limfomiPET/pythonScripts/runStat.py

import statUtils
import os
import radiomics
import SimpleITK
import sys
import json

def main(parFile='../templates/statistics.json'):
    setup=statUtils.loadSetup(parFile)
    rFile='radiomics.json'
    with open(rFile,'w') as f:
        f.write(json.dumps(setup['radiomics']))
    setup['db'],setup['fb']=statUtils.connectDB('onko-nix')
    users=statUtils.getUsers(setup['db'],setup['project'])
    qFilter=[]
    try:
        vList=';'.join(setup['participants'])    
        qFilter.append({'variable':'ParticipantId','value':vList,'oper':'in'})
    except KeyError:
        pass
    ds=setup['db'].selectRows(setup['project'],'study',setup['imagingDataset'],qFilter)
    if not os.path.isdir(setup['localDir']):
        os.mkdir(setup['localDir'])
    #select just the first row; debugging
    rows=ds['rows']
    setup['values']=['COM','MTV','TLG','SUVmean','SUVmax']
    #params=os.path.join('..','templates','radiomics.yaml')
    setup['featureExtractor']=radiomics.featureextractor.RadiomicsFeatureExtractor(rFile)
    for r in rows:
        print(r)
        for q in ['petResampled']:
            localPath=statUtils.getImage(setup,r,q)
        if localPath=="NONE":
            continue
        segPaths=statUtils.getSegmentations(setup,r)
        if "NONE" in segPaths.values():
            os.remove(localPath)
            continue
        segKeys=list(segPaths.keys())
        for x in segPaths:
            print('Loaded {}/{}'.format(users[x],segPaths[x]))
        pet=SimpleITK.ReadImage(localPath)
        seg={x:SimpleITK.ReadImage(segPaths[x]) for x in segPaths}
        #find labels associated with each (non-overlaping) segmentation
        ids=statUtils.getSegments(list(seg.values())[0])
        for id in ids:
            print('{} {}'.format(id,ids[id]))
            for x in seg:
                try:
                    output=statUtils.getRadiomicsComponentStats(setup,pet,seg[x],ids[id])
                except ValueError:
                    continue
                output.update({x:r[x] for x in ['ParticipantId','SequenceNum','patientCode','visitCode']})
                output['User']=x
                output['segment']=ids[id]
                statUtils.updateDatasetRows(setup['db'],setup['project'],setup['SUVdataset'],[output])
                #print(output)
        #cleanup
        for x in segPaths:
            os.remove(segPaths[x])
        os.remove(localPath)
    os.remove(rFile)
if __name__=='__main__':
    main(sys.argv[1])