k-Wave

1. Alexander
   

   Member
   Joined: Jun '17
   Posts: 19

   Hi,

   I am currently using GNU/Octave with k-wave and wanted to make an animation of some of the simulations I am running. The default way to do this in k-wave isn't supported in octave (or newer versions of matlab) by passing ‘RecordMovie’ as true in kspaceFirstOrder2D(...). Therefore I am looking to capture the pressure field at each point in time and then plot it as a mesh plot.

   I was able to do something similar using FOCUS (http://www.egr.msu.edu/~fultras-web/index.php) with the following code (using matlab)...

   nt = size(p_tsd, 4); % The amount of time points in the array 
   
   for it = 1:nt
   mesh(z*100, x*100, squeeze(p_tsd(:, :, :, it)))
   title(['FNM TSD Example, t = ', sprintf('%0.3f',(it/fs) * 1e6), '\mu','s'])
   zlabel('pressure (Pa)')
   xlabel('z (cm)')
   ylabel('x (cm)')
   temp=axis();
   temp(5)=-maxpressure;
   temp(6)=maxpressure;
   axis(temp);
   cb = colorbar();
   caxis([-maxpressure maxpressure]);
   ylabel(cb, 'Pressure (Pa)');
   drawnow
   
   frame = getframe(1);
    im = frame2im(frame);
    [imind,cm] = rgb2ind(im,256);
   
    if it == 1
        imwrite(imind,cm,'x-z_transient_bone.gif','gif', 'Loopcount',inf);
    else
        imwrite(imind,cm,'x-z_transient_bone.gif','gif','WriteMode','append','DelayTime', 0);
    end
   end

   So would something similar be possible in k-wave?

   Posted 7 years ago #

2. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,643

   Hi eu7209,

   We have actually switched to using VideoWriter for V1.2. The release should be out very soon. Unfortunately, I'm not sure about compatibility with Octave.

   Brad.

   Posted 7 years ago #

3. Alexander
   

   Member
   Joined: Jun '17
   Posts: 19

   Thanks Brad,

   I'll re-post here once I test it out in octave. However, is there a way to capture the pressure field as it is? So for FOCUS I could get the pressure field as an array with properties (x,y,z,t) and just loop through t to plot the pressure field (as seen in the above code). Because from my understanding sensor_data is only used for image reconstruction, whereas I just what the pressure field as the simulation runs.

   Posted 7 years ago #

4. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,643

   Hi eu7209,

   Yes, you can just set your sensor mask to cover the whole domain. See the "Defining A Sensor Mask By Opposing Corners Example".

   Brad.

   Posted 7 years ago #

5. Alexander
   

   Member
   Joined: Jun '17
   Posts: 19

   Thank you Brad. Everything seems to be working great now. I look forward to using v1.2 soon.

   Posted 7 years ago #

6. ahd123
   

   Member
   Joined: Mar '19
   Posts: 6

   Just started using k-wave with Octave. Unfortunately, Octave does not have the videoWriter functionality. It does have a video package which provides 'addframe', 'avifile','aviinfo',and 'aviread' functions.

   Does anyone know if these functions can be wrapped into a pseudofunction to provide videoWriter-like functionality that k-wave could use without having to rewrite the underlying K-wave movie functionality?

   Posted 5 years ago #

7. ahd123
   

   Member
   Joined: Mar '19
   Posts: 6

   Just a heads up, the patch() command does not appear to be fully implemented in Octave, specifically transparency. As a result, running voxelPlot() does not work unless line 114
   set(hp2, 'FaceAlpha', transparency); is commented out. Also, the edge color does not seem to work. Output is not optimal, but is usable.

   Posted 5 years ago #

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