How to use saveas for binary images?

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Veronika
Veronika 2017-4-8
评论： Veronika 2017-4-16
Dear all,
I would like to saveas jpg my DICOM images, which I transform to binary images. So I would like to save these binary images. But I only did, that all of these images are in one .jpg picture, but I want to save them separately, for example: binaryImage1.jpg, binaryImage2.jpg,.....binaryImage37.jpg. This is my code:
Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';
for i=0;
i = i+1;
for p = 48:86
filename = fullfile(Folder, sprintf('%06d.dcm', p));
grayImage(:,:,1,p - 47)= dicomread(filename);
grayImage_pater(:,:,1,p - 47)= dicomread(filename);
[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);%ekvalizace pomocí histogramu obrazu
[rows, columns, numberOfColorChannels] = size(grayImage_pater);
if numberOfColorChannels > 1
% Máme barevný obraz, musíme ho převést na černobílý = vybereme zelený kanál
grayImage_pater = grayImage_pater(:, :, 2); % zelený kanál
end
eq_grayImage_pater = histeq(grayImage_pater);
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, 750);
%Roztažení binárního obrazu pro přesnější segmentaci
se = strel('line',5,100);
binaryImage_okoli= imdilate(binaryImage_okoli,se);
imshow(binaryImage_okoli, []);
% X(:,:,1,p - 47) = imadjust(X(:,:,1,p - 47),[0 0.022],[]); % increase contrast
saveas(gcf(i),'Binarizace_okoli.png')
end
end
Can you advise me? Thank you for your answers.
  2 个评论
Guillaume
Guillaume 2017-4-11
A bit off topic, but saving a binary image as JPEG is not a good idea. Unless you use the rarely used non-lossy compression option, JPEG will result in colour gradients at the transitions between black and white.
Thankfully, in the answers that have been provided I see that the format has been changed to PNG which is a much better format for saving binary images.
Veronika
Veronika 2017-4-11
Yes, I save images in PNG format, but still, first two are saved right, but the other images are only black.
Do you know, where is a problem, please?
This is my recent code:
Folder = 'C:/Users/ced0005/DP/DP_framework/DICOM/slicesCT/';
for p = 54:86
filename = fullfile(Folder, sprintf('%06d.dcm', p));
grayImage(:,:,1,p - 53)= dicomread(filename);
%grayImage_pater(:,:,1,p - 53)= dicomread(filename);
[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);%ekvalizace pomocí histogramu obrazu
%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);
imshow(binaryImage_okoli, []);
output_name = sprintf('Binarizace_okoli_%3d_%3d.png', p)
imwrite(logical(binaryImage_okoli), output_name);

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采纳的回答

Walter Roberson
Walter Roberson 2017-4-8
  13 个评论
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Image Analyst
Image Analyst 2017-4-12
The poorly-named "temp" is, or should be a filename. However you're sticking an actual binary image into it for some reason. Why are you doing that? You should not.
Use sprintf() to make up a valid filename. Check what it is before you just blindly use it.
Also, why do you have this:
for p = numel(Index)
for k = 1:p figure(k);
for p = 54:66
You have a loop over p inside an outer loop over p. What is your thought process there????
Veronika
Veronika 2017-4-12
So I must rename temp to binaryImage_okoli?
for p = numel(Index)
this I have for counting the number of images in file
for k = 1:p figure(k);
this is for create figure (1-33)
and this
for p = 54:66
for better name of file.
Please, if you can, transform my code for better function.

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更多回答（2 个）

Image Analyst
Image Analyst 2017-4-9
Try this:
uint8Image = uint8(255 * binaryImage_okoli);
imwrite(uint8Image, 'Binarizace_okoli.png') ;
  9 个评论
显示 7更早的评论
Image Analyst
Image Analyst 2017-4-16
This works perfectly fine as far as I can tell.
% 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\Mark\Documents\MATLAB\work\Tests\Scans';
% 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');
Veronika
Veronika 2017-4-16
Thank you, sooo much. You are amazing!

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Payam Khoshkenar
Payam Khoshkenar 2017-4-9
编辑：Walter Roberson 2017-4-9
I have a microscope image with three channels (RED, GREEN and BLUE), each channel is unit 16 intensity image. I want to show each channel in a subplot (1,3), but in their color form (RGB). I figured it out that with the following command, I can all channels into one RGB image, but I want to show each channel in one subplot.
overlay=cat(3,imadjust(mat2gray(RED)),imadjust(mat2gray(GREEN)),imadjust(mat2gray(BLUE)));
Is there anyway to show/convert my intensity grayscale images into RGB format? I also found in one of your replies that following line can show each channel in RGB format but the output image is not adjusted and also I cannot adjust the output of following code by imadjust because it's not grayscale anymore:
red_IM = cast(cat(3, RED, zeros(size(RED)), zeros(size(RED))), class(RED));
I would appreciate if you could help me.
Thanks
  1 个评论
Walter Roberson
Walter Roberson 2017-4-9
red_IM = cast(cat(3, imadjust(mat2gray(RED)), zeros(size(RED)), zeros(size(RED))), class(RED));

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