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MuonLifeTime.py
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MuonLifeTime.py
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#!/usr/bin/env python
import os
import shutil
import struct
import subprocess as subp
import sys
import time
from ConfigParser import ConfigParser
from optparse import OptionParser
import ROOT as ro
import numpy as np
import cPickle as pickle
from Channel_Caen import Channel_Caen
from Settings_Caen import Settings_Caen
from Utils import *
# from memory_profiler import profile
trig_rand_time = 0.2
wait_time_hv = 7
class MuonLifeTime:
def __init__(self, infile='None', settingsObj=None):
print 'Starting Muon Life Time program ...'
self.infile = infile
if self.infile != 'None':
self.settings = Settings_Caen(self.infile)
self.settings.ReadInputFile()
elif settingsObj:
self.settings = settingsObj
else:
ExitMessage('No setting file was given, or settings object. Quittint!')
self.settings.SetOutputFiles()
# Create channel objects for signal, trigger and veto
self.signal_ch = {sigi: Channel_Caen(self.settings.sigCh[sigi], signal_number=sigi, is_trigger=False, is_veto=False) for sigi in xrange(self.settings.num_signals)}
for sigi in xrange(self.settings.num_signals):
self.signal_ch[sigi].Set_Channel(self.settings)
self.trigger_ch = Channel_Caen(self.settings.trigCh, signal_number=-1, is_trigger=True, is_veto=False)
self.trigger_ch.Set_Channel(self.settings)
self.veto_ch = Channel_Caen(self.settings.vetoCh, signal_number=-1, is_trigger=False, is_veto=True)
self.veto_ch.Set_Channel(self.settings)
# declare extra variables that will be used
self.fs0, self.ft0, self.fv0 = None, None, None
self.fs0 = {sigi: None for sigi in xrange(self.settings.num_signals)}
self.utils = Utils()
self.RemoveFiles()
self.t0, self.t1, self.t2 = None, None, None
self.p, self.pconv = None, None
self.total_events = 0
self.written_events_sig, self.written_events_trig, self.written_events_veto = 0, 0, 0
self.total_events_sig, self.total_events_trig, self.total_events_veto = 0, 0, 0
self.session_measured_data_sig, self.session_measured_data_trig, self.session_measured_data_veto = 0, 0, 0
self.total_merged_data_sig, self.total_merged_data_trig, self.total_merged_data_veto = 0, 0, 0
self.doMerge = False
self.min_measured_data = 0
self.min_data_to_write = 0
self.events_to_write = 0
self.read_size = 0
self.sig_written, self.trg_written, self.veto_written = 0, 0, 0
self.session_written_events_sig, self.session_written_events_trg, self.session_written_events_veto = 0, 0, 0
self.fins, self.fint, self.finv = None, None, None
self.datas, self.datat, self.datav = None, None, None
self.bar = None
def RemoveFiles(self):
'''
Removes old files in the directory where the MuonLifeTime.py file is. Useful to eliminate lingering files after a crash
:return:
'''
for sigi in xrange(self.settings.num_signals):
# close and delete instances of signal channels
if self.fs0[sigi]:
if not self.fs0[sigi].closed:
self.fs0[sigi].close()
del self.fs0[sigi]
if self.ft0:
# close ane delete instance of trigger channel
if not self.ft0.closed:
self.ft0.close()
del self.ft0
if self.fv0:
# close and delete instance of veto channel
if not self.fv0.closed:
self.fv0.close()
del self.fv0
channels = self.settings.sigCh.values() + [self.settings.trigCh] + [self.settings.vetoCh]
for ch in channels:
# remove lingering files for signals, trigger and veto channels
if os.path.isfile('raw_waves{c}.dat'.format(c=ch)):
os.remove('raw_waves{c}.dat'.format(c=ch))
if os.path.isfile('waves{c}.dat'.format(c=ch)):
os.remove('waves{c}.dat'.format(c=ch))
del channels
def CreateEmptyFiles(self):
'''
Creates empty data files for each signal channel, the veto channel and the trigger channel
:return:
'''
self.ft0 = open('raw_wave{t}.dat'.format(t=self.trigger_ch.caen_ch), 'wb')
self.fv0 = open('raw_wave{a}.dat'.format(a=self.veto_ch.caen_ch), 'wb')
for sigi in xrange(self.settings.num_signals):
self.fs0[sigi] = open('raw_wave{s}.dat'.format(s=self.signal_ch[sigi].caen_ch), 'wb')
