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POImage manipulation with Matlab - intensity and tif image
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copied!<p>I have to analyse a set of images, and these are the operations I need to perform:</p> <ol> <li>sum another set of images (called open beam in the code), calculate the median and rotate it by 90 degrees;</li> <li>load a set of images, listed in the file "list.txt";</li> <li>the images have been collected in groups of 3. For each group, I want to produce an image whose intensity values are 3 times the image median above a certain threshold and otherwise equal to the sum of the intensity values;</li> <li>for each group of three images, subtract the open beam median (calculated in 1.) from the combined image (calculated in 3.)</li> </ol> <p>Considering one of the tifs produced using the process above, I have that the maximum value is 65211, which is not 3* the median for the three images of the corresponding group (I checked considering the pixel position). Do you have any suggestion on why this happens, and how I could fix it?</p> <p>The code is reported below. Thanks!</p> <pre><code>%Here we calculate the average for the open beam clear; j = 0; for i=1:5 s = sprintf('/Users/Alberto/Desktop/Midi/17_OB_2.75/midi_%04i.fits',i); j = j+1; A(j,:,:) = uint16(fitsread(s)); end OB_median = median(A,1); OB_median = squeeze(OB_median); OB_median_rot=rot90(OB_median); %Here we calculate, for each projection, the average value from the three datasets %Read list of images from text file fid = fopen('/Users/Alberto/Desktop/Midi/list.txt', 'r'); a = textscan(fid, '%s'); fclose(fid); %load images j = 0; for i = 1:1:42 %556 entries; 543 valid values s = sprintf('/Users/Alberto/Desktop/Midi/%s',a{1,1}{i,1}); j = j+1; A(j,:,:) = uint16(fitsread(s)); end threshold = 80 %This is a discretional number. I put it after noticing %that we get the same number of pixels with a value >100 if we use 80 or 50. k = 0; for ii = 1:3:42 N(1,:,:) = A(ii,:,:); N(2,:,:) = A(ii+1,:,:); N(3,:,:) = A(ii+2,:,:); median_N = median(N,1); median_N = squeeze(median_N); B(:,:) = zeros(2160,2592); for i = 1:1:2160 for j = 1:1:2592 RMS(i,j) = sqrt((double(N(1,i,j).^2) + double(N(2,i,j).^2) + double(N(3,i,j).^2))/3); if RMS(i,j) > threshold %B(i,j) = 30; B(i,j) = 3*median_N(i,j); else B(i,j) = A(ii,i,j) + A(ii+1,i,j) + A(ii+2,i,j); %B(i,j) = A(ii,i,j); end end end k = k+1; filename = sprintf('/Users/Alberto/Desktop/Midi/Edited_images/Despeckled_images/despeckled_image_%03i.tif',k); %Now we rotate the matrix B_rot=rot90(B); imwrite(B_rot, filename); %imwrite(uint16(B_rot), filename); %Now we subtract the OB median B_final_rot = double(B_rot) - 3*double(OB_median_rot); filename = sprintf('/Users/Alberto/Desktop/Midi/Edited_images/Final_image/final_image_%03i.tif',k); imwrite(uint16(B_final_rot), filename); end </code></pre>

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