run_TOFPET.py

#! /usr/bin/env python

import os
import sys
import optparse
import datetime
import subprocess
from glob import glob
from collections import defaultdict
from collections import OrderedDict
from array import array
import time
import re

from ROOT import *

usage = "usage: run from Timing-TOFPET: \n Test (options from config_main.txt): python run_TOFPET.py -c config_main.txt \n Physics run (with options): python run_TOFPET.py -c config_main.txt --runType PHYS -d my_acquire_sipm_data -t 10 -v 3 --ovref 3 -l NoSource_1 -g 15 -o output/ScanTest \n Pedestal run (with options): python run_TOFPET.py -c config_main.txt --runType PED -d acquire_pedestal_data -t 1 -v 3 --ovref 3 -l Ped_1 -g 15 -o output/ScanTest"

parser = optparse.OptionParser(usage)

parser.add_option("-c", "--config", dest="configFile",
                  help="config file")

parser.add_option("-v", "--ov", dest="overVoltage",
                  help="sipm over voltage")

parser.add_option("--ovref", dest="overVoltageRef",
                  help="reference sipm over voltage")

parser.add_option("-g", "--gate", dest="gate",
                  help="signal integration gate = DeltaT[ns]/20: gate=15 -> DeltaT=300 ns")

parser.add_option("-t", "--time", dest="duration",
                  help="run duration")

parser.add_option("-d", "--daq", dest="daqType",
                  help="data acquisition type (i.e. pedestal or SiPM data)")

parser.add_option("-l", "--label", dest="outputLabel",
                  help="label of output file")

parser.add_option("-o", "--outFolder", dest="outputFolder",
                  help="output directory")

parser.add_option("--runType", dest="runType",
                  help="runType (PHYS or PED)")

parser.add_option("--pedAllChannels", dest="pedAllChannels", default=0, 
                  help="Set to 1 to collect pedestals for all channels (default is 0)")

parser.add_option("--enabledChannels", dest="enabledChannels", default="",
                  help="List of channels with trigger enabled. The string format is 0_1_2_3 to eanble channels CH0, CH1, CH2, CH3 accordingly to configuration file. If nothing is specified all channels in configuration file can trigger. For pedestal run: ignored if pedAllChannels is set to 1.")

parser.add_option("--energyThr", dest="energyThr", default="", 
                  help="List of energy thresholds for triggering. The string format is 0_10_5_3 to reduce the energy thresholds with respect to the config file by to 0, 10, 5, 3 for channels CH0, CH1, CH2, CH3. For pedestal run: ignored.")

parser.add_option("--energyThrT1", dest="energyThrT1", default="", 
                  help="List of energy thresholds for triggering. The string format is 0_10_5_3 to set the absolute value of t1 thresholds for channels CH0, CH1, CH2, CH3. For pedestal run: ignored.")

(opt, args) = parser.parse_args()

if not opt.configFile:   
    parser.error('config file not provided')

################################################

gROOT.SetBatch(True)

#####################################################
### 0) Edit config file based on command line options
#####################################################

tempConfig = "config_main_temp.txt"
file_tempConfig = open(tempConfig, "w")
cfg = open(opt.configFile, "r")
for line in cfg:

    #skip commented out lines or empty lines
    if (line.startswith("#")):
        file_tempConfig.write(line)
        continue
    if line in ['\n','\r\n']:
        file_tempConfig.write(line)
        continue

    line = line.rstrip('\n')
    splitline = line.split()
    linetype = splitline[0]
    linesize = len(splitline)
    #print line

    if (linetype == "TIME" and linesize==2 and opt.duration):
        line = re.sub(splitline[1],opt.duration,line)
        print "Line of config file changed: ... ", line

    if (linetype == "DAQSCRIPT" and linesize==3 and opt.daqType):
        line = re.sub(splitline[1],opt.daqType,line)
        line = re.sub(splitline[2],opt.runType,line)
        print "Line of config file changed: ... ", line

    if (linetype == "OUTPUT_DIR" and linesize==2 and opt.outputFolder):
        line = re.sub(splitline[1],opt.outputFolder,line)
        print "Line of config file changed: ... ", line

