data/lung_seashore_plot.m

%% MATLAB script for generating M-Mode Seashore plots from real-time 
%  recordings of pleural region from files '*_rt_recon.mat' for B-Mode data

clear;
% clc;
% close;

%% Image params
log_compression = true;
dB_range = 40;
orthogonal = false;
slice_dir = 'yz';
video_out = false;
display_plot = true;
frame_rate = 5.394;

%% Load saved B-Mode complex data for plotting in MATLAB/
%    exporting into image data for Origin

%Data file path
filepath = './datasets_lung/';

%File name
filename = 'lung_dataset1_rt_recon';

%Load Complex data
bmode_data_struct = load(strcat(filepath, filename, '.mat'));

%Assign variables
bmode_data = bmode_data_struct.bmode_data;

zI = bmode_data_struct.zI;
if (slice_dir=='xz')
    xI = bmode_data_struct.xI;
elseif (slice_dir=='yz')
    yI = bmode_data_struct.yI;
end

N_frame = size(bmode_data, 3);

%% Generate seashore plot

%Magnitude of complex data
bmode_data = abs(bmode_data);

b_mode = bmode_data/max(bmode_data(:));

%Log compression
b_mode_temp = 20*log10(b_mode);
b_mode = (b_mode_temp+dB_range).*(b_mode_temp>-dB_range);

b_mode = uint8(255*b_mode/dB_range);

%Set Seashore Parameters and Index the region
seashore_center = 0;
seashore_roi = 0.12;

seashore_depth = 4.4;

seashore_width = [-0.5*seashore_roi 0.5*seashore_roi]*1e-2;
seashore_depth = [0.15 seashore_depth]*1e-2;

% Get Seashore coordinates
if(slice_dir == "xz")
    seashore_index = (xI>=seashore_width(1) & xI<=seashore_width(2) & ...
        zI>=seashore_depth(1) & zI<=seashore_depth(2));
else
    seashore_index = (yI>=seashore_width(1) & yI<=seashore_width(2) & ...
        zI>=seashore_depth(1) & zI<=seashore_depth(2));
end

if(slice_dir == "xz")
    seashore_y = xI(seashore_index);
else
    seashore_y = yI(seashore_index);
end
seashore_z = zI(seashore_index);

% Get Seashore Data
seashore_index = repmat(seashore_index, [1 1 N_frame]);
seashore_data = b_mode(seashore_index);
seashore_data = reshape(seashore_data, size(seashore_y, 1), []);

%Interpolate from Scattered XY onto Uniform grid 
F = scatteredInterpolant(seashore_y, seashore_z, double(seashore_data));

[y_interp, z_interp] = meshgrid(linspace(seashore_width(1), seashore_width(2), 20), ...
    linspace(seashore_depth(1), seashore_depth(2), 1024));

seashore_interp = F(y_interp, z_interp);

%Average along Y
seashore_interp = reshape(seashore_interp, size(y_interp, 1), size(y_interp, 2), []);
seashore_interp = squeeze(mean(seashore_interp, 2));

seashore_interp = uint8(255*seashore_interp/(max(seashore_interp, [], 'all')));

%Time axis and plot
time_end = (N_frame-1)/frame_rate;

time_axis = (0:N_frame-1)/frame_rate;
depth_axis = 100*z_interp(:, 1);

figure();
pcolor(time_axis, depth_axis, seashore_interp);
axis ij tight
shading flat
ylabel('Z (depth) [cm]');
xlabel('Time [s]');
colormap hot
c = colorbar;
clim([0 255]);
c.YTick = [0 255];
c.YTickLabel = {'0 dB',strcat(num2str(dB_range), ' dB')};

yticks(1:4);
xticks(0:4:20);