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muVES_3D_visualize.m
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% =============================== µVES ================================== %
% Copyrights © 2021 Alberto Rota, Luca Possenti
%
% For informations please contact:
% alberto1.rota@polimi.it
% or alberto_rota@outlook.com
% luca.possenti@polimi.it
% ========================================================================%
%% VISUALIZATION OF 3D MICROVASCULAR NETWORK
tot_branches = size(mvn.branchdata,1);
vol = mvn.raw;
[h,w,l] = size(mvn.bw);
[x_sk,y_sk,z_sk]=ind2sub([h,w,l],find(mvn.skel.sk));
[x_ep,y_ep,z_ep]=ind2sub([h,w,l],find(mvn.skel.bp));
[x_bp,y_bp,z_bp]=ind2sub([h,w,l],find(mvn.skel.ep));
%% 2D PROJECTION
if flat_img
figure('Name','2D Projection');
imagesc(mvn.flat);
ca = gca;
ca.Title.String = '2D projection';
end
%% SLICE VIEWER
if slices
sliceViewer(vol);
end
%% SEGMENTATION
if segmentation
figure('Name','Segmentation');
vhandle = volshow(double(mvn.bw));
vhandle.Renderer = 'Isosurface';
vhandle.IsosurfaceColor = [1 0 0];
vhandle.BackgroundColor = [0.4 0.4 0.4];
end
%% SKELETON
if skeleton
figure('Name','3D Discrete skeleton');
plot3(x_sk,y_sk,z_sk,'square','Markersize',2,'MarkerFaceColor',[1 1 1],...
'Color',[1 1 1]);
hold on
scatter3(x_ep,y_ep,z_ep,'filled','CData',[87 192 255]./255);
scatter3(x_bp,y_bp,z_bp,'filled','CData',[255 0 0]./255);
hold off
set(gca,'Color',[0.2 0.2 0.2]);
ca = gca;
ca.Title.String = 'Skeleton';
daspect([1 1 1]);
view(3);
end
%% INTERPOLATION
if interpolation
figure('Name','Interpolated skeleton');
hold on;
set(gca,'Color',[0.2 0.2 0.2]);
title('Interpolated Skeleton');
view(3);
daspect([1 1 1]);
for i=1:tot_branches
fnplt(mvn.branchdata.Interp{i},'y',2);
end
from = mvn.branchdata.From; to = mvn.branchdata.To;
scatter3(from(:,1),from(:,2),from(:,3),'filled','CData',[87 192 255]./255);
scatter3(to(:,1),to(:,2),to(:,3),'filled','CData',[255 0 0]./255);
end
%% GRAPH
if graph
figure('Name','Graph conversion');
ph = plot(mvn.skel.graph,'XData',mvn.skel.graph.Nodes.x,'YData',...
mvn.skel.graph.Nodes.y,'ZData',mvn.skel.graph.Nodes.z);
title('Graph');
try
for sn=1:max(mvn.skel.graph.Nodes.subN)
highlight(ph,mvn.skel.graph.Nodes.subN == sn,'NodeColor',abs(rand([1 3])),...
'MarkerSize',4);
end
catch
end
end
%% HISTOGRAMS
if histograms
% ISTOGRAMMA: Lenhezze
figure('Name','Histgrams: mesurement distribution for different metrics');
subplot(2,2,1);
histogram(mvn.branchdata.Len(:),'FaceColor','r','Normalization','probability');
xline(mean(mvn.branchdata.Len(:)),'k-.','LineWidth',2);
title('Length');
xlabel('Length [\mum]');
ylabel('Occurrences [%]');
% ISTOGRAMMA: Tortuosità
subplot(2,2,2);
histogram(mvn.branchdata.Tort(:),'FaceColor','b','Normalization','probability');
xline(mean(mvn.branchdata.Tort(:)),'k-.','LineWidth',2);
xlabel('Tortuosity [adim.]');
ylabel('Occurrences');
title('Tortuosity');
% ISTOGRAMMA: Raggio
subplot(2,2,3);
histogram(mvn.branchdata.Rad(~isnan(mvn.branchdata.Rad)),'FaceColor','g',...
'Normalization','probability');
xline(mean(mvn.branchdata.Rad(~isnan(mvn.branchdata.Rad))),'k-.','LineWidth',2);
xlabel('Radius [\mum]');
ylabel('Occurrences [%]');
title('Radius');
% ISTOGRAMMA: Eccentricità
subplot(2,2,4);
histogram(mvn.branchdata.Eccent(:),'FaceColor',[234,179,10]./255,...
'Normalization','probability');
axis tight
title('Eccentricity');
xline(mean(mvn.branchdata.Eccent(:)),'k-.','LineWidth',2);
xlabel('Eccentricity [adim.]');
ylabel('Occurrences [%]');
end
%% TORTUOSITY
% Viene riplottato lo scheletro, ma questa volta il colore di ogni branch
% dipende dalla tortuosità
if tortuosity
figure('Name','Tortuosity branch-wise')
cm = colormap(jet);
for b = 1:tot_branches
currcolor_idx = 1+round((mvn.branchdata.Tort_new(b)-min(mvn.branchdata.Tort_new(:)))...
