data/bmode_image_plot.m

%% MATLAB Script for displaying 2D and 3D plots of reconstructed B-Mode data in
%  files named "*3d_recon.mat"

% See "multiframe_bmode_plot.m" for displaying real-time B-Mode data in files 
% named "*rt_recon.mat"

% See "image_recon_3d.m" and "image_recon_rt.m" for reconstructing B-Mode data from
% raw RF data in files names "*_raw.zip"

clear;
% clc;
% close;

%% Image params
log_compression = true;
dB_range = 30;
orthogonal = false;
slice_dir = 'yz';
video_out = false;

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

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

%File name
filename = 'neck_yz_3d_recon';

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

%Check how many fields in struct for 2-D/3-D
num_dim = length(fieldnames(bmode_data_struct))-1;

%Assign variables
bmode_data = bmode_data_struct.bmode_data;

zI = bmode_data_struct.zI;
if (num_dim==2 & slice_dir=='xz')
    xI = bmode_data_struct.xI;
elseif (num_dim==2 && slice_dir=='yz')
    xI = bmode_data_struct.yI;
elseif(num_dim == 3)
    xI = bmode_data_struct.xI;
    yI = bmode_data_struct.yI;
    grid_res = size(bmode_data, 1);
    grid_res_orth = size(bmode_data, 3);
end

%% Imaging

if(num_dim == 2)
%% Plot 2-D images
    bmode_data = abs(bmode_data);

    if(log_compression)
        %Log compression
        b_mode_temp = 20*log10(bmode_data/max(max(bmode_data)));
        b_mode = (b_mode_temp+dB_range).*(b_mode_temp>-dB_range);
        b_mode = uint8(255*b_mode/dB_range);
        
        %Plot Image
        figure();
        
        if(slice_dir == "xz")
            hP = pcolor(xI*1e2,zI*1e2,b_mode);
        elseif(slice_dir == "yz")
            hP = pcolor(yI*1e2,zI*1e2,b_mode);
        end
        set(gca, 'XAxisLocation', 'bottom', 'XTickMode', 'auto');
        shading interp, axis ij tight
        c = colorbar;
        clim([0 255]);
        c.YTick = [0 255];
        c.YTickLabel = {'0 dB',strcat(num2str(dB_range), ' dB')};
        ylabel('[cm]')
        xlabel('[cm]')
        set(gca,'XColor','none','box','off')
        colormap hot
        % title(test_name, 'Interpreter', 'none');
        % view(2)
        % hP.DataTipTemplate.DataTipRows(3).Value   = 'CData';
    else
        %Normalization
        b_mode_temp = bmode_data/max(max(bmode_data));
        
        %Plot Image
        figure();
        
        if(slice_dir == "xz")
            hP = pcolor(xI*1e2,zI*1e2,b_mode_temp);
        elseif(slice_dir == "yz")
            hP = pcolor(yI*1e2,zI*1e2,b_mode_temp);
        end
        shading interp, axis equal ij tight
        c = colorbar;
        xlabel('[cm]')
        clim([0 1]);
        c.YTick = [0 1];
        c.YTickLabel = {'0','1'};
        ylabel('[cm]')
        set(gca,'XColor','none','box','off')
        colormap hot
        % title(test_name, 'Interpreter', 'none');
        % view(2)
        % hP.DataTipTemplate.DataTipRows(3).Value   = 'CData';
    end   

elseif(num_dim == 3)
%% Plot 3-D images
    
    %Magnitude of complex number
    bmode_data = abs(bmode_data);
    
    if(log_compression)
        %Log compression
        b_mode_temp = 20*log10(bmode_data/max(bmode_data,[],'all'));
        b_mode = (b_mode_temp+dB_range).*(b_mode_temp>-dB_range);
        b_mode = uint8(255*b_mode/dB_range);

        %Plot real-tim image
        figure();
    
        if(~orthogonal)
            % for i=1:grid_res_orth
            for i=27
                % b_mode_temp = 20*log10(bmode_data(:, :, i)/max(bmode_data(:, :, i), [],'all'));
                % b_mode(:, :, i) = (b_mode_temp+dB_range).*(b_mode_temp>-dB_range);
                % b_mode(:, :, i) = uint8(255*b_mode(:, :, i)/dB_range);
                % figure();
                if(strcmp(slice_dir,'xz'))
                    hP = pcolor(xI(:,:,i)*1e2,zI(:,:,i)*1e2,b_mode(:,:,i));
                elseif(strcmp(slice_dir,'yz'))
                    hP = pcolor(yI(:,:,i)*1e2,zI(:,:,i)*1e2,b_mode(:,:,i));
                end
                shading interp, axis equal ij tight
                c = colorbar;
                clim([0 255]);
                c.YTick = [0 255];
                c.YTickLabel = {'0 dB', strcat(num2str(dB_range),' dB')};
                % c.YTickLabel = {'0 dB', strcat(num2str(dB_range),' dB')};
                ylabel('Z (depth) [cm]')
                yticks(1:1:4)
                xticks(-2:1:2)

