def testBuildJsonSR(self, *_):
study_json_copy = _MOCK_STUDY_JSON.copy()
builder = dicom_builder.DicomBuilder()
dicom_json_sr = builder.BuildJsonSR(_REPORT_CONTENT, _MOCK_STUDY_JSON)
# Ensure the study json is not affected by the builder.
self.assertEqual(_MOCK_STUDY_JSON, study_json_copy)
# Test the UIDs, order doesn't matter.
self.assertCountEqual(
(dicom_json_sr.series_uid, dicom_json_sr.instance_uid), (_UID1, _UID2))
dicom_dict = dicom_json_sr.dicom_dict
# Test Study Level Tags
for item in _MOCK_STUDY_JSON:
self.assertIn(item, dicom_dict)
self._AssertJsonTag(dicom_dict, tags.STUDY_INSTANCE_UID, _STUDY_UID)
# Test instance level tags.
self._AssertJsonTag(dicom_dict, tags.SPECIFIC_CHARACTER_SET,
dicom_builder._ISO_CHARACTER_SET)
self._AssertJsonTag(dicom_dict, tags.MEDIA_STORAGE_SOP_INSTANCE_UID,
dicom_json_sr.instance_uid)
self._AssertJsonTag(dicom_dict, tags.MEDIA_STORAGE_SOP_CLASS_UID,
tag_values.BASIC_TEXT_SR_CUID)
self._AssertJsonTag(dicom_dict, tags.SOP_CLASS_UID,
tag_values.BASIC_TEXT_SR_CUID)
self._AssertJsonTag(dicom_dict, tags.MODALITY, tag_values.SR_MODALITY)
# Test content sequence tags including inference text.
content_sequence = dicom_json.GetValue(dicom_dict, tags.CONTENT_SEQUENCE)
self._AssertJsonTag(content_sequence, tags.TEXT_VALUE, _REPORT_CONTENT)
self._AssertJsonTag(content_sequence, tags.VALUE_TYPE, 'TEXT')
self._AssertJsonTag(content_sequence, tags.RELATIONSHIP_TYPE, 'CONTAINS')
def BuildJsonSC(self, image_array: np.ndarray, metadata_json: Dict[Text,
Any],
series_uid: Text) -> dicom_json.ObjectWithBulkData:
"""Builds and returns a DICOM Secondary Capture.
Args:
image_array: Image array (RGB) to embed in DICOM instance.
metadata_json: Dict of tags (including study-level information) to add.
series_uid: UID of the series to create the SC in.
Returns:
DICOM JSON Object containing JSON and bulk data of the Secondary Capture.
"""
# Copy over any study and instance level tags.
instance_uid = self.GenerateUID()
metadata_json = metadata_json.copy()
dicom_json.Insert(metadata_json, tags.SOP_CLASS_UID,
tag_values.SECONDARY_CAPTURE_CUID)
dicom_json.Insert(metadata_json, tags.MODALITY, tag_values.OT_MODALITY)
dicom_json.Insert(metadata_json, tags.SERIES_INSTANCE_UID, series_uid)
dicom_json.Insert(metadata_json, tags.SPECIFIC_CHARACTER_SET,
_ISO_CHARACTER_SET)
dicom_json.Insert(metadata_json, tags.SOP_INSTANCE_UID, instance_uid)
dicom_json.Insert(metadata_json, tags.TRANSFER_SYNTAX_UID,
_IMPLICIT_VR_LITTLE_ENDIAN)
dicom_json.Insert(metadata_json, tags.MEDIA_STORAGE_SOP_CLASS_UID,
tag_values.SECONDARY_CAPTURE_CUID)
dicom_json.Insert(metadata_json, tags.MEDIA_STORAGE_SOP_INSTANCE_UID,
instance_uid)
# Assures URI is unique.
study_uid = dicom_json.GetValue(metadata_json, tags.STUDY_INSTANCE_UID)
uri = '{}/{}/{}'.format(study_uid, series_uid, instance_uid)
metadata_json[tags.PIXEL_DATA.number] = {
'vr': tags.PIXEL_DATA.vr,
'BulkDataURI': uri
}
dicom_json.Insert(metadata_json, tags.PHOTOMETRIC_INTERPRETATION,
'RGB')
dicom_json.Insert(metadata_json, tags.SAMPLES_PER_PIXEL, 3)
# Indicates we store pixel data as R1,G1,B1,R2,G2,B2...
dicom_json.Insert(metadata_json, tags.PLANAR_CONFIGURATION, 0)
dicom_json.Insert(metadata_json, tags.ROWS, image_array.shape[0])
dicom_json.Insert(metadata_json, tags.COLUMNS, image_array.shape[1])
dicom_json.Insert(metadata_json, tags.BITS_ALLOCATED, 8)
dicom_json.Insert(metadata_json, tags.BITS_STORED, 8)
dicom_json.Insert(metadata_json, tags.HIGH_BIT, 7)
dicom_json.Insert(metadata_json, tags.PIXEL_REPRESENTATION, 0)
bulkdata = dicom_web.DicomBulkData(
uri=uri,
data=image_array.tobytes(),
content_type='application/octet-stream')
return dicom_json.ObjectWithBulkData(metadata_json, [bulkdata])
def _AssertJsonTag(self, dicomjson: Dict[Text, Any], tag: tags.DicomTag,
expected: Text) -> None:
"""Given a DICOM JSON asserts whether the tag's value is the expected value.
Args:
dicomjson: Dict representing the DICOM JSON structure.
tag: A tuple representing a DICOM Tag and its associated VR.
expected: String value to compare the value of the tag in the dicomjson
to.
"""
self.assertEqual(dicom_json.GetValue(dicomjson, tag), expected)
def _IsMammoInstance(instance_path):
# type: dicom_path.Path -> bool
"""Returns whether the DICOM instance is of type MG modality.
Args:
instance_path: dicom_path.Path of DICOM instance.
Returns:
ParsedMessage or None if the message is invalid.
"""
series_url = posixpath.join(_HEALTHCARE_API_URL_PREFIX,
str(instance_path.GetSeriesPath()))
qido_url = ('%s/instances?SOPInstanceUID=%s&includefield=%s' %
(series_url, instance_path.instance_uid, tags.MODALITY.number))
parsed_content = _QidoRs(qido_url)[0]
modality = dicom_json.GetValue(parsed_content, tags.MODALITY)
if modality is None or modality != tag_values.MG_MODALITY:
return False
return True
def testGetValue(self, tag, expected_value): """Tests expected return values for `GetValue()`.""" actual_value = dicom_json.GetValue(_DICOM_JSON, tag) self.assertEqual(actual_value, expected_value)