Observation 1: You have
currentFile = files(l).name;
so currentFile is the name of the file only, without any absolute or relative path, so when you do this:
Str=importdata(currentFile);
you are asking to importdata a file in the current directory that may or may not exist.
Instead, to be sure you are referring to the correct file, you can use:
currentFile = fullfile(files(l).folder,files(l).name);
That doesn't sound like the problem you ran into, because you say the code does generate fig files but the figures are empty. (However, if you make the same mistake as above when checking for the fig files, you may not be looking at the files that were generated in the most recent run of the code, if any were generated at all.)
Observation 2: z and w are both NaN with the example file
z = str2double(parts{3}(3:end));
w = str2double(parts{4}(2:end));
The code doesn't seem to conform to the file naming convention, at least for this example file.
If you change it to:
z = str2double(parts{3});
w = str2double(parts{4});
Then you get 0 and 1 for z and w, respectively. Is that what is intended? (Or should they have been NaN? If you want to allow NaNs for z and w, you should use isnan(A(i, trackIDColumn)) instead of A(i, trackIDColumn)==z, etc., because NaN==NaN is false.)
Making those two changes (and removing the redundant readtable call whose result is immediately overwritten) produces a fig file containing a non-empty figure:
% Specify the folder containing your files
folderPath = '.';
saveFolderPath = '.';
% Get a list of all files in the folder
files = dir(fullfile(folderPath, 'export*.csv')); % Assuming filenames start with 'export' and have a '.csv' extension
for l = 1:length(files)
% Get the current file name
% currentFile = files(l).name;
currentFile = fullfile(files(l).folder,files(l).name);
% Extract values of z and w from the filename
[~, fileName, ~] = fileparts(currentFile);
parts = strsplit(fileName, '_');
% z = str2double(parts{3}(3:end));
% w = str2double(parts{4}(2:end));
z = str2double(parts{3});
w = str2double(parts{4});
% % Load data from the current file
% A = readtable(currentFile);
%import table values on matlab
Str=importdata(currentFile);
A=Str.data(:,:);
%i=line in the table
% Determine the column indices for TrackID and Intensity based on the data structure
trackIDColumn = 2; % Adjust this based on the actual structure of your data
intensityColumn = 12; % Adjust this based on the actual structure of your data
% Initialize variables
j = 0;
x0 = [];
k = 0;
x1 = [];
notvalid = 0;
sz = size(A);
% Loop through the data
for i = 1:sz(1)
if A(i, trackIDColumn) == z
j = j + 1;
x0(j, 1) = A(i, 7); % time 0
x0(j, 2) = A(i, intensityColumn); % intensity 0
elseif A(i, trackIDColumn) == w
k = k + 1;
x1(k, 1) = A(i, 7); % time 1
x1(k, 2) = A(i, intensityColumn); % intensity 1
else
notvalid = notvalid + 1;
end
end
% Rest of your existing script...
MS2 = zeros(481, 2);
for TrackID = 0:200
temp = A(A(:, trackIDColumn) == TrackID, [7, intensityColumn]);
MS2(temp(:, 1) + 1, TrackID + 1) = temp(:, 2);
end
% Check if w+1 is a valid index for MS2
if w+1 >= 1 && w + 1 <= size(MS2, 2)
MS2_mirror = -MS2(:, w + 1); % Adjusted for 'w'
MS2_mirror = -MS2(:, w + 1); % Adjusted for 'w'
timeframe = (1:481)';
time = timeframe * 3 - 3;
% TSS1=MS2(:,z),
% Plot
plot(time, MS2(:, z + 1), 'DisplayName', ['TSS 1']) % Adjusted for 'z'
hold on
plot(time, MS2_mirror, 'DisplayName', ['TSS 2']) % Adjusted for 'w'
xlabel('Time (min)', 'FontSize', 10)
xlim([0 1440])
ylabel('Fluorescent intensity', 'FontSize', 10)
legend(['TSS 1'], ['TSS 2'])
else
disp(['Invalid TrackID for w: ' num2str(w)]);
end
% Optionally, you can include a pause or any other necessary delay here
pause(0.5); % Adjust as needed
% Save the figure as JPEG
figJPEGName = fullfile(saveFolderPath, ['Figure_' num2str(z) '_and_' num2str(w) '_' fileName '.jpg']);
saveas(gcf, figJPEGName, 'jpeg');
% Save the figure as MATLAB Figure file
figMatName = fullfile(saveFolderPath, ['Figure_' num2str(z) '_and_' num2str(w) '_' fileName '.fig']);
saveas(gcf, figMatName, 'fig');
% Optionally, you can include a pause or any other necessary delay here
pause(0.5); % Adjust as needed
% End of the loop
close(gcf); % Close the current figure to avoid overlapping in the next iteration
end
% Additional cleanup or finalization code can be added here
disp('Processing complete.');
% open the fig files to check:
fig_files = dir(fullfile(saveFolderPath,'*.fig'));
for ii = 1:numel(fig_files)
openfig(fullfile(fig_files(ii).folder,fig_files(ii).name))
end
