How to convert .NetCDF reterive from NCEP/NCAR to ASCII files of each month

I have air.mon.mean.nc file prepared by NCEP/NCAR. This file contain monthly temperature. I want to get temperature data in text file for each month since 1985 to 2015.

When i try ncdisp('air.mon.mean.nc')

I got

Source:
           E:\meta data\new\data _thesis\NCEP\.Net files\air.mon.mean.nc
Format:
           netcdf4_classic
Global Attributes:
           description = ' Data from NCEP initialized reanalysis (4x/day).  These are interpolated to pressure surfaces from model (sigma) surfaces.'
           platform    = 'Model'
           Conventions = 'COARDS'
           NCO         = '20121012'
           history     = 'Mon Jul  5 21:45:36 1999: ncrcat air.mon.mean.nc /Datasets/ncep.reanalysis.derived/pressure/air.mon.mean.nc /dm/dmwork/nmc.rean.ingest/combinedMMs/air.mon.mean.nc
                         /home/hoop/crdc/cpreanjuke2farm/cpreanjuke2farm Tue Oct 17 20:07:08 1995 from air.85.nc
                         created 95/02/06 by Hoop (netCDF2.3)
                         Converted to chunked, deflated non-packed NetCDF4 2014/09'
           title       = 'monthly mean air from the NCEP Reanalysis'
           References  = 'http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis.derived.html'
Dimensions:
           level = 17
           lat   = 73
           lon   = 144
           time  = 818   (UNLIMITED)
Variables:
    level
           Size:       17x1
           Dimensions: level
           Datatype:   single
           Attributes:
                       units        = 'millibar'
                       long_name    = 'Level'
                       positive     = 'down'
                       GRIB_id      = 100
                       GRIB_name    = 'hPa'
                       actual_range = [1.00e+03 1.00e+01]
                       axis         = 'Z'
    lat  
           Size:       73x1
           Dimensions: lat
           Datatype:   single
           Attributes:
                       units         = 'degrees_north'
                       actual_range  = [9.00e+01 -9.00e+01]
                       long_name     = 'Latitude'
                       standard_name = 'latitude'
                       axis          = 'Y'
    lon  
           Size:       144x1
           Dimensions: lon
           Datatype:   single
           Attributes:
                       units         = 'degrees_east'
                       long_name     = 'Longitude'
                       actual_range  = [0.00e+00 3.58e+02]
                       standard_name = 'longitude'
                       axis          = 'X'
    time 
           Size:       818x1
           Dimensions: time
           Datatype:   double
           Attributes:
                       long_name       = 'Time'
                       delta_t         = '0000-01-00 00:00:00'
                       avg_period      = '0000-01-00 00:00:00'
                       prev_avg_period = '0000-00-01 00:00:00'
                       standard_name   = 'time'
                       axis            = 'T'
                       units           = 'hours since 1800-01-01 00:00:0.0'
                       actual_range    = [1.30e+06 1.89e+06]
    air  
           Size:       144x73x17x818
           Dimensions: lon,lat,level,time
           Datatype:   single
           Attributes:
                       long_name               = 'Monthly Mean of Air temperature'
                       units                   = 'degC'
                       precision               = 2
                       least_significant_digit = 1
                       var_desc                = 'Air Temperature'
                       level_desc              = 'Multiple levels'
                       statistic               = 'Mean'
                       parent_stat             = 'Other'
                       missing_value           = -9.97e+36
                       valid_range             = [-2.00e+02  3.00e+02]
                       dataset                 = 'NCEP Reanalysis Derived Products'
                       actual_range            = [-1.09e+02  4.32e+01]
>>

These are my inputs to dimensions in nc files.

time: 444(means for January 1985 and it will be 445 for February 1985 and soon on till 2015)

Level: 0:1:16 (remains same in each file)

Lat:21:1:28 (remains same in each file)

Lon:24:1:31 (remains same in each file)

Save these text files in name like jan, feb,march,aparil,.....dec and make a folder with name of each year like 1985, 1986,1987...2015 where this code save monthly text files of the same year.

