k-Wave User Forum » Topic: problem saving .h5 for c++ simulation

k-Wave User Forum » Topic: problem saving .h5 for c++ simulation http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation Support for the k-Wave MATLAB toolbox en-US Wed, 13 May 2026 00:26:38 +0000 http://bbpress.org/?v=1.0.2 <![CDATA[Search]]> q http://www.k-wave.org/forum/search.php sheun on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4298 Tue, 04 Feb 2014 02:10:53 +0000 sheun 4298@http://www.k-wave.org/forum/ Sorry to bother you. It was my mistake. Thanks for the help though!! Bradley Treeby on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4296 Mon, 03 Feb 2014 09:49:11 +0000 Bradley Treeby 4296@http://www.k-wave.org/forum/ Hi sheun, If you use the option <code>'SaveToDisk</code>' the simulation isn't actually run (it stops after the input data is saved to disk), so no output is returned, hence the error message. You should either use: <code>kspaceFirstOrder3D(kgrid, medium, source, sensor, 'SaveToDisk', filetype, input_args{:});</code> and then call the C++ code yourself from the command line, or: <code>sensor_data = kspaceFirstOrder3DC(kgrid, medium, source, sensor, input_args{:});</code> and let the wrapper function …3DC add the <code>'SaveToDisk</code>' argument and call the C++ code for you. Brad. sheun on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4295 Mon, 03 Feb 2014 00:54:36 +0000 sheun 4295@http://www.k-wave.org/forum/ Bradley, I get the same error with other 3D examples as well.. I get the following when I type "clock" in the cmd line, "ans = 1.0e+03 * 2.0140 0.0020 0.0030 0.0080 0.0470 0.0559" The whole error message I get is, "Error in kspaceFirstOrder3D (line 427) start_time = clock; Output argument "sensor_data" (and maybe others) not assigned during call to "C:\Users\LS\Desktop\k-Wave Toolbox\kspaceFirstOrder3D.m>kspaceFirstOrder3D". Error in example_pr_3D_TR_planar_sensor (line 76) sensor_data = kspaceFirstOrder3D(kgrid, medium, source, sensor, 'SaveToDisk',filetype, input_args{:}); " Bradley Treeby on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4292 Thu, 30 Jan 2014 21:08:53 +0000 Bradley Treeby 4292@http://www.k-wave.org/forum/ Hi sheun, That's a puzzling message... Are you able to run any of the other 3D examples in the toolbox? What happens if you type <code>clock</code> at the command line? Is there any more to the error message? Brad. sheun on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4286 Wed, 22 Jan 2014 00:31:23 +0000 sheun 4286@http://www.k-wave.org/forum/ Brad, Sorry I confused you but the real error message I get is (which was mentioned in the subsequent post) "Error in kspaceFirstOrder3D (line 427) start_time = clock; Output argument "sensor_data" (and maybe others) not assigned during call to "C:\Users\Desktop\k-Wave Toolbox\kspaceFirstOrder3D.m>kspaceFirstOrder3D"." This happens even without the improper attempt to save the final pressure field. Bradley Treeby on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4284 Tue, 21 Jan 2014 09:54:44 +0000 Bradley Treeby 4284@http://www.k-wave.org/forum/ Hi sheun, The answer is in the error message: "The output field_data has been deprecated. Please use sensor.record = {'p_final'} (etc) to return the final pressure field". You need to replace <code>[sensor_data,p_final] = ...</code> with <code>sensor_data = ...</code> If you want to record the final pressure field in addition to the time varying pressure, after you define the sensor, add the line: <code>sensor.record = {'p', 'p_final'};</code> Brad. sheun on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4283 Tue, 21 Jan 2014 02:48:32 +0000 sheun 4283@http://www.k-wave.org/forum/ modification to the post, the error message I get using "[sensor_data] = kspaceFirstOrder3D(kgrid, medium, transducer, transducer,'SaveToDisk',filename, input_args{:})" is that, "Error in kspaceFirstOrder3D (line 427) start_time = clock; Output argument "sensor_data" (and maybe others) not assigned during call to "C:\Users\Desktop\k-Wave Toolbox\kspaceFirstOrder3D.m>kspaceFirstOrder3D"." sorry for the confusion. sheun on "problem saving .h5 for c++ simulation" http://www.k-wave.org/forum/topic/problem-saving-h5-for-c-simulation#post-4282 Tue, 21 Jan 2014 01:57:51 +0000 sheun 4282@http://www.k-wave.org/forum/ Hi, I am trying to save input file and run it on C++ (as suggested in the manual) in hope for reducing some calculation time. However, when I run kspaceFirstOrder3D with optional input 'savetodisk', I get a following message. "Error using kspaceFirstOrder_inputChecking (line 34) The output field_data has been deprecated. Please use sensor.record = {'p_final'} (etc) to return the final pressure field." I am a little lost here as to how I should solve this issue. I really would appreciate if you could give me a guidance. I am using multi element UT in a heterogeneous medium(with a ball in the medium using a makeBall function). Below is the code I used FYI, % set the size of the perfectly matched layer (PML) PML_X_SIZE = 20; % [grid points] PML_Y_SIZE = 10; % [grid points] PML_Z_SIZE = 10; % [grid points] % set total number of grid points not including the PML Nx = 168 - 2*PML_X_SIZE; % [grid points] Ny = 84 - 2*PML_Y_SIZE; % [grid points] Nz = 84 - 2*PML_Z_SIZE; % [grid points] % set desired grid size in the x-direction not including the PML