dynamicSPECT/pythonScripts/segmentation.py

import numpy
import config
import SimpleITK
import os
import getData

def guessPixelPosition(sx=-1,sy=-1,sz=-1):
    #guess position of segments
    if sx<0:
        sx=12
    if sy<0:
        sy=28
    if sz<0:
        sz=32
    rz=4
    oz=0

    slc=[sx,sy,sz]
    p1=[sx,sy,sz]

    #tip
    fp={'0':[\
            [sx,sy,sz],   
            [sx-5,sy,sz],\
            [sx-2,sy,sz-rz],\
            [sx+3,sy,sz-rz],\
            [sx-2,sy,sz+rz-1],\
            [sx+3,sy,sz+rz]],\
        '1':[\
            [sx,sy,sz],  
            [sx-5,sy,sz],\
            [sx-1,sy-rz,sz],\
            [sx-1,sy+rz-1,sz],\
            [sx+3,sy-rz,sz],\
            [sx+3,sy+rz,sz]],\
        '2':[\
            [sx,sy,sz],
            [sx,sy+rz+oz,sz],\
            [sx,sy+0.3*rz+oz,sz-rz],\
            [sx,sy-0.3*rz+oz,sz-rz],\
            [sx,sy-rz+oz,sz],\
            [sx,sy-0.3*rz+oz,sz+rz],\
            [sx,sy+0.3*rz+oz,sz+rz]]}
    return fp

    
def getPatientNIM(r,setup):
    locDir=config.getLocalDir(r,setup)
    fileName=config.getNodeName(r,setup,'NM',19)+'.nrrd'
    f=os.path.join(locDir,fileName)
    im=SimpleITK.ReadImage(f)
    nim=SimpleITK.GetArrayFromImage(im)
    return nim

def writeSegmentation(db,r,setup):
    locDir=config.getLocalDir(r,setup)
    fileName='{}_Segmentation.txt'.format(config.getCode(r,setup))
    idFilter={'variable':'PatientId','value':config.getPatientId(r,setup),'oper':'eq'}
    visitFilter={'variable':'visitName','value':config.getVisitId(r,setup),'oper':'eq'}
    rows=getData.getSegmentation(db,setup,[idFilter,visitFilter])
    v=numpy.zeros((len(rows),3))
    for qr in rows:
        region=int(qr['regionId'])
        v[region,2]=float(qr['x'])
        v[region,1]=float(qr['y'])
        v[region,0]=float(qr['z'])
    #for i in range(len(rows)):
    #    print(v[i,:])
    numpy.savetxt(os.path.join(locDir,fileName),v)