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Diagnostic & Visualisation
• Introduction• Diagnostic
• cdo• Visualisation• gnuplot• GrADS• GMT• cdat
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6fetching data
from data base
Ferret
ncar
idl
gnuplot2
GrADS
3gmt
4
cdat
5
diagnosticcdo
1
graphictools
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• Introduction• Diagnostic
• cdos• info• change formats• extract regions• extract time slices• interpolate grids• build means, mins, maxs• change values• prepare for visualisation
• Visualisation• gnuplot• GrADS• GMT• cdat
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CDOThere are more than 250 operators available.
•File information (info, sinfo, diff, ...)•File operations (copy, cat, merge, split, ...)•Selection (selcode, selvar, sellevel, seltimestep, ...)•Missing values (setctomiss, setmisstoc, setrtomiss)•Arithmetic (add, sub, mul, div, ...)•Mathematical functions (sqrt, exp, log, sin, cos, ...)•Comparision (eq, ne, le, lt, ge, gt, ...)•Conditions (ifthen, ifnotthen, ifthenc, ifnotthenc)•Field statistic (fldsum, fldavg, fldstd, fldmin, fldmax, ...)•Vertical statistic (vertsum, vertavg, vertstd, vertmin, ...)•Time range statistic (timavg, yearavg, monavg, dayavg, ...)•Ensemble statistic (enssum, ensavg, ensstd, ensmin, ...)•Regression (detrend)•Field interpolation (remapbil, remapcon, remapdis, ...)•Vertical interpolation (ml2pl, ml2hl)•Time interpolation (inttime, intyear)
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CDOUsage:
cdo [options] \ operator[,op[,op]] \ [-operator] \ ifile [ifile ...] [ofile]
For:
GRIB-, NetCDF-, ieg-, Service-, Extra- formatted files
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CDOcdo info: info, infov
sophie 29%cdo info zzz.grb-1 : Date Time Code Level Size Miss : Minimum Mean Maximum 1 : 24-01-01 18:00 214 0 8192 0 : 229.31 279.04 327.19cdo info : Processed 1 variable 1 timestep. ( 0.00s 0B )sophie 30%cdo infov zzz.grb-1 : Date Time Varname Level Size Miss : Minimum Mean Maximum 1 : 24-01-01 18:00 var214 0 8192 0 : 229.31 279.04 327.19sophie 33%cdo -f nc copy zzz.grb zzz.nccdo copy : Processed 1 variable 1 timestep. ( 0.01s 0B )sophie 34%cdo infov zzz.nc-1 : Date Time Varname Level Size Miss : Minimum Mean Maximum 1 : 24-01-01 18:00 var214 0 8192 0 : 229.31 279.04 327.19cdo infov : Processed 1 variable 1 timestep. ( 0.00s 0B )sophie 35%cdo -f nc -t echam4 copy zzz.grb zzz.nccdo copy : Processed 1 variable 1 timestep. ( 0.01s 0B )sophie 36%cdo infov zzz.nc-1 : Date Time Varname Level Size Miss : Minimum Mean Maximum 1 : 24-01-01 18:00 tsmax 0 8192 0 : 229.31 279.04 327.19cdo infov : Processed 1 variable 1 timestep. ( 0.00s 0B )
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CDOcdo info: mapsophie 28%cdo sellonlatbox,-10,30,35,70 tsmax.grb tsmaxeuropa.grbsophie 29%cdo map tsmaxeuropa.grb
00000000011111 12345678901234
01 44455555533211 0102 45555555332211 0203 55566533333322 0304 66666433334432 0405 64566665455332 0506 55566655553222 0607 76555432222210 0708 7765432101100m 0809 77744332211111 0910 75445884332228 1011 65568888888588 1112 8889899M899788 12 00000000011111 123456789012340=[+2.611e+02,+2.656e+02] 1=[+2.656e+02,+2.688e+02] 2=[+2.688e+02,+2.720e+02] 3=[+2.720e+02,+2.752e+02] 4=[+2.752e+02,+2.784e+02] 5=[+2.784e+02,+2.816e+02]6=[+2.816e+02,+2.848e+02] 7=[+2.848e+02,+2.880e+02] 8=[+2.880e+02,+2.912e+02] 9=[+2.912e+02,+2.929e+02] *=0 .=miss m=min=+2.611e+02 M=max=+2.929e+02
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CDOcdo -r -f nc -t echam4 copy zzz.grb zzz.nc
-r relative time axis-f nc output format is netcdf-t echam4 use parameter table echam4
converting a GRIB-file to NetCDF...