x = 0.75/2/1000; % [m]Nx % calculate the spacing between the grid points dx = x; % [m] dy = dx; % [m] dz = dx; % [m] % create the k-space grid kgrid = makeGrid(Nx, dx, Ny, dy, Nz, dz); scalef = 1.0667; % ========================================================================= % DEFINE THE MEDIUM PARAMETERS % ========================================================================= if hetero % define the properties of the propagation medium medium.sound_speed = 2000*ones(Nx,Ny,Nz) ; % [m/s] 2nd medium.sound_speed(1:round(Nx/scalef),:,:) = 1000 ; % [m/s] 1st 101 medium.density = 5000*ones(Nx,Ny,Nz); % [kg/m^3] 2nd medium.density(1:round(Nx/scalef),:,:) = 1134 ; % [kg/m^3] 1st medium.alpha_coeff = 0.001*ones(Nx,Ny,Nz); % [dB/(MHz^y cm)] 2nd medium.alpha_coeff(1:round(Nx/scalef),:,:)=0.011083 ; % [dB/(MHz^y cm)] 1st medium.alpha_power = 1.05; medium.BonA = 6; %6 , 0 ussed else % define the properties of the propagation medium medium.sound_speed = 1000*ones(Nx,Ny,Nz) ; % [m/s] 2nd medium.density = 1134*ones(Nx,Ny,Nz); % [kg/m^3] 2nd medium.alpha_coeff = 0.011083*ones(Nx,Ny,Nz); % [dB/(MHz^y cm)] 2nd medium.alpha_power = 1.05; medium.BonA = 6; %6 end % create the time array t_end = 175e-6; % [s] kgrid.t_array = makeTime(kgrid, medium.sound_speed, [], t_end); % ========================================================================= % Flaw Characteristics % ========================================================================= if void_inclusion %void_size = 0.75*10/1000; %% in grid points %object = makeSphere(round(Nx/scalef), Ny/2, Nz/2, void_size); %center_pos = [round(Nx/2), Ny/2, Nz/2]; scattering_map = randn([Nx,Ny,Nz]); scattering_c0 = 1000 + 25 + 75*scattering_map; scattering_c0(scattering_c0 > 1600) = 2600; scattering_c0(scattering_c0 < 1400) = 100; scattering_rho0 = (scattering_c0/100)*7747; flaw = makeBall(Nx,Ny,Nz,Nx/scalef,Ny/2,Nz/2,3,0); % last argument "1" is for plotting medium.sound_speed(flaw == 1) = scattering_c0(flaw == 1);; % m/s steel ball medium.density(flaw == 1) = scattering_rho0(flaw == 1);; end % ========================================================================= % DEFINE THE SOURCE % ========================================================================= % define properties of the input signal source_strength = 20e6; % [Pa] tone_burst_freq = 2.25e6; % [Hz] tone_burst_cycles = 3; % create the input signal using toneBurst %input_signal = toneBurst(1/kgrid.dt, tone_burst_freq, tone_burst_cycles); input_signal = toneBurst(1/(1*kgrid.dt), tone_burst_freq, tone_burst_cycles); % scale the source magnitude by the source_strength divided by the % impedance (the source is assigned to the particle velocity) input_signal = (source_strength./(1000*1134)).*input_signal; % ========================================================================= % DEFINE THE ULTRASOUND TRANSDUCER % ========================================================================= % physical properties of the transducer transducer.number_elements = 16; % total number of transducer elements transducer.element_width = 2; % width of each element [grid points/voxels] transducer.element_length = 32; % length of each element [grid points/voxels] transducer.element_spacing = 0; % spacing (kerf width) between the elements [grid points/voxels] transducer.radius = inf; % radius of curvature of the transducer [m] % calculate the width of the transducer in grid points transducer_width = transducer.number_elements*transducer.element_width ... + (transducer.number_elements - 1)*transducer.element_spacing; % use this to position the transducer in the middle of the computational grid transducer.position = round([1, Ny/2 - transducer_width/2, Nz/2 - transducer.element_length/2]); % properties used to derive the beamforming delays transducer.sound_speed = 1000; % sound speed [m/s] transducer.focus_distance = 28/1000; % focus distance [m] transducer.elevation_focus_distance = 28/1000; % focus distance in the elevation plane [m] transducer.steering_angle = 0; % steering angle [degrees] % apodization transducer.transmit_apodization = 'Hanning'; transducer.receive_apodization = 'Rectangular'; % define the transducer elements that are currently active number_active_elements = 16; transducer.active_elements = ones(transducer.number_elements, 1); %transducer.active_elements = zeros(transducer.number_elements, 1); %transducer.active_elements(21:52) = 1; % append input signal used to drive the transducer transducer.input_signal = input_signal; % create the transducer using the defined settings transducer = makeTransducer(kgrid, transducer); % print out transducer properties transducer.properties; if run_simulation % ========================================================================= % RUN THE SIMULATION % ========================================================================= % set the input settings input_args = {'DisplayMask', transducer.active_elements_mask, ... 'PMLInside', false, 'PlotPML', false, 'PMLSize', [PML_X_SIZE, PML_Y_SIZE, PML_Z_SIZE], ... 'DataCast', DATA_CAST, 'PlotScale', [-source_strength/7, source_strength/7]}; % run the simulation %[sensor_data] = kspaceFirstOrder3D(kgrid, medium, transducer, transducer, input_args{:}); filename = 'kwave_input_data.h5'; [sensor_data,p_final] = kspaceFirstOrder3D(kgrid, medium, transducer, transducer,'SaveToDisk',filename, input_args{:});