def BuildJsonInstanceFromPng(
self, image: bytes,
sop_class_uid: Text) -> dicom_json.ObjectWithBulkData:
"""Builds and returns a DICOM instance from a PNG.
This function will create a new DICOM study and series. Converts all
incoming
images to grayscale.
Args:
image: Image bytes of DICOM instance.
sop_class_uid: UID of the SOP class for DICOM instance.
Returns:
DICOM JSON Object containing JSON and bulk data of the Secondary Capture.
"""
study_uid = self.GenerateUID()
series_uid = self.GenerateUID()
instance_uid = self.GenerateUID()
metadata_json = {}
dicom_json.Insert(metadata_json, tags.PLANAR_CONFIGURATION, 0)
# Converts colored images to grayscale.
dicom_json.Insert(metadata_json, tags.PHOTOMETRIC_INTERPRETATION,
'MONOCHROME2')
dicom_json.Insert(metadata_json, tags.SOP_CLASS_UID, sop_class_uid)
dicom_json.Insert(metadata_json, tags.STUDY_INSTANCE_UID, study_uid)
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,
_EXPLICIT_VR_LITTLE_ENDIAN)
dicom_json.Insert(metadata_json, tags.MEDIA_STORAGE_SOP_CLASS_UID,
sop_class_uid)
dicom_json.Insert(metadata_json, tags.MEDIA_STORAGE_SOP_INSTANCE_UID,
instance_uid)
# Assures URI is unique.
uri = '{}/{}/{}'.format(study_uid, series_uid, instance_uid)
metadata_json[tags.PIXEL_DATA.number] = {
'vr': tags.PIXEL_DATA.vr,
'BulkDataURI': uri
}
bulkdata = dicom_web.DicomBulkData(
uri=uri, data=image, content_type='image/png; transfer-syntax=""')
return dicom_json.ObjectWithBulkData(metadata_json, [bulkdata])
def testObjectWithBulkData(self):
"""Tests methods of ObjectWithBulkData class."""
# Construct dicom_json.ObjectWithBulkData object
dicom_dict = dict()
instance_uid = 'instance_uid'
study_uid = 'study_uid'
series_uid = 'series_uid'
dicom_json.Insert(dicom_dict, tags.SOP_INSTANCE_UID, instance_uid)
dicom_json.Insert(dicom_dict, tags.STUDY_INSTANCE_UID, study_uid)
dicom_json.Insert(dicom_dict, tags.SERIES_INSTANCE_UID, series_uid)
bulkdata = dicom_web.DicomBulkData(
uri='uri',
data=bytearray('image_array', encoding='utf8'),
content_type='type')
bulkdata_list = [bulkdata]
dicom_object = dicom_json.ObjectWithBulkData(dicom_dict, bulkdata_list)
# Test properties
self.assertEqual(dicom_object.instance_uid, instance_uid)
self.assertEqual(dicom_object.series_uid, series_uid)
self.assertEqual(dicom_object.study_uid, study_uid)
def CreateMockStudyJsonResponse(study_uid: Text) -> Dict[Text, Any]:
"""Creates a Dict representing a DICOM JSON response to a Study Level QIDO."""