                % ylim([0 4])
                if(strcmp(slice_dir,'xz'))
                    xlabel('X [cm]')
                elseif(strcmp(slice_dir,'yz'))
                    xlabel('Y [cm]')
                end

                % set(gca,'XColor','none','box','off')
                colormap hot
                if(strcmp(slice_dir,'xz'))
                    % title(strcat('Y =', {' '}, num2str(round(100*yI(64, 64, i), 2)), ' cm'), 'Interpreter', 'none');
                    title(strcat('Slice #', num2str(i)));
                else
                    title(strcat('X =', {' '}, num2str(round(100*xI(64, 64, i), 2)), ' cm'), 'Interpreter', 'none');
                    % title('Center Slice – YZ');
                end
                drawnow limitrate;
                F = getframe(gcf) ;
                img{i} = frame2im(F);
            end
        else
            for i=1:grid_res
            % for i = 51
                % b_mode_temp = 20*log10(bmode_data(i, :, :)/max(bmode_data(i, :, :), [],'all'));
                % b_mode(i, :, :) = (b_mode_temp+dB_range).*(b_mode_temp>-dB_range);
                % b_mode(i, :, :) = uint8(255*b_mode(i, :, :)/dB_range);
                if(strcmp(slice_dir,'xz') && orthogonal)
                    hP = pcolor(squeeze(yI(i,:,:))*1e2,squeeze(zI(i,:,:))*1e2,squeeze(b_mode(i,:,:)));
                    % hP = pcolor(squeeze(b_mode(i,:,:)));
                elseif(strcmp(slice_dir,'yz') && orthogonal)
                    hP = pcolor(squeeze(xI(i,:,:))*1e2,squeeze(zI(i,:,:))*1e2,squeeze(b_mode(i,:,:)));
                end
                shading interp, axis equal ij tight
                c = colorbar;
                clim([0 255]);
                c.YTick = [0 255];
                c.YTickLabel = {'0 dB', strcat(num2str(dB_range),' dB')};
                ylabel('Z (depth) [cm]')
                yticks([1 2 3 4])

                if(strcmp(slice_dir,'xz'))
                    xlabel('Y [cm]')
                elseif(strcmp(slice_dir,'yz'))
                    xlabel('X [cm]')
                end

                % set(gca,'XColor','none','box','off')
                colormap hot
                if(strcmp(slice_dir,'xz'))
                    % title('Center Slice – YZ')
                    % title(strcat('X =', {' '}, num2str(round(100*xI(i, 64, 26), 2)), ' cm'), 'Interpreter', 'none');
                else
                    % title('YZ – Orthogonal Reconstruction at Center')
                    title(strcat('Y =', {' '}, num2str(round(100*yI(i, 64, 26), 2)), ' cm'), 'Interpreter', 'none');
                end
                drawnow limitrate;
                F = getframe(gcf) ;
                img{i} = frame2im(F);
            end
        end
    else
        %Normalization
        b_mode = bmode_data/max(bmode_data,[],'all');
        
        %Plot real-tim image
        figure();
        if(~orthogonal)
            for i=1:grid_res_orth
            % for i=84
                % b_mode_temp = 20*log10(bmode_data(:, :, i)/max(bmode_data(:, :, i), [],'all'));
                % b_mode(:, :, i) = (b_mode_temp+dB_range).*(b_mode_temp>-dB_range);
                % b_mode(:, :, i) = uint8(255*b_mode(:, :, i)/dB_range);
                if(strcmp(slice_dir,'xz'))
                    hP = pcolor(xI(:,:,i)*1e2,zI(:,:,i)*1e2,b_mode(:,:,i));
                elseif(strcmp(slice_dir,'yz'))
                    hP = pcolor(yI(:,:,i)*1e2,zI(:,:,i)*1e2,b_mode(:,:,i));
                end
                shading interp, axis equal ij tight
                c = colorbar;
                clim([0 1]);
                c.YTick = [0 1];
                c.YTickLabel = {'0','1'};
                ylabel('Z (depth) [cm]')
                xlabel('X [cm]')
                set(gca,'XColor','none','box','off')
                colormap hot
                title(strcat('Slice: ',num2str(i)), 'Interpreter', 'none');
                drawnow limitrate;
                F = getframe(gcf) ;
                img{i} = frame2im(F);
            end
        else
            for i=1:grid_res
                b_mode_temp = 20*log10(bmode_data(:, :, i)/max(bmode_data(:, :, i), [],'all'));
                b_mode(:, :, i) = (b_mode_temp+dB_range).*(b_mode_temp>-dB_range);
                b_mode(:, :, i) = uint8(255*b_mode(:, :, i)/dB_range);
                if(strcmp(slice_dir,'xz') && orthogonal)
                    hP = pcolor(squeeze(yI(i,:,:))*1e2,squeeze(zI(i,:,:))*1e2,squeeze(b_mode(i,:,:)));
                elseif(strcmp(slice_dir,'yz') && orthogonal)
                    hP = pcolor(squeeze(xI(i,:,:))*1e2,squeeze(zI(i,:,:))*1e2,squeeze(b_mode(i,:,:)));
                end
                shading interp, axis equal ij tight
                c = colorbar;
                clim([0 1]);
                c.YTick = [0 1];
                c.YTickLabel = {'0','1'};
                ylabel('Z (depth) [cm]')
                xlabel('Y [cm]')
                set(gca,'XColor','none','box','off')
                colormap hot
                title(strcat('Slice: ',num2str(i), ' Angle = ', num2str((i-grid_res/2-0.5)/(grid_res/2-0.5)*30), ' degrees'), 'Interpreter', 'none');
                drawnow limitrate;
                F = getframe(gcf) ;
                img{i} = frame2im(F);
            end
        end
    end
    
    %Find frame with minimum elements (/3 for uint8)
    elementCounts = cellfun(@numel, img)/3;
    [~, min_index] = min(elementCounts);
    
    %Frame parameters
    frameheight = size(img{min_index},1);
    framewidth = size(img{min_index},2);
    
    %% Write Video for RT multiframe

    if(video_out)
        % create the video writer with 1 fps
        writerObj = VideoWriter(strcat(filepath, filename, '.mp4'), 'MPEG-4');
        % set the seconds per image
        writerObj.FrameRate = 1;
        % open the video writer
        open(writerObj);
        % write the frames to the video
        if(~orthogonal)
            for i=1:grid_res_orth
                % convert the image to a frame
                img{i} = imresize(img{i},[frameheight framewidth]);
                writeVideo(writerObj, img{i});
            end
        else
            for i=1:grid_res
                % convert the image to a frame
                img{i} = imresize(img{i},[frameheight framewidth]);
                writeVideo(writerObj, img{i});
            end
        end
        % close the writer object
        close(writerObj);
    end

    % view(2)
    % hP.DataTipTemplate.DataTipRows(3).Value   = 'CData';

end

%% 3-D scatter plot from scattered data

plot_thresh_lower = 90;
plot_thresh_upper = 180;

index_3D = b_mode>plot_thresh_lower & b_mode<plot_thresh_upper & zI>0.005;
x_3D = 100*xI(index_3D);
y_3D = 100*yI(index_3D);
z_3D = 100*zI(index_3D);

bmode_3D = b_mode(index_3D);

figure();
h = scatter3(x_3D, y_3D, z_3D, 20, y_3D,  'o', 'filled');
set(h, 'MarkerFaceAlpha', 0.5)
% set(h, 'MarkerFaceColor', "#444444")
constantplane([0 1 0], 0, "FaceColor", "k", "FaceAlpha", 0.1);

c = colorbar('eastoutside');
clim([-0.8 0.8]);
c.YTick = [-0.8 0 0.8];
c.Label.String = 'Y coordinate [cm]';
% c.Label.Rotation = 270;
cpos = c.Position;
cpos(3) = 0.6*cpos(3);
cpos(4) = 0.6*cpos(4);
cpos(2) = 0.8-cpos(4);
c.Position = cpos;

% colormap sky
set(gca, 'Zdir', 'reverse');
% axis equal 
xlabel('X [cm]')
xlim([-0.8 0.8])
ylabel('Y [cm]')
ylim([-0.8 0.8])
yticks(-0.5:0.5:0.5)
zlabel('Z [cm]')
zlim([0.8 2.1])
zticks(1:0.5:2.5)

%% Interpolate volume data for oblique slices

bmode_3D_func = scatteredInterpolant(xI(:), yI(:), zI(:), double(b_mode(:)), 'linear', 'none');

%% Query Interpolant

x_axis = (-1:0.02:1)*1e-2;
y_axis = (-2:0.02:2)*1e-2;
z_axis = (0:0.02:4.5)*1e-2;

[xq, yq, zq] = meshgrid(x_axis, y_axis, z_axis);

bmode_q = bmode_3D_func(xq, yq, zq);

