How to calculate median matrix of many .tif files with MATLAB?

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Rafat
Rafat 2023-11-1
评论： Rafat 2023-11-3
Hi
I have for example 15 .tif files, some pixels with "NaN". How to find a matrix of the median of the 15 tif files
Is it possible?
to be more precice
The following link to subsample of the data:
https://www.dropbox.com/scl/fo/bwb5bek75hv6d0hiyv0ey/h?rlkey=7xsqnc762ta8ezcj8e8x53qap&dl=0
input: 15 .tif files x m rows x n columns
output: so I want the out put be 1 median x m rows x n columns
Cheers
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Walter Roberson
Walter Roberson 2023-11-2
If you have 120 files in the directory then how do you want to select the 15 of them you want to process?

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Walter Roberson
Walter Roberson 2023-11-2
Ran in:
format long g
master_size = [87, 207];
unzip Test.zip
Warning: Cannot open file "" for reading.
files = dir('*.tif');
filenames = fullfile({files.folder},{files.name});
N = numel(files);
for ii = 1:N
files(ii).data = imresize(imread(filenames{ii}), master_size);
end
datablock = cat(3, files.data);
image_median = median(datablock, 3, 'omitnan');
[min(image_median(:)), max(image_median(:))]
ans = 1×2
1.0e+00 * -1.06638e+13 7.329353e+11
image(image_median)
After that you want to write the median out to a tiff, and you probably want the same data range (rather than converting the image to uint8). imwrite() cannot itself write single precision tiff, so you need the Tiff library. More information is at https://www.mathworks.com/matlabcentral/answers/7184-how-can-i-write-32-bit-floating-point-tifs-with-nans . Or you could use the File Exchange contribution https://www.mathworks.com/matlabcentral/fileexchange/30519-export-image-to-tif-or-tiff-file-of-selected-data-type which you could install using the Add-On Explorer
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Walter Roberson
Walter Roberson 2023-11-2
Ran in:
You might be interested in standardizeMissing
format long g
master_size = [87, 207];
unzip Test.zip
Warning: Cannot open file "" for reading.
files = dir('*.tif');
filenames = fullfile({files.folder},{files.name});
N = numel(files);
for ii = 1:N
thisimg = imread(filenames{ii});
minval = min(thisimg(:));
if minval < -1e12
thisimg = standardizeMissing(thisimg, minval);
end
files(ii).data = imresize(thisimg, master_size);
end
datablock = cat(3, files.data);
image_median = median(datablock, 3, 'omitnan');
[min(image_median(:)), max(image_median(:))]
ans = 1×2
45.09927 214.264
image(image_median)
Rafat
Rafat 2023-11-3
Hello Walter,
I went through the script, then I understand the wierd values other than the 1- "FillValues" and 2- the normal range of data from 0-1000
"master_size = [87, 207];"
this produce the wierd values in .tif files if rows> 87 and columns > 207; so to that end, I tested
"master_size = [88, 208];" for .tif files if rows= 88 and columns = 208; the wierd values disappierd, so I think we need to deliet the rows > 87 and the columns > 207 then apply from "master_size = [87, 207];" to the end of script.
I appriciat any help of that!!
Cheers,
rafat

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