loop to read netcdf files

hi, I have hundreds of netcdf files to work and I want to generate a loop to read all of them and save the result in other folder. The result it is a cut (a smaller region of interest) and then I will calculate the mean value. I have done the code for a single file and it works:

ncid1=netcdf.open('ESACCI-SOILMOISTURE-L3S-SSMV-COMBINED-20100101000000-fv02.2.nc', 'NC_NOWRITE');

varname = netcdf.inqVar(ncid1,4);

varid = netcdf.inqVarID(ncid1,varname);

data = netcdf.getVar(ncid1,varid);

lon1=netcdf.getVar(ncid1,0,0,1440);

lat1=netcdf.getVar(ncid1,1,0,720);

[longrid,latgrid]=meshgrid(lon1,lat1);

data2=data((longrid>-1)&(longrid<0)&(latgrid>39)&(latgrid<40));

(the mean value I will calculate it when I have all the files cut). I have found some information on previous answers but I am still not able to solve it. It works until sentence "%Now do whatever you want with this file name" because it is copied from internet and I don't know how to continue:

% Specify the folder where the files are.
myFolder = 'G:\DATA_validation\ESA\data\daily_files\COMBINED\v02.2\2010\files';

% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isdir(myFolder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', myFolder);
  uiwait(warndlg(errorMessage));
  return;
end

% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(myFolder, '*.nc'); 
theFiles = dir(filePattern);

for k = 1 : length(theFiles)
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(myFolder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);

    % Now do whatever you want with this file name

    ncid=netcdf.open(theFiles(k), 'NC_NOWRITE');
    varname = netcdf.inqVar(ncid,4);
    varid = netcdf.inqVarID(ncid,varname);
    data(k) = netcdf.getVar(ncid,varid);
    end

Thanks in advanced, I'm not good coding... if you don't understand me just ask!

Answer 1

[Maite M.]

just in case someone need it, I could solve it and I share the code, I haven't finished yet, but my doubt is solved as:

% Specify the folder where the files are.
myFolder = 'G:\SWICCA\DATA_validation\ESA\data\daily_files\COMBINED\v02.2\2010\files';

% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isdir(myFolder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', myFolder);
  uiwait(warndlg(errorMessage));
  return;
end

filePattern = fullfile(myFolder, '*.nc'); 
theFiles = dir(filePattern);

% Loop for each nc-file
for i = 1:length(theFiles)
  baseFileName = theFiles(i).name;
  fullFileName = fullfile(myFolder, baseFileName);
%     fprintf(1, 'Now reading %s\n', fullFileName);
%     ncdisp(ncfiles(i).name) ;
     ncid=netcdf.open(fullFileName, 'NC_NOWRITE');
     varname= netcdf.inqVar(ncid,4);
     varid = netcdf.inqVarID(ncid,varname);
%      data = netcdf.getVar(ncid,varid);
     netcdf.close(ncid);
end

Answer 2

[KSSV]

% Read the names of nc-files in the folder 
ncfiles = dir('*.nc') ;
Nfiles = length(ncfiles) ;     % Total number of nc files 
% Loop for each nc-file
for i = 1:Nfiles
    % display the nc file 
    ncdisp(ncfiles(i).name) ;   % call the nc file by ncfiles(i).name
    % do what you want %
end

In the above I am displaying nc-files in the loop; you can do what ever you want instead. hope the above hint helps you.

[Maite M.]

thank you a lot for answering, it's much simpler now but still I can't read the files...

for i = 1:Nfiles
    ncid=netcdf.open('ncfiles(i)', 'NC_NOWRITE');
    varname = netcdf.inqVar(ncid,4);
    varid = netcdf.inqVarID(ncid,varname);
    data(i) = netcdf.getVar(ncid,varid);
end

How should I write the inside part of the loop? I want to read every file and save each one as a matrix "data" in other folder. This matrix should contain only "varname" data.

[KSSV]

You make your code to read single variable into a function and call it inside the loop.