function parse_dir {
# Syntax: parse_dir
[]
# $1: directory to parse
# $2: directory structure
# [$3...]: := patches
# Purpose: parse directory with structure and export all variables.
# If $dataset = $dset, the value of obtain with parsing is replaced with .
local d s
d=$1; shift; s=$1; shift
while :; do
$(eval echo "export ${s%%/*}=${d%%/*}")
s=${s#*/}; d=${d#*/}
if [ "$s" = "${s#*/}" ]; then break; fi
done
while [ $# -ge 1 ]; do if [ $dataset = ${1%:*} ]; then eval export ${1#*:}; fi; shift; done
unset d s
}
#==================================================================================
function replace_1 {
# $1: string $2: =
local out=$1
while [ "${out%${2%=*}*}" != "$out" ]; do out=${out%${2%=*}*}"${2#*=}"${out##*${2#=*}*}; done
echo $out; unset out; return 0
}
#==================================================================================
function replace {
# same as "replace_1", but with several = arguments.
local out=$1; shift
while [ $# -ne 0 ]; do out=$(replace_1 $out "$1"); shift; done
echo $out; unset out; return 0
}
#==================================================================================
function addc {
local s="$1"; while [ ${#s} -lt $2 ]; do s="_$s"; done ; echo "$s"; unset s
}
#==================================================================================
function progress_bar {
# $1: iteration $2: iterations number $3: length of the bar
local n bar
bar=`echo "scale=1 ; (100*$1)/$2" | bc`
bar="`addc "$bar" 5`% ["
n=`echo "scale=0 ; ($3*$1)/$2" | bc`
if [ $n -ne 0 ]; then bar="$bar"`eval "printf '='%.0s {1..$n}"`; fi
n=$(($3-$n))
if [ $n -ne 0 ]; then bar="$bar"`eval "printf '.'%.0s {1..$n}"`']\r'; fi
echo -ne $bar; if [ $2 -eq $1 ]; then echo; fi
unset n bar
}
#==================================================================================
function extract {
# Input arguments:
# $1: v_in,v_ou (input/output variable names)
# $2: f_in,f_ou (input/output files names)
# $3: Ymin,Ymax,dY (min/max available years, years/file number)
# $4: nmrg (number of additional months before and after)
#
# Purpose:
# * Extract year $Y for variable $v_in from files $f_in containing data from
# $Ymin to $Ymax, where each input file contains $dY years
# * Outputs are stored in file $f_ou, and variable renamed $v_ou.
# * Optionally, add before/after the 12 months the $nmrg previous/next months.
# - Y=Ymin (missing Ymin-1) => $nmrg last months of year $Y used instead.
# - Y=Ymax (missing Ymax+1) => $nmrg first months of year $Y used instead.
#
# Remark: First record of first file has to be january $Ymin.
#
local v_in v_ou d_in f_ou Ymin Ymax Yb Ye Y dY nbm nmrg it fin fou fm ff fp ib ie
v_in="${1%%,*}"; v_ou="${1#*,}"; shift
f_in="${1%%,*}"; f_ou="${1#*,}"; shift
Ymin="${1%%,*}"; Ymax="${1#*,}"; dY="${Ymax#*,}"; Ymax="${Ymax%%,*}"; shift
Y=$1; shift; if [ $# -eq 1 ]; then nmrg=$1; else nmrg=0; fi
if [ $dY -eq $((Ymax-Ymin+1)) ]; then dY=0; fi #--- SINGLE FILE
ff=actu_${v_in}_${Y}.nc; fm=""; fp=""
#--- INITIAL AND FINAL YEAR OF FILE CONTAINING CURRENT YEAR
if [ $dY -eq 0 ]; then
Yb=$Ymin; Ye=$Ymax
else
Yb=$((dY*(Y/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye))
fi
nbm=$((12*(Ye-Yb+1)-1)) #--- MONTHS NUMBER OF CURRENT FILE
it=$((12*(Y-Yb))) #--- JANUARY INDEX IN CURRENT FILE
fin=`var=$v_in; Yb=$Yb; Ye=$Ye; eval echo $f_in` #--- CURRENT FILE NAME
fou=`var=$v_ou; Y=$Y; eval echo $f_ou` #--- OUTPUT FILE NAME
ib=$(($it<=nmrg?0:$((it-nmrg)))) #--- INDEX OF FIRST USED MONTH
ie=$(($((it+11+mrg))>=$nbm?$nbm:$((it+11+nmrg)))) #--- INDEX OF LAST USED MONTHF
rm -f $ff ; rm -f $ff ; ncks -d time,$ib,$ie $fin $ff
#--- MISSING PREVIOUS YEAR LAST MONTHS => CURRENT YEAR INSTEAD
if [ $it -lt $nmrg ]; then fm="prev_${v_in}_${Y}.nc"; rm -f $fm
if [[ $Y -eq $Ymin || $dY -eq 0 ]]; then ncks -d time,$((it-nmrg+12)),11 $fin $fm
else Yb=$((dY*((Y-1)/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye))
ncks -d time,$((12*(Ye-Yb+1)-nmrg+it)),$((12*(Ye-Yb+1)-1)) `var=$v_in; Yb=$Yb; Ye=$Ye; eval echo $f_in` $fm
fi
fi
#--- MISSING FOLLOWING YEAR FIRST MONTHS => CURRENT YEAR INSTEAD
if [ $((it+nmrg+11)) -gt $nbm ]; then fp="next_${v_in}_${Y}.nc"; rm -f $fp
if [[ $Y -eq $Ymax || $dY -eq 0 ]]; then ncks -d time,$((nbm-11)),$((it+nmrg-1)) $fin $fp
else Yb=$((dY*((Y+1)/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye))
ncks -d time,0,$((nmrg-1)) `var=$v_in; Yb=$Yb; Ye=$Ye; eval echo $f_in` $fp
fi
fi
if [ ! -d ${fou%/*} ]; then mkdir -p ${fou%/*}; fi
if [[ "$fm" != "" || "$fp" != "" ]]; then
rm -f $fou ; ncrcat $fm $ff $fp $fou ; rm -f $fm $ff $fp
else
mv $ff $fou
fi
if [ "$v_in" != "$v_ou" ]; then
ncrename -v $v_in,$v_ou $fou > /dev/null 2>&1
fi
}
#==================================================================================
function make_clim {
# Input arguments:
# $1: variable name $2: input files name
# $3: beg-end years $4: index for january (optional, starting from 0)
#
# Purpose:
# Create a 12 months climatology for a variable using 1-year monthly files.
#
# Remark:
# Files with additional months are usable if the index for january is given (default: 0)
#
local f_ou f0 Yb Ye ib ie M MM
Yb="${3%%-*}"; Ye="${3#*-}"
if [ $# -eq 4 ]; then ib=$4; else ib=0; fi; ie=$((ib+11)) #=== INDEX $ib FOR JANUARY
for M in $(eval echo {$ib..$ie}); do
MM=$((M+1-ib)); if [ $MM -le 9 ]; then MM=0$MM; fi
for Y in `eval echo {${Yb}..${Ye}}`; do
f_ou=$(var=$1; Y=$Y; eval echo $2)
rm -f ${1}_$Y$MM.nc ; ncks -d time,$M $(var=$1; Y=$Y; eval echo $f_ou) ${1}_$Y$MM.nc
done
rm -f ${1}_$MM.nc ; ncra ${1}_????$MM.nc ${1}_$MM.nc ; rm -f ${1}_????$MM.nc
progress_bar $((M+1-ib)) $((ie-ib+1)) 50
done
f_ou=$(var=$1; Y=${Yb}_${Ye}_clim; eval echo $2)
if [ ! -p ${f_ou%/*} ]; then mkdir -p ${f_ou%/*}; fi
rm -f $f_ou ; ncrcat ${1}_??.nc $f_ou ; rm -f ${1}_??.nc
f0=`var=$1; Y='YYYY'; eval echo $2`; f0=$(var=$1; Y='YYYY'; eval echo $f0); f0=${f0##*/}
ncatted -a comment,global,a,c,"\nClimatology from $Yb to $Ye using file(s) $f0" $f_ou
}
#==================================================================================
function str2ascii() {
LC_CTYPE=C printf '%d' "'$1"
}
#==================================================================================
function deblank {
#--- REMOVE UNEXPECTED CHARACTERS (IN PARTICULAR THOSE WEIRD ASCII(0) CHARS)
local a
a=$1; while [ `str2ascii ${a:0:1}` -lt 32 ]; do a=${a:1:${#a}}; done; echo $a
}
#==================================================================================
function dim_nam {
#--- GET DIMENSION $2 (X/Y/Z/T) NAME FOR FILE $1
#--- SPECIAL CASE: RETURN 'Seasons' IF "$2" = "S".
