def test_adjust_machine_name():
new_name = 'new_name'
original_ds = dicom_dataset_from_dict({
'BeamSequence': [
{
'TreatmentMachineName': 'hello'
},
{
'TreatmentMachineName': 'george'
}
]
})
expected_ds = dicom_dataset_from_dict({
'BeamSequence': [
{
'TreatmentMachineName': new_name
},
{
'TreatmentMachineName': new_name
}
]
})
adjusted_ds = adjust_machine_name(original_ds, new_name)
assert adjusted_ds != original_ds
assert adjusted_ds == expected_ds
command = (
'pymedphys dicom adjust-machine-name'.split() +
[ORIGINAL_DICOM_FILENAME, ADJUSTED_DICOM_FILENAME, new_name])
compare_dicom_cli(command, original_ds, expected_ds)
def test_structure_name_based_RED_append():
electron_density_to_use = 0.5
original_ds = dicom_dataset_from_dict({
"StructureSetROISequence": [
{
"ROINumber": 1,
"ROIName":
"a_structure RED={}".format(electron_density_to_use),
},
{
"ROINumber": 2,
"ROIName": "dont_change_me"
},
],
"RTROIObservationsSequence": [
{
"ReferencedROINumber": 1
},
{
"ReferencedROINumber": 2
},
],
})
expected_ds = dicom_dataset_from_dict(
{
"RTROIObservationsSequence": [
{
"ReferencedROINumber":
1,
"ROIPhysicalPropertiesSequence":
[{
"ROIPhysicalProperty": "REL_ELEC_DENSITY",
"ROIPhysicalPropertyValue": electron_density_to_use,
}],
},
{
"ReferencedROINumber": 2
},
]
},
template_ds=original_ds,
)
adjusted_ds = adjust_RED_by_structure_name(original_ds)
assert adjusted_ds != original_ds
assert str(expected_ds) == str(adjusted_ds)
command = "pymedphys dicom adjust-RED-by-structure-name".split() + [
ORIGINAL_DICOM_FILENAME,
ADJUSTED_DICOM_FILENAME,
]
compare_dicom_cli(command, original_ds, expected_ds)
def test_structure_name_based_RED_append():
electron_density_to_use = 0.5
original_ds = dicom_dataset_from_dict({
'StructureSetROISequence': [
{
'ROINumber': 1,
'ROIName': 'a_structure RED={}'.format(electron_density_to_use)
},
{
'ROINumber': 2,
'ROIName': 'dont_change_me'
}
],
'RTROIObservationsSequence': [
{
'ReferencedROINumber': 1,
},
{
'ReferencedROINumber': 2,
}
]
})
expected_ds = dicom_dataset_from_dict({
'RTROIObservationsSequence': [
{
'ReferencedROINumber': 1,
'ROIPhysicalPropertiesSequence': [
{
'ROIPhysicalProperty': 'REL_ELEC_DENSITY',
'ROIPhysicalPropertyValue': electron_density_to_use
}
]
},
{
'ReferencedROINumber': 2
},
]
}, template_ds=original_ds)
adjusted_ds = adjust_RED_by_structure_name(original_ds)
assert adjusted_ds != original_ds
assert str(expected_ds) == str(adjusted_ds)
command = (
'pymedphys dicom adjust-RED-by-structure-name'.split()
+ [ORIGINAL_DICOM_FILENAME, ADJUSTED_DICOM_FILENAME])
compare_dicom_cli(command, original_ds, expected_ds)
def test_copy():
dont_change_string = "don't change me"
to_be_changed_string = 'do change me'
new_manufactuer = 'george'
dataset_to_be_copied = dicom_dataset_from_dict(
{'Manufacturer': dont_change_string})
dataset_to_be_viewed = dicom_dataset_from_dict(
{'Manufacturer': to_be_changed_string})
dicom_base_copy = DicomBase(dataset_to_be_copied)
dicom_base_view = DicomBase(dataset_to_be_viewed, copy=False)
dicom_base_copy.dataset.Manufacturer = new_manufactuer
dicom_base_view.dataset.Manufacturer = new_manufactuer
assert dataset_to_be_copied.Manufacturer == dont_change_string
assert dataset_to_be_viewed.Manufacturer == new_manufactuer
def test_anonymise():
expected_dataset = dicom_dataset_from_dict({
'Manufacturer': 'PyMedPhys',
'PatientName': 'Anonymous'
})
dicom = DicomBase.from_dict({
'Manufacturer': 'PyMedPhys',
'PatientName': 'Python^Monte'
})
dicom.anonymise(inplace=True)