study_json = {}
dicom_json.Insert(study_json, tags.ACCESSION_NUMBER, _ACCESSION_NUMBER)
dicom_json.Insert(study_json, tags.STUDY_INSTANCE_UID, study_uid)
dicom_json.Insert(study_json, tags.STUDY_ID, _STUDY_ID)
dicom_json.Insert(study_json, tags.STUDY_DATE, _STUDY_DATE)
dicom_json.Insert(study_json, tags.STUDY_DESCRIPTION, _STUDY_DESCRIPTION)
dicom_json.Insert(study_json, tags.REFERRING_PHYSICIAN_NAME,
_REFERRING_PHYSICIAN_NAME)
dicom_json.Insert(study_json, tags.STUDY_TIME, _STUDY_TIME)
dicom_json.Insert(study_json, tags.PATIENT_BIRTH_DATE, _PATIENT_BIRTH_DATE)
dicom_json.Insert(study_json, tags.PATIENT_BIRTH_TIME, _PATIENT_BIRTH_TIME)
dicom_json.Insert(study_json, tags.PATIENT_NAME, _PATIENT_NAME)
dicom_json.Insert(study_json, tags.PATIENT_ID, _PATIENT_ID)
dicom_json.Insert(study_json, tags.PATIENT_SEX, _PATIENT_SEX)
dicom_json.Insert(study_json, tags.PATIENT_AGE, _PATIENT_AGE)
dicom_json.Insert(study_json, tags.PATIENT_SIZE, _PATIENT_SIZE)
dicom_json.Insert(study_json, tags.PATIENT_WEIGHT, _PATIENT_WEIGHT)
dicom_json.Insert(study_json, tags.NAME_OF_PHYSICIAN_READING_STUDY,
_NAME_OF_PHYSICIAN_READING)
dicom_json.Insert(study_json, tags.ADMITTING_DIAGNOSES_DESCRIPTION,
_ADMITTING_DIAGNOSES_DESCRIPTION)
dicom_json.Insert(study_json, tags.ISSUER_OF_PATIENT_ID,
_ISSUER_OF_PATIENT_ID)
dicom_json.Insert(study_json, tags.OTHER_PATIENT_IDS, _OTHER_PATIENT_IDS)
dicom_json.Insert(study_json, tags.OTHER_PATIENT_NAMES,
_OTHER_PATIENT_NAMES)
dicom_json.Insert(study_json, tags.ETHNIC_GROUP, _ETHNIC_GROUP)
dicom_json.Insert(study_json, tags.OCCUPATION, _OCCUPATION)
dicom_json.Insert(study_json, tags.ADDITIONAL_PATIENT_HISTORY,
_ADDITIONAL_PATIENT_HISTORY)
dicom_json.Insert(study_json, tags.PATIENT_COMMENTS, _PATIENT_COMMENTS)
procedure_sequence = {}
dicom_json.Insert(procedure_sequence, tags.CODE_VALUE, _CODE_VALUE)
dicom_json.Insert(procedure_sequence, tags.CODE_SCHEME_DESIGNATOR,
_CODE_SCHEME_DESIGNATOR)
dicom_json.Insert(procedure_sequence, tags.CODE_SCHEME_VERSION,
_CODE_SCHEME_VERSION)
dicom_json.Insert(procedure_sequence, tags.CODE_MEANING, _CODE_MEANING)
dicom_json.Insert(study_json, tags.PROCEDURE_CODE_SEQUENCE,
procedure_sequence)
referenced_study_sequence = {}
dicom_json.Insert(referenced_study_sequence, tags.REFERENCED_SOP_CLASS_UID,
_REFERENCED_SOP_CLASS_UID)
dicom_json.Insert(referenced_study_sequence,
tags.REFERENCED_SOP_INSTANCE_UID,
_REFERENCED_SOP_INSTANCE_UID)
dicom_json.Insert(study_json, tags.REFERENCED_STUDY_SEQUENCE,
referenced_study_sequence)
referenced_patient_sequence = {}
dicom_json.Insert(referenced_patient_sequence,
tags.REFERENCED_SOP_CLASS_UID, _REFERENCED_SOP_CLASS_UID)
dicom_json.Insert(referenced_patient_sequence,
tags.REFERENCED_SOP_INSTANCE_UID,
_REFERENCED_SOP_INSTANCE_UID)
dicom_json.Insert(study_json, tags.REFERENCED_PATIENT_SEQUENCE,
referenced_patient_sequence)
return study_json
def CreateMockSRDict(sr_text: Text) -> Dict[Text, Any]:
"""Creates a DICOM JSON dictionary representing a structured report."""
