orthancInterface/pythonScripts/scanOrthancQuickLocal.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
import datetime

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']['orthancInterface'])
   sys.path.insert(0,setup['paths']['labkeyInterface'])
   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={}
      pid=dicom['PatientID']
      if len(pid)>32:
         pid=pid[:32]
      row[participantField]=pid
      
      try:
         row['birthDate']=datetime.datetime.strptime(dicom['PatientBirthDate'],'%Y-%m-%d %H:%M')
      except (KeyError,ValueError):
         pass
      
      row['PatientName']=dicom['PatientName']
      row['OrthancId']=p
      prows.append(row)

   if len(prows)>0:

      resp=db.modifyRows('insert',project,opars['schemaName'],\
         opars['demographicsQuery'],prows)
      print(resp)

   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']
      if len(patientId)>32:
         patientId=patientId[:32]

#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=datetime.datetime.strptime(sdicom['StudyDate'],'%Y-%m-%d %H:%M')
         except (KeyError,ValueError):
             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)
            #this is a weird O that appears sometimes
            seDesc=seDesc.replace(chr(212),'O')


            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])