def OpenFiles(self, mode='rb'):
'''
:param mode:
:return:
'''
for sigi in xrange(self.settings.num_signals):
if not self.fs0[sigi]:
self.fs0[sigi] = open('raw_wave{s}.dat'.format(s=self.signal_ch[sigi].caen_ch), mode)
if not self.ft0:
self.ft0 = open('raw_wave{t}.dat'.format(t=self.trigger_ch.caen_ch), mode)
if not self.fv0:
self.fv0 = open('raw_wave{a}.dat'.format(a=self.veto_ch.caen_ch), mode)
def CloseFiles(self):
if self.ft0:
self.ft0.close()
if self.ft0.closed:
del self.ft0
self.ft0 = None
if self.fv0:
self.fv0.close()
if self.fv0.closed:
del self.fv0
self.fv0 = None
for sigi in xrange(self.settings.num_signals):
if self.fs0[sigi]:
self.fs0[sigi].close()
if self.fs0[sigi].closed:
del self.fs0[sigi]
self.fs0[sigi] = None
def GetWaveforms(self, events=1, stdin=False, stdout=False):
self.t1 = time.time()
# if self.settings.do_hv_control: self.hv_control.UpdateHVFile()
# if events == 1:
# # while self.p.poll() is None:
# time.sleep(1)
# self.p.stdin.write('c')
# self.p.stdin.flush()
# time.sleep(1)
# self.p.stdin.write('s')
# self.p.stdin.flush()
# if self.settings.plot_waveforms:
# # time.sleep(1)
# self.p.stdin.write('P')
# self.p.stdin.flush()
# # time.sleep(1)
# self.p.stdin.write('w')
# self.p.stdin.flush()
# # time.sleep(1)
# self.p.stdin.write('t')
# self.p.stdin.flush()
# time.sleep(1)
# self.p.stdin.write('s')
# self.p.stdin.flush()
# time.sleep(1)
# self.p.stdin.write('q')
# self.p.stdin.flush()
# while self.p.poll() is None:
# continue
# if self.settings.do_hv_control: self.hv_control.UpdateHVFile()
# self.ConcatenateBinaries()
# self.CloseSubprocess('wave_dump', stdin=stdin, stdout=stdout)
# self.settings.RemoveBinaries()
# else:
time.sleep(1)
self.p.stdin.write('c')
self.p.stdin.flush()
time.sleep(1)
self.p.stdin.write('W')
self.p.stdin.flush()
if self.settings.plot_waveforms:
# time.sleep(1)
self.p.stdin.write('P')
self.p.stdin.flush()
# time.sleep(1)
self.p.stdin.write('s')
self.p.stdin.flush()
self.written_events_sig, self.written_events_trig, self.written_events_veto = 0, 0, 0
# time.sleep(1)
self.t2 = time.time()
while self.p.poll() is None:
if time.time() - self.t1 >= self.settings.time_calib:
self.p.stdin.write('s')
self.p.stdin.flush()
self.settings.RemoveBinaries()
self.p.stdin.write('c')
self.p.stdin.flush()
self.p.stdin.write('q')
self.p.stdin.flush()
time.sleep(1)
# if self.settings.do_hv_control: self.hv_control.UpdateHVFile()
elif self.written_events_sig + self.sig_written >= events:
self.p.stdin.write('s')
self.p.stdin.flush()
self.settings.RemoveBinaries()
self.p.stdin.write('q')
self.p.stdin.flush()
time.sleep(1)
# if self.settings.do_hv_control: self.hv_control.UpdateHVFile()
else:
# if self.settings.random_test and (time.time() - self.t2 > trig_rand_time):
# self.p.stdin.write('t')
# self.p.stdin.flush()
# self.t2 = time.time()
self.ConcatenateBinaries()
if not self.settings.simultaneous_conversion:
self.bar.update(int(min(self.written_events_sig + self.sig_written, self.settings.num_events)))
del self.t1
self.t1 = None
self.CloseSubprocess('wave_dump', stdin=stdin, stdout=stdout)
time.sleep(1)
del self.t2
self.t2 = None
self.total_events_sig = self.CalculateEventsWritten(self.settings.sigCh[0])
self.total_events_trig = self.CalculateEventsWritten(self.settings.trigCh)
self.total_events_veto = self.CalculateEventsWritten(self.settings.vetoCh)
if self.total_events_sig == self.total_events_trig and self.total_events_sig == self.total_events_veto:
self.total_events = self.total_events_sig
else:
print 'Written events are of different sizes (signal: {s}, trigger: {t}, veto: {v}). Missmatch!'.format(s=self.total_events_sig, t=self.total_events_trig, v=self.total_events_veto)
exit()
del self.total_events_sig, self.total_events_trig, self.total_events_veto
self.total_events_sig, self.total_events_trig, self.total_events_veto = None, None, None
def CloseSubprocess(self, pname='wave_dump', stdin=False, stdout=False):
p = self.p if pname == 'wave_dump' else self.pconv if pname == 'converter' else None
if not p:
print 'Something failed! Exiting!'