%% Plot XY slices from volume data

figure();
tiledlayout(3, 3, "TileSpacing", "compact", "Padding", "compact")
for z = 65:2:82
    nexttile;
    pcolor(1e2*squeeze(yq(:, :, z)), 1e2*squeeze(xq(:, :, z)), squeeze(bmode_q(:, :, z)));
    axis equal tight ij
    shading interp;
    colorbar;
    colormap gray;
    title(strcat("Z = ", num2str(1e2*z_axis(z)), " cm"));
end


figure();
tiledlayout(3, 3, "TileSpacing", "compact", "Padding", "compact")
for z = 41:3:67
    nexttile;
    pcolor(1e2*squeeze(yq(:, :, z)), 1e2*squeeze(xq(:, :, z)), squeeze(bmode_q(:, :, z)));
    axis equal tight ij
    shading interp;
    colorbar;
    colormap gray;
    title(strcat("Z = ", num2str(1e2*z_axis(z)), " cm"));
end

%% Plot oblique slices in 3D space

slice_point = [0 0 189];
% slice_point = [51 101 0];
slice_normal = [0 0 1];

[B_slice, x_slice, y_slice, z_slice] = obliqueslice(bmode_q, slice_point, slice_normal);

x_slice = (x_slice./size(xq, 2) - 0.5)*2;
y_slice = (y_slice./size(yq, 1) - 0.5)*4;
z_slice = z_slice./size(zq, 3)*4.5;

% B_slice(y_slice<-1.6 | y_slice>1.4) = NaN;

figure();
surf(x_slice,y_slice, z_slice, B_slice, 'FaceAlpha', 0.9);
colormap(hot);
clim([20 204])
c = colorbar('eastoutside');
c.YTick = [20 204];
c.YTickLabel = {'0 dB', '30 dB'};
cpos = c.Position;
cpos(3) = 0.6*cpos(3);
cpos(4) = 0.6*cpos(4);
cpos(2) = 0.8-cpos(4);
c.Position = cpos;
shading interp
set(gca, 'Zdir', 'reverse');

axis equal tight
xlabel('X [cm]');
xlim([-1 1]);
xticks(-1:1);
ylabel('Y [cm]');
ylim([-2 2]);
yticks(-2:1:2);
zlabel('Z [cm]');
zlim([1 4.5]);
zticks(1:1:4);
view([0 90]);

%% Scatter plot with interpolated data

plot_thresh_lower = 18;
plot_thresh_upper = 20;

index_vessel = (bmode_q>plot_thresh_lower & bmode_q<plot_thresh_upper & zq>0.019 &  zq<0.042 & yq>-0.01 & yq<0.01);
x_vessel = 100*xq(index_vessel);
y_vessel = 100*yq(index_vessel);
z_vessel = 100*zq(index_vessel);

bmode_vessel = bmode_q(index_vessel);

% plot_thresh_lower = 80;
% plot_thresh_upper = 255;
% 
% index_3D = (bmode_q>plot_thresh_lower & bmode_q<plot_thresh_upper & zq>0.019 & yq>-0.015 & yq<0.008);
% x_3D = 100*xq(index_3D);
% y_3D = 100*yq(index_3D);
% z_3D = 100*zq(index_3D);

% bmode_3D = bmode_q(index_3D);

hold on
% h1 = scatter3(x_3D, y_3D, z_3D, 1, 'w', 'o', 'filled');
% set(h1, 'MarkerFaceAlpha', 0.2)

h2 = scatter3(x_vessel, y_vessel, z_vessel, 15, 'k', 'o', 'filled');
set(h2, 'MarkerFaceAlpha', 0.6)
set(h2, 'MarkerFaceColor', "#555555")

colormap gray

% c = colorbar('eastoutside');
% c.Limits = [-1 1];
% c.YTick = [-1 1];
% c.YTickLabel = {'-1', '1'};
% c.Label.String = 'X coordinate [cm]';
% clim([-1 2])
% cpos = c.Position;
% cpos(3) = 0.6*cpos(3);
% cpos(4) = 0.6*cpos(4);
% cpos(2) = 0.8-cpos(4);
% c.Position = cpos;

set(gca, 'Zdir', 'reverse');
ax = gca;
% ax.Color = 'k'; 
% ax.GridColor = 'w';
ax.GridLineWidth = 1.5;

grid on
axis equal
view([48 13]);

constantplane([38 3 0], 0, "FaceColor", "r", "FaceAlpha", 0.2);
constantplane([-3 38 0], 0, "FaceColor", "g", "FaceAlpha", 0.2);
constantplane([0 0 1], 2.6, "FaceColor", "b", "FaceAlpha", 0.2);
constantplane([0 0 1], 3.75, "FaceColor", "b", "FaceAlpha", 0.2);

xlabel('X [cm]');
xlim([-1 1]);
xticks(-1:1);
ylabel('Y [cm]');
ylim([-1.7 1.7]);
yticks(-1:1:1);
zlabel('Z [cm]');
zlim([1.5 4.5]);
zticks(1:1:4);