Ultrasound B-Mode Phased Array: Image not detected

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Ultrasound B-Mode Phased Array: Image not detected

(6 posts) (2 voices)

Started 3 years ago by kpalac
Latest reply from kpalac

kpalac

Member
Joined: Apr '20
Posts: 4

Greetings users,

I am experiencing some issues with my code. I'll be writing master thesis about b-mode phased ultrasound imaging using k-Wave. Unfortunately, I cannot get a proper image on the output. The output image is almost completely black and it is not the fault of contrast. I ask You for Your help. Here is my code (the array size is locked, I am obliged to keep kerf, width and length of transducer array)

Code:

clearvars;

% simulation settings
DATA_CAST = 'single'; % set to 'single' or 'gpuArray-single' to speed up computations
RUN_SIMULATION = true; % set to false to reload previous results instead of running simulation

% =========================================================================
% DEFINE THE K-WAVE GRID
% =========================================================================

% set the size of the perfectly matched layer (PML)
pml_x_size = 15; % [grid points]
pml_y_size = 10; % [grid points]
pml_z_size = 10; % [grid points]

% set total number of grid points not including the PML
sc = 1;
Nx = 300/sc - 2*pml_x_size; % [grid points]
Ny = 300/sc - 2*pml_y_size; % [grid points]
Nz = 300/sc - 2*pml_z_size; % [grid points]

% set desired grid size in the x-direction not including the PML
x = 50e-3; % [m]

% calculate the spacing between the grid points
dx = x / Nx; % [m]
dy = dx; % [m]
dz = dx; % [m]

% create the k-space grid
kgrid = kWaveGrid(Nx, dx, Ny, dy, Nz, dz);

% =========================================================================
% DEFINE THE MEDIUM PARAMETERS
% =========================================================================

% define the properties of the propagation medium
c0 = 1496.727708; % [m/s]
rho0 = 997.0751; % [kg/m^3]
medium.alpha_coeff = 0.7642; % [dB/(MHz^y cm)]
medium.alpha_power = 1.5;
medium.BonA = 6;

% create the time array
t_end = (Nx * dx) * 2.2 / c0; % [s]
kgrid.makeTime(c0, [], t_end);

% =========================================================================
% DEFINE THE INPUT SIGNAL
% =========================================================================

% define properties of the input signal
source_strength = 2e6; % [Pa]
tone_burst_freq = 2e6 / sc; % [Hz]
tone_burst_cycles = 4;

% create the input signal using toneBurst
input_signal = toneBurst(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 ./ (c0 * rho0)) .* input_signal;

% =========================================================================
% DEFINE THE ULTRASOUND TRANSDUCER
% =========================================================================

% define the physical properties of the phased array transducer
transducer.number_elements = 32 / sc; % total number of transducer elements
transducer.element_width = 5; % width of each element [grid points]
transducer.element_length = 170 / sc; % length of each element [grid points]
transducer.element_spacing = 3; % spacing (kerf width) between the elements [grid points]

% 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 = c0; % sound speed [m/s]
transducer.focus_distance = 25e-3; % focus distance [m]
transducer.elevation_focus_distance = 25e-3; % focus distance in the elevation plane [m]
transducer.steering_angle = 15; % steering angle [degrees]
transducer.steering_angle_max = 25; % maximum steering angle [degrees]

% apodization
transducer.transmit_apodization = 'Hanning';
transducer.receive_apodization = 'Rectangular';

% define the transducer elements that are currently active
transducer.active_elements = ones(transducer.number_elements, 1);

% append input signal used to drive the transducer
transducer.input_signal = input_signal;

% create the transducer using the defined settings
transducer = kWaveTransducer(kgrid, transducer);

% print out transducer properties
transducer.properties;

% =========================================================================
% DEFINE THE MEDIUM PROPERTIES
% =========================================================================

% define a random distribution of scatterers for the medium
background_map_mean = 1;
background_map_std = 0.008;
background_map = background_map_mean + background_map_std * randn([Nx, Ny, Nz]);

% define a random distribution of scatterers for the highly scattering
% region
scattering_map = randn([Nx, Ny, Nz]);
scattering_c0 = c0 + 25 + 150 * scattering_map; %
%scattering_c0(scattering_c0 > 1600) = 1600;
%scattering_c0(scattering_c0 < 1400) = 1400;
scattering_rho0 = scattering_c0 / 1.5;

scattering_c1 = 4080 + 10 + 100 * scattering_map; %bone
scattering_rho1 = scattering_c1/1.5;
%scattering_c2 = 1530 + 10 + 75 * scattering_map;
%scattering_rho2 = scattering_c2/1.5;
%scattering_c3 = 1573 + 10 + 100 * scattering_map;
%scattering_rho3 = scattering_c3/1.6;
%scattering_c4 = 1570 + 10 + 50 * scattering_map;
%scattering_rho4 = scattering_c4/1.35;