    if (linetype == "OUTPUT_LABEL" and linesize==2 and opt.outputLabel):
        line = re.sub(splitline[1],opt.outputLabel ,line)
        print "Line of config file changed: ... ", line

    if (linetype == "OVERWRITE_OV_REF" and linesize==2 and opt.overVoltageRef):
        line = re.sub(splitline[1],opt.overVoltageRef ,line)
        print "Line of config file changed: ... ", line

    if (linetype == "OVERWRITE_OV" and linesize==2 and opt.overVoltage):
        line = re.sub(splitline[1],opt.overVoltage ,line)
        print "Line of config file changed: ... ", line

    if (linetype == "MIN_INTG_TIME" and linesize==2 and opt.gate):
        line = re.sub(splitline[1],opt.gate ,line)
        print "Line of config file changed: ... ", line

    if (linetype == "MAX_INTG_TIME" and linesize==2 and opt.gate):
        line = re.sub(splitline[1],opt.gate ,line)
        print "Line of config file changed: ... ", line

    file_tempConfig.write(line+'\n')

cfg.close()    
file_tempConfig.close()

commandCpConfigtxt = "mv "+tempConfig+" "+opt.configFile
print commandCpConfigtxt
os.system(commandCpConfigtxt)

###############################
### 0.1) Read config file
###############################
cfg = open(opt.configFile, "r")

config_template_file = ""
hv_dac = ""
run_calib = ""
calib_dir = ""
tdc_calib = ""
qdc_calib = ""
disc_calib = ""
sipm_bias = ""
disc_settings = ""
channel_map = ""
trigger_map = ""
lsb_t1 = ""
lsb_t2 = ""
min_intg_time = 0
max_intg_time = 0
daqscript = ""
daqscriptlabel = ""
convertsinglescript = ""
convertcoincidencescript = ""
#convertNcoincidencescript = ""
temperaturefile = ""
mode = ""
runtime = ""
output_dir = ""
output_label = ""
overwrite_ov = -99
overwrite_ov_ref = -99
dic_channels = {}
channels = []

for line in cfg:

    #skip commented out lines or empty lines
    if (line.startswith("#")):
        continue
    if line in ['\n','\r\n']:
        continue
        
    line = line.rstrip('\n')
    splitline = line.split()
    linetype = splitline[0]
    linesize = len(splitline)

    if (linetype == "CONFIG_INI_TEMPLATE" and linesize==2):
        config_template_file = splitline[1]

    if (linetype == "HV_DAC" and linesize==2):
        hv_dac = splitline[1]

    if (linetype == "RUN_CALIB" and linesize==2):
        run_calib = splitline[1]

    if (linetype == "CALIB_DIR" and linesize==2):
        calib_dir = splitline[1]

    if (linetype == "TDC_CALIB" and linesize==2):
        tdc_calib = splitline[1]

    if (linetype == "QDC_CALIB" and linesize==2):
        qdc_calib = splitline[1]

    if (linetype == "DISC_CALIB" and linesize==2):
        disc_calib = splitline[1]

    if (linetype == "SIPM_BIAS" and linesize==2):
        sipm_bias = splitline[1]

    if (linetype == "DISC_SETTINGS" and linesize==2):
        disc_settings = splitline[1]

    if (linetype == "CHANNEL_MAP" and linesize==2):
        channel_map = splitline[1]

    if (linetype == "TRIGGER_MAP" and linesize==2):
        trigger_map = splitline[1]

    if (linetype == "LSB_T1" and linesize==2):
        lsb_t1 = splitline[1]

    if (linetype == "LSB_T2" and linesize==2):
        lsb_t2 = splitline[1]

    if (linetype == "MIN_INTG_TIME" and linesize==2):
        min_intg_time = splitline[1]

    if (linetype == "MAX_INTG_TIME" and linesize==2):
        max_intg_time = splitline[1]

    if (linetype == "DAQSCRIPT" and linesize==3):
        daqscript = splitline[1]
        daqscriptlabel = splitline[2]

    if (linetype == "CONVERTSINGLESCRIPT" and linesize==2):
        convertsinglescript = splitline[1]

    if (linetype == "CONVERTCOINCIDENCESCRIPT" and linesize==2):
        convertcoincidencescript = splitline[1]

