Adding scanOrthanc.py

pythonScripts/scanOrthanc.py

@@ -0,0 +1,104 @@
+#scans orthanc database and updates Demographics datataset and 
+#series list in project Imaging dataset
+
+import os
+import json
+import re
+import sys
+
+
+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']['labkeyInterface'])
+import labkeyInterface
+import labkeyDatabaseBrowser
+
+sys.path.insert(0,setup['paths']['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)
+
+i=0
+project='Orthanc/Database'
+
+patients=odb.getPatients()
+
+for p in patients:
+    pdata=odb.getPatientData(p)
+    dicom=pdata['MainDicomTags']
+    patientId=dicom['PatientID']
+    
+    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))
+
+            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")