or "var:field"
action = action.get('action') # "REPLACE"
# Validate the action
if action not in valid_actions:
bot.warning('%s in not a valid choice. Defaulting to blanked.' %
action)
action = "BLANK"
# If there is an expander applied to field, we iterate over
fields = expand_field_expression(field=field,
dicom=dicom,
contenders=fields)
# Keep track of fields we have seen
seen = []
# An expanded field must END with that field
expanded_regexp = "__%s$" % field
for field in fields:
seen.append(field)
# Handle top level field
_perform_action(dicom=dicom,
field=field,
item=item,
action=action,
value=value)
# Expand sequences
if item:
expanded_fields = [x for x in item if re.search(expanded_regexp, x)]
# FieldA__FieldB
for expanded_field in expanded_fields:
_perform_expanded_action(dicom=dicom,
expanded_field=expanded_field,
item=item,
action=action,
value=value)
if return_seen:
return dicom, seen
return dicom
def parse_label(section, config, section_name, members, label=None):
"""parse label will add a (optionally named) label to the filter
section, including one or more criteria
Parameters
==========
section: the section name (e.g., header) must be one in sections
config: the config (dictionary) parsed thus far
section_name: an optional name for a section
members: the lines beloning to the section/section_name
label: an optional name for the group of commands
"""
criteria = {"filters": [], "coordinates": []}
if label is not None:
label = label.replace("label", "", 1).split("#")[0].strip()
criteria["name"] = label
while len(members) > 0:
member = members.pop(0).strip()
# We have a coordinate line (coordinates to remove, mask 0)
if member.lower().startswith("coordinates"):
coordinate = member.replace("coordinates", "").strip()
criteria["coordinates"].append([0, coordinate])
continue
# Coordinates to keep (mask 1)
elif member.lower().startswith("keepcoordinates"):
coordinate = member.replace("keepcoordinates", "").strip()
criteria["coordinates"].append([1, coordinate])
continue
operator = None
entry = None
if member.startswith("+"):
operator = "and"
member = member.replace("+", "", 1).strip()
elif member.startswith("||"):
operator = "or"
member = member.replace("||", "", 1).strip()
# Skip over comments
if member.startswith("#"):
continue
# Now that operators removed, parse member
if not member.lower().startswith(filters):
bot.warning("%s filter is not valid, skipping." % member.lower())
else:
# Returns single member with field, values, operator,
# Or if multiple or/and in statement, a list
entry = parse_member(member, operator)
if entry is not None:
criteria["filters"].append(entry.copy())
config[section][section_name].append(criteria)
return config
def extract_values_list(dicom, actions, fields=None):
"""Given a list of actions for a named group (a list) extract values from
the dicom based on the list of actions provided. This function
always returns a list intended to update some lookup to be used
to further process the dicom.
"""
values = set()
# The function can be provided fields to save re-parsing
if not fields:
fields = get_fields(dicom)
for action in actions:
# Extract some subset of fields based on action
subset = expand_field_expression(
field=action["field"], dicom=dicom, contenders=fields
)
# Just grab the entire value string for a field, no parsing
if action["action"] == "FIELD":
for uid, field in subset.items():
if field.element.value not in ["", None]:
values.add(field.element.value)
# Split action, can optionally have a "by" and/or minlength parameter
elif action["action"] == "SPLIT":
# Default values for split are length 1 and character empty space
bot.debug("Parsing action %s" % action)
split_by = " "
minlength = 1
if "value" in action:
for param in action["value"].split(";"):
param_name, param_val = param.split("=")
param_name = param_name.strip()
param_val = param_val.strip()
# Set a custom parameter legnth
if param_name == "minlength":
minlength = int(param_val)
bot.debug("Minimum length set to %s" % minlength)
elif param_name == "by":
split_by = param_val.strip("'").strip('"')
bot.debug("Splitting value set to %s" % split_by)
for uid, field in subset.items():
new_values = (str(field.element.value) or "").split(split_by)
for new_value in new_values:
if len(new_value) >= minlength:
values.add(new_value)
else:
bot.warning(
"Unrecognized action %s for values list extraction." % action["action"]
)
return list(values)
def __init__(self, deid=None, base=False, default_base='dicom'):
# If deid is None, use the default
if deid is None:
bot.warning('No specification, loading default base deid.%s' % default_base)
base = True
self._init_deid(deid, base=base, default_base=default_base)
def _perform_action(field, item, action, value=None):
'''_perform_action is the base function for performing an action.
It is equivalent to the dicom module version, except we work with
dictionary field/value instead of dicom headers.
