#!/bin/sh
# shell to run ocean heat content time series and geographic
# distribution from in situ ocean profile data (World Ocean Database, WOD)

#MAINDIR is the directory in whose subdirectories all of the files for
# OHC calculations are found and to which the output files will be written.
# In this example shell this is simply the present directory above
# the 'shells' directory in which 'run_ohc.shell' resides.
# Change as necessary. But take care, full pathnames + file names
# must be <= 80 characters.
MAINDIR="."

#SHELLDIR is location for shells for OHC (including this one)
SHELLDIR="$MAINDIR"/shells

#EXECDIR is the directory in which executables are stored
EXECDIR="$MAINDIR"/executables

#WORKDIR is the directory in which shells/programs are run.
# This present shell should be run from the work directory
# In this example shell, from necessity, the WORKDIR=MAINDIR.
# Since this shell does not clean up after itself, there will
# be numerous files copied to the work area and lefft there.
#WORKDIR="$MAINDIR"/work
WORKDIR="$MAINDIR"

#INFOFILEDIR: directory for information files for program runs
INFOFILEDIR="$MAINDIR"/info_files

#CLIMATOLOGYDIR: directory for climatological mean fields and statistics
#                including anomaly fields
CLIMATOLOGYDIR="$MAINDIR"/climatology
#CLIMATOLOGYSTATSDIR: directory for anomaly error statistics
CLIMATOLOGYSTATSDIR="$CLIMATOLOGYDIR"/stats

#NETCDFDIR is the directory for the OHC netcdf files
NETCDFDIR="$MAINDIR"/netcdf

#YEARSTART: starting year to run anomaly fields (YEAR - 1900)
YEARSTART="116"
YEARSTARTFULL="2016"
#YEAREND: ending year to run anomaly fields (YEAR - 1900)
YEAREND="116"
YEARENDFULL="2016"

#SEAS_START: starting season (1-4) of first year for anomaly run
SEAS_START="1"
#SEAS_END: ending season (1-4) of last year for anomaly run
SEAS_END="4"

#DEP1: starting depth level for analysis (1=surface)
DEP1="1"
#DEP2: ending depth level for analysis (16=700m depth)
DEP2="16"

#subset.sheet: subsetting instructions for WOD system
#empty for OHC.
cp "$INFOFILEDIR"/subset.sheet_empty "$WORKDIR"/subset.sheet

#maskchoice.t : WOD quality flags for ocean profile data
cp "$INFOFILEDIR"/maskchoice.t "$WORKDIR"/maskchoice.d

#probefile.allt_ohc: data set information/selections for WOD system
cp "$INFOFILEDIR"/probefile.allt_ohc "$WORKDIR"/probefile.d

#devfile_anom.3month: instructions for run of finalsd.exe
cp "$INFOFILEDIR"/devfile_anom.3month "$WORKDIR"/devfile.d 
#loop through each requested year
for (( YEAR = "$YEARSTART"; YEAR <= "$YEAREND"; YEAR++))
 do

#if any but first year start in first season (1)
#for first year, use user input start season
  SEAS1="1"
  if [ "$YEAR" -eq "$YEARSTART" ]
   then
    SEAS1="$SEAS_START"
   fi

#if any but last year end in last season (4)
#for last year, use user input end season
  SEAS2="4"
  if [ "$YEAR" -eq "$YEAREND" ]
   then
    SEAS2="$SEAS_END"
   fi

# run loop for each designated season for each year
  for (( SEAS = "$SEAS1"; SEAS <= "$SEAS2"; SEAS++))
   do

#enter year, season into short information file for analysis.exe
    cat>"$WORKDIR"/dum2<<END
$YEAR $SEAS
END

#enter directory path to statistical mean files (line 1)
# and analyzed data files (line 2).  "1.00" will be added
# as a subdirectory for both directory paths (one degree grid size).
# "mean", "num", "sd", will be added as another additional subdirectory
# for first directory paht, for statistical mean, number of
# observations, and standard deviation.
    cat>"$WORKDIR"/statpath.d<<END
$CLIMATOLOGYDIR
$CLIMATOLOGYDIR
END