sr_dict = CreateMockStudyJsonResponse(_STUDY_UID)
dicom_json.Insert(sr_dict, tags.SOP_CLASS_UID,
tag_values.BASIC_TEXT_SR_CUID)
dicom_json.Insert(sr_dict, tags.MODALITY, tag_values.SR_MODALITY)
dicom_json.Insert(sr_dict, tags.SERIES_INSTANCE_UID, _SR_SERIES_UID)
dicom_json.Insert(sr_dict, tags.SPECIFIC_CHARACTER_SET,
dicom_builder._ISO_CHARACTER_SET)
dicom_json.Insert(sr_dict, tags.SOP_INSTANCE_UID, _SR_INSTANCE_UID)
content_json = {}
dicom_json.Insert(content_json, tags.RELATIONSHIP_TYPE, 'CONTAINS')
dicom_json.Insert(content_json, tags.VALUE_TYPE, 'TEXT')
dicom_json.Insert(content_json, tags.TEXT_VALUE, sr_text)
dicom_json.Insert(sr_dict, tags.CONTENT_SEQUENCE, content_json)
dicom_json.Insert(sr_dict, tags.TRANSFER_SYNTAX_UID,
dicom_builder._IMPLICIT_VR_LITTLE_ENDIAN)
dicom_json.Insert(sr_dict, tags.MEDIA_STORAGE_SOP_CLASS_UID,
tag_values.BASIC_TEXT_SR_CUID)
dicom_json.Insert(sr_dict, tags.MEDIA_STORAGE_SOP_INSTANCE_UID,
_SR_INSTANCE_UID)
return sr_dict
def _CreateMockInstanceMetadata() -> Dict[Text, Any]:
instance_metadata = {}
dicom_json.Insert(instance_metadata, tags.STUDY_INSTANCE_UID, 1)
dicom_json.Insert(instance_metadata, tags.SERIES_INSTANCE_UID, 2)
dicom_json.Insert(instance_metadata, tags.SOP_INSTANCE_UID, 3)
return instance_metadata
def BuildJsonSR(
self, report_text: Text,
metadata_json: Dict[Text, Any]) -> dicom_json.ObjectWithBulkData:
"""Builds and returns a Basic Text DICOM JSON Structured Report instance.
This function will create a new DICOM series.
Args:
report_text: Text string to use for the Basic Text DICOM SR.
metadata_json: Dict of tags (including study-level information) to add.
Returns:
DICOM JSON Object containing the Structured Report.
"""
# Dicom StowJsonRs expects a list with DICOM JSON as elements.
# Add study level tags to the SR.
dataset = metadata_json.copy()
series_uid = self.GenerateUID()
instance_uid = self.GenerateUID()
dicom_json.Insert(dataset, tags.SOP_CLASS_UID,
tag_values.BASIC_TEXT_SR_CUID)
dicom_json.Insert(dataset, tags.MODALITY, tag_values.SR_MODALITY)
dicom_json.Insert(dataset, tags.SERIES_INSTANCE_UID, series_uid)
dicom_json.Insert(dataset, tags.SPECIFIC_CHARACTER_SET,
_ISO_CHARACTER_SET)
logging.log(
logging.INFO,
'Creating DICOM JSON SR with Series UID: %s and Instance UID: %s',
series_uid, instance_uid)
dicom_json.Insert(dataset, tags.SOP_INSTANCE_UID, instance_uid)
content_dataset = {}
dicom_json.Insert(content_dataset, tags.RELATIONSHIP_TYPE, 'CONTAINS')
dicom_json.Insert(content_dataset, tags.VALUE_TYPE, 'TEXT')
dicom_json.Insert(content_dataset, tags.TEXT_VALUE, report_text)
dicom_json.Insert(dataset, tags.CONTENT_SEQUENCE, content_dataset)
dicom_json.Insert(dataset, tags.TRANSFER_SYNTAX_UID,
_IMPLICIT_VR_LITTLE_ENDIAN)
