def test_get_patient_age_with_field(self, dicom_generator):
age = '10Y'
filename, dataset = dicom_generator(PatientAge=age)
dcm = Dicom(filename, dcm=dataset)
assert dcm._patient_age() == age
def test_get_patient_age_with_birth_date(self, dicom_generator):
filename, dataset = dicom_generator(PatientBirthDate='20180101',
StudyDate='20190701')
dcm = Dicom(filename, dcm=dataset)
assert dcm._patient_age() == '001Y'
def test_sort_test(self, dicom_generator, tmpdir, capsys):
filename, dicom = dicom_generator(
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Base Directory
root = str(tmpdir)
# Subdirectories
directory = [
'%(SeriesDescription)s',
'%(SeriesDescription)s',
]
# Filename format
file_format = '%(ImageType)s'
dcm.sort(root, directory, file_format, keep_original=False, test=True)
destination = tmpdir.join('desc_Series0001').join('desc_Series0001')
destination = destination.join('Unknown')
# The original is unmodified
assert os.path.exists(filename)
# The file was not actually copied
assert os.path.exists(str(destination)) is False
captured = capsys.readouterr()
assert captured.out == str(destination) + '\n'
def test_sort_discard_original(self, dicom_generator, tmpdir):
filename, dicom = dicom_generator(
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Base Directory
root = str(tmpdir)
# Subdirectories
directory = [
'%(SeriesDescription)s',
'%(SeriesDescription)s',
]
# Filename format
file_format = '%(ImageType)s'
dcm.sort(root, directory, file_format, keep_original=False)
destination = tmpdir.join('desc_Series0001').join('desc_Series0001')
destination = destination.join('Unknown')
assert os.path.exists(filename) is False
assert os.path.exists(str(destination))
def test_get_item_override_value(self, dicom_generator):
filename, dicom = dicom_generator()
dcm = Dicom(filename, dcm=dicom)
dcm.set_anonymization_rules({'Field': 'Value'})
assert dcm['Field'] == 'Value'
def test_get_image_type_3drecon(self, dicom_generator):
filename, dataset = dicom_generator(ImageType=['CSA 3D EDITOR', ''])
dcm = Dicom(filename, dcm=dataset)
assert dcm._image_type() == '3DRecon'
assert dataset.InstanceNumber == dataset.SeriesNumber
def test_get_series_description(self, dicom_generator):
filename, dataset = dicom_generator(SeriesDescription=' My Series',
SeriesNumber=1)
dcm = Dicom(filename, dcm=dataset)
assert dcm._series_description() == 'My Series_Series0001'
def test_get_series_description_no_description(self, dicom_generator):
filename, dicom = dicom_generator(SeriesNumber=1)
del dicom.SeriesDescription
dcm = Dicom(filename, dcm=dicom)
assert dcm._series_description() == 'Series0001'
def test_sort_inplace(self, dicom_generator, tmpdir):
filename, dicom = dicom_generator(
'image.dcm',
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Base Directory
root = str(tmpdir)
# Subdirectories
directory = None
# Filename format
file_format = '%(ImageType)s'
dcm.sort(
root,
directory,
file_format,
rootdir=[os.path.dirname(filename)],
)
destination = str(tmpdir.join('image.dcm'))
assert os.path.exists(destination)
def test_get_destination_bad_directory_attr(self, dicom_generator):
filename, dicom = dicom_generator(
'image.dcm',
PatientName='name',
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Base Directory
root = '/my/base/directory'
# Sub-directories
directory = [
'%(Invalid)s', # Invalid attribute
'%(SeriesDescription)s %(PatientName)s'
]
# Filename format
filename = '%(SeriesNumber)d file'
dest = dcm.get_destination(root, directory, filename)
expected = '/my/base/directory/UNKNOWN/desc_Series0001 name/1 file'
assert dest == expected
def test_anonymization_invalid_input(self, dicom_generator):
filename, dataset = dicom_generator()
dcm = Dicom(filename, dcm=dataset)
with pytest.raises(Exception) as excinfo:
dcm.set_anonymization_rules('')
assert excinfo.value.args[0] == 'Anon rules must be a dictionary'
def test_anonymize_birthdate(self, dicom_generator):
date = '20191101'
filename, dataset = dicom_generator(PatientBirthDate='20200101')
dcm = Dicom(filename, dcm=dataset)
dcm.set_anonymization_rules({'PatientBirthDate': date})
assert dcm.overrides['PatientBirthDate'] == date
assert dcm['PatientBirthDate'] == date
def test_anonymize_age(self, dicom_generator):
filename, dataset = dicom_generator(PatientAge='030Y',
PatientBirthDate='19890201',
StudyDate='20190301')
dcm = Dicom(filename, dcm=dataset)
dcm.set_anonymization_rules({'PatientBirthDate': ''})
assert dcm['PatientAge'] == '030Y'
assert dcm['PatientBirthDate'] == '19890101'
def test_anonymization(self, dicom_generator):
filename, dataset = dicom_generator()
dcm = Dicom(filename, dcm=dataset)
adict = {'Key': 'Value'}
dcm.set_anonymization_rules(adict)
assert dcm.anonymization_lookup == adict
assert dcm.overrides['Key'] == 'Value'
assert dcm['Key'] == 'Value'
def test_constructor_without_dicom(self, dicom_generator, mocker):
func = mocker.patch.object(pydicom, 'read_file', return_value='dicom')
filename, _ = dicom_generator()
dcm = Dicom(filename)
func.assert_called_once_with(filename)
assert dcm.dicom == 'dicom'
def test_constructor_with_dicom(self, dicom_generator, mocker):
func = mocker.patch.object(pydicom, 'read_file', return_value='dicom')
