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_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_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_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)