local a v Units
case $2 in
X) Units='degrees_east degree_east degree_e degrees_e "degrees east" "degree east" degreee degreese' ;;
Y) Units='degrees_north degree_north degree_n degrees_n "degrees north" "degree north" degreen degreesn' ;;
Z) Units='pa pascal pascals hpa millibar millibars mbar mbars mb bar bars atm atms atmosphere atmospheres' ;;
T) Units=' since' ;;
S) echo Seasons; return 0 ;;
*) echo "error in dim_nam: unrecognized axis $2"; return 1 ;;
esac
for u in $Units; do
case $2 in
X|Y|Z) a=`ncdump -h $1 | grep -i ':units = "'"$u"'"'` ;;
T) a=`ncdump -h $1 | grep -i $u | grep ':units = "'` ;;
esac
if [ "$a" != "" ]; then
if [ "$2" = "Z" ]; then v=${a%%:*}; v=`deblank $v`
if [ "`ncdump -h $1 | grep -i "$v($v)"`" != "" ]; then break; fi
else break
fi
fi
done
if [[ "$a" = "" && "$2" = "Z" ]]; then a=`ncdump -h $1 | grep -i ':positive = "'`; fi
if [ "$a" = "" ]; then echo "error in dim_nam: unable to recognize axis $2"; return 1; fi
echo ${a%%:*}; return 0
}
#==================================================================================
function test_var {
# Input arguments:
# $1: file name $2: variable name
ncdump -h $1 | grep "double $2" > /dev/null; if [ $? -eq 0 ]; then return 0; fi
ncdump -h $1 | grep "float $2" > /dev/null; return $?
}
#==================================================================================
function get_boundsvar {
# Input arguments:
# $1: file name $2: variable name
local a=$(ncdump -h $1 | grep -P "\t$2:bounds")
if [ "$a" != "${a#*\"}" ]; then a=${a#*\"}; echo ${a%\"*}; else echo ""; fi
}
#==================================================================================
function rename_bounds {
# Input arguments:
# $1: file name $2: variable name $3: new variable name
# returns: $old_var,$old_boundvar,$new_boundvar
local vin=$(get_boundsvar $1 $2) beg end vou
if [ "$vin" = "" ]; then return 1; fi
beg=${vin##*$2}; if [ "$beg" = "$vin" ]; then beg=$vin; fi
beg=${vin%%$2*}; if [ "$end" = "$vin" ]; then end=$vin; fi
if [[ "$beg" = "" && "$end" = "" ]]; then return 1; fi
vou=$beg$3$end
echo "$2,$vin,$vou"
}
#==================================================================================
