CDO

Hi Fabio,

I would guess the answer is no. But you can write a short shell script using a loop to select all points.
Here is an example Korn-Shell script which selects 4 points (in your case you can read the x and y arrays
from file):

#!/bin/ksh

#-- delete existing ASCII output file
rm -rf outfile.txt

#-- name of the input file
infile=inputfile.nc

#-- arrays of the points lon lat locations
set -A lon 0.0 5.0 10.0 15.0
set -A lat 0.0 5.0 10.0 15.0

#-- loop to retrieve the data of the selected points 
for i in $(seq 0 3)
do
   cdo -O remapnn,lon=${lon[$i]}/lat=${lat[$i]} $infile tmp.nc
   cdo -outputtab,lon,lat,lev,date,value tmp.nc >> outfile.txt
done

#-- delete the multiple entries of the header line in output file
header="#" 
awk '!header[$0]++' outfile.txt > tmp2.txt
mv tmp2.txt outfile.txt

#-- remove temporary file
rm tmp.nc

exit

Take care whether your data file has levels or not.

-Karin

Hi Karin,

Thanks for your help.
Sorry, I'm not very familiar with the ksh and I'm having some troubles running this script.

I installed the mksh in the cygwin environment, put your script in a .ksh file and tried to run it but it gives me the following error indicating the line where the for loop starts:

file.ksh[15]: syntax error: unexpected 'do

In addition, I'd really appreciate if you could give me some guidance in how I should edit the script to go take the lon lat arrays from a file like the one attached.
Thank you very much

The script is a Korn Shell script so you need to have ksh installed.
You can modify the script and run it, lets assume the script name is your_script.ksh:

ksh your_script.ksh

But you can rewrite it to use another shell scripting language as you like, it's on you.

-Karin

Hello Karin
Sorry, I've then realized that there was a problem of Windows/UNIX encoding in the line ending of the script, because I used a normal EditPad Lite 7 to write down a script inspired by yours instead of writing it down directly in a vi editor.
The editor I used was using the Windows encoding to end the lines in the code and that was causing the syntax error. The encoding is specifically:

^M

Once this issue was fixed, the code was running smoothly. This methodology, however, is extremely costly in processing time. The domain in my .nc file has almost 4 million cells for more than 14 thousands time steps, I need to extract time series for about 400 thousands points. This script would do that sequentially for each of the lon/lat combinations. In each time step, the procedure would spend about 800/1000 seconds only in the remapnn step.
It would be nice to have a more efficient way to extract data for specific set of coordinates.

Thank you very much again.

Best,
F

Hi there, thanks for this script!

I am trying to extract from negative longitudes or latitudes, and run into an error:

test1¹⁰: set: -0: unknown option
test1¹⁰: set: -.: unknown option
test1¹⁰: set: -9: unknown option
test1¹⁰: set: -6: unknown option
test1¹⁰: set: -3: unknown option
test1¹⁰: set: -2: unknown option
test1¹⁰: set: -4: unknown option
test1¹⁰: set: -6: unknown option

This is for example for longitude -0.963246

I tried to fix it with the conversion using -convertlon or -convertlat but this only gives another error.
In that case all my extracted values become 1e+20

Any help would be appreciated!

Thanks
Max

script and inputfile are attached!

Hi Max,

what did you do exactly? -- Sorry didn't noticed that test1 is a script. It is always a good style to name a script including a suffix, e.g. test1.ksh.

-Karin

if you want to extract only one single point than you don't have to use arrays.

cdo -O remapnn,lon=-0.963246/lat=38.308579 $infile tmp.nc
cdo -outputtab,lon,lat,date,value tmp.nc >> outfile.txt

Or in a script

#!/bin/ksh

#-- delete existing ASCII output file
rm -rf outfile.txt

#-- name of the input file
infile=euin.nc

#-- lon lat location
lon=-0.963246
lat=38.308579

#-- retrieve the data of the selected points 
cdo -O remapnn,lon=${lon}/lat=${lat} $infile tmp.nc
cdo -outputtab,lon,lat,date,value tmp.nc >> outfile.txt

#-- remove temporary file
rm tmp.nc

exit

-Karin

Thanks for the quick reply. I will have to extract more than one pair of points. I just put one pair in for the sake of testing it :-)
I think the problem that I have is related to korn shell and how it deals with negative values.. Could that be the case?

I solved it!

Instead of

set -A lon -0.963246
set -A lat 38.308579

it has to be

set A lon - 0.963246
set -A lat - 38.308579

Got the hint from this thread:
https://www.unix.com/shell-programming-and-scripting/186579-solved-capturing-output-korn-variable.html

Best
Max

I solved it!

Instead of

set -A lon -0.963246
set -A lat 38.308579

it has to be

set -A lon -- -0.963246
set -A lat -- 38.308579

Got the hint from this thread:
https://www.unix.com/shell-programming-and-scripting/186579-solved-capturing-output-korn-variable.html

Best
Max

Yup, that's the way when you want to use arrays. I should have mentioned that, too.

-Karin