| 1 | function parse_dir { |
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| 2 | # Syntax: export variables from directory $1 with structure var1/var2/.../varN ($2) |
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| 3 | # Each variable ${vari} is exported. |
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| 4 | local d=$1 s=$2 |
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| 5 | while :; do |
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| 6 | export ${s%%/*}=${d%%/*} |
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| 7 | s=${s#*/}; d=${d#*/} |
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| 8 | if [ "$s" = "${s#*/}" ]; then break; fi |
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| 9 | done |
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| 10 | } |
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| 11 | #================================================================================== |
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| 12 | function addc { |
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| 13 | local s |
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| 14 | s="$1"; while [ ${#s} -lt $2 ]; do s="_$s"; done ; echo "$s"; unset s |
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| 15 | } |
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| 16 | #================================================================================== |
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| 17 | function progress_bar { |
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| 18 | # $1: iteration $2: iterations number $3: length of the bar |
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| 19 | local n bar |
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| 20 | bar=`echo "scale=1 ; (100*$1)/$2" | bc` |
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| 21 | bar="`addc "$bar" 5`% [" |
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| 22 | n=`echo "scale=0 ; ($3*$1)/$2" | bc` |
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| 23 | if [ $n -ne 0 ]; then bar="$bar"`eval "printf '='%.0s {1..$n}"`; fi |
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| 24 | n=$(($3-$n)) |
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| 25 | if [ $n -ne 0 ]; then bar="$bar"`eval "printf '.'%.0s {1..$n}"`']\r'; fi |
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| 26 | echo -ne $bar; if [ $2 -eq $1 ]; then echo; fi |
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| 27 | unset n bar |
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| 28 | } |
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| 29 | #================================================================================== |
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| 30 | function extract { |
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| 31 | # Input arguments: |
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| 32 | # $1: v_in,v_ou (input/output variable names) |
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| 33 | # $2: f_in,f_ou (input/output files names) |
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| 34 | # $3: Ymin,Ymax,dY (min/max available years, years/file number) |
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| 35 | # $4: nmrg (number of additional months before and after) |
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| 36 | # |
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| 37 | # Purpose: |
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| 38 | # * Extract year $Y for variable $v_in from files $f_in containing data from |
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| 39 | # $Ymin to $Ymax, where each input file contains $dY years |
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| 40 | # * Outputs are stored in file $f_ou, and variable renamed $v_ou. |
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| 41 | # * Optionally, add before/after the 12 months the $nmrg previous/next months. |
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| 42 | # - Y=Ymin (missing Ymin-1) => $nmrg last months of year $Y used instead. |
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| 43 | # - Y=Ymax (missing Ymax+1) => $nmrg first months of year $Y used instead. |
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| 44 | # |
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| 45 | # Remark: First record of first file has to be january $Ymin. |
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| 46 | # |
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| 47 | local v_in v_ou d_in f_ou Ymin Ymax Yb Ye Y dY nbm nmrg it fin fou fm ff fp ib ie |
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| 48 | v_in="${1%%,*}"; v_ou="${1#*,}"; shift |
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| 49 | f_in="${1%%,*}"; f_ou="${1#*,}"; shift |
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| 50 | Ymin="${1%%,*}"; Ymax="${1#*,}"; dY="${Ymax#*,}"; Ymax="${Ymax%%,*}"; shift |
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| 51 | Y=$1; shift; if [ $# -eq 1 ]; then nmrg=$1; else nmrg=0; fi |
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| 52 | if [ $dY -eq $((Ymax-Ymin+1)) ]; then dY=0; fi #--- SINGLE FILE |
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| 53 | ff=actu_${v_in}_${Y}.nc; fm=""; fp="" |
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| 54 | #--- INITIAL AND FINAL YEAR OF FILE CONTAINING CURRENT YEAR |
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| 55 | if [ $dY -eq 0 ]; then |
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| 56 | Yb=$Ymin; Ye=$Ymax |