At end i have 30 folders(from 1985 to 2015) and 12 text files exporting from nc file in each folder.

My nc file exceeding 5Mb upload size that why i am sharing link NCEP/NCAR where i download my air.mon.mean.nc file. and i am using Rmatlab2013b version of matlab.

output text files for 1985 has been attached remaining are just like of that. Please help!

[Muhammad Usman Saleem]

At NetCDF to text i find some build in tool to get data from Netcdf files and export it to ASCII file. But no idea how to use it for my requirement?

[Muhammad Usman Saleem]

i start from this but not know what i am doing??

file = 'air.mon.mean.nc';
ncdisp(file)
 longitude = ncread(file,'lon');
  latitude = ncread(file,'lat');
  time = ncread(file,'time');
  temp = ncread(file,'air',[444], [0:1:16], [21 1 28],[24:1:31]);

error

   file = 'air.mon.mean.nc';
  ncdisp(file)
   longitude = ncread(file,'lon');
    latitude = ncread(file,'lat');
    time = ncread(file,'time');
    temp = ncread(file,'air',[444], [0:1:16], [21 1 28],[24:1:31]);
  Source:
             E:\meta data\new\data _thesis\NCEP\.Net files\air.mon.mean.nc
  Format:
             netcdf4_classic
  Global Attributes:
             description = ' Data from NCEP initialized reanalysis (4x/day).  These are interpolated to pressure surfaces from model (sigma) surfaces.'
             platform    = 'Model'
             Conventions = 'COARDS'
             NCO         = '20121012'
             history     = 'Mon Jul  5 21:45:36 1999: ncrcat air.mon.mean.nc /Datasets/ncep.reanalysis.derived/pressure/air.mon.mean.nc /dm/dmwork/nmc.rean.ingest/combinedMMs/air.mon.mean.nc
                           /home/hoop/crdc/cpreanjuke2farm/cpreanjuke2farm Tue Oct 17 20:07:08 1995 from air.85.nc
                           created 95/02/06 by Hoop (netCDF2.3)
                           Converted to chunked, deflated non-packed NetCDF4 2014/09'
             title       = 'monthly mean air from the NCEP Reanalysis'
             References  = 'http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis.derived.html'
  Dimensions:
             level = 17
             lat   = 73
             lon   = 144
             time  = 818   (UNLIMITED)
  Variables:
      level
             Size:       17x1
             Dimensions: level
             Datatype:   single
             Attributes:
                         units        = 'millibar'
                         long_name    = 'Level'
                         positive     = 'down'
                         GRIB_id      = 100
                         GRIB_name    = 'hPa'
                         actual_range = [1.00e+03 1.00e+01]
                         axis         = 'Z'
      lat  
             Size:       73x1
             Dimensions: lat
             Datatype:   single
             Attributes:
                         units         = 'degrees_north'
                         actual_range  = [9.00e+01 -9.00e+01]
                         long_name     = 'Latitude'
                         standard_name = 'latitude'
                         axis          = 'Y'
      lon  
             Size:       144x1
             Dimensions: lon
             Datatype:   single
             Attributes:
                         units         = 'degrees_east'
                         long_name     = 'Longitude'
                         actual_range  = [0.00e+00 3.58e+02]
                         standard_name = 'longitude'
                         axis          = 'X'
      time 
             Size:       818x1
             Dimensions: time
             Datatype:   double
             Attributes:
                         long_name       = 'Time'
                         delta_t         = '0000-01-00 00:00:00'
                         avg_period      = '0000-01-00 00:00:00'
                         prev_avg_period = '0000-00-01 00:00:00'
                         standard_name   = 'time'
                         axis            = 'T'
                         units           = 'hours since 1800-01-01 00:00:0.0'
                         actual_range    = [1.30e+06 1.89e+06]
      air  
             Size:       144x73x17x818
             Dimensions: lon,lat,level,time
             Datatype:   single
             Attributes:
                         long_name               = 'Monthly Mean of Air temperature'
                         units                   = 'degC'
                         precision               = 2
                         least_significant_digit = 1
                         var_desc                = 'Air Temperature'
                         level_desc              = 'Multiple levels'
                         statistic               = 'Mean'
                         parent_stat             = 'Other'
                         missing_value           = -9.97e+36
                         valid_range             = [-2.00e+02  3.00e+02]
                         dataset                 = 'NCEP Reanalysis Derived Products'
                         actual_range            = [-1.09e+02  4.32e+01]
  Error using ncread (line 56)
  Too many input arguments.

