Pre-ACCESS CMIP5/MODIS analysis scripts

The fifth phase of the Coupled Model Intercomparison Project (CMIP5) provides a multi-model framework for comparing the mechanisms and responses of climate models from around the world. However, the workload of retrieving a certain climate statistic from all these models, each of which includes several ensemble members, is tremendous. Not only that, it is too often a repetitive process which impedes new research and hypothesis testing. Our NASA ACCESS project is designed to simplify and accelerate this process. To begin, we have documented below a prototypical example of CMIP5 analysis and evaluation using traditional NCO commands on netCDF3-format model and HDF-EOS format observational (NASA MODIS satellite instrument) datasets. These examples complement the NCO User's Guide by detailing in-depth data analysis in a frequently encountered “real world” context. Graphical representations of the results (NCL scripts available upon request) are provided to illustrate physical meaning of the analysis. Over the summer of 2013, we will add scripts which make use of new NCO features that combine all the loops in the analysis into single commands by exploiting NCO's new group aggregation and arithmetic features.

Sample Scripts

  1. Combine Files
    Sometimes, the data of one ensemble member will be stored in several files to reduce single file size. This script illustrates how to concatenate these files into one, including:
    1. Obtain the number and names (or partial names) of files in directory;
    2. Concatenate files along record dimension (the left-most dimension) using ncrcat.
  2. Global Distribution of Long-term Average (see Fig. 1)
    1. Average the ensemble members of each model using ncea;
    2. Average along the record dimension (the left-most) using ncra;
    3. Store the results of one model as a group in the output file using ncecat with the option of –gag;
  3. Annual Average over Regions (see Fig. 2)
    1. Spatial average using ncap2 and ncwa;
    2. Change the order of dimensions using ncpdq;
    3. Annual average using ncra;
    4. Anomaly from long-term average using ncbo;
    5. Standard deviation using ncbo and ncea;
    6. Rename variables using ncrename;
    7. Edit attributions using ncatted;
    8. Linear regression using ncap2;
    9. Use ncap2 with commands file (i.e., .nco file);
    10. Move variables around using ncks.
  4. Monthly Cycle (see Fig. 3)
    1. Anomaly from annual-average
  5. Regrid MODIS Data
    1. Regrid using bilinear interpolation;
    2. Rename variables, dimensions and attributions using ncrename.
  6. Add Coordinates to MODIS Data
  7. Permute MODIS Coordinates
    The latitude of MODIS data is from 90oN to -90oN, and the longitude is from -180oE to 180oE. However, CMIP5 is from -90oN to 90oN, and from 0oE to 360oE. So this script illustrates how to change MODIS coordinate to that of CMIP5.

PIC PIC
 

 
 PIC
 

 

 
Fig. 1 Global Distribution of Long-term Average. Fig. 2 Annual Average over Regions. Fig. 3 Monthly Cycle.

 

1 Combine Files

#!/bin/bash         ## shell type  
shopt -s extglob ## enable extended globbing  
 
##===========================================================================  
## Some of the models cut one ensemble member into several files, which include data of different time periods.  
## We’d better concatenate them into one at the beginning so that we won’t have to think about which files we need if we want to retrieve a specific time period later.  
##  
## Method:  
## - Make sure ’time’ is the record dimension (i.e., left-most)  
## - ncrcat  
##===========================================================================  
 
drc_in=’/home/wenshanw/data/cmip5/’## directory of input files  
 
var=( ’snc’ ’snd’ ) ## variables  
rlm=’LImon’## realm  
xpt=( ’historical’ ) ## experiment ( could be more )  
 
for var_id in {0..1}; do ## loop over two variables  
  ## names of all the models (ls [get file names]; cut [get the part for model names]; sort; uniq [remove duplicates]; awk [print])  
  mdl_set=$( ls ${drc_in}${var[var_id]}_${rlm}_*_${xpt[0]}_*.nc | cut -d ’_’ -f 3 | sort | uniq -c | awk ’{print $2}’ )  
  ## number of models (echo [print contents]; wc [count])  
  mdl_nbr=$( echo ${mdl_set} | wc -w )  
  echo "=============================="  
  echo "There are" ${mdl_nbr} "models for" ${var[var_id]}.  
 