exit()
pid = p.pid
if stdin:
p.stdin.close()
if stdout:
p.stdout.close()
if p.wait() is None:
print 'Could not terminate subprocess... forcing termination'
p.kill()
if p.wait() is None:
print 'Could not kill subprocess... quitting'
exit()
try:
os.kill(pid, 0)
except OSError:
pass
else:
print 'The subprocess is still running. Killing it with os.kill'
os.kill(pid, 15)
try:
os.kill(pid, 0)
except OSError:
pass
else:
print 'The process does not die... quitting program'
exit()
del p, pid
if pname == 'wave_dump':
del self.p
self.p = None
elif pname == 'converter':
del self.pconv
self.pconv = None
def ConcatenateBinaries(self):
self.session_measured_data_sig, self.session_measured_data_trig, self.session_measured_data_veto = 0, 0, 0
data_channels = self.settings.sigCh.values() + [self.settings.trigCh] + [self.settings.vetoCh]
data_files = ['wave{s}.dat'.format(s=ch) for ch in data_channels]
bool_cont = True
for data_file in data_files:
if not os.path.isfile(data_file):
bool_cont = False
if bool_cont:
self.session_measured_data_sig = int(os.path.getsize('wave{s}.dat'.format(s=self.settings.sigCh[0])))
self.session_measured_data_trig = int(os.path.getsize('wave{t}.dat'.format(t=self.settings.trigCh)))
self.session_measured_data_veto = int(os.path.getsize('wave{a}.dat'.format(a=self.settings.vetoCh)))
else:
print 'Waiting for first event...'
# ExitMessage('Stop!!! something is wrooong!!!!', os.EX_DATAERR)
return
self.total_merged_data_sig = int(os.path.getsize('raw_wave{s}.dat'.format(s=self.settings.sigCh[0])))
self.total_merged_data_trig = int(os.path.getsize('raw_wave{t}.dat'.format(t=self.settings.trigCh)))
self.total_merged_data_veto = int(os.path.getsize('raw_wave{a}.dat'.format(a=self.settings.vetoCh)))
self.doMerge = (self.session_measured_data_sig + self.sig_written * self.settings.struct_len > self.total_merged_data_sig) and (self.session_measured_data_trig + self.trg_written * self.settings.struct_len > self.total_merged_data_trig) and (self.session_measured_data_veto + self.veto_written * self.settings.struct_len > self.total_merged_data_veto)
if self.doMerge:
# self.OpenFiles(mode='ab')
self.min_measured_data = min(self.session_measured_data_sig, self.session_measured_data_trig, self.session_measured_data_veto)
data_to_write_sig = self.min_measured_data - self.total_merged_data_sig + self.sig_written * self.settings.struct_len
data_to_write_trg = self.min_measured_data - self.total_merged_data_trig + self.trg_written * self.settings.struct_len
data_to_write_aco = self.min_measured_data - self.total_merged_data_veto + self.veto_written * self.settings.struct_len
self.min_data_to_write = min(data_to_write_sig, data_to_write_trg, data_to_write_aco)
del data_to_write_sig, data_to_write_trg, data_to_write_aco
self.events_to_write = int(np.floor(self.min_data_to_write / float(self.settings.struct_len)))
self.read_size = self.events_to_write * self.settings.struct_len
for sigi in xrange(self.settings.num_signals):
with open('wave{s}.dat'.format(s=self.signal_ch[sigi].caen_ch), 'rb') as self.fins:
self.fins.seek(self.written_events_sig * self.settings.struct_len, 0)
self.datas = self.fins.read(self.read_size)
del self.fins
self.fins = None
with open('raw_wave{s}.dat'.format(s=self.signal_ch[sigi].caen_ch), 'ab') as self.fs0[sigi]:
self.fs0[sigi].write(self.datas)
self.fs0[sigi].flush()
del self.fs0[sigi], self.datas
self.fs0[sigi], self.datas = None, None
with open('wave{t}.dat'.format(t=self.trigger_ch.caen_ch), 'rb') as self.fint:
self.fint.seek(self.written_events_trig * self.settings.struct_len, 0)
self.datat = self.fint.read(self.read_size)
del self.fint
self.fint = None
with open('raw_wave{t}.dat'.format(t=self.trigger_ch.caen_ch), 'ab') as self.ft0:
self.ft0.write(self.datat)
self.ft0.flush()
del self.ft0, self.datat
self.ft0, self.datat = None, None
with open('wave{a}.dat'.format(a=self.veto_ch.caen_ch), 'rb') as self.finv:
self.finv.seek(self.written_events_veto * self.settings.struct_len, 0)
self.datav = self.finv.read(self.read_size)
del self.finv
self.finv = None
with open('raw_wave{a}.dat'.format(a=self.veto_ch.caen_ch), 'ab') as self.fv0:
self.fv0.write(self.datav)
self.fv0.flush()
del self.fv0, self.datav
self.fv0, self.datav = None, None
self.written_events_sig += int(self.events_to_write)
self.written_events_trig += int(self.events_to_write)
self.written_events_veto += int(self.events_to_write)
del self.events_to_write, self.read_size
self.events_to_write, self.read_size = None, None
self.doMerge = False
def CalculateEventsWritten(self, ch):
return int(round(float(os.path.getsize('raw_wave{c}.dat'.format(c=ch))) / float(self.settings.struct_len)))
def ReadBaseLines(self):
# Read ADCs from files for trigger and veto scintillators
with open('raw_wave{t}.dat'.format(t=self.trigger_ch.ch), 'rb') as self.ft0:
self.ft0.seek(0)
self.datat = self.ft0.read(self.settings.struct_len)
t = struct.Struct(self.settings.struct_fmt).unpack_from(self.datat)
triggADCs = np.array(t, 'H')
mean_t = triggADCs.mean()
std_t = triggADCs.std()
with open('raw_wave{ac}.dat'.format(ac=self.veto_ch.ch), 'rb') as self.fv0:
self.fv0.seek(0)
self.datav = self.fv0.read(self.settings.struct_len)
ac = struct.Struct(self.settings.struct_fmt).unpack_from(self.datav)
acADCs = np.array(ac, 'H')
mean_ac = acADCs.mean()
std_ac = acADCs.std()
# clear possible ADCs with non-baseline signals
for i in xrange(10):
condition_t = (np.abs(triggADCs - mean_t) < 3 * std_t)
mean_t = np.extract(condition_t, triggADCs).mean()
std_t = np.extract(condition_t, triggADCs).std()
condition_ac = (np.abs(acADCs - mean_ac) < 3 * std_ac)
mean_ac = np.extract(condition_ac, acADCs).mean()
std_ac = np.extract(condition_ac, acADCs).std()
# set channels such that the baselines are near the maximum ADC's leaving space for the scintillator signals. Adjust threshold values
self.trigger_ch.Correct_Base_Line(mean_adc=mean_t, sigma_adc=std_t, settings=self.settings)
self.trigger_ch.Correct_Threshold(sigma=std_t)
self.settings.trig_base_line = np.multiply(self.trigger_ch.base_line_u_adcs, self.settings.sigRes, dtype='f8')
self.settings.trig_thr_counts = self.trigger_ch.thr_counts
self.veto_ch.Correct_Base_Line(mean_adc=mean_ac, sigma_adc=std_ac, settings=self.settings)
self.veto_ch.Correct_Threshold(sigma=std_ac)
self.settings.ac_base_line = np.multiply(self.veto_ch.base_line_u_adcs, self.settings.sigRes, dtype='f8')
self.settings.ac_thr_counts = self.veto_ch.thr_counts
del self.ft0, self.datat, t, triggADCs, mean_t, std_t
del self.fv0, self.datav, ac, acADCs, mean_ac, std_ac
self.ft0, self.datat= None, None
self.fv0, self.datav = None, None
# @profile(precision=12)
def GetData(self):
self.t0 = time.time()
self.CreateEmptyFiles()
self.CloseFiles()
self.total_events = 0
print 'Getting {n} events...'.format(n=self.settings.num_events)
if self.settings.simultaneous_conversion:
self.CreateRootFile(files_moved=False)
else:
self.bar = CreateProgressBarUtils(self.settings.num_events)
self.bar.start()
