set NaN as another color than default using imagesc

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Hello, I have a matrix filled probability numbers (i.e. ranging from 0 to 1) or NaN when the probability is not computed. I would like to display this matrix as a color table (e.g. using imagesc), in order to have a quick visualisation of the result. The colorbar range is thus set as 0 to 1 since I am interested in probability values. However, I would like the NaN fields to appear with another color than the default "-inf" (here the color of 0 since the down limit for the color is set for value 0), for example gray. How can I do this? Thank you very much, Gaelle

Accepted Answer

Kelly Kearney
Kelly Kearney on 12 Jul 2013
Edited: Kelly Kearney on 12 Jul 2013
Do you need to use imagesc, or are you open to using pcolor? The latter will leave NaNs blank, so they will appear the same color as the axis background.
Example:
data = rand(10);
data(data > 0.9) = NaN;
[nr,nc] = size(data);
subplot(2,1,1);
imagesc(data);
subplot(2,1,2);
pcolor([data nan(nr,1); nan(1,nc+1)]);
shading flat;
set(gca, 'ydir', 'reverse');
(The NaN-padding in the pcolor call is so the last row and column are shown, similar to imagesc)
  3 Comments
Kelly Kearney
Kelly Kearney on 20 Jan 2017
Just set the 'clim' property of the axes:
data = rand(10);
data(data > 0.9) = NaN;
[nr,nc] = size(data);
ax(1) = subplot(2,1,1);
imagesc(data);
ax(2) = subplot(2,1,2);
pcolor([data nan(nr,1); nan(1,nc+1)]);
shading flat;
set(gca, 'ydir', 'reverse');
set(ax, 'clim', [0 1]);

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More Answers (5)

Charles Krzysik
Charles Krzysik on 27 Apr 2017
If you want to use imagesc rather than pcolor, you can set the AlphaData property to zero everywhere you have a NaN. This will show the background wherever there is no data; you can then additionally set the background colour, if you so choose. In this example I'm setting it to black:
imAlpha=ones(size(Data_Array));
imAlpha(isnan(Data_Array))=0;
imagesc(Data_Array,'AlphaData',imAlpha);
set(gca,'color',0*[1 1 1]);
  4 Comments
TheStranger
TheStranger on 2 Jun 2021
Edited: TheStranger on 2 Jun 2021
This is the most useful comment of this thread, yet not with the most votes!
Maria Cristina Araya Rodriguez
I agree, many thanks, in fact this is a good solution when using a ".cpt" colour scale.

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Lauren
Lauren on 7 Nov 2017
imagesc(data,'AlphaData',~isnan(data))
  8 Comments
Walter Roberson
Walter Roberson on 17 Nov 2023
If you have RGB data, some elements of which might be NaN, then
%with sufficiently new versions of MATLAB
scaled_data = rescale(YourRGBData, 0, 1);
alpha_data = 0 + ~any(isnan(YourRGBData), 3);
image(scaled_data, 'AlphaData', alpha_data);
%older versions of MATLAB
scaled_data = mat2gray(YourRGBData);
alpha_data = 0 + ~any(isnan(YourRGBData), 3);
image(scaled_data, 'AlphaData', alpha_data);
In practice if your RGB data is single or double precision data that uses only integral values 0 to 255, but also has some NaN, then you would probably use slightly different code,
scaled_data = uint8(YourRGBData);
alpha_data = 0 + ~any(isnan(YourRGBData), 3);
image(scaled_data, 'AlphaData', alpha_data);

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Evan
Evan on 12 Jul 2013
Edited: Evan on 12 Jul 2013
You can use the isnan function to find the indices of all NaNs, then set those elements to another value:
Example:
>>A = [4 NaN 3;NaN 2 1];
>>A(isnan(A)) = 255
A =
4 255 3
255 2 1
  6 Comments
Gaëlle
Gaëlle on 12 Jul 2013
Moved: DGM on 25 Mar 2023
But one thing which is bad using your way: the colorbar scale is not set according to the values of the probabilities. So actually, I cannot use your trick...
Adil Masood
Adil Masood on 10 Dec 2015
Moved: DGM on 25 Mar 2023
Thanks you for a smart solution. There is just one correction: Instead of
scatter(ii,jj,'ok','MarkerEdgeColor',[1 1 1],'MarkerFaceColor',[0 0 0],'LineWidth',2,'SizeData',100)
it should be
scatter(jj,ii,'ok','MarkerEdgeColor',[1 1 1],'MarkerFaceColor',[0 0 0],'LineWidth',2,'SizeData',100)
Its because imagesc() plots elements of matrix indexed as (row,column), while scatter() handles elements as (x,y).

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Gaëlle
Gaëlle on 12 Jul 2013
Hi, I am open to use pcolor, it just seemed more complicated to use than imagesc. I will try to implement it. Thank you!

Ben
Ben on 4 Dec 2014
Edited: Ben on 10 Dec 2014
If using pcolor, NaNs are set to the axis background color. So you can set your colormap to color non-NaNs, and set the axis background color to set the color for NaNs. For example, to set NaNs black you can use: set(gca,'color','k')
  1 Comment
Walter Roberson
Walter Roberson on 20 Jan 2017
For pcolor the nan are not exactly set to the axes background color: instead a hole is created that allows whatever is under to be visible. If nothing else is there that would be the axes background, but there could also be a different graphics object there.

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