source: TOOLS/CMIP6_FORCING/OZONE/tools.bash @ 3870

Last change on this file since 3870 was 3870, checked in by cugnet, 4 years ago

Available datasets list on ciclad extended.
Genral tools contained in tools.bash are now fully independent of the main script clims_CMIP6.

File size: 13.4 KB
Line 
1function parse_dir {
2# Syntax:   parse_dir <dir> <dir_struct> [<patch1 ... patchN>]
3#       $1:     directory to parse
4#       $2:     directory structure
5#      [$3...]: <dset>:<var>=<val> patches
6# Purpose: parse directory <dir> with structure <dir_struct> and export all variables.
7# If $dataset = $dset, the value of <var> obtain with parsing is replaced with <val>.
8  local d s
9  d=$1; shift; s=$1; shift
10  while :; do
11    $(eval echo "export ${s%%/*}=${d%%/*}")
12    s=${s#*/}; d=${d#*/}
13    if [ "$s" = "${s#*/}" ]; then break; fi
14  done
15  while [ $# -ge 1 ]; do if [ $dataset = ${1%:*} ]; then eval export ${1#*:}; fi; shift; done
16  unset d s
17}
18#==================================================================================
19function replace_1 {
20  # $1: string  $2: <patch>=<replacement string>
21  local out=$1
22  while [ "${out%${2%=*}*}" != "$out" ]; do out=${out%${2%=*}*}"${2#*=}"${out##*${2#=*}*}; done
23  echo $out; unset out; return 0
24}
25#==================================================================================
26function replace {
27  # same as "replace_1", but with several <patch>=<replacement string> arguments.
28  local out=$1; shift
29  while [ $# -ne 0 ]; do out=$(replace_1 $out "$1"); shift; done
30  echo $out; unset out; return 0
31}
32#==================================================================================
33function addc {
34  local s="$1"; while [ ${#s} -lt $2 ]; do s="_$s"; done ; echo "$s"; unset s
35}
36#==================================================================================
37function progress_bar {
38# $1: iteration  $2: iterations number  $3: length of the bar
39  local n bar
40  bar=`echo "scale=1 ; (100*$1)/$2" | bc`
41  bar="`addc "$bar" 5`% ["
42  n=`echo "scale=0 ; ($3*$1)/$2" | bc`
43  if [ $n -ne 0 ]; then bar="$bar"`eval "printf '='%.0s {1..$n}"`; fi
44  n=$(($3-$n))
45  if [ $n -ne 0 ]; then bar="$bar"`eval "printf '.'%.0s {1..$n}"`']\r'; fi
46  echo -ne $bar; if [ $2 -eq $1 ]; then echo; fi
47  unset n bar
48}
49#==================================================================================
50function extract {
51# Input arguments:
52#    $1: v_in,v_ou     (input/output variable names)
53#    $2: f_in,f_ou     (input/output files names)
54#    $3: Ymin,Ymax,dY  (min/max available years, years/file number)
55#    $4: nmrg          (number of additional months before and after)
56#
57# Purpose:
58#  * Extract year $Y for variable $v_in from files $f_in containing data from
59#    $Ymin to $Ymax, where each input file contains $dY years
60#  * Outputs are stored in file $f_ou, and variable renamed $v_ou.
61#  * Optionally, add before/after the 12 months the $nmrg previous/next months.
62#    - Y=Ymin (missing Ymin-1) => $nmrg last  months of year $Y used instead.
63#    - Y=Ymax (missing Ymax+1) => $nmrg first months of year $Y used instead.
64#
65# Remark:  First record of first file has to be january $Ymin.
