#!/bin/bash

#################################################################################################################
#
# Description:
#        This is the GUI generated bash script used to run the MIRS testbed.
#
# Record of revisions:
#           Date        Ver.        Programmer               Description of change
#       ============   =====   =======================   ============================================
#        09/03/2005     v0      Sid-Ahmed Boukabara       Original script created
#                               (NOAA/NESDIS/ORA/IMSG)
#
#        02/20/2006     v1      Ninghai Sun               Modify script for operational testbed
#                               (NOAA/NESDIS/ORA/IMSG)
#
#        03/20/2006     v2      Ninghai Sun               Modify script to compromise to SSM/IS
#                               (NOAA/NESDIS/ORA/IMSG)    Change the way to find GDAS data to standard
#
#        03/31/2006     v3      Sid Ahmed Boukabara       Changes related to :
#                                                         (1) new footprint-matching, 
#                                                         (2) addition of new covariance matrix
#                                                         (3) sensor ID (to distinguish sensor-dependent classifiers),
#                                                         (4) flexible handling of scanlines shift (mhs vs amsu)
#                                                         (5) bias correction method (bias removal or slope/intercept)
#                                                         (6) Added threshold checking of relative humidity
#        05/31/2006     v4      Sid Ahmed Boukabara       Changes related to directory structure more in line with oper.
#
#
#        12/19/2006     v5      Sid Ahmed Boukabara       Added the capability to run the scripts in
#                              (IMSG@NOAA/NESDIS/STAR)    orbital mode in addition to daily mode.
#
#        12/22/2006     v6      Sid Ahmed Boukabara       Major changes to make the script as simple as possible to 
#                                                         maintain and ultimately to be generated through the JAVA GUI.
#
#        12/28/2006     v7      Sid Ahmed Boukabara       Extensive revision to make all functions general.
#                              (IMSG@NOAA/NESDIS/STAR)    Scripts to be generated automatically through a Java GUI.
#                                                         This removes the need to maintain as many scripts as sensors.
#        03/10/2010     v8      Wanchun Chen              Many functions previously in script are moved into library.
#                              (QSS/PSGS/DELL)
#        11/04/2016     v9      Junye Chen                Modified GUI to generate JPSS-1(N20)/ATMS enabled scripts.
#                              (ESSIC/UMD@NOAA/NESDIS/STAR)
#
#
#################################################################################################################

#------Store arguments & set starting date
script=$0
oldargs=("$@")
nargs=$#
sdate=`date`
MIRS_ROOT=`grep ^MIRS_ROOT ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`
HDF4LIB=`grep HDF4LIB ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`
HDF5LIB=`grep HDF5LIB ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`
HDF5BIN=`grep HDF5BIN ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`
HDFEOSLIB=`grep HDFEOSLIB ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`
SZIPLIB=`grep SZIPLIB ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`
ZLIBLIB=`grep ZLIBLIB ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`
NETCDF4LIB=`grep NETCDF4LIB ../setup/paths | cut -f2 -d '=' | sed -e 's/^[ 	]*//'`


#-----Include libraries and setup Info
. ../scripts/script_functions.bash
. ../setup/n18_pcf_daily_ECMWF.bash
# Add more colon-separated shared libraries here:
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$HDF4LIB:$HDFEOSLIB:$SZIPLIB:$ZLIBLIB:$HDF5LIB:$NETCDF4LIB
# set stack size to unlimited
ulimit -s unlimited

displayVerif ${script} ${logFile} ${processMode} ${sensorId}\
	${outFMAccuracy} ${prefixFMAccuracy} ${nProfs2Retr} ${nProfs2Fwd}\
	${addDeviceNoise} ${monitorIterative} ${nAttempts} ${extBkgAtmUse} \
	${externalDataAvailable} ${monitorRetrieval} ${monitorFwd} ${geoLimit}\
	${minLat} ${maxLat} ${minLon} ${maxLon} ${maxDaysArchived} ${nDaysBack}\
	${tdrFormat} ${cend} ${dayUsed4Bias} ${dayUsed4Alg} ${nOrbits2Process}\
	${gifDensity} ${externalDataSrc} ${fmType} ${biasComputeMethod} \
	${nChoppedFilesPerOrbit} ${retrOnOrbitOrSubOrbit} ${retrOnWhichSDR}\
	${fwdMatrix2Use} ${sweClimoUse} ${makeOrNot} ${useCPU}

extResol=`determineSpatialResol ${satId} ${fmType}`

version='9999'
if [[ -s ${rootPath}/version.txt ]] ; then
    version=`cat ${rootPath}/version.txt`
fi

os=`uname -s`
#Linux g95 and gfortran is the same as AIX xlf90/95(stream,unformatted)
#Linux ifort is (sequential,binary)
accessStr='sequential'
formStr='binary'
if [[ ${os} == 'Linux' ]] ; then
  accessStr='sequential'
  formStr='binary'
elif [[ ${os} == 'AIX' ]] ; then
  accessStr='stream'
  formStr='unformatted'
fi

gdasData=1
ecmwfData=2
gfsData=3

#----Construct date extension(s) for building directories
if [[ ${nargs} -eq 0 ]] ; then
   extensions=`DetermineYesterdExtAndAlanysExt ${nDaysBack}`
   date=$(echo ${extensions}|cut -c1-10)
   rdrSensor1Dir=${rdrSensor1Path}/${date}
   rdrSensor2Dir=${rdrSensor2Path}/${date}
elif [[ ${nargs} -eq 1 ]] ; then
   #----Check 3 different paths (absolute/relative/a nude dir name)
   indx_slash=`echo ${oldargs} | awk -v slash="/" '{printf index($1,slash)}'`
   if [[ ${indx_slash} -eq 1 ]] ; then # =1: absolute path
     inputPath=${oldargs}
   elif [[ ${indx_slash} -gt 1 ]] ; then # >1: relative path
     inputPath=$(readlink -f ${oldargs}) # to get absolute full path
   else # <1: a nude dir name with no slash in it
     inputPath=${rdrSensor1Path}/${oldargs}
   fi
   date=`getDateFromFile ${satId} ${inputPath}`
   echo ${satId} 
   echo ${inputPath}
   if [[ ${date} == 'xxxx-xx-xx' ]] ; then # something wrong
     op_msg "Error: date $date is incorrect"
     exit 1
   fi
   rdrSensor1Dir=${inputPath}
   rdrSensor2Dir=${inputPath}
   extensions=`DetermineExtAndAlanysExtFromArgument ${date}`
else
   ErrMessDue2UsageInDailyMode
fi

rdirExt=$(echo ${extensions}|cut -c1-10)
rdirAnalysExt=$(echo ${extensions}|cut -c12-21)
rdirNextAnalysExt=$(echo ${extensions}|cut -c23-32)
#----set the generic extension
fileExt=`determineFileExt ${rdirExt}`
fileAnalysExt=`determineFileExt ${rdirAnalysExt}`
orbitInfo=Dummy