self.settings.SetupDigitiser(signal=self.signal_ch, trigger=self.trigger_ch, veto=self.veto_ch)
while self.total_events < self.settings.num_events:
self.sig_written = self.CalculateEventsWritten(self.settings.sigCh[0])
self.trg_written = self.CalculateEventsWritten(self.settings.trigCh)
self.veto_written = self.CalculateEventsWritten(self.settings.vetoCh)
self.p = subp.Popen(['{p}/wavedump'.format(p=self.settings.wavedump_path), '{d}/WaveDumpConfig_muon.txt'.format(d=self.settings.outdir)], bufsize=-1, stdin=subp.PIPE, stdout=subp.PIPE, close_fds=True)
self.GetWaveforms(self.settings.num_events, stdin=True, stdout=True)
self.CloseFiles()
if not self.settings.simultaneous_conversion:
print 'Time getting {n} events: {t} seconds'.format(n=self.total_events, t=time.time() - self.t0)
self.bar.finish()
else:
while self.pconv.poll() is None:
time.sleep(2)
self.CloseSubprocess('converter', stdin=False, stdout=False)
return self.total_events
def CreateRootFile(self, files_moved=False):
settings_bin_path = os.path.abspath(self.settings.outdir + '/Runs/{f}/{f}.settings'.format(f=self.settings.filename))
data_bin_path = os.path.abspath(self.settings.outdir + '/Runs/{f}'.format(f=self.settings.filename)) if files_moved else os.getcwd()
self.pconv = subp.Popen(['python', 'Converter_Caen_Raw.py', settings_bin_path, data_bin_path], close_fds=True) if self.settings.simultaneous_conversion else subp.Popen(['python', 'Converter_Caen_Raw.py', settings_bin_path, data_bin_path, 0], close_fds=True)
del settings_bin_path
def SavePickles(self):
# save objects of settings, signal_ch, trigger_ch and veto_ch
with open('{d}/Runs/{f}/{f}.settings'.format(d=self.settings.outdir, f=self.settings.filename), 'wb') as fs0:
pickle.dump(self.settings, fs0, pickle.HIGHEST_PROTOCOL)
for sigi in xrange(self.settings.num_signals):
with open('{d}/Runs/{f}/{f}.signal_ch{c}'.format(c=sigi, d=self.settings.outdir, f=self.settings.filename), 'wb') as fs0ig:
pickle.dump(self.signal_ch[sigi], fs0ig, pickle.HIGHEST_PROTOCOL)
with open('{d}/Runs/{f}/{f}.trigger_ch'.format(d=self.settings.outdir, f=self.settings.filename), 'wb') as ft:
pickle.dump(self.trigger_ch, ft, pickle.HIGHEST_PROTOCOL)
with open('{d}/Runs/{f}/{f}.veto'.format(d=self.settings.outdir, f=self.settings.filename), 'wb') as fv:
pickle.dump(self.veto_ch, fv, pickle.HIGHEST_PROTOCOL)
def PrintPlotLimits(self, ti=-5.12e-7, tf=4.606e-6, vmin=-0.7, vmax=0.05):
print np.double([(tf-ti)/float(self.settings.time_res) +1, ti-self.settings.time_res/2.0,
tf+self.settings.time_res/2.0, (vmax-vmin)/self.settings.sigRes, vmin, vmax])
def main():
parser = OptionParser()
parser.add_option('-i', '--infile', dest='infile', default='None', type='string',
help='Input configuration file. e.g. CAENCalibration.cfg')
parser.add_option('-a', '--automatic', dest='auto', default=False, help='Toggles automatic data taking and conversion', action='store_true')
(options, args) = parser.parse_args()
infile = str(options.infile)
auto = bool(options.auto)
mlt = MuonLifeTime(infile)
if auto:
mlt.SavePickles()
written_events = mlt.GetData()
mlt.settings.num_events = written_events
mlt.SavePickles() # update pickles with the real amount of written events
mlt.settings.MoveBinaryFiles()
mlt.settings.RenameDigitiserSettings()
if not mlt.settings.simultaneous_conversion:
mlt.CreateRootFile(files_moved=True)
while mlt.pconv.poll() is None:
time.sleep(3)
mlt.CloseSubprocess('converter', stdin=False, stdout=False)
print 'Finished :)'
sys.stdout.write('\a\a\a')
sys.stdout.flush()
if __name__ == '__main__':
main()