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how to mask or extract data from nc files by one certain region? thanks
Added by Wi Du over 7 years ago
Hi everyone,
I have many nc files, which are global climate data (50 years). Now I am want to focus one country region (I have the shapefile) to do statistic analysis (such as region mean,trend, and so on). So now I tried:
First to turn the shapefile into nc file using ARCGIS.
Second, I use the cdo command:
du@ubuntu:~/model/CC$ cdo div country.nc precipitation_2051-2110.nc out.nc
But I got errors:
cdo div: Open failed on >cdd_yr_HFB_4K_CC_m102_2051-2110.nc<
Unsupported file type (library support not compiled in)
It seems the cdo can not open the nc files. And I checked the nc files using ncdump
du@ubuntu:~/CC$ ncdump -h precipitation_2051-2110.nc
netcdf precipitation_2051-2110 {
dimensions:
bnds = 2 ;
time = UNLIMITED ; // (60 currently)
lon = 116 ;
lat = 71 ;
variables:
double time(time) ;
time:units = "days since 2051-1-1" ;
time:standard_name = "time" ;
time:long_name = "Time" ;
time:calendar = "standard" ;
time:axis = "T" ;
double time_bnds(time, bnds) ;
double lon(lon) ;
lon:units = "degrees_east" ;
lon:standard_name = "longitude" ;
lon:long_name = "longitude" ;
lon:axis = "X" ;
double lat(lat) ;
lat:units = "degrees_north" ;
lat:standard_name = "latitude" ;
lat:long_name = "latitude" ;
lat:axis = "Y" ;
float precipi(time, lat, lon) ;
cddETCCDI:units = "days" ;
cddETCCDI:_FillValue = 1.e+20f ;
cddETCCDI:long_name = "Precipitation" ;
cddETCCDI:grid_type = "gaussian" ;
// global attributes:
Anyone can help me?
Thanks a lot!
check if netcdf is compiled in with
cdo -V
Thanks.
I checked the data, and the information is as follows.
Climate Data Operators version 1.6.2 (http://code.zmaw.de/projects/cdo)
Compiler: gcc -std=gnu99 -g -O2 -fPIE -fstack-protector --param=ssp-buffer-size=4 -Wformat -Werror=format-security -Wall -pedantic -fPIC -pthread
version: gcc (Ubuntu/Linaro 4.8.2-4ubuntu1) 4.8.2
Compiled: by buildd on allspice (x86_64-unknown-linux-gnu) Nov 15 2013 17:10:54
Features: PTHREADS Z JASPER PROJ.4 MAGICS
Libraries: proj/4.7
Filetypes: srv ext ieg grb grb2 nc
CDI library version : 1.6.2 of Nov 15 2013 17:10:44
GRIB_API library version : 1.10.4
netCDF library version : 4.1.3 of Feb 24 2014 21:05:37 $
HDF5 library version : 1.8.11
SERVICE library version : 1.3.1 of Nov 15 2013 17:10:28
EXTRA library version : 1.3.1 of Nov 15 2013 17:10:20
IEG library version : 1.3.1 of Nov 15 2013 17:10:24
FILE library version : 1.8.2 of Nov 15 2013 17:10:20
Use commandline option -h for help.
Error (operatorInqModID) : operator missing! cdd_yr_HFB_4K_CC_m102_2051-2110.nc is a file on disk!
So how can I modify these data and make them can be used in CDO?
Thanks a lot!
Please, upload some of tour data!
Hello, I attached the sample nc files. Please check.
Thanks a lot!
Best regards,
cdo mul -selname,altcddETCCDI altcdd_yr_HFB_4K_CC_m101_2051-2110.nc China.nc masked.nc
works with cdo-1.8.2. Can you update your CDO version?
I uploaded the results.
hth
ralf
Hi,Dr.Ralf,
Thanks a lot. I updated the cdo and it can be run.
But I checked the results using grads and I found the results are headstand.
Please check the attached figure.
So how to modify it. I tried several times, but failed.
Thanks!
Best regards,
Du
the grids in China.nc and the other file a quite different although they have the same dimension size. longitudes are a little different abd latitudes are in reversed order.
1. remap data to the China.nc grid
cdo remapnn,China.nc -selname,altcddETCCDI altcdd_yr_HFB_4K_CC_m101_2051-2110.nc alt.nc
2. multiply mask and data
cdo mul alt.nc China.nc alt_masked.nc
3. results look like this
Hello, Dr.Ralf,
Thank you very much!
It is ok now.
Best regards,
Du
Hi, Dr.Ralf,
Sorry to disturb you again.
I found the value are changed after the mask. Them are much bigger than the original value
Thanks again!
Regards,
Du
Wi Du wrote:
Hi, Dr.Ralf,
Sorry to disturb you again.
I found the value are changed after the mask. Them are much bigger than the original value
Thanks again!
Regards,
Du
That's because the China variable is not a 0-1 mask, it has values from 0 to ca. 950. You can create such a field by dividing China.nc by itself and do the multiplication afterwards - or as a one line
cdo mul alt.nc -div China.nc China.nc alt_realMaskedOut.nc
hth
ralf
Hello, Dr. Ralf,
Thanks a lot.
But I faced another problem for some dataset. Of them, the mask value is very strange. Like the zero value could not be deleted.
Would you please check it for me?
Thanks!
Du
no problem, you can add 1.0 before doing the devision like this
f=mask_r99p_yr_HFB_4K_CC_m101_2051-2110.nc
cdo -L -div -addc,1 -abs $f -addc,1 -abs $f newMask.nc
newMask.nc has no new missing values (introduced by devision by zero)
hth
ralf
Sorry, Dr.Ralf,
I just want to ask how to put this step, because I tried several times and got the constant(1) value for the final results.
Thanks a lot!
Best regards,
Du
Do I get it right, that you want the data from r99p_yr_HFB_4K_CC_m101_2051-2110.nc masked out to the china region???
cdo selname,r99pETCCDI r99p_yr_HFB_4K_CC_m101_2051-2110.nc r99Mask.nc
f=China.nc
cdo -L -div -addc,1 -abs $f -addc,1 -abs $f chinaMask.nc
cdo remapnn,r99Mask.nc chinaMask.nc r99ChinaMask.nc
cdo div -selname,r99pETCCDI r99p_yr_HFB_4K_CC_m101_2051-2110.nc r99ChinaMask.nc r99Masked2China.nc
looks like
is that what you had in mind?
Hi, Dr.Ralf,
Thanks a lot!
Best regards,
Du
HELLO ALL,
I want to extrct djf from a .nc file (starting fro december of 1st year to february of last year) using cdo. I used cdo -selmon,12,1,2 -shifttime,-1mo infile.nc outfile.nc. but it show wrong in values......2nd year january data show as 1st year december ... Please help me in this regards. Here I attach the infile (sst_dec.nc) and outfile (124.nc) Thank you
Anyone can help me?
Thanks a lot!
Hi Sanjukta,
please, create always a new forum question unless your question depends of an old one.
Why do you do a shifttime one month backwards? This is what the wrong month are coming from.
It should be
cdo -selmon,12,1,2 infile.nc outfile.nc
Another way to select DJF is to use the select operator
cdo select,season=DJF infile.nc outfile.nc
But at the beginning it will select only JF and for the last year only D because of missing years.
-Karin
hi Karin sir,
I am so sorry. Actually I am new here and i dont know how to start a new forum...And my question was little similar to this forum so i was query here. Thanks for replr me. when i used cdo select,season=DJF infile.nc outfile.nc
i got this
cdo select : Enter parameter list >
after this i dont know what to do.
kindly help
Thank You
Do you really enter the cdo command above or do you have a blank between select, and season? That's where I would get the 'cdo select : Enter parameter list >' request.
You have to enter
cdo select,season=DJF infile.nc outfile.nc
If this won't work which cdo version are you using(cdo -V)? The current version is 1.9.5.
-Karin
