CDO

See https://code.mpimet.mpg.de/projects/cdo/embedded/cdo.pdf#subsection.2.14.6 there is a table of the outputtab keywords and as you can see there is lev that can be used to retrieve the levels too.

This ticket is linked to the previous https://code.mpimet.mpg.de/boards/2/topics/13777

Thanks

Hi

I am trying to run this command on the netcdf file but getting the error please

cdo outputtab,date,lon,lat,lev,value precipitation_2017.nc > 2017.txt

the error message is please

cdo outputtab: Open failed on >precipitation_2017.nc<
Unsupported file type

Have a look at your data file.

ncdump -h precipitation_2017.nc 
ncdump: precipitation_2017.nc: NetCDF: Unknown file format

file precipitation_2017.nc 
precipitation_2017.nc: gzip compressed data, was "dataset-satellite-precipitation-ec25f67a-d1b5-43de-aead-454aa09d0700.tar", last modified: Mon Dec 12 11:20:01 2022, max compression, original size modulo 2^32 389120

Hello

I am trying to run the following code. cdo outputtab command is triminng the values of lat and longitude. How I can keep the full length of the lat and longitude as given in the coords.txt please

Thanks

#!/bin/bash

infile="X_2021.nc" 
coords="coords.txt" 

while read line
do
   line=$(echo $line | sed -e 's/\r//g')
   station=$(echo $line | cut -d ' ' -f 1)
   #-- skip header line
   if [[ "$station" == "station" ]]; then continue; fi
   #-- select station coordinates
   lat=$(echo $line | cut -d ' ' -f 2)
   lon=$(echo $line | cut -d ' ' -f 3)
   station="${station}_${lat}_${lon}" 
   #-- extract the station data
   cdo -remapnn,"lon=${lon}_lat=${lat}" ${infile} ${station}_out.nc
   cdo outputtab,date,time,year,month,day,x,y,lon,lat,lev,name,value ${station}_out.nc > ${station}_out.txt
done < $coords

You can set the number of digits for lon and lat in outputtab with lon:<num_digits> and lat:<num_digits>. In your case:

cdo outputtab,date,time,year,month,day,x,y,lon:10,lat:10,lev,name,value ${station}_out.nc > ${station}_out.txt

Thanks

it is not working please I am getting the same output please

cdo outputtab,date,time,year,month,day,x,y,lon:10,lat:10,lev,name,value ${station}_out.nc > ${station}_out.txt

Please see the attached files.

Thanks

Hm, that seems not to work anymore for version 2.1.0 and 2.0.5 too. You can use a workaround to replace the wrong lon and lat values by the correct ones:

  cdo -outputtab,date,time,year,month,day,x,y,lon,lat,lev,name,value \
        outputs/${station}_out.nc | \
        awk '{$8="'${lon}'"; $9="'${lat}'";print}' > outputs/${station}_out.txt

E.g. Output:

# date time year month day x 72.57155787 36.44991823 lat lev name value
2021-01-01 00:00:00 2021 1 1 72.5716 36.4499 72.57155787 36.44991823 0 u10 -0.001083623
2021-01-01 00:00:00 2021 1 1 72.5716 36.4499 72.57155787 36.44991823 0 v10 -0.05580788
2021-01-01 00:00:00 2021 1 1 72.5716 36.4499 72.57155787 36.44991823 0 si10 1.121761
...