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| 57 | else |
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| 58 | Yb=$((dY*(Y/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye)) |
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| 59 | fi |
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| 60 | nbm=$((12*(Ye-Yb+1)-1)) #--- MONTHS NUMBER OF CURRENT FILE |
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| 61 | it=$((12*(Y-Yb))) #--- JANUARY INDEX IN CURRENT FILE |
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| 62 | fin=`var=$v_in; Yb=$Yb; Ye=$Ye; eval echo $f_in` #--- CURRENT FILE NAME |
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| 63 | fou=`var=$v_ou; Y=$Y; eval echo $f_ou` #--- OUTPUT FILE NAME |
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| 64 | ib=$(($it<=nmrg?0:$((it-nmrg)))) #--- INDEX OF FIRST USED MONTH |
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| 65 | ie=$(($((it+11+mrg))>=$nbm?$nbm:$((it+11+nmrg)))) #--- INDEX OF LAST USED MONTHF |
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| 66 | rm -f $ff ; rm -f $ff ; ncks -d time,$ib,$ie $fin $ff |
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| 67 | #--- MISSING PREVIOUS YEAR LAST MONTHS => CURRENT YEAR INSTEAD |
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| 68 | if [ $it -lt $nmrg ]; then fm="prev_${v_in}_${Y}.nc"; rm -f $fm |
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| 69 | if [[ $Y -eq $Ymin || $dY -eq 0 ]]; then ncks -d time,$((it-nmrg+12)),11 $fin $fm |
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| 70 | else Yb=$((dY*((Y-1)/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye)) |
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| 71 | 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 |
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| 72 | fi |
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| 73 | fi |
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| 74 | #--- MISSING FOLLOWING YEAR FIRST MONTHS => CURRENT YEAR INSTEAD |
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| 75 | if [ $((it+nmrg+11)) -gt $nbm ]; then fp="next_${v_in}_${Y}.nc"; rm -f $fp |
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| 76 | if [[ $Y -eq $Ymax || $dY -eq 0 ]]; then ncks -d time,$((nbm-11)),$((it+nmrg-1)) $fin $fp |
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| 77 | else Yb=$((dY*((Y+1)/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye)) |
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| 78 | ncks -d time,0,$((nmrg-1)) `var=$v_in; Yb=$Yb; Ye=$Ye; eval echo $f_in` $fp |
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| 79 | fi |
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| 80 | fi |
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| 81 | if [ ! -d ${fou%/*} ]; then mkdir -p ${fou%/*}; fi |
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| 82 | if [[ "$fm" != "" || "$fp" != "" ]]; then |
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| 83 | rm -f $fou ; ncrcat $fm $ff $fp $fou ; rm -f $fm $ff $fp |
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| 84 | else |
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| 85 | mv $ff $fou |
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| 86 | fi |
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| 87 | if [ "$v_in" != "$v_ou" ]; then |
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| 88 | ncrename -v $v_in,$v_ou $fou > /dev/null 2>&1 |
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| 89 | fi |
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| 90 | } |
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| 91 | #================================================================================== |
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| 92 | function make_clim { |
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| 93 | # Input arguments: |
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| 94 | # $1: variable name $2: input files name |
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| 95 | # $3: beg-end years $4: index for january (optional, starting from 0) |
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| 96 | # |
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| 97 | # Purpose: |
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| 98 | # Create a 12 months climatology for a variable using 1-year monthly files. |
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| 99 | # |
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| 100 | # Remark: |
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| 101 | # Files with additional months are usable if the index for january is given (default: 0) |
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| 102 | # |
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| 103 | local f_ou f0 Yb Ye ib ie M MM |
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| 104 | Yb="${3%%-*}"; Ye="${3#*-}" |
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| 105 | if [ $# -eq 4 ]; then ib=$4; else ib=0; fi; ie=$((ib+11)) #=== INDEX $ib FOR JANUARY |
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| 106 | for M in $(eval echo {$ib..$ie}); do |
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| 107 | MM=$((M+1-ib)); if [ $MM -le 9 ]; then MM=0$MM; fi |
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| 108 | for Y in `eval echo {${Yb}..${Ye}}`; do |
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| 109 | f_ou=$(var=$1; Y=$Y; eval echo $2) |
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| 110 | rm -f ${1}_$Y$MM.nc ; ncks -d time,$M $(var=$1; Y=$Y; eval echo $f_ou) ${1}_$Y$MM.nc |
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| 111 | done |
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| 112 | rm -f ${1}_$MM.nc ; ncra ${1}_????$MM.nc ${1}_$MM.nc ; rm -f ${1}_????$MM.nc |
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| 113 | progress_bar $((M+1-ib)) $((ie-ib+1)) 50 |
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| 114 | done |
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| 115 | f_ou=$(var=$1; Y=${Yb}_${Ye}_clim; eval echo $2) |
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| 116 | rm -f $f_ou ; ncrcat ${1}_??.nc $f_ou ; rm -f ${1}_??.nc |
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| 117 | f0=`var=$1; Y='YYYY'; eval echo $2`; f0=$(var=$1; Y='YYYY'; eval echo $f0); f0=${f0##*/} |
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| 118 | ncatted -a comment,global,a,c,"\nClimatology from $Yb to $Ye using file(s) $f0" $f_ou |
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| 119 | echo ">> Done for variable $1." |
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| 120 | } |
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| 121 | #================================================================================== |
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| 122 | function str2ascii() { |
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| 123 | LC_CTYPE=C printf '%d' "'$1" |
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| 124 | } |
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| 125 | |
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| 126 | #================================================================================== |
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| 127 | function deblank { |
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| 128 | #--- REMOVE UNEXPECTED CHARACTERS (IN PARTICULAR THOSE WEIRD ASCII(0) CHARS) |
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| 129 | local a |
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| 130 | a=$1; while [ `str2ascii ${a:0:1}` -lt 32 ]; do a=${a:1:${#a}}; done; echo $a |
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| 131 | } |
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| 132 | |
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| 133 | #================================================================================== |
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| 134 | function dim_nam { |
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| 135 | #--- GET DIMENSION $2 (X/Y/Z/T) NAME FOR FILE $1 |
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| 136 | #--- SPECIAL CASE: RETURN 'Seasons' IF "$2" = "S". |
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| 137 | local a v Units |
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| 138 | case $2 in |
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| 139 | X) Units='degrees_east degree_east degree_e degrees_e "degrees east" "degree east" degreee degreese' ;; |
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| 140 | Y) Units='degrees_north degree_north degree_n degrees_n "degrees north" "degree north" degreen degreesn' ;; |
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| 141 | Z) Units='pa pascal pascals hpa millibar millibars mbar mbars mb bar bars atm atms atmosphere atmospheres' ;; |
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| 142 | T) Units=' since' ;; |
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| 143 | S) echo Seasons; return 0 ;; |
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| 144 | *) echo "error in dim_nam: unrecognized axis $2"; return 1 ;; |
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| 145 | esac |
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| 146 | for u in $Units; do |
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| 147 | case $2 in |
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| 148 | X|Y|Z) a=`ncdump -h $1 | grep -i ':units = "'"$u"'"'` ;; |
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| 149 | T) a=`ncdump -h $1 | grep -i $u | grep ':units = "'` ;; |
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| 150 | esac |
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| 151 | if [ "$a" != "" ]; then |
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| 152 | if [ "$2" = "Z" ]; then v=${a%%:*}; v=`deblank $v` |
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| 153 | if [ "`ncdump -h $1 | grep -i "$v($v)"`" != "" ]; then break; fi |
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| 154 | else break |
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| 155 | fi |
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| 156 | fi |
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| 157 | done |
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| 158 | if [[ "$a" = "" && "$2" = "Z" ]]; then a=`ncdump -h $1 | grep -i ':positive = "'`; fi |
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| 159 | if [ "$a" = "" ]; then echo "error in dim_nam: unable to recognize axis $2"; return 1; fi |
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| 160 | echo ${a%%:*}; return 0 |
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| 161 | } |
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| 162 | |
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| 163 | #================================================================================== |
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| 164 | function test_var { |
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| 165 | # Input arguments: |
