Modifying scanOrthanc.py to run from a configuration script

pythonScripts/scanOrthanc.py

@@ -6,99 +6,116 @@ import json
 import re
 import sys
 
+def main(parameterFile):
 
-fhome=os.path.expanduser('~')
-fsetup=os.path.join(fhome,'.labkey','setup.json')
+    fhome=os.path.expanduser('~')
+    fsetup=os.path.join(fhome,'.labkey','setup.json')
 
-with open(fsetup,'r') as f:
-    setup=json.load(f)
+    with open(fsetup,'r') as f:
+        setup=json.load(f)
 
-sys.path.insert(0,setup['paths']['labkeyInterface'])
-import labkeyInterface
-import labkeyDatabaseBrowser
+    sys.path.insert(0,setup['paths']['labkeyInterface'])
+    import labkeyInterface
+    import labkeyDatabaseBrowser
 
-sys.path.insert(0,setup['paths']['orthancInterface'])
-import orthancInterface
-import orthancDatabaseBrowser
+    sys.path.insert(0,setup['paths']['orthancInterface'])
+    import orthancInterface
+    import orthancDatabaseBrowser
 
-fconfig=os.path.join(fhome,'.labkey','network.json')
+    fconfig=os.path.join(fhome,'.labkey','network.json')
 
-net=labkeyInterface.labkeyInterface()
-net.init(fconfig)
-db=labkeyDatabaseBrowser.labkeyDB(net)
+    net=labkeyInterface.labkeyInterface()
+    net.init(fconfig)
+    db=labkeyDatabaseBrowser.labkeyDB(net)
 
 
-onet=orthancInterface.orthancInterface()
-onet.init(fconfig)
-odb=orthancDatabaseBrowser.orthancDB(onet)
+    onet=orthancInterface.orthancInterface()
+    onet.init(fconfig)
+    odb=orthancDatabaseBrowser.orthancDB(onet)
 
-i=0
-project='Orthanc/Database'
 
-patients=odb.getPatients()
+    with open(parameterFile) as f:
+        pars=json.load(f)
 
-for p in patients:
-    pdata=odb.getPatientData(p)
-    dicom=pdata['MainDicomTags']
-    patientId=dicom['PatientID']
+    i=0
+    opars=pars['Orthanc']
+    project=opars['project']
     
-    print("Patient: {} ID: {}".format(p,patientId))
-
-    qfilter={'variable':'PatientId','value':patientId,'oper':'eq'}
-    ds=db.selectRows(project,'study','Demographics',[qfilter])
-    if len(ds['rows'])==0:
-        row={}
-        row['PatientId']=patientId
-        row['birthDate']=dicom['PatientBirthDate']
-        row['PatientName']=dicom['PatientName']
-        row['OrthancId']=p
-        db.modifyRows('insert',project,'study','Demographics',[row])
-
-    for s in pdata['Studies']:
-        sdata=odb.getStudyData(s)
-        sdicom=sdata['MainDicomTags']
-        sid=sdicom['StudyInstanceUID']
-        print('Study: {}/{}'.format(s,sid))
-        #print('Data: {}'.format(sdata))
-        sdate=sdicom['StudyDate']
-        #continue
-        
-        
-        for se in sdata['Series']:
-
-            qfilter={'variable':'orthancSeries','value':se,'oper':'eq'}
-            ds=db.selectRows(project,'study','Imaging',[qfilter])
-            if len(ds['rows'])>0:
-                continue
-
-            #count existing entries for patient
-            qfilter={'variable':'PatientId','value':patientId,'oper':'eq'}
-            ds=db.selectRows(project,'study','Imaging',[qfilter])
-            seqNum=len(ds['rows'])
-
-            sedata=odb.getSeriesData(se)
-            sedicom=sedata['MainDicomTags']
-            seid=sedicom['SeriesInstanceUID']
-            print('Series: {}/{}'.format(se,seid))
-            #print('Data: {}'.format(sedata))
-            seDesc="NONE"
-            try:
-                seDesc=sedicom['SeriesDescription']
-            except KeyError:
-                pass
-
-            print('ID: {}.'.format(seDesc))
+    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['PatientId']=patientId
-            row['sequenceNum']=seqNum
-            row['dicomStudy']=sid
-            row['orthancStudy']=s
-            row['dicomSeries']=seid
-            row['orthancSeries']=se
-            row['studyDate']=sdate
-            row['seriesDescription']=seDesc
-            db.modifyRows('insert',project,'study','Imaging',[row])
-
-
-print("Done")
+            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('\tStudy: {}/{}'.format(s,sid))
+            #print('Data: {}'.format(sdata))
+            sdate=sdicom['StudyDate']
+            #continue
+        
+        
+            for se in sdata['Series']:
+
+                qfilter={'variable':'orthancSeries','value':se,'oper':'eq'}
+                ds=db.selectRows(project,opars['schemaName'],\
+                        opars['queryName'],[qfilter])
+                if len(ds['rows'])>0:
+                    continue
+
+                #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'])
+
+                sedata=odb.getSeriesData(se)
+                sedicom=sedata['MainDicomTags']
+                seid=sedicom['SeriesInstanceUID']
+                #print('Data: {}'.format(sedata))
+                seDesc="NONE"
+                try:
+                    seDesc=sedicom['SeriesDescription']
+                except KeyError:
+                    pass
+
+                print('\t\tSeries[{}]: {}/{}'.format(seDesc,se,seid))
+
+                row={}
+                row[participantField]=patientId
+                row['sequenceNum']=seqNum
+                row['dicomStudy']=sid
+                row['orthancStudy']=s
+                row['dicomSeries']=seid
+                row['orthancSeries']=se
+                row['studyDate']=sdate
+                row['seriesDescription']=seDesc
+                db.modifyRows('insert',project,opars['schemaName'],\
+                        opars['queryName'],[row])
+
+
+        i+=1
+    print("Done")
+
+if __name__=="__main__":
+    main(sys.argv[1])