def main(): """ Entry point for command line tool """ try: parser = AslOptionParser(usage="asl_mask -i <asl_image> [options...]", version=__version__) parser.add_option("--calib", "-c", help="Calibration image", default=None) parser.add_option( "--use-pwi", help= "Use the perfusion weighted average rather than the timeseries mean", action="store_true", default=False) parser.add_category(image.AslImageOptions()) parser.add_category(struc.StructuralImageOptions()) parser.add_category(GenericOptions()) options, _ = parser.parse_args(sys.argv) options.mask = None # No point in using command line tool if you already have a mask! wsp = Workspace(**vars(options)) if not options.asldata: sys.stderr.write("Input file not specified\n") parser.print_help() sys.exit(1) wsp.asldata = AslImage(wsp.asldata, **parser.filter(vars(options), "image")) wsp.asldata.summary() wsp.generate_mask() if wsp.output is None: wsp.output = wsp.asldata.name + "_mask" wsp.rois.mask.save(wsp.output) except ValueError as exc: sys.stderr.write("ERROR: " + str(exc) + "\n") sys.exit(1)
def main(): """ Entry point for oxasl_calib command line program """ debug = False try: parser = AslOptionParser( usage= "oxasl_calib -i <perfusion image> -c <calibration image> --calib-method <voxelwise|refregion> -o <output filename> [options]" ) parser.add_category(CalibOptions()) parser.add_category(GenericOptions(output_type="file")) options, _ = parser.parse_args(sys.argv) if not options.perf: sys.stderr.write("Perfusion input file not specified\n") parser.print_help() sys.exit(1) if not options.calib: sys.stderr.write("Calibration input file not specified\n") parser.print_help() sys.exit(1) wsp = Workspace(**vars(options)) summary(wsp.perf) summary(wsp.calib) if wsp.output is None: wsp.output = "%s_calib" % wsp.perf.name calibrated_img = calibrate(wsp, wsp.perf) summary(calibrated_img) calibrated_img.save(wsp.output) except ValueError as exc: sys.stderr.write("ERROR: " + str(exc) + "\n") if debug: traceback.print_exc() sys.exit(1)