Modifying a TIFF file and saving it to a new one with the same size

Question

Matt086 2021-2-19

0
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此问题的直接链接

https://ww2.mathworks.cn/matlabcentral/answers/750454-modifying-a-tiff-file-and-saving-it-to-a-new-one-with-the-same-size

评论： Walter Roberson 2021-2-22

Good day everyone,

I'm stucked with this code. I need to load a bounch of TIF files, merge them, and finally save everything to a new file.

However, the resulting file is smaller (in size) than the original one when I load it with another program, thus usless for my purpose.

The original files that I need to process are too large to attach them here. Anyway, when I "imfinfo" one of them what I get is:

                     Filename: 'C:\Users\usr1\Desktop\w1.mccd'
                  FileModDate: '17-feb-2021 18:46:59'
                     FileSize: 8392704
                       Format: 'tif'
                FormatVersion: []
                        Width: 2048
                       Height: 2048
                     BitDepth: 16
                    ColorType: 'grayscale'
              FormatSignature: [73 73 42 0]
                    ByteOrder: 'little-endian'
               NewSubFileType: 0
                BitsPerSample: 16
                  Compression: 'Uncompressed'
    PhotometricInterpretation: 'BlackIsZero'
                 StripOffsets: 4096
              SamplesPerPixel: 1
                 RowsPerStrip: 2048
              StripByteCounts: 8388608
                  XResolution: 126.3137
                  YResolution: 126.3137
               ResolutionUnit: 'Centimeter'
                     Colormap: []
          PlanarConfiguration: 'Chunky'
                    TileWidth: []
                   TileLength: []
                  TileOffsets: []
               TileByteCounts: []
                  Orientation: 1
                    FillOrder: 1
             GrayResponseUnit: 0.0100
               MaxSampleValue: 65535
               MinSampleValue: 0
                 Thresholding: 1
                       Offset: 8
                  UnknownTags: [1×1 struct]

This is the code I'm using

clearvars; close all; clc;
SaveFileName='test.tif';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
[name,path]=uigetfile('*.mccd','MultiSelect','on');
I=imfinfo(name{1});
[D,~] = imread([path name{1}]);
[Xsize,Ysize] = size(D);
Max=max(max(D));
disp([name{1} ' loaded...']);
A1 = double(D);
for i = 2:length(name)
    A1 = A1 + double(imread(name{i}));
    disp([name{i} ' loaded...']);
end
A1=A1/length(name);
A = uint16(A1);
Xlength = 10*I.Width/I.XResolution;
Ylength = 10*I.Height/I.YResolution;
figure('units','normalized','outerposition',[.12 .41 .31 .31]); hold on; 
s{1}=subplot(1,2,1,'color','none'); hold on; pbaspect([1 1 1]); xlabel('X (pixels)'); ylabel('Y (pixels)'); 
s{1}.Title.String = 'Frame #1';
im = imagesc(D); 
    im.AlphaData = 0.75;     view([0 -90]);     colormap(copper)
    xlim([1 length(D(1,:))]);    ylim([1 length(D(:,1))]);    
    
s{2}=subplot(1,2,2,'color','none'); hold on; pbaspect([1 1 1]); xlabel('X (pixels)'); ylabel('Y (pixels)'); 
s{2}.Title.String = 'All Frames Summed and Averaged';
im = imagesc(A); 
    im.AlphaData = 0.75;     view([0 -90]);     colormap(copper)
    xlim([1 length(A(1,:))]);    ylim([1 length(A(:,1))]);   
% save Summed Frames into new TIFF
t = Tiff(SaveFileName,'w'); %%
 setTag(t,'Photometric',Tiff.Photometric.MinIsBlack);%%
 setTag(t,'Compression',Tiff.Compression.None);
 if I.ResolutionUnit=='Centimeter'
     res=3;
 elseif I.ResolutionUnit=='Inch'
     res=2;
 elseif I.ResolutionUnit=='None'
     res=1;
 end
 setTag(t,'ResolutionUnit',res);
 t.setTag('XResolution',I.XResolution)
 t.setTag('YResolution',I.YResolution)
 setTag(t,'SampleFormat',Tiff.SampleFormat.UInt);
 setTag(t,'ExtraSamples',Tiff.ExtraSamples.Unspecified);
 setTag(t,'ImageLength',I.Width);%%
 setTag(t,'ImageWidth',I.Height);%% 2048
 setTag(t,'PlanarConfiguration',Tiff.PlanarConfiguration.Chunky);
 tagstruct.BitsPerSample = I.BitsPerSample;
 tagstruct.SamplesPerPixel = I.SamplesPerPixel;
 tagstruct.RowsPerStrip = I.RowsPerStrip; %2
 
 setTag(t,tagstruct)
 
write(t,A);
close(t);   
    
F=imfinfo(SaveFileName);

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Matt086 2021-2-22

在 MATLAB Online 中打开

Hi,

Yes, the detector in this example is an old MAR165 (165 mm diameters). But in principle I'd like to use the same script for other 2D detectors. Xlength and Ylength result in 162.1361, which are the edges of the original picture shown on the left. However, these pars are actually not used in my script.

The iminfo of the generated file is:

F = 
  struct with fields:
                     Filename: 'C:\Users\usr1\Desktop\test.tif'
                  FileModDate: '22-feb-2021 08:38:23'
                     FileSize: 8388818
                       Format: 'tif'
                FormatVersion: []
                        Width: 2048
                       Height: 2048
                     BitDepth: 16
                    ColorType: 'grayscale'
              FormatSignature: [73 73 42 0]
                    ByteOrder: 'little-endian'
               NewSubFileType: 0
                BitsPerSample: 16
                  Compression: 'Uncompressed'
    PhotometricInterpretation: 'BlackIsZero'
                 StripOffsets: 8
              SamplesPerPixel: 1
                 RowsPerStrip: 2048
              StripByteCounts: 8388608
                  XResolution: 126.3137
                  YResolution: 126.3137
               ResolutionUnit: 'Centimeter'
                     Colormap: []
          PlanarConfiguration: 'Chunky'
                    TileWidth: []
                   TileLength: []
                  TileOffsets: []
               TileByteCounts: []
                  Orientation: 1
                    FillOrder: 1
             GrayResponseUnit: 0.0100
               MaxSampleValue: 65535
               MinSampleValue: 0
                 Thresholding: 1
                       Offset: 8388616
                 ExtraSamples: 0
                 SampleFormat: 'Unsigned integer'

I have no experience in generating image files (TIF) and I think I'm just missing some simple step that perhaps is obvious to someone with more experience... I don't understand whether I have to modify the converted data (A) or the right tag in the generated Tiff (t).

Thanks

Matt086 2021-2-22

Dear Walter,

I think the problem is solved now. As you noticed, the problem was not in the MATLAB script. There is a conversion that gsas applies and it was not working on my current version. After installing a more stable version of gsas the conversion seems to be working fine.

Thank you very much!