cdo formats: -f
cdo -f ext copy zzz.grb zzz.ext
-f ext output format is extra
converting a GRIB-file to extra...
output is a formatted text file...
cdo outputf,f8.3,5 zzz.grb zzz.asc
f8.3 fortran format convention5 values per line
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CDOcdo -t mpiom1 -f nc setgrid,grob15s.nc \ -selindexbox,2,255,1,220 -setgrid,r256x220 \ filein.ext inter.nccdo remapcon,r360x180 inter.nc fileout.nc
interpolate a curve linear (extra file) to a regular grid (NetCDF)(MPI-OM1 to regular 360*180 grid for CMOR)
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CDOexample: piping, missing_values, etc
cdo -f ext daymean MSLP.grb A1_pslcdo -f ext daymin T2MIN.grb A1_tasmincdo -f ext daymax T2MAX.grb A1_tasmaxcdo -f ext add -daymean APRL.grb -daymean APRC.grb A1_prcdo -f ext sub -daymean TRADS.grb \ -daymean TRADSU.grb A1_rldscdo -f ext sub -daymean SRADS.grb \ -daymean SRADSU.grb zwisch1_rsdscdo gtc,0.0 zwisch1_rsds zwisch2_rsdscdo setmisstoc,0.0 -ifthen zwisch2_rsds \ zwisch1_rsds A1_rsdscdo -f ext mulc,-1. -daymean AHFL.grb A1_hfls
ifthen = i2(t,x) if i1 != 0 = miss if i1 = 0
gtc = 1 if i1 > 0 = 0 if i1 <= 0
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CDOexample: preparing for excel
Step 1: time selection and download from data basejblob -datasetname EH4OPYC_TPREC -rmin 71941 -rmax 93544Step 2: daily mean:cdo daymean EH4OPYC_TPREC_71941-93544.grb EH4OPYC_TPREC_day.grbStep 3: select region:cdo sellonlatbox,239,251,48,55 EH4OPYC_TPREC_day.grb \ EH4OPYC_TPREC_daycs.grbStep 4: set values < 0 to 0,change from ms-1 to mmd-1:cdo gtc,0.0 EH4OPYC_TPREC_daycs.grb EOmaskcdo setmisstoc,0.0 -ifthen EOmask EH4OPYC_TPREC_daycs.grb \ EH4OPYC_TPREC_erg.grbcdo mulc,86400000 EH4OPYC_TPREC_erg.grb EH4OPYC_TPREC_mmd.grbStep 5: convert from GRIB to ascii:cdo outputf,%10.4f,5 EH4OPYC_TPREC_mmd.grb > EH4OPYC_TPREC.ascStep 6:convert from mac to windows (interactive editor)Step 7:pack:gzip EH4OPYC_22723GSDIO_TPREC.win.asc
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CDOcdo gradsdes: GrADS description file
cdo gradsdes zzz.grb
zzz.ctl ---the GrADS description filezzz.gmp ---the INDEX file
creates
cdo outputbounds zzz.grb > zzz.txt
creates
sophie 25% more zzz.asc# File = zzz.nc# Name = T_2M# Code = -1# Level = 2# Date = 1950-01-01# Time = 03:00#> -Z287.575 -10.7 34.5 -10.5 34.5 -10.5 34.7 -10.7 34.7 -10.7 34.5> -Z287.542 -10.5 34.5 -10.3 34.5 -10.3 34.7 -10.5 34.7 -10.5 34.5.....
