k-Wave User Forum » Topic: Absorption coeff. of the target

k-Wave User Forum » Topic: Absorption coeff. of the target http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target Support for the k-Wave MATLAB toolbox en-US Tue, 12 May 2026 22:34:34 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php Bradley Treeby on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-8200 Wed, 09 Jun 2021 08:57:26 +0000 Bradley Treeby 8200@http://www.k-wave.org/forum/ If you don't specify the absorption, the simulation will be lossless. If you have already specified the medium properties, you can remove it by: <pre><code>medium = rmfield(medium, 'alpha_coeff'); medium = rmfield(medium, 'alpha_power');</code></pre> zengqw2021 on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-8197 Wed, 09 Jun 2021 08:17:44 +0000 zengqw2021 8197@http://www.k-wave.org/forum/ Hi Brad, Ok, I see. Is there a way for me to turn absorption off during reconstruction? Zeng Bradley Treeby on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-8196 Tue, 08 Jun 2021 17:39:26 +0000 Bradley Treeby 8196@http://www.k-wave.org/forum/ Hi Zeng, The second simulation is run on a different sized grid (to avoid the inverse crime). So you will either need to use the same grid, or redefine <code>medium.alpha_coeff</code> to be Nx by Ny. Note though, you probably want to turn absorption off anyway for the reconstruction (or invert it as described in the attenuation compensation examples). Brad. zengqw2021 on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-8171 Mon, 07 Jun 2021 16:06:11 +0000 zengqw2021 8171@http://www.k-wave.org/forum/ Dear treeby, I’m a new user of k-Wave toolbox. It is great. Now, I'm trying to run a simulation with different absorption coeff. The alfa_coeff is change to a matrix, the simulation encounter the following error: Matrix dimensions must agree. Error in kspaceFirstOrder2D (line 864) (rhox + rhoy) ... Error in PAT_Heterogeneous (line 93) p0_recon = kspaceFirstOrder2D(kgrid_recon, medium, source, sensor, input_args{:}); %%The code is as follows: clearvars;clear;close all;clc; % ========================================================================= % SIMULATION % ========================================================================= % assign the grid size and create the computational grid PML_size = 20; % size of the PML in grid points Nx = 256 - 2 * PML_size; % number of grid points in the x direction Ny = 256 - 2 * PML_size; % number of grid points in the y direction x = 20e-3; % total grid size [m] y = 20e-3; % total grid size [m] dx = x / Nx; % grid point spacing in the x direction [m] dy = y / Ny; % grid point spacing in the y direction [m] kgrid = kWaveGrid(Nx, dx, Ny, dy); % create initial pressure distribution medium.sound_speed = 330; % [m/s] medium.alpha_coeff = ones(kgrid.Nx,kgrid.Ny)*0.75; % [dB/(MHz^y cm)] %ones(kgrid.Nx,kgrid.Ny)* medium.alpha_power = 1.5; medium.alpha_mode = 'no_dispersion'; Cp_heat_cap = 1.002; % the specific heat capacity at constant pressure Heat_beta = 1/273.15; % the coefficient of the thermal expansion disc_H0 = 30; % [kJ/m3] disc_x_pos = floor(Nx/2); % [grid points] disc_y_pos = floor(Ny/2); % [grid points] disc_radius = 4/2/sqrt(log(2)); % [grid points] disc_1 = Heat_beta*medium.sound_speed^2/Cp_heat_cap*disc_H0*makeDisc(Nx, Ny, disc_x_pos, disc_y_pos, disc_radius); % Heat_beta*medium.sound_speed^2/Cp_heat_cap* p0 = disc_1 ; % imagesc(p0); source.p0 = disc_1 ; init_p0 = source.p0; %for output % smooth the initial pressure distribution and restore the magnitude source.p0 = smooth(source.p0, true); % define a centered Cartesian circular sensor sensor_radius = 2e-3; % [m] sensor_angle = 2*pi ; % [rad] sensor_pos = [0, 0]; % [m] num_sensor_points = 30; cart_sensor_mask = makeCartCircle(sensor_radius, num_sensor_points, sensor_pos, sensor_angle); % assign to sensor structure sensor.mask = cart_sensor_mask; % create the time array t1=kgrid.makeTime(medium.sound_speed); % set the input arguements: force the PML to be outside the computational % grid; switch off p0 smoothing within kspaceFirstOrder2D input_args1 = {'PMLInside', false, 'PMLSize', PML_size, 'PlotPML', false, 'Smooth', false}; % %% save the simulation animations as a movie % input_args2 = {'RecordMovie', true, 'MovieName', 'example_movie'}; % input_args = [input_args1 input_args2]; input_args = input_args1; % run the simulation sensor_data = kspaceFirstOrder2D(kgrid, medium, source, sensor, input_args{:}); % add noise to the recorded sensor data signal_to_noise_ratio = 40; % [dB] sensor_data = addNoise(sensor_data, signal_to_noise_ratio, 'peak'); % create a second computation grid for the reconstruction to avoid the % inverse crime Nx = 300; % number of grid points in the x direction Ny = 300; % number of grid points in the y direction dx = x/Nx; % grid point spacing in the x direction [m] dy = y/Ny; % grid point spacing in the y direction [m] kgrid_recon = kWaveGrid(Nx, dx, Ny, dy); % use the same time array for the reconstruction kgrid_recon.setTime(kgrid.Nt, kgrid.dt); % reset the initial pressure source.p0 = 0; % assign the time reversal data sensor.time_reversal_boundary_data = sensor_data; % run the time-reversal reconstruction p0_recon = kspaceFirstOrder2D(kgrid_recon, medium, source, sensor, input_args{:}); Could you give me some advice? I appreciate any help in this regard. Zeng DuuMushishi on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-3883 Mon, 26 Aug 2013 21:00:21 +0000 DuuMushishi 3883@http://www.k-wave.org/forum/ Hello Brad, I followed your instructions and it seems the simulation is now running without problems. Thank you for your quick reply. I really appreciate your help. Thanks again Andre Bradley Treeby on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-3882 Mon, 26 Aug 2013 17:10:00 +0000 Bradley Treeby 3882@http://www.k-wave.org/forum/ Hi Andre, This particular simulation works by assigning larger heterogenous maps of sound and density, and then assigning a portion of these to <code>medium.sound_speed</code> and <code>medium.density</code> for the simulation of each scan line. If you want to follow the same format for the absorption, you should define an additional absorption coefficient variable that is Nx_tot by Ny_tot by Nz_tot, and then for the simulation of each scan line, assign the appropriate portion of this to <code>medium.alpha_coeff</code>. You can see how this is done for the sound speed and density at line 235/236. Hope that helps, Brad. DuuMushishi on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-3880 Mon, 26 Aug 2013 16:27:11 +0000 DuuMushishi 3880@http://www.k-wave.org/forum/ OK, I've just corrected that typo and I got this error: ....medium.alpha_coeff = ones(kgrid.Nx,kgrid.Ny,kgrid.Nz)*0.2; % [dB/(MHz^y cm)] medium.alpha_power = 1.0; medium.alpha_mode = 'no_dispersion';..... ??? Attempt to grow array along ambiguous dimension. Error in ==> example_us_bmode_linear_transducer at 189 medium.alpha_coeff(scattering_region1==1)=0.6; So I assumed that it was because the scattering_region1 had different size than kgrid (Ny_tot = Ny + number_scan_lines*transducer.element_width;) thus, I changed the dimension of the alpha_coeff matrix to: medium.alpha_coeff = ones(Nx_tot,Ny_tot,Nz_tot)*0.2; but then this error comes out: ??? Array dimensions must match for binary array op. Error in ==> kspaceFirstOrder_createAbsorptionVariables at 40 absorb_tau = -2*medium.alpha_coeff.