[Muhammad Usman Saleem]

according to documentation , i am trying this

temp = ncread(file, 'air', [24 21 0 444], [31 28 16 444]);
%file means nc files with air variable
%[24 21 0 444] means start lon 24 lati 21 level 0 and time 444 
%[31 28 16 444] means till lon 31 lati 28 level 16 and time of 444 ???

But i am getting this error

Error using ncread
Expected start to be positive.

Error in internal.matlab.imagesci.nc/read (line 557)
                    validateattributes(start,{'numeric'},...

Error in ncread (line 58)
vardata = ncObj.read(varName, varargin{:});

[Muhammad Usman Saleem]

I find this code, but not idea how can i use it for or how can i set input arguments according to my requirement?

function [ value pressure latitude longitude] = get_NCEP_NCAR(year,month,field)
%Field is the type of variable you want : geopotential_height,temperature,u,v,w
%Dimension of output value is (time,pressure_level,latitude,longitude)         
folder='/where_the_netcdf_are/';
%List the files in selected folder
air_list=dir([folder,'air.',num2str(year,'%04i'),'*']);
hgt_list=dir([folder,'hgt.',num2str(year,'%04i'),'*']);
omega_list=dir([folder,'omega.',num2str(year,'%04i'),'*']);
uwnd_list=dir([folder,'uwnd.',num2str(year,'%04i'),'*']);
vwnd_list=dir([folder,'vwnd.',num2str(year,'%04i'),'*']); 
if(strcmp(field,'temperature'))
filename=air_list.name;
filepath=[folder,filename];
ncid=netcdf.open(filepath,'NC_NOWRITE');
varid=netcdf.inqVarID(ncid,'air');                
end  
if(strcmp(field,'geopotential_height'))
filename=hgt_list.name;
filepath=[folder,filename];
ncid=netcdf.open(filepath,'NC_NOWRITE');varid=netcdf.inqVarID(ncid,'hgt');                                   
end
if(strcmp(field,'w'))
filename=omega_list.name;
filepath=[folder,filename];
ncid=netcdf.open(filepath,'NC_NOWRITE');
varid=netcdf.inqVarID(ncid,'omega');
end
if(strcmp(field,'u'))
filename=uwnd_list.name;
filepath=[folder,filename];
ncid=netcdf.open(filepath,'NC_NOWRITE');
varid=netcdf.inqVarID(ncid,'uwnd');
end  
if(strcmp(field,'v'))
filename=vwnd_list.name;
filepath=[folder,filename];
ncid=netcdf.open(filepath,'NC_NOWRITE');
varid=netcdf.inqVarID(ncid,'vwnd');
end
varidp=netcdf.inqVarID(ncid,'level');
varidlat=netcdf.inqVarID(ncid,'lat');
varidlon=netcdf.inqVarID(ncid,'lon');
varidt=netcdf.inqVarID(ncid,'time');
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
value=netcdf.getVar(ncid,varid,'short');
scale = netcdf.getAtt(ncid,varid,'scale_factor');
offset= netcdf.getAtt(ncid,varid,'add_offset');
value=double(value)*scale+offset;
value=single(permute(value,[4 3 2 1]));
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
pressure=single(netcdf.getVar(ncid,varidp));
latitude=single(netcdf.getVar(ncid,varidlat));
longitude=single(netcdf.getVar(ncid,varidlon));
%to keep only the time asked for
time=netcdf.getVar(ncid,varidt);     
dayssince111=time/24;
datevalue=dayssince111+datenum(1,1,1)-2;  
mm=datevec(datevalue); mm=mm(:,2);
value=value(month==mm,:,:,:);                
netcdf.close(ncid);
value(value>10^14)=nan;
%pads the data for the month with NAN if not all month is available yet
theoreticaltime=datenum(year,month,1):(datenum(year,month+1,1)-1);
ts=length(theoreticaltime)*4;
dummy=zeros([ts,length(pressure),length(latitude),length(longitude)]);
dummy=dummy*0/0;
dummy(1:size(value,1),:,:,:)=value;
value=dummy;
end

