How to save pixel values from set of images and store them in ASCII format?

I have set of TIFF images, each corresponding to particular wavelength. For example, first image corresponds to 225.197nm, while the next one corresponds to 225.198nm. This way I have images that corresponds to about 100 different wavelengths. For a particular pixel in each of those images, I would like to extract the pixel values and put them like the attached file in two different columns. Any help will be greatly appreciated.

[Walter Roberson]

Do I understand correctly that if your image was (for example) 512 pixels by 768 pixels, that you would want (512*768) = 393216 different files created, one for each pixel position, each file containing the information for all of the wavelengths at that position ?

[Syed Mashruk]

Yes. That's right.

Answer 1

[Image Analyst]

Use the FAQ to create a 3-D image, if there are not too many of them. Let's say you have 50 images, each with a different wavelength, then you'd do

image3d = zeros(rows, columns, numImages);
for k = 1 : numImages
    thisImage = imread(...........
    image3d(:,:,k) = thisImage;
end

Then scan the image, writing out each spectrum. You should have an array that says what the wavelength is for each image.

[rows, columns, numImages] = size(image3d);
count = 1;
for row = 1 : rows
    for col = 1 : columns
        thisSpectrum = image3d(row, col, :);
        filename = sprintf('Spectrum %d.txt', count);
        fileID = fopen(filename, 'wt');
        fprintf(fileID, '%f, %f\n', wavelengths, thisSpectrum);
        fclose(fileID);
    end
end

[Syed Mashruk]

Thanks for your help. How would I define the array that says what the wavelength for each image? Sorry, I am very new in Matlab. Also how would I create 3D image and I have 500 TIFF images to work with, each represent different wavelengths.

[Image Analyst]

I thought you already HAD the images like you got them from your camera or other instrument. And if so you should know the wavelength they were created with.

[Syed Mashruk]

Yes, I know the wavelengths but just do not know how to assign them. For example, the wavenumbers are from 44406 - 44505 with a step of 0.2 for every image. How would I assign the array? Something like this perhaps:

for l=1:500
wavenumbers = [44406 44505];
end

[Image Analyst]

No. Like this

wavelengths = 44406 : 0.2 : 44505;

By the way, wavenumbers are a different concept than wavelengths - the units are different.

[Syed Mashruk]

Thanks. Yes I know they are different.

When I am defining the wavelength the way you said, in the text file, all the wavelengths are coming first, then the pixel values but I want them side by side as the text file I attached in the beginning.

Also the run time is quite high with this code. If I define the text file as a matrix like (numImages, 2), would it help? Here's the code:

[listOfFiles, folder] = uigetfile ('*.tif', 'Select your image', 'MultiSelect', 'on');
fullFileName = fullfile(folder, listOfFiles{1});
[I, cmap] = imread(fullFileName);
[rows, columns] = size(I);
image3d = zeros(rows, columns, 5);
for k = 1 : length(listOfFiles)
    fullFileName = fullfile(folder, listOfFiles{k});
    thisImage = imread(fullFileName);
    image3d(:,:,k) = thisImage;
end
wavenumbers=44406 : 0.2 : 44406.8;
[rows, columns, numImages] = size(image3d);
count = 1;
for row = 1 : rows
    for col = 1 : columns
        thisSpectrum = image3d(row, col, :);
        filename = sprintf('Spectrum %d.txt', count);
        fileID = fopen(filename, 'wt');
        fprintf(fileID, '%f %f\n', wavenumbers, thisSpectrum);
        fclose(fileID);
    end
end

[Image Analyst]

You'll need this:

fprintf(fileID, '%f %f\n', wavenumbers(count), thisSpectrum);

and it would run faster if you put the inner loop as rows rather than columns.

And you have

image3d = zeros(rows, columns, 5);

Why 5 instead of length(listOfFiles)? And what if your user picks 3 files? Why are you taking only the first file? And if you take just one file, representing only one wavelength, then you cannot build a spectrum. You need lots of files.

[Syed Mashruk]

I was testing with 5 images. At first,listOfFliles{1} was used to get the row and column sizes only. All the 5 files were read afterwards anyway with 'this image'. Does 'count=1' means to get pixel value only for 1 pixel?

[Image Analyst]

Count is the number of the text file you are on. Eventually it will be the total number of pixels since you said that you want as many text files as there are pixels in the image. That seems like a huge amount. If I were you I'd downsize the images to get the average spectrum over a rectangular patch rather than the spectrum at each and every pixel.

[Syed Mashruk]

I am still not getting my text file in the desired following form:

44406 216
44406.2 216
44406.4 215
44406.6 215
44406.8 214

Instead getting in the following form:

44406 44406.2
44406.4 44406.6
44406.8 216
216 215
215 214

I tried following code:

fprintf(fileID, '%f %f\n', wavenumbers(count), thisSpectrum);

And I am getting following message:

Error using vertcat
Dimensions of matrices being concatenated are not consistent.

Any suggestions?

[Syed Mashruk]

solved it with the following code:

fprintf(fileID, '%f %f\n', [wavenumbers(:), thisSpectrum(:)].');

Many thanks for your help.

Answer 2

[Walter Roberson]

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

Read the files in and store into a 3D array, with the third dimension increasing with wavelength. Once you have everything read in, loop over the pixels, fopen() an appropriate file name, fprintf() the wavelengths and a 3D column extracted from the array.

[Syed Mashruk]

Thanks Walter but when I am trying to use fopen() like the following code:

   [listOfFiles, folder] = uigetfile ('*.tif', 'Select your image', 'MultiSelect', 'on');
    for j=1:length(listOfFiles)
            fullFileName = fullfile(folder, listOfFiles{j});
            fileID=fopen(fullFileName);
    end

I selected 500 tiff files and I am getting the following message:

Too many open files. Close files to prevent MATLAB instability.

Caused by: Message Catalog MATLAB:services was not loaded from the file. Please check file location, format or contents

Is there any way around it?

[Walter Roberson]

Do not fopen() the tif files yourself. Use imread(), or use the Tiff class (and make sure you clear the tiff object when you are done with it.)