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Convert a series of single cell timeseries to a NetCDF file

Added by Alonso Arriagada 8 months ago

Hi all!
I have text files with time series (3-hourly) with 6 variables. Each file represents a cell with specific lat-long coordinate.

¿Someone knows how to convert those txt files to one single NetCDF file?

All the txt files represent a grid over Chile, the spatial resolution is 0.05° X 0.05°.

I attach a few files.

Thanks all in advance!

Alonso.


Replies (4)

RE: Convert a series of single cell timeseries to a NetCDF file - Added by Karin Meier-Fleischer 8 months ago

Hi Alonso,

to convert such an ASCII file where the columns are the 6 different variables you have to write a script to select each variable from the input ASCII file, create a grid description file, and define the starting time.

I've tested it using a ksh script:

#!/bin/ksh

input=data_-17.475_-69.475

ncols=6                                 #-- number of variables
variables=("var1" "var2" "var3" "var4" "var5" "var6") #-- variable names

time="1950-01-01,00:00:00,3hour"        #-- init time axis

lat=$(echo $input | cut -d "_" -f 2)    #-- latitude value
lon=$(echo $input | cut -d "_" -f 3)    #-- longitude value

#-- generate the grid description file for $input
cat << EOF > gridfile_${input}.txt
gridtype = lonlat
xsize    = 1
ysize    = 1
xvals    = $lon
yvals    = $lat
EOF

#-- loop over all variables
j=0
for i in $(seq 1 ${ncols})
do
   echo "--> variable: ${variables[j]}" 
   $(cat  $input | cut -d " " -f ${i} > tmp.txt)
   cdo -s -f nc -settaxis,$time -setname,${variables[$j]} -input,gridfile_${input}.txt out_$i.nc < tmp.txt
   j=$(expr $j + 1)
done

#-- merge all variable into one netCDF file
cdo -O -s merge out_*.nc ${input}.nc

-Karin

RE: Convert a series of single cell timeseries to a NetCDF file - Added by Alonso Arriagada 8 months ago

Hi Karin!

Thanks for your quick response!

I will try to use your script.

Best!:)
A.

RE: Convert a series of single cell timeseries to a NetCDF file - Added by Alonso Arriagada 8 months ago

Hi Karin,
Your script worked fine for a single file, so I have tried to loop over all the files in my folder, but I am not able to run it.
I created a txt file with the names of the files in my forlder called "dirlist.txt"
I have use Cygwyn in Windows10. This is my script:

#!/bin/mksh

for file in $(cat  dirlist.txt) 
do
    input=$file

    ncols=6                                 #-- number of variables
    variables=("pr_mm" "WS_m_s" "T_grC" "HR" "SWR_W_m2" "LWR_W_m2") #-- variable names

    time="1979-01-01,00:00:00,3hour"        #-- init time axis

    lat=$(echo $input | cut -d "_" -f 2)    #-- latitude value
    lon=$(echo $input | cut -d "_" -f 3)    #-- longitude value

    #-- generate the grid description file for $input
    cat << EOF > gridfile_${input}.txt
    gridtype = lonlat
    xsize    = 1
    ysize    = 1
    xvals    = $lon
    yvals    = $lat
    EOF

    #-- loop over all variables
    j=0
    for i in $(seq 1 ${ncols})
    do
          echo "--> variable: ${variables[j]}" 
          $(cat  $input | cut -d " " -f ${i} > tmp.txt)
          cdo -f nc -settaxis,$time -setname,${variables[$j]} -input,gridfile_${input}.txt out_$i.nc < tmp.txt
          j=$(expr $j + 1)
    done

    #-- merge all variable into one netCDF file
    cdo merge out_*.nc ${input}.nc
done

Do you have any comments about it?

Thank you in advance!
Best,

Alonso.

RE: Convert a series of single cell timeseries to a NetCDF file - Added by Alonso Arriagada 7 months ago

Hi Karin,
I have solved it! After some time of messing around, I have found the useful script.
I have solve it with a `ls data*.*` in the first for loop. This is the code:

#!/bin/mksh

ncols=6
variables=("pr_mm" "WS_m_s" "T_grC" "HR" "SWR_W_m2" "LWR_W_m2")

time="1979-01-01,00:00:00,3hour"

for var in `ls data_*.*`;
do
input=$var
echo "$input"

lat=$(echo $input | cut -d "_" -f 2)
lon=$(echo $input | cut -d "_" -f 3)
newfile=${myroot}/gridfile_${input}.txt
echo "$newfile"
echo "gridtype = lonlat"  > $newfile
echo "xsize = 1" >> $newfile
echo "ysize = 1" >> $newfile
echo "xvals = $lon" >> $newfile
echo "yvals = $lat" >> $newfile
j=0
for i in $(seq 1 ${ncols})
do
echo "j: $j i: $i"
echo "--> variable: ${variables[j]}"
$(cat $input | cut -d " " -f ${i} > tmp.txt)
cdo -s -f nc -settaxis,$time -setname,${variables[$j]} -input,$newfile out_$i.nc < tmp.txt
j=$(expr $j + 1)
done
cdo -s merge out_*.nc ${input}.nc

done

Thank you! This would not have been possible without your initial help.;)

Best Regards.
Alonso.

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