assert dicom.dataset == expected_dataset
def test_anonymise():
expected_dataset = dicom_dataset_from_dict({
"Manufacturer": "PyMedPhys",
"PatientName": "Anonymous"
})
dicom = DicomBase.from_dict({
"Manufacturer": "PyMedPhys",
"PatientName": "Python^Monte"
})
dicom.anonymise(inplace=True)
assert dicom.dataset == expected_dataset
def test_adjust_machine_name():
new_name = "new_name"
original_ds = dicom_dataset_from_dict({
"BeamSequence": [
{
"TreatmentMachineName": "hello"
},
{
"TreatmentMachineName": "george"
},
]
})
expected_ds = dicom_dataset_from_dict({
"BeamSequence": [
{
"TreatmentMachineName": new_name
},
{
"TreatmentMachineName": new_name
},
]
})
adjusted_ds = adjust_machine_name(original_ds, new_name)
assert adjusted_ds != original_ds
assert adjusted_ds == expected_ds
command = "pymedphys dicom adjust-machine-name".split() + [
ORIGINAL_DICOM_FILENAME,
ADJUSTED_DICOM_FILENAME,
new_name,
]
compare_dicom_cli(command, original_ds, expected_ds)
def test_dicom_from_dict():
baseline_dataset = pydicom.Dataset()
baseline_dataset.Manufacturer = "PyMedPhys"
beam_sequence = pydicom.Dataset()
beam_sequence.Manufacturer = "PyMedPhys"
baseline_dataset.BeamSequence = [beam_sequence]
created_dataset = dicom_dataset_from_dict({
"Manufacturer":
"PyMedPhys",
"BeamSequence": [{
"Manufacturer": "PyMedPhys"
}]
})
assert created_dataset == baseline_dataset
def test_dicom_from_dict():
baseline_dataset = pydicom.Dataset()
baseline_dataset.Manufacturer = 'PyMedPhys'
beam_sequence = pydicom.Dataset()
beam_sequence.Manufacturer = 'PyMedPhys'
baseline_dataset.BeamSequence = [beam_sequence]
created_dataset = dicom_dataset_from_dict({
'Manufacturer':
'PyMedPhys',
'BeamSequence': [{
'Manufacturer': 'PyMedPhys'
}]
})
assert created_dataset == baseline_dataset
def test_pull_structure():
dicom_structure = dicom_dataset_from_dict({
'StructureSetROISequence': [{
'ROIName': A_STRUCTURE.name,
'ROINumber': A_STRUCTURE.number
}, {
'ROIName': ANOTHER_STRUCTURE.name,
'ROINumber': ANOTHER_STRUCTURE.number
}],
'ROIContourSequence': [
# Sequence purposely placed in reverse order to ensure ROI
# number is being used and not list order.
create_contour_sequence_dict(ANOTHER_STRUCTURE),
create_contour_sequence_dict(A_STRUCTURE)
]
})
x, y, z = pull_structure(A_STRUCTURE.name, dicom_structure)
assert np.all(x == np.array(A_STRUCTURE.coords)[:, 0, :])
assert np.all(y == np.array(A_STRUCTURE.coords)[:, 1, :])
assert np.all(z == np.array(A_STRUCTURE.coords)[:, 2, :])
def test_electron_density_append():
adjustment_map = {
"to_be_changed 1": 1.0,
"to_be_changed 2": 0.5,
"to_be_changed 3": 1.5,
}
excess_adjustment_map = {
**adjustment_map,
**{
"this_structure_doesnt_exist": 1.0
}
}
original_ds = dicom_dataset_from_dict({
"StructureSetROISequence": [
{
"ROINumber": 1,
"ROIName": "to_be_changed 1"
},
{
"ROINumber": 2,
"ROIName": "dont_change_me"
},
{
"ROINumber": 10,
"ROIName": "to_be_changed 2"
},
{
"ROINumber": 99,
"ROIName": "to_be_changed 3"
},
],
"RTROIObservationsSequence": [
{
"ReferencedROINumber":
1,
"ROIPhysicalPropertiesSequence": [{
"ROIPhysicalProperty":
"EFFECTIVE_Z",
"ROIPhysicalPropertyValue":
6,
}],
},
{
"ReferencedROINumber": 2
},
{
"ReferencedROINumber": 10
},
{
"ReferencedROINumber":
99,
"ROIPhysicalPropertiesSequence": [{
"ROIPhysicalProperty":
"REL_ELEC_DENSITY",
"ROIPhysicalPropertyValue":
0,
}],
},
],
})
expected_ds = dicom_dataset_from_dict(
{
"RTROIObservationsSequence": [
{
"ReferencedROINumber":
1,
"ROIPhysicalPropertiesSequence": [
