set NaN as another color than default using imagesc

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Gaëlle
Gaëlle 2013-7-12
评论： Walter Roberson 2023-11-17
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

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Kelly Kearney
Kelly Kearney 2013-7-12
编辑：Kelly Kearney 2013-7-12
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)
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Kelly Kearney
Kelly Kearney 2017-1-20
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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更多回答（5 个）

Charles Krzysik
Charles Krzysik 2017-4-27
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]);
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TheStranger
TheStranger 2021-6-2
编辑：TheStranger 2021-6-2
This is the most useful comment of this thread, yet not with the most votes!
Maria Cristina Araya Rodriguez
Maria Cristina Araya Rodriguez 2023-11-17
I agree, many thanks, in fact this is a good solution when using a ".cpt" colour scale.

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Lauren
Lauren 2017-11-7
imagesc(data,'AlphaData',~isnan(data))
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Walter Roberson
Walter Roberson 2023-11-17
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 2013-7-12
编辑：Evan 2013-7-12
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
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Gaëlle
Gaëlle 2013-7-12
移动：DGM 2023-3-25
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 2015-12-10
移动：DGM 2023-3-25
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 2013-7-12
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 2014-12-4
编辑：Ben 2014-12-10
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')
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Walter Roberson
Walter Roberson 2017-1-20
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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