Adding scanOrthancLocal that only uses local copy of the software

pythonScripts/scanOrthancLocal.py

@@ -0,0 +1,159 @@
+#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'])
+    sys.path.insert(0,setup['paths']['labkeyInterface'])
+    sys.path.insert(0,setup['paths']['orthancInterface'])
+    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)
+
+    i=0
+    opars=pars['Orthanc']
+    project=opars['project']
+    
+    participantField=opars['participantField']
+
+    patients=odb.getPatients()
+    n=len(patients)
+
+    for p in patients:
+        pdata=odb.getPatientData(p)
+        dicom=pdata['MainDicomTags']
+        patientId=dicom['PatientID']
+    
+        print("[{}/{}] Patient: {} ID: {}".format(i,n,p,patientId))
+
+        qfilter={'variable':participantField,'value':patientId,'oper':'eq'}
+        ds=db.selectRows(project,opars['schemaName'],\
+                opars['demographicsQuery'],[qfilter])
+        if len(ds['rows'])==0:
+            row={}
+            row[participantField]=patientId
+            row['birthDate']=dicom['PatientBirthDate']
+            row['PatientName']=dicom['PatientName']
+            row['OrthancId']=p
+            db.modifyRows('insert',project,opars['schemaName'],\
+                    opars['demographicsQuery'],[row])
+
+        for s in pdata['Studies']:
+            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])
+                
+                mode='insert'
+
+                if len(ds['rows'])>0:
+                    mode='update'
+                    #use existing row data
+                    row=ds['rows'][0]
+
+                else:
+
+                    #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
+                db.modifyRows(mode,project,opars['schemaName'],\
+                        opars['queryName'],[row])
+
+
+        i+=1
+    print("Done")
+
+if __name__=="__main__":
+    main(sys.argv[1])