A problem with a code that works as it is but gives an index error when is used inside a function

Hi,

I am writting a code that basically reads force curves from my microscope and then auto-align them based on their baseline and the offset. After it does it, I then divide the data into 30 graphs blocks so that I can remove bad curves. I basically 113 curves so there are 4 blocks where the last block has only 23 curves.

The problem is that when I run the code by itself it works perfectly. However when I put it inside a function, I am getting when it enter the 4th block the following error message: "Index in position 2 exceeds array bounds. Index must not exceed 100. Error in cleaner (line 118) z_corrj = z_corr(:, j);" - I just can't understand why it works perfectly but crashes when it is part of the function.

Here is the original code:

block_size = 30;
% Calculate the number of blocks
num_blocks = ceil(size((d_corr),1) / block_size)
% Loop through each dataset
for i = 1:num_blocks
    figure;
    hold on;
    start_idx = (i-1) * block_size + 1;
    end_idx = min(i*block_size, size((d_corr),1));
    % Extract the i-th column for X and Y
    for j = start_idx:end_idx
        z_corrj = z_corr(:, j);
        d_corrj = d_corr(:, j);
        % Assign a constant Z value for this dataset
        Zj = ones(size(z_corrj)) * j;
        
        % Plot using plot3
        plot3(z_corrj, d_corrj, Zj);
    end
    % Customize the plot
    xlabel('Z [nm]');
    ylabel('Deflection [V]');
    zlabel('Index');
    title('3D Plot of 10 XY sets');
    grid on;
    % Set the view orientation
    azimuth = 117.4; % Azimuth angle in degrees
    elevation = 50; % Elevation angle in degrees
    view(azimuth, elevation);
    hold off;
    %Remove bad curves
    trash = 0;
    trash = input('If you want to remove a curve, input its number x (press Enter if you are done): ');
    if trash
        z_corr(:,trash) = [];
        d_corr(:,trash) = [];
    else
        
    end
    if i<num_blocks
        disp('Press Enter to display the next block')  ;
        pause;
    end
end

Answer 1

[Voss]

Based on the error message, "Index in position 2 exceeds array bounds. Index must not exceed 100. Error in cleaner (line 118) z_corrj = z_corr(:, j);" we know that z_corr has 100 columns. And since you say you have 113 curves, I'll assume that each curve corresponds to a row of z_corr, so that z_corr has 113 rows. I'll also assume d_corr and z_corr have the same size.

If those assumptions are correct, then the problem is that you are taking the jth column of z_corr and d_corr here

z_corrj = z_corr(:, j);

d_corrj = d_corr(:, j);

when you should be taking the jth row

z_corrj = z_corr(j, :);

d_corrj = d_corr(j, :);

because curves correspond to rows. Your num_blocks and end_idx are based on the number of rows of d_corr (size(d_corr,1)), so you need to take a row from each matrix, not a column.

Making that change (and also commenting out the user-interaction section for running in this environment - and fixing the plot titles to correctly indicate the number of curves while I'm at it) the code runs without error, using random 113-by-100 matrices for d_corr and z_corr:

d_corr = rand(113,100);
z_corr = rand(113,100);

block_size = 30;
% Calculate the number of blocks
num_blocks = ceil(size((d_corr),1) / block_size)

num_blocks = 4

% Loop through each dataset
for i = 1:num_blocks
    figure;
    hold on;
    start_idx = (i-1) * block_size + 1;
    end_idx = min(i*block_size, size((d_corr),1));
    % Extract the j-th row for X and Y
    for j = start_idx:end_idx
        z_corrj = z_corr(j, :);
        d_corrj = d_corr(j, :);
        % Assign a constant Z value for this dataset
        Zj = ones(size(z_corrj)) * j;
        
        % Plot using plot3
        plot3(z_corrj, d_corrj, Zj);
    end
    % Customize the plot
    xlabel('Z [nm]');
    ylabel('Deflection [V]');
    zlabel('Index');
    title(sprintf('3D Plot of %d XY sets',end_idx-start_idx+1));
    grid on;
    % Set the view orientation
    azimuth = 117.4; % Azimuth angle in degrees
    elevation = 50; % Elevation angle in degrees
    view(azimuth, elevation);
    hold off;
    % %Remove bad curves
    % trash = 0;
    % trash = input('If you want to remove a curve, input its number x (press Enter if you are done): ');
    % if trash
    %     z_corr(:,trash) = [];
    %     d_corr(:,trash) = [];
    % else
    % 
    % end
    % if i<num_blocks
    %     disp('Press Enter to display the next block')  ;
    %     pause;
    % end
end