/max(mvn.branchdata.Tort(:))*255);
plot3(mvn.branchdata.xPath{b}, mvn.branchdata.yPath{b}, mvn.branchdata.zPath{b},...
'Color', cm(currcolor_idx,:),'LineWidth',3);
hold on
scatter3(mvn.branchdata.From(b,1), mvn.branchdata.From(b,2), mvn.branchdata.From(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
scatter3(mvn.branchdata.To(b,1), mvn.branchdata.To(b,2), mvn.branchdata.To(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
end
hold off
set(gca,'CLim',[min(mvn.branchdata.Tort_new(:)) max(mvn.branchdata.Tort_new(:))]);
set(gca,'Color',[0.2 0.2 0.2]);
colorbar
title('Tortuosity');
daspect([1 1 1]);
view(3);
end
%% RADIUS
if radius
figure('Name','Radius branch-wise')
cool = colormap(jet);
for b = 1:tot_branches
currcolor_idx = ceil(mvn.branchdata.Rad(b)/max(mvn.branchdata.Rad(:))*256);
plot3(mvn.branchdata.xPath{b}, mvn.branchdata.yPath{b}, mvn.branchdata.zPath{b},...
'Color', cool(currcolor_idx,:),'LineWidth',3);
hold on
scatter3(mvn.branchdata.From(b,1), mvn.branchdata.From(b,2), mvn.branchdata.From(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
scatter3(mvn.branchdata.To(b,1), mvn.branchdata.To(b,2), mvn.branchdata.To(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
end
hold off
set(gca,'CLim',[min(mvn.branchdata.Rad(:)) max(mvn.branchdata.Rad(:))]);
set(gca,'Color',[0.2 0.2 0.2]);
colorbar;
title('Radius');
daspect([1 1 1]);
view(3);
end
%% LENGTH
if lengthh
figure('Name','Length branch-wise');
cool = colormap(jet);
for b = 1:tot_branches
currcolor_idx = ceil(mvn.branchdata.Len(b)/max(mvn.branchdata.Len(:))*256);
plot3(mvn.branchdata.xPath{b}, mvn.branchdata.yPath{b}, mvn.branchdata.zPath{b},...
'Color', cool(currcolor_idx,:),'LineWidth',3);
hold on
scatter3(mvn.branchdata.From(b,1), mvn.branchdata.From(b,2), mvn.branchdata.From(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
scatter3(mvn.branchdata.To(b,1), mvn.branchdata.To(b,2), mvn.branchdata.To(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
end
hold off
set(gca,'CLim',[min(mvn.branchdata.Len(:)) max(mvn.branchdata.Len(:))]);
set(gca,'Color',[0.2 0.2 0.2]);
colorbar;
title('Length');
daspect([1 1 1]);
view(3);
end
%% ECCENTRICITY
if eccentricity
figure('Name','Eccenticity branch-wise');
cool = colormap(jet);
for b = 1:tot_branches
currcolor_idx = ceil(mvn.branchdata.Eccent(b)/max(mvn.branchdata.Eccent(:))*256);
plot3(mvn.branchdata.xPath{b}, mvn.branchdata.yPath{b}, mvn.branchdata.zPath{b},...
'Color', cool(currcolor_idx,:),'LineWidth',3);
hold on
scatter3(mvn.branchdata.From(b,1), mvn.branchdata.From(b,2), mvn.branchdata.From(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
scatter3(mvn.branchdata.To(b,1), mvn.branchdata.To(b,2), mvn.branchdata.To(b,3),'o',...
'filled','MarkerFaceColor', [1 1 1]);
end
hold off
set(gca,'CLim',[min(mvn.branchdata.Eccent(:)) max(mvn.branchdata.Eccent(:))]);
set(gca,'Color',[0.2 0.2 0.2]);
colorbar;
title('Eccentricity');
daspect([1 1 1]);
view(3);
end
%% PTS CLASSIFICATION
if pts_classification
figure('Name','.pts classification');
for i=1:tot_branches
plot3(mvn.branchdata.xInt(i,:), mvn.branchdata.yInt(i,:), mvn.branchdata.zInt(i,:),...
'LineWidth',2);
hold on
text(mvn.branchdata.xInt(i,round(end/2)), mvn.branchdata.yInt(i,round(end/2)),...
mvn.branchdata.zInt(i,round(end/2)),string(i),'FontSize',6);
scatter3(mvn.branchdata.From(i,1),mvn.branchdata.From(i,2),mvn.branchdata.From(i,3),'o');
text(mvn.branchdata.From(i,1),mvn.branchdata.From(i,2),mvn.branchdata.From(i,3),...
mvn.branchdata.CatFr(i),'FontSize',10);
scatter3(mvn.branchdata.To(i,1),mvn.branchdata.To(i,2),mvn.branchdata.To(i,3),'o');
text(mvn.branchdata.To(i,1),mvn.branchdata.To(i,2),mvn.branchdata.To(i,3),...
mvn.branchdata.CatTo(i),'FontSize',10);
end
daspect([1 1 1]);
title('Node classification ');
end