How to save binary images png into one tiff format file?

Dear all,

I have saved binary images by this code in format png:

% Initialization steps.
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
% Specify the folder where the files live.
folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';
% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isdir(folder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', folder);
  uiwait(warndlg(errorMessage));
  return;
end
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(folder, '*.dcm'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
for k = 1 : length(theFiles)
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(folder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);
  % Now do whatever you want with this file name,
  % such as reading it in as an image array with imread()
  grayImage= dicomread(fullFileName);
  subplot(1, 2, 1);
  imshow(grayImage, []);  % Display image.
  axis on;
  title(baseFileName, 'FontSize', fontSize);
  drawnow; % Force display to update immediately.
  
  % Convert to gra scale if necessary.
  [rows, columns, numberOfColorChannels] = size(grayImage);
  if numberOfColorChannels > 1
    %   % Máme barevný obraz, musíme ho převést na černobílý = vybereme %zelený kanál
    grayImage = grayImage(:, :, 2); % zelený kanál
  end
  
  % Do totally unnecessary histogram equalization.
  eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
  
  % Do morphological processing
  % Práh pro vytvoření binárního obrazu okolí
  thresholdValue = 900;
  binaryImage_okoli = grayImage > thresholdValue;
  % Odstranění okolí.
  binaryImage_okoli = imclearborder(binaryImage_okoli);
  % Vyplnění otvorů.
  binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
  % Vymazání menších otvorů.
  binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);
  % Roztažení binárního obrazu pro přesnější segmentaci
  se = strel('line',5,100);
  binaryImage_okoli= imdilate(binaryImage_okoli,se);
  
  % Display the image.
  subplot(1, 2, 2);
  imshow(binaryImage_okoli, []);
  title('Binarized', 'FontSize', fontSize);
  % Enlarge figure to full screen.
  set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
  drawnow;
  
  % Save output image.
  baseOutputFileName = sprintf('Binarizace_okoli_%3d.png', k);
  fullOutputFileName = fullfile(folder, baseOutputFileName);
  imwrite(logical(binaryImage_okoli), fullOutputFileName);
  fprintf('Saved %s.\n', fullOutputFileName);
  
  promptMessage = sprintf('Do you want to Continue processing,\nor Quit processing?');
  titleBarCaption = 'Continue?';
  buttonText = questdlg(promptMessage, titleBarCaption, 'Continue', 'Quit', 'Continue');
  if strcmpi(buttonText, 'Quit')
    break;
  end
end
% Set up figure properties:
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
% Get rid of tool bar and pulldown menus that are along top of figure.
set(gcf, 'Toolbar', 'none', 'Menu', 'none');
% Give a name to the title bar.
set(gcf, 'Name', 'Demo by ImageAnalyst for Veronika', 'NumberTitle', 'Off')
msgbox('Done with Program');

I would like to save these binary images into one file. And this file has tiff format. Is it possible? Thank you for your answers.

Answer 1

[Walter Roberson]

https://www.mathworks.com/help/matlab/ref/imwrite.html#btwmoig-1

imwrite() with 'WriteMode', 'append' can be used with TIFF files.

[Veronika]

Okay, it works, but in my case there is saved only the last binary image, please advice me, where in my code I add for loop for adding the other binary images into tiff file.

% Initialization steps.
clc;    % Clear the command window.
close all;  % Close all figures (except those of imtool.)
clear;  % Erase all existing variables. Or clearvars if you want.
workspace;  % Make sure the workspace panel is showing.
format long g;
format compact;
fontSize = 20;
% Specify the folder where the files live.
folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';
% Check to make sure that folder actually exists.  Warn user if it doesn't.
if ~isdir(folder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', folder);
  uiwait(warndlg(errorMessage));
  return;
end
% Get a list of all files in the folder with the desired file name pattern.
filePattern = fullfile(folder, '*.dcm'); % Change to whatever pattern you need.
theFiles = dir(filePattern);
for k = 1 : length(theFiles)
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(folder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);
  % Now do whatever you want with this file name,
  % such as reading it in as an image array with imread()
  grayImage= dicomread(fullFileName);
  subplot(1, 2, 1);
  imshow(grayImage, []);  % Display image.
  axis on;
  title(baseFileName, 'FontSize', fontSize);
  drawnow; % Force display to update immediately.
  
  % Convert to gra scale if necessary.
  [rows, columns, numberOfColorChannels] = size(grayImage);
  if numberOfColorChannels > 1
    %   % Máme barevný obraz, musíme ho převést na černobílý = vybereme %zelený kanál
    grayImage = grayImage(:, :, 2); % zelený kanál
  end
  
  % Do totally unnecessary histogram equalization.
  eq_grayImage = histeq(grayImage);%ekvalizace pomocí histogramu obrazu
  
  % Do morphological processing
  % Práh pro vytvoření binárního obrazu okolí
  thresholdValue = 900;
  binaryImage_okoli = grayImage > thresholdValue;
  % Odstranění okolí.
  binaryImage_okoli = imclearborder(binaryImage_okoli);
  % Vyplnění otvorů.
  binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
  % Vymazání menších otvorů.
  binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);
  % Roztažení binárního obrazu pro přesnější segmentaci
  se = strel('line',5,100);
  binaryImage_okoli= imdilate(binaryImage_okoli,se);
  
  % Display the image.
  subplot(1, 2, 2);
  imshow(binaryImage_okoli, []);
  title('Binarizovaný obraz', 'FontSize', fontSize);
  % Enlarge figure to full screen.
  set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
  drawnow;
  
  % Save output image.
  baseOutputFileName = sprintf('Binarizace_okoli_%3d.png', k);
  fullOutputFileName = fullfile(folder, baseOutputFileName);
  imwrite(logical(binaryImage_okoli), fullOutputFileName);
  fprintf('Saved %s.\n', fullOutputFileName);
    imwrite(binaryImage_okoli,'myMultipageFile.tif')

[Walter Roberson]

if k == 1
  imwrite(binaryImage_okoli,'myMultipageFile.tif')
else
  imwrite(binaryImage_okoli,'myMultipageFile.tif', 'writemode, 'append')
end

[Veronika]

Okay, thank you so much. I added these raws here:

clc;    
close all;  
clear;  
workspace;  
format long g;
format compact;
fontSize = 20;

folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';

if ~isdir(folder)
  errorMessage = sprintf('Error: The following folder does not exist:\n%s', folder);
  uiwait(warndlg(errorMessage));
  return;
end

filePattern = fullfile(folder, '*.dcm'); 
theFiles = dir(filePattern);
for k = 1 : length(theFiles)
  baseFileName = theFiles(k).name;
  fullFileName = fullfile(folder, baseFileName);
  fprintf(1, 'Now reading %s\n', fullFileName);
  
  grayImage= dicomread(fullFileName);
  subplot(1, 2, 1);
  imshow(grayImage, []);  
  axis on;
  title(baseFileName, 'FontSize', fontSize);
  drawnow; 
  
  
  [rows, columns, numberOfColorChannels] = size(grayImage);
  if numberOfColorChannels > 1
    %   % Máme barevný obraz, musíme ho převést na černobílý = vybereme %zelený kanál
    grayImage = grayImage(:, :, 2); % zelený kanál
  end
  

  eq_grayImage = histeq(grayImage);
  
  
  % Práh pro vytvoření binárního obrazu okolí
  thresholdValue = 900;
  binaryImage_okoli = grayImage > thresholdValue;
  % Odstranění okolí.
  binaryImage_okoli = imclearborder(binaryImage_okoli);
  % Vyplnění otvorů.
  binaryImage_okoli = imfill(binaryImage_okoli, 'holes');
  % Vymazání menších otvorů.
  binaryImage_okoli = bwareaopen(binaryImage_okoli, 1150);
  % Roztažení binárního obrazu pro přesnější segmentaci
  se = strel('line',5,100);
  binaryImage_okoli= imdilate(binaryImage_okoli,se);
  
  
  subplot(1, 2, 2);
  imshow(binaryImage_okoli, []);
  title('Binarizovaný obraz', 'FontSize', fontSize);
  
  set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
  drawnow;
  
  
  baseOutputFileName = sprintf('Binarizace_okoli_%3d.png', k);
  fullOutputFileName = fullfile(folder, baseOutputFileName);
  imwrite(logical(binaryImage_okoli), fullOutputFileName);
  fprintf('Uloženo %s.\n', fullOutputFileName);
    *if k == 1
        imwrite(binaryImage_okoli,'myMultipageFile.tif')
    else
         imwrite(binaryImage_okoli,'myMultipageFile.tif','writemode','append')
    end*
end
set(gcf, 'Units', 'Normalized', 'OuterPosition', [0 0 1 1]);
set(gcf, 'Toolbar', 'none', 'Menu', 'none');
set(gcf, 'Name', 'Binarizace testovacích CT skenů', 'NumberTitle', 'Off')

Is it right or not? Because I still see only one image in this myMultipageFile.tif.

[Walter Roberson]

The code correctly writes multiple images to the tif file.

When a TIFF has multiple images, then when you issue a single imread() to read back from the file, you do not get all of the images at one time -- not beside each other, and not as a 3D array or 4D array of images. You have to loop reading the images using indexing.

filename = 'myMultipageFile.tif'
metadata = imfinfo(filename);
num_img = length(metadata);
image_data = imread(filename);
if num_img > 1; image_data(:,:,:,num_img) = 0; end  %pre-allocate
for img_num = 2 : num_img
  image_data(:,:,:,img_num) = imread(filename, img_num);
end