Reading multiple nc files in different subfolders within a directory

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skanwal
skanwal 2018-12-11
评论： skanwal 2018-12-12
Hi,
My data is stored in a folder withch contains subfolders cyc001, cyc002, cyc003...cyc258 each with 15 .nc files. I have written this code to explore the main data data directory and each cyc* subdirectories (total 258),read data from 15 nc files, retrieve certain fields in each .nc filesand store/save as output (passes). My code works well for one cyc001 folder but it failes to read the 2nd and subsequen folders.
currentdir= '/Users/Documents/test1';
cd(currentdir);
% For each cyc subdirectory
list_cycle= textscan(ls(),'%s');
cyclelist=list_cycle{1,1}(:,:)
j=1;
for c=1:length(cyclelist)
cd(cyclelist{c,1});%change into current cyc
list_dir= textscan(ls('-d','*.nc'),'%s');
dirlist=list_dir{1,1}(:,:)
%read nc files
myFolder=pwd;% folder of each cy
filePattern = fullfile(myFolder, '*.nc');
theFiles = dir(filePattern);
findFileInFolder(pwd,{'.nc'})
% Loop for each nc-file
for k = 1:length(theFiles)
baseFileName = theFiles(k).name;
fullFileName = fullfile(myFolder, baseFileName);
ncid=netcdf.open(fullFileName, 'NC_NOWRITE');
varname= netcdf.inqVar(ncid,4);
varid = netcdf.inqVarID(ncid,varname);
netcdf.close(ncid);
end
ncfiles = dir('*.nc'); % get all nc files in the folder
nfiles = length(ncfiles) ; % total number of files
end
% For each pass (.nc file)
for d=1:length(dirlist)
cd(dirlist{d,1});
data=read_nc(fullFileName); % Read the selected nc files using read_nc func
fprintf('Reading track: %d/%d of pass %d/%d. To read tracks: %d\n',d, length(dirlist),c,length(cyclelist),i);
ind=find((data.glat.Value<lat1)&(data.glat.Value>lat2)&(data.glon.Value<lon1|data.glon.Value>lon2));%find the indices
passe(j).lat= data.glat.Value(ind); % copy the fields in the data structure
passe(j).lon= data.glon.Value(ind); % copy the fields in the data structure
j=j+1;
clear data;
cd('..')
end
cd('..')
cd(currentdir)
It gives me eorror that
Error using cd
Cannot CD to cycle002 (Name is nonexistent or not a directory).
Ithink porblem is where I am trying to read nc files in each cyc... subfolder. Anyone, please help to fix this loop? I am not an expert matlab user so maybe I cam forgetting something and doing something wrong here.
  1 个评论
Stephen23
Stephen23 2018-12-11
编辑：Stephen23 2018-12-11
Do NOT use cd like that. Do NOT change directories just to access data files. It is faster and more robust to use absolute/relative filenames, which you can easily construct using fullfile.
Do NOT use ls in code to get a list of folder contents (it is intended for visual display, not for processing in code). Use dir instead.

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采纳的回答

Stephen23
Stephen23 2018-12-11
编辑：Stephen23 2018-12-11
You should start again, because all of those cd calls are absolute chaos.
Start with something like this:
D = '/Users/Documents/test1';
S = dir(fullfile(D,'cyc*'));
S = {S([S.isdir]).name};
Z = struct('lat',{},'lon',{});
for ii = 1:numel(S)
T = dir(fullfile(D,S{ii},'*.nc'));
T = {T.name};
for jj = 1:numel(T)
F = fullfile(D,S{ii},T{jj})
... your code
Z(ii,jj).lat = ...
Z(ii,jj).lon = ...
end
end
end
https://www.mathworks.com/help/matlab/import_export/process-a-sequence-of-files.html
  1 个评论
skanwal
skanwal 2018-12-12
Hi Stephen, I simply delete the redundant lines and rewrite the code according to the format you advised after adding the above code. It worked. I really ppreciate your help. Thank you,

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更多回答（1 个）

KSSV
KSSV 2018-12-11
ncfiles = dir('*nc') ;
N = length(ncfiles) ;
for i = 1:N
ncfile = ncfiles(i).name ;
% do what you want
end

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