If no action is done, None is returned
'''
done = False
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 item and action != "ADD":
# Blank the value
if action == "BLANK":
item[field] = ""
done = True
# Code the value with something in the response
elif action == "REPLACE":
value = parse_value(item, value)
if value is not None:
done = True
item[field] = value
else:
bot.warning("REPLACE failed for %s" % field)
# Code the value with something in the response
elif action == "JITTER":
value = parse_value(item, value)
if value is not None:
done = True
item = jitter_timestamp(field=field, value=value, item=item)
else:
bot.warning('JITTER failed for %s' % field)
# Do nothing. Keep the original
elif action == "KEEP":
done = True
bot.debug('KEEP %s' % field)
# Remove the field entirely
elif action == "REMOVE":
del item[field]
done = True
if not done:
bot.warning("%s not done for %s" % (action, field))
elif action == "ADD":
value = parse_value(item, value)
if value is not None:
item[field] = value
else:
bot.warning('ADD failed for %s' % field)
return item
def jitter_timestamp(dicom, field, value):
"""if present, jitter a timestamp in dicom
field "field" by number of days specified by "value"
The value can be positive or negative.
Parameters
==========
dicom: the pydicom Dataset
field: the field with the timestamp
value: number of days to jitter by. Jitter bug!
"""
if not isinstance(value, int):
value = int(value)
original = dicom.get(field)
if original is not None:
# Create default for new value
new_value = None
# If we have a string, we need to create a DataElement
if isinstance(field, str):
dcmvr = dicom.data_element(field).VR
else:
dcmvr = dicom.get(field).VR
original = dicom.get(field).value
# DICOM Value Representation can be either DA (Date) DT (Timestamp),
# or something else, which is not supported.
if dcmvr == "DA":
# NEMA-compliant format for DICOM date is YYYYMMDD
new_value = get_timestamp(original,
jitter_days=value,
format="%Y%m%d")
elif dcmvr == "DT":
# NEMA-compliant format for DICOM timestamp is
# YYYYMMDDHHMMSS.FFFFFF&ZZXX
new_value = get_timestamp(original,
jitter_days=value,
format="%Y%m%d%H%M%S.%f%z")
else:
# Do nothing and issue a warning.
bot.warning("JITTER not supported for %s with VR=%s" %
(field, dcmvr))
if new_value is not None and new_value != original:
# Only update if there's something to update AND there's been change
dicom = update_tag(dicom, field=field, value=new_value)
return dicom
def blank_tag(dicom, field):
'''blank tag calls update_tag with value set to an
empty string. If the tag cannot be found, warns the user
and doesn't touch (in case of imaging data, or not found)
'''
# We cannot blank VR types of US or SS
element = dicom.data_element(field)
if element is not None:
if element.VR not in ['US', 'SS']:
return update_tag(dicom, field, "")
bot.warning('Cannot determine tag for %s, skipping blank.' % field)
return dicom
def replace_identifiers(
dicom_files,
ids=None,
deid=None,
save=False,
overwrite=False,
output_folder=None,
force=True,
config=None,
strip_sequences=False,
remove_private=False,
):
"""replace identifiers using pydicom, can be slow when writing
and saving new files. If you want to replace sequences, they need
to be extracted with get_identifiers and expand_sequences to True.
"""
if not isinstance(dicom_files, list):
dicom_files = [dicom_files]
# Warn the user that we use the default deid recipe
if not deid:
bot.warning("No deid specification provided, will use defaults.")
# ids (a lookup) is not required
ids = ids or {}
# Parse through dicom files, update headers, and save
updated_files = []
for dicom_file in dicom_files:
parser = DicomParser(dicom_file, force=force, config=config, recipe=deid)
# If a custom lookup was provided, update the parser
if parser.dicom_file in ids:
parser.lookup.update(ids[parser.dicom_file])
parser.parse(strip_sequences=strip_sequences, remove_private=remove_private)
# Save to file, otherwise return updated objects
if save is True:
ds = save_dicom(
dicom=parser.dicom,
dicom_file=parser.dicom_file,
output_folder=output_folder,
overwrite=overwrite,
)
updated_files.append(ds)
else:
updated_files.append(parser.dicom)
return updated_files
def blank_field(self, field):
"""Blank a field"""
element = self.get_nested_field(field)
# Assert we have a data element, and can blank a string
if element:
if not isinstance(element, DataElement):
bot.warning("Issue parsing %s as a DataElement, not blanked." %
field)
elif element.VR in ["US", "SS"]:
element.value = ""
else:
bot.warning("Unrecognized VR for %s, skipping blank." % field)
def perform_action(self, field, value, action):
"""perform action takes an action (dictionary with field, action, value)
and performs the action on the loaded dicom.
