Adding a fast version of scanOrthanc that looks for new entries only

pythonScripts/scanOrthancQuick.py

@@ -0,0 +1,182 @@
+#labkey/orthanc interface
+
+#scans the orthanc internal database and fills labkey table
+
+#"Orthanc" section expected in the configuration file, with
+#"queryName": query to be filled for each image 
+#"demographicsQuery": query to be filled for every patient
+#"schemaName": the schema both queries are part of
+#"project": name of the project under labkey that collects Orthanc data,
+#           typically named Orthanc or similar
+#"participantField": sorting participant field label in labkey study
+
+
+import os
+import json
+import re
+import sys
+
+def main(parameterFile):
+
+    fhome=os.path.expanduser('~')
+    fsetup=os.path.join(fhome,'.labkey','setup.json')
+
+    with open(fsetup,'r') as f:
+        setup=json.load(f)
+
+    sys.path.insert(0,setup['paths']['nixWrapper'])
+    import nixWrapper
+
+    nixWrapper.loadLibrary("labkeyInterface")
+    import labkeyInterface
+    import labkeyDatabaseBrowser
+
+    nixWrapper.loadLibrary('orthancInterface')
+    import orthancInterface
+    import orthancDatabaseBrowser
+
+    fconfig=os.path.join(fhome,'.labkey','network.json')
+
+    net=labkeyInterface.labkeyInterface()
+    net.init(fconfig)
+    db=labkeyDatabaseBrowser.labkeyDB(net)
+
+
+    onet=orthancInterface.orthancInterface()
+    onet.init(fconfig)
+    odb=orthancDatabaseBrowser.orthancDB(onet)
+
+
+    with open(parameterFile) as f:
+        pars=json.load(f)
+
+    opars=pars['Orthanc']
+    project=opars['project']
+    
+    participantField=opars['participantField']
+
+    patients=odb.getPatients()
+
+
+    #equivalent for labkey side?
+    dsDemo=db.selectRows(project,opars['schemaName'],\
+            opars['demographicsQuery'],[])
+    dsPatients=[row['OrthancId'] for row in dsDemo['rows']]
+    pMissing=[p for p in patients if p not in dsPatients]
+    print('Missing : {}'.format(len(pMissing)))
+
+    #we need details for all patients (some might have just a study uploaded
+    pdata={p:odb.getPatientData(p) for p in patients}
+    
+    #update patient data for missing patients
+    prows=[]
+    for p in pMissing:
+        dicom=pdata[p]['MainDicomTags']
+        row={}
+        row[participantField]=dicom['PatientID']
+        row['birthDate']=dicom['PatientBirthDate']
+        row['PatientName']=dicom['PatientName']
+        row['OrthancId']=p
+        prows.append(row)
+
+    db.modifyRows('insert',project,opars['schemaName'],\
+                    opars['demographicsQuery'],prows)
+
+    n=len(patients)
+    i=0
+    #download the full images dataset (~1000 rows)
+    ds=db.selectRows(project,opars['schemaName'],opars['queryName'],[])
+    for p in patients:
+        dicom=pdata[p]['MainDicomTags']
+        patientId=dicom['PatientID']
+
+        #get all studies for pateint
+        #qfilter={'variable':participantField,'value':patientId,'oper':'eq'}
+        dsStudies=[row['orthancStudy'] for row in ds['rows'] if row[participantField]==patientId]
+        #number of entries for patient (if new must be inserted)
+        seqNum=len(dsStudies)
+        
+        #unique
+        dsStudies=list(set(dsStudies))
+        studies=pdata[p]['Studies']
+        pHex=p.split('-')
+
+        print("[{:>3d}/{:>3d}] ID: {:>10s} [{}] Studies: {:>2}/{:>2} Entries in DB: {:>4d}".format(i,n,patientId,pHex[-1],len(dsStudies),len(studies),seqNum))
+        missingStudies=[s for s in studies if s not in dsStudies]
+        #print('Missing studies: {}'.format(len(missingStudies)))
+
+        srows=[]
+        for s in missingStudies:
+
+            sdata=odb.getStudyData(s)
+            sdicom=sdata['MainDicomTags']
+            sid=sdicom['StudyInstanceUID']
+            #print('Data: {}'.format(sdata))
+            #this is try/except protetcted in previous version...
+            sdate="19700101"
+            try:
+                sdate=sdicom['StudyDate']
+            except KeyError:
+                pass
+            #continue
+        
+            print('\tStudy[{}]: {}/{}'.format(sdate,s,sid))
+        
+            for se in sdata['Series']:
+
+                sedata=odb.getSeriesData(se)
+                sedicom=sedata['MainDicomTags']
+                    
+                seid=sedicom['SeriesInstanceUID']
+                #print('Data: {}'.format(sedata))
+                seDesc="NONE"
+                try:
+                    seDesc=sedicom['SeriesDescription']
+                except KeyError:
+                    pass
+
+                #replace letters that might trip the database
+                spanishOAcute=''.join([chr(3619),chr(3603)])
+                spanishAAcute=''.join([chr(3619),chr(3585)])
+                seDesc=re.sub(spanishOAcute,'o',seDesc)
+                seDesc=re.sub(spanishAAcute,'a',seDesc)
+
+
+                print('\t\tSeries[{}]: {}/{}'.format(seDesc,se,seid))
+
+                #qfilter={'variable':'orthancSeries','value':se,'oper':'eq'}
+                #ds=db.selectRows(project,opars['schemaName'],\
+                #        opars['queryName'],[qfilter])
+                
+                #count existing entries for patient
+                #qfilter={'variable':participantField,'value':patientId,'oper':'eq'}
+                #ds=db.selectRows(project,opars['schemaName'],\
+                #opars['queryName'],[qfilter])
+                #    seqNum=len(ds['rows'])
+                    
+                #create new row
+                row={}
+                row[participantField]=patientId
+                row['sequenceNum']=seqNum
+                row['orthancSeries']=se
+                
+                
+                row['dicomStudy']=sid
+                row['orthancStudy']=s
+                row['dicomSeries']=seid
+                row['studyDate']=sdate
+                row['seriesDescription']=seDesc
+                srows.append(row)
+                seqNum+=1
+
+        #upload updates
+        if len(srows)>0:
+            db.modifyRows('insert',project,opars['schemaName'],\
+                opars['queryName'],srows)
+
+
+        i+=1
+    print("Done")
+
+if __name__=="__main__":
+    main(sys.argv[1])