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CDOcdo: infos, downloads, installations
Current officially released version is cdo 0.9.11
http://www.mpimet.mpg.de/fileadmin/software/cdo/
SUN ( Solaris 8): /client/binSUN (Solaris 10)(zetta, jango): /pf/k/k204016/binLINUX: /client/bin
or local installations ( LINUX, Mac OS X):
configure --with-netcdf=/swmake
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• Introduction• Diagnostic
• cdos• Visualisation• gnuplot
• timeseries daily & monthly• 2d field with contour & pm3d• installation, etc...
•GrADS• GMT• cdat
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cdo sellonlatbox,-10,30,35,70 -monmean TSMAX.grb eh5_mon_europe.grbcdo sellonlatbox,-10,30,35,70 $FILE eh5_day_europe.grbcdo info eh5_mon_europe.grb | tail +2 | head -12 \ | cut -c 10-19,72-79 > eur_mon.asccdo info eh5_day_europe.grb | tail +2 | head -365 \ | cut -c 10-19,72-79 > eur_day.asc
cdo + gnuplot for timeseries
sophie 27%cdo info EH4_OPYC_SRES_A2_TSMAX_day.grb -1 : Date Time Code Level Size Miss : Minimum Mean Maximum 1 : 24-01-01 18:00 214 0 8192 0 : 229.31 279.04 327.19 2 : 24-01-02 18:00 214 0 8192 0 : 227.92 279.11 332.09 3 : 24-01-03 18:00 214 0 8192 0 : 228.69 279.23 331.56 4 : 24-01-04 18:00 214 0 8192 0 : 227.97 279.06 328.30 5 : 24-01-05 18:00 214 0 8192 0 : 228.06 278.88 326.79
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if (-e REINDA) rm REINDAcat > REINDA << ENDEset terminal post colorset xdata timeset timefmt "%Y-%m-%d"set format x "%m"set output "eur_mon_day.ps"plot "eur_day.asc" u 1:2 title "daily mean" w l , \ "eur_mon.asc" u 1:2 title "monthly mean" w lquitENDEgnuplot < REINDA
cdo + gnuplot for timeseries
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cdo selrec,1,1 EH4_OPYC_SRES_A2_TSMAX_day.grb tsmax.grbcdo griddes tsmax.grb > tsmax.gridcdo -f ext copy tsmax.grb tsmax.extf90 -o gp.x gp.f90gp.x
cdo + gnuplot for 2d field
produces a file tsmax.asc:
sophie 40%more tsmax.asc 0.0000 87.8638 262.2228 2.8125 87.8638 262.5333 5.6250 87.8638 262.8868 8.4375 87.8638 263.1720 11.2500 87.8638 263.4376 14.0625 87.8638 263.7111 16.8750 87.8638 263.5919 .....
gp.f90:reads tsmax.ext (tsmax)reads tsmax.grid (lon, lat)
writes ascii file (lon, lat, tsmax)
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gnuplotgnuplot> set pm3dgnuplot> unset surfacegnuplot> set contour basegnuplot> set view 0,0,1.2,1.2 gnuplot> set palette model RGBgnuplot> set palette defined \( 0 "#0033ff", 2 "#ffff33", 3 "#ffcccc", 5 "#ff0033") gnuplot> splot [0:360][-90:90][220:330] "tsmax.asc" with pm3d gnuplot> set term postscript colorgnuplot> set output "gnutemp.ps"gnuplot> replotgnuplot> quit
gnuplot for 2d field (pm3d only version 4.0)
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6gnuplot: infos, downloads, installations
Current officially released version is gnuplot 4.0
http://www.gnuplot.info/
http://www.gnuplot.info/download.html
cross (version 3.7) : /usr/binsun solaris (version 3.7) : /client/binLINUX (version 3.7) : /usr/bin
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• Introduction• Diagnostic
• cdos• Visualisation• gnuplot• GrADS
• plot with default values• plot with different colours• plot with frames• plot with additional text• plot with vectors• animation• installation, etc...