dicom_json.Insert(dataset, tags.MEDIA_STORAGE_SOP_CLASS_UID,
tag_values.BASIC_TEXT_SR_CUID)
dicom_json.Insert(dataset, tags.MEDIA_STORAGE_SOP_INSTANCE_UID,
instance_uid)
return dicom_json.ObjectWithBulkData(dataset)
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 testBuildJsonSC(self, *_):
num_rows = 10
num_columns = 10
hufloat = np.ones([num_rows, num_columns, 1])
image_position_tag_value = '1'
study_time_tag_value = '2'
study_instance_uid = '1.2.3.4'
series_uid = '5.6.7'
study_dict = {}
dicom_json.Insert(study_dict, tags.IMAGE_POSITION, image_position_tag_value)
dicom_json.Insert(study_dict, tags.STUDY_TIME, study_time_tag_value)
dicom_json.Insert(study_dict, tags.STUDY_INSTANCE_UID, study_instance_uid)
study_dict_copy = study_dict.copy()
builder = dicom_builder.DicomBuilder()
dicom_json_sc = builder.BuildJsonSC(hufloat, study_dict, series_uid)
# Ensure the study_dict is not affected by the builder.
self.assertEqual(study_dict, study_dict_copy)
# Test the UIDs.
self.assertEqual(dicom_json_sc.instance_uid, _UID1)
dicom_dict = dicom_json_sc.dicom_dict
# Test study/series level tags.
self._AssertJsonTag(dicom_dict, tags.STUDY_INSTANCE_UID, study_instance_uid)
self._AssertJsonTag(dicom_dict, tags.SERIES_INSTANCE_UID, series_uid)
self._AssertJsonTag(dicom_dict, tags.STUDY_TIME, study_time_tag_value)
self._AssertJsonTag(dicom_dict, tags.MODALITY, tag_values.OT_MODALITY)
# 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_sc.instance_uid)
self._AssertJsonTag(dicom_dict, tags.MEDIA_STORAGE_SOP_CLASS_UID,
tag_values.SECONDARY_CAPTURE_CUID)
self._AssertJsonTag(dicom_dict, tags.SOP_CLASS_UID,
tag_values.SECONDARY_CAPTURE_CUID)
self._AssertJsonTag(dicom_dict, tags.TRANSFER_SYNTAX_UID,
dicom_builder._IMPLICIT_VR_LITTLE_ENDIAN)
# Test positional tags.
self._AssertJsonTag(dicom_dict, tags.IMAGE_POSITION,
image_position_tag_value)
# Test image tags.
self._AssertJsonTag(dicom_dict, tags.PHOTOMETRIC_INTERPRETATION, 'RGB')
self._AssertJsonTag(dicom_dict, tags.SAMPLES_PER_PIXEL, 3)
self._AssertJsonTag(dicom_dict, tags.PLANAR_CONFIGURATION, 0)
self._AssertJsonTag(dicom_dict, tags.ROWS, num_rows)
self._AssertJsonTag(dicom_dict, tags.COLUMNS, num_columns)
self._AssertJsonTag(dicom_dict, tags.BITS_ALLOCATED, 8)
self._AssertJsonTag(dicom_dict, tags.BITS_STORED, 8)
self._AssertJsonTag(dicom_dict, tags.HIGH_BIT, 7)
self._AssertJsonTag(dicom_dict, tags.PIXEL_REPRESENTATION, 0)
bulkdata_uri = '{}/{}/{}'.format(study_instance_uid, series_uid, _UID1)
self.assertEqual(dicom_dict[tags.PIXEL_DATA.number]['BulkDataURI'],
bulkdata_uri)
# Test image bulkdata.
bulkdata = dicom_json_sc.bulkdata_list[0]
self.assertEqual(bulkdata.uri, bulkdata_uri)
self.assertEqual(bulkdata.data, hufloat.tobytes())
self.assertEqual(bulkdata.content_type, 'application/octet-stream')