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Disallow measurement report with no measurement groups #325

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Disallow measurement report with no measurement groups #325

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66af872
Explicitly disallow MeasurementReport with no imaging measurements
CPBridge Feb 12, 2025
d93c3f2
Fix indentation bug in ImageLibrary
CPBridge Feb 12, 2025
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150 changes: 85 additions & 65 deletions src/highdicom/sr/templates.py
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Original file line number Diff line number Diff line change
Expand Up @@ -4269,31 +4269,46 @@ def __init__(
PlanarROIMeasurementsAndQualitativeEvaluations |
VolumetricROIMeasurementsAndQualitativeEvaluations
)
if imaging_measurements is not None:
measurement_types = (
PlanarROIMeasurementsAndQualitativeEvaluations,
VolumetricROIMeasurementsAndQualitativeEvaluations,
MeasurementsAndQualitativeEvaluations,

# Since only imaging meansurements are currently supported, at least
# one is required. This could be relaxed in the future if evaluations
# or derived measurements (rows 10 or 12 of the TID1500 table) are
# supported
if imaging_measurements is None:
raise TypeError(
"Argument 'imaging_measurements' is required."
)
container_item = ContainerContentItem(
name=codes.DCM.ImagingMeasurements,
relationship_type=RelationshipTypeValues.CONTAINS

if len(imaging_measurements) == 0:
raise ValueError(
"Argument 'imaging_measurements' must contain at least "
"one item."
)
container_item.ContentSequence = ContentSequence()
for measurements in imaging_measurements:
if not isinstance(measurements, measurement_types):
raise TypeError(
'Measurements must have one of the following types: '
'"{}"'.format(
'", "'.join(
[
t.__name__
for t in measurement_types
]
)

measurement_types = (
PlanarROIMeasurementsAndQualitativeEvaluations,
VolumetricROIMeasurementsAndQualitativeEvaluations,
MeasurementsAndQualitativeEvaluations,
)
container_item = ContainerContentItem(
name=codes.DCM.ImagingMeasurements,
relationship_type=RelationshipTypeValues.CONTAINS
)
container_item.ContentSequence = ContentSequence()
for measurements in imaging_measurements:
if not isinstance(measurements, measurement_types):
raise TypeError(
'Measurements must have one of the following types: '
'"{}"'.format(
'", "'.join(
[
t.__name__
for t in measurement_types
]
)
)
container_item.ContentSequence.extend(measurements)
)
container_item.ContentSequence.extend(measurements)
item.ContentSequence.append(container_item)
super().__init__([item], is_root=True)

Expand Down Expand Up @@ -5119,58 +5134,63 @@ def __init__(

"""
super().__init__()

if len(datasets) == 0:
raise ValueError(
"Argument 'datasets' must contain at least one item."
)

library_item = ContainerContentItem(
name=codes.DCM.ImageLibrary,
relationship_type=RelationshipTypeValues.CONTAINS
)
library_item.ContentSequence = ContentSequence()
if datasets is not None:
groups = collections.defaultdict(list)
for ds in datasets:
modality = _get_coded_modality(ds.SOPClassUID)
image_item = ImageContentItem(
name=CodedConcept(
value='260753009',
meaning='Source',
scheme_designator='SCT'
),
referenced_sop_instance_uid=ds.SOPInstanceUID,
referenced_sop_class_uid=ds.SOPClassUID,
relationship_type=RelationshipTypeValues.CONTAINS
groups = collections.defaultdict(list)
for ds in datasets:
modality = _get_coded_modality(ds.SOPClassUID)
image_item = ImageContentItem(
name=CodedConcept(
value='260753009',
meaning='Source',
scheme_designator='SCT'
),
referenced_sop_instance_uid=ds.SOPInstanceUID,
referenced_sop_class_uid=ds.SOPClassUID,
relationship_type=RelationshipTypeValues.CONTAINS
)
descriptors = ImageLibraryEntryDescriptors(ds)

image_item.ContentSequence = ContentSequence()
image_item.ContentSequence.extend(descriptors)
if 'FrameOfReferenceUID' in ds:
# Only type 1 attributes
shared_descriptors = (
modality,
ds.FrameOfReferenceUID,
)
descriptors = ImageLibraryEntryDescriptors(ds)

image_item.ContentSequence = ContentSequence()
image_item.ContentSequence.extend(descriptors)
if 'FrameOfReferenceUID' in ds:
# Only type 1 attributes
shared_descriptors = (
modality,
ds.FrameOfReferenceUID,
)
else:
shared_descriptors = (
modality,
)
groups[shared_descriptors].append(image_item)

