# Make white portions of slice of flow data transparent

17 views (last 30 days)
Nathaniel H Werner on 6 Apr 2020
Edited: darova on 6 Apr 2020
I have created this figure (one of five) with the code (I have edited it for the question) below.
I would like to make the white [1 1 1] portions of the cylinder sections transparent. I know that MatLab cannot work with RGBa in the colormap, so is there some other way to do that? I do not want the entire cylinder surface to be transparent, just the white part. I found this question here which seems to work for png images, but that is not what I am looking for. I'm pretty sure something like what I am asking can be done since I've seen it before but I don't have the source code to work with.
Here is an image from a recent paper Li, C., Dong, H., & Cheng, B. (2020). Tip vortices formation and evolution of rotating wings at low Reynolds numbers. Physics of Fluids, 32(2), 021905.
Correction: I do not know if this figure was made in MatLab.
I cannot load the variables X, Y, Z, or V since they are too large. You can use the flow data built into MatLab.
Please let me know if you have any questions or if there are issues with the code, I will make any necessary edits if I forgot something.
Ny = 1000;
[X,Y,Z,V] = flow(10);
% these variables are needed, I forgot them in the previous version
y = [-0.7344,0.7031];
dt = 0.0258; % Size of time step
dtheta = 7.5; % Differential angle size [deg]
theta = 180 + dtheta;
iso = -3;
for q=1:2
for i=1:3
if ~and(q==2,i==1)
if i==1
AR = 3;
elseif i==2
AR = 5;
elseif i==3
AR = 7;
end
RoLoc = (0.2:0.1:0.9)*AR;
% don't bother to draw the rectangular patch in the image
figure(sub2ind([2,3],q,i))
xlabel('x'), ylabel('y'), zlabel('z')
hold on
fh = gcf();
axh = findall(fh, 'Type', 'Axes');
for r=1:length(RoLoc)
sweep = floor(2.1*Ny*RoLoc(r));
[Xc,Yc,Zc] = cylinder2(RoLoc(r)*ones(1,Ny),[0,1,0],sweep); % you can find this here https://www.mathworks.com/matlabcentral/fileexchange/64007-generate-cylinder-with-custom-axis
H = [1 0 0 0;
0 1 0 min(y); % vertical translation
0 0 1 0;
0 0 0 1]*...
[1 0 0 0;
0 peak2peak(y) 0 0; % vertical stretching
0 0 1 0;
0 0 0 1]*...
[ones(1,Ny);Yc(:,1)';ones(1,Ny);ones(1,Ny)];
Yc = repmat(H(2,1:Ny)',1,sweep+1);
clear H
% angle for part of the cylinder
Phi_prime = atand(delta/RoLoc(r));
theta_prime = linspace(360,0,sweep+1)';
if r==1
T = 3;
elseif r==2
T = 4;
elseif r==3
T = 5;
elseif r>3 && r<6
T = 6;
else
T = 9;
end
theta_q = theta - T*Phi_prime;
clear T
theta_p = theta + 2*Phi_prime;
[~,l] = min(abs(theta_prime - theta_p));
[~,m] = min(abs(theta_prime - theta_q));
Vsli{q,i,r} = slice(axh,X,Y,Z,V,Xc(:,l:m),Yc(:,l:m),Zc(:,l:m),'linear');
Vsli{q,i,r}.EdgeColor = 'none';
% Setup color axis range
V_min(q,i,r) = sign(min(caxis))*ceil(abs(min(caxis))); % min value in flow
V_max(q,i,r) = ceil(max(caxis)); % max value in flow
end
end
end
end
% this portion changes the colors of the cylinder sections
n = 1000;
for q = 1:2
for i = 1:3
if ~and(q==2, i==1)
figure(sub2ind([2,3],q,i))
colorbar
fh = gcf();
axh = findall(fh, 'Type','Axes');
cbh = findall(fh, 'Type', 'ColorBar');
% these numbers are tuned to my data
M1 = nanmin(V_min,[],'all');
M2 = nanmax(V_max,[],'all');
vPmin = 1/3;
vPmax = 1/2;
M1prime = sign(M1)*ceil(abs(vPmin*M1)/5)*5;
M2prime = floor(vPmax*M2/5)*5;
caxis([M1prime,M2prime])
% I have adapted the code for making your own interpolated colormap here https://stackoverflow.com/questions/30851050/how-to-create-an-interpolated-colormap-or-color-palette-from-two-colors
% Set white to be zero with blue as negative and red as positive
n0 = floor(interp1([M1prime,M2prime],[1,n],0)); % interpolate color index to zero
nN2 = floor(interp1([M1prime,M2prime],[1,n],iso-1)); % blue to cyan
nN1 = floor(interp1([M1prime,M2prime],[1,n],iso)); % cyan to white
nP1 = floor(interp1([M1prime,M2prime],[1,n],-iso)); % white to yellow
nP2 = floor(interp1([M1prime,M2prime],[1,n],-(iso-1))); % yellow to red
cmap = zeros(5,3);
cmap(1,:) = [0 0 1]; %// color first row - blue
cmap(2,:) = [0 1 1]; % cyan
cmap(3,:) = [1 1 1]; %// color 1/2*nth row - white
cmap(4,:) = [1 1 0]; % yellow
cmap(5,:) = [1 0 0]; %// color nth row - red
[xcs,ycs] = meshgrid(1:3,1:n); %// mesh of indices
cmapN = interp2(xcs([1,nN2,nN1],:),ycs([1,nN2,nN1],:),[cmap(1:2,:);cmap(2,:)],xcs,ycs); %// interpolate blue to cyan
cmapN(nN1+1:end,:) = [];
cmapZ1 = interp2(xcs([nN1+1,nN1+1+floor((n0-(nN1+1))/2),n0],:),ycs([nN1+1,nN1+1+floor((n0-(nN1+1))/2),n0],:),[cmap(2:3,:);cmap(3,:)],xcs,ycs); %// interpolate cyan to white
cmapZ1(1:nN1,:) = []; Lz1 = length(cmapZ1);
cmapZ1(Lz1-(n-n0)+1:Lz1,:) = [];
cmapZ2 = interp2(xcs([n0+1,n0+1+floor((nP1-(n0+1))/2),nP1],:),ycs([n0+1,n0+1+floor((nP1-(n0+1))/2),nP1],:),[cmap(3,:);cmap(3:4,:)],xcs,ycs); %// interpolate white to yellow
cmapZ2(1:n0,:) = []; Lz2 = length(cmapZ2);
cmapZ2(Lz2-(n-nP1)+1:Lz2,:) = [];
cmapP = interp2(xcs([nP1+1,nP2,n],:),ycs([nP1+1,nP2,n],:),[cmap(4,:);cmap(4:5,:)],xcs,ycs); %// interpolate yellow to red
cmapP(1:nP1,:) = [];
cmapNtot = [cmapN;cmapZ1];
cmapPtot = [cmapZ2;cmapP];
cmap = [cmapNtot;cmapPtot];
colormap(cmap) %// set color map
% I found this pause helps to make sure the colorbar changes, sometimes MatLab doesn't change it without being in debug mode
pause(3)
end
end
end
Nathaniel H Werner on 6 Apr 2020
No not really. You need high numbers for the grid to make the contours look smooth enough. But feel free to lower them if you have some ideas.