  for mdl in ${mdl_set}; do ## loop over models  
    ## names of all the ensemble members  
    nsm_set=$( ls ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*.nc | cut -d ’_’ -f 5 | sort | uniq -c | awk ’{print $2}’ )  
    nsm_nbr=$( echo ${nsm_set} | wc -w ) ## number of ensemble members in each model  
    echo "------------------------------"  
    echo "Model" ${mdl} "includes" ${nsm_nbr} "ensemble member(s):"  
    echo ${nsm_set}"."  
 
    for nsm in ${nsm_set}; do ## loop over ensemble members  
      fl_nbr=$( ls ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_${nsm}_*.nc | wc -w ) ## number of files in this ensemble member  
 
      if [ ${fl_nbr} -le 1 ] ## if there is only 1 file, continue to next loop  
      then  
       echo "There is only 1 file in" ${nsm}.  
       continue  
      fi  
 
      echo "There are" ${fl_nbr} "files in" ${nsm}.  
 
      ## starting date of data (sed [the name of the first file includes the starting date])  
      yyyymm_str=$( ls ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_${nsm}_*.nc | sed -n ’1p’ | cut -d ’_’ -f 6 | cut -d ’-’ -f 1 )  
      ## ending date of data (sed [the name of the last file includes the ending date])  
      yyyymm_end=$( ls ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_${nsm}_*.nc | sed -n "${fl_nbr}p" | cut -d ’_’ -f 6 | cut -d ’-’ -f 2 )  
 
      ## concatenate the files of one ensemble member into one along the record dimension (now is time)  
      ncrcat -O ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_${nsm}_*.nc ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_${nsm}_${yyyymm_str}-${yyyymm_end}  
 
      ## remove useless files  
      rm ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_${nsm}_!(${yyyymm_str}-${yyyymm_end})  
    done  
  done  
done

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2 Global Distribution of Long-term Average

#!/bin/bash  
 
##===========================================================================  
## After one-ensemble-one-file.sh  
## Example: Long-term average of each model globally  
##===========================================================================  
 
##---------------------------------------------------------------------------  
## parameters  
drc_in=’/home/wenshanw/data/cmip5/’## directory of input files  
drc_out=’/home/wenshanw/data/cmip5/output/’## directory of output files  
 
var=( ’snc’ ’snd’ ) ## variables  
rlm=’LImon’## realm  
xpt=( ’historical’ ) ## experiment ( could be more )  
 
fld_out=( ’snc/’ ’snd/’ ) ## folders of output files  
##---------------------------------------------------------------------------  
 
for var_id in {0..1}; do ## loop over two variables  
## names of all models (ls [get file names]; cut [get the part for model names]; sort; uniq [remove duplicates]; awk [print])  
  mdl_set=$( ls ${drc_in}${var[var_id]}_${rlm}_*_${xpt[0]}_*.nc | cut -d ’_’ -f 3 | sort | uniq -c | awk ’{print $2}’ )  
  mdl_num=$( echo ${mdl_set} | wc -w ) ## number of models (echo [print contents]; wc [count])  
 
  for mdl in ${mdl_set}; do ## loop over models  
   ## average all the ensemble members of each model  
   ncea -O -4 -d time,"1956-01-01 00:00:0.0","2005-12-31 23:59:9.9" ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_195601-200512.nc  
 
   ## average along time  
   ncra -O ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_195601-200512.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${mdl}.nc  
 
   echo Model ${mdl} done!  
  done  
 
## Remove temporary files to avoid file name confliction  
rm ${drc_out}${fld_out[var_id]}${var[var_id]}*historical*.nc  
 
  ## Store models as groups in the output file  
  ncecat -O --gag ${drc_out}${fld_out[var_id]}${var[var_id]}_*.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_all-mdl_${xpt[0]}_all-nsm_clm.nc  
 
echo Var ${var[var_id]} done!  
done

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3 Annual Average over Regions