function rename_dims {
# Input arguments:
# $1: file name $2...: : (axis=X,Y,Z or T)
#
# Purpose:
# Rename dimensions, dimensional variables.
# In case of boundary grid variables with bounds_ names are available,
# they are renamed together with the corresponding "bounds" attributes.
local vio f=$1 att="" ren="" nam_in nam_ou
shift
while [ $# -ge 1 ]; do
nam_ou=${1##*:}; nam_in=$(dim_nam $f ${1%:*}); shift
if [ "$nam_in" != "$nam_ou" ]; then
ren="$ren -d $nam_in,$nam_ou -v $nam_in,$nam_ou"
#--- CHECK WETHER "bounds" ATTRIBUTE IS THERE
vio="$(rename_bounds $f $nam_in $nam_ou)"
if [ "$vio" != "" ]; then
att="$att -a bounds,$nam_ou,m,c,${vio##*,}"; ren="$ren -v ${vio#*,}"
fi
fi
done
if [ "$ren" != "" ]; then ncrename $ren $f 2>&1 > /dev/null ; fi
if [ "$att" != "" ]; then ncatted $att $f 2>&1 > /dev/null ; fi
}
#==================================================================================
function zonal_mean {
# Input arguments:
# $1: input file $2: output file
local tmp=tmp.$$.nc
if [ ! -d ${2%/*} ]; then mkdir -p ${2%/*}; fi
ncwa -a longitude $1 $tmp ; mv $tmp $2 #--- Zonal mean
ncks -O -x -v longitude $2 $tmp ; mv $tmp $2 #--- Remove longitude
v="bounds_longitude"; test_var $2 $v #--- Remove bounds vars
if [ $? -eq 0 ]; then ncks -O -x -v $v $2 $tmp ; mv $tmp $2; fi
}
#==================================================================================
function get_date {
# Assumes the following filename structure: *_${Yb}*-${Ye}*.* (Yb/e: 4 digits)
# $1: varname
# $2: datatype
# $3: dirin
# $4: dirin structure patch
# $5...$N: files_in
# [$N+1...]: := to overwrite value of variables evaluated from parsing.
local v_in dtyp d_in dstr f_in Yb Ye St a f first date dates files_in=""
v_in=$1; shift; dtyp=$1; shift; d_in=$1; shift; dstr=$1; shift; f0=$1
while [ "$1" = "${1##*=}" ]; do files_in="$files_in $1"; shift; done
for f_in in $files_in; do date=$(get_date_1 $v_in $dtyp $d_in $dstr $f_in $*)
if [ $f_in = $f0 ]; then dates=$date; else dates="$dates $date"; fi
done
echo $dates
}
#==================================================================================
function get_date_1 {
# Assumes the following filename structure: *_${Yb}*-${Ye}*.* (Yb/e: 4 digits)
# $1: varname
# $2: datatype
# $3: base directory for files
# $4: dirin structure patch
# $5: file_in
# [$6...]: := to overwrite value of variables evaluated from parsing.
local v_in dtyp d_in d_str f_in Yb Ye St a f first
v_in=$1; shift; dtyp=$1; shift; d_in=$1; shift; dstr=$1; shift; f_in=$1; shift
parse_dir $f_in $dstr $*; Yb=1000000; Ye=0; first='t'
for f in $(var=$v_in; Yb=????; Ye=????; datatype=$dtyp; eval ls $d_in/$f_in); do
a=${f##*_}; if [ ${a::4} -le $Yb ]; then Yb=${a::4}; fi
a=${a##*-}; if [ ${a::4} -ge $Ye ]; then Ye=${a::4}; fi
if [ $first = 't' ]; then St=$((Ye-Yb+1)); first='f'; fi
done
echo $Yb-$Ye-$St
}
#==================================================================================
function dim_len {
local n
if [ "$2" = "T" ]; then
n=$(ncdump -h $1 | grep 'UNLIMITED'); n=${n#*// (}; echo ${n% currently*}
else
n=$(ncdump -h $1 | grep $2' = '); n=${n#* = }; echo ${n% ;*}
fi
}
#==================================================================================
function get_grid {
# $1: filename $2: varname
X=$(dim_nam $1 X); if [ $? -ne 0 ]; then X=""; else lX=$(dim_len $1 $X); fi
Y=$(dim_nam $1 Y); if [ $? -ne 0 ]; then Y=""; else lY=$(dim_len $1 $Y); fi
Z=$(dim_nam $1 Z); if [ $? -ne 0 ]; then Z=""; else lZ=$(dim_len $1 $Z); fi
T=$(dim_nam $1 T); if [ $? -ne 0 ]; then T=""; else lT=$(dim_len $1 T); fi
t=$(ncdump -h $1 | grep "double $2")
if [ $? -ne 0 ]; then t=$(ncdump -h $1 | grep "float $2"); fi
t=${t##*$2(}; t=${t%)*}; g=""; r=""
while :; do s=${t##*, }; t=${t%,*}
case $s in
$X) g=${g}X; r=${r}x$lX ;;
$Y) g=${g}Y; r=${r}x$lY ;;
$Z) g=${g}Z; r=${r}x$lZ ;;
$T) g=${g}T; r=${r}x$lT ;;
esac
if [ "$s" = "$t" ]; then break; fi
done
echo $g=${r:1:${#r}}
}
#==================================================================================