[Muhammad Usman Saleem]

I have one .nc file with name air.nc which contains temperature data. I am getting confusion in these line?

function [ value pressure latitude longitude] = get_NCEP_NCAR(year,month,field)

How can i set inputs to my requirements??

%Field is the type of variable you want : geopotential_height,temperature,u,v,w %Dimension of output value is (time,pressure_level,latitude,longitude)

folder='/where_the_netcdf_are/';

my air.nc file is in E:\meta data\new\data _thesis\NCEP\.Net files and this function is also save in the same folder. Tell me how can i arrange my nc files according to below code requirements?

%List the files in selected folder
air_list=dir([folder,'air.',num2str(year,'%04i'),'*']);
hgt_list=dir([folder,'hgt.',num2str(year,'%04i'),'*']);
omega_list=dir([folder,'omega.',num2str(year,'%04i'),'*']);
uwnd_list=dir([folder,'uwnd.',num2str(year,'%04i'),'*']);
vwnd_list=dir([folder,'vwnd.',num2str(year,'%04i'),'*']);

Please assist?

Answer 1

[KSSV]

Reading nc file is very easy in MATLAB. Use ncdisp('air.mon.mean.nc') to view the contents of the file. ncdisp shows you variables, dimensions of the file. After looking into variables, you can read what ever the variable you want. To read longitude and latitude: lon = ncread('air.mon.mean.nc','Lon') ; % Lon is variable as given above lat = ncread('air.mon.mean.nc','Lat') ; % LAt is variable as given above

Like wise using ncread you can read all the variables. Once you have the data in workspace, you can write it into any format you want.

[Muhammad Usman Saleem]

Thanks for your kind assistance.

I am getting that error

a=ncdisp('air.mon.mean.nc')
Error using ncdisp
Too many output argument

[KSSV]

ncdisp cannot be taken as output. Simply try ncdisp. Or a = ncinfo('air.mon.mean.nc') ; a will be your structure with all information.

[Muhammad Usman Saleem]

Now this is an error with no variable in workspace

>> a = ncinfo('air.mon.mean.nc') ;
Error using netcdflib
The NetCDF library encountered an error during execution of 'open' function - 'HDF error
(NC_EHDFERR)'.
Error in netcdf.open (line 59)
        [varargout{:}] = netcdflib ( 'open', filename, varargin{1} );
Error in internal.matlab.imagesci.nc/openToRead (line 1257)
            this.ncRootid = netcdf.open(this.Filename,'NOWRITE');
Error in internal.matlab.imagesci.nc (line 121)
                    this.openToRead();
Error in ncinfo (line 80)
ncObj   = internal.matlab.imagesci.nc(ncFile);

but when i try to read others nc files of my data sets its works and creating a structure in workspace

>> a = ncinfo('pottmp.mon.mean.nc') ;
>> b = ncinfo('pottmp.mon.mean.nc') ;
>> b = ncinfo('rhum.mon.mean.nc') ;
>> c = ncinfo('pottmp.mon.mean.nc') ;

Now what i do next?