#----Names of directories for both orbital and Daily processing
tdrSensor1Dir=${tdrSensor1Path}/${rdirExt}
tdrSensor2Dir=${tdrSensor2Path}/${rdirExt}
sdrSensor1Dir=${sdrSensor1Path}/${rdirExt}
sdrSensor2Dir=${sdrSensor2Path}/${rdirExt}
fmsdrDir=${fmsdrPath}/${rdirExt}
fmsdrChoppDir=${choppPath}/${rdirExt}
edrDir=${edrPath}/${rdirExt}
depDir=${depPath}/${rdirExt}
sfrDir=${sfrPath}/${rdirExt}
gridDir=${gridPath}/${rdirExt}
ncDir=${ncPath}/${rdirExt}
figsDir=${figsPath}/${rdirExt}
regressRetrDir=${regressRetrPath}/${rdirExt}
prepSweClimoDir=${prepSweClimoPath}/${rdirExt}
ffCollocDir=${ffCollocPath}/${rdirExt}
imsCollocDir=${imsCollocPath}/${rdirExt}
orbitMonPath=${perfsMonitorPath}/orbitmon/
#----control file and input file identifiers depending on processing mode
if [[ ${processMode} -eq 0 ]] ; then
  identifier=${orbitInfo}
else
  identifier=${rdirExt}
fi
#----Control file
rdr2tdrSensor1ControlFile=${rdr2tdrSensor1ControlFile}_${identifier}.in
rdr2tdrSensor2ControlFile=${rdr2tdrSensor2ControlFile}_${identifier}.in
mergeNedtControlFile=${mergeNedtControlFile}_${identifier}.in
tdr2sdrSensor1ControlFile=${tdr2sdrSensor1ControlFile}_${identifier}.in
tdr2sdrSensor2ControlFile=${tdr2sdrSensor2ControlFile}_${identifier}.in
fmControlFile=${fmControlFile}_${identifier}.in
modifyNedtControlFile=${modifyNedtControlFile}_${identifier}.in
fmsdr2edrControlFile=${fmsdr2edrControlFile}_${identifier}.in
grid2nwpControlFile=${grid2nwpControlFile}_${identifier}.in
fwdControlFile=${fwdControlFile}_${identifier}.in
regressControlFile=${regressControlFile}_${identifier}.in
prepSweClimoControlFile=${prepSweClimoControlFile}_${identifier}.in
ffCollocControlFile=${ffCollocControlFile}_${identifier}.in
imsCollocControlFile=${imsCollocControlFile}_${identifier}.in
choppControlFile=${choppControlFile}_${identifier}.in
mergeEdrControlFile=${mergeEdrControlFile}_${identifier}.in
vippControlFile=${vippControlFile}_${identifier}.in
sfrControlFile=${sfrControlFile}_${identifier}.in
sfr2depControlFile=${sfr2depControlFile}_${identifier}.in
gridControlFile=${gridControlFile}_${identifier}.in
nwpGridControlFile=${nwpGridControlFile}_${identifier}.in
fwdGridControlFile=${fwdGridControlFile}_${identifier}.in
biasGridControlFile=${biasGridControlFile}_${identifier}.in
biasCompuControlFile=${biasCompuControlFile}_${identifier}.in
biasVerifControlFile=${biasVerifControlFile}_${identifier}.in
regressGenControlFile=${regressGenControlFile}_${identifier}.in
figsGenControlFile=${figsGenControlFile}_${identifier}.in
#---- Input file list
rdrSensor1List=${rdrSensor1List}_${identifier}.list
rdrSensor2List=${rdrSensor2List}_${identifier}.list
tdrSensor1List=${tdrSensor1List}_${identifier}.list
tdrSensor2List=${tdrSensor2List}_${identifier}.list
sdrSensor1List=${sdrSensor1List}_${identifier}.list
sdrSensor2List=${sdrSensor2List}_${identifier}.list
fmsdrList=${fmsdrList}_${identifier}.list
fmsdr4ChoppList=${fmsdr4ChoppList}_${identifier}.list
fmsdr4NwpList=${fmsdr4NwpList}_${identifier}.list
fmsdr4BiasList=${fmsdr4BiasList}_${identifier}.list
fmsdr4RegressList=${fmsdr4RegressList}_${identifier}.list
fmsdr4ApplyRegressList=${fmsdr4ApplyRegressList}_${identifier}.list
fmsdr4PrepSweList=${fmsdr4PrepSweList}_${identifier}.list
fmsdr4ffCollocList=${fmsdr4ffCollocList}_${identifier}.list
fmsdr4SfrList=${fmsdr4SfrList}_${identifier}.list
fmsdr4imsCollocList=${fmsdr4imsCollocList}_${identifier}.list
imsColloc4nwpList=${imsColloc4nwpList}_${identifier}.list
imsColloc4retrList=${imsColloc4retrList}_${identifier}.list
prepSweClimo4VippList=${prepSweClimo4VippList}_${identifier}.list
ffColloc4VippList=${ffColloc4VippList}_${identifier}.list
edrList=${edrList}_${identifier}.list
edr4BiasList=${edr4BiasList}_${identifier}.list
dep4BiasList=${dep4BiasList}_${identifier}.list
edr4MergeList=${edr4MergeList}_${identifier}.list
depList=${depList}_${identifier}.list
sfrList=${sfrList}_${identifier}.list
gridNwpSfrList=${gridNwpSfrList}_${identifier}.list
nedtList=${nedtList}_${identifier}.list
nedtSensor1List=${nedtSensor1List}_${identifier}.list
nedtSensor2List=${nedtSensor2List}_${identifier}.list
gridSfcNwpAnalysList=${gridSfcNwpAnalysList}_${identifier}.list
gridAtmNwpAnalysList=${gridAtmNwpAnalysList}_${identifier}.list
nwpAnalysList=${nwpAnalysList}_${identifier}.list
nwpAnalysRetrList=${nwpAnalysRetrList}_${identifier}.list
nwpAnalys4BiasList=${nwpAnalys4BiasList}_${identifier}.list
nwpAnalys4RegressList=${nwpAnalys4RegressList}_${identifier}.list
fwdAnalys4BiasList=${fwdAnalys4BiasList}_${identifier}.list