% define properties
sound_speed_map = c0 * ones(Nx, Ny, Nz) .* background_map;
density_map = rho0 * ones(Nx, Ny, Nz) .* background_map;

% define a sphere for a highly scattering region
radius = 25e-3;
x_pos = 25e-3;
y_pos = dy * Ny/2;
scattering_region1 = makeBall(Nx, Ny, Nz, round(x_pos / dx), round(y_pos / dx), Nz/2, round(radius / dx));
scattering_region2 = makeBall(Nx, Ny, Nz, round(25e-3 / dx), round(25e-3 / dx), Nz/2, round(2e-3 / dx));
%scattering_region3 = makeBall(Nx, Ny, Nz, round(20e-3 / dx), round(15 / dx), Nz/2, round(3e-3 / dx));
%scattering_region4 = makeBall(Nx, Ny, Nz, round(25e-3 / dx), round(30 / dx), Nz/2, round(4e-3 / dx));
%scattering_region5 = makeBall(Nx, Ny, Nz, round(45e-3 / dx), round(40 / dx), Nz/2, round(2e-3 / dx));

% assign region
sound_speed_map(scattering_region1 == 1) = scattering_c0(scattering_region1 == 1);
density_map(scattering_region1 == 1) = scattering_rho0(scattering_region1 == 1);
sound_speed_map(scattering_region2 == 1) = scattering_c1(scattering_region2 == 1);
density_map(scattering_region2 == 1) = scattering_rho1(scattering_region2 == 1);
%sound_speed_map(scattering_region3 == 1) = scattering_c2(scattering_region3 == 1);
%density_map(scattering_region3 == 1) = scattering_rho2(scattering_region3 == 1);
%sound_speed_map(scattering_region4 == 1) = scattering_c3(scattering_region4 == 1);
%density_map(scattering_region4 == 1) = scattering_rho3(scattering_region4 == 1);
%sound_speed_map(scattering_region5 == 1) = scattering_c4(scattering_region5 == 1);
%density_map(scattering_region5 == 1) = scattering_rho4(scattering_region5 == 1);

% assign to the medium inputs
medium.sound_speed = sound_speed_map;
medium.density = density_map;

% =========================================================================
% RUN THE SIMULATION
% =========================================================================

% range of steering angles to test
steering_angles = -25:5:25;

% preallocate the storage
number_scan_lines = length(steering_angles);
scan_lines = zeros(number_scan_lines, kgrid.Nt);

% set the input settings
input_args = {...
'PMLInside', false, 'PMLSize', [pml_x_size, pml_y_size, pml_z_size], ...
'DataCast', DATA_CAST, 'DataRecast', true, 'PlotSim', false};

% run the simulation if set to true, otherwise, load previous results
if RUN_SIMULATION

% loop through the range of angles to test
for angle_index = 1:number_scan_lines

% update the command line status
disp('');
disp(['Computing scan line ' num2str(angle_index) ' of ' num2str(number_scan_lines)]);

% update the current steering angle
transducer.steering_angle = steering_angles(angle_index);

% run the simulation
sensor_data = kspaceFirstOrder3D(kgrid, medium, transducer, transducer, input_args{:});

% extract the scan line from the sensor data
scan_lines(angle_index, :) = transducer.scan_line(sensor_data);

end

% save the scan lines to disk
save example_us_phased_array_scan_lines scan_lines;

else

% load the scan lines from disk
load example_us_phased_array_scan_lines

end

% trim the delay offset from the scan line data
t0_offset = round(length(input_signal) / 2) + (transducer.appended_zeros - transducer.beamforming_delays_offset);
scan_lines = scan_lines(:, t0_offset:end);

% get the new length of the scan lines
Nt = length(scan_lines(1, :));

% =========================================================================
% PROCESS THE RESULTS
% =========================================================================

% -----------------------------
% Remove Input Signal
% -----------------------------

% create a window to set the first part of each scan line to zero to remove
% interference from the input signal
scan_line_win = getWin(Nt * 2, 'Tukey', 'Param', 0.05).';
scan_line_win = [zeros(1, t0_offset * 2), scan_line_win(1:end/2 - t0_offset * 2)];

% apply the window to each of the scan lines
scan_lines = bsxfun(@times, scan_line_win, scan_lines);

% -----------------------------
% Time Gain Compensation
% -----------------------------

% create radius variable
r = c0 * (1:Nt) * kgrid.dt / 2; % [m]

% define absorption value and convert to correct units
tgc_alpha_db_cm = medium.alpha_coeff * (tone_burst_freq * 1e-6)^medium.alpha_power;
tgc_alpha_np_m = tgc_alpha_db_cm / 8.686 * 100;

% create time gain compensation function based on attenuation value and
% round trip distance
tgc = exp(tgc_alpha_np_m * 2 * r);

% apply the time gain compensation to each of the scan lines
scan_lines = bsxfun(@times, tgc, scan_lines);