Main Script

#!/bin/bash  
# includes gsl_rgr.nco  
 
##===========================================================================  
## After one-ensemble-one-file.sh  
## Example: Annual trend of each model over Greenland and Tibet ( time- and spatial-average, standard deviation, anomaly and linear regression)  
##===========================================================================  
 
##---------------------------------------------------------------------------  
## parameters  
drc_in=’/home/wenshanw/data/cmip5/’## directory of input files  
drc_out=’/home/wenshanw/data/cmip5/output/’## directory of output files  
 
var=( ’snc’ ’snd’ ) ## variables  
rlm=’LImon’## realm  
xpt=( ’historical’ ) ## experiment ( could be more )  
 
fld_out=( ’snc/’ ’snd/’ ) ## folders of output files  
##------------------------------------------------------------  
 
for var_id in {0..1}; do ## loop over two variables  
## names of all models (ls [get file names]; cut [get the part for model names]; sort; uniq [remove duplicates]; awk [print])  
  mdl_set=$( ls ${drc_in}${var[var_id]}_${rlm}_*_${xpt[0]}_*.nc | cut -d ’_’ -f 3 | sort | uniq -c | awk ’{print $2}’ )  
 
  for mdl in ${mdl_set}; do ## loop over models  
    for fn in $( ls ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*.nc ); do ## loop over ensemble members  
      pfx=$( echo ${fn} | cut -d’/’ -f6 | cut -d’_’ -f1-5 ) ## part of the file name  
 
      ## retrieve the 2 zones  
      ## calculate the geographical weight first  
      ncap2 -O -s ’gw = cos(lat*3.1415926/180.); gw@long_name="geographical weight";gw@units="ratio"’ ${fn} ${drc_out}${fld_out[var_id]}${pfx}_gw.nc  
      ## Greenland  
      ncwa -O -w gw -d lat,60.0,75.0 -d lon,300.0,340.0 -a lat,lon ${drc_out}${fld_out[var_id]}${pfx}_gw.nc ${drc_out}${fld_out[var_id]}${pfx}_gw_1.nc  
      ## Tibet  
      ncwa -O -w gw -d lat,30.0,40.0 -d lon,80.0,100.0 -a lat,lon ${drc_out}${fld_out[var_id]}${pfx}_gw.nc ${drc_out}${fld_out[var_id]}${pfx}_gw_2.nc  
 
      ## concatenate 2 zones together  
      ncecat -O -u zone ${drc_out}${fld_out[var_id]}${pfx}_gw_?.nc ${drc_out}${fld_out[var_id]}${pfx}_gw_zone4.nc  
 
      ## change the order of the dimension so that the record dimension is ’time’  
      ncpdq -O -a time,zone ${drc_out}${fld_out[var_id]}${pfx}_gw_zone4.nc ${drc_out}${fld_out[var_id]}${pfx}_gw_zone4.nc  
 
      ## remove the temporary files (optional)  
      rm ${drc_out}${fld_out[var_id]}${pfx}_gw_?.nc ${drc_out}${fld_out[var_id]}${pfx}_gw.nc  
 
      ## annual average (use the feature of ’Duration’)  
      ncra -O --mro -d time,"1956-01-01 00:00:0.0","2005-12-31 23:59:9.9",12,12 ${drc_out}${fld_out[var_id]}${pfx}_gw_zone4.nc ${drc_out}${fld_out[var_id]}${pfx}_yrly.nc  
 
      ## anomaly  
      ## long-term average  
      ncwa -O -a time ${drc_out}${fld_out[var_id]}${pfx}_yrly.nc ${drc_out}${fld_out[var_id]}${pfx}_clm.nc  
      ## subtract long-term average  
      ncbo -O --op_typ=- ${drc_out}${fld_out[var_id]}${pfx}_yrly.nc ${drc_out}${fld_out[var_id]}${pfx}_clm.nc ${drc_out}${fld_out[var_id]}${pfx}_anm.nc  
    done  
 
    rm ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*_yrly.nc  
 
    ## average over all the ensemble members  
    ncea -O -4 ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*_anm.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_anm.nc  
 