{
"ROIPhysicalProperty": "EFFECTIVE_Z",
"ROIPhysicalPropertyValue": 6,
},
{
"ROIPhysicalProperty":
"REL_ELEC_DENSITY",
"ROIPhysicalPropertyValue":
adjustment_map["to_be_changed 1"],
},
],
},
{
"ReferencedROINumber": 2
},
{
"ReferencedROINumber":
10,
"ROIPhysicalPropertiesSequence": [{
"ROIPhysicalProperty":
"REL_ELEC_DENSITY",
"ROIPhysicalPropertyValue":
adjustment_map["to_be_changed 2"],
}],
},
{
"ReferencedROINumber":
99,
"ROIPhysicalPropertiesSequence": [{
"ROIPhysicalProperty":
"REL_ELEC_DENSITY",
"ROIPhysicalPropertyValue":
adjustment_map["to_be_changed 3"],
}],
},
]
},
template_ds=original_ds,
)
adjusted_ds = adjust_rel_elec_density(original_ds, adjustment_map)
assert adjusted_ds != original_ds
assert str(expected_ds) == str(adjusted_ds)
adjusted_with_excess_ds = adjust_rel_elec_density(
original_ds, excess_adjustment_map, ignore_missing_structure=True)
assert adjusted_with_excess_ds != original_ds
assert str(expected_ds) == str(adjusted_with_excess_ds)
excess_adjustment_map_as_list = [[
"{}".format(key), item
] for key, item in excess_adjustment_map.items()]
excess_adjustment_map_flat = np.concatenate(
excess_adjustment_map_as_list).tolist()
command = ("pymedphys dicom adjust-RED -i ".split() +
[ORIGINAL_DICOM_FILENAME, ADJUSTED_DICOM_FILENAME] +
excess_adjustment_map_flat)
compare_dicom_cli(command, original_ds, expected_ds)
def test_anonymise_dataset_and_all_is_anonymised_functions():
# Create dict with one instance of every identifying keyword and
# run basic anonymisation tests
non_anon_dict = dict.fromkeys(IDENTIFYING_KEYWORDS)
for key in non_anon_dict:
non_anon_dict[key] = _get_non_anonymous_replacement_value(key)
ds = dicom_dataset_from_dict(non_anon_dict)
_check_is_anonymised_dataset_file_and_dir(ds, anon_is_expected=False)
ds_anon = anonymise_dataset(ds)
_check_is_anonymised_dataset_file_and_dir(ds_anon, anon_is_expected=True)
# Test anonymisation (and check thereof) for each identifying
# element individually.
for elem in ds_anon.iterall():
ds_single_non_anon_value = deepcopy(ds_anon)
setattr(ds_single_non_anon_value, elem.keyword,
_get_non_anonymous_replacement_value(elem.keyword))
_check_is_anonymised_dataset_file_and_dir(ds_single_non_anon_value,
anon_is_expected=False)
ds_single_anon = anonymise_dataset(ds_single_non_anon_value)
_check_is_anonymised_dataset_file_and_dir(ds_single_anon,
anon_is_expected=True)
# Test correct handling of private tags
ds_anon.add(DataElement(0x0043102b, 'SS', [4, 4, 0, 0]))
_check_is_anonymised_dataset_file_and_dir(ds_anon,
anon_is_expected=False,
ignore_private_tags=False)
_check_is_anonymised_dataset_file_and_dir(ds_anon,
anon_is_expected=True,
ignore_private_tags=True)
ds_anon.remove_private_tags()
_check_is_anonymised_dataset_file_and_dir(ds_anon,
anon_is_expected=True,
ignore_private_tags=False)
# Test blank anonymisation
# # Sanity check
_check_is_anonymised_dataset_file_and_dir(ds, anon_is_expected=False)
ds_anon_blank = anonymise_dataset(ds, replace_values=False)
_check_is_anonymised_dataset_file_and_dir(ds_anon_blank,
anon_is_expected=True)
# Test handling of unknown tags by removing PatientName from
# baseline dict
patient_name_tag = tag_for_keyword('PatientName')
try:
patient_name = BaselineDicomDictionary.pop(patient_name_tag)
with pytest.raises(ValueError) as e_info:
anonymise_dataset(ds)
assert str(e_info).count("At least one of the non-private tags "
"within your DICOM file is not within "
"PyMedPhys's copy of the DICOM dictionary.")