% -----------------------------
% Frequency Filtering
% -----------------------------

% filter the scan lines using both the transmit frequency and the second
% harmonic
scan_lines_fund = gaussianFilter(scan_lines, 1/kgrid.dt, tone_burst_freq, 100, true);
scan_lines_harm = gaussianFilter(scan_lines, 1/kgrid.dt, 2 * tone_burst_freq, 30, true);

% -----------------------------
% Envelope Detection
% -----------------------------

% envelope detection
scan_lines_fund = envelopeDetection(scan_lines_fund);
scan_lines_harm = envelopeDetection(scan_lines_harm);

% -----------------------------
% Log Compression
% -----------------------------

% normalised log compression
compression_ratio = 3;
scan_lines_fund = logCompression(scan_lines_fund, compression_ratio, true);
scan_lines_harm = logCompression(scan_lines_harm, compression_ratio, true);

% -----------------------------
% Scan Conversion
% -----------------------------

% set the desired size of the image
image_size = [Nx * dx, Ny * dy];

% convert the data from polar coordinates to Cartesian coordinates for
% display
b_mode_fund = scanConversion(scan_lines_fund, steering_angles, image_size, c0, kgrid.dt);
b_mode_harm = scanConversion(scan_lines_harm, steering_angles, image_size, c0, kgrid.dt);

% =========================================================================
% VISUALISATION
% =========================================================================

% create the axis variables
x_axis = [0, Nx * dx * 1e3]; % [mm]
y_axis = [0, Ny * dy * 1e3]; % [mm]

% plot the data before and after scan conversion
figure;
subplot(1, 3, 1);
imagesc(steering_angles, x_axis, scan_lines.');
axis square;
xlabel('Steering angle [deg]');
ylabel('Depth [mm]');
title('Raw Scan-Line Data');

subplot(1, 3, 2);
imagesc(steering_angles, x_axis, scan_lines_fund.');
axis square;
xlabel('Steering angle [deg]');
ylabel('Depth [mm]');
title('Processed Scan-Line Data');

subplot(1, 3, 3);
imagesc(y_axis, x_axis, b_mode_fund);
axis square;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('B-Mode Image');
colormap(gray);

scaleFig(2, 1);

% plot the medium and the B-mode images
figure;
subplot(1, 3, 1);
imagesc(y_axis, x_axis, medium.sound_speed(:, :, end/2));
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('Scattering Phantom');

subplot(1, 3, 2);
imagesc(y_axis, x_axis, b_mode_fund);
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('B-Mode Image');

subplot(1, 3, 3);
imagesc(y_axis, x_axis, b_mode_harm);
colormap(gray);
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('Harmonic Image');

scaleFig(2, 1);

Posted 3 years ago #
kpalac

Member
Joined: Apr '20
Posts: 4

Posted 3 years ago #
Bradley Treeby

Developer
Joined: Mar '10
Posts: 1,640

Hi kpalac,

Can you highlight which lines of code you changed from the example?

Brad.

Posted 3 years ago #
kpalac

Member
Joined: Apr '20
Posts: 4

Sure. I will add code again. "$" will be put at the beginning of each line that was modified:

clearvars;

% simulation settings
DATA_CAST = 'single'; % set to 'single' or 'gpuArray-single' to speed up computations
RUN_SIMULATION = true; % set to false to reload previous results instead of running simulation

% =========================================================================
% DEFINE THE K-WAVE GRID
% =========================================================================

% set the size of the perfectly matched layer (PML)
pml_x_size = 15; % [grid points]
pml_y_size = 10; % [grid points]
pml_z_size = 10; % [grid points]

% set total number of grid points not including the PML
sc = 1;
$ Nx = 300/sc - 2*pml_x_size; % [grid points]
$ Ny = 300/sc - 2*pml_y_size; % [grid points]
$ Nz = 300/sc - 2*pml_z_size; % [grid points]

% set desired grid size in the x-direction not including the PML
$ x = 50e-3; % [m]

% calculate the spacing between the grid points
dx = x / Nx; % [m]
dy = dx; % [m]
dz = dx; % [m]

% create the k-space grid
kgrid = kWaveGrid(Nx, dx, Ny, dy, Nz, dz);

% =========================================================================
% DEFINE THE MEDIUM PARAMETERS
% =========================================================================

% define the properties of the propagation medium
$ c0 = 1496.727708; % [m/s]
$ rho0 = 997.0751; % [kg/m^3]
$ medium.alpha_coeff = 0.7642; % [dB/(MHz^y cm)]
$ medium.alpha_power = 1.5;
medium.BonA = 6;

% create the time array
t_end = (Nx * dx) * 2.2 / c0; % [s]
kgrid.makeTime(c0, [], t_end);

% =========================================================================
% DEFINE THE INPUT SIGNAL
% =========================================================================