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| 166 | # $1: file name $2: variable name |
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| 167 | ncdump -h $1 | grep "double $2" > /dev/null; if [ $? -eq 0 ]; then return 0; fi |
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| 168 | ncdump -h $1 | grep "float $2" > /dev/null; return $? |
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| 169 | } |
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| 170 | #================================================================================== |
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| 171 | function get_boundsvar { |
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| 172 | # Input arguments: |
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| 173 | # $1: file name $2: variable name |
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| 174 | local a=$(ncdump -h $1 | grep -P "\t$2:bounds") |
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| 175 | if [ "$a" != "${a#*\"}" ]; then a=${a#*\"}; echo ${a%\"*}; else echo ""; fi |
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| 176 | } |
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| 177 | #================================================================================== |
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| 178 | function rename_bounds { |
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| 179 | # Input arguments: |
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| 180 | # $1: file name $2: variable name $3: new variable name |
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| 181 | # returns: $old_var,$old_boundvar,$new_boundvar |
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| 182 | local vin=$(get_boundsvar $1 $2) beg end vou |
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| 183 | if [ "$vin" = "" ]; then return 1; fi |
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| 184 | beg=${vin##*$2}; if [ "$beg" = "$vin" ]; then beg=$vin; fi |
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| 185 | beg=${vin%%$2*}; if [ "$end" = "$vin" ]; then end=$vin; fi |
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| 186 | if [[ "$beg" = "" && "$end" = "" ]]; then return 1; fi |
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| 187 | vou=$beg$3$end |
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| 188 | echo "$2,$vin,$vou" |
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| 189 | } |
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| 190 | #================================================================================== |
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| 191 | function rename_dims { |
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| 192 | # Input arguments: |
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| 193 | # $1: file name $2...: <axis>:<target_name> (axis=X,Y,Z or T) |
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| 194 | # |
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| 195 | # Purpose: |
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| 196 | # Rename dimensions, dimensional variables. |
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| 197 | # In case of boundary grid variables with bounds_<variable> names are available, |
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| 198 | # they are renamed together with the corresponding "bounds" attributes. |
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| 199 | local vio f=$1 att="" ren="" nam_in nam_ou |
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| 200 | shift |
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| 201 | while [ $# -ge 1 ]; do |
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| 202 | nam_ou=${1##*:}; nam_in=$(dim_nam $f ${1%:*}); shift |
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| 203 | if [ "$nam_in" != "$nam_ou" ]; then |
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| 204 | ren="$ren -d $nam_in,$nam_ou -v $nam_in,$nam_ou" |
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| 205 | #--- CHECK WETHER "bounds" ATTRIBUTE IS THERE |
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| 206 | vio="$(rename_bounds $f $nam_in $nam_ou)" |
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| 207 | if [ "$vio" != "" ]; then |
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| 208 | att="$att -a bounds,$nam_ou,m,c,${vio##*,}"; ren="$ren -v ${vio#*,}" |
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| 209 | fi |
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| 210 | fi |
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| 211 | done |
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| 212 | if [ "$ren" != "" ]; then ncrename $ren $f 2>&1 > /dev/null ; fi |
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| 213 | if [ "$att" != "" ]; then ncatted $att $f 2>&1 > /dev/null ; fi |
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| 214 | } |
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| 215 | #================================================================================== |
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| 216 | function zonal_mean { |
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| 217 | # Input arguments: |
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| 218 | # $1: input file $2: output file |
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| 219 | local tmp=tmp.$$.nc |
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| 220 | ncwa -a longitude $1 $tmp ; mv $tmp $2 #--- Zonal mean |
