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.

[Ryan]

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

[Dominic Lawson]

Yes that's right

To be precise:-

Run20120629.103217 Multiple Image - 00000

Run20120629.103217 Multiple Image - 00001 etc...

Answer 1

[Steve Eddins]

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

[Dominic Lawson]

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

[Steve Eddins]

So ... what happened when you tried it?

[Dominic Lawson]

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)

[Ryan]

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));

[Dominic Lawson]

Thank you very much for your help

Answer 2

[Image Analyst]

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

[Dominic Lawson]

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

[Image Analyst]

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.

[Dominic Lawson]

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?