orthancInterface/pythonScripts/scanOrthancLocal.py

#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']
   demoQuery=opars['demographicsQuery']
   schema=opars['schemaName']
   query=opars['queryName']

   participantField=opars['participantField']

   patients=odb.getPatients()
   n=len(patients)
   print('Npatients: {}'.format(n))

   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'}
      print('selectRows({},{},{})'.format(project,schema,demoQuery))
      ds=db.selectRows(project,schema,demoQuery,[qfilter])
      if len(ds['rows'])==0:
         row={}
         row[participantField]=patientId
         try:
            row['birthDate']=dicom['PatientBirthDate']
         except KeyError:
            pass
         row['PatientName']=dicom['PatientName']
         row['OrthancId']=p
         db.modifyRows('insert',project,schema,demoQuery,[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,schema,query,[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,schema,query,[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,schema,query,[row])


      i+=1
   print("Done")

if __name__=="__main__":
    main(sys.argv[1])