How to read netCDF file ?

l downloaded netCDF master. zip and GEBCO_2020.nc file.

I want to read this netCDF file and plot. But l met this error. What should I do?

Error using internal.matlab.imagesci.nc/openToRead (line 1272)
Could not open GEBCO_2020.nc for reading.

Error in internal.matlab.imagesci.nc (line 121)
                    this.openToRead();

Error in ncdisp (line 62)
ncObj   = internal.matlab.imagesci.nc(ncFile);

Error in read_necdf (line 12)
ncdisp(file)

Below is the code I used.

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
clear all; close all;
% set(0,'Units','pixels');
% scnsize = get(0,'ScreenSize');
% pos1 = [10, 10, 1910, 1070];

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 
file = 'GEBCO_2020.nc';

% 
ncdisp(file)

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
% 
time = ncread(file,'time')

% 
shot = ncread(file,'shot');
depth = ncread(file,'depth');
SS = ncread(file,'SS',[1 1],[Inf Inf]);
% SS = ncread(file,'temp',[1 1],[Inf Inf]);
% SS = ncread(file,'sal',[1 1],[Inf Inf]);

figure(1);
plot(shot);

figure(3);
plot(depth);

% % 
% SS_struct = struct( 'shot', shot, 'depth', depth, 'SS', SS );
% SS_mod = struct('SS',SS_struct);
% 
% [xx,yy] = meshgrid(SS_mod.SS_struct.shot,SS_mod.SS_struct.depth);
% zz = SS_mod.SS_struct.SS_struct(:,:,1);

figure(2);
% pcolor(double(xx),double(yy),double(zz))
pcolor( double(SS) );
% caxis([1500 1520]);
colorbar('location','EastOutside'); set(gca,'linewidth',1,'fontsize',16);
shading flat; axis('ij');

[Walter Roberson]

Either it could not find the file on the MATLAB path, or else it found the file but you do not have read permission for the file.

[KSSV]

What does this line show?

ncdisp(file)

[Walter Roberson]

I am downloading the file from https://www.gebco.net/data_and_products/gridded_bathymetry_data/ but it is a bit slow...

[주향 이]

ncdisp.m file in the netCDP master.zip. Do you want i show you thid code?

[주향 이]

@Walter Roberson

yes this file is 7GB😂

[Walter Roberson]

I went to https://www.gebco.net/data_and_products/gridded_bathymetry_data/ and downloaded https://www.bodc.ac.uk/data/open_download/gebco/gebco_2020/zip/ which contains gebco_2020_netcdf.zip which contains a directory gebco_2020_netcdf which contains two .pdf files and GEBCO_2020.nc . The .zip is 4 Gigabytes, expanding to 7 gigabytes.

However.. that nc file does not have any time information, only lat, lon, and elevation.

Which file are you looking at?

[주향 이]

Ah... I just thught this funtion reads my netCDF file and plots figure.

I don't need time information.

So l delete time = ncread(file,'time') ?

Answer 1

[KSSV]

I will recommend you to use this file exchange function:

https://in.mathworks.com/matlabcentral/fileexchange/46669-gebconetcdf-file-wlon-elon-slat-nlat

[주향 이]

Thank you !

But l met error...

Error: File: gebconetcdf.m Line: 1 Column: 46

Invalid expression. Check for missing multiplication operator, missing or unbalanced delimiters, or other syntax

error. To construct matrices, use brackets instead of parentheses.

I followed example's code. GEBCO_2020.nc file in the matlab folder.

l copied location of this file's properties.

%   --Example--------------------------------------------------------------
%
%   Retrieve the bathymetry data for the Baltic Sea:
%
%   [BATHY XGRID YGRID] = gebconetcdf('C:\GISdata\gebco_08.nc',...
%   +10.0, +26.0, +52.00, +66.00)

Below code has problem ?