#----Names of directories exclusively for Daily processing
figs4BiasDir=${perfsMonitorPath}/${rdirAnalysExt}
qcCheckDir=${perfsMonitorPath}/${rdirExt}
figs4RegressDir=${perfsMonitorPath}/${rdirAnalysExt}
nwpAnalysDir=${nwpAnalysPath}/${rdirAnalysExt}
fwdAnalysDir=${fwdAnalysPath}/${rdirAnalysExt}
fmsdr4BiasDir=${fmsdrPath}/${rdirAnalysExt}
edr4BiasDir=${edrPath}/${rdirAnalysExt}
dep4BiasDir=${depPath}/${rdirAnalysExt}
grid4BiasDir=${gridPath}/${rdirAnalysExt}
#----Names of the files dynamically generated
sensor1Nedt=${nedtSensor1Path}/${satId}_${sensor1}_nedt_${fileExt}.dat
sensor2Nedt=${nedtSensor2Path}/${satId}_${sensor2}_nedt_${fileExt}.dat
nedtExt=${fileExt}
if [[ ${satId} == "f16" || ${satId} == "aqua" || ${satId} == "gcomw1" || ${satId} == "f17" || ${satId} == "f18" || ${satId} == "f19" || ${satId} == "fy3ri" || ${satId} == "trmm" || ${satId} == "gpm" || ${satId} == "mtma" || ${satId} == "mtsa" ]] ; then
  nedtBefFMFile=${nedtSensor1Path}/${satId}_${sensor1}_nedt_${fileExt}_befFM.dat
  nedtAftFMFile=${nedtSensor1Path}/${satId}_${sensor1}_nedt_${fileExt}_aftFM.dat
  nedtDir=${nedtSensor1Path}/${rdirExt}
elif [[ ${satId} == "npp" || ${satId} == "n20" || ${satId} == "n21" || ${satId} == "metopSGA1" ]]; then
  nedtExt=`determineNedtExt ${satId} ${rdrSensor1Dir} ${rdrType}`
  nedtBefFMFile=${nedtSensor1Path}/${satId}_${sensor1}_nedt_${nedtExt}_befFM.dat
  nedtAftFMFile=${nedtSensor1Path}/${satId}_${sensor1}_nedt_${nedtExt}_aftFM.dat
  nedtDir=${nedtSensor1Path}/${rdirExt}
else
  nedtBefFMFile=${nedtSensor1Sensor2Path}/${satId}_${sensor1}_${sensor2}_nedt_${fileExt}_befFM.dat
  nedtAftFMFile=${nedtSensor1Sensor2Path}/${satId}_${sensor1}_${sensor2}_nedt_${fileExt}_aftFM.dat
  nedtDir=${nedtSensor1Sensor2Path}/${rdirExt}
fi
sensor1Wt=${nedtSensor1Path}/${satId}_${sensor1}_wt_${fileExt}.dat
sensor2Wt=${nedtSensor2Path}/${satId}_${sensor2}_wt_${fileExt}.dat
sensor1Sensor2Wt=${nedtSensor1Sensor2Path}/${satId}_${sensor1}_${sensor2}_wt_${fileExt}.dat
modelErrFile=${biasPath}/ModelErrFile_${satId}_${fileExt}.dat	      #Model err file that will be generated
if [[ ${satId} == "npp" || ${satId} == "n20" || ${satId} == "n21" || ${satId} == "metopSGA1" ]]; then
  modelErrFile=${biasPath}/ModelErrFile_${satId}_${nedtExt}.dat
fi
logFile=${logFile}_${fileExt}.dat
#----Names of files dynamically generated only for daily processing 
biasFile=${biasPath}/biasCorrec_${satId}_${fileAnalysExt}.dat	      #bias file that will be generated
if [[ ${satId} == "npp" || ${satId} == "n20" || ${satId} == "n21" || ${satId} == "metopSGA1" ]]; then
  biasFile=${biasPath}/biasCorrec_${satId}_${nedtExt}.dat
fi
biasCheckFile=${biasPath}/biasAfterCorr_${satId}_${fileAnalysExt}.dat #bias residual file
#----EDR/DEP/NWP grid/p2p products list
edrGridStr="angle,chisq,em,nattempt,niter,psfc,qc,scanday,scanpos,sfc,tbf,tbu,tbc,tbl,temp,tskin,wv,clwp,rainp,graupelp,pressure"
edrP2PStr="em,scanpos,sfc,tbu,tskin,wspd,temp,psfc,wv"
depGridStr="clw,gs,iwp,lwp,rr,rwp,sfc2,sice,sicefy,sicemy,snow,swe,tpw,sfr,sfrprob"
depP2PStr="angle,clw,iwp,lat,lon,lwp,rr,rwp,sfc2,swe,tpw"
nwpGridStr="angle,chisq,clw,em,iwp,nattempt,niter,psfc,rr,scanday,scanpos,sfc,swe,tbf,tbu,tbc,tbl,temp,tpw,tskin,wv,clwp,rainp,graupelp,pressure"
nwpP2PStr="clw,em,iwp,lwp,rwp,sfc,swe,tbu,tpw,tskin,temp,psfc,wv"
if [[ ${satId} == "f16" || ${satId} == "f17" || ${satId} == "f18" || ${satId} == "f19" || ${satId} == "trmm" || ${satId} == "gpm" || ${satId} == "mtma" || ${satId} == "mtsa" ]] ; then
  depGridStr="clw,gs,iwp,lwp,rr,rwp,sfc2,sice,sicefy,sicemy,snow,swe,tpw,wspd"
  depP2PStr="angle,clw,iwp,lat,lon,lwp,rr,rwp,sfc2,swe,tpw,wspd"
  nwpGridStr="angle,chisq,clw,em,iwp,nattempt,niter,psfc,rr,scanday,scanpos,sfc,swe,tbf,tbu,tbc,tbl,temp,tpw,tskin,wspd,wv,clwp,rainp,graupelp,pressure"
  nwpP2PStr="clw,em,iwp,lwp,rwp,sfc,swe,tbu,tpw,tskin,temp,wspd,psfc,wv"
fi

