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

7 次查看（过去 30 天）

显示更早的评论

Rafat 2023-11-1

0
链接

此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2041681-how-to-calculate-median-matrix-of-many-tif-files-with-matlab

评论： Rafat 2023-11-3

采纳的回答： Walter Roberson

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

11 个评论
显示 9更早的评论隐藏 9更早的评论

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?

Rafat 2023-11-2

I gave an example here for 15

请先登录，再进行评论。

请先登录，再回答此问题。

采纳的回答

Walter Roberson 2023-11-2

2
链接

此回答的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/2041681-how-to-calculate-median-matrix-of-many-tif-files-with-matlab#answer_1345586

在 MATLAB Online 中打开

Test.zip

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

4 个评论
显示 2更早的评论隐藏 2更早的评论

Walter Roberson 2023-11-2

在 MATLAB Online 中打开

Test.zip

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 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

请先登录，再进行评论。