# compute mean, number of observations, standard deviation of
# temperature anomalies from the surface (level 1) to 3000 m
# depth (level 28).  Depths below 700 m (level 16) are calculated
# as part of the full profile quality check
# output files will be in subdirectory listed in statpath.d,of
# in further subdirectories "mean" (statistical mean), "num"
# number of observations), and "sd" (standard deviation).  Files
# are of the form "t0y[Y1][Y2][M(M)]-[N(N)]00AM" where
#Y1 is start year (-1900; for years 2000 to 2009, Y1=
# A[Y], where Y=0-9, for 2010-2019, Y1=B[Y] where Y=0-9,
# For 1900, Y1=00. Y2 is ending year, same form as Y1.
#M(M) is one or two digit starting month (January=1, October=10).
#N(N) is one or two digit ending month.
    "$EXECDIR"/finalsd.exe

# transfer year, season to short information file for analysis.exe
   cp "$WORKDIR"/dum2 "$WORKDIR"/year.counter

# run loop through each depth level
   for (( DEPTH = "$DEP1"; DEPTH <= "$DEP2"; DEPTH++ ))
    do
     
#enter depth level in short information file
cat>"$WORKDIR"/dum<<END
$DEPTH
END

#enter directory path to statistical mean files (line 1)
# and analyzed data files (line 2).  "1.00" will be added
# as a subdirectory for both directory paths (one degree grid size).
# "mean" will be added as another additional subdirectory
# for first directory path for statistical mean.
    cat>"$WORKDIR"/statpath.d<<END
$CLIMATOLOGYDIR
$CLIMATOLOGYDIR
END
#anlyfile_3month_anom.regulart is the information file for
# analysis.exe for normal objective analysis
   cp "$INFOFILEDIR"/anlyfile_3month_anom.regulart "$WORKDIR"/anlyfile.d

# compute objectively analyzed grided field of 
# temperature anomalies from the surface (level 1) to 700 m
# depth (level 16).
# output files will be in subdirectory listed in statpath.d,
# under subdirectory 1.00.  Files are of the form
# are of the form "t0y[Y1][Y2][M(M)]-[N(N)]00AM" where
#Y1 is start year (-1900; for years 2000 to 2009, Y1=
# A[Y], where Y=0-9, for 2010-2019, Y1=B[Y] where Y=0-9,
# For 1900, Y1=00. Y2 is ending year, same form as Y1.
#) is one or two digit starting month (January=1, October=10).
#N(N) is one or two digit ending month.
# run objective analysis on year/season/depth level as designated
# input files are the results from finalsd.exe above.
# Along with objectively analyed field files, a file of the
# form "t0y[Y1][Y2][M(M)]-[N(N)]00AM.points" is output,
# containing the number of gridboxes with data within the
# radius of influence of each gridbox.
# 
     "$EXECDIR"/analysis.exe

# set statpath.d for error statistics output, same structure
# as above, except output error statistics add a "stats"
# directory before "1.00" subdirectory
    cat>"$WORKDIR"/statpath.d<<END
$CLIMATOLOGYDIR
$CLIMATOLOGYSTATSDIR
END

#anlyfile_3month_anom.errort is the information file for
# analysis.exe for error statistics for objective analysis
   cp "$INFOFILEDIR"/anlyfile_3month_anom.errort "$WORKDIR"/anlyfile.d

# run objective analysis on year/season/depth level as designated
# output files of the form "t0y[Y1][Y2][M(M)]-[N(N)]00AM.s"
# for standard error for the objective analysis procedure.
     "$EXECDIR"/analysis.exe

    done

  done

done

#layer_field_10ann_climatology.inf is the information file
#for layer_field_10ann_climatology.exe.  Note that the
# given file is set up for year 2016.  Any change must
# be made directly in the file
cp "$INFOFILEDIR"/layer_field_10ann_climatology.inf "$WORKDIR"/.

# calculate OHC for given layer (in this case, levels 1-16,
# surface to 700m.  Output files are in subdirectory OHC
# and of the form
# "h18-[D(D)(D)(D)]-[E(E)(E)(E)]-[Y1][Y2][M(M)]-[N(N)].1"
# where D=start depth, E=end depth, lowest possible value
#is "0", highest is "3000" (in meters).  Y1=start year,
# year -1900; for years 2000 to 2009, Y1= A[Y], where Y=0-9,
# for 2010-2019, Y1=B[Y] where Y=0-9,
# For 1900, Y1=00. Y2 is ending year, same form as Y1.
#M(M) is one or two digit starting month (January=1, October=10).
#N(N) is one or two digit ending month.

 "$EXECDIR"/layer_field_10ann_climatology.exe

#layer_fieldSE_K05.inf is the information file
#for layer_fieldSE_K05.exe.  Note that the
# given file is set up for year 2016.  Any change must
# be made directly in the file
cp "$INFOFILEDIR"/layer_fieldSE_K05.inf "$WORKDIR"/.

# calculate OHC standard error for given layer (in this case, levels 1-16,
# surface to 700m.  Output files are in subdirectory OHC
# and of the form
# "h18-[D(D)(D)(D)]-[E(E)(E)(E)]-[Y1][Y2][M(M)]-[N(N)].se"
# see comments for layer_field_10ann_climatology.exe for
# file name form explanation
 "$EXECDIR"/layer_fieldSE_K05.exe

#basin_layer10ann_climatology.inf is the information file
# for basin_layer10ann_climatology.exe.  Note that
# given file is set up for year 2016.  Any change must
# be made directly in the file.  There are information files for
# global (WO), Northern Hemisphere (NH) and Southern Hemisphere (SH)
cp "$INFOFILEDIR"/basin_layer10ann_climatology_WO.inf "$WORKDIR"/basin_layer10ann_climatology.inf

# OCL_basin_[BB].dat are basin definition files for
# BB=WO - world, BB=AO - Atlantic Ocean
# BB=PO - Pacific Ocean, BB=IO - Indian Ocean
cp "$INFOFILEDIR"/OCL_basin_WO.dat "$WORKDIR"/.
cp "$INFOFILEDIR"/OCL_basin_AO.dat "$WORKDIR"/.
cp "$INFOFILEDIR"/OCL_basin_PO.dat "$WORKDIR"/.
cp "$INFOFILEDIR"/OCL_basin_IO.dat "$WORKDIR"/.

# calculate OHC integrated over requested basins.
# input files from layer_field_10ann_climatology.exe and
# and layer_fieldSE_K05.exe output.  
# subdirectory OHC, with form 
# "3mon-h22-[B][D(D)(D)(D)]-[E(E)(E)(E)]m[SL][H][NL][I].dat"
# where D=start depth, E=end depth, lowest possible value
# is "0", highest is "3000" (in meters).  Y1=start year,
"$EXECDIR"/basin_layer10ann_climatology.exe

cp "$INFOFILEDIR"/basin_layer10ann_climatology_NH.inf "$WORKDIR"/basin_layer10ann_climatology.inf
"$EXECDIR"/basin_layer10ann_climatology.exe

cp "$INFOFILEDIR"/basin_layer10ann_climatology_SH.inf "$WORKDIR"/basin_layer10ann_climatology.inf
"$EXECDIR"/basin_layer10ann_climatology.exe

# convert temperature anomaly and OHC files from binary to
# Climate-Forecast (CF) compliant netCDF files

cp "$INFOFILEDIR"/global_attributes_anomaly.d "$WORKDIR"/.
cp "$INFOFILEDIR"/woa_field_definitionsnc.dat "$WORKDIR"/.
cp "$INFOFILEDIR"/timeseries_area_info.txt "$WORKDIR"/.
 "$SHELLDIR"/woatoncfile_tempanom_seas.shell "$MAINDIR" "$WORKDIR" "$YEARSTARTFULL" "$SEAS_START" "$YEARENDFULL" "$SEAS_END" "$NETCDFDIR"
 "$SHELLDIR"/woatoncfile_heatanom_seas.shell "$MAINDIR" "$WORKDIR" "$YEARSTARTFULL" "$SEAS_START" "$YEARENDFULL" "$SEAS_END" "$NETCDFDIR"