#---- fwd model error matrix
modelErrFile1ToUse=${biasPath}/ModelErrFile_${satId}.dat
modelErrFile2ToUse=${biasPath}/ModelErrFile_${satId}.dat

#---Check existence of the directories. If negative, make them
DirGen ${tdrSensor1Dir} "TDR-${sensor1}"
if [[ $sensor2 != "dummy" ]] ; then 
  DirGen ${tdrSensor2Dir} "TDR-${sensor2}"
fi
DirGen ${sdrSensor1Dir} "SDR-${sensor1}"
if [[ $sensor2 != "dummy" ]] ; then 
  DirGen ${sdrSensor2Dir} "SDR-${sensor2}"
fi
if [[ ${satId} == "npp" || ${satId} == "n20" || ${satId} == "n21" || ${satId} == "metopSGA1" ]] ; then
  DirGen ${nedtDir} "NEDT"
fi
DirGen ${fmsdrDir} "FM-SDR"
DirGen ${fmsdrChoppDir} "CHOPPED FMSDRs"
DirGen ${edrDir} "EDR"
DirGen ${depDir} "DEP"
DirGen ${gridDir} "GRID"
DirGen ${ncDir} "NETCDF4"
DirGen ${figsDir} "FIGS"
DirGen ${sfrDir} "SFR"
DirGen ${figs4BiasDir} "FIGS"
DirGen ${grid4BiasDir} "GRID-BIAS"
DirGen ${qcCheckDir} "QCCheck"
DirGen ${figs4RegressDir} "regr-FIGS"
DirGen ${nwpAnalysDir} "NWP-ANALYSIS"
DirGen ${fwdAnalysDir} "FWD SIMUL on Analyses"
DirGen ${orbitMonPath} "QC Monitor"
DirGen ${regressRetrDir} "Regression-Based Retrievals"
DirGen ${prepSweClimoDir} "SWE Climatology"
DirGen ${ffCollocDir} "FF Collocation"
DirGen ${imsCollocDir} "IMS Collocation"

#--------------------------------------------------------------------------------
#      NPP/ATMS special case: to generate NEDT from SDR files
#--------------------------------------------------------------------------------
if [[ "${step_rdr2tdrSensor1}" -eq 1 && ${satId} == "npp" && ${rdrType} -eq 1 ]] ; then
  rdrType2=3
  nfile_gatmo=`ls -1 ${rdrSensor1Dir}/GATMO_npp* 2> /dev/null | wc -l`
  nfile_satms=`ls -1 ${rdrSensor1Dir}/SATMS_npp* 2> /dev/null | wc -l`
  #---- only do this when SDR files exist and have equal numer of GATMO files
  if [[ ${nfile_satms} -ge 1 && ${nfile_gatmo} -eq ${nfile_satms} ]] ; then
    rdr2tdr ${rdrSensor1Dir} ${rdrSensor1List} ${sensor1} ${tdrSensor1Dir} ${sensor1Nedt}\
    ${instrumentSensor1File} ${sensor1Wt} ${nOrbits2Process} ${logFile}\
    ${rdr2tdrSensor1ControlFile} ${rdr2tdrSensor1Src} ${makeOrNot} ${binPath}\
    ${processMode} ${orbitInfo} ${satId} "${rdirExt}" ${controlDataPath}\
    ${calibBiasFitFile} ${calibDTRlutFile} ${accessStr} ${formStr} ${rdrType2}
    #---- clean up ( only need remove TDR to avoid conflict )
    rm -f ${tdrSensor1Dir}/TDR*
  fi
fi

#--------------------------------------------------------------------------------
#      N20/ATMS special case: to generate NEDT from SDR files
#--------------------------------------------------------------------------------
if [[ "${step_rdr2tdrSensor1}" -eq 1 && ${satId} == "n20" && ${rdrType} -eq 1 ]] ; then
  rdrType2=3
  nfile_gatmo=`ls -1 ${rdrSensor1Dir}/GATMO_j01* 2> /dev/null | wc -l`
  nfile_satms=`ls -1 ${rdrSensor1Dir}/SATMS_j01* 2> /dev/null | wc -l`
  #---- only do this when SDR files exist and have equal numer of GATMO files
  if [[ ${nfile_satms} -ge 1 && ${nfile_gatmo} -eq ${nfile_satms} ]] ; then
    rdr2tdr ${rdrSensor1Dir} ${rdrSensor1List} ${sensor1} ${tdrSensor1Dir} ${sensor1Nedt}\
    ${instrumentSensor1File} ${sensor1Wt} ${nOrbits2Process} ${logFile}\
    ${rdr2tdrSensor1ControlFile} ${rdr2tdrSensor1Src} ${makeOrNot} ${binPath}\
    ${processMode} ${orbitInfo} ${satId} "${rdirExt}" ${controlDataPath}\
    ${calibBiasFitFile} ${calibDTRlutFile} ${accessStr} ${formStr} ${rdrType2}
    #---- clean up ( only need remove TDR to avoid conflict )
    rm -f ${tdrSensor1Dir}/TDR*
  fi
fi

#--------------------------------------------------------------------------------
#      N20/ATMS special case: to generate NEDT from SDR files
#--------------------------------------------------------------------------------
if [[ "${step_rdr2tdrSensor1}" -eq 1 && ${satId} == "n21" && ${rdrType} -eq 1 ]] ; then
  rdrType2=3
  nfile_gatmo=`ls -1 ${rdrSensor1Dir}/GATMO_j02* 2> /dev/null | wc -l`
  nfile_satms=`ls -1 ${rdrSensor1Dir}/SATMS_j02* 2> /dev/null | wc -l`
  #---- only do this when SDR files exist and have equal numer of GATMO files
  if [[ ${nfile_satms} -ge 1 && ${nfile_gatmo} -eq ${nfile_satms} ]] ; then
    rdr2tdr ${rdrSensor1Dir} ${rdrSensor1List} ${sensor1} ${tdrSensor1Dir} ${sensor1Nedt}\
    ${instrumentSensor1File} ${sensor1Wt} ${nOrbits2Process} ${logFile}\
    ${rdr2tdrSensor1ControlFile} ${rdr2tdrSensor1Src} ${makeOrNot} ${binPath}\
    ${processMode} ${orbitInfo} ${satId} "${rdirExt}" ${controlDataPath}\
    ${calibBiasFitFile} ${calibDTRlutFile} ${accessStr} ${formStr} ${rdrType2}
    #---- clean up ( only need remove TDR to avoid conflict )
    rm -f ${tdrSensor1Dir}/TDR*
  fi
fi