Parameters
==========
fields: if provided, a filtered list of fields for expand
action: the action from the parsed deid to take
"field" (eg, PatientID) the header field to process
"action" (eg, REPLACE) what to do with the field
"value": if needed, the field from the response to replace with
"""
# Validate the action
if action not in valid_actions:
bot.warning("%s in not a valid choice. Defaulting to blanked." %
action)
action = "BLANK"
# A values list returns fields with the value (can be private tags if not removed)
if re.search("^values", field):
values = self.lookup.get(re.sub("^values:", "", field), [])
fields = self.find_by_values(values=values)
# A fields list is used vertabim
elif re.search("^fields", field):
listing = {}
for uid, contender in self.lookup.get(
re.sub("^fields:", "", field), {}).items():
listing.update(
expand_field_expression(
field=contender.element.keyword,
dicom=self.dicom,
contenders=self.fields,
))
fields = listing
else:
# If there is an expander applied to field, we iterate over
fields = expand_field_expression(field=field,
dicom=self.dicom,
contenders=self.fields)
# If it's an addition, we might not have fields
if action == "ADD":
self.add_field(field, value)
# Otherwise, these are operations on existing fields
else:
for uid, field in fields.items():
self._run_action(field=field, action=action, value=value)
def parse_label(section,config,section_name,members,label=None):
'''parse label will add a (optionally named) label to the filter
section, including one or more criteria
Parameters
==========
section: the section name (e.g., header) must be one in sections
config: the config (dictionary) parsed thus far
section_name: an optional name for a section
members: the lines beloning to the section/section_name
label: an optional name for the group of commands
'''
criteria = {'filters':[],
'coordinates':[]}
if label is not None:
label = (label.replace('label','',1)
.split('#')[0]
.strip())
criteria['name'] = label
while len(members) > 0:
member = members.pop(0).strip()
# We have a coordinate line
if member.lower().startswith('coordinates'):
coordinate = member.lower().replace('coordinates','').strip()
criteria['coordinates'].append(coordinate)
continue
operator = None
entry = None
if member.startswith('+'):
operator = 'and'
member = member.replace('+','',1).strip()
elif member.startswith('||'):
operator = 'or'
member = member.replace('||','',1).strip()
# Now that operators removed, parse member
if not member.lower().startswith(filters):
bot.warning('%s filter is not valid, skipping.' %member.lower())
else:
# Returns single member with field, values, operator,
# Or if multiple or/and in statement, a list
entry = parse_member(member, operator)
if entry is not None:
criteria['filters'].append(entry.copy())
config[section][section_name].append(criteria)
return config
def save_png(self, output_folder=None, image_type="cleaned", title=None):
"""save an original or cleaned dicom as png to disk.
Default image_format is "cleaned" and can be set
to "original." If the image was already clean (not
flagged) the cleaned image is just a copy of original
"""
if hasattr(self, image_type):
png_file = self._get_clean_name(output_folder, "png")
plt = self.get_figure(image_type=image_type, title=title)
plt.savefig(png_file)
plt.close()
return png_file
else:
bot.warning("use detect() --> clean() before saving is possible.")
def save_dicom(self, output_folder=None, image_type="cleaned"):
'''save a cleaned dicom to disk. We expose an option to save
an original (change image_type to "original" to be consistent,
although this is not incredibly useful given it would duplicate
the original data.
'''
# Having clean also means has dicom image
if hasattr(self, image_type):
dicom_name = self._get_clean_name(output_folder)
dicom = read_file(self.dicom_file, force=True)
dicom.PixelData = self.clean.tostring()
dicom.save_as(dicom_name)
return dicom_name
else:
bot.warning('use detect() --> clean() before saving is possible.')
def jitter_timestamp(dicom, field, value):
'''if present, jitter a timestamp in dicom
field "field" by number of days specified by "value"
The value can be positive or negative.
Parameters
==========
dicom: the pydicom Dataset
field: the field with the timestamp
value: number of days to jitter by. Jitter bug!
'''
if not isinstance(value, int):
value = int(value)
original = dicom.get(field, None)
if original is not None:
dcmvr = dicom.data_element(field).VR
'''
DICOM Value Representation can be either DA (Date) DT (Timestamp),
or something else, which is not supported.
'''
if (dcmvr == 'DA'):
'''
NEMA-compliant format for DICOM date is YYYYMMDD
'''
new_value = get_timestamp(original,
jitter_days=value,
format='%Y%m%d')
elif (dcmvr == 'DT'):
'''
NEMA-compliant format for DICOM timestamp is
YYYYMMDDHHMMSS.FFFFFF&ZZXX
'''
new_value = get_timestamp(original,
jitter_days=value,
format='%Y%m%d%H%M%S.%f%z')
else:
# Do nothing and issue a warning.
new_value = None
bot.warning("JITTER not supported for %s with VR=%s" %
(field, dcmvr))
if (new_value is not None and new_value != original):
# Only update if there's something to update AND there's been change
dicom = update_tag(dicom, field=field, value=new_value)
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 _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 parse_value(item, value):
'''parse_value will parse the value field of an action,
either returning the string, or a variable looked up
in the case of var:FieldName
'''
# Does the user want a custom value?
if re.search('[:]', value):
value_type, value_option = value.split(':')
if value_type.lower() == "var":
# If selected variable not provided, skip
if value_option not in item:
return None
return item[value_option]
bot.warning('%s is not a valid value type, skipping.' % (value_type))
return None
return value