% define properties of the input signal
$ source_strength = 2e6; % [Pa]
$ tone_burst_freq = 2e6 / sc; % [Hz]
tone_burst_cycles = 4;

% create the input signal using toneBurst
input_signal = toneBurst(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 ./ (c0 * rho0)) .* input_signal;

% =========================================================================
% DEFINE THE ULTRASOUND TRANSDUCER
% =========================================================================

% define the physical properties of the phased array transducer
$ transducer.number_elements = 32 / sc; % total number of transducer elements
$ transducer.element_width = 5; % width of each element [grid points]
$ transducer.element_length = 170 / sc; % length of each element [grid points]
$ transducer.element_spacing = 3; % spacing (kerf width) between the elements [grid points]

% 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 = c0; % sound speed [m/s]
$transducer.focus_distance = 25e-3; % focus distance [m]
$transducer.elevation_focus_distance = 25e-3; % focus distance in the elevation plane [m]
$transducer.steering_angle = 20; % steering angle [degrees]
$transducer.steering_angle_max = 20; % maximum steering angle [degrees]

% apodization
transducer.transmit_apodization = 'Hanning';
transducer.receive_apodization = 'Rectangular';

% define the transducer elements that are currently active
transducer.active_elements = ones(transducer.number_elements, 1);

% append input signal used to drive the transducer
transducer.input_signal = input_signal;

% create the transducer using the defined settings
transducer = kWaveTransducer(kgrid, transducer);

% print out transducer properties
transducer.properties;

% =========================================================================
% DEFINE THE MEDIUM PROPERTIES
% =========================================================================

% define a random distribution of scatterers for the medium
background_map_mean = 1;
background_map_std = 0.008;
background_map = background_map_mean + background_map_std * randn([Nx, Ny, Nz]);

% define a random distribution of scatterers for the highly scattering
% region
scattering_map = randn([Nx, Ny, Nz]);
$scattering_c0 = c0 + 25 + 150 * scattering_map; %
$scattering_c0(scattering_c0 > 1600) = 1600;
$scattering_c0(scattering_c0 < 1400) = 1400;
$scattering_rho0 = scattering_c0 / 1.5;

$scattering_c1 = 4080 + 10 + 100 * scattering_map; %bone
scattering_rho1 = scattering_c1/1.5;
%scattering_c2 = 1530 + 10 + 75 * scattering_map;
%scattering_rho2 = scattering_c2/1.5;
%scattering_c3 = 1573 + 10 + 100 * scattering_map;
%scattering_rho3 = scattering_c3/1.6;
%scattering_c4 = 1570 + 10 + 50 * scattering_map;
%scattering_rho4 = scattering_c4/1.35;

% define properties
sound_speed_map = c0 * ones(Nx, Ny, Nz) .* background_map;
density_map = rho0 * ones(Nx, Ny, Nz) .* background_map;

% define a sphere for a highly scattering region
$radius = 25e-3;
$x_pos = 25e-3;
y_pos = dy * Ny/2;
scattering_region1 = makeBall(Nx, Ny, Nz, round(x_pos / dx), round(y_pos / dx), Nz/2, round(radius / dx));
$scattering_region2 = makeBall(Nx, Ny, Nz, round(25e-3 / dx), round(25e-3 / dx), Nz/2, round(2e-3 / dx));
%scattering_region3 = makeBall(Nx, Ny, Nz, round(20e-3 / dx), round(15 / dx), Nz/2, round(3e-3 / dx));
%scattering_region4 = makeBall(Nx, Ny, Nz, round(25e-3 / dx), round(30 / dx), Nz/2, round(4e-3 / dx));
%scattering_region5 = makeBall(Nx, Ny, Nz, round(45e-3 / dx), round(40 / dx), Nz/2, round(2e-3 / dx));

% assign region
sound_speed_map(scattering_region1 == 1) = scattering_c0(scattering_region1 == 1);
density_map(scattering_region1 == 1) = scattering_rho0(scattering_region1 == 1);
$sound_speed_map(scattering_region2 == 1) = scattering_c1(scattering_region2 == 1);
$density_map(scattering_region2 == 1) = scattering_rho1(scattering_region2 == 1);
%sound_speed_map(scattering_region3 == 1) = scattering_c2(scattering_region3 == 1);
%density_map(scattering_region3 == 1) = scattering_rho2(scattering_region3 == 1);
%sound_speed_map(scattering_region4 == 1) = scattering_c3(scattering_region4 == 1);
%density_map(scattering_region4 == 1) = scattering_rho3(scattering_region4 == 1);
%sound_speed_map(scattering_region5 == 1) = scattering_c4(scattering_region5 == 1);
%density_map(scattering_region5 == 1) = scattering_rho4(scattering_region5 == 1);

% assign to the medium inputs
medium.sound_speed = sound_speed_map;
medium.density = density_map;

% =========================================================================
% RUN THE SIMULATION
% =========================================================================