    #if (linetype == "CONVERTNCOINCIDENCESCRIPT" and linesize==2):
    #    convertNcoincidencescript = splitline[1]

    if (linetype == "TEMPERATUREFILE" and linesize==2):
        temperaturefile = splitline[1]

    if (linetype == "MODE" and linesize==2):
        mode = splitline[1]

    if (linetype == "TIME" and linesize==2):
        runtime = splitline[1]

    if (linetype == "OUTPUT_DIR" and linesize==2):
        output_dir = splitline[1]

    if (linetype == "OUTPUT_LABEL" and linesize==2):
        output_label = splitline[1]

    if (linetype == "OVERWRITE_OV" and linesize==2):
        overwrite_ov = splitline[1]

    if (linetype == "OVERWRITE_OV_REF" and linesize==2):
        overwrite_ov_ref = splitline[1]

    #print linetype, linesize

    if (linetype == "CH" and linesize==16):
        #read channel settings
        chId = splitline[1]
        channels.append(chId)        

        NHV = splitline[2]
        VBR = splitline[3]
        OV = splitline[4]
        NCHIP = splitline[5]
        NCH = splitline[6]
        VTH_1 = splitline[7]
        VTH_2 = splitline[8]
        VTH_E = splitline[9]
        SIPM_CODE = splitline[10]
        SIPM_TYPE = splitline[11]
        X = splitline[12]
        Y = splitline[13]
        Z = splitline[14]
        CRYSTAL = splitline[15]
        #write channel settings in dictionary
        dic_channels[(chId,"NHV")]=NHV
        dic_channels[(chId,"VBR")]=VBR
        dic_channels[(chId,"OV")]=OV
        dic_channels[(chId,"NCHIP")]=NCHIP
        dic_channels[(chId,"NCH")]=NCH
        dic_channels[(chId,"VTH_1")]=VTH_1
        dic_channels[(chId,"VTH_2")]=VTH_2
        dic_channels[(chId,"VTH_E")]=VTH_E
        dic_channels[(chId,"SIPM_CODE")]=SIPM_CODE
        dic_channels[(chId,"SIPM_TYPE")]=SIPM_TYPE
        dic_channels[(chId,"X")]=X
        dic_channels[(chId,"Y")]=Y
        dic_channels[(chId,"Z")]=Z
        dic_channels[(chId,"CRYSTAL")]=CRYSTAL
        #overwrite overvoltage
        if(float(overwrite_ov) > 0. and float(chId) > 0.):
            dic_channels[(chId,"OV")]=overwrite_ov
        if(float(overwrite_ov_ref) > 0. and float(chId) == 0.):
            dic_channels[(chId,"OV")]=overwrite_ov_ref


cfg.close()

#print config_template_file, hv_dac, run_calib, calib_dir, tdc_calib, qdc_calib, disc_calib, sipm_bias, disc_settings, channel_map, trigger_map, lsb_t1, lsb_t2, min_intg_time, max_intg_time, daqscript, convertsinglescript, convertcoincidencescript, temperaturefile, mode, runtime,  output_dir, output_label, overwrite_ov, overwrite_ov_ref
#print dic_channels[("0","VBR")]
print "Active channels: ", channels

###############################
### 1) Check calibration status
###############################
tdc_calib_path = calib_dir+"/"+tdc_calib
qdc_calib_path = calib_dir+"/"+qdc_calib
disc_calib_path = calib_dir+"/"+disc_calib

tdc_calib_exists = os.path.isfile(tdc_calib_path)
qdc_calib_exists = os.path.isfile(qdc_calib_path)
disc_calib_exists = os.path.isfile(disc_calib_path)

if run_calib=="1" and (tdc_calib_exists or qdc_calib_exists or disc_calib_exists):
    print "WARNING: Not possible to run calibration since at least one calibration file already exists"
    print "Exit..."
    sys.exit()

if run_calib=="0" and ( not (tdc_calib_exists and qdc_calib_exists and disc_calib_exists) ):
    print "WARNING: Not possible to run daq since at least one calibration file is missing"
    print "Exit..."
    sys.exit()

