def total_curv(fudge_parameters, spectra): non_ext, extending, pulses, prop = fudge_parameters for s in spectra.values(): print s exit(1) corr_spectra = [correct_deadtime(non_ext, extending, pulses, prop, s) for s in spectra] curv = [np.sum(spectrum_curvature(s)) for s in corr_spectra] return np.sum(np.abs(curv))
def main():
parser = argparse.ArgumentParser(description='Correct clusters for deadtime.')
parser.add_argument('clusters',
help='file containing cluster filenames')
parser.add_argument('outputdir',
help='directory to write corrected clusters to')
parser.add_argument('-d','--ext', dest='ext', type=float, default=5.,
help='extending deadtime (ns)')
parser.add_argument('-D','--non', dest='non', type=float, default=0.,
help='non-extending deadtime (ns)')
parser.add_argument('-s','--scantime', dest='ST', type=float, default=0.23,
help='scan time (s)')
parser.add_argument('-c','--cycletime', dest='CT', type=float, default=45.,
help='cycletime (μs)')
parser.add_argument('-l','--length', dest='L', type=float, default=1078.,
help='effective TOF path length (mm)')
parser.add_argument('-v','--voltage', dest='V', type=float, default=5630.,
help='effective accelerating voltage (V)')
args = parser.parse_args()
dt = [args.ext,args.non]
pulses = args.ST / (args.CT * 1E-6)
prop = (args.L * 1E-3) / (2 * 96485333.7 * args.V)**0.5
try:
with open(args.clusters, 'r') as inf:
files = [line.split()[0] for line in inf]
except IOError:
print "error opening ", args.clusters
return -1
try:
os.mkdir(args.outputdir)
except OSError:
print args.outputdir, " already exists"
return -1
lre = re.compile('(\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)\s+(\d+\.\d+)')
for file in files:
spectrum={}
scannums={}
try:
with open(file, 'r') as f:
for line in f:
res = lre.search(line)
if res:
RT = float(res.group(2))
if RT not in spectrum:
spectrum[RT] = {}
spectrum[RT][float(res.group(3))] = float(res.group(4))
scannums[RT] = res.group(1)
except IOError:
next
spectrum = correct_deadtime(dt,pulses,prop,spectrum)
outputfilename = os.path.join(args.outputdir, os.path.basename(file))
with open(outputfilename, 'w') as f:
for RT, scan in sorted(spectrum.iteritems()):
for mz, I in sorted(scan.iteritems()):
f.write("%s %.3f %.3f %.3f\n" % (scannums[RT],RT,mz,I))
return 0