def run(self):
global args, events, hist
p = Parse(args.infile)
data = None
while True:
if self._abort_flag:
print("Worker aborted")
return
if self._pause_flag:
time.sleep(0.1)
continue
try:
data = p.next()
except StopIteration:
time.sleep(0.5)
continue
vals = integrate(data)
e_summ, e_baseline = vals.summ, vals.bl
if self._notify_window.ready:
self._notify_window.ready = False
wx.PostEvent(self._notify_window, DataReadyEvent(data))
sys.stderr.write("progress: %2.3f%%\n" %
(100.0 * p.progress()))
events.append(data)
#TODO: if hist:
hist.append(e_summ)
def main():
parser = argparse.ArgumentParser(description=__doc__, formatter_class=argparse.RawTextHelpFormatter)
parser.add_argument('infile', nargs='?', type=str, default='-',
help="raw data file (stdin by default)")
parser.add_argument('-o', '--outfile', type=lambda x: check_file_not_exists(parser, x), default=sys.stdout,
metavar='FILE',
help="redirect output to a file")
parser.add_argument('-b','--baseline', type=str, default="0:20",
metavar = 'A:B',
help='a range for baseline samples (int means from the beginning, negative int means from the end)'
)
parser.add_argument('-s','--signal', type=str, default=None,
metavar = 'C:D',
help='a range for signal samples to integrate (default: from baseline to the end, for negative baseline is from 0 to baseline)'
)
parser.add_argument('--skip', type=int, default=0,
metavar = 'N',
help='skip first N events (useful if first timestamps are not consequent)')
parser.add_argument('--csv', action='store_true',
help='output as a .csv')
parser.add_argument('--debug', action='store_true')
parser.add_argument('--save-bl', action='store_true',
help='save calculated baseline value')
parser.add_argument('--save-bl-var', action='store_true',
help='save baseline standard deviation (to estimate noise)')
parser.add_argument('--save-min', action='store_true',
help='save the value of absolute minimum')
parser.add_argument('--save-max', action='store_true',
help='save the value and the bin number of absolute maximum')
parser.add_argument('--save-max-idx', action='store_true',
help='save sample index of the maximum value')
parser.add_argument('--save-len', action='store_true',
help='save a number of values more than baseline around the maximum')
parser.add_argument('--progress', action='store_true',
help="print progress to stderr")
args = parser.parse_args()
global debug, nevents
# --debug, --outfile
debug = args.debug
outfile = args.outfile
# --baseline, --signal
rbaseline = map(int, str.split(args.baseline, ':')) # acceptable values: "0:10", "10" , "-10", "-10:-5"
if len(rbaseline) > 2:
raise ValueError('rbaseline is a:b')
if len(rbaseline) is 1:
rbaseline = [0] + rbaseline # [10] -> [0,10]
if args.signal:
rsignal = map(int, str.split(args.signal, ':'))
if len(rsignal) is 1:
rsignal = [rbaseline[1] ] + rsignal
else:
rsignal = (rbaseline[1], None) # from just after baseline to the end
# --infile
infile = sys.stdin
if args.infile != '-':
try:
infile = io.open(args.infile, 'rb')
except IOError as e:
sys.stderr.write('Err: ' + e.strerror+': "' + e.filename +'"\n')
exit(e.errno)
splitter = '\t'
# --csv
if args.csv:
splitter = ';'
# --skip
skip = args.skip
# Init parser
try:
p = Parse(infile)
except ValueError as e:
sys.stderr.write("Err: %s \n" % e)
exit(1)
# Catch Ctrl+C
signal.signal(signal.SIGINT, fin)
# Parse events
nevents = 0
fields = list(Features._fields)
if not args.save_max:
fields.remove('max')
if not args.save_min:
fields.remove('min')
if not args.save_max_idx:
fields.remove('max_idx')
if not args.save_bl:
fields.remove('bl')
if not args.save_bl_var:
fields.remove('bl_var')
if not args.save_len:
fields.remove('len')
# Print file header
outfile.write('# ' + splitter.join(fields) +'\n')
for event in p:
nevents += 1
if skip and nevents <= skip:
continue
vals = rintegrate(event, rbaseline, rsignal, fields)
if args.progress and (nevents % 10000 == 0):
sys.stderr.write("progress: {0:.1f}%\r".format( 100.0 * p.progress()))
vals = [getattr(vals, k) for k in fields ]
line = splitter.join( map(str, vals) )
outfile.write(line + '\n')
sys.stderr.write("{}: ".format(outfile.name))
fin()