darova on 6 Apr 2020
An example of how to make some faces transparent
[X,Y] = meshgrid(-10:10); % generate mesh
Z = -X.^2-Y.^2; % Z values (paraboloid)
alpha1 = Z*0+1; % alphadata (all '1')
ix = -20 > Z & Z > -60; % find Z values between -20 and -60
alpha1(ix) = 0.5; % assign alpha 0.5 (transparency
h = surf(X,Y,Z,...
'facealpha','interp',... % interpolate transparency
'alphadatamapping','none'); % don't know what is this
axis vis3d
Result
darova on 6 Apr 2020
Here is an example with using slice
clc,clear
opengl software
[X,Y,Z,V] = flow(20);
xx = linspace(min(X(:)),max(X(:)),50);
yy = linspace(min(Y(:)),max(Y(:)),50);
[X1,Y1] = meshgrid(xx,yy);
Z1 = Y1;
V1 = interp3(X,Y,Z,V,X1,Y1,Z1); % values of flow on plane
h = slice(X,Y,Z,V,X1,Y1,Z1);
alpha1 = Z1*0+1; % alphadata (all '1')
ix = -2 > V1 & V1 > -4; % find V1 values between -2 and -4
alpha1(ix) = 0.5; % assign alpha 0.5 (transparency
set(h,...
'edgecolor','none',...
'facealpha','interp',... % interpolate transparency
'alphadatamapping','none'); % don't know what is this
axis vis3d
colorbar

R2018b

### Community Treasure Hunt

Find the treasures in MATLAB Central and discover how the community can help you!

Start Hunting!