#--------------------------------------------------------------------------------
#      step: RDR to TDR conversion (sensor1)
#--------------------------------------------------------------------------------
if [[ "${step_rdr2tdrSensor1}" -eq 1 ]] ; then
  rdr2tdr ${rdrSensor1Dir} ${rdrSensor1List} ${sensor1} ${tdrSensor1Dir} ${sensor1Nedt}\
  ${instrumentSensor1File} ${sensor1Wt} ${nOrbits2Process} ${logFile}\
  ${rdr2tdrSensor1ControlFile} ${rdr2tdrSensor1Src} ${makeOrNot} ${binPath}\
  ${processMode} ${orbitInfo} ${satId} "${rdirExt}" ${controlDataPath}\
  ${calibBiasFitFile} ${calibDTRlutFile} ${accessStr} ${formStr} ${rdrType}
fi

#--------------------------------------------------------------------------------
#      step: RDR to TDR conversion (sensor2)
#--------------------------------------------------------------------------------
if [[ "${step_rdr2tdrSensor2}" -eq 1 ]] ; then
  rdr2tdr ${rdrSensor2Dir} ${rdrSensor2List} ${sensor2} ${tdrSensor2Dir} ${sensor2Nedt}\
  ${instrumentSensor2File} ${sensor2Wt} ${nOrbits2Process} ${logFile}\
  ${rdr2tdrSensor2ControlFile} ${rdr2tdrSensor2Src} ${makeOrNot} ${binPath}\
  ${processMode} ${orbitInfo} ${satId} "${rdirExt}" ${controlDataPath}\
  ${calibBiasFitFile} ${calibDTRlutFile} ${accessStr} ${formStr} ${rdrType}
fi

#--------------------------------------------------------------------------------
#      step: Merge Different Sensor NEDT files into a single file
#--------------------------------------------------------------------------------
if [[ "${step_mergeNedt}" -eq 1 ]] ; then
  mergeNedt ${sensor1Nedt} ${sensor2Nedt} ${nedtBefFMFile} ${logFile}\
  ${mergeNedtControlFile} ${mergeNedtSrc} ${makeOrNot} ${binPath} ${satId}\
  "${nedtNominalFile}"  "${nedtDir}" 
fi

#--------------------------------------------------------------------------------
#      step: TDR to SDR conversion (sensor1)
#--------------------------------------------------------------------------------
if [[ "${step_tdr2sdrSensor1}" -eq 1 ]] ; then
  tdr2sdr ${tdrSensor1Dir} ${tdrSensor1List} ${sensor1} ${tdrFormat} ${sdrSensor1Dir}\
  ${antennaSensor1File} ${nOrbits2Process} ${logFile} ${tdr2sdrSensor1ControlFile}\
  ${makeOrNot} ${binPath} ${processMode} ${orbitInfo} ${tdr2sdrSrc}
fi

#--------------------------------------------------------------------------------
#      step: TDR to SDR conversion (sensor2)
#--------------------------------------------------------------------------------
if [[ "${step_tdr2sdrSensor2}" -eq 1 ]] ; then
  tdr2sdr ${tdrSensor2Dir} ${tdrSensor2List} ${sensor2} ${tdrFormat} ${sdrSensor2Dir}\
  ${antennaSensor2File} ${nOrbits2Process} ${logFile} ${tdr2sdrSensor2ControlFile}\
  ${makeOrNot} ${binPath} ${processMode} ${orbitInfo} ${tdr2sdrSrc}
fi

#--------------------------------------------------------------------------------
#      step: Footprint Matching (FM) sensor1/sensor2
#--------------------------------------------------------------------------------
if [[ "${step_fm}" -eq 1 ]] ; then
  fm ${sdrSensor1Dir} ${sdrSensor1List} ${sdrSensor2Dir} ${sdrSensor2List}\
  ${sensor1} ${sensor2} ${fmsdrDir} ${outFMAccuracy} ${perfsMonitorPath}\
  ${prefixFMAccuracy} ${fmType} ${nScanLineSensor1Skip} ${nScanLineSensor2Skip}\
  ${scanLineIndexSensor2TimeColloc} ${nOrbits2Process} ${logFile} ${fmControlFile}\
  ${fmSrc} ${makeOrNot} ${binPath} ${processMode} ${orbitInfo} ${satId}\
  ${nedtBefFMFile} ${nedtAftFMFile} ${modifyNedtControlFile} ${figs4BiasDir}\
  ${identifier} ${outFMAccuracy} ${inputDataPath} ${controlDataPath}\
  ${geoLimit} ${minLat} ${maxLat} ${minLon} ${maxLon}
fi

#--------------------------------------------------------------------------------
#      step: Collocate FMSDRs with the IMS Snow/Ice surface type analysis (for nwp step)
#--------------------------------------------------------------------------------
if [[ "${step_ims4nwp}" -eq 1 ]] ; then
   if [[ ${processMode} -eq 0 ]] ; then
      yyyy=`echo ${orbitInfo} | cut -c1-4`
      mm=`echo ${orbitInfo} | cut -c5-6`
      dd=`echo ${orbitInfo} | cut -c7-8`
      date=${yyyy}-${mm}-${dd}
   fi
  yyyy=`echo ${date} | cut -c1-4`
  let ndays=${ndayLagIms}+1
  yyyymmdd=`date -d "${date} $ndays days" +%Y-%m-%d`
  yyyy=`echo ${yyyymmdd} | cut -c1-4`
  jjj=`yyyymmdd2jjj $yyyymmdd`
  #imsFile=${imsAnalysisPath}/"ims"${yyyy}${jjj}"_4km_v1.3.asc"
  imsFile=${imsAnalysisPath}/"NIC.IMS_v3_"${yyyy}${jjj}"00_4km.asc"
  echo "imsFile=" ${imsFile}
  if [ ! -e ${imsFile} ]; then
     op_msg "Warning in imsColloc: file not found"
     imsSfcUse=0
  fi
  if [ -e ${imsFile} ]; then
     imsColloc ${fmsdrDir} "${extResol}" ${fmsdr4imsCollocList} ${imsCollocDir}\
     ${imsFile} ${ndayLagIms} ${logFile} ${imsCollocControlFile}\
     ${imsCollocSrc} ${makeOrNot} ${binPath} ${processMode} ${orbitInfo}\
     ${retrOnOrbitOrSubOrbit} ${fmsdrChoppDir} ${sensorId}\
     ${nOrbits2Process} ${version}
  fi
fi