% range of steering angles to test
$steering_angles = -20:10:20;

% preallocate the storage
number_scan_lines = length(steering_angles);
scan_lines = zeros(number_scan_lines, kgrid.Nt);

% set the input settings
input_args = {...
'PMLInside', false, 'PMLSize', [pml_x_size, pml_y_size, pml_z_size], ...
'DataCast', DATA_CAST, 'DataRecast', true, 'PlotSim', false};

% run the simulation if set to true, otherwise, load previous results
if RUN_SIMULATION

% loop through the range of angles to test
for angle_index = 1:number_scan_lines

% update the command line status
disp('');
disp(['Computing scan line ' num2str(angle_index) ' of ' num2str(number_scan_lines)]);

% update the current steering angle
transducer.steering_angle = steering_angles(angle_index);

% run the simulation
sensor_data = kspaceFirstOrder3D(kgrid, medium, transducer, transducer, input_args{:});

% extract the scan line from the sensor data
scan_lines(angle_index, :) = transducer.scan_line(sensor_data);

end

% save the scan lines to disk
save example_us_phased_array_scan_lines scan_lines;

else

% load the scan lines from disk
load example_us_phased_array_scan_lines

end

% trim the delay offset from the scan line data
t0_offset = round(length(input_signal) / 2) + (transducer.appended_zeros - transducer.beamforming_delays_offset);
scan_lines = scan_lines(:, t0_offset:end);

% get the new length of the scan lines
Nt = length(scan_lines(1, :));

% =========================================================================
% PROCESS THE RESULTS
% =========================================================================

% -----------------------------
% Remove Input Signal
% -----------------------------

% create a window to set the first part of each scan line to zero to remove
% interference from the input signal
scan_line_win = getWin(Nt * 2, 'Tukey', 'Param', 0.05).';
scan_line_win = [zeros(1, t0_offset * 2), scan_line_win(1:end/2 - t0_offset * 2)];

% apply the window to each of the scan lines
scan_lines = bsxfun(@times, scan_line_win, scan_lines);

% -----------------------------
% Time Gain Compensation
% -----------------------------

% create radius variable
r = c0 * (1:Nt) * kgrid.dt / 2; % [m]

% define absorption value and convert to correct units
tgc_alpha_db_cm = medium.alpha_coeff * (tone_burst_freq * 1e-6)^medium.alpha_power;
tgc_alpha_np_m = tgc_alpha_db_cm / 8.686 * 100;

% create time gain compensation function based on attenuation value and
% round trip distance
tgc = exp(tgc_alpha_np_m * 2 * r);

% apply the time gain compensation to each of the scan lines
scan_lines = bsxfun(@times, tgc, scan_lines);

% -----------------------------
% Frequency Filtering
% -----------------------------

% filter the scan lines using both the transmit frequency and the second
% harmonic
scan_lines_fund = gaussianFilter(scan_lines, 1/kgrid.dt, tone_burst_freq, 100, true);
scan_lines_harm = gaussianFilter(scan_lines, 1/kgrid.dt, 2 * tone_burst_freq, 30, true);

% -----------------------------
% Envelope Detection
% -----------------------------

% envelope detection
scan_lines_fund = envelopeDetection(scan_lines_fund);
scan_lines_harm = envelopeDetection(scan_lines_harm);

% -----------------------------
% Log Compression
% -----------------------------

% normalised log compression
compression_ratio = 3;
scan_lines_fund = logCompression(scan_lines_fund, compression_ratio, true);
scan_lines_harm = logCompression(scan_lines_harm, compression_ratio, true);

% -----------------------------
% Scan Conversion
% -----------------------------

% set the desired size of the image
image_size = [Nx * dx, Ny * dy];

% convert the data from polar coordinates to Cartesian coordinates for
% display
b_mode_fund = scanConversion(scan_lines_fund, steering_angles, image_size, c0, kgrid.dt);
b_mode_harm = scanConversion(scan_lines_harm, steering_angles, image_size, c0, kgrid.dt);

% =========================================================================
% VISUALISATION
% =========================================================================

% create the axis variables
x_axis = [0, Nx * dx * 1e3]; % [mm]
y_axis = [0, Ny * dy * 1e3]; % [mm]

% plot the data before and after scan conversion
figure;
subplot(1, 3, 1);
imagesc(steering_angles, x_axis, scan_lines.');
axis square;
xlabel('Steering angle [deg]');
ylabel('Depth [mm]');
title('Raw Scan-Line Data');

subplot(1, 3, 2);
imagesc(steering_angles, x_axis, scan_lines_fund.');
axis square;
xlabel('Steering angle [deg]');
ylabel('Depth [mm]');
title('Processed Scan-Line Data');

subplot(1, 3, 3);
imagesc(y_axis, x_axis, b_mode_fund);
axis square;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('B-Mode Image');
colormap(gray);

scaleFig(2, 1);

% plot the medium and the B-mode images
figure;
subplot(1, 3, 1);
imagesc(y_axis, x_axis, medium.sound_speed(:, :, end/2));
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('Scattering Phantom');

subplot(1, 3, 2);
imagesc(y_axis, x_axis, b_mode_fund);
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('B-Mode Image');

subplot(1, 3, 3);
imagesc(y_axis, x_axis, b_mode_harm);
colormap(gray);
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('Harmonic Image');

scaleFig(2, 1);

Posted 3 years ago #
Bradley Treeby

Developer
Joined: Mar '10
Posts: 1,640

I didn't run your simulation to completion, but the following is given on the command line:

WARNING: time step may be too large for a stable simulation.

