EMBRACE/loadPatient.py

#load all relevant patient data
#requires labkeyInterface through labkeyDatabrowser db, labkeyFileBrowser fb, fbDMR, importDicom iDicom and loadDicom lDicom

       
def getOICode(db, project, label):
        idFilter={"variable":"EMBRACE_ID",
            "oper":"eq",
            "value":label}
        fSet=db.selectRows(project,'study','PopisneStevilke',[idFilter])
        try:
            row=fSet["rows"][0]
        except:
            print("OI code for {} not found").format(label)
            return None
        return row["OICode"]


def load(db,fb,fbDMR,iDicom,lDicom,project,label):

    print('loadPatient.load ver: 1.0.3')



    idFilter={'variable':'EMBRACE_ID','value':label,'oper':'eq'}
    ctFilter={'variable':'type','value':'CT','oper':'eq'}
    dsCT=db.selectRows(project,'study','ImagingVisitsManaged',[idFilter,ctFilter])
    returnObj={}

    try:
        ctRow=dsCT['rows'][0]
    except IndexError:
        return returnObj
    
    oiCode=getOICode(db,project,label)
    
    #load ct
    seqNum=ctRow['pseudoTransverseID']
    oiFilter={'variable':'PatientId','value':oiCode,'oper':'eq'}
    sFilter={'variable':'SequenceNum','value':'{:.0f}'.format(seqNum),'oper':'eq'}
    
    dsDicom=db.selectRows('Test/Transfer','study','Imaging',[oiFilter,sFilter])
    try:
        rDicom=dsDicom['rows'][0]
    except IndexError:
        return returnObj
    
    iPath=['dicom',rDicom['Study'],rDicom['Series']]
    dicomReadFilter={'seriesNumber':"SeriesLabel",
                        'studyInstanceUid':None,
                        'frameOfReferenceInstanceUid':None}

    ctVolumes=iDicom.loadVolumes(fb,'Test/Transfer',iPath,dicomReadFilter)
    ctNode=ctVolumes[0]['node']
    ctNode.SetName(label+'_CT')

    #load dmr
    #uses different server!!!
    dmrFilter={'variable':'type','value':'DMR','oper':'eq'}
    dsDMR=db.selectRows(project,'study','ImagingVisitsManaged',[idFilter,dmrFilter])
    try:
        dmrRow=dsDMR['rows'][0]
    except IndexError:
        return returnObj
    
    dmrName=dmrRow['Name']
    iPath=['PRETVORJENE',dmrName,'DICOM']
    dicomReadFilter={'seriesNumber':"SeriesLabel",
                        'sequenceName':"*tse2d1_3",
                        'percentPhaseFieldOfView':90,
                        'studyInstanceUid':None,
                        'frameOfReferenceInstanceUid':None,
                        'scanningSequence':None,
                        'sequenceVariant':None}

    dmrVolumes=iDicom.loadVolumes(fbDMR,project,iPath,dicomReadFilter)
    try:
        dmrNode=dmrVolumes[0]['node']
        dmrNode.SetName(label+'_DMR')
    except IndexError:
        return returnObj

    #load CT-RS
    ctrsFilter={'variable':'type','value':'CT-RS','oper':'eq'}
    dsCTRS=db.selectRows(project,'study','ImagingVisitsManaged',[idFilter,ctrsFilter])
    try:
        ctrsRow=dsCTRS['rows'][0]
        print('CTRS: {}'.format(len(dsCTRS['rows'])))
    except IndexError:
        return returnObj
    seqNum=ctrsRow['pseudoTransverseID']
    sFilter={'variable':'SequenceNum','value':'{:.0f}'.format(seqNum),'oper':'eq'}
    
    dsDicomRT=db.selectRows('Test/Transfer','study','Imaging',[oiFilter,sFilter])
    try:
        rDicomRT=dsDicomRT['rows'][0]
        print('CT-RS Dicom: {}'.format(len(dsDicomRT['rows'])))
        print('ID: {}'.format(rDicomRT['PatientId']))
    except IndexError:
        return returnObj

    iPath=['dicom',rDicomRT['Study'],rDicomRT['Series']]
    dicomReadFilter={'seriesNumber':"SeriesLabel",
                       'studyInstanceUid':None,
                       'frameOfReferenceInstanceUid':None}

    rtSeg=lDicom.loadSegmentations(fb,'Test/Transfer',iPath,dicomReadFilter)
    rtNode=rtSeg[0]['node']
    rtNode.SetName(label+'_CTRS')

    return {'CT':ctNode,'DMR':dmrNode,'CTRS':rtNode,
        'metadataCT':ctVolumes[0]['metadata'],
        'metadataDMR':dmrVolumes[0]['metadata'],
        'metadataCTRS':rtSeg[0]['metadata']
        }