# To get a list of specific filters under a group
recipe.get_filters('blacklist')
################################################################################
# Header Actions
# A header action is a step (e.g., replace, remove, blank) to be applied to
# a dicom image header. The headers are also part of the deid recipe, and you
# don't need to necessarily use header actions and filters at the same time.
################################################################################
# For the example we were doing above, the recipe didn't have a header section.
# Let's load one that does.
recipe = DeidRecipe()
# We can get a complete list of actions
recipe.get_actions()
# We can filter to an action type
recipe.get_actions(action='ADD')
#[{'action': 'ADD',
# 'field': 'IssuerOfPatientID',
# 'value': 'STARR. In an effort to remove PHI all dates are offset from their original values.'},
# {'action': 'ADD',
# 'field': 'PatientBirthDate',
# 'value': 'var:entity_timestamp'},
# {'action': 'ADD', 'field': 'StudyDate', 'value': 'var:item_timestamp'},
# {'action': 'ADD', 'field': 'PatientID', 'value': 'var:entity_id'},
# {'action': 'ADD', 'field': 'AccessionNumber', 'value': 'var:item_id'},
# {'action': 'ADD', 'field': 'PatientIdentityRemoved', 'value': 'Yes'}]
##################################
# Create the DeidRecipe Instance from deid.dicom
from deid.config import DeidRecipe
recipe = DeidRecipe("deid.dicom")
# To see an entire (raw in a dictionary) recipe just look at
recipe.deid
# What is the format?
recipe.get_format()
# dicom
# What actions do we want to do on the header?
recipe.get_actions()
"""
[{'action': 'REPLACE',
'field': 'StudyInstanceUID',
'value': 'func:generate_uid'},
{'action': 'REPLACE',
'field': 'SeriesInstanceUID',
'value': 'func:generate_uid'},
{'action': 'REPLACE',
'field': 'FrameOfReferenceUID',
'value': 'func:generate_uid'}]
"""
# We can filter to an action type (not useful here, we only have one type)
recipe.get_actions(action="REPLACE")
##################################
# Create the DeidRecipe Instance from deid.dicom
from deid.config import DeidRecipe
recipe = DeidRecipe('deid.dicom')
# To see an entire (raw in a dictionary) recipe just look at
recipe.deid
# What is the format?
recipe.get_format()
# dicom
# What actions do we want to do on the header?
recipe.get_actions()
'''
[{'action': 'REPLACE',
'field': 'StudyInstanceUID',
'value': 'func:generate_uid'},
{'action': 'REPLACE',
'field': 'SeriesInstanceUID',
'value': 'func:generate_uid'},
{'action': 'REPLACE',
'field': 'FrameOfReferenceUID',
'value': 'func:generate_uid'}]
'''
# We can filter to an action type (not useful here, we only have one type)
recipe.get_actions(action='REPLACE')
# To get a list of specific filters under a group
recipe.get_filters("blacklist")
################################################################################
# Header Actions
# A header action is a step (e.g., replace, remove, blank) to be applied to
# a dicom image header. The headers are also part of the deid recipe, and you
# don't need to necessarily use header actions and filters at the same time.
################################################################################
# For the example we were doing above, the recipe didn't have a header section.
# Let's load one that does.
recipe = DeidRecipe()
# We can get a complete list of actions
recipe.get_actions()
# We can filter to an action type
recipe.get_actions(action="ADD")
# [{'action': 'ADD',
# 'field': 'IssuerOfPatientID',
# 'value': 'STARR. In an effort to remove PHI all dates are offset from their original values.'},
# {'action': 'ADD',
# 'field': 'PatientBirthDate',
# 'value': 'var:entity_timestamp'},
# {'action': 'ADD', 'field': 'StudyDate', 'value': 'var:item_timestamp'},
# {'action': 'ADD', 'field': 'PatientID', 'value': 'var:entity_id'},
# {'action': 'ADD', 'field': 'AccessionNumber', 'value': 'var:item_id'},
# {'action': 'ADD', 'field': 'PatientIdentityRemoved', 'value': 'Yes'}]
def test_get_functions(self):
recipe = DeidRecipe(self.deid)
# Format
self.assertEqual(recipe.get_format(), "dicom")
# Actions for header
print("Testing get_actions")
actions = recipe.get_actions()
self.assertTrue(isinstance(actions, list))
for key in ["action", "field", "value"]:
self.assertTrue(key in actions[0])
self.assertTrue(recipe.has_actions())
# Filters
print("Testing get_filters")
filters = recipe.get_filters()
self.assertTrue(isinstance(filters, dict))
# whitelist, blacklist, graylist
for key in recipe.ls_filters():
self.assertTrue(key in filters)
recipe = DeidRecipe()
filters = recipe.get_filters()
self.assertTrue(isinstance(filters["whitelist"], list))
# Test that each filter has a set of filters, coords, name
for key in ["filters", "coordinates", "name"]:
self.assertTrue(key in filters["whitelist"][0])
# Each filter is a list of actions, name is string, coords are list
self.assertTrue(isinstance(filters["whitelist"][0]["filters"], list))
self.assertTrue(isinstance(filters["whitelist"][0]["name"], str))
self.assertTrue(
isinstance(filters["whitelist"][0]["coordinates"], list))
# Check content of the first filter
for key in ["action", "field", "operator", "InnerOperators", "value"]:
self.assertTrue(key in filters["whitelist"][0]["filters"][0])
# Fields and Values
print("Testing get_fields_lists and get_values_lists")
self.assertEqual(recipe.get_fields_lists(), None)
self.assertEqual(recipe.get_values_lists(), None)
self.assertEqual(recipe.ls_fieldlists(), [])
self.assertEqual(recipe.ls_valuelists(), [])
self.assertTrue(not recipe.has_fields_lists())
self.assertTrue(not recipe.has_values_lists())
# Load in recipe with values and fields
deid = os.path.abspath("%s/../examples/deid/deid.dicom-groups" %
self.pwd)
recipe = DeidRecipe(deid)
assert "values" in recipe.deid
assert "fields" in recipe.deid
self.assertTrue(isinstance(recipe.deid["values"], dict))
self.assertTrue(isinstance(recipe.deid["fields"], dict))
self.assertTrue(recipe.get_fields_lists() is not None)
self.assertTrue(recipe.get_values_lists() is not None)
self.assertEqual(recipe.ls_fieldlists(), ["instance_fields"])
self.assertEqual(recipe.ls_valuelists(),
["cookie_names", "operator_names"])
self.assertTrue(recipe.has_fields_lists())
self.assertTrue(recipe.has_values_lists())
