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:
Related
I am trying to create a filled contour plot from an image in MATLAB. However, the command imcontour does not seem to have an option for filled contours. If I use contourf, it draws all the contour lines in black. Since the image has a lot of contour levels, it is shown almost completely in black.
Does anybody know how to make a filled imcontour or how to meaningfully apply contourf on an image?
There is no filled version of imcontour because in theory, the image itself is the filled version.
data = load('clown');
img = ind2rgb(data.X, data.map);
imshow(img);
hold on
imcontour(img(:,:,1), 3);
You could use contourf though, and specify the line color. By specifying a value of 'none' no lines will be shown.
c = contourf(data, 2, 'LineColor', 'none')
I have some data I would like to display in a picture form. In one case I want to rescale the x and y axis, which leads me to using imagesc. The issue is that the same colormap (jet) looks different in imagesc as compared to image.
Is there a way to make them the same?
I am using MATLAB R2014a.
Demonstration:
Here is how I show them:
figure; image(cancelledmap); colormap(jet); %image
figure; imagesc(y,x,cancelledmap); colormap(jet); %imagesc
And the output:
The colormap settings for both figures are somehow the same, however:
imagesc scales the color axis, whereas image does not. That's why the colors look different. If you click the colorbar button you'll see that they are on different color scales.
You can change the colorscale with caxis.
By the way, if you only want to scale the X- and Y-axes, you can use either function. Just supply your own scaled x and y vectors.
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)
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.
I have obtained the following figure using a 120x120 matrix and the surf function.
Is there a simple way to make the lines between different colors look smoother?
First of all, surf may not be the best way to display 2D-image - if you don't actually need the height information, imagesc will work just fine. Even better, it won't show the differently colored lines between hexagons, since it's not going through the colormap at intersections.
However, regardless of your approach, a low-resolution bitmap will not be automatically transformed into a "arbitrary"-resolution vector graphics - and you may not want that, anyway, if you use the figure to allow you to inspect at which combination of (x,y) you obtained at a given value.
There are three approaches to make your image prettier - (1) segment the hexagons, and use patch to create a vector-graphics image. (2) upsample the image with imresample. (3) create a RGB image and smoothen each color separately to get softer transitions:
%# assume img is your image
nColors = length(unique(img));
%# transform the image to rgb
rgb = ind2rgb((img+fliplr(img)),jet(nColors)); %# there are much better colormaps than jet
%# filter each color
for i=1:3,rgbf(:,:,i)=imfilter(rgb(:,:,i),fspecial('gaussian',9,3),'replicate');end