• GMT• cdat
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6'reinit''set vpage 0 8.5 0 11''set display color white''clear'*'sdfopen $FILE1'*'set lon -180 180''set gxout shaded''set parea 0.5 6.5 0.5 5.25''set t 1''display sic''draw title sea ice cover Jan'
'set lon -180 180''set gxout shaded''set parea 0.5 6.5 5.75 10.5''set t 8''display sic''draw title sea ice cover Aug'*'run cbar.gs''printim icex2.gif gif x480 y640 white'
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6function palette()******************************* color palette fuer arktis* weiss-tuerkis-werte* Nr red green blue'set rgb 16 240 250 250''set rgb 17 225 240 245''set rgb 18 210 230 240''set rgb 19 195 220 235''set rgb 20 180 210 230''set rgb 21 165 200 225''set rgb 22 150 190 220''set rgb 23 135 180 215''set rgb 24 120 170 210''set rgb 25 105 160 205''set rgb 26 90 150 200''set rgb 27 75 140 195''set rgb 28 60 130 190''set rgb 29 45 120 185''set rgb 30 30 110 180'
'set cmin 0''set cmax 100''set clevs 8 16 24 32 40 48 56 64 \ 72 80 88 96''set ccols 16 17 18 19 20 21 22 23 \ 24 25 26 27 28 29'
additive color system
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6'reinit''set vpage 0 8.5 0 11''set display color white''clear''run palette.arktis.gs''sdfopen sic_O1_1860-2000.nc''set cmin 0''set cmax 100''set clevs 8 16 24 32 ... 64 72 80 88 96''set ccols 16 17 ...23 24 25 26 27 28 29''set lon -180 180''set gxout shaded''set parea 0.5 6.5 0.75 4.5''set t 1''display sic''draw title sea ice cover Jan''set cmin 0''set cmax 100''set clevs 8 16 24 32 ...64 72 80 88 96''set ccols 16 17 ...23 24 25 26 27 28 29''set lon -180 180''set gxout shaded''set parea 0.5 6.5 5.5 9.25''set t 8''display sic''draw title sea ice cover Aug''run cbar.gs'
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6'reinit''set vpage 0 8.5 0 11''set display color white''clear''run palette.arktis.gs'*'sdfopen $FILE1'*'draw rec 0.5 0.5 6.5 5.25''draw string 0.6 0.6 first window''draw rec 0.5 5.75 6.5 10.5''draw string 0.6 5.85 second window''draw rec 7.0 2 7.7 9'*'set cmin 0''set cmax 100''set clevs 8 16 24 32 ... 64 72 80 88 96''set ccols 16 17 ...23 24 25 26 27 28 29''set lon -180 180''set gxout shaded''set parea 0.5 6.5 0.5 5.25''set t 1''display sic''draw title sea ice cover Jan'
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'set cmin 0''set cmax 100''set clevs 8 16 24 32 ...64 72 80 88 96''set ccols 16 17 ...23 24 25 26 27 28 29''set lon -180 180''set gxout shaded''set parea 0.5 6.5 5.75 10.5''set t 8''display sic''draw title sea ice cover Aug'*'run cbar.gs''set string 4 c 2 0''draw string 7.35 8.9 %''set font 4''set string 2 l 30 55''set strsiz 1''draw string 0.6 1 GrADS 1.9b''printim icex2.gif gif x480 y640 white'
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6#!/bin/tcsh## Script fuer ein gradsbild#set WORK = "$HOME/GRADStest"set FILE1 = uas_A1.ncset FILE2 = vas_A1.ncset FILE3 = speed_A1.nc#cd $WORK#cat > REIN.gs <<ENDE'reinit''set vpage 0 11 0.5 8.5''set display color white''clear''run palette.joerg3.gs'*'sdfopen $FILE1''sdfopen $FILE2''sdfopen $FILE3''set parea 1 10 1 8''set map 2 1 10'*'set cmin 0''set cmax 27''set clevs 3 6 9 12 15 18 21 24 27''set ccols 38 39 40 ... 46 47 48'