    ## standard deviation ------------------------------  
    for fn in $( ls ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*_anm.nc ); do  
      pfx=$( echo ${fn} | cut -d’/’ -f8 | cut -d’_’ -f1-5 )  
 
      ## difference between each ensemble member and the average of all members  
      ncbo -O --op_typ=- ${fn} ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_anm.nc ${drc_out}${fld_out[var_id]}${pfx}_dlt.nc  
    done  
 
    ## RMS  
    ncea -O -y rmssdn ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*_dlt.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_sdv.nc  
    ## rename variables  
    ncrename -v ${var[var_id]},sdv ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_sdv.nc  
    ## edit attributions  
    ncatted -a standard_name,sdv,a,c,"_standard_deviation_over_ensemble" -a long_name,sdv,a,c," Standard Deviation over Ensemble" -a original_name,sdv,a,c," sdv" ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_sdv.nc  
    ##------------------------------------------------------------  
 
    ## linear regression -----------------------------------------  
    ##!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!  
    ## have to change the name of variable in the commands file of gsl_rgr.nco manually (gsl_rgr.nco is listed below)  
    ncap2 -O -S gsl_rgr.nco ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_anm.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_anm_rgr.nc  
    ##!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!  
 
    ## get rid of temporary variables  
    ncks -O -v c0,c1,pval,${var[var_id]},gw ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_anm_rgr.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${mdl}.nc  
    ##------------------------------------------------------------  
 
    ## move the variable ’sdv’ into the anomaly files (i.e., *anm.nc files)  
    ncks -A -v sdv ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_sdv.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${mdl}.nc  
    rm ${drc_out}${fld_out[var_id]}${var[var_id]}_*historical*  
 
    echo Model ${mdl} done!  
  done  
 
  ## Store models as groups in the output file  
  ncecat -O --gag ${drc_out}${fld_out[var_id]}${var[var_id]}_*.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_all-mdl_${xpt[0]}_all-nsm_annual.nc  
 
  echo Var ${var[var_id]} done!  
done

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gsl_rgr.nco

//linear regression  
//Caution: make sure the variable name is in agreement with the main script (now is ’snd’)  
 
//declare variables  
*c0[$zone]=0.;        //intercept  
*c1[$zone]=0.;        //slope  
*sdv[$zone]=0.;       //standard deviation  
*covxy[$zone]=0.;     //covariance  
*x = double(time);  
 
for (*zone_id=0;zone_id<$zone.size;zone_id++)   //loop over zones  
{  
gsl_fit_linear(time,1,snd(:,zone_id),1,$time.size, &tc0, &tc1, &cov00, &cov01,&cov11,&sumsq); //linear regression function  
c0(zone_id) = tc0;    //store the results  
c1(zone_id) = tc1;  
covxy(zone_id) = gsl_stats_covariance(time,1,$time.size,double(snd(:,zone_id)),1,$time.size); //covariance function  
sdv(zone_id) = gsl_stats_sd(snd(:,zone_id), 1, $time.size);   //standard deviation function  
}  
 
//pval------------------------------------------------------------  
*time_sdv = gsl_stats_sd(time, 1, $time.size);  
*r_value = covxy/(time_sdv*sdv);  
*t_value = r_value/sqrt((1-r_value^2)/($time.size-2));  
pval = abs(gsl_cdf_tdist_P(t_value, $time.size-2) - gsl_cdf_tdist_P(-t_value, $time.size-2));  
//----------------------------------------------------------------  
 
//write RAM variables to disk  
//------------------------------------------------------------  
//usually NCO writes the outputs directly to disk  
//inside .nco files, using RAM variables, declared by *, will shorten running time  
//write the final outputs using ram_write()  
//------------------------------------------------------------  
ram_write(c0);  
ram_write(c1);

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4 Monthly Cycle

#!/bin/bash  
 
##============================================================  
## After one-ensemble-one-file.sh  
## Example: Monthly cycle of each model in Greenland  
##============================================================  
 
