Loading images with their names into single arrays

Hi, I'm trying to load multiple .tif files into MATLAB from a folder. I tried this:

files= dir('*.tif')

for k=1:length(files);

imagename = files(k).name;

image1 = imread(imagename);

images{k} = image1;

end

But I need these files to be loaded separately, so every one of them will be one single array, but this code writes them all into a cell. I also need these single array variables to have the same names that .tif files had. How can I do that?

[Sindar]

This writes them each into a cell of a cell array. You could create a separate cell array containing the corresponding names. Or, you could work with a more complicated data type like structure arrays, tables, or datastores.

separate cell arrays:

files= dir('*.tif')
for k=1:length(files);
   imagename = files(k).name;
   image1 = imread(imagename);
   images{k} = image1;
   imagenames{k} = imagename;
end

structure array:

files= dir('*.tif')
for k=1:length(files);
   imagename = files(k).name;
   image1 = imread(imagename);
   images(k).image = image1;
   images(k).name = imagename;
end

If what you want is an entirely separate variable for each image, named according to the filename... reconsider

The closest thing that is not completely terrible would be creating a structure where fields are named according to the filename, but there are issues

files= dir('*.tif')
for k=1:length(files);
   imagename = files(k).name;
   image1 = imread(imagename);
   % many filenames are not valid fieldnames (or variable names)
   valid_fieldname = genvarname(imagename);
   images.(valid_variable_name) = image1;
end

[Izabela Wojciechowska]

Thank you a lot for your answer @Sindar

First and second methods work good, but trying to use third, I only get one image and one imagename. Isn't there something wrong?

Ok, so which method you proposed will be better if what I want to do in the next step is to find couples of images which has the same part of title (which is the date, because I have measured two parameters same time) and do some calculations on it?

[Sindar]

hmm, not sure what's up with the third method, but for your purposes I'd recommend the first. Cell arrays of character vectors are easy to do text-checking on (if you're familiar with Matlab string arrays, you could also convert)

files= dir('*.tif')
for k=1:length(files);
   imagename = files(k).name;
   image1 = imread(imagename);
   images{k} = image1;
   imagenames{k} = imagename;
end
my_date = '28-Sep-2020';
% find indices of names which include the given date
idx = contains(imagenames,my_date);
% extract the names and images for that date
date_names = imagenames(idx);
date_images = images(idx);
% do something with each image
for ind=1:length(date_images)
    % here, just displaying
    imshow(date_images{idx})
end

[Stephen23]

"But I need these files to be loaded separately, so every one of them will be one single array..."

They already are: every cell of images contains one single array. They can be trivially accessed using indexing.

":..but this code writes them all into a cell."

Which is one of the best and simplest ways to store data from multiple files, and is exactly what the MATLAB documentation recommends: https://www.mathworks.com/help/matlab/import_export/process-a-sequence-of-files.html

"I also need these single array variables to have the same names that .tif files had."

That would be about the worst way to write MATLAB code. Forcing meta-data into variable names is one way that some beginners force themselves into writing slow, complex, inefficient, obfuscated, buggy code that is hard to debug:

https://www.mathworks.com/matlabcentral/answers/304528-tutorial-why-variables-should-not-be-named-dynamically-eval

Consider what would happen if you tried to name variables after filenames, and some of the files had these names: '-1.tif', 'a-b.tif', '0.tif', '@.tif'

[Izabela Wojciechowska]

Thank you for help @Sindar and for the explanation @Stephen Cobeldick.

Answer 1

[Stephen23]

One of the best approaches is to simply import the file data into the same structure that dir returns, then for each file you have all of the file data and file meta-data in one simple structure element:

D = 'absolute or relative path to where the files are saved';
S = dir(fullfile(D,'*.tif'))
for k = 1:numel(S);
    F = fullfile(D,S(k).name);
    S(k).data = imread(F);
end

You can trivially access any file using indexing, e.g. the third file:

S(3).name
S(3).data

See also:

https://www.mathworks.com/help/matlab/matlab_prog/comma-separated-lists.html

https://www.mathworks.com/matlabcentral/answers/320713-how-to-operate-on-comma-separated-lists

[Izabela Wojciechowska]

I'm afraid this doesn't solve the problem. How can I get only selected values from data in the structure, for example using "find"?

I mean when I have single array I can do this:

Regions=imread('RegionsFile.tif');

FirstParameterDate=imread('FirstParameterDate.tif');

SecondParameterDate=imread('SecondParameterDate.tif');

x=find(Regions==5);

MyRegionFirstParameter=FirstParameterDate(x);

MyRegionSecondParameter=SecondParameterDate(x);

Answer=find(MyRegionFirstParameter>=2&MyRegionSecondParameter<5);

But how can I do this, when my data is in the structure? This doesn't work:

MyRegionFirstParameter(:).data=find(FirstParameter(:).data==x);

I'm sorry if my problem sounds trivial to you, but I really don't know how to do calculations on structures. I only used arrays so far.

[Stephen23]

@Izabela Wojciechowska : there are two ways to use data stored n container arrays:

1. assign the content to a temporary variable
2. refer to the content of the container array directly

The first is very intuitive and makes it easy to use your existing code:

for k = 1:numel(S)
    Regions = S(k).data;
    x = find(Regions==5);
    ... your code here
end

The second you simply replace every instance of Regions with S(k).data, e.g.:

for k = 1:numel(S)
    x = find(S(k).data==5);
    ... your code here
end

[Izabela Wojciechowska]

Thank you, it works. I really appreciate your help.