for shared_descriptors, image_items in groups.items():
image = image_items[0]
group_item = ContainerContentItem(
name=codes.DCM.ImageLibraryGroup,
relationship_type=RelationshipTypeValues.CONTAINS
else:
shared_descriptors = (
modality,
)
group_item.ContentSequence = ContentSequence()

if 'FrameOfReferenceUID' in image:
group_item.ContentSequence.append(
UIDRefContentItem(
name=codes.DCM.FrameOfReferenceUID,
value=shared_descriptors[1],
relationship_type=RelationshipTypeValues.HAS_ACQ_CONTEXT # noqa: E501
)
groups[shared_descriptors].append(image_item)

for shared_descriptors, image_items in groups.items():
image = image_items[0]
group_item = ContainerContentItem(
name=codes.DCM.ImageLibraryGroup,
relationship_type=RelationshipTypeValues.CONTAINS
)
group_item.ContentSequence = ContentSequence()

if 'FrameOfReferenceUID' in image:
group_item.ContentSequence.append(
UIDRefContentItem(
name=codes.DCM.FrameOfReferenceUID,
value=shared_descriptors[1],
relationship_type=RelationshipTypeValues.HAS_ACQ_CONTEXT # noqa: E501
)
group_item.ContentSequence.extend(image_items)
)
group_item.ContentSequence.extend(image_items)
if len(group_item) > 0:
library_item.ContentSequence.append(group_item)

Expand Down
61 changes: 60 additions & 1 deletion tests/test_sr.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3851,6 +3851,18 @@ def test_from_sequence(self):
assert len(qualitative_evaluations) == 1
assert isinstance(qualitative_evaluations[0], QualitativeEvaluation)

def test_construction_none(self):
# Since only imaging meansurements are currently supported, at least
# one is required. This could be relaxed in the future if evaluations
# or derived measurements (rows 10 or 12 of the TID1500 table) are
# supported
msg = ("Argument 'imaging_measurements' is required.")
with pytest.raises(TypeError, match=msg):
_ = MeasurementReport(
observation_context=self._observation_context,
procedure_reported=self._procedure_reported,
)


class TestEnhancedSR(unittest.TestCase):

Expand Down Expand Up @@ -5717,7 +5729,9 @@ def test_construction(self):

library_items = ImageLibrary([self._ref_sm_dataset])
assert len(library_items) == 1
library_group_item = library_items[0].ContentSequence[0]
library_groups = library_items[0].ContentSequence
assert len(library_groups) == 1
library_group_item = library_groups[0]
assert len(library_group_item.ContentSequence) == 1
assert library_group_item.name == codes.DCM.ImageLibraryGroup
content_item = library_group_item.ContentSequence[0]
Expand All @@ -5730,3 +5744,48 @@ def test_construction(self):
self._ref_sm_dataset.SOPInstanceUID
assert ref_sop_class_uid == \
self._ref_sm_dataset.SOPClassUID

def test_construction_multiple_groups(self):
file_path = Path(__file__)
data_dir = file_path.parent.parent.joinpath('data')
self._ref_sm_dataset = dcmread(
str(data_dir.joinpath('test_files', 'sm_image.dcm'))
)
self._ref_ct_dataset = dcmread(
str(data_dir.joinpath('test_files', 'ct_image.dcm'))
)

library_items = ImageLibrary(
[self._ref_sm_dataset, self._ref_ct_dataset]
)
assert len(library_items) == 1
library_groups = library_items[0].ContentSequence
assert len(library_groups) == 2

sm_group_item = library_items[0].ContentSequence[0]
assert len(sm_group_item.ContentSequence) == 1
assert sm_group_item.name == codes.DCM.ImageLibraryGroup
content_item = sm_group_item.ContentSequence[0]
assert isinstance(content_item, ImageContentItem)
ref_sop_instance_uid = \
content_item.ReferencedSOPSequence[0].ReferencedSOPInstanceUID
ref_sop_class_uid = \
content_item.ReferencedSOPSequence[0].ReferencedSOPClassUID
assert ref_sop_instance_uid == \
self._ref_sm_dataset.SOPInstanceUID
assert ref_sop_class_uid == \
self._ref_sm_dataset.SOPClassUID

ct_group_item = library_items[0].ContentSequence[1]
assert len(ct_group_item.ContentSequence) == 1
assert ct_group_item.name == codes.DCM.ImageLibraryGroup
content_item = ct_group_item.ContentSequence[0]
assert isinstance(content_item, ImageContentItem)
ref_sop_instance_uid = \
content_item.ReferencedSOPSequence[0].ReferencedSOPInstanceUID
ref_sop_class_uid = \
content_item.ReferencedSOPSequence[0].ReferencedSOPClassUID
assert ref_sop_instance_uid == \
self._ref_ct_dataset.SOPInstanceUID
assert ref_sop_class_uid == \
self._ref_ct_dataset.SOPClassUID