If the sensor data is filled with nans, then it sounds like classic instability. You will need to make the time step smaller.

Posted 3 years ago #
kpalac

Member
Joined: Apr '20
Posts: 4

I'm back with the code. Still cannot see the objects. It's quite interesting since i used three different impedances and densities. Can you help me find and fix the issue?

% Simulating B-mode Ultrasound Images Example

% This example illustrates how k-Wave can be used for the simulation of
% B-mode ultrasound images using a phased-array or sector transducer. It
% builds on the Simulating B-mode Ultrasound Images Example.
%
% To allow the simulated scan line data to be processed multiple times with
% different settings, the simulated RF data is saved to disk. This can be
% reloaded by setting RUN_SIMULATION = false within the example m-file. The
% data can also be downloaded from
% http://www.k-wave.org/datasets/example_us_phased_array_scan_lines.mat
%
% author: Bradley Treeby
% date: 7th September 2012
% last update: 22nd January 2020
%
% This function is part of the k-Wave Toolbox (http://www.k-wave.org)
% Copyright (C) 2012-2020 Bradley Treeby

% This file is part of k-Wave. k-Wave is free software: you can
% redistribute it and/or modify it under the terms of the GNU Lesser
% General Public License as published by the Free Software Foundation,
% either version 3 of the License, or (at your option) any later version.
%
% k-Wave is distributed in the hope that it will be useful, but WITHOUT ANY
% WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
% FOR A PARTICULAR PURPOSE. See the GNU Lesser General Public License for
% more details.
%
% You should have received a copy of the GNU Lesser General Public License
% along with k-Wave. If not, see <http://www.gnu.org/licenses/>.

%#ok<*UNRCH
clearvars;
addpath('/home/kpalac/k-Wave')

% simulation settings
DATA_CAST = 'single'; % set to 'single' or 'gpuArray-single' to speed up computations
RUN_SIMULATION = false; % set to false to reload previous results instead of running simulation

% =========================================================================
% DEFINE THE K-WAVE GRID
% =========================================================================

% set the size of the perfectly matched layer (PML)
pml_x_size = 15; % [grid points]
pml_y_size = 10; % [grid points]
pml_z_size = 10; % [grid points]

% set total number of grid points not including the PML
sc = 1;
Nx = 256/sc - 2*pml_x_size; % [grid points]
Ny = 256/sc - 2*pml_y_size; % [grid points]
Nz = 256/sc - 2*pml_z_size; % [grid points]

% set desired grid size in the x-direction not including the PML
x = 50e-3; % [m]

% calculate the spacing between the grid points
dx = x / Nx; % [m]
dy = dx; % [m]
dz = dx; % [m]

% create the k-space grid
kgrid = kWaveGrid(Nx, dx, Ny, dy, Nz, dz);

% =========================================================================
% DEFINE THE MEDIUM PARAMETERS
% =========================================================================

% define the properties of the propagation medium
c0 = 1496.727708; % [m/s]
rho0 = 997.0751; % [kg/m^3]
medium.alpha_coeff = 0.5; % [dB/(MHz^y cm)]
medium.alpha_power = 1.5;
medium.BonA = 6;

% create the time array
t_end = (Nx * dx) * 2.2 / c0; % [s]
kgrid.makeTime(c0, [], t_end);

% =========================================================================
% DEFINE THE INPUT SIGNAL
% =========================================================================

% define properties of the input signal
source_strength = 2e6; % [Pa]
tone_burst_freq = 2e6 / sc; % [Hz]
tone_burst_cycles = 4;

% create the input signal using toneBurst
input_signal = toneBurst(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 ./ (c0 * rho0)) .* input_signal;

% =========================================================================
% DEFINE THE ULTRASOUND TRANSDUCER
% =========================================================================

% define the physical properties of the phased array transducer
transducer.number_elements = 32 / sc; % total number of transducer elements
transducer.element_width = 2; % width of each element [grid points]
transducer.element_length = 85 / sc; % length of each element [grid points]
transducer.element_spacing = 2; % spacing (kerf width) between the elements [grid points]