##------------------------------------------------------------  
## parameters  
drc_in=’/home/wenshanw/data/cmip5/’## directory of input files  
drc_out=’/home/wenshanw/data/cmip5/output/’## directory of output files  
 
var=( ’snc’ ’snd’ ) ## variables  
rlm=’LImon’## realm  
xpt=( ’historical’ ) ## experiment ( could be more )  
 
fld_out=( ’snc/’ ’snd/’ ) ## folders of output files  
##------------------------------------------------------------  
 
for var_id in {0..1}; do ## loop over two variables  
  ## names of all models (ls [get file names]; cut [get the part for model names]; sort; uniq [remove duplicates]; awk [print])  
  mdl_set=$( ls ${drc_in}${var[var_id]}_${rlm}_*_${xpt[0]}_*.nc | cut -d ’_’ -f 3 | sort | uniq -c | awk ’{print $2}’ )  
 
  for mdl in ${mdl_set}; do ## loop over models  
    ## average all the ensemble members in each model  
    ncea -O -4 -d time,"1956-01-01 00:00:0.0","2005-12-31 23:59:9.9" ${drc_in}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_*.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm.nc  
 
    ## retrieve Greenland  
    ## calculate the geographical weight first  
    ncap2 -O -s ’gw = cos(lat*3.1415926/180.); gw@long_name="geographical weight";gw@units="ratio"’ ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm.nc  
    ## Greenland  
    ncwa -O -w gw -d lat,60.0,75.0 -d lon,300.0,340.0 -a lat,lon ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN.nc  
 
    ## anomaly----------------------------------------  
    for moy in {1..12}; do ## loop over months  
      mm=$( printf "%02d" ${moy} ) ## change the format of month into 2-digit  
 
      for yr in {1956..2005}; do ## loop over years  
        if [ ${moy} -eq 1 ]; then ## if January, calculate the annual average of this year  
         ncra -O -d time,"${yr}-01-01 00:00:0.0","${yr}-12-31 23:59:9.9" ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_${yr}.nc  
        fi  
 
        ## retrieve this month  
        ncks -O -d time,"${yr}-${mm}-01 00:00:0.0","${yr}-${mm}-31 23:59:9.9" ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_${yr}${mm}.nc  
        ## subtract the annual average from the month data  
        ncbo -O --op_typ=- ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_${yr}${mm}.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_${yr}.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_${yr}${mm}_anm.nc  
      done  
 
      ## average over years  
      ncra -O ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_????${mm}_anm.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_${mm}_anm.nc  
    done  
    ##--------------------------------------------------  
 
    ## concatenate the months data together  
    ncrcat -O ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_${mdl}_${xpt[0]}_all-nsm_GN_??_anm.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${mdl}.nc  
 
    echo Model ${mdl} done!  
  done  
 
  rm -f ${drc_out}${fld_out[var_id]}${var[var_id]}*historical*  
 
  ## Store models as groups in the output file  
  ncecat -O --gag -v ${var[var_id]} ${drc_out}${fld_out[var_id]}${var[var_id]}_*.nc ${drc_out}${fld_out[var_id]}${var[var_id]}_${rlm}_all-mdl_${xpt[0]}_all-nsm_GN_mthly-anm.nc  
 
  echo Var ${var[var_id]} done!  
done

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5 Regrid MODIS Data

Main Script

#!/bin/bash  
## include bi_interp.nco  
 
##===========================================================================  
## Example for  
## - regrid (using bi_interp.nco): the spatial resolution of MODIS data  
## is much finer than those of CMIP5 models. In order to compare  
## the two, we can regrid MODIS data to comform to CMIP5.  
##===========================================================================  
 
var=( ’MCD43C3’ ) ## variable  
fld_in=( ’monthly/’ ) ## folder of input files  
fld_out=( ’cesm-grid/’ ) ## folder of output files  
drc_in=’/media/grele_data/wenshan/modis/mcd43c3/’## directory of input files  
 
for fn in $( ls ${drc_in}${fld_in}${var}.*.nc ); do ## loop over files  
  sfx=$( echo $fn | cut -d ’/’ -f 8 | cut -d ’.’ -f 2 ) ## part of file names  
 
  ## regrid  
  ncap2 -O -S bi_interp.nco ${fn} ${drc_in}${fld_out}${var}.${sfx}.regrid.nc  
  ## retrieve only the new variables  
  ncks -O -v wsa_sw_less,bsa_sw_less ${drc_in}${fld_out}${var}.${sfx}.regrid.nc ${drc_in}${fld_out}${var}.${sfx}.regrid.nc  
  ## rename the new variables, dimensions and attributions  
  ncrename -O -d latn,lat -d lonn,lon -v latn,lat -v lonn,lon -v wsa_sw_less,wsa_sw -v bsa_sw_less,bsa_sw -a missing_value,_FillValue ${drc_in}${fld_out}${var}.${sfx}.regrid.nc  
 
  echo $sfx done.  
done

bi_interp.nco

// bilinear interpolation  
 
defdim("latn",192); // define new dimension: latitude  
defdim("lonn",288); // define new dimension: longitude  
latn[$latn] = {90,89.0576 ,88.1152 ,87.1728 ,86.2304 ,85.288  ,84.3456 ,83.4031 ,82.4607 ,81.5183 ,80.5759 ,79.6335 ,78.6911 ,77.7487 ,76.8063 ,75.8639 ,74.9215 ,73.9791 ,73.0367 ,72.0942 ,71.1518 ,70.2094 ,69.267  ,68.3246 ,67.3822 ,66.4398 ,65.4974 ,64.555  ,63.6126 ,62.6702 ,61.7277 ,60.7853 ,59.8429 ,58.9005 ,57.9581 ,57.0157 ,56.0733 ,55.1309 ,54.1885 ,53.2461 ,52.3037 ,51.3613 ,50.4188 ,49.4764 ,48.534  ,47.5916 ,46.6492 ,45.7068 ,44.7644 ,43.822  ,42.8796 ,41.9372 ,40.9948 ,40.0524 ,39.11   ,38.1675 ,37.2251 ,36.2827 ,35.3403 ,34.3979 ,33.4555 ,32.5131 ,31.5707 ,30.6283 ,29.6859 ,28.7435 ,27.8011 ,26.8586 ,25.9162 ,24.9738 ,24.0314 ,23.089  ,22.1466 ,21.2042 ,20.2618 ,19.3194 ,18.377  ,17.4346 ,16.4921 ,15.5497 ,14.6073 ,13.6649 ,12.7225 ,11.7801 ,10.8377 ,9.89529 ,8.95288 ,8.01047 ,7.06806 ,6.12565 ,5.18325 ,4.24084 ,3.29843 ,2.35602 ,1.41361 ,0.471204,-0.471204,-1.41361,-2.35602,-3.29843,-4.24084,-5.18325,-6.12565,-7.06806,-8.01047,-8.95288,-9.89529,-10.8377,-11.7801,-12.7225,-13.6649,-14.6073,-15.5497,-16.4921,-17.4346,-18.377 ,-19.3194,-20.2618,-21.2042,-22.1466,-23.089 ,-24.0314,-24.9738,-25.9162,-26.8586,-27.8011,-28.7435,-29.6859,-30.6283,-31.5707,-32.5131,-33.4555,-34.3979,-35.3403,-36.2827,-37.2251,-38.1675,-39.11  ,-40.0524,-40.9948,-41.9372,-42.8796,-43.822 ,-44.7644,-45.7068,-46.6492,-47.5916,-48.534 ,-49.4764,-50.4188,-51.3613,-52.3037,-53.2461,-54.1885,-55.1309,-56.0733,-57.0157,-57.9581,-58.9005,-59.8429,-60.7853,-61.7277,-62.6702,-63.6126,-64.555 ,-65.4974,-66.4398,-67.3822,-68.3246,-69.267 ,-70.2094,-71.1518,-72.0942,-73.0367,-73.9791,-74.9215,-75.8639,-76.8063,-77.7487,-78.6911,-79.6335,-80.5759,-81.5183,-82.4607,-83.4031,-84.3456,-85.288,-86.2304,-87.1728,-88.1152,-89.0576,-90}; // the copy of CCSM4 latitude  
