Effacer les filtres
Effacer les filtres

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

2 vues (au cours des 30 derniers jours)
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.
  2 commentaires
Bob Thompson
Bob Thompson le 15 Nov 2018
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
Brendan Wolan le 16 Nov 2018
This is the directory copied directly from my terminal:
/Users/andromache/Desktop/Research/data/other/180319_114103_A1\ 20X\ PL\ FL\ Phase\ \(3\)

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Réponse acceptée

Ken Atwell
Ken Atwell le 21 Nov 2018
Modifié(e) : Ken Atwell le 21 Nov 2018
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
  1 commentaire
Brendan Wolan
Brendan Wolan le 23 Nov 2018
The simpler filepath solved the issue. Thanks all for the suggestions and help.

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Plus de réponses (1)

Image Analyst
Image Analyst le 16 Nov 2018
Modifié(e) : Image Analyst le 16 Nov 2018
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
  2 commentaires
Brendan Wolan
Brendan Wolan le 19 Nov 2018
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
Image Analyst le 19 Nov 2018
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.

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