#!/bin/ksh
# Do not forget to exectute module load R and module load cdo on obelix
# ${1} can take tree value : all= cdo extract + reformating R script + eval_figure R script
#                            rscript= reformating R script + eval_figure R script
#                            figure= eval_figure R script
# ${2} wich step do you want : STOI, ORC-1, FIN, HIST
# S{3} Output temporal frequency : Daily=D, Monthly=M
# ${5} A name that describe your simulation experiment ex: reference, V1.X, r5800 etc....
# ${4} choose between SRF and SBG
# $[6...X] A name that describe simulation experiment for wich you want to compare with ${2}
# 
# Here your can put any variables you would like to extract

if [ ${4} -eq 'SBG' ];then
var='LAI,RDI,AGE_STAND,DIAMETER,IND,HEIGHT,RDI_TARGET_UPPER,RDI_TARGET_LOWER,GPP,NPP,IND_DOM,HEIGHT_DOM,DIAMETER_DOM,BA,CCTRW_001,CCTRW_002,CCTRW_003,MOISTRESS,HET_RESP,PLANT_STATUS,WOOD_VOLUME_PIX_CUT'
else
var='GPP,NPP,NEE,HUMREL,EVAP,ASSIMI,GS,GSMEAN,LAI,TVEG,POTEVAP,VC'
fi

OUTPATHS=/home/scratch01/$USER/IGCM_OUT/OL2/PROD/ensemble\

if [ X${1} == 'Xall' ]; then

	for i in DE-Bay DE-Hai DE-Tha DE-Wet DK-Sor FI-Hyy FI-Sod FR-Fon FR-Hes FR-LBr FR-Pue IT-Col IT-Cpz IT-Non IT-PT1 IT-Ren IT-SRo NL-Loo SE-Fla SE-Nor SE-Sk1 SE-Sk2 AU-Tum AU-Wac CZ-BK1 ES-ES1 IL-Yat IS-Gun IT-Lav IT-Lec IT-Non IT-Ro1 IT-Ro2 PT-Esp PT-Mi1 RU-Fyo RU-Ha1 RU-Ha2 RU-Zot SK-Tat UK-Gri UK-Ham UK-PL3 US-Blo US-Me4 US-SP1 US-SP2 US-SP3 US-SP4 US-Ho1 US-Ho2 US-Wi0 US-Wi2 US-Wi4 US-Wi5 US-Wi9 AU-Tum AU-Wac US-MMS US-MOz US-WBW US-Bar US-Ha1 US-Oho US-UMB US-WCr US-Wi1 US-Wi8 CA-Man CA-NS1 CA-NS2 CA-NS3 CA-NS4 CA-NS5 CA-Qcu CA-Qfo CA-SF1 CA-SF2 RU-Ha3 US-Aud US-FPe US-Goo US-Var AT-Neu CH-Oe1 DE-Gri DE-Meh DK-Lva ES-VDA FR-Lq1 FR-Lq2 HU-Bug HU-Mat IE-Dri IT-LMa IT-Mal IT-MBo NL-Cal NL-Haa NL-Hor UK-EBu UK-Tad US-Bkg DK-Ris FR-Gri NL-Lut US-Bo1 US-Ne1 US-Ne2 US-Ne3 NL-Lan BE-Vie CH-Lae IT-Cp2 CH-Dav DE-Obe BE-Bra 
	do
            if [ ${2} -eq 'HIST' ];then
               if [ ${4} -eq 'SBG' ];then
                     PATHS=${OUTPATHS}/FLUXNET/${i}FLUXNETHIST/SBG/Output/MO/
               else
                     PATHS=${OUTPATHS}/FLUXNET/${i}FLUXNETHIST/SRF/Output/MO/
               fi
            else
               if [ ${4} -eq 'SBG' ];then
                     PATHS=${OUTPATHS}/FLUXNET/${i}FLUXNET/SPIN/Output/${i}FLUXNET${2}/SBG/Output/MO/
               else
                     PATHS=${OUTPATHS}/FLUXNET/${i}FLUXNET/SPIN/Output/${i}FLUXNET${2}/SRF/Output/MO/
               fi
            fi

            if [ ! -d ${PATHS} ];then
              continue
	    fi
            if [ ${4} -eq 'SBG' ];then
                cdo select,name=${var} $PATHS*1M_stomate_history.nc $OUTPATHS/FLUXNET/${i}_ALL.nc
            else
                cdo select,name=${var} $PATHS*1M_sechiba_history.nc $OUTPATHS/FLUXNET/${i}_ALL.nc
            fi
	done
	Rscript --vanilla convert_nc_txt.R ${OUTPATHS}/FLUXNET/ ${OUTPATHS}/ ${@}
	Rscript --vanilla make_eval_figure.R ${OUTPATHS}/FLUXNET/ ${OUTPATHS}/ ${@}
	tar Jcvf $OUTPATHS/All_${5}.tar.xz $OUTPATHS/FLUXNET/*_ALL.nc

fi


if [ X${1} == 'Xrscript' ] ; then
     tar Jxvf $OUTPATHS/All_${5}.tar.xz -C $OUTPATHS/
     mv ${OUTPATHS}/${OUTPATHS}/FLUXNET/*_ALL.nc $OUTPATHS/
     Rscript --vanilla convert_nc_txt.R $OUTPATHS/ $OUTPATHS/  ${@} 
     Rscript --vanilla make_eval_figure.R $OUTPATHS/ $OUTPATHS/ ${@}
     rm -rf *_ALL.nc
fi


if [ X${1} == 'Xfigure' ] ; then
     tar Jxvf $OUTPATHS/All_${5}.tar.xz -C $OUTPATHS/
     mv ${OUTPATHS}/${OUTPATHS}/FLUXNET/*_ALL.nc $OUTPATHS/
     Rscript --vanilla make_eval_figure.R $OUTPATHS/ $OUTPATHS/ ${@}
     rm -rf *_ALL.nc
fi