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SRCDParser.py
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SRCDParser.py
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from DICOMParser import DICOMParser
import pydicom
import copy
class SRCDParser(DICOMParser):
def parse(self):
modality = self.dcm.Modality
if modality == "SR":
if hasattr(self.dcm, "ContentTemplateSequence"):
if self.dcm.ContentTemplateSequence[0].TemplateIdentifier == "QIICR_2000":
self.readTopLevelAttributes("CompositeContext")
self.readTopLevelAttributes("CD")
self.ClinicalDataParser("CD")
else:
super(SRCDParser,self).parse()
else:
super(SRCDParser, self).parse()
def ClinicalDataParser(self, modality):
completedContainers = []
self.tables['CD']=[self.tables['CD']]
for container in ('ProblemList','SocialHistory','TumorStaging','MedicalHistory','Biopsy','Surgery','Radiotherapy',
'Chemotherapy','OriginalPathology','CervicalLymphNodeGroupExcision','DiseaseOutcome'):
str(getattr(self, "readCD%s" % container)(container))
completedContainers.append(container)
def readCDProblemList(self, container):
dataElement = getattr(self, "getCD%sContainer" % container)()
if not dataElement is None:
dataElement=dataElement[0].ContentSequence
self.readCDValue(container, 'Code', 'Problem', 'Problem', dataElement[0])
srcTables=self.tables['CD']
self.tables['CD']=[]
for i in range(1,len(dataElement)):
destTables=copy.deepcopy(srcTables)
self.readCDValueMulti(container, 'Code', 'Therapy', 'Therapy', dataElement[i], destTables)
self.tables['CD'] += destTables
def readCDSocialHistory(self, container):
dataElement = getattr(self, "getCD%sContainer" % container)()
if not dataElement is None:
self.readCDValue(container, 'Code', 'TobaccoSmokingBehavior', 'Tobacco Smoking Behavior', dataElement)
self.readCDValue(container, 'Code', 'AlcoholConsumption', 'Alcohol consumption', dataElement)
self.readCDValue(container, 'Code', 'DetailsOfTobaccoChewing', 'Details of tobacco chewing', dataElement)
def readCDTumorStaging(self, container):
dataElement = getattr(self, "getCD%sContainer" % container)()
if not dataElement is None:
self.readCDValue(container, 'Code', "PrimaryTumorSite", "Primary tumor site", dataElement)
self.readCDValue(container, "Code", "TumorStageFinding", "Tumor stage finding", dataElement)
dataElement = self.getContainerByConceptNameMeaning(dataElement, "TNM Category")
if not dataElement is None:
self.readCDValue(container, "Code", "TStage", "T Stage", dataElement)
self.readCDValue(container, "Code", "NStage", "N Stage", dataElement)
self.readCDValue(container, "Code", "MStage", "M Stage", dataElement)
def readCDMedicalHistory(self, container):
dataElement = getattr(self, "getCD%sContainer" % container)()
if not dataElement is None:
self.readCDValue(container, "Code", "RadiationTherapy", "History of radiation therapy", dataElement)
self.readCDValue(container, "Code", "MalignantNeoplasm", "History of malignant neoplasm", dataElement)
def readCDBiopsy(self, container):
dataElements = getattr(self, "getCD%sContainer" % container)()
if not dataElements is None and dataElements.VM>0:
srcTables=self.tables['CD']
self.tables['CD']=[]
for dataElement in dataElements:
destTables=copy.deepcopy(srcTables)
dataElement = dataElement.ContentSequence
self.readCDValueMulti(container, "Date", "DateOfProcedure", "Date of procedure", dataElement,
destTables)
self.readCDValueMulti(container, "TextValue", "Site", "Biopsy Site", dataElement,
destTables)
self.tables['CD'] += destTables
def readCDSurgery(self, container):
dataElements = getattr(self, "getCD%sContainer" % container)()
if not dataElements is None and len(dataElements)>0:
srcTables=self.tables['CD']
self.tables['CD']=[]
for dataElement in dataElements:
destTables=copy.deepcopy(srcTables)
self.readCDValueMulti(container, "Date", "DateOfProcedure", "Date of procedure", dataElement,
destTables)
self.readCDValueMulti(container, "TextValue", "ProcedureDescription", "Procedure Description",
dataElement, destTables)
self.readCDValueMulti(container, "Code", "ResectionOfPrimaryTumor", "Resection of primary tumor",
dataElement, destTables)
self.readCDValueMulti(container, "Code", "BlockDissectionOfCervicalLymphNodes",
"Block dissection of cervical lymph nodes", dataElement, destTables)
self.tables['CD'] += destTables
def readCDRadiotherapy(self, container):
dataElements = getattr(self, "getCD%sContainer" % container)()
if not dataElements is None and len(dataElements)>0:
srcTables=self.tables['CD']
self.tables['CD']=[]
for dataElement in dataElements:
destTables=copy.deepcopy(srcTables)
self.readCDValueMulti(container, "Date", "DateTreatmentStarted", "Date treatment started", dataElement,
destTables)
self.readCDValueMulti(container, "Date", "DateTreatmentStopped", "Date treatment stopped", dataElement,
destTables)
self.readCDValueMulti(container, "NumericValue", "TotalRadiationDoseDelivered",
"Total radiation dose delivered", dataElement, destTables)
self.readCDValueMulti(container, "NumericValue", "RadiationDosePerFraction", "Radiation dose per fraction",
dataElement, destTables)
self.readCDValueMulti(container, "TextValue", "ProcedureDescription", "Procedure Description", dataElement,
destTables)
self.tables['CD'] += destTables
def readCDChemotherapy(self, container):
dataElements = getattr(self, "getCD%sContainer" % container)()
if not dataElements is None and len(dataElements)>0:
srcTables = self.tables['CD']
self.tables['CD'] = []
for dataElement in dataElements:
destTables=copy.deepcopy(srcTables)
self.readCDValueMulti(container, "Date", "DateTreatmentStarted", "Date treatment started", dataElement,
destTables)
self.readCDValueMulti(container, "Date", "DateTreatmentStopped", "Date treatment stopped", dataElement,
destTables)
self.readCDValueMulti(container, "Code", "AntineoplasticAgent", "Antineoplastic agent",
dataElement, destTables) # Need to support up to 3
self.tables['CD'] += destTables
def readCDOriginalPathology(self, container):
dataElement = getattr(self, "getCD%sContainer" % container)()
if not dataElement is None:
self.readCDValue(container, "Code", "Pathology", "Pathology", dataElement)
dataElement = dataElement[0].data_element('ContentSequence')
if not dataElement is None:
self.readCDValue(container, "Code", "HistologicalGradeFinding", "Histological grade finding",
dataElement)
self.readCDValue(container, "Code", "MalignancyType", "Malignancy Type", dataElement)
self.readCDValue(container, "Code", "TumorMarginStatus", "Tumor margin status", dataElement)
self.readCDValue(container, "Code", "PerineuralInvasionFinding", "Perineural invasion finding",
dataElement)
self.readCDValue(container, "Code", "StatusOfVascularInvasionByTumor",
"Status of vascular invasion by tumor", dataElement)
def readCDCervicalLymphNodeGroupExcision(self, container):
dataElements = getattr(self, "getCD%sContainer" % container)()
if not dataElements is None:
lymphNodeGroup = [dataElement for dataElement in dataElements if
self.readCDValue(container, "Code", "StatusOfExtraCapsularExtensionOfNodalTumor",
"Status of extra-capsular extension of nodal tumor", dataElement) +
self.readCDValue(container, "TextValue", "Comment", "Comment", dataElement) == 0]
if len(lymphNodeGroup)>0:
srcTables=self.tables['CD']
self.tables['CD']=[]
for dataElement in lymphNodeGroup:
destTables=copy.deepcopy(srcTables)
self.readCDValueMulti(container,"Code","CervicalLymphNodeGroup","Cervical lymph node group",dataElement,
destTables)
try:
dataElement = dataElement.data_element('ContentSequence')
self.readCDValueMulti(container, "Code", "Sidedness", "Sidedness", dataElement, destTables)
self.readCDValueMulti(container, "NumericValue", "NumberOfNodesRemoved", "Number of nodes removed",
dataElement, destTables)
self.readCDValueMulti(container, "NumericValue", "NumberOfNodesPositive", "Number of nodes positive",
dataElement, destTables)
except:
pass
self.tables['CD'] += destTables
def readCDDiseaseOutcome(self, container):
dataElement = getattr(self, "getCD%sContainer" % container)()
if not dataElement is None:
self.readCDValue(container, "Date", "FollowupVisitDate", "Follow-up visit date", dataElement)
self.readCDValue(container, "Code", "FollowupStatus", "Followup status", dataElement)
self.readCDValue(container, "Date", "DateOfDeath", "Date of death", dataElement)
self.readCDValue(container, "Code", "CauseOfDeath", "Cause of death", dataElement)
self.readCDValue(container, "Code", "PostRadiotherapyTreatment", "Post-radiotherapy treatment", dataElement)
self.readCDValue(container, "Date", "DateOfCancerRecurrence", "Date of cancer recurrence", dataElement)
self.readCDValue(container, "Code", "LocationOfFirstRecurrence", "Location of first recurrence",
dataElement)
dataElement = self.getContainerByConceptNameMeaning(dataElement, "Pathology of recurrent tumor")
if not dataElement is None:
dataElement = dataElement[0].data_element('ContentSequence')
self.readCDValue(container, "Code", "Pathology", "Pathology", dataElement)
dataElement = dataElement[0].data_element('ContentSequence')
self.readCDValue(container, "Code", "HistologicalGradeFinding", "Histological grade finding",
dataElement)
self.readCDValue(container, "Code", "MalignancyType", "Malignancy Type", dataElement)
self.readCDValue(container, "Code", "TumorMarginStatus", "Tumor margin status", dataElement)
self.readCDValue(container, "Code", "PerineuralInvasionFinding", "Perineural invasion finding",
dataElement)
self.readCDValue(container, "Code", "StatusOfVascularInvasionByTumor",
"Status of vascular invasion by tumor", dataElement)
def readCDValueMulti(self, container, valueType, field, codeMeaning, dataElement,destTables):
value = None
if type(dataElement) == pydicom.dataset.Dataset:
if dataElement.ConceptNameCodeSequence[0].CodeMeaning == codeMeaning:
if valueType == "Date" or valueType == "TextValue":
value = dataElement.data_element(valueType).value
elif valueType == "NumericValue":
value = dataElement.MeasuredValueSequence[0].NumericValue
elif valueType == "Code":
value = dataElement.ConceptCodeSequence[0]
else:
for item in dataElement:
if item.ConceptNameCodeSequence[0].CodeMeaning == codeMeaning:
if valueType == "Date" or valueType == "TextValue":
value = item.data_element(valueType).value
elif valueType == "NumericValue":
value = item.MeasuredValueSequence[0].NumericValue
elif valueType == "Code":
value = item.ConceptCodeSequence[0]
break
if not value is None:
for table in destTables:
if valueType == "Code":
table["%s_%s_CodeValue" % (container, field)] = value.CodeValue
table["%s_%s_CodingSchemeDesignator" % (container, field)] = value.CodingSchemeDesignator
table["%s_%s_CodeMeaning" % (container, field)] = value.CodeMeaning
else:
table["%s_%s" % (container, field)] = value
return not value is None
def readCDValue(self, container, valueType, field, codeMeaning, dataElement):
value = None
if type(dataElement) == pydicom.dataset.Dataset:
if dataElement.ConceptNameCodeSequence[0].CodeMeaning == codeMeaning:
if valueType == "Date" or valueType == "TextValue":
value = dataElement.data_element(valueType).value
elif valueType == "NumericValue":
value = dataElement.MeasuredValueSequence[0].NumericValue
elif valueType == "Code":
value = dataElement.ConceptCodeSequence[0]