###############################
### 2) Create new sipm bias table
###############################
sipm_bias_table_template = sipm_bias
sipm_bias_table_current = "data/sipm_bias_current.tsv"
sipmbiasTemplate = open(sipm_bias_table_template, "r")
sipmbiasCurrent = open(sipm_bias_table_current, "w")
for line in sipmbiasTemplate:

    #skip commented out lines or empty lines
    if (line.startswith("#")):
        sipmbiasCurrent.write(line)
        continue
    if line in ['\n','\r\n']:
        sipmbiasCurrent.write(line)
        continue

    line = line.rstrip('\n')
    splitline = line.split()
    #print line

    HVfound = 0
    for ch in channels:
        if(splitline[2]==dic_channels[(ch,"NHV")] and len(splitline)==6 and HVfound==0):
            HVfound=1
            sipmbiasCurrent.write("0\t0\t"+
                                  dic_channels[(ch,"NHV")]+"\t"+
                                  str(float(dic_channels[(ch,"VBR")])-5)+"\t"+
                                  dic_channels[(ch,"VBR")]+"\t"+
                                  dic_channels[(ch,"OV")]+"\n"
                              )

    if HVfound==0:
        sipmbiasCurrent.write(line+'\n')
    
sipmbiasCurrent.close()
sipmbiasTemplate.close()

###############################
### 3) Create new discriminator threshold table
###############################
disc_settings_table_template = disc_settings
disc_settings_table_current = "data/disc_settings_current.tsv"
discSetTemplate = open(disc_settings_table_template, "r")
discSetCurrent = open(disc_settings_table_current, "w")
for line in discSetTemplate:

    #skip commented out lines or empty lines
    if (line.startswith("#")):
        discSetCurrent.write(line)
        continue
    if line in ['\n','\r\n']:
        discSetCurrent.write(line)
        continue

    line = line.rstrip('\n')
    splitline = line.split()
    #print line

    CHfound = 0
    for ch in channels:
        if(splitline[2]==dic_channels[(ch,"NCHIP")] 
           and splitline[3]==dic_channels[(ch,"NCH")] 
           and len(splitline)==7):
            CHfound=1
            discSetCurrent.write("0\t0\t"+
                                  dic_channels[(ch,"NCHIP")]+"\t"+
                                  dic_channels[(ch,"NCH")]+"\t"+
                                  dic_channels[(ch,"VTH_1")]+"\t"+
                                  dic_channels[(ch,"VTH_2")]+"\t"+
                                  dic_channels[(ch,"VTH_E")]+"\n"
                              )

    if CHfound==0:
        discSetCurrent.write(line+'\n')
    
discSetCurrent.close()
discSetTemplate.close()

###############################
### 4) Create new configuration file
###############################
config_template = config_template_file
config_current = "config_current.ini"
configFileTemplate = open(config_template, "r")
configFileCurrent = open(config_current, "w")
for line in configFileTemplate:

    #skip commented out lines or empty lines
    if (line.startswith("#")):
        configFileCurrent.write(line)
        continue
    if line in ['\n','\r\n']:
        configFileCurrent.write(line)
        continue

    line = line.rstrip('\n')

    if "HV_DAC" in line:
        line = line.replace("HV_DAC",hv_dac)
    if "TDC_CALIB" in line:
        line = line.replace("TDC_CALIB",tdc_calib_path)
    if "QDC_CALIB" in line:
        line = line.replace("QDC_CALIB",qdc_calib_path)
    if "DISC_CALIB" in line:
        line = line.replace("DISC_CALIB",disc_calib_path)
    if "SIPM_BIAS" in line:
        line = line.replace("SIPM_BIAS",sipm_bias_table_current)
    if "DISC_SETTINGS" in line:
        line = line.replace("DISC_SETTINGS",disc_settings_table_current)
    if "CHANNEL_MAP" in line:
        line = line.replace("CHANNEL_MAP",channel_map)
    if "TRIGGER_MAP" in line:
        line = line.replace("TRIGGER_MAP",trigger_map)
    if "LSB_T1" in line:
        line = line.replace("LSB_T1",lsb_t1)
    if "LSB_T2" in line:
        line = line.replace("LSB_T2",lsb_t2)
    if "MIN_INTG_TIME" in line:
        line = line.replace("MIN_INTG_TIME",min_intg_time)
    if "MAX_INTG_TIME" in line:
        line = line.replace("MAX_INTG_TIME",max_intg_time)