ds_anon_delete_unknown = anonymise_dataset(ds,
delete_unknown_tags=True)
_check_is_anonymised_dataset_file_and_dir(ds_anon_delete_unknown,
anon_is_expected=True)
with pytest.raises(AttributeError) as e_info:
ds_anon_delete_unknown.PatientName
assert str(e_info).count("'Dataset' object has no attribute "
"'PatientName'")
ds_anon_ignore_unknown = anonymise_dataset(ds,
delete_unknown_tags=False)
_check_is_anonymised_dataset_file_and_dir(ds_anon_ignore_unknown,
anon_is_expected=True)
assert patient_name_tag in ds_anon_ignore_unknown
finally:
BaselineDicomDictionary.setdefault(patient_name_tag, patient_name)
# Test copy_dataset=False:
anonymise_dataset(ds, copy_dataset=False)
assert is_anonymised_dataset(ds)
def test_electron_density_append():
adjustment_map = {
'to_be_changed 1': 1.0,
'to_be_changed 2': 0.5,
'to_be_changed 3': 1.5
}
excess_adjustment_map = {
**adjustment_map,
**{
'this_structure_doesnt_exist': 1.0
}
}
original_ds = dicom_dataset_from_dict({
'StructureSetROISequence': [
{
'ROINumber': 1,
'ROIName': 'to_be_changed 1'
},
{
'ROINumber': 2,
'ROIName': 'dont_change_me'
},
{
'ROINumber': 10,
'ROIName': 'to_be_changed 2'
},
{
'ROINumber': 99,
'ROIName': 'to_be_changed 3'
},
],
'RTROIObservationsSequence': [
{
'ReferencedROINumber': 1,
'ROIPhysicalPropertiesSequence': [
{
'ROIPhysicalProperty': 'EFFECTIVE_Z',
'ROIPhysicalPropertyValue': 6
}
]
},
{
'ReferencedROINumber': 2,
},
{
'ReferencedROINumber': 10,
},
{
'ReferencedROINumber': 99,
'ROIPhysicalPropertiesSequence': [
{
'ROIPhysicalProperty': 'REL_ELEC_DENSITY',
'ROIPhysicalPropertyValue': 0
}
]
}
]
})
expected_ds = dicom_dataset_from_dict({
'RTROIObservationsSequence': [
{
'ReferencedROINumber': 1,
'ROIPhysicalPropertiesSequence': [
{
'ROIPhysicalProperty': 'EFFECTIVE_Z',
'ROIPhysicalPropertyValue': 6
},
{
'ROIPhysicalProperty': 'REL_ELEC_DENSITY',
'ROIPhysicalPropertyValue': adjustment_map['to_be_changed 1']
}
]
},
{
'ReferencedROINumber': 2
},
{
'ReferencedROINumber': 10,
'ROIPhysicalPropertiesSequence': [
{
'ROIPhysicalProperty': 'REL_ELEC_DENSITY',
'ROIPhysicalPropertyValue': adjustment_map['to_be_changed 2']
}
]
},
{
'ReferencedROINumber': 99,
'ROIPhysicalPropertiesSequence': [
{
'ROIPhysicalProperty': 'REL_ELEC_DENSITY',
'ROIPhysicalPropertyValue': adjustment_map['to_be_changed 3']
}
]
}
]
}, template_ds=original_ds)
adjusted_ds = adjust_rel_elec_density(
original_ds, adjustment_map)
assert adjusted_ds != original_ds
assert str(expected_ds) == str(adjusted_ds)
adjusted_with_excess_ds = adjust_rel_elec_density(
original_ds, excess_adjustment_map, ignore_missing_structure=True)
assert adjusted_with_excess_ds != original_ds
assert str(expected_ds) == str(adjusted_with_excess_ds)
excess_adjustment_map_as_list = [
['{}'.format(key), item] for key, item in excess_adjustment_map.items()
]
excess_adjustment_map_flat = np.concatenate(
excess_adjustment_map_as_list).tolist()
command = (
'pymedphys dicom adjust-RED -i '.split()
+ [ORIGINAL_DICOM_FILENAME, ADJUSTED_DICOM_FILENAME]
+ excess_adjustment_map_flat)
compare_dicom_cli(command, original_ds, expected_ds)