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| 221 | ncks -O -x -v longitude $2 $tmp ; mv $tmp $2 #--- Remove longitude |
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| 222 | v="bounds_longitude"; test_var $2 $v #--- Remove bounds vars |
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| 223 | if [ $? -eq 0 ]; then ncks -O -x -v $v $2 $tmp ; mv $tmp $2; fi |
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| 224 | } |
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| 225 | #================================================================================== |
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| 226 | function get_date { |
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| 227 | # $1: varname $2: datatype $3: dirin $4:...: files_in |
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| 228 | # Assumes the following filename structure: *_${Yb}*-${Ye}*.* (Yb/e: 4 digits) |
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| 229 | local v_in dtyp d_in f_in ixf Yb Ye St a f first dates |
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| 230 | v_in=$1; shift; dtyp=$1; shift; d_in=$1; shift |
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| 231 | for f_in in $@; do parse_dir ${f_in} $DIRSTRUCT; Yb=1000000; Ye=0; first='t' |
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| 232 | #=== /!\ ERROR IN THE STORAGE TREE ON CICLAD FOR PCMDI-AMIP-1-1-0 |
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| 233 | if [ $dataset = "PCMDI-AMIP-1-1-0" ]; then grid='gs1x1'; fi |
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| 234 | for f in $(var=$v_in; Yb=????; Ye=????; datatype=$dtyp; eval echo $d_in/$f_in); do |
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| 235 | a=${f##*_}; if [ ${a::4} -le $Yb ]; then Yb=${a::4}; fi |
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| 236 | a=${a##*-}; if [ ${a::4} -ge $Ye ]; then Ye=${a::4}; fi |
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| 237 | if [ $first = 't' ]; then St=$((Ye-Yb+1)); first='f'; fi |
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| 238 | done |
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| 239 | if [ $f_in = $1 ]; then dates="$Yb-$Ye-$St"; else dates="$dates $Yb-$Ye-$St"; fi |
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| 240 | done |
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| 241 | echo $dates |
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| 242 | } |
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| 243 | #================================================================================== |
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| 244 | function dim_len { |
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| 245 | local n |
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| 246 | if [ "$2" = "T" ]; then |
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| 247 | n=$(ncdump -h $1 | grep 'UNLIMITED'); n=${n#*// (}; echo ${n% currently*} |
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| 248 | else |
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| 249 | n=$(ncdump -h $1 | grep $2' = '); n=${n#* = }; echo ${n% ;*} |
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| 250 | fi |
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| 251 | } |
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| 252 | #================================================================================== |
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| 253 | function get_grid { |
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| 254 | # $1: filename $2: varname |
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| 255 | X=$(dim_nam $1 X); if [ $? -ne 0 ]; then X=""; else lX=$(dim_len $1 $X); fi |
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| 256 | Y=$(dim_nam $1 Y); if [ $? -ne 0 ]; then Y=""; else lY=$(dim_len $1 $Y); fi |
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| 257 | Z=$(dim_nam $1 Z); if [ $? -ne 0 ]; then Z=""; else lZ=$(dim_len $1 $Z); fi |
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| 258 | T=$(dim_nam $1 T); if [ $? -ne 0 ]; then T=""; else lT=$(dim_len $1 T); fi |
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| 259 | t=$(ncdump -h $1 | grep "double $2") |
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| 260 | if [ $? -ne 0 ]; then t=$(ncdump -h $1 | grep "float $2"); fi |
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| 261 | t=${t##*$2(}; t=${t%)*}; g=""; r="" |
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| 262 | while :; do s=${t##*, }; t=${t%,*} |
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| 263 | case $s in |
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| 264 | $X) g=${g}X; r=${r}x$lX ;; |
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| 265 | $Y) g=${g}Y; r=${r}x$lY ;; |
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| 266 | $Z) g=${g}Z; r=${r}x$lZ ;; |
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| 267 | $T) g=${g}T; r=${r}x$lT ;; |
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| 268 | esac |
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| 269 | if [ "$s" = "$t" ]; then break; fi |
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| 270 | done |
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| 271 | echo $g=${r:1:${#r}} |
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| 272 | } |
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| 273 | #================================================================================== |
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| 274 | |
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