lonn[$lonn] = {-178.75,-177.5,-176.25,-175,-173.75,-172.5,-171.25,-170,-168.75,-167.5,-166.25,-165,-163.75,-162.5,-161.25,-160,-158.75,-157.5,-156.25,-155,-153.75,-152.5,-151.25,-150,-148.75,-147.5,-146.25,-145,-143.75,-142.5,-141.25,-140,-138.75,-137.5,-136.25,-135,-133.75,-132.5,-131.25,-130,-128.75,-127.5,-126.25,-125,-123.75,-122.5,-121.25,-120,-118.75,-117.5,-116.25,-115,-113.75,-112.5,-111.25,-110,-108.75,-107.5,-106.25,-105,-103.75,-102.5,-101.25,-100,-98.75,-97.5,-96.25,-95,-93.75,-92.5,-91.25,-90,-88.75,-87.5,-86.25,-85,-83.75,-82.5,-81.25,-80,-78.75,-77.5,-76.25,-75,-73.75,-72.5,-71.25,-70,-68.75,-67.5,-66.25,-65,-63.75,-62.5,-61.25,-60,-58.75,-57.5,-56.25,-55,-53.75,-52.5,-51.25,-50,-48.75,-47.5,-46.25,-45,-43.75,-42.5,-41.25,-40,-38.75,-37.5,-36.25,-35,-33.75,-32.5,-31.25,-30,-28.75,-27.5,-26.25,-25,-23.75,-22.5,-21.25,-20,-18.75,-17.5,-16.25,-15,-13.75,-12.5,-11.25,-10,-8.75,-7.5,-6.25,-5,-3.75,-2.5,-1.25,0,1.25,2.5,3.75,5,6.25,7.5,8.75,10,11.25,12.5,13.75,15,16.25,17.5,18.75,20,21.25,22.5,23.75,25,26.25,27.5,28.75,30,31.25,32.5,33.75,35,36.25,37.5,38.75,40,41.25,42.5,43.75,45,46.25,47.5,48.75,50,51.25,52.5,53.75,55,56.25,57.5,58.75,60,61.25,62.5,63.75,65,66.25,67.5,68.75,70,71.25,72.5,73.75,75,76.25,77.5,78.75,80,81.25,82.5,83.75,85,86.25,87.5,88.75,90,91.25,92.5,93.75,95,96.25,97.5,98.75,100,101.25,102.5,103.75,105,106.25,107.5,108.75,110,111.25,112.5,113.75,115,116.25,117.5,118.75,120,121.25,122.5,123.75,125,126.25,127.5,128.75,130,131.25,132.5,133.75,135,136.25,137.5,138.75,140,141.25,142.5,143.75,145,146.25,147.5,148.75,150,151.25,152.5,153.75,155,156.25,157.5,158.75,160,161.25,162.5,163.75,165,166.25,167.5,168.75,170,171.25,172.5,173.75,175,176.25,177.5,178.75,180}; // the copy of CCSM4 longitude  
 
*out[$time,$latn,$lonn]=0.0; // output structure  
 
// bi-linear interpolation  
bsa_sw_less=bilinear_interp_wrap(bsa_sw,out,latn,lonn,lat,lon);  
wsa_sw_less=bilinear_interp_wrap(wsa_sw,out,latn,lonn,lat,lon);  
 
// add attributions  
latn@units = "degree_north";  
lonn@units = "degree_east";  
latn@long_name = "latitude";  
lonn@long_name = "longitude";  
bsa_sw_less@hdf_name = "Albedo_BSA_shortwave";  
bsa_sw_less@calibrated_nt = 5;  
bsa_sw_less@missing_value = 32767.0;  
bsa_sw_less@units = "albedo, no units";  
bsa_sw_less@long_name = "Global_Albedo_BSA_shortwave";  
wsa_sw_less@hdf_name = "Albedo_WSA_shortwave";  
wsa_sw_less@calibrated_nt = 5;  
wsa_sw_less@missing_value = 32767.0;  
wsa_sw_less@units = "albedo, no units";  
wsa_sw_less@long_name = "Global_Albedo_WSA_shortwave";

