YildizLabCode/SpotlistData2XML.py at master · petercombs/YildizLabCode · GitHub

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#/usr/bin/python


from scipy import io
from optparse import OptionParser

if __name__ == "__main__":
    parser = OptionParser(usage="Usage: %prog inputfile.mat outputfile.xml")

    opts, args = parser.parse_args()
    assert len(args) == 2

    Data = io.loadmat(args[0], squeeze_me = True)
    imgname = Data['imgname']

    framesets = zip(Data["tpmins"], Data["tpmaxes"]+1)
    plotpoints = []
    if 'xl_fids' in Data:
        plotpoints.append((Data['xl_fids'], Data['yl_fids'], Data['framesetnum_fids']))
        plotpoints.append((Data['xr_fids'], Data['yr_fids'], Data['framesetnum_fids']))
        plotpoints.append((Data['xl_exp'], Data['yl_exp'], Data['framesetnum_exp']))
        plotpoints.append((Data['xr_exp'], Data['yr_exp'], Data['framesetnum_exp']))
    else:
        plotpoints.append((Data['xl'], Data['yl'], Data['framesetnum']))
        plotpoints.append((Data['xr'], Data['yr'], Data['framesetnum']))


    plotpoints.append((Data['DQ_varbig_x'], Data['DQ_varbig_y'], Data['DQ_varbig_t']))
    plotpoints.append((Data['DQ_nomatch_x'], Data['DQ_nomatch_y'], Data['DQ_nomatch_t']))

    outfile = open(args[1], 'w')
    outfile.write('<?xml version="1.0" encoding="UTF-8"?>\n')
    outfile.write("<CellCounter_Marker_File>\n")
    outfile.write("<Image_Properties>\n"
     "\t<Image_Filename>%s</Image_Filename>\n"
    "</Image_Properties>\n" % imgname)

    outfile.write('<Marker_Data>\n')
    outfile.write('\t<Current_Type>1</Current_Type>\n')


    marker_type = 1
    for xs, ys, fsnums in plotpoints:
        outfile.write('\t<Marker_Type> \n')
        outfile.write('\t\t<Type>%d</Type>\n' % marker_type)
        for x, y, fsnum in zip(xs, ys, fsnums):
            for fnum in range(*map(int,framesets[int(fsnum)])):
                outfile.write('\t\t<Marker><MarkerX>%d</MarkerX> '
                                    '<MarkerY>%d</MarkerY> '
                                    '<MarkerZ>%d</MarkerZ> '
                                    '</Marker>\n' % (int(x), int(y), int(fnum)))
        outfile.write('\t</Marker_Type>\n')
        marker_type += 1
    print "Almost",
    outfile.write('</Marker_Data>\n')

    outfile.write("</CellCounter_Marker_File>\n")
    outfile.close()
    print "There!"