irAEMM/pythonScripts/runSegmentation.py

import os
import json
import re
import subprocess
import nibabel
import shutil
import sys

#nothing gets done if you do import

def getPatientLabel(row,participantField='PatientId'):
    return row[participantField].replace('/','_') 

def getVisitLabel(row):
    return 'VISIT_'+str(int(row['SequenceNum']))

def getStudyLabel(row,participantField='PatientId'):
    return getPatientLabel(row,participantField)+'-'+getVisitLabel(row)


def updateRow(project,dataset,row,imageResampledField,gzFileNames,\
        participantField='PatientId'):
    row['patientCode']=getPatientLabel(row,participantField)
    row['visitCode']=getVisitLabel(row)
    for im in imageResampledField:
        row[imageResampledField[im]]=gzFileNames[im]
    db.modifyRows('update',project,'study',dataset,[row])
 
def replacePatterns(infile,outfile,replacePatterns):
    of=open(outfile,'w')
    with open(infile,'r') as f:
        data=f.read()
        for p in replacePatterns:
            val=replacePatterns[p]
            data=re.sub(p,val,data)
    of.write(data)
    of.close()
    
def valueSubstitution(pars,val):
    if val.find('__home__')>-1:
        val=re.sub(r'__home__',os.path.expanduser('~'),val)

    return path

def main(parameterFile):
    
    fhome=os.path.expanduser('~')
    with open(os.path.join(fhome,".labkey","setup.json")) as f:
        setup=json.load(f)

    sys.path.insert(0,setup["paths"]["labkeyInterface"])
    import labkeyInterface
    import labkeyDatabaseBrowser
    import labkeyFileBrowser

    sys.path.append(setup['paths']['parseConfig'])
    import parseConfig


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

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

    with open(parameterFile) as f:
        pars=json.load(f)

    pars=parseConfig.convert(pars)
    pars=parseConfig.convertValues(pars)

    hi=0
    project=pars['project']
    dataset=pars['targetQuery']
    schema=pars['targetSchema']


    tempBase=pars['tempBase']
    if not os.path.isdir(tempBase):
        os.makedirs(tempBase)


    participantField=pars['participantField']

    #all images from database
    ds=db.selectRows(project,schema,dataset,[])

    
    #imageSelector={"CT":"CT","PET":"PETWB_orthancId"}
    #input
    images=pars['images']
    #use webdav to transfer file (even though it is localhost)

    tempNames={im:os.path.join(tempBase,images[im]['tempFile']) for im in images}
 

    #update the config
    cfg=pars['deepmedic']['config']
    for c in cfg:
        replacePatterns(cfg[c]['template'],\
                cfg[c]['out'],\
                pars['replacePattern'])
    i=0
    for row in ds["rows"]:
        
        #download to temp file (could be a fixed name)
        baseDir=fb.formatPathURL(project,pars['imageDir']+'/'+\
            getPatientLabel(row,participantField)+'/'+\
            getVisitLabel(row))
        for im in images:
            fb.readFileToFile(baseDir+'/'+row[images[im]['queryField']],
                os.path.join(tempBase,images[im]['tempFile']))
            
        break        
        i=i+1

    print("Done")


if __name__ == '__main__':
    main(sys.argv[1])
    #sys.exit()