    configFileCurrent.write(line+"\n")
 
configFileCurrent.close()
configFileTemplate.close()

###############################
### 5) Run calibration
###############################
#calibration scripts
disc_calib_script = "acquire_threshold_calibration"
disc_calib_process_script = "process_threshold_calibration"
tdc_calib_script = "acquire_tdc_calibration"
tdc_calib_process_script = "process_tdc_calibration"
qdc_calib_script = "acquire_qdc_calibration"
qdc_calib_process_script = "process_qdc_calibration"

if run_calib=="1":
    
    commandOutputCalibDir = "mkdir -p "+calib_dir
    print commandOutputCalibDir
    os.system(commandOutputCalibDir)

    print "Starting discriminator calibration..."
    commandDiscCalib = "./"+disc_calib_script+" --config "+config_current+" -o "+calib_dir+"/"+"disc_calibration"
    commandDiscCalibProcess = "./"+disc_calib_process_script+" --config "+config_current+" -i "+calib_dir+"/"+"disc_calibration"+" -o "+disc_calib_path+" --root-file "+disc_calib_path.split(".tsv")[0]+".root"
    print commandDiscCalib    
    os.system(commandDiscCalib)
    print commandDiscCalibProcess    
    os.system(commandDiscCalibProcess)
    print "End discriminator calibration"
    print "\n"

    print "Starting TDC and QDC calibration..."
    commandTdcCalib = "./"+tdc_calib_script+" --config "+config_current+" -o "+calib_dir+"/"+"tdc_calibration"
    commandTdcCalibProcess = "./"+tdc_calib_process_script+" --config "+config_current+" -i "+calib_dir+"/"+"tdc_calibration"+" -o "+tdc_calib_path.split(".tsv")[0]
    commandQdcCalib = "./"+qdc_calib_script+" --config "+config_current+" -o "+calib_dir+"/"+"qdc_calibration"
    commandQdcCalibProcess = "./"+qdc_calib_process_script+" --config "+config_current+" -i "+calib_dir+"/"+"qdc_calibration"+" -o "+qdc_calib_path.split(".tsv")[0]
    print commandTdcCalib    
    os.system(commandTdcCalib)
    print commandQdcCalib    
    os.system(commandQdcCalib)
    print commandTdcCalibProcess    
    os.system(commandTdcCalibProcess)
    print commandQdcCalibProcess    
    os.system(commandQdcCalibProcess)
    print "End TDC and QDC calibration"
    print "\n"

    commandCpConfigForCalib = "cp "+opt.configFile+" "+calib_dir+"/"+"config_for_calibration.txt"
    print commandCpConfigForCalib
    os.system(commandCpConfigForCalib)

###############################
### 6) Run daq
###############################

#copy content and clear temporary file with temperatures
commandCopyTemp = "cat "+temperaturefile+" >> arduino/temperature/temperature_all.txt"
print commandCopyTemp
os.system(commandCopyTemp)
commandRmTemp = "rm -f "+temperaturefile
print commandRmTemp
os.system(commandRmTemp)
time.sleep(3) #wait until 1 line of the temporary temperature file is recreated

###########################################

#current_time = datetime.datetime.now()
#simpletimeMarker = "%04d-%02d-%02d__%02d-%02d-%02d" % (current_time.year,current_time.month,current_time.day,current_time.hour,current_time.minute,current_time.second)
unixTimeStart = long(time.time())

###########################################

commandOutputDir = "mkdir -p "+output_dir
print commandOutputDir
os.system(commandOutputDir)

