orthancInterface/pythonScripts/scanOrthanc.py

#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")