Oops, it also changes the header line $8 and $9

Okay, to keep the header untouched and delete the last two cdo info messages from the output file do

  cdo -s -outputtab,date,time,year,month,day,x,y,lon,lat,lev,name,value \
        outputs/${station}_out.nc | \
        awk 'NR>1 {$8="'${lon}'"; $9="'${lat}'"}1' > outputs/${station}_out.txt

Thanks

I am getting the following error message please

do remapnn: Nearest neighbor weights from lonlat (69x55) to lonlat (1x1) grid
cdo remapnn: Processed 273240 values from 6 variables over 12 timesteps [0.02s 46MB].
./values2.sh: line 22: outputs/1_36.44991823_72.57155787_out.txt: No such file or directory
cdo outputtab: Open failed on >outputs/1_36.44991823_72.57155787_out.nc<
No such file or directory
cdo remapnn: Nearest neighbor weights from lonlat (69x55) to lonlat (1x1) grid
cdo remapnn: Processed 273240 values from 6 variables over 12 timesteps [0.02s 45MB].
./values2.sh: line 22: outputs/2_35.89191425_71.72687311_out.txt: No such file or directory
cdo outputtab: Open failed on >outputs/2_35.89191425_71.72687311_out.nc<
No such file or directory
cdo remapnn: Nearest neighbor weights from lonlat (69x55) to lonlat (1x1) grid
cdo remapnn: Processed 273240 values from 6 variables over 12 timesteps [0.02s 46MB].
./values2.sh: line 22: outputs/3_35.16956641_71.8344582_out.txt: No such file or directory
cdo outputtab: Open failed on >outputs/3_35.16956641_71.8344582_out.nc<
No such file or directory
cdo remapnn: Nearest neighbor weights from lonlat (69x55) to lonlat (1x1) grid
cdo remapnn: Processed 273240 values from 6 variables over 12 timesteps [0.02s 45MB].
./values2.sh: line 22: outputs/4_35.42472896_72.16393117_out.txt: No such file or directory
cdo outputtab: Open failed on >outputs/4_35.42472896_72.16393117_out.nc<
No such file or directory
cdo remapnn: Nearest neighbor weights from lonlat (69x55) to lonlat (1x1) grid
cdo remapnn: Processed 273240 values from 6 variables over 12 timesteps [0.02s 45MB].
./values2.sh: line 22: outputs/5_35.00569553_71.77647769_out.txt: No such file or directory
cdo outputtab: Open failed on >outputs/5_35.00569553_71.77647769_out.nc<
No such file or directory
cdo remapnn: Nearest neighbor weights from lonlat (69x55) to lonlat (1x1) grid
cdo remapnn: Processed 273240 values from 6 variables over 12 timesteps [0.02s 46MB].
./values2.sh: line 22: outputs/6_34.94443242_71.65510941_out.txt: No such file or directory
cdo outputtab: Open failed on >outputs/6_34.94443242_71.65510941_out.nc<
No such file or directory

You have to delete the outputs/ in front of the file names. I didn't want to have all the files in the same directory as the script.

You should read and understand what I have send you because it's on you to take further care on it.

Thanks

it worked but new code is repeating the observations

1. date time year month day x y lon lat lev name value
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 u10 0.2442991
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 u10 0.2442991
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 v10 -1.768886
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 v10 -1.768886
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 si10 1.956628
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 si10 1.956628
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 t2m 277.643
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 t2m 277.643
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 sp 86510.81
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 sp 86510.81
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 tp 0.0006449826
   2021-01-01 00:00:00 2021 1 1 71.6551 34.9444 71.65510941 34.94443242 0 tp 0.0006449826

See the corrected command without the print in the awk call.

Hello

can you please help to modify the code in values2.sh , I have to run this code on multiple files air.1948 ... air.2020. and I want to the name of the txt files be name of filein front of the txt files. please help me how I can achieve this please

This not really a CDO question. If you need to work with shell scripts you have to learn more about it. There are multiple tutorials about bash, zsh and other Shells available.

To strip off the path prefix and the .nc suffix to get only the base name of a file, e.g.:

infile="/home/mygroup/myid/folder1/file1.nc" 

infile_base=$(basename -s .nc $infile)

Result: file1

Hello

I am working on the similar thing , this time nc file have lev variable I only want the values when lev variable is 1000, 925 and 850 in the txt files, how to d this in the code. the nc files have 17 layers of temperature, while running the values2.sh code its taking a lot of time.

Please help me with this

Thanks