#integration gate in ns (min_intg_time=max_intg_time)
#integration_gate = int(min_intg_time) * 4 units of clock * 5 ns tdc clock 
integration_gate = int(min_intg_time)
print integration_gate 

outputFileLabel = output_label+"_"+daqscriptlabel+"_"+mode+"_Time"+runtime+"_Gate"+str(integration_gate)
if opt.overVoltage:
    outputFileLabel = output_label+"_"+daqscriptlabel+"_"+mode+"_Time"+runtime+"_Gate"+str(integration_gate)+"_Ov"+opt.overVoltage
if opt.overVoltageRef:
    outputFileLabel = output_label+"_"+daqscriptlabel+"_"+mode+"_Time"+runtime+"_Gate"+str(integration_gate)+"_OvRef"+opt.overVoltageRef
if opt.overVoltage and opt.overVoltageRef:
    outputFileLabel = output_label+"_"+daqscriptlabel+"_"+mode+"_Time"+runtime+"_Gate"+str(integration_gate)+"_OvRef"+opt.overVoltageRef+"_Ov"+opt.overVoltage

newname = output_dir+"/"+outputFileLabel
newconfignametxt = newname+".txt"
newconfignameini = newname+".ini"

commandCpConfigtxt = "cp "+opt.configFile+" "+newconfignametxt
print commandCpConfigtxt
os.system(commandCpConfigtxt)

commandCpConfigini = "cp "+config_current+" "+newconfignameini
print commandCpConfigini
os.system(commandCpConfigini)

print "Starting run..."
commandRun = ""
print daqscript
if (daqscript == "acquire_pedestal_data"):
    commandRun = "./"+daqscript+" --config "+ config_current +" --mode "+ mode +" --time "+ runtime +" -o "+newname+" --cfgChannels "+opt.configFile+" --pedAllChannels " + str(opt.pedAllChannels)
    if (opt.enabledChannels != ""):
        commandRun = commandRun +" --enabledChannels " + str(opt.enabledChannels)         
else:
    commandRun = "./"+daqscript+" --config "+ config_current +" --mode "+ mode +" --time "+ runtime +" -o "+newname+" --cfgChannels "+opt.configFile
    if (opt.enabledChannels != ""):
        commandRun = commandRun +" --enabledChannels " + str(opt.enabledChannels)         
        if (opt.energyThr != ""):
            commandRun = commandRun + " --energyThr " + str(opt.energyThr)
        if (opt.energyThrT1 != ""):
            commandRun = commandRun + " --energyThrT1 " + str(opt.energyThrT1)
          
print commandRun
os.system(commandRun)
print "End run"
print "\n"

'''
###############################
### 7) Convert output to ROOT trees
###############################
print "Creating root file with tree (singles)..."
commandConvertSingles = "./"+convertsinglescript+" --config "+ config_current +" -i "+newname+" -o "+newname+"_singles.root"+" --writeRoot"
print commandConvertSingles
os.system(commandConvertSingles)
print "File created."
print "\n"

## Add branches to root tree (singles)
print "Update root file with tree (singles)..."
inputfilename = newname+"_singles.root"
tfileinput = TFile.Open(inputfilename,"update")
treeInput = tfileinput.Get("data")
unixTime = array( 'l' , [0])
tempInt = array( 'd' , [-999.])
tempExt = array( 'd' , [-999.])
tempBoardTest = array( 'd' , [-999.])
tempBoardRef = array( 'd' , [-999.])
tempSiPMTest = array( 'd' , [-999.])
tempSiPMRef = array( 'd' , [-999.])

unixTimeBranch = treeInput.Branch( 'unixTime', unixTime, 'unixTime/L' )
tempIntBranch = treeInput.Branch( 'tempInt', tempInt, 'tempInt/D' )
tempExtBranch = treeInput.Branch( 'tempExt', tempExt, 'tempExt/D' )
tempBoardTestBranch = treeInput.Branch( 'tempBoardTest', tempBoardTest, 'tempBoardTest/D' )
tempBoardRefBranch = treeInput.Branch( 'tempBoardRef', tempBoardRef, 'tempBoardRef/D' )
tempSiPMTestBranch = treeInput.Branch( 'tempSiPMTest', tempSiPMTest, 'tempSiPMTest/D' )
tempSiPMRefBranch = treeInput.Branch( 'tempSiPMRef', tempSiPMRef, 'tempSiPMRef/D' )

ReadNewTemperature = 0 
TInt = -999. 
TExt = -999.
TBoardTest = -999. 
TBoardRef = -999. 
TSiPMTest = -999.
TSiPMRef = -999.

previousTime = 0
for event in treeInput:
    unixTime[0] = long(event.time * 10**-12) + unixTimeStart #unix time in seconds of the current event

    ## Read temperatures from file every fixed DeltaT (10^12 ps = 1 s by default)
    if previousTime==0:
        ReadNewTemperature=1 
        previousTime = event.time
    elif (event.time - previousTime) <= 10**12:
        tempInt[0] = TInt
        tempExt[0] = TExt
        tempBoardTest[0] = TBoardTest
        tempBoardRef[0] = TBoardRef
        tempSiPMTest[0] = TSiPMTest
        tempSiPMRef[0] = TSiPMRef
    elif (event.time - previousTime) > 10**12:
        ReadNewTemperature=1
        previousTime = event.time

    if ReadNewTemperature==1:
        tempFile = open(temperaturefile, "r")    
        for line in tempFile:
            #skip commented out lines or empty lines
            if (line.startswith("#")):
                continue
            if line in ['\n','\r\n']:
                continue
        
            line = line.rstrip('\n')
            splitline = line.split()

            linesize = len(splitline)
            if (linesize==7):
                # find match within 2 seconds
                if( abs(long(unixTime[0])-long(splitline[0])) < 2):
                    TInt = float(splitline[2])+0.16
                    TExt = float(splitline[3])-0.03
                    TBoardTest = float(splitline[4])-0.88
                    TBoardRef = float(splitline[1])-0.75
                    TSiPMTest = float(splitline[6])+0.09
                    TSiPMRef = float(splitline[5])+0.22
                    tempInt[0] = TInt
                    tempExt[0] = TExt
                    tempBoardTest[0] = TBoardTest
                    tempBoardRef[0] = TBoardRef
                    tempSiPMTest[0] = TSiPMTest
                    tempSiPMRef[0] = TSiPMRef
                    break
        ReadNewTemperature=0
        tempFile.close()
        
    unixTimeBranch.Fill()
    tempIntBranch.Fill()
    tempExtBranch.Fill()
    tempBoardTestBranch.Fill()
    tempBoardRefBranch.Fill()
    tempSiPMTestBranch.Fill()
    tempSiPMRefBranch.Fill()

treeInput.Write("",TFile.kOverwrite)
tfileinput.Close()
print "File updated."
print "\n"

#print "Creating root file with tree (coincidences)..."
#commandConvertCoincidences = "./"+convertcoincidencescript+" --config "+ config_current +" -i "+newname+" -o "+newname+"_coincidences.root"+" --writeRoot"
#print commandConvertCoincidences
#os.system(commandConvertCoincidences)
#print "File created."
#print "\n"

if( len(channels)<2 ):
    sys.exit()

print "Creating root file with tree (N-coincidences) from singles..."
commandConvertCoincidences = "python "+convertcoincidencescript+" -c "+ opt.configFile +" -i "+ newname+"_singles.root" +" -n "+str(len(channels))+" -o "+newname+"_coincidences.root"
print commandConvertCoincidences
os.system(commandConvertCoincidences)
print "File created."
print "\n"
'''

## Copy content and clear temporary file with temperatures

#copy in output dir
newtemperaturetxt = newname+".temp"
commandCopyTempFinal = "cp "+temperaturefile+" "+newtemperaturetxt
print commandCopyTempFinal
os.system(commandCopyTempFinal)
#copy in file temperature_all
print commandCopyTemp
os.system(commandCopyTemp)
#rm file
print commandRmTemp
os.system(commandRmTemp)