k-Wave

1. jf
   

   Member
   Joined: May '20
   Posts: 3

   Hi,
   I just installed the k-wave toolbox and tried to run the examples, but I always get the same error (Matlab 2018b):

   Matrix dimensions must agree.

   Error in kspaceFirstOrder2D (line 920)
   ux_sgx = dt .* rho0_sgx_inv .* real(ifft2( bsxfun(@times, ddx_k_shift_pos,
   kappa .* fft2(p)) )) / 2;

   Error in example_3_ivp_opposing_corners_sensor_mask (line 82)
   sensor_data = kspaceFirstOrder2D(kgrid, medium, source, sensor);

   The reason for the error is that in the function 'bsxfun(@times, ddx_k_shift_pos, kappa .* fft2(p))' the variable 'kappa' is of size NxN (128x128 in example_ivp_homogeneous_medium), while 'fft2(p)' is of the size (N^2)x1 (16384).

   Posted 4 years ago #

2. jf
   

   Member
   Joined: May '20
   Posts: 3

   I guess I found the reason for this error, in 'kspaceFirstOrder_inputChecking' line 1540:

   source.p0 = smooth(source.p0, true);

   outputs a vector even though the input is a matrix. I replaced this line with

   source.p0 = smoothdata(source.p0, true);

   which returns a matrix, and it seems to be working (at least the output seems similar to the one in the documentation for this example).

   EDIT: I just realized that k-wave has its own smoothing function implemented, but as far I can tell, matlab is prioritizing using its own version. I just renamed the smoothing function in the toolbox folder from 'smooth' to 'smooth_k' and changed the line to

   source.p0 = smooth_k(source.p0, true);

   which also seems to work I guess as intended.

   EDIT2: Since 'smooth_k' recalls itself recursively line 62

   mat_sm = smooth(varargin{2:end});

   has to be changed to the renamed function aswell:

   mat_sm = smooth_k(varargin{2:end});

   Posted 4 years ago #

3. jf
   

   Member
   Joined: May '20
   Posts: 3

   As far I can tell there is also another reason for this error appearance: While setting the path of the toolbox, i moved it to the bottom of the list. This prevented the toolbox integrated 'smooth' function to overload the matlab version, I think this is the reason that this error did not occur more often. Since I do not know how this interacts with other scripts I stick with renaming the smooth function and keep the toolbox at the bottom of the path-list.

   Posted 4 years ago #

4. alhareth
   

   Member
   Joined: Mar '20
   Posts: 1

   Dear jf

   I am facing the same problem. How to set the path of the toolbox and solve the problem?

   Posted 4 years ago #

5. Bradley Treeby
   

   Developer
   Joined: Mar '10
   Posts: 1,643

   Hi jf,

   Thanks for the report. We'll make an effort to migrate the name of smooth to something that doesn't conflict with the curve fitting toolbox.

   Brad.

   Posted 4 years ago #

RSS feed for this topic

Reply

You must log in to post.