else:
for item in dataElement:
if item.ConceptNameCodeSequence[0].CodeMeaning == codeMeaning:
if valueType == "Date" or valueType == "TextValue":
value = item.data_element(valueType).value
elif valueType == "NumericValue":
value = item.MeasuredValueSequence[0].NumericValue
elif valueType == "Code":
value = item.ConceptCodeSequence[0]
break
if not value is None:
for table in self.tables['CD']:
if valueType == "Code":
table["%s_%s_CodeValue" % (container, field)] = value.CodeValue
table["%s_%s_CodingSchemeDesignator" % (container, field)] = value.CodingSchemeDesignator
table["%s_%s_CodeMeaning" % (container, field)] = value.CodeMeaning
else:
table["%s_%s" % (container, field)] = value
return not value is None
def getCDProblemListContainer(self):
container = self.getCDSummaryClinicalDocumentContainer()[2]
try:
return container.data_element('ContentSequence')
except:
return None
def getCDSocialHistoryContainer(self):
return self.getCDSummaryClinicalDocumentContainer()[3].data_element('ContentSequence')
def getCDTumorStagingContainer(self):
return self.getCDSummaryClinicalDocumentContainer()[4].data_element('ContentSequence')
def getCDTNMCategoryContainer(self):
dataElement = self.getCDTumorStagingContainer()
return self.getContainerByConceptNameMeaning(dataElement, "TNM Category")
def getCDMedicalHistoryContainer(self):
return self.getCDSummaryClinicalDocumentContainer()[5].data_element('ContentSequence')
def getCDDiagnosticProcedureContainer(self):
try:
return self.getCDSummaryClinicalDocumentContainer()[6].data_element('ContentSequence')
except:
return None
def getCDBiopsyContainer(self):
return self.getCDDiagnosticProcedureContainer()
def getCDTherapeuticProcedureContainer(self):
return self.getCDSummaryClinicalDocumentContainer()[7].data_element('ContentSequence')
def getCDSurgeryContainer(self):
containers = self.getCDTherapeuticProcedureContainer()
surgeryContainers = []
for container in containers:
if container.ConceptNameCodeSequence[0].CodeMeaning == "Surgical Procedure":
surgeryContainers.append(container.ContentSequence)
return surgeryContainers
def getCDRadiotherapyContainer(self):
containers = self.getCDTherapeuticProcedureContainer()
surgeryContainers = []
for container in containers:
if container.ConceptNameCodeSequence[0].CodeMeaning == "Radiotherapy Procedure":
surgeryContainers.append(container.ContentSequence)
return surgeryContainers
def getCDChemotherapyContainer(self):
containers = self.getCDTherapeuticProcedureContainer()
surgeryContainers = []
for container in containers:
if container.ConceptNameCodeSequence[0].CodeMeaning == "Chemotherapy":
surgeryContainers.append(container.ContentSequence)
return surgeryContainers
def getCDPathologyOfOriginalTumorContainer(self):
return self.getCDSummaryClinicalDocumentContainer()[8].data_element('ContentSequence')
def getCDOriginalPathologyContainer(self):
dataElement = self.getCDPathologyOfOriginalTumorContainer()
return self.getContainerByConceptNameMeaning(dataElement, "Pathology Results")
def getCDCervicalLymphNodeGroupExcisionContainer(self):
dataElement = self.getCDPathologyOfOriginalTumorContainer()
return self.getContainerByConceptNameMeaning(dataElement, "Excision of cervical lymph nodes group")
def getCDDiseaseOutcomeContainer(self):
return self.getCDSummaryClinicalDocumentContainer()[9].data_element('ContentSequence')
def getCDSummaryClinicalDocumentContainer(self):
return self.dcm.data_element("ContentSequence")
def getContainerByConceptNameMeaning(self, dataElement, conceptNameMeaning):
if not dataElement is None:
for item in dataElement:
if item.ConceptNameCodeSequence[0].CodeMeaning == conceptNameMeaning:
try:
return item.data_element('ContentSequence')
except:
return None
return None