#--------------------------------------------------------------------------------
#      step: colocation of NWP ECMWF analyses with radiances (for bias)
#	note: In this step, if you get data allocate problem, you need do this:
#		ulimit -d unlimited  ( on IBM or Linux )
#	Or	limit datasize unlimited ( on other platforms )
#--------------------------------------------------------------------------------
if [[ "${step_nwp}" -eq 1 ]] ; then
  checkNWP=`prepNWP ${fmsdrPath} ${rdirAnalysExt} "${extResol}" ${satId} ${ecmwfData}\
  ${nwpGenAnalysSrc} ${makeOrNot} ${binPath} ${controlDataPath} ${nwpEcmwfGridPath}\
  ${gridSfcNwpAnalysList} ${gridAtmNwpAnalysList}`
  if [[ ${checkNWP} == "1" ]] ; then
    echo NWP files needed are complete
  else
    echo NWP files needed are NOT complete
    exit 1
  fi
  nwp ${nwpEcmwfGridPath} ${rdirAnalysExt} ${gridSfcNwpAnalysList} ${gridAtmNwpAnalysList}\
  ${fmsdrPath} "${extResol}" ${fmsdr4NwpList} ${nwpAnalysDir} ${topographyFile}\
  ${covBkgAtm1File} ${nOrbits2Process} ${logFile} ${nProfs2Fwd} ${grid2nwpControlFile}\
  ${nwpGenAnalysSrc} ${makeOrNot} ${binPath} ${sensorId} ${rdirNextAnalysExt}\
  ${CRTMcoeffPath} ${ecmwfData}\
  ${imsSfcUse} ${imsCollocDir} ${imsColloc4nwpList} ${processMode} ${orbitInfo}
fi

#--------------------------------------------------------------------------------
#	step: Application of forward operator on NWP ECMWF analyses
#--------------------------------------------------------------------------------
if [[ "${step_fwd}" -eq 1 ]] ; then
  fwd ${fwdSrc} ${makeOrNot} ${nwpAnalysDir} ${nwpAnalysList} ${nOrbits2Process}\
  ${fwdAnalysDir} ${CRTMcoeffPath} ${instrumentSensor1Sensor2File} ${nProfs2Fwd}\
  ${addDeviceNoise} ${nedtAftFMFile} ${monitorFwd} ${logFile} ${fwdControlFile} \
  ${binPath} ${satId} ${sensorId} ${ecmwfData} ${fwdCloudOffOrOn} "${rdirExt}"
fi

#--------------------------------------------------------------------------------
#      step: Determination of the bias (by comparing FWD simul and meas)
#--------------------------------------------------------------------------------
if [[ "${step_biasGen}" -eq 1 ]] ; then
  biasGen ${determineBiasSrc} ${nwpAnalysDir} "${extResol}" ${nwpAnalys4BiasList}\
  ${fwdAnalysDir} ${fwdAnalys4BiasList} ${fmsdr4BiasDir} ${fmsdr4BiasList}\
  ${biasCompuControlFile} ${biasComputeMethod} ${biasFile} ${modelErrFile}\
  ${figs4BiasDir} ${nOrbits2Process} ${satId} ${IDL} ${sensorId}\
  ${topographyFile} ${binPath} "${modelErrNominalFile}" ${controlDataPath} ${ecmwfData} ${minLat} ${maxLat} ${minLon} ${maxLon}
fi

#--------------------------------------------------------------------------------
#	step: Chopping the FMSDR file  into pieces for faster processing
#--------------------------------------------------------------------------------
if [[ "${step_choppRadFiles}" -eq 1 ]] ; then
  chopp ${fmsdrDir} ${fmsdr4ChoppList} ${sensor1}${sensor2} ${fmsdrChoppDir}\
  ${nChoppedFilesPerOrbit} ${logFile} ${choppControlFile} ${choppSrc} ${makeOrNot}\
  ${binPath} ${processMode} ${orbitInfo} "${extResol}"
fi

#--------------------------------------------------------------------------------
#      step: Collocate FMSDRs with the IMS Snow/Ice surface type analysis (for 1dvar step)
#--------------------------------------------------------------------------------
if [[ "${step_ims4retr}" -eq 1 ]] ; then
   if [[ ${processMode} -eq 0 ]] ; then
      yyyy=`echo ${orbitInfo} | cut -c1-4`
      mm=`echo ${orbitInfo} | cut -c5-6`
      dd=`echo ${orbitInfo} | cut -c7-8`
      date=${yyyy}-${mm}-${dd}
   fi
  yyyy=`echo ${date} | cut -c1-4`
  let ndays=${ndayLagIms}+1
  yyyymmdd=`date -d "${date} $ndays days" +%Y-%m-%d`
  yyyy=`echo ${yyyymmdd} | cut -c1-4`
  jjj=`yyyymmdd2jjj $yyyymmdd`
  #imsFile=${imsAnalysisPath}/"ims"${yyyy}${jjj}"_4km_v1.3.asc"
  imsFile=${imsAnalysisPath}/"NIC.IMS_v3_"${yyyy}${jjj}"00_4km.asc"
  echo "imsFile=" ${imsFile}
  if [ ! -e ${imsFile} ]; then
     op_msg "Warning in imsColloc: file not found"
     imsSfcUse=0
  fi
  if [ -e ${imsFile} ]; then
     imsColloc ${fmsdrDir} "${extResol}" ${fmsdr4imsCollocList} ${imsCollocDir}\
     ${imsFile} ${ndayLagIms} ${logFile} ${imsCollocControlFile}\
     ${imsCollocSrc} ${makeOrNot} ${binPath} ${processMode} ${orbitInfo}\
     ${retrOnOrbitOrSubOrbit} ${fmsdrChoppDir} ${sensorId}\
     ${nOrbits2Process} ${version}
  fi
fi

#--------------------------------------------------------------------------------
#      step: Apply regression-based algorithms on FM-SDR radiances
#--------------------------------------------------------------------------------
if [[ "${step_externalDataFromRegress}" -eq 1 ]] ; then
  applyRegress ${fmsdrDir} "${extResol}" ${fmsdr4ApplyRegressList} ${regressRetrDir}\
  ${topographyFile} ${covBkgAtm1File} ${covBkgSfc1File} ${logFile} ${regressControlFile}\
  ${applyRegressAlgSrc} ${makeOrNot} ${binPath} ${processMode} ${orbitInfo}\
  ${regressCoeffOceanClwFile}   ${regressCoeffSeaIceClwFile}   ${regressCoeffLandClwFile}   ${regressCoeffSnowClwFile}\
  ${regressCoeffOceanTskinFile} ${regressCoeffSeaIceTskinFile} ${regressCoeffLandTskinFile} ${regressCoeffSnowTskinFile}\
  ${regressCoeffOceanTpwFile}   ${regressCoeffSeaIceTpwFile}   ${regressCoeffLandTpwFile}   ${regressCoeffSnowTpwFile}\
  ${regressCoeffOceanEmFile}    ${regressCoeffSeaIceEmFile}    ${regressCoeffLandEmFile}    ${regressCoeffSnowEmFile}\
  ${regressCoeffOceanWvFile}    ${regressCoeffSeaIceWvFile}    ${regressCoeffLandWvFile}    ${regressCoeffSnowWvFile}\
  ${regressCoeffOceanTempFile}  ${regressCoeffSeaIceTempFile}  ${regressCoeffLandTempFile}  ${regressCoeffSnowTempFile}\
  ${regressCoeffOceanGwpFile}   ${regressCoeffSeaIceGwpFile}   ${regressCoeffLandGwpFile}   ${regressCoeffSnowGwpFile}\
  ${retrOnOrbitOrSubOrbit} ${fmsdrChoppDir} ${sensorId}\
  ${nOrbits2Process} ${biasFileToUse} ${tune1File} ${version}
fi

#--------------------------------------------------------------------------------
#      step: EDRs retrieval from the FM-SDRs
#--------------------------------------------------------------------------------
if [[ "${step_fmsdr2edr}" -eq 1 ]] ; then
  fmsdr2edr ${fmsdr2edrSrc} ${makeOrNot} ${retrOnWhichSDR} ${fmsdrDir}\
  ${fwdAnalysDir} ${retrOnOrbitOrSubOrbit} ${fmsdrChoppDir} ${fmsdrList}\
  ${nOrbits2Process} ${externalDataAvailable} ${externalDataSrc} ${nwpAnalysDir}\
  ${nwpAnalysRetrList} ${regressRetrDir} ${edrDir} ${nProfs2Retr}\
  ${monitorIterative} ${nAttempts} ${monitorRetrieval} ${geoLimit}\
  ${minLat} ${maxLat} ${minLon} ${maxLon} ${cend} ${sensorId}\
  ${tune1File} ${tune2File} ${covBkgAtm1File} ${covBkgAtm2File}\
  ${covBkgSfc1File} ${covBkgSfc2File} ${modelErrFile1ToUse} ${modelErrFile2ToUse} \
  ${extBkgAtmFile} ${extBkgAtmUse}\
  ${imsSfcUse} ${imsCollocDir} ${imsColloc4retrList}\
  ${nedtAftFMFile} ${monitorFile} ${topographyFile}\
  ${CRTMcoeffPath} ${logFile} ${fmsdr2edrControlFile} ${useCPU} ${processMode}\
  ${orbitInfo} ${binPath} ${biasFileToUse} ${version} "${extResol}" "${rdirExt}" \
  ${TBbias_NNModelFile} ${TPW_NNModelFile} ${Tskin_NNModelFile} 
fi

#--------------------------------------------------------------------------------
#      step: Merge the mini EDR files into full orbit file
#--------------------------------------------------------------------------------
if [[ "${step_mergeEdr}" -eq 1 ]] ; then
  mergeEdr ${edrDir} "${extResol}" ${edr4MergeList} ${sensor1}${sensor2}\
  ${nChoppedFilesPerOrbit} ${logFile} ${mergeEdrControlFile} ${mergeEdrSrc}\
  ${makeOrNot} ${binPath} ${processMode} ${orbitInfo}
fi

#--------------------------------------------------------------------------------
#      step: Prepare files with SWE climatology information (for vipp)
#--------------------------------------------------------------------------------
if [[ "${step_prepSweClimo}" -eq 1 ]] ; then
  prepSweClimo ${fmsdrDir} "${extResol}" ${fmsdr4PrepSweList} ${prepSweClimoDir}\
  ${SweClimoMeanFile} ${SweClimoStdevFile} ${logFile} ${prepSweClimoControlFile}\
  ${prepSweSrc} ${makeOrNot} ${binPath} ${processMode} ${orbitInfo}\
  ${retrOnOrbitOrSubOrbit} ${fmsdrChoppDir} ${sensorId}\
  ${nOrbits2Process} ${version}
fi

#--------------------------------------------------------------------------------
#      step: Collocate FMSDRs with the VIIRS-based forest fraction (for vipp)
#--------------------------------------------------------------------------------
if [[ "${step_ffColloc}" -eq 1 ]] ; then
  ffColloc ${fmsdrDir} "${extResol}" ${fmsdr4ffCollocList} ${ffCollocDir}\
  ${ffFile} ${ffLatLonFile} ${logFile} ${ffCollocControlFile}\
  ${ffCollocSrc} ${makeOrNot} ${binPath} ${processMode} ${orbitInfo}\
  ${retrOnOrbitOrSubOrbit} ${fmsdrChoppDir} ${sensorId}\
  ${nOrbits2Process} ${version}
fi

#--------------------------------------------------------------------------------
#      step: To generate vertical integrated products
#--------------------------------------------------------------------------------
if [[ "${step_vipp}" -eq 1 ]] ; then
  vipp ${edrList} ${edrDir} ${prepSweClimoDir} ${prepSweClimo4VippList}\
  ${sweClimoUse} ${ffCollocDir} ${ffColloc4VippList} ${ffUse}\
  ${depDir}  ${logFile} ${nOrbits2Process} ${nProfs2Retr}\
  ${sensorId} ${processMode} ${orbitInfo} "${extResol}" ${vippControlFile}\
  ${vippSrc} ${binPath} ${siceEmissCatalogFile} ${snowEmissCatalogFile}
fi

