Suppose we have two images:
1) RGB Image:
% initialize RGB image:
rgbIm = zeros(100, 100, 3);
rgbIm(20:80, 20:80, 1) = 1;
2) Grayscale Image:
% initialize grayscale image:
grayIm = zeros(100);
grayIm(20:80, 20:80) = 1;
Lets show both of them:
figure, imshow(rgbIm), colormap('jet'), colorbar;
figure, imshow(grayIm), colormap('jet'), colorbar;
As we can see, the colorbar in the 2nd figure (i.e. grayscale image) makes total sense. On the other hand I can't really understand the information given by the colormap in the 1st figure.
What I would like to achieve is to display the colorbar of the grayscale image in the figure corresponding to the RGB image.
It might seem that this does not make sense but this is just a very minimal example that I just made up to show what I would like to do in a larger project.
Any thoughts?
Thanks a lot :)
EDIT1: Allow me to explain why I would need this
Suppose I compute some physiological parameters one MRI slice in certain regions of interest, yielding something like this:
Now I want to superimpose these parameters on top of the original slice, and I create one RGB image to achieve this:
The colormap does not make sense, and this is why I would like to display the colormap corresponding to the parametric image in the RGB image (i.e. the superimposition image).
Any ideas?
Thank you for your attention.
I still think what you are asking does not make sense.
Let me explain:
What is colorbar? Colorbar is a representation of a function (mapping) from gray-level (scalar) to color. Using jet, in your example, you map the 0 to dark blue and 1 to red.
By asking for a colorbar for an RGB image, you are actually asking for a mapping from RGB triplet to RGB color -- this mapping is the identity mapping! you do not need a colorbar to see this mapping, each pixel represent it!
EDIT
After seeing the edited question, I revise my answer a bit:
Since both MRI signal and whatever physiological parameters you computed makes no sense in RGB space, you have two 1D mappings:
1. MRI signal at each voxel to gray level ("gray" colormap)
2. Physiological measure at each voxel to "jet" color
What I usually do in this cases is convert the 2D MRI slice into RGB gray image by simply replicate it along the third dimension
rgbSlice = twoDSlice(:,:,[1 1 1]);
Now show the images on top of each other
figure;
imshow( rgbSlice );
hold on;
h = imshow( physiologicalParams );
colormap jet;
set(h, 'AlphaData', .5 );
colorbar
You might need to play with the color mapping of the axes using caxis or clim to get it right.
(Answering my own question so I can hopefully help someone in the future)
I just accomplished what I intended, with the help of the above answer and a post from Steve Eddins' blog.
Here's how:
baseImage = baseImage/(max(baseImage(:))); % normalize base (anatomical) image
rgbSlice = baseImage(:,:,[1 1 1]); % converting to RGB (ignore colormaps)
imshow(parameterROIImage, []); % show parametric image
colormap('jet'); % apply colormap
hold on;
h = imshow(rgbSlice); % superimpose anatomical image
set(h, 'AlphaData', ~bwROIlocations); % make pixels in the ROI transparent
colorbar;
where parameterROIImage is:
bwROIlocations is the logical matrix containing the ROI pixels:
Final result:
Thanks for the help Shai.
Related
I have 2 matrices. Matrix A contains values between 0 and 1 and matrix B contains values between 0 and 90. I would like to display an image with a different color for the numbers in each matrix.
When I use the colormap function with:
figure; colormap(jet); imshow(A);
The image displayed has several levels of gray, when I am supposed to have several colors (because I am using jet).
When I use the colormap function with:
figure; colormap(jet); imshow(B);
The image displayed is completely white, probably because my values are higher than 64 (which is the max of jet).
How can I solve these two problems? I read a lot of tutorials in several forums but I can't find the answer...
Thank you very much for answering my problem!
Just normalize the matrix by its max value if the values are more than 1. So for your B matrix try:
imshow(B/max(B(:)))
You can specify the colormap scaling and the number of actual colors within the colormap like so:
figure; imshow( A, [0 1], 'Colormap', jet(100) );
figure; imshow( B, [0 100], 'Colormap', jet(100) );
The jet(100) indicates 100 unique colors within the colormap to be used.
You are using the wrong function for the task in hand.
imshow expects an N by M by 3 array input, of the RGB channels of an image. When you use a 2D matrix the function assumes it's a grayscale image (it's like replicating it to 3 identical matrices to create these three channels - if all the channels in RGB have the same values you get grayscale colors). You can use this function together with a colormap to get a colored matrix, but there are much more convenient alternatives.
One simple function for getting a colored representation of a matrix is imagesc or (image if you want to scale the values by yourself). This function takes the values in your matrix, and assign them a color from the colormap you choose:
A = rand(10);
figure; colormap(jet); imagesc(A);
Another option is pcolor, which works a little different but give a similar result. pcolor attach the values to the vertices of the cells (in oppose to the center, as imagesc does), and interpolate the color in each cell from its' vertices. The resulted colored matrix is always smaller in one row and one column because it takes n+1 points (values in the original matrix) to define n gaps (the cells in the colored matrix). Here is an example:
A = rand(10);
figure; colormap(jet); pcolor(A);
shading flat
I'd like to read a custom image and apply a colormap like in the example from matlab. How can I do that? I see the example imageext uses custom images and applies colormaps and I'd like to do the same with my images. How can it be done? I want just to use my own picture for an example like imageext in matlab.
This does not work:
I = im2double(imread('niklas3.png')); figure(1); imshow(I,[]); daspect([1 1 1]); axis off; colormap gray;
niklas3.png:
But this code works:
I = im2double(imread('cameraman.tif')); figure(1); imshow(I,[]); daspect([1 1 1]); axis off; colormap summer;
You can apply a colormap in any image you want if it was previously displayed into a figure.
I recommend you to use imagesc or imshow to display images. In order to do that, you need to load the image with imread. A good practice is to convert your image data to double precision.
I = im2double(imread('cameraman.tif'));
As you can see, im2double converts image data to double precision ranging from 0 values to 1 values. If you do not want this, you can use the double function, ranging from 0 values to 255 value.
Later, you need to display the image into a figure. I strongly recommend to use imagesc instead of imshow, because imagesc allows you to customize your data and your display (for example, adding a different colormap).
figure(1); imagesc(I); daspect([1 1 1]); axis off;
Now, you can use the colormap you want. Type help colormap for more information, but you can use a jet colormap (default), gray, hot, bones, or whatever you want, just typing:
colormap gray;
If you plotted several images, you need to indicate the aimed image with:
figure(1); colormap gray;
If you want to use imshow, just type:
figure(1); imshow(I,[]); daspect([1 1 1]); axis off; colormap gray;
Edited: Once I saw your image, I knew your problem is that you are trying to apply a colormap into a RGB image. That is, you are trying to apply it into a 3D matrix, where rows and columns identify the pixel value and the third dimension identifies the RGB components.
So, you need to convert your RGB image into a 2D matrix (a black and white one). You can do it by performing the mean along the third dimension.
I = nanmean(I,3);
Finally, you should apply the colormap as I said it before. The final code would be:
I = im2double(imread('niklas3.jpg'));
I = nanmean(I,3);
figure(1); imshow(I,[]); daspect([1 1 1 ]); axis off;
colormap jet;
This is the result using a jet colormap:
I would like to define a transparent color within the color map how do I do that?
The reason I need this is that I have a multiple layers in my axes (produced both by imagesc and plot). I know I could simply first use imagesc and then plot but I want to draw the lines behind non-zero values of the imagesc representation.
To color the zeros white I use
jet = colormap('jet');
jet(1:2,:) = 1;
colormap(jet);
Now I would like to make white transparent.
The colormap doesn't have a fourth element for alpha, it's RGB only, so the way I do this sort of thing is to make a mask of the desired transparency layer - binary or greyscale will work - and then apply that to the image. To do this you need to store the handle of the image
% make random image
im = rand(100,100);
% make example alphamask
alphamask = im<0.3;
% store handle
hnd = imagesc(im);
% apply mask
set(hnd, 'AlphaData', alphamask);
I guess, I've got an colormap issue with Matlab2013. I plot a 3d surface plot with colormap hot and I would like to have in the same plot an bitmap (8bit colour image) on the x-y plane. Plotting both separately from each other works fine but as soon as I plot them in one figure the first surface plot is only black. I guess it is because the RGB image on the x-y plane uses a different colour map. Is there an option in Matlab to plot two different type of images in the same plot?
surf(X,Y,density,'FaceColor','texturemap','Edgecolor','none')
colormap hot
...
%// define the location of the bitmap
xImage = [miX maX; miX maX]; %// The y data for the image corners
yImage = [miY miY; maY maY]; %// The x data for the image corners
zImage = [zDist zDist; zDist zDist]; %// The z data for the image corners
surf(xImage,yImage,zImage,... %// Plot the surface
'CData',RGBImage,...
'FaceColor','texturemap');
Thanks!
Durin
I think this is an issue with the relative scaling of density and zImage. I can replicate this by doing the following:
1) Plot a surf where the third input is n x m which is scaled like some real data (-0.2 to +0.2, for example). This responds to changes in colormap as you'd expect.
2) After hold on, plot another surf where the third input is n x m x 3, like a RGB image, double values scaled between 0 and 1.
This causes the first image to go "dark" (or whatever the lowest color in that particular colormap is). The issue is that they share their CLim, being in the same axis, although the RGBImage doesn't, in fact, reference the colormap.
This is "fixable" by scaling/normalising the first plot (your density values) to be between 0 and 1 (in this case) - although this quick fix is going to give you issues if you then want to add a colorbar. Alternatively, first grab the "CLim" from your axis after plotting the first surf:
trueC = get(gca,'CLim');
Then set it back after you plot the image:
set(gca,'CLim',trueC)
I have a similar question than the one in this post.
I have a grayscale image and I plot points on it. Fro plotting the points I use colormap('jet') but as I want the image to be grayscale, after plotting the points I reset the colormap, colormap('gray').
But I want to show a colorbar! And the colorbar is plotted in grayscale, not 'jet'.
How can I do that?
EDIT:
I want a Colorbar showing the color of the points!
You should convert your image to RGB by putting the same data into R-, G-, and B-channels (this will be grayscale RGB image). Colormap in MatLab is not applied to RGB images, only to indexed ones. Then plot your points over the image with colormap you like.
As discussed here, there's a few ways:
If you have the image processing toolbox, use subimage to create an independent image with a separate colormap. Then plot the image, your points, and join them into one using linkaxes.
Use freezeColors from the file exchange (or multiple colormaps, which I haven't ever tested personally). This is a very easy way to create a larger colormap, and automatically selecting the right portion of the colormap for display of images and colorbars.
As answered by anandr, convert your greyscale image to RGB; Matlab doesn't use colormaps on RGB images, which leaves you freedom to plot your points and show their colorbar independent of the image.
Example code for (3):
I = imread('cameraman.tif');
imshow(cat(3,I,I,I))
hold on
x = #() round(size(I,1) * rand(50,1));
y = #() round(size(I,2) * rand(50,1));
plot(x(), y(), 'r.')
plot(x(), y(), 'g.')
plot(x(), y(), 'b.')
colormap('jet')
colorbar
result: