Analysing a few .tiff files

I have a bunch of .tiff files that are pictures of a diffraction pattern evolving with time. Each file is an array 480x640 where each entry in the array is an intensity value.

I want to load the .tiff files automatically into Matlab and obtain the total intensity for each file by adding each entry together until the total is reached. I want these total values to be remembered and at the end the total intensities are recalled and plotted as intensity vs. time.

I know how to load up an individual .tiff file using the imread function. I have spent a lot of time trying to figure out what commands I need but haven’t gotten far.

Does anyone have any thoughts on my problem please? Any help would be greatly appreciated.

How are the .tiff files named? Is it something like Image_namestuff_1.tiff, Image_namestuff_2.tiff... etc?

Yes that's right

To be precise:-

Run20120629.103217 Multiple Image - 00000

Run20120629.103217 Multiple Image - 00001 etc...

Answer 1

Are the different time slices stored in different TIFF files? Then try something like this:

d = dir('myfiles*.tiff');
total = zeros(480,640);
for k = 1:length(d)
  I = imread(d(k).name);
  total = total + double(I);
end

Or are the different time slices all stored in a single TIFF file? Then try something like this:

total = zeros(480,640);
info = imfinfo('myfile.tiff');
num_slices = length(info);
for k = 1:num_slices
  I = imread('myfile.tiff','Info',info,'Index',k);
  total = total + double(I);
end

Thanks very much for you're help. Sadly I couldn't get it to work. I'll keep at it though...

So ... what happened when you tried it?

I've come back to MATLAB this morning having had time to relax and gather my thoughts. I can load in my data files using your code above. Thanks very much indeed.

I still want each file to be uploaded and each file to have its entire contents added up and the values stored in a separate array or something. This seems to be partially happening just now but I keep getting a value of 255 for the total of each array. I know their totals should be greater than this.

Any thoughts please?

clear all

t = 0;

d = dir('*.tif');

total = zeros(480,640);

for k = 1:length(d)

    I = imread(d(k).name);

    total = total + double(I);

    for i = 1:numel(I)

        t = t + I(i);

    end

end

disp(t)

If you're looking for the sum of all of the pixel values in a particular image use this in your loop:

 SumOfPixelValues(k) = sum(sum(I));

Thank you very much for your help

Answer 2

As I said in your duplicate question ( http://www.mathworks.com/matlabcentral/answers/43372-importing-multiple-tiff-files-by-mfile-for-further-processing:

Two code examples are given in the FAQ:

http://matlab.wikia.com/wiki/FAQ#How_can_I_process_a_sequence_of_files.3F

Thanks had already looked and tried these example codes but didn't work sadly.

Strange. I'll take a look at the FAQ, find the bug in it, and fix the code there. I don't want non-working code in the FAQ.

Dear Image Analyst,

Here is my code thus far:-

clear all

t = 0;

d = dir('*.tif');

z = [ ];

z = zeros(11,1);

for k = 1:length(d)

    I = imread(d(k).name); 

    for i = 1:numel(I)

        z(:,1) = t + I(i)

    end

end

I want to have each file loaded in, the array elements all added together, this value stored then move onto the next file. When all files have been read I want an array that has these total values in it.

I've been looking at examples and tried them but haven't been successful so far. Any pointers at all please?