*c.^(medium.alpha_power - 1); Error in ==> kspaceFirstOrder3D at 705 kspaceFirstOrder_createAbsorptionVariables; Error in ==> example_us_bmode_linear_transducer at 247 sensor_data = kspaceFirstOrder3D(kgrid, medium, transducer, transducer, input_args{:}); Am I missing something? Thanks, Andre Bradley Treeby on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-3876 Sat, 24 Aug 2013 09:41:44 +0000 Bradley Treeby 3876@http://www.k-wave.org/forum/ The problem is just a small typo: <code>alfa_coeff</code> must be spelt <code>alpha_coeff</code>. DuuMushishi on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-3875 Fri, 23 Aug 2013 22:02:39 +0000 DuuMushishi 3875@http://www.k-wave.org/forum/ Oh, I'm sorry, I didn´t copy the entire error message ??? Error using ==> checkFieldNames at 51 alfa_coeff is not a valid field for the structure medium Bradley Treeby on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-3874 Fri, 23 Aug 2013 18:31:27 +0000 Bradley Treeby 3874@http://www.k-wave.org/forum/ Hi Andre, Is there an error message above where it says "Error in ..." ? Brad. DuuMushishi on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-3873 Fri, 23 Aug 2013 16:47:48 +0000 DuuMushishi 3873@http://www.k-wave.org/forum/ Hello Dr.Cox I'm trying to run a simulation whit different absorption coeff. in the medium (i.e 0.75,0.5) and I'm using the B-mode image example file. However, when the alfa_coeff is change to a matrix, the simulation encounter the following error: Error in ==> kspaceFirstOrder_inputChecking at 83 checkFieldNames(medium, {'sound_speed', 'sound_speed_ref', 'density', 'alpha_coeff', 'alpha_power', 'alpha_mode', 'alpha_filter', 'alpha_sign', 'BonA'}); Error in ==> kspaceFirstOrder3D at 495 kspaceFirstOrder_inputChecking; Error in ==> simulation at 135 sensor_data = kspaceFirstOrder3D(kgrid, medium, transducer, transducer, input_args{:}); Is there any other value that I must set/correct in order to properly simulate a medium with two different absorption properties? Andre bencox on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-324 Wed, 22 Feb 2012 10:38:31 +0000 bencox 324@http://www.k-wave.org/forum/ That's right, yes. Hope you get it working! Ben Tim Wang on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-320 Wed, 22 Feb 2012 00:47:54 +0000 Tim Wang 320@http://www.k-wave.org/forum/ Thanks Dr. Cox. This is what I was trying to do. So originally, if alpha_coeff =0.75, that means both disc source and the background meduim has the same absorption coeff.? (All pixels coeff = 0.75?) Tim bencox on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-319 Tue, 21 Feb 2012 23:27:10 +0000 bencox 319@http://www.k-wave.org/forum/ Hi Tim, Instead of being a single number, alpha_coeff can be a matrix the same size as your image, so alpha_coeff takes a different value for each pixel (in 2D) or voxel (in 3D). If you want just two values - one or the background and one for an object - you have to define values for all pixels. Here's an example for a disc with higher absorption: <code> object = makeDisc(kgrid.Nx, kgrid.Ny, kgrid.Nx/2, kgrid.Ny/2, 5); medium.alpha_coeff = ones(kgrid.Nx,kgrid.Ny)*0.75; medium.alpha_coeff(object==1) = 2; </code> Is something like this what you're trying to do? Ben Tim Wang on "Absorption coeff. of the target" http://www.k-wave.org/forum/topic/absorption-coeff-of-the-target#post-318 Tue, 21 Feb 2012 18:55:19 +0000 Tim Wang 318@http://www.k-wave.org/forum/ Hello Dr. Cox, The alpha_coeff in the code now is set to 0.75, it is the propagation medium absorption, right? Where can I find the target source absorption coefficient right now? Thanks, Tim