orthancInterface/pythonScripts/scanOrthanc.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'])
    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])