66#
67  local v_in v_ou d_in f_ou Ymin Ymax Yb Ye Y dY nbm nmrg it fin fou fm ff fp ib ie
68  v_in="${1%%,*}"; v_ou="${1#*,}"; shift
69  f_in="${1%%,*}"; f_ou="${1#*,}"; shift
70  Ymin="${1%%,*}"; Ymax="${1#*,}"; dY="${Ymax#*,}"; Ymax="${Ymax%%,*}"; shift
71  Y=$1; shift; if [ $# -eq 1 ]; then nmrg=$1; else nmrg=0; fi
72  if [ $dY -eq $((Ymax-Ymin+1)) ]; then dY=0; fi    #--- SINGLE FILE
73  ff=actu_${v_in}_${Y}.nc; fm=""; fp=""
74  #--- INITIAL AND FINAL YEAR OF FILE CONTAINING CURRENT YEAR
75  if [ $dY -eq 0 ]; then
76    Yb=$Ymin; Ye=$Ymax
77  else
78    Yb=$((dY*(Y/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye))
79  fi
80  nbm=$((12*(Ye-Yb+1)-1))                           #--- MONTHS NUMBER OF CURRENT FILE
81  it=$((12*(Y-Yb)))                                 #--- JANUARY INDEX IN CURRENT FILE
82  fin=`var=$v_in; Yb=$Yb; Ye=$Ye; eval echo $f_in`  #--- CURRENT FILE NAME
83  fou=`var=$v_ou; Y=$Y; eval echo $f_ou`            #--- OUTPUT FILE NAME
84  ib=$(($it<=nmrg?0:$((it-nmrg))))                  #--- INDEX OF FIRST USED MONTH
85  ie=$(($((it+11+mrg))>=$nbm?$nbm:$((it+11+nmrg)))) #--- INDEX OF LAST USED MONTHF
86  rm -f $ff ; rm -f $ff ; ncks -d time,$ib,$ie $fin $ff
87  #--- MISSING PREVIOUS YEAR LAST  MONTHS => CURRENT YEAR INSTEAD
88  if [ $it           -lt $nmrg ]; then fm="prev_${v_in}_${Y}.nc"; rm -f $fm
89    if [[ $Y -eq $Ymin || $dY -eq 0  ]]; then ncks -d time,$((it-nmrg+12)),11 $fin $fm
90    else Yb=$((dY*((Y-1)/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye))
91      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
92    fi
93  fi
94  #--- MISSING FOLLOWING YEAR FIRST MONTHS => CURRENT YEAR INSTEAD
95  if [ $((it+nmrg+11)) -gt $nbm ]; then fp="next_${v_in}_${Y}.nc"; rm -f $fp
96    if [[ $Y -eq $Ymax || $dY -eq 0  ]]; then ncks -d time,$((nbm-11)),$((it+nmrg-1)) $fin $fp
97    else Yb=$((dY*((Y+1)/dY))); Ye=$((Yb+dY-1)); Ye=$(($Ye>$Ymax?$Ymax:$Ye))
98      ncks -d time,0,$((nmrg-1)) `var=$v_in; Yb=$Yb; Ye=$Ye; eval echo $f_in` $fp
99    fi
100  fi
101  if [ ! -d ${fou%/*} ]; then mkdir -p ${fou%/*}; fi
102  if [[ "$fm" != "" || "$fp" != "" ]]; then
103    rm -f $fou ; ncrcat $fm $ff $fp $fou ; rm -f $fm $ff $fp
104  else
105    mv $ff $fou
106  fi
107  if [ "$v_in" != "$v_ou" ]; then
108    ncrename -v $v_in,$v_ou $fou > /dev/null 2>&1
109  fi
110}
111#==================================================================================
112function make_clim {
113# Input arguments:
114#    $1: variable name   $2: input files name
115#    $3: beg-end years   $4: index for january (optional, starting from 0)
116#
117# Purpose:
118#    Create a 12 months climatology for a variable using 1-year monthly files.
119#
120# Remark:
121#    Files with additional months are usable if the index for january is given (default: 0)
122#
123  local f_ou f0 Yb Ye ib ie M MM
124  Yb="${3%%-*}"; Ye="${3#*-}"
125  if [ $# -eq 4 ]; then ib=$4; else ib=0; fi; ie=$((ib+11))  #=== INDEX $ib FOR JANUARY
126  for M in $(eval echo {$ib..$ie}); do
127    MM=$((M+1-ib)); if [ $MM -le 9 ]; then MM=0$MM; fi
128    for Y in `eval echo {${Yb}..${Ye}}`; do
129      f_ou=$(var=$1; Y=$Y; eval echo $2)
130      rm -f ${1}_$Y$MM.nc ; ncks -d time,$M $(var=$1; Y=$Y; eval echo $f_ou) ${1}_$Y$MM.nc
131    done
132    rm -f ${1}_$MM.nc ; ncra ${1}_????$MM.nc ${1}_$MM.nc ; rm -f ${1}_????$MM.nc
133    progress_bar $((M+1-ib)) $((ie-ib+1)) 50
134  done
135  f_ou=$(var=$1; Y=${Yb}_${Ye}_clim; eval echo $2)
136  if [ ! -p ${f_ou%/*} ]; then mkdir -p ${f_ou%/*}; fi
137  rm -f $f_ou ; ncrcat ${1}_??.nc $f_ou ; rm -f ${1}_??.nc
138  f0=`var=$1; Y='YYYY'; eval echo $2`; f0=$(var=$1; Y='YYYY'; eval echo $f0); f0=${f0##*/}
139  ncatted -a comment,global,a,c,"\nClimatology from $Yb to $Ye using file(s) $f0" $f_ou
140}
141#==================================================================================
142function str2ascii() {
143  LC_CTYPE=C printf '%d' "'$1"
144}
145
146#==================================================================================
147function deblank {
148#--- REMOVE UNEXPECTED CHARACTERS (IN PARTICULAR THOSE WEIRD ASCII(0) CHARS)
149  local a
150  a=$1; while [ `str2ascii ${a:0:1}` -lt 32 ]; do a=${a:1:${#a}}; done; echo $a
151}
152
153#==================================================================================
154function dim_nam {
155  #--- GET DIMENSION $2 (X/Y/Z/T) NAME FOR FILE $1
156  #--- SPECIAL CASE: RETURN 'Seasons' IF "$2" = "S".