#--------------------------------------------------------------------------------
#      step: To generate sfr products
#--------------------------------------------------------------------------------
if [[ "${step_sfr}" -eq 1 ]] ; then
 sfr ${satId} ${sensor1} ${fmsdrDir} "${extResol}" ${fmsdr4SfrList} ${sfrDir} ${sfrDataPath}\
     ${logFile} ${sfrSrc} ${makeOrNot} ${binPath}\
     ${processMode} ${orbitInfo} ${retrOnOrbitOrSubOrbit} ${fmsdrChoppDir}\
     ${nOrbits2Process} ${sfrControlFile} ${nwpSfrGridPath} ${gridNwpSfrList}\
     ${nProfs2Retr} ${sfr2depSrc} ${sfr2depControlFile} ${sfrList} ${depDir} ${depList}
fi

#--------------------------------------------------------------------------------
#      step: To generate gridded products
#--------------------------------------------------------------------------------
if [[ "${step_grid}" -eq 1 ]] ; then
  gridGen_parallel ${processMode} ${edrDir} ${depDir} ${orbitInfo} ${edrList} ${depList}\
  "${extResol}" ${satId} ${fileExt} ${gridSrc} ${gridDir} ${makeOrNot} ${binPath}\
  ${gridControlFile} ${gridFactor} ${minLat} ${maxLat} ${minLon} ${maxLon}\
  ${fmType} "${edrGridStr}" "${edrP2PStr}" "${depGridStr}" "${depP2PStr}"
fi

#--------------------------------------------------------------------------------
#      step: To convert EDR & DEP into netcdf4 format
#--------------------------------------------------------------------------------
if [[ "${step_nc}" -eq 1 ]] ; then
  mirs2nc_parallel ${edrDir} ${depDir} ${ncDir} ${binPath} ${satId} ${rdrSensor1List} ${rdrType} ${HDF5BIN} ${production_site} ${production_environment}
fi

#--------------------------------------------------------------------------------
#      step: EDRs Figures Generation
#--------------------------------------------------------------------------------
if [[ "${step_figsGen}" -eq 1 ]] ; then
  figsGen_parallel ${satId} ${gridFactor} ${gridDir} ${gridSrc} ${figsDir} ${IDL}\
  ${identifier} ${figsGenControlFile} ${processMode} ${controlDataPath} ${version}\
  ${minLat} ${maxLat} ${minLon} ${maxLon}
fi

#--------------------------------------------------------------------------------
#      step: Bias Figures Generation (NWP ECMWF) 
#--------------------------------------------------------------------------------
if [[ "${step_biasFigsGen}" -eq 1 ]] ; then
  biasFigsGen_parallel ${edr4BiasDir} ${nwpAnalysDir} ${fwdAnalysDir} ${edr4BiasList}\
  ${nwpAnalys4BiasList} ${fwdAnalys4BiasList} ${processMode} ${orbitInfo}\
  "${extResol}" ${satId} ${rdirAnalysExt} ${gridSrc} ${grid4BiasDir} ${makeOrNot}\
  ${binPath} ${nwpGridControlFile} ${fwdGridControlFile} ${biasGridControlFile}\
  ${gridFactor} ${gridSrc} ${figs4BiasDir} ${IDL} ${rdirAnalysExt}\
  ${figsGenControlFile} ${controlDataPath}  ${dep4BiasDir} ${dep4BiasList}\
  ${version} ${biasPath} ${minLat} ${maxLat} ${minLon} ${maxLon} ${ecmwfData}\
  ${fmType} "${nwpGridStr}" "${nwpP2PStr}" "${nedtExt}"
fi

#--------------------------------------------------------------------------------
#      step: Data monitoring (plots)
#--------------------------------------------------------------------------------
if [[ "${step_dataMonitor}" -eq 1 ]] ; then
  qcRetrieval ${depDir} ${depList} ${orbitMonPath} ${IDL} ${gridSrc}\
  ${controlDataPath}/qcRetrieval_abnormal_${satId}_${fileExt}\
  ${controlDataPath}/qcRetrieval_namelist_${satId}_${fileExt}\
  "${email}" "${website}" ${controlDataPath} ${satId} ${date} ${binPath}

  dataQualityMonitor ${nedtSensor1Sensor2Path} ${nedtList} ${nedtMonitorSrc} ${IDL}\
  ${orbitMonPath} ${figsDir} ${processMode} ${fileExt} ${satId} ${controlDataPath} ${perfsMonitorPath}
fi

#--------------------------------------------------------------------------------
#      step: Cleaning Up
#--------------------------------------------------------------------------------
if [[ "${step_clean}" -eq 1 ]] ; then
  if [[ "${satId}" == "f16" || "${satId}" == "f17" || "${satId}" == "f18" || "${satId}" == "f19" || "${satId}" == "gpm" || "${satId}" == "npp" || "${satId}" == "n20" || ${satId} == "n21" || ${satId} == "metopSGA1" ]] ; then
	tdrSensor2Path='Dummy'
	sdrSensor2Path='Dummy'
	rdr2tdrSensor2Src='Dummy'
	nedtSensor2Path='Dummy'
	nedtSensor1Sensor2Path='Dummy'
  fi
  clean ${satId} ${maxDaysArchived} ${tdrSensor1Path} ${tdrSensor2Path} ${sdrSensor1Path}\
  ${sdrSensor2Path} ${fmsdrPath} ${choppPath} ${edrPath} ${depPath}\
  ${figsPath} ${nwpAnalysPath} ${fwdAnalysPath} ${regressRetrPath}\
  ${perfsMonitorPath} ${makeOrNot} ${rdr2tdrSensor1Src} ${rdr2tdrSensor2Src}\
  ${mergeNedtSrc} ${tdr2sdrSrc} ${fmSrc} ${nwpGenAnalysSrc} ${fwdSrc} \
  ${applyRegressAlgSrc} ${fmsdr2edrSrc} ${controlDataPath} ${inputDataPath} ${binPath}\
  ${logPath} ${prefixFMAccuracy} ${determineBiasSrc} \
  ${applyRegressAlgSrc} ${rootPath} ${processMode} ${makeClean} ${nedtSensor1Path}\
  ${nedtSensor2Path} ${nedtSensor1Sensor2Path} ${regressPath} ${biasPath} ${gridPath}
fi