irAEMM/pythonScripts/populateImagingFromOrthanc.py

import os
import json
import re
import sys
import datetime
import re

fhome=os.path.expanduser('~')
sys.path.insert(1,fhome+'/software/src/labkeyInterface')
import labkeyInterface
import labkeyDatabaseBrowser

fconfig=os.path.join(fhome,'.labkey','network.json')

net=labkeyInterface.labkeyInterface()
net.init(fconfig)
db=labkeyDatabaseBrowser.labkeyDB(net)


i=0
projectOrthanc='Orthanc/Database'
inputDataset='Imaging'
projectStudy='iPNUMMretro/Study'
outputDataset='Imaging1'

ds=db.selectRows(projectOrthanc,'study',inputDataset,[])


#single entry for the patientId/dicomStudy pair
selectVars=['PatientId','dicomStudy']

dates=[datetime.datetime.strptime(row['studyDate'],'%Y/%m/%d %H:%M:%S') for row in ds['rows']]
idx=sorted(range(len(dates)),key=lambda k:dates[k])

for j in range(len(dates)):
    #row in ds['rows']:
    row=ds['rows'][idx[j]]

    #skip series which don't match selected filters
    outvar='NONE'
    sd=row['seriesDescription']
    if sd=='PET WB':
        outvar='PETWB'
    if sd.find('CT WB')==0:
        if sd.find('fov')<0:
            outvar='CT'

    if outvar=='NONE':
        continue

    filters=[]
    for v in selectVars:
        filters.append({'variable':v,'value':row[v],'oper':'eq'})
    ds2=db.selectRows(projectStudy,'study',outputDataset,
            [{'variable':'PatientId','value':row['PatientId'],'oper':'eq'}])
    ds1=db.selectRows(projectStudy,'study',outputDataset,filters)
    if len(ds1['rows'])>1:
        print('ERROR: too many matches for {}/{}'.format(row['PatientId'],row['dicomStudy']))
        continue
    mode='update'
    outRow={}
    if len(ds1['rows'])==0:
        mode='insert'
        outRow['PatientId']=row['PatientId']
        outRow['SequenceNum']=len(ds2['rows'])
        outRow['dicomStudy']=row['dicomStudy']
    else:
        outRow=ds1['rows'][0]
        
    outRow[outvar]=row['orthancSeries']
    outRow['studyDate']=row['studyDate']

    status=db.modifyRows(mode,projectStudy,'study',outputDataset,[outRow])
    print('{}'.format(status))
    if j==50:
        break
        
print("Done")