[KSSV]

what version of MATLAB you are using? As it is reading other ncfiles...are you giving the ncfile name properly? Is ncfile lying in the path?

[Muhammad Usman Saleem]

I am using Rmat2013b, i download new air.mon.mean.nc and run

a = ncinfo('air.mon.mean.nc') ;

which is creating a structure in workspace now what i do for latitude and longitude , pressure levels, and time of my requirements.?

[KSSV]

Dear friend ...

I have already answered that.

[Muhammad Usman Saleem]

what you answered related to nc not with structure. Now i have structure in hand what to do when i make a call to latitude,lon,level,time. I am never experience with nc files so sending you more detail of structure variable created in my workspace

when i click on one of the structure variable, i got

when i click on dimension , i got

'level'  8  false
'lat'  73  false
'lon'  144  false
'time'  818  true

when i click on variable , i got

'level'  1x1 struct

  8  'single'  1x7 struct

  []  9.9692100e+36  []  false
'lat'  1x1 struct

  73  'single'  1x5 struct

  []  9.9692100e+36  []  false
'lon'  1x1 struct

  144  'single'  1x5 struct

  []  9.9692100e+36  []  false
'time'  1x1 struct

  818  'double'  1x8 struct

  1  9.96920996838687e+36  []  false
'rhum'  1x4 struct

  [144,73,8,818]  'single'  1x12 struct
  [144,73,1,1]  9.9692100e+36  2  true

when i click on attributes, i got

'description'  'Data from NCEP initialized reanalysis (4x/day).  These are interpolated to pressure surfaces from model (sigma) surfaces'
'platform'  'Model'
'Conventions'  'COARDS'
'NCO'  '20121012'
'history'  'Thu May  4 18:11:03 2000: ncrcat -d time,0,622 /Datasets/ncep.reanalysis.derived/pressure/rhum.mon.mean.nc ./pressure/rhum.mon.mean.nc
Mon Jul  5 22:22:51 1999: ncrcat rhum.mon.mean.nc /Datasets/ncep.reanalysis.derived/pressure/rhum.mon.mean.nc /dm/dmwork/nmc.rean.ingest/combinedMMs/rhum.mon.mean.nc
created by Cathy Smith 12/5/95
(netCDF2.3)
Converted to chunked, deflated non-packed NetCDF4 2014/09'
'title'  'monthly mean rhum from the NCEP Reanalysis'
'References'  'http://www.esrl.noaa.gov/psd/data/gridded/data.ncep.reanalysis.derived.html'

when i click on group, i got empty array

when i click on format i got

'netcdf4_classic'

Please read my question and my requirement and please then answer.

[Muhammad Usman Saleem]

Dear Dr. Siva Srinivas Kolukula ;

I am trying this but last line is not running finely.

ncid1 = netcdf.open('air.mon.mean.nc','NC_NOWRITE'); 
level1 = netcdf.getVar(ncid1,0,1,16)
lat1 = netcdf.getVar(ncid1,1,21,28)
lon1 = netcdf.getVar(ncid1,2,24,31)
time1 = netcdf.getVar(ncid1,3,444,455)

other two lines are fine.

Error

Error using netcdf.open (line 44) Error using netcdflib The NetCDF library encountered an error during execution of 'getVaraDouble' function - 'Start+count exceeds dimension bound (NC_EEDGE)'.

Error in netcdf.getVar (line 136)
    data = netcdflib(funcstr,ncid,varid,varargin{:});

Although when i check no of variables by using

    [ndim, nvar, natt, unlim] = netcdf.inq(ncid1)

output

>> [ndim, nvar, natt, unlim] = netcdf.inq(ncid1)

ndim =

       4

nvar =

       5

natt =

       7

unlim =

       3