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:
    print("Extracting patient: {}".format(p))
    pdata=odb.getPatientData(p)
    dicom=pdata['MainDicomTags']
    patientId=dicom['PatientID']

    queryPatientId=re.sub(r' ',r'%20',patientId)
    
    print("Patient: {} ID: {}".format(p,patientId))

    qfilter={'variable':'ParticipantId','value':queryPatientId,'oper':'eq'}
    ds=db.selectRows(project,'study','Demographics',[qfilter])
    if len(ds['rows'])==0:
        row={}
        row['ParticipantId']=patientId
        try:
            row['birthDate']=dicom['PatientBirthDate']
            row['PatientName']=dicom['PatientName']
        except KeyError:
            pass
    

        row['OrthancId']=p
        db.modifyRows('insert',project,'study','Demographics',[row])

    for s in pdata['Studies']:
        sdata=odb.getStudyData(s)
        sdicom=sdata['MainDicomTags']

        sdate='19700101'
        try:
            sid=sdicom['StudyInstanceUID']
            sdate=sdicom['StudyDate']
            print('Study: {}/{}'.format(s,sid))
        except KeyError:
            pass
        #print('Data: {}'.format(sdata))
        #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':'ParticipantId','value':queryPatientId,'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

            #remove strange characters
            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("seDesc")
            #fc=[ord(c) for c in seDesc]
            #for f in fc:
            #    print("{}".format(f))
            #
            
            print('ID: {}.'.format(seDesc))

            row={}
            row['ParticipantId']=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")