*'set lon -30 40''set lat 20 75''set gxout shaded''display uas.3''set gxout vector''set t 1''set arrscl .3 10''display uas.1;vas.2'*'run cbar.gs''draw string 1.9 0.2 Windspeed und Direction''printim gifimage.out gif x800 y600 white'*'quit'*ENDE#gradsnc -lc 'run REIN.gs'#
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6#!/bin/tcsh -vx set work = $HOME/DKRZcourse/GRADStestset bild = $work/gifsset ifile = templev.nccd $workforeach z ( 6 ... 5720) cat > REINDA << ENDE'reinit''set vpage 0 11 0.5 8.5''set display color white''clear''run palette.joerg3.gs''sdfopen $ifile''set parea 1 10 1 8''set cmin 270''set cmax 302''set clevs 270 273 276 279 282 285 288 291 293 296 299 302''set ccols 37 38 39 40 41 42 43 44 45 46 47 48 49 50''set gxout shaded''set lev $z''display thetao''run cbar.gs''draw string 3 0.2 Temp from surface to bottom: $z''printim ./gifs/temp.$z.gif gif x600 y400 white''quit'ENDEgradsnc -lbc 'run REINDA'rm REINDAend
set loopdim zset lev 6 5720set z 1 40display thetao
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temp.0006.gif temp.0150.gif temp.0740.gif temp.2290.giftemp.0017.gif temp.0183.gif temp.0845.gif temp.2525.giftemp.0027.gif temp.0220.gif temp.0960.gif temp.2785.giftemp.0037.gif temp.0263.gif temp.1085.gif temp.3070.giftemp.0047.gif temp.0310.gif temp.1220.gif temp.3395.giftemp.0057.gif temp.0363.gif temp.1365.gif temp.3770.giftemp.0069.gif temp.0420.gif temp.1525.gif temp.4195.giftemp.0083.gif temp.0485.gif temp.1700.gif temp.4670.giftemp.0100.gif temp.0560.gif temp.1885.gif temp.5170.giftemp.0123.gif temp.0645.gif temp.2080.gif temp.5720.gif
convert -delay 20 temp.*.gif ani20.gif
cd ./gifsforeach z ( 6 17 27 37 47 57 69 83 100 123 150 183 220 263 310 363 420 485 \ 560 645 740 845 960 1085 1220 1365 1525 1700 \ 1885 2080 2290 2525 2785 3070 3395 3770 4195 4670 5170 5720 )if ( $z < 10 ) then mv temp.$z.gif temp.000$z.gifelse if ( $z < 100 ) then mv temp.$z.gif temp.00$z.gifelse if ( $z < 1000 ) then mv temp.$z.gif temp.0$z.gifendif end
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Zur Anzeige wird der QuickTime™ Dekompressor „GIF“
benötigt.
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6GrADS: infos, downloads, installations
Current officially released version is GrADS 1.8s11
http://www.iges.org/grads/
http://www.iges.org/grads/downloads.html
cross (version 1.8sl11) : /pool/ia64/grads/ia32/binsun solaris (version 1.8sl9): /client/binLINUX (version 1.8) : /client/binRunning Version 1.9b4: MacOS X.4
setenv GADDIR ~/grads-1.9b4/datasetenv GRADSDIR ~/bin
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• Introduction• Diagnostic
• cdos• Visualisation• gnuplot• GrADS• GMT
• plot europe• plot europe "conic"• plot europe "and world"• plot ocean data on curve linear grid• installation, etc...