% 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 = c0; % sound speed [m/s]
transducer.focus_distance = 25e-3; % focus distance [m]
transducer.elevation_focus_distance = 25e-3; % focus distance in the elevation plane [m]
transducer.steering_angle = 30; % steering angle [degrees]
transducer.steering_angle_max = 30; % maximum steering angle [degrees]

% apodization
transducer.transmit_apodization = 'Hanning';
transducer.receive_apodization = 'Rectangular';

% define the transducer elements that are currently active
transducer.active_elements = ones(transducer.number_elements, 1);

% append input signal used to drive the transducer
transducer.input_signal = input_signal;

% create the transducer using the defined settings
transducer = kWaveTransducer(kgrid, transducer);

% print out transducer properties
transducer.properties;

% =========================================================================
% DEFINE THE MEDIUM PROPERTIES
% =========================================================================

% define a random distribution of scatterers for the medium
background_map_mean = 1;
background_map_std = 0.008;
background_map = background_map_mean + background_map_std * randn([Nx, Ny, Nz]);

% define a random distribution of scatterers for the highly scattering
% region
scattering_map = randn([Nx, Ny, Nz]);
scattering_c0 = c0 + 25 + 50 * scattering_map; %
scattering_c0(scattering_c0 > 1900) = 1900;
scattering_c0(scattering_c0 < 1400) = 1400;
scattering_rho0 = scattering_c0 / 1.5;

scattering_c1 = 1550 + 10 + 60 * scattering_map; %bone
scattering_rho1 = scattering_c1/1;
scattering_c2 = 1570 + 10 + 60 * scattering_map;
scattering_rho2 = scattering_c2/2;
%scattering_c3 = 1573 + 10 + 100 * scattering_map;
%scattering_rho3 = scattering_c3/1.6;
%scattering_c4 = 1570 + 10 + 50 * scattering_map;
%scattering_rho4 = scattering_c4/1.35;

% define properties
sound_speed_map = c0 * ones(Nx, Ny, Nz) .* background_map;
density_map = rho0 * ones(Nx, Ny, Nz) .* background_map;

% define a sphere for a highly scattering region
radius = 25e-3;
x_pos = 25e-3;
y_pos = dy * Ny/2;
scattering_region1 = makeBall(Nx, Ny, Nz, round(x_pos / dx), round(y_pos / dx), Nz/2, round(radius / dx));
scattering_region2 = makeBall(Nx, Ny, Nz, round(25e-3 / dx), round(25e-3 / dx), Nz/2, round(7e-3 / dx));
scattering_region3 = makeBall(Nx, Ny, Nz, round(20e-3 / dx), round(15e-3 / dx), Nz/2, round(4e-3 / dx));
%scattering_region4 = makeBall(Nx, Ny, Nz, round(25e-3 / dx), round(30 / dx), Nz/2, round(4e-3 / dx));
%scattering_region5 = makeBall(Nx, Ny, Nz, round(45e-3 / dx), round(40 / dx), Nz/2, round(2e-3 / dx));

% assign region
sound_speed_map(scattering_region1 == 1) = scattering_c0(scattering_region1 == 1);
density_map(scattering_region1 == 1) = scattering_rho0(scattering_region1 == 1);
sound_speed_map(scattering_region2 == 1) = scattering_c1(scattering_region2 == 1);
density_map(scattering_region2 == 1) = scattering_rho1(scattering_region2 == 1);
sound_speed_map(scattering_region3 == 1) = scattering_c2(scattering_region3 == 1);
density_map(scattering_region3 == 1) = scattering_rho2(scattering_region3 == 1);
%sound_speed_map(scattering_region4 == 1) = scattering_c3(scattering_region4 == 1);
%density_map(scattering_region4 == 1) = scattering_rho3(scattering_region4 == 1);
%sound_speed_map(scattering_region5 == 1) = scattering_c4(scattering_region5 == 1);
%density_map(scattering_region5 == 1) = scattering_rho4(scattering_region5 == 1);

% assign to the medium inputs
medium.sound_speed = sound_speed_map;
medium.density = density_map;

% =========================================================================
% RUN THE SIMULATION
% =========================================================================

% range of steering angles to test
steering_angles = -30:10:30;

% preallocate the storage
number_scan_lines = length(steering_angles);
scan_lines = zeros(number_scan_lines, kgrid.Nt);

% set the input settings
input_args = {...
'PMLInside', false, 'PMLSize', [pml_x_size, pml_y_size, pml_z_size], ...
'DataCast', DATA_CAST, 'DataRecast', true, 'PlotSim', false};

% run the simulation if set to true, otherwise, load previous results
if RUN_SIMULATION

% loop through the range of angles to test
for angle_index = 1:number_scan_lines

% update the command line status
disp('');
disp(['Computing scan line ' num2str(angle_index) ' of ' num2str(number_scan_lines)]);

% update the current steering angle
transducer.steering_angle = steering_angles(angle_index);

% run the simulation
sensor_data = kspaceFirstOrder3D(kgrid, medium, transducer, transducer, input_args{:});

% extract the scan line from the sensor data
scan_lines(angle_index, :) = transducer.scan_line(sensor_data);

end

% save the scan lines to disk
save example_us_phased_array_scan_lines scan_lines;

else

% load the scan lines from disk
load example_us_phased_array_scan_lines

end

% trim the delay offset from the scan line data
t0_offset = round(length(input_signal) / 2) + (transducer.appended_zeros - transducer.beamforming_delays_offset);
scan_lines = scan_lines(:, t0_offset:end);

% get the new length of the scan lines
Nt = length(scan_lines(1, :));

% =========================================================================
% PROCESS THE RESULTS
% =========================================================================

% -----------------------------
% Remove Input Signal
% -----------------------------

% create a window to set the first part of each scan line to zero to remove
% interference from the input signal
scan_line_win = getWin(Nt * 2, 'Tukey', 'Param', 0.05).';
scan_line_win = [zeros(1, t0_offset * 2), scan_line_win(1:end/2 - t0_offset * 2)];

% apply the window to each of the scan lines
scan_lines = bsxfun(@times, scan_line_win, scan_lines);

% -----------------------------
% Time Gain Compensation
% -----------------------------

% create radius variable
r = c0 * (1:Nt) * kgrid.dt / 2; % [m]

% define absorption value and convert to correct units
tgc_alpha_db_cm = medium.alpha_coeff * (tone_burst_freq * 1e-6)^medium.alpha_power;
tgc_alpha_np_m = tgc_alpha_db_cm / 8.686 * 100;

% create time gain compensation function based on attenuation value and
% round trip distance
tgc = exp(tgc_alpha_np_m * 2 * r);

% apply the time gain compensation to each of the scan lines
scan_lines = bsxfun(@times, tgc, scan_lines);

% -----------------------------
% Frequency Filtering
% -----------------------------

% filter the scan lines using both the transmit frequency and the second
% harmonic
scan_lines_fund = gaussianFilter(scan_lines, 1/kgrid.dt, tone_burst_freq, 100, true);
scan_lines_harm = gaussianFilter(scan_lines, 1/kgrid.dt, 2 * tone_burst_freq, 30, true);

% -----------------------------
% Envelope Detection
% -----------------------------

% envelope detection
scan_lines_fund = envelopeDetection(scan_lines_fund);
scan_lines_harm = envelopeDetection(scan_lines_harm);

% -----------------------------
% Log Compression
% -----------------------------

% normalised log compression
compression_ratio = 3;
scan_lines_fund = logCompression(scan_lines_fund, compression_ratio, true);
scan_lines_harm = logCompression(scan_lines_harm, compression_ratio, true);

% -----------------------------
% Scan Conversion
% -----------------------------

% set the desired size of the image
image_size = [Nx * dx, Ny * dy];

% convert the data from polar coordinates to Cartesian coordinates for
% display
b_mode_fund = scanConversion(scan_lines_fund, steering_angles, image_size, c0, kgrid.dt);
b_mode_harm = scanConversion(scan_lines_harm, steering_angles, image_size, c0, kgrid.dt);

% =========================================================================
% VISUALISATION
% =========================================================================

% create the axis variables
x_axis = [0, Nx * dx * 1e3]; % [mm]
y_axis = [0, Ny * dy * 1e3]; % [mm]

% plot the data before and after scan conversion
figure;
subplot(1, 3, 1);
imagesc(steering_angles, x_axis, scan_lines.');
axis square;
xlabel('Steering angle [deg]');
ylabel('Depth [mm]');
title('Raw Scan-Line Data');

subplot(1, 3, 2);
imagesc(steering_angles, x_axis, scan_lines_fund.');
axis square;
xlabel('Steering angle [deg]');
ylabel('Depth [mm]');
title('Processed Scan-Line Data');

subplot(1, 3, 3);
imagesc(y_axis, x_axis, b_mode_fund);
axis square;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('B-Mode Image');
colormap(gray);

scaleFig(2, 1);

% plot the medium and the B-mode images
figure;
subplot(1, 3, 1);
imagesc(y_axis, x_axis, medium.sound_speed(:, :, end/2));
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('Scattering Phantom');

subplot(1, 3, 2);
imagesc(y_axis, x_axis, b_mode_fund);
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('B-Mode Image');

subplot(1, 3, 3);
imagesc(y_axis, x_axis, b_mode_harm);
colormap(gray);
axis image;
xlabel('Horizontal Position [mm]');
ylabel('Depth [mm]');
title('Harmonic Image');

scaleFig(2, 1);

Posted 2 years ago #

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k-Wave

A MATLAB toolbox for the time-domain simulation of acoustic wave fields

Ultrasound B-Mode Phased Array: Image not detected

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A MATLAB toolbox for the time-domain
simulation of acoustic wave fields