MATLAB: Centreline fitting in 3d (3D line fitting)

3d centreline fitting

Hello everyone,

I've got a centreline data set of a vessel and I want to connect the points to get an estimation of the length, however there are a few anomalous points off the main vessel ( i.e. noise ).

Any thoughts about how to fit the line / remove the points?

So far I was thinking of using the datatip to manually select unwanted points, but this would obviously take ages. I've tried using "smooth3" to clean up the data, but it didn't do much for me.

Here's the image below:

Cheers, Will

Best Answer

What I would try is to calculate the distances from every point to all other points. Then I would sort those distances in order of decreasing distance. Now it looks like some outliers might be fairly close to other outliers but in general the outliers are not close to more than 3 or 4 other outliers. So for a point to be valid, meaning close to a big group of other coordinates, the 5th closest (5th smallest) distance should be closer (smaller) than some specified tolerance distance. If that distance it larger, then it's far away and an outlier. So untested code would be something like

% Extract individual x, y, z vectors from the 3D data array.
allX = xyz(:, 1);
allY = xyz(:, 2);
allZ = xyz(:, 3);
fixed_xyz = xyz; % Initialize our good output array.
largestAllowableDistance = 10;  % Whatever works for you.
for k = 1 : size(xyz, 1)
    thisX = xyz(k, 1);
    thisY = xyz(k, 2);
    thisZ = xyz(k, 3);
    distances = sqrt((thisX-allX).^2 + (thisY-allY).^2 + (thisZ - allZ).^2);
    [sortedDistances, sortOrder] = sort(distances, 'descend');
    if sortedDistances(5) > largestAllowableDistance
        % It's an outlier so remove it.
        fixed_xyz(k, :) = []; % Setting to null removes that row.
    else
        % It's near the curve.
    end
end

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MATLAB: Store NaN and remove in for loop

There are multiple issues with your code. Here are a few that I quickly picked out:

using = to test for equivalency, whereas the correct code to test for equivalency is == . In MATLAB = is used only to assign a value.
using CP(k)=NaN to test if an element is NaN. It is important to learn that in floating point number convention NaN is not equal to anything, not even itself. To test if an element is NaN, use the function isnan .
defining the loop with for k=1:size(CP), which may not be giving you the range that you think it is: size(CP) will give (at minimum) a 1x2 numeric vector, which if you check the documentation for the : operator, the syntax a:[b,c] will be treated as a:b, so your code will only iterate up to the number of rows of CP.

If you want to remove all NaN elements from matrix CP, and the corresponding elments from matrix fixed_xyz, you can use MATLAB's rather powerful indexing and vectorization abilities. I would advise not removing the data, but just keeping an index to use whenever you need the data without the NaN's, something like this:

>> A = [1,2,3;4,NaN,6;NaN,NaN,9];
>> B = reshape(11:19,3,[]).';
>> X = isnan(A);
>> A(~X) % gives the elements of A without NaN's
>> B(~X) % and the corresponding ones for B.

You could even use this index within a loop, as you seem to be attempting something like this in your equation at the beginning of your question:

>> for k=1:size(A,1), B(k,~X(k,:)), end
ans =
    11    12    13
ans =
    14    16
ans =
    19

MATLAB: How to get those object and turn background color into white of the binary image

Try this:

clc;    % Clear the command window.
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%===============================================================================
% Read in a color reference image.
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rgbImage = imread(fullFileName);
% Get the dimensions of the image.  numberