Extremely slow imshow() when using 16-bit images

I'm starting by taking a matrix of data from a DICOM file and making it indexed (so that I can apply a user-specified colormap).

shades = 2^bit_val
grayData = mat2gray(dicomData);
% Limiting to shades-1 to allow for a special mark-up color
indexedData = gray2ind(data, shades-1);

%Then code to calculate cmap with the special color at the end
...
imshow(indexedData, cmap, handles.Axes);

If bit_val is 8, then the code takes 0.01 seconds to display which is fine. However, if bit_val is 16, then it takes nearly a whole second to display.

The primary issue is that I want to be able to quickly/smoothly switch between different slices being displayed.

Is there any way to improve the rendering time?

Edit:

According to Wikipedia's entry for palette ( http://en.wikipedia.org/wiki/Palette_%28computing%29#System_and_logical_palettes_under_Microsoft_Windows )

Under Windows, "When a given application intends to output colorized graphics and/or images, it can set their own logical palette, that is, its own private selection of colors (up to 256)."

Perhaps this explains why an 8-bit color map (with only 256 colors) displays faster than a 16-bit color map (with 65536 colors) on Windows.

[Walter Roberson]

Which platform are you using? I have read that MS Windows is not designed to be able to handle colormaps with more than 256 entries.

[Sean de Wolski]

How are you timing it?

[Christopher]

@Walter: I am, indeed, using Windows. (XP to be precise. Company isn't upgrading to Windows 7 until next year.)

@Sean: With tic and toc.

Answer 1

[Sean de Wolski]

X = uint16(rand(1000)*60000);
t = 0;
figure;ax = axes;
for ii = 1:10
  tic;
  imshow(X,'parent',ax);
  drawnow;
  t = t+toc;
  cla;
  drawnow;
end

disp(t/10);
%    0.0335 on my system

Also Have you seen implay()?

doc implay

[Christopher]

I'm getting about the same when running that code.

However, with my code, I have:

disp(toc(tstart));
iH = imshow(indexedSlice, [cvalues; highlight], 'Parent', handles.([type 'Axes']));
disp(toc(tstart));

For 8-bit colormaps, this gives:

    0.0021

    0.0162

For 16-bit colormaps, this gives:

    0.0047

    0.4363

Yesterday, it was giving 0.9. Maybe something was running in the background.

[Image Analyst]

You don't need to put tic and toc inside a disp() function.

[Sean de Wolski]

@Christopher: Put this in a loop (like I did) and run it in a script file. That way you don't get any overhead that may be introduced by the command window.

[Christopher]

@Sean: Your script doesn't use an indexed image with a colormap. If I use just a grayscale version of the image with imshow(), it's very fast. However, the slowdown is in adding/applying the colormap.

Could you tell me what you get for:

X = uint16(rand(1000)*60000);
X = mat2gray(X);
X = gray2ind(X, 2^16);
cmap = gray(2^16);

t = 0;
figure;ax = axes;
for ii = 1:10
  tic;
  imshow(X, cmap,'parent',ax);
  drawnow;
  t = t+toc;
  cla;
  drawnow;
end

disp(t/10);

I get an average of 1.75

Edit: I've even tried displaying the indexed image (without the colormap as it was already set) and this doesn't seem to have increased the speed all that much.

Edit2: I noticed this from "help image":

For uint8 and uint16 matrices, color intensities are on the range [0, 255].