•cdat
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cdo outputbounds ifile > ofile.ascpsbasemap -R-15/40/35/75 -JM6i \ -B15/5:."Europa mit GMT":\ -P -K >! zzz.ps psxy -R -J -M zzz.asc -L \ -Czzz.cpt -P -O -K >> zzz.pspscoast -R -J -Dc -W0.5p -P -O >> zzz.ps
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6cdo outputbounds ifile > ofile.ascmakecpt -Crainbow -T240/300/3 > zzz.cptpsbasemap -R-15/40/35/75 -JB-10/30/35/65/6i \ -B15/5:."Europe Albers Conic": -P -K >! zzz.ps psxy -R -J -M zzz.asc -L -Czzz.cpt -P -O -K >> zzz.pspscoast -R -J -Dc -W0.5p -P -O >> zzz.ps
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6#!/bin/tcsh#makecpt -Crainbow -T240/300/3 > zzz.cptpscoast -R-180/180/-90/90 -JG10/35/6i -Bg30/g15 -Dc \ -A5000 -G255/255/255 \ -S150/50/150 -P -K >! zz1.pspsxy -R-12/37/35/70 -M zzz.asc -J -L -O -K -Czzz.cpt >> zz1.pspscoast -R-180/180/-90/90 -JG10/35/6i -Bg30/g15 -Dc -A5000 -W0.5p \ -P -O >> zz1.ps
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6#!/bin/tcsh -vxset IFILE = $1set OFILE = $2set GFILE = $OFILE:r.gmtset CFILE = colorj.cptset PFILE = $OFILE:r.ps#change from extra to netcdf and cutting the overlapscdo -t mpiom1 -f nc setgrid,$HOME/cdogrids/grob15s.nc \ -selindexbox,2,255,1,220 \ -setgrid,r256x220 $IFILE $OFILE#create inputfile for gmtcdo outputbounds $OFILE > $GFILE#Cylindrical equidistant GMT outputpsbasemap -Rd -JQ0/8.0i -X1.5i -Y2.0i \ -Ba60f30/a30f15:."MPIOM ZO - Height above geoid": \ -K >! $PFILEpsxy -R -J -M $GFILE -L -C./$CFILE -W0.5p \ -O -K >> $PFILEpscoast -R -J -W0.5p -G102/187/80 -Dc \ -O -K >> $PFILEpsbasemap -R -J -Bg30/g15 -U/0.0i/-1.6i/"joergwegner" \ -O -K >> $PFILEpsscale -C./$CFILE -D4.0i/-0.5i/4.0i/0.2ih -B2/:"[m]": \ -O >> $PFILE
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6psbasemap -Rd -JG-35/50/6.0i -X1.0i -Y2.0i \ -Ba60f30/a30f15:."MPIOM ZO - Height above geoid":\ -P -K >! $PFILE
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6gmt: infos, downloads, installations
Current officially released version is gmt 4.1
http://gmt.soest.hawaii.edu/
http://gmt.soest.hawaii.edu/
cross (version ?) : not installedsun solaris (version 3.41) : /client/binLINUX (version ?) : ?
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• Introduction• Diagnostic
• cdos• Visualisation• gnuplot• GrADS• GMT•cdat
•overview• example• installation, etc...
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6#!/usr/bin/env pythonimport cdms, vcs, cdutil, Numeric, genutil, os, sysfrom cdms import MVfrom Numeric import *#f=cdms.open('clmt.nc', 'r')temp = f('T', time = ('1960-3-7 3:0:0.0', '1960-3-7 3:0:0.0'),\ level = (29, 29),\ rlat = (-22.0275, 22.1925),\ rlon = (-24.8825, 17.0275),\ squeeze = 0, order = '0123')lob = f('lon')lab = f('lat')tla = temp.getLatitude()tlo = temp.getLongitude()#b=cdms.open('zbounds.bin','r')labb=b('variable_2195043')lobb=b('variable_2195044') la=cdms.createVariable(labb)lo=cdms.createVariable(lobb)print la.shapeprint lo.shapetla.setBounds(la)tlo.setBounds(lo)vis=vcs.init()te=temp[:]#vis.plot(te)vis.gif('zb3.eu0123.gif','r','l')
cdat example on CLM outputloading bounds for lon and latfrom file and plotting temperature
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6cdat: infos, downloads, installations
Current officially released version is cdat 4.0
http://www-pcmdi.llnl.gov/software/support.php
http://sourceforge.net/project/showfiles.php?group_id=11356
cross (version 4.0) : no Fortran support, no postscript outputsun solaris (version 4.0) : no Fortran supportLINUX (version ?) : not installedRunning Version 4.0: MacOS X.4, LINUX (SUSE, Debian)(with gcc 4.0 or higher)
setenv CDATHOME "/pf/k/k204083/cdat"setenv PYTHONHOME "/pf/k/k204083/cdat"setenv PYTHONPATH "$CDATHOME/lib/python2.4:$CDATHOME/bin: \ $CDATHOME/lib:."#set my_path = ( $PINGO ./ $CDO $PYTHONPATH )
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