"Error using textscan Invalid file identifier. Use fopen to generate a valid file identifier." - why am i getting this error?

% Read the data from the file

fid = fopen('gc-data-2.txt', 'r');
data = textscan(fid, '%f %s %f');

Error using textscan
Invalid file identifier. Use fopen to generate a valid file identifier.

fclose(fid);

% 1.Identify the lines that contain data

ind = regexp(data{1}, 'Data');
ind = find(~cellfun(@isempty, ind));

% 2.Get the number of data points
npoints = length(ind);

% Read up to the data
x = data{1}(1:ind(1)-1);
y = data{2}(1:ind(1)-1);

% 3.    Initialize the data vectors
time = zeros(npoints, 1);
signal = zeros(npoints, 1);

% Read in the data
for i = 1:npoints
    time(i) = data{1}(ind(i));
    signal(i) = data{2}(ind(i));
end

% 4.Plot the data
figure
plot(time, signal)
xlabel('Time (s)')
ylabel('Signal')
title('data')

% Correct for non-zero baseline
signal = signal - mean(signal);

% 5.Implementing a fitting procedure using a decaying gaussian function
% Define the decaying gaussian function
gauss = @(p, x) p(1)*exp(-((x - p(2))./p(3)).^2) + p(4);

% Define the objective function
obj = @(p) sum((gauss(p, time) - signal).^2);

% Define the initial guess for the parameters
p0 = [1, mean(time), std(time), 0];

% Optimize the parameters
p = fminsearch(obj, p0);

% 6. implementing a fitting procedure with two peaks and plot the fitting function with an initial guess for each parameter
% Define the function that adds two decaying gaussian functions
gauss2 = @(p, x) p(1)*exp(-((x - p(2))./p(3)).^2) + p(4) + p(5)*exp(-((x - p(6))./p(7)).^2) + p(8);

% 7. Plot fitting function with an initial guess for each parameter
% First we define Define the initial guess for the parameters
p0 = [1, mean(time), std(time), 0, 1, mean(time), std(time), 0];

% Plot the fitting function with the initial guess for the parameters
figure
plot(time, gauss2(p0, time))
xlabel('Time (s)')
ylabel('Signal')
title('fitting function with initial guess')

% 8.using nonlinear fitting to get the parameters that best fit our data, and ploting the fit on the graph 
% Optimize the parameters
p2 = lsqnonlin(obj2, p0);

% Plot the fit on the graph
figure
plot(time, signal)
hold on
plot(time, gauss2(p2, time))
xlabel('Time (s)')
ylabel('Signal')

% 9.extracting out the two peaks and integrating the areas 
% Extract the two peaks
peak1 = gauss(p2(1:4), time);
peak2 = gauss(p2(5:8), time);
% Display the two peaks extracted
figure
plot(time, peak1)
hold on
plot(time, peak2)
xlabel('Time (s)')
ylabel('Signal')
legend('Peak 1', 'Peak 2')
title('the two extracted peaks')

% Integrate the areas
area1 = trapz(time, peak1);
area2 = trapz(time, peak2);
% Display the integrated areas
fprintf('Integrated area 1: %f\n', area1)
fprintf('Integrated area 2: %f\n', area2)

% 10.Compute the relative amounts
rel1 = area1/(area1 + area2);
rel2 = area2/(area1 + area2);
% Display the relative amounts
fprintf('Relative amount 1: %f\n', rel1)
fprintf('Relative amount 2: %f\n', rel2)

[RIHANA ALI]

what am i supposed to fix

ind = regexp(data{1}, 'Data');
ind = find(~cellfun(@isempty, ind));

Error using cellfun

Input #2 expected to be a cell array, was double instead

[Jeslyn]

why does it say index exceeds the number of array elements.

[Voss]

@Jeslyn: That error happens when attempting to access an element beyond the size of the array.

Example:

x = [10 20 30]

x = 1x3

10 20 30

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x(1) % ok

ans = 10

x(2) % ok

ans = 20

x(3) % ok

ans = 30

x(4) % error: no x(4), x has only 3 elements

Index exceeds the number of array elements. Index must not exceed 3.

[Walter Roberson]

ind = regexp(data{1}, 'Data');

The default output from regexp is a numeric vector of indices of matches.

ind = find(~cellfun(@isempty, ind));

You cannot cellfun() over a numeric vector.

But

data = textscan(fid, '%f %s %f');

textscan() returns a cell array with one entry for each un-suppressed format specifier. The cell array entries have datatype according to the format specifier. The %f format will result in the cell array entry being an array of double.

You then try to regexp() that array of doubles, which is likely to fail.

Answer 1

[Cris LaPierre]

The most likely reason is because the file you are trying to open does not exist. Check that you have spelled the file name correctly, and that the file is either in your current folder, or in a folder that has been added to your MATLAB Path.

You many need to include the path to the file (relative or absolute) along with the filename to fopen. You may want to consider using fullfile to construct that.

[RIHANA ALI]

yes , your right the file name was spelled wrong.Thank you