How to avoid filling in certain geometries in a 3D plot

Hello there, I'm currently creating a script that takes in binarised 2D .png slices and creates 3D models from the slices. I used bwboundaries to draw the plots for each image slice with 'holes':

[B] = bwboundaries(binaryImage_new,'holes');

I then used fill3 to draw the plots in 3D and cover the empty white spaces with a cyan colour and the whole process loops again with a new slice. Unfortunately, I have run into an issue where the fill3 property covers over the 'holes' of the plots.

As shown above, the base of my 3D benchy model has letters that should be indented but aren't, as the fill3 properties covers everything. I want to fill in the parts outside the letters in cyan and leave parts inside the letters empty.

Another example are the two holes above benchy, which should be hollow but are covered up by the fill3 property. I want to fill the outer geometry but leave the 'holes' empty.

Here's the main line of code for the plotting:

fill3(boundary(:,1), boundary(:,2), z, 'c', 'EdgeColor', [0 0.4470 0.7410], 'EdgeAlpha', 0.15, 'LineWidth', 0.25/resolution) %fill3 generates 3D plots and also fills in enclosed geometry with color

Is it possible to fill in certain parts?

[Suleman Sial]

Okay, so I managed to get it to work, *slightly*. I decided to concatencate cell array B entirely (made by bwboundaries), thus removing the nested for loop (shown below):

for k = 1:length(B)                                             %for every cell in B...
        boundary = B{k};
        z = repmat(i*(0.25/resolution),(height(boundary)),1);       %z coordinates is an array of repeated numbers that is iterated by 1 every loop 
        ...the size of the array changes depending on the size of the chosen cell array of B
        fill3(boundary(:,1), boundary(:,2), z, 'c', 'EdgeColor', [0 0.4470 0.7410], 'EdgeAlpha', 0.15, 'LineWidth', 0.25/resolution)
        ...%fill3 generates 3D plots and also fills in enclosed geometry with color
end

replacing it instead with:

    boundary = cell2mat(B);
    boundary(:,3) = (0.25*i);
    fill3(boundary(:,1), boundary(:,2), boundary(:,3), 'c', 'EdgeColor', [0 0.4470 0.7410], 'EdgeAlpha', 0.15, 'LineWidth', 0.25/resolution)
    ...%fill3 generates 3D plots and also fills in enclosed geometry with color

Unfortunately, this has caused another issue:

It appears that concatencating all of the points into a single 2d matrix means that boundaries are being connected with a single line, shown below:

Is there a way to remove these unwanted lines that are disrupting the fill3 tool? Adding NaN inbetween boundaries results in the fill3 tool not filling the region, due to the NaN values in the 2d matrix.

Any help would be greatly appreciated!

Answer 1

[Suleman Sial]

It appears I've answered my own question. When dealing with image slices, utilising matlab's Volume Viewer app and volshow() is the best tool for this scenario, not bwboundaries or fill3 or any other plotting methods.

It created the holes and boundaries AND runs 8 times faster, since parfor can be utilised in the 'for loop' for stacking the images in an array.

Refer to this post for more info: https://au.mathworks.com/matlabcentral/answers/488639-converting-large-stack-of-2d-images-into-3d-image-how-to-improve-performance