filename, dataset = dicom_generator()
dcm = Dicom(filename, dcm=dataset)
func.assert_not_called()
assert dcm.dicom == dataset
def test_create_default_overrides(self, dicom_generator):
filename, dataset = dicom_generator()
dcm = Dicom(filename, dcm=dataset)
assert 'ImageType' in dcm.default_overrides
assert 'FileExtension' in dcm.default_overrides
assert 'SeriesDescription' in dcm.default_overrides
assert dcm.overrides == dcm.default_overrides
def test_sort_anonymize(self, dicom_generator, tmpdir):
filename, dicom = dicom_generator(
PatientName='TO^BE^REMOVED',
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Overwrite the PatientName
dcm.set_anonymization_rules({'PatientName': 'ANON'})
# Base Directory
root = str(tmpdir)
# Subdirectories
directory = [
'%(PatientName)s',
'%(SeriesDescription)s',
]
# Filename format
file_format = '%(ImageType)s'
dcm.sort(root, directory, file_format, keep_original=False)
destination = tmpdir.join('ANON').join('desc_Series0001')
destination = str(destination.join('Unknown'))
assert os.path.exists(destination)
# Ensure the DICOM was modified
newdcm = pydicom.read_file(destination)
assert newdcm.PatientName == 'ANON'
def test_sort_anonymize_invalid_field(self, dicom_generator, tmpdir):
filename, dicom = dicom_generator(
PatientName='TO^BE^REMOVED',
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Overwrite the PatientID (this field does not exist)
dcm.set_anonymization_rules({'PatientID': 'ANON'})
# Base Directory
root = str(tmpdir)
# Subdirectories
directory = [
'%(PatientID)s',
'%(SeriesDescription)s',
]
# Filename format
file_format = '%(ImageType)s'
dcm.sort(root, directory, file_format, keep_original=False)
destination = tmpdir.join('ANON').join('desc_Series0001')
destination = str(destination.join('Unknown'))
assert os.path.exists(destination)
# Make sure the field was not added to the new DICOM
newdcm = pydicom.read_file(destination)
assert 'PatientID' not in newdcm
def test_get_destination(self, dicom_generator):
filename, dicom = dicom_generator(
PatientName='name',
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Base Directory
root = '/my/base/directory'
# Sub-directories
directory = ['%(ImageType)s', '%(SeriesDescription)s %(PatientName)s']
# Filename format
filename = '%(SeriesNumber)d file'
dest = dcm.get_destination(root, directory, filename)
expected = '/my/base/directory/Unknown/desc_Series0001 name/1 file'
assert dest == expected
def test_get_destination_bad_filename_attr(self, dicom_generator):
filename, dicom = dicom_generator(
'image.dcm',
PatientName='name',
SeriesDescription='desc',
SeriesNumber=1,
)
dcm = Dicom(filename, dcm=dicom)
# Base Directory
root = '/my/base/directory'
# Sub-directories
directory = ['%(ImageType)s', '%(SeriesDescription)s %(PatientName)s']
# Filename format which uses attributes that are not defined
filename = '%(Invalid)d file'
dest = dcm.get_destination(root, directory, filename)
expected = '/my/base/directory/Unknown/desc_Series0001 name/image.dcm'
assert dest == expected
def test_is_anonymous(self, dicom_generator):
filename, dataset = dicom_generator()
dcm = Dicom(filename, dcm=dataset)
assert dcm.is_anonymous() is False
# Set anonimization rules
dcm.set_anonymization_rules({'PatientName': 'ANON'})
assert dcm.is_anonymous() is True
def test_anonymize_empty_birthdate(self, dicom_generator):
filename, dataset = dicom_generator(
PatientBirthDate='20170601',
StudyDate='20180201',
)
dcm = Dicom(filename, dcm=dataset)
dcm.set_anonymization_rules({'PatientBirthDate': ''})
# Maintains the patient age but uses January 01
assert dcm.overrides['PatientBirthDate'] == '20180101'
assert dcm['PatientBirthDate'] == '20180101'
# 1-day Old
dataset.PatientBirthDate = '20180131'
dcm.set_anonymization_rules({'PatientBirthDate': ''})
assert dcm.overrides['PatientBirthDate'] == '20180101'
assert dcm['PatientBirthDate'] == '20180101'
def test_get_image_type_magnitude(self, dicom_generator):
filename, dataset = dicom_generator(ImageType=['FFE', 'M', 'JUNK'])
dcm = Dicom(filename, dcm=dataset)
assert dcm._image_type() == 'Mag'
def test_get_image_type_phase(self, dicom_generator):
filename, dataset = dicom_generator(ImageType=['P', 'BLAH'])
dcm = Dicom(filename, dcm=dataset)
assert dcm._image_type() == 'Phase'
def test_get_image_type_phoenix(self, dicom_generator):
filename, dataset = dicom_generator(ImageType=['CSA REPORT', ''])
dcm = Dicom(filename, dcm=dataset)
assert dcm._image_type() == 'Phoenix'
def test_get_file_extension_empty(self, dicom_generator):
filename, _ = dicom_generator('image')
dcm = Dicom(filename)
assert dcm._file_extension() == ''
def test_get_item_dicom_attribute(self, dicom_generator):
filename, dicom = dicom_generator(PatientName='Suever')
dcm = Dicom(filename, dcm=dicom)
assert dcm['PatientName'] == 'Suever'
def test_get_image_type_no_type(self, dicom_generator):
filename, dataset = dicom_generator()
dcm = Dicom(filename, dcm=dataset)
assert dcm._image_type() == 'Unknown'
def test_get_image_type_generic(self, dicom_generator):
filename, dataset = dicom_generator(ImageType=['A', 'B'])
dcm = Dicom(filename, dcm=dataset)
assert dcm._image_type() == 'Image'