157  local a v Units
158  case $2 in
159    X) Units='degrees_east  degree_east  degree_e degrees_e "degrees east"  "degree east"  degreee degreese' ;;
160    Y) Units='degrees_north degree_north degree_n degrees_n "degrees north" "degree north" degreen degreesn' ;;
161    Z) Units='pa pascal pascals hpa millibar millibars mbar mbars mb bar bars atm atms atmosphere atmospheres' ;;
162    T) Units=' since' ;;
163    S) echo Seasons; return 0 ;;
164    *) echo "error in dim_nam: unrecognized axis $2"; return 1 ;;
165  esac
166  for u in $Units; do
167    case $2 in
168      X|Y|Z) a=`ncdump -h $1 | grep -i ':units = "'"$u"'"'` ;;
169      T)     a=`ncdump -h $1 | grep -i $u | grep ':units = "'` ;;
170    esac
171    if [ "$a" != "" ]; then
172      if [ "$2" = "Z" ]; then v=${a%%:*}; v=`deblank $v`
173        if [ "`ncdump -h $1 | grep -i "$v($v)"`" != "" ]; then break; fi
174      else break
175      fi
176    fi
177  done
178  if [[ "$a" = "" && "$2" = "Z" ]]; then a=`ncdump -h $1 | grep -i ':positive = "'`; fi
179  if [ "$a" = "" ]; then echo "error in dim_nam: unable to recognize axis $2"; return 1; fi
180  echo ${a%%:*}; return 0
181}
182
183#==================================================================================
184function test_var {
185# Input arguments:
186#    $1: file name  $2: variable name
187  ncdump -h $1 | grep "double $2" > /dev/null; if [ $? -eq 0 ]; then return 0; fi
188  ncdump -h $1 | grep "float  $2" > /dev/null; return $?
189}
190#==================================================================================
191function get_boundsvar {
192# Input arguments:
193#    $1: file name  $2: variable name
194  local a=$(ncdump -h $1 | grep -P "\t$2:bounds")
195  if [ "$a" != "${a#*\"}" ]; then a=${a#*\"}; echo ${a%\"*}; else echo ""; fi
196}
197#==================================================================================
198function rename_bounds {
199# Input arguments:
200#    $1: file name  $2: variable name  $3: new variable name
201#    returns: $old_var,$old_boundvar,$new_boundvar
202  local vin=$(get_boundsvar $1 $2) beg end vou
203  if [ "$vin" = "" ]; then return 1; fi
204  beg=${vin##*$2}; if [ "$beg" = "$vin" ]; then beg=$vin; fi
205  beg=${vin%%$2*}; if [ "$end" = "$vin" ]; then end=$vin; fi
206  if [[  "$beg" = ""  &&  "$end" = ""  ]]; then return 1; fi
207  vou=$beg$3$end
208  echo "$2,$vin,$vou"
209}
210#==================================================================================
211function rename_dims {
212# Input arguments:
213#    $1: file name  $2...: <axis>:<target_name> (axis=X,Y,Z or T)
214#
215# Purpose:
216#    Rename dimensions, dimensional variables.
217#    In case of boundary grid variables with bounds_<variable> names are available,
218#    they are renamed together with the corresponding "bounds" attributes.
219  local vio f=$1 att="" ren="" nam_in nam_ou
220  shift
221  while [ $# -ge 1 ]; do
222    nam_ou=${1##*:}; nam_in=$(dim_nam $f ${1%:*}); shift
223    if [ "$nam_in" != "$nam_ou" ]; then
224      ren="$ren -d $nam_in,$nam_ou -v $nam_in,$nam_ou"
225      #--- CHECK WETHER "bounds" ATTRIBUTE IS THERE
226      vio="$(rename_bounds $f $nam_in $nam_ou)"
227      if [ "$vio" != "" ]; then
228        att="$att -a bounds,$nam_ou,m,c,${vio##*,}"; ren="$ren -v ${vio#*,}"
229      fi
230    fi
231  done
232  if [ "$ren" != "" ]; then ncrename $ren $f 2>&1 > /dev/null ; fi
233  if [ "$att" != "" ]; then ncatted  $att $f 2>&1 > /dev/null ; fi
234}
235#==================================================================================
236function zonal_mean {
237# Input arguments:
238#    $1: input file  $2: output file
239  local tmp=tmp.$$.nc
240  if [ ! -d ${2%/*} ]; then mkdir -p ${2%/*}; fi
241  ncwa       -a longitude $1 $tmp ; mv $tmp $2    #--- Zonal mean
242  ncks -O -x -v longitude $2 $tmp ; mv $tmp $2    #--- Remove longitude
243  v="bounds_longitude"; test_var $2 $v            #--- Remove bounds vars
244  if [ $? -eq 0 ]; then ncks -O -x -v $v $2 $tmp ; mv $tmp $2; fi
245}
246#==================================================================================
247function get_date {
248# Assumes the following filename structure: *_${Yb}*-${Ye}*.* (Yb/e: 4 digits)
249# $1: varname
250# $2: datatype
251# $3: dirin
252# $4: dirin structure patch
253# $5...$N: files_in
254# [$N+1...]: <dset>:<var>=<val> to overwrite value of variables evaluated from parsing.
255  local v_in dtyp d_in dstr f_in Yb Ye St a f first date dates files_in=""
256  v_in=$1; shift; dtyp=$1; shift; d_in=$1; shift; dstr=$1; shift; f0=$1
257  while [ "$1" = "${1##*=}" ]; do files_in="$files_in $1"; shift; done
258  for f_in in $files_in; do date=$(get_date_1 $v_in $dtyp $d_in $dstr $f_in $*)
259    if [ $f_in = $f0 ]; then dates=$date; else dates="$dates $date"; fi
260  done
261  echo $dates
262}
263#==================================================================================
264function get_date_1 {
265# Assumes the following filename structure: *_${Yb}*-${Ye}*.* (Yb/e: 4 digits)
266# $1: varname
267# $2: datatype
268# $3: base directory for files
269# $4: dirin structure patch
270# $5: file_in
271# [$6...]: <dset>:<var>=<val> to overwrite value of variables evaluated from parsing.
272  local v_in dtyp d_in d_str f_in Yb Ye St a f first
273  v_in=$1; shift; dtyp=$1; shift; d_in=$1; shift; dstr=$1; shift; f_in=$1; shift
274  parse_dir $f_in $dstr $*; Yb=1000000; Ye=0; first='t'
275  for f in $(var=$v_in; Yb=????; Ye=????; datatype=$dtyp; eval ls $d_in/$f_in); do
276    a=${f##*_}; if [ ${a::4} -le $Yb ]; then Yb=${a::4}; fi
277    a=${a##*-}; if [ ${a::4} -ge $Ye ]; then Ye=${a::4}; fi
278    if [ $first = 't' ]; then St=$((Ye-Yb+1)); first='f'; fi
279  done
280  echo $Yb-$Ye-$St
281}
282#==================================================================================
283function dim_len {
284  local n
285  if [ "$2" = "T" ]; then
286    n=$(ncdump -h $1 | grep 'UNLIMITED'); n=${n#*// (}; echo ${n% currently*}
287  else
288    n=$(ncdump -h $1 | grep $2' = '); n=${n#* = }; echo ${n% ;*}
289  fi
290}
291#==================================================================================
292function get_grid {
293  # $1: filename $2: varname
294  X=$(dim_nam $1 X); if [ $? -ne 0 ]; then X=""; else lX=$(dim_len $1 $X); fi
295  Y=$(dim_nam $1 Y); if [ $? -ne 0 ]; then Y=""; else lY=$(dim_len $1 $Y); fi
296  Z=$(dim_nam $1 Z); if [ $? -ne 0 ]; then Z=""; else lZ=$(dim_len $1 $Z); fi
297  T=$(dim_nam $1 T); if [ $? -ne 0 ]; then T=""; else lT=$(dim_len $1  T); fi
298  t=$(ncdump -h $1 | grep "double $2")
299  if [ $? -ne 0 ]; then t=$(ncdump -h $1 | grep "float $2"); fi
300  t=${t##*$2(}; t=${t%)*}; g=""; r=""
301  while :; do s=${t##*, }; t=${t%,*}
302    case $s in
303      $X) g=${g}X; r=${r}x$lX ;;
304      $Y) g=${g}Y; r=${r}x$lY ;;
305      $Z) g=${g}Z; r=${r}x$lZ ;;
306      $T) g=${g}T; r=${r}x$lT ;;
307    esac
308    if [ "$s" = "$t" ]; then break; fi
309  done
310  echo $g=${r:1:${#r}}
311}
312#==================================================================================
313
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