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6 Add Coordinates to MODIS Data

Main Script

#!/bin/bash  
 
##============================================================  
## Example for  
## - regrid (using bi_interp.nco): the spatial resolution of MODIS data  
## is much finer than those of CMIP5 models. In order to compare  
## the two, we can regrid MODIS data to comform to CMIP5.  
## - add coordinates (using coor.nco): there is no coordinate information  
## in MODIS data. We have to add it manually now.  
##============================================================  
 
var=( ’MOD10CM’ ) ## variable  
fld_in=( ’snc/nc/’ ) ## folder of input files  
drc_in=’/media/grele_data/wenshan/modis/’## directory of input files  
 
for fn in $( ls ${drc_in}${fld_in}${var}*.nc ); do ## loop over files  
  sfx=$( echo ${fn} | cut -d ’/’ -f 8 | cut -d ’.’ -f 2-4 ) ## part of file names  
  echo ${sfx}  
 
  ## rename dimension names since they are too long  
  ncrename -d YDim_MOD_CMG_Snow_5km,lat -d XDim_MOD_CMG_Snow_5km,lon -O ${drc_in}${fld_in}${var}.${sfx}.nc ${drc_in}${fld_in}${var}.${sfx}.nc  
  ## add coordinates  
  ncap2 -O -S coor.nco ${drc_in}${fld_in}${var}.${sfx}.nc ${drc_in}${fld_in}${var}.${sfx}.nc  
done

coor.nco

// add coordinate to MODIS HDF data  
lon = array(0.f, 0.05, $lon) - 180;  
lat = 90.f- array(0.f, 0.05, $lat);

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7 Permute MODIS Coordinates

Main Script

#!/bin/bash  
 
##===========================================================================  
## Example for  
## - permute coordinates (using inverse-lat.nco): the grid of MODIS is  
## from (-180 degE, 90 degN), the left-up corner, to  
## (180 degE, -90 degN), the right-low corner. However, CMIP5 is  
## from (0 degE, -90 degN) to (360 degE, 90 degN). The script  
## here changes the MODIS grid to CMIP5 grid.  
##===========================================================================  
 
##---------------------------------------------------------------------------  
## permute coordinates  
## - inverse lat from (90,-90) to (-90,90)  
## - permute lon from (-180,180) to (0,360)  
for fn in $( ls MCD43C3.*.nc ); do ## loop over files  
  sfx=$( echo ${fn} | cut -d ’.’ -f 1-3 ) ## part of file names  
  echo ${sfx}  
 
  ## lat  
  ncap2 -O -S inverse-lat.nco ${fn} ${fn} ## inverse latitude  
 
  ## lon  
  ## break into east and west hemispheres in order to switch the two  
  ncks -O -d lon,0.0,180.0 ${fn} ${sfx}.part1.nc  
  ncks -O -d lon,-180.0,-1.25 ${fn} ${sfx}.part2.nc  
  ## make longitude the record dimension  
  ncpdq -O -a lon,lat,time ${sfx}.part1.nc ${sfx}.part1.nc  
  ncpdq -O -a lon,lat,time ${sfx}.part2.nc ${sfx}.part2.nc  
  ## concatenate the two hemispheres along longitude  
  ncrcat -O ${sfx}.part?.nc ${fn}  
  ## reorder dimensions  
  ncpdq -O -a time,lat,lon ${fn} ${fn}  
  ## add new longitude coordinates  
  ncap2 -O -s ’lon=array(0.0,1.25,$lon)’ ${fn} ${fn}  
done

inverse-lat.nco

// inverse lat from (90,-90) to (-90,90)  
bsa_sw=bsa_sw.reverse($lat);  
wsa_sw=wsa_sw.reverse($lat);  
lat=lat.reverse($lat);

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