Index exceeds array bounds error when trying to reach .tif images from file

I'm working on a program that tracks the movement of particles across many images and as such, it needs to access the file where these images are stored. However, I continue to run into the following issue when trying to access the images:

srcFiles = 

  0×1 empty struct array with fields:

    name
    folder
    date
    bytes
    isdir
    datenum

Index exceeds array bounds.

Error in Particletracking (line 16)
        filename = strcat('/Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\
        Phase\ \(3\)',srcFiles(i).name);%Change filepath here

This corresponds to the following code:

%% Read File, filter signal, localize and track particles
 
srcFiles=dir('/Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\ Phase\ \(3\)*.tif ') %Change filepath here
pos_list=[];
dt=0.15;
nbimage=180;
for i=1:nbimage
    
   
    
    %Analyze picture n°a to b
    i;
        filename = strcat('/Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\ Phase\ \(3\)',srcFiles(i).name);%Change filepath here
    a = imread(filename);
    a=2^16-a;
    %BandPass
    b = bpass(a,1,10);
    %Findparticles
    pk = pkfnd(b,5000,11);
    cnt = cntrd(b,pk,15);
    
    %Create list of positions
    if find(cnt) ~=0 
       pos_list=[pos_list; cnt(:,1),cnt(:,2), ones(length(cnt(:,1)),1).*i*dt];
    end
end

Solutions attempted include running the code on both mac and windows as well as moving the filepath, and adjusting the filepath ad nauseum. I've inherited this project and code from a growing line who have successively added to the project, so I don't have a full understanding of the code and, given that I can't run it, am haivng a tough time trying to build an understanding of it.

Any suggestions are appreciated.

[Bob Thompson]

The error is occurring because srcFiles is empty. I suspect there is an issue with your file path, as you have some folders separated with / and some separated with \.

[Brendan Wolan]

This is the directory copied directly from my terminal:

/Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\ Phase\ \(3\)

Answer 1

[Ken Atwell]

Those backslashes are likely not really part of the folder name, but inserted by the Terminal program to escape spaces in the folder name. As others have suggest, renaming the folder to something simplier is the easiest way forward.

Or, try this: Replace your use of dir with:

srcFiles=dir('/Users/

This press the Tab key. Use tab-completion to drill down to the desired folder, then close the string.

I suspect you'll send up with an assignment like this (some line wrapping inserted by MATLAB Answers):

srcFiles=dir('/Users/andromache/Desktop/Research/data/other/180319_114103_A1 20X PL FL
        Phase (3)');

Later, don't use strcat, but fullfile to create the filename:

filename = fullfile(srcFiles(i).folder, srcFiles(i).name)

Hope that helps

[Brendan Wolan]

The simpler filepath solved the issue. Thanks all for the suggestions and help.

Answer 2

[Image Analyst]

Try making it more robust to discover what the problem is:

folder = 'C:/Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\ Phase\ \(3\)'
if ~exist(folder, 'dir')
	message = sprintf('Directory does not exist:\n%s', folder)
	uiwait(errordlg(message));
	return;
end
filePattern = fullfile(folder, '*.tif')
sourceFiles = dir(filePattern)
if isempty(sourceFiles)
	message = sprintf('No TIF files exist in folder:\n%s', folder);
	uiwait(errordlg(message));
	return;
end
for k = 1 : length(sourceFiles)
	fullFileName = fullfile(folder, sourceFiles(k).name); % Change filepath here
	fprintf('Found TIF file: %s\n', fullFileName);
end

[Brendan Wolan]

It exits with the message

srcFiles = 

  0×1 empty struct array with fields:

    name
    folder
    date
    bytes
    isdir
    datenum


folder =

    '/Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\ Phase\ \(3\)'


message =

    'Directory does not exist:
     /Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\ Phase\ \(3\)'

Clearly the code isn't finding the directory, however the above directory is a direct copy of the directory from the terminal on my mac. Is there a better way to find the file directory?

[Image Analyst]

I don't know - I don't use a Mac. Perhaps move the files to a folder that doesn't have so many spaces, parentheses, and slashes. I've added the tag "mac" to your post so maybe some mac people will answer. Or else call tech support.