def generateJSON4DcmSR(self, dcmSegmentationFile, sourceVolumeNode):
measurements = []
sourceImageSeriesUID = ModuleLogicMixin.getDICOMValue(sourceVolumeNode, "0020,000E")
logging.debug("SourceImageSeriesUID: {}".format(sourceImageSeriesUID))
segmentationSOPInstanceUID = ModuleLogicMixin.getDICOMValue(dcmSegmentationFile, "0008,0018")
logging.debug("SegmentationSOPInstanceUID: {}".format(segmentationSOPInstanceUID))
for segmentID in self.statistics["SegmentIDs"]:
if not self.isSegmentValid(segmentID):
continue
data = dict()
data["TrackingIdentifier"] = self.statistics[segmentID, "Segment"]
data["ReferencedSegment"] = len(measurements)+1
data["SourceSeriesForImageSegmentation"] = sourceImageSeriesUID
data["segmentationSOPInstanceUID"] = segmentationSOPInstanceUID
segment = self.segmentationNode.GetSegmentation().GetSegment(segmentID)
terminologyEntry = DICOMSegmentationExporter.getDeserializedTerminologyEntry(segment)
data["Finding"] = self.createJSONFromTerminologyContext(terminologyEntry)["SegmentedPropertyTypeCodeSequence"]
anatomicContext = self.createJSONFromAnatomicContext(terminologyEntry)
if anatomicContext.has_key("AnatomicRegionSequence"):
data["FindingSite"] = anatomicContext["AnatomicRegionSequence"]
data["measurementItems"] = self.createMeasurementItemsForLabelValue(segmentID)
measurements.append(data)
return measurements
def getPatientInformation(self):
if not self.patientInfo:
masterVolume = ModuleLogicMixin.getReferencedVolumeFromSegmentationNode(self.segmentationNode)
self.patientInfo = self.patientInfoTemplate.format(ModuleLogicMixin.getDICOMValue(masterVolume,
DICOMTAGS.PATIENT_NAME),
ModuleLogicMixin.getDICOMValue(masterVolume,
DICOMTAGS.PATIENT_ID),
ModuleLogicMixin.getDICOMValue(masterVolume,
DICOMTAGS.PATIENT_BIRTH_DATE))
return self.patientInfo
def getPatientInformation(self):
if not self.patientInfo:
masterVolume = ModuleLogicMixin.getReferencedVolumeFromSegmentationNode(self.segmentationNode)
self.patientInfo = self.patientInfoTemplate.format(ModuleLogicMixin.getDICOMValue(masterVolume,
DICOMTAGS.PATIENT_NAME),
ModuleLogicMixin.getDICOMValue(masterVolume,
DICOMTAGS.PATIENT_ID),
ModuleLogicMixin.getDICOMValue(masterVolume,
DICOMTAGS.PATIENT_BIRTH_DATE))
return self.patientInfo
def getSeriesAttributes(self): attributes = dict() volumeNode = self.getReferencedVolumeFromSegmentationNode(self.segmentationNode) seriesNumber = ModuleLogicMixin.getDICOMValue(volumeNode, DICOMTAGS.SERIES_NUMBER) attributes["SeriesNumber"] = "100" if seriesNumber in [None,''] else str(int(seriesNumber)+100) attributes["InstanceNumber"] = "1" return attributes
def getSeriesAttributes(self):
attributes = dict()
volumeNode = self.getReferencedVolumeFromSegmentationNode(
self.segmentationNode)
seriesNumber = ModuleLogicMixin.getDICOMValue(volumeNode,
DICOMTAGS.SERIES_NUMBER)
attributes["SeriesNumber"] = "100" if seriesNumber in [
None, ''
] else str(int(seriesNumber) + 100)
attributes["InstanceNumber"] = "1"
return attributes
def generateJSON4DcmSR(self, dcmSegmentationFile, sourceVolumeNode):
measurements = []
sourceImageSeriesUID = ModuleLogicMixin.getDICOMValue(
sourceVolumeNode, "0020,000E")
logging.debug("SourceImageSeriesUID: {}".format(sourceImageSeriesUID))
segmentationSOPInstanceUID = ModuleLogicMixin.getDICOMValue(
dcmSegmentationFile, "0008,0018")
logging.debug("SegmentationSOPInstanceUID: {}".format(
segmentationSOPInstanceUID))
for segmentID in self.statistics["SegmentIDs"]:
if not self.isSegmentValid(segmentID):
continue
data = dict()
data["TrackingIdentifier"] = self.statistics[segmentID, "Segment"]
data["ReferencedSegment"] = len(measurements) + 1
data["SourceSeriesForImageSegmentation"] = sourceImageSeriesUID
data["segmentationSOPInstanceUID"] = segmentationSOPInstanceUID
segment = self.segmentationNode.GetSegmentation().GetSegment(
segmentID)
terminologyEntry = DICOMSegmentationExporter.getDeserializedTerminologyEntry(
segment)
data["Finding"] = self.createJSONFromTerminologyContext(
terminologyEntry)["SegmentedPropertyTypeCodeSequence"]
anatomicContext = self.createJSONFromAnatomicContext(
terminologyEntry)
if "AnatomicRegionSequence" in anatomicContext:
data["FindingSite"] = anatomicContext["AnatomicRegionSequence"]
data[
"measurementItems"] = self.createMeasurementItemsForLabelValue(
segmentID)
measurements.append(data)
return measurements
def updateInformationFromWatchBoxAttribute(self, attribute):
if attribute.tags and self.sourceFile:
values = []
for tag in attribute.tags:
currentValue = ModuleLogicMixin.getDICOMValue(self.sourceFile, tag, "")
if tag in self.DATE_TAGS_TO_FORMAT:
currentValue = self._formatDate(currentValue)
elif tag == DICOMTAGS.PATIENT_NAME:
currentValue = self._formatPatientName(currentValue)
elif tag == self.CURRENTDIRTAG:
path = os.path.normpath(self.sourceFile)
folderList = path.split(os.sep)
if len(folderList)>=4:
currentValue = folderList[-4]
values.append(currentValue)
return self._getTagValueFromTagValues(values)
return ""
def _processData(self, caller=None, event=None):
self._seriesTypeLabel.text = "{}: {}".format(
ModuleLogicMixin.getDICOMValue(self._seriesType.getVolume(),
DICOMTAGS.SERIES_NUMBER),
self._seriesType.getName())