function [BATHY, XGRID, YGRID] = gebconetcdf('C:\Users\wngid\OneDrive\5744~1-DESKTOP-2A49GC5\GEBCO_2020.nc', +10.0, +26.0, +52.00, +66.00);
%[BATHY, XGRID, YGRID] = gebconetcdf(FILE, Wlon, Elon, Slat, Nlat)
%
%   This function opens a GEBCO bathymetry NetCDF file and retrieves data 
%   for a desired latitude/longitude window. Note: Be careful when 
%   selecting a very large area of the world (e.g. entire oceans) as the 
%   GEBCO data are stored as 16-bit and memory can run out quickly.
%
%   Author: Bryan C. Lougheed. Date: May 2014.
%   Written using MatLab version 2012a.
%
%   --Input parameters-----------------------------------------------------
%
%   FILE is a string specifying the location of the GEBCO bathymetry NetCDF
%   file, e.g. 'gebco_08.nc'. Both the half-minute and one-minute datasets
%   should be automatically recognised. HOWEVER, to avoid crash, it is best 
%   to use the half-minute NetCDF for the entire world, as this script is
%   optimised for that one, and GEBCO aren't particularly consistent in how
%   they design NetCDF files for different resolutions/regions.
%   
%   Wlon, Elon, Slat and Nlat are the decimal degree values of the
%   western, eastern, southern and northern limits of the desired lat/lon
%   window, whereby degrees N should be entered as positive, degrees S as
%   negative, degrees W as negative and degrees E as positive. The nearest
%   possible coordinates in the GEBCO bathymetry NetCDF file will be
%   used.
%
%   --Output data----------------------------------------------------------
%   
%   BATHY: Matrix containing the gridded elevation/bathymetry data for the
%   desired lat/lon window.
%
%   XGRID, YGRID: Matrices of same dimensions as BATHY, containing the
%   longitude (XGRID) and latitude (YGRID) coordinates for each datapoint
%   in BATHY. Coordinates are in decimal degrees and represent the
%   centre-of-pixel coordinates.
%
%   --Example--------------------------------------------------------------
%
%   Retrieve the bathymetry data for the Baltic Sea:
%
%   [BATHY XGRID YGRID] = gebconetcdf('C:\GISdata\gebco_08.nc',...
%   +10.0, +26.0, +52.00, +66.00)
%

% Open the NetCDF file
gebconc = netcdf.open(FILE, 'GEBCO_2020.nc');

% Find information about the data contained within the file
west = netcdf.getVar(gebconc,0,0,1);
east = netcdf.getVar(gebconc,0,1,1);
north = netcdf.getVar(gebconc,1,1,1);
south = netcdf.getVar(gebconc,1,0,1);
resdata = netcdf.getVar(gebconc,3,0,1);

% All avaliable lat and lon coordinates in GEBCO file
cols = west+(resdata/2)  :  resdata : east-(resdata/2);
rows = north-(resdata/2) : -resdata : south+(resdata/2);
      
% find col and row indexes nearest to desired window
[~, start_col] = min(abs(cols - (Wlon+1*10e-100)));
[~, end_col] = min(abs(cols - (Elon-1*10e-100)));
[~, start_row] = min(abs(rows - (Nlat-1*10e-100)));
[~, end_row] = min(abs(rows - (Slat+1*10e-100)));

% Prep output matrix
BATHY = NaN(length(start_row:1:end_row),length(start_col:1:end_col));

% Read out data row by row
output_row = 0;
for i = start_row:1:end_row;

    start_index = ((i-1)*length(cols)) + start_col - 1; %subtract one (zero based indexing in NetCDF)

    count = length(start_col:1:end_col);

    row_slice = netcdf.getVar(gebconc,5,start_index,count);

    output_row = output_row+1;
    BATHY(output_row,:) = row_slice(:,:);
end

% Close the NetCDF file
netcdf.close(gebconc);

% Make meshgrid
[XGRID YGRID] = meshgrid( cols(start_col):resdata:cols(end_col) , rows(start_row):-resdata:rows(end_row) );

end

[KSSV]

You download the function and save it in a folder. The function will be saved on the name gebconetcdf.m. Now go to the folder, where this function is present. You have to call the function now. Call usig:

file = 'C:\Users\wngid\OneDrive\5744~1-DESKTOP-2A49GC5\GEBCO_2020.nc' ; 
[BATHY, XGRID, YGRID] = gebconetcdf(file, +10.0, +26.0, +52.00, +66.00);

You are getting error because, you are inputting the values staright away to the function, this is not allowed.

[주향 이]

Thank you!

Out of memory. The likely cause is an infinite recursion within the program.

l met this error..

[KSSV]

Reduce the bounding box.... The data which you are trying to read is huge and your RAM cannot support that much size.