How to save unint16 class as tiff image.

Hello

I have 36 tiff images ( CT scans) :

Imported them and store in a cell array :C

I stacked row slices of each image to generate 3d matrix or 2d cell array : Sinogram

Converted the 2D cell array into uint16 : A

Now Iam looking to save the A (3d matrix) as a tiff image.

However imwrite is not allowing me to do. Kindly requesting for help. Below is my code

% Uploading images
myPath = 'G:\My Drive\Research-Ph.D\Matlab codes\4.23\20220422_5anglestep_001';
fileNames = dir(fullfile(myPath, '*.tif')); % Assigning the output of dir directly into fileNames

% First, define the cell array to have the right size to store all images in a single collection
C = cell(length(fileNames), 1);
I = cell(length(fileNames), 1);

% Now storing each image into a different cell:
for k = 1:length(fileNames)
    filename = fileNames(k).name;
     C{k, 1} = imread(filename);
     I{k} = im2gray(C{k});
end

figure(1)
%% sinogram
sinogram_image= montage(permute(C, [3,2,1]));

sinogram = permute(C, [3,2,1]);

%{
for i=1:size(sinogram, 3)
        for k=1:size(sinogram, 1)
            sinogram(k,:,i)=C(i,:,k);

        end
end
%}

%% Saving each image of the sinogram - Not required
%for k = 1:numel(sinogram)
 %   imwrite(sinogram{k}, sprintf('s%d.tiff', k), 'compression', 'none');
%end


%% 
A = cell2mat(sinogram);
imwrite(A,'resultimage.tif')

%% %% Volshow
%volshow(A)

[Geoff Hayes]

@Anand Rathnam - please clarify what you mean by imwrite is not allowing me to. If there is an error message, please copy and paste the full message to this question.

[Anand Ra]

@Geoff Hayes Sorry should have included that. Below was the error I received:

Error using writetif (line 40)

Writing TIFFs with 36 components is not supported with IMWRITE.

Use Tiff instead. Type "help Tiff" for more information.

Error in imwrite (line 566)

feval(fmt_s.write, data, map, filename, paramPairs{:});

Error in fullprg_2 (line 42)

imwrite(A,'resultimage.tif')

Answer 1

[Walter Roberson]

See https://www.mathworks.com/matlabcentral/fileexchange/30519-export-image-to-tif-or-tiff-file-of-selected-data-type?s_tid=srchtitle for code that can write to TIFF integer and floating point formats.

If you do not want to use that contribution then see the code outline at https://www.mathworks.com/matlabcentral/answers/7184-how-can-i-write-32-bit-floating-point-tifs-with-nans#comment_15023

[Anand Ra]

@Walter Roberson Hey, Thanks for the reference.

I incorpiorated your silution, but I am getting the following error

Error using tifflib

If SampleFormat is IEEEFP, the image datatype is

restricted to one of the following: single,

double.

Error in Tiff/writeAllStrips (line 1979)

tifflib('writeEncodedStrip',obj.FileID,stripNum-1,imageData(row_inds,:,:));

Error in Tiff/write (line

1486)

obj.writeAllStrips(varargin{:});

Error in fullprg_2 (line 63)

t.write(A);

Also tried converting the class to double instead of uint16, still the error persists

clc;

% Uploading images
myPath = 'G:\My Drive\Research-Ph.D\Matlab codes\4.23\20220422_5anglestep_001';
fileNames = dir(fullfile(myPath, '*.tif')); % Assigning the output of dir directly into fileNames

% First, define the cell array to have the right size to store all images in a single collection
C = cell(length(fileNames), 1);
I = cell(length(fileNames), 1);

% Now storing each image into a different cell:
for k = 1:length(fileNames)
    filename = fileNames(k).name;
     C{k, 1} = imread(filename);
     I{k} = im2gray(C{k});
end

figure(1)
% sinogram
sinogram_image= montage(permute(C, [3,2,1]));

sinogram = permute(C, [3,2,1]);

%{
for i=1:size(sinogram, 3)
        for k=1:size(sinogram, 1)
            sinogram(k,:,i)=C(i,:,k);

        end
end
%}

%% Saving each image of the sinogram - Not required
%for k = 1:numel(sinogram)
 %   imwrite(sinogram{k}, sprintf('s%d.tiff', k), 'compression', 'none');
%end


%% 
%A = str2double(sinogram);
A= cell2mat(sinogram);
% imwrite(A,'resultimage.tif')

% imgdata = imread('A.tif');
% imwrite2tif(imgdata,[],'new_mri.tif','int32','Copyright','MRI','Compression',1);

%% %% Volshow
%volshow(A)

%% Saving A as tiff
filename = 'testtifffp.tiff';

t = Tiff(filename, 'w');
tagstruct.ImageLength = size(A, 1);
tagstruct.ImageWidth = size(A, 2);
tagstruct.Compression = Tiff.Compression.None;
tagstruct.SampleFormat = Tiff.SampleFormat.IEEEFP;
tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
tagstruct.BitsPerSample = 16;
tagstruct.SamplesPerPixel = size(A,3);
tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
t.setTag(tagstruct);
t.write(A);
t.close();

[Anand Ra]

@Walter Roberson Also wanted to update you that I receive the following warning when I used the file exchange. Btw, the saved tif cannot be opened in normal windows photo viewer?

Warning: Sum of Photometric color channels and ExtraSamples does

not match the value specified in SamplesPerPixel.

Writing with this configuration will error in a future release. To

correct the configuration, define the non-color channels as

ExtraSamples.

> In Tiff/writeAllStrips (line 1979)

In Tiff/write (line 1486)

In imwrite2tif (line 154)

In fullprg_2 (line 53)

>>

[Walter Roberson]

% Uploading images
myPath = 'G:\My Drive\Research-Ph.D\Matlab codes\4.23\20220422_5anglestep_001';
fileNames = dir(fullfile(myPath, '*.tif')); % Assigning the output of dir directly into fileNames

% First, define the cell array to have the right size to store all images in a single collection
C = cell(length(fileNames), 1);
I = cell(length(fileNames), 1);

% Now storing each image into a different cell:
for k = 1:length(fileNames)
    filename = fileNames(k).name;
     C{k, 1} = imread(filename);
     I{k} = im2gray(C{k});
end

figure(1)
% sinogram
sinogram_image= montage(permute(C, [3,2,1]));

sinogram = permute(C, [3,2,1]);

A= cell2mat(sinogram);

%% Saving A as tiff
filename = 'testtifffp.tiff';

t = Tiff(filename, 'w');
tagstruct.ImageLength = size(A, 1);
tagstruct.ImageWidth = size(A, 2);
tagstruct.Compression = Tiff.Compression.None;
tagstruct.SampleFormat = Tiff.SampleFormat.UInt;
if size(A,3) == 1
    tagstruct.Photometric = Tiff.Photometric.MinIsBlack;
else
    tagstruct.Photometric = Tiff.Photometric.RGB;
end
tagstruct.BitsPerSample = 16;
tagstruct.SamplesPerPixel = size(A,3);
tagstruct.PlanarConfiguration = Tiff.PlanarConfiguration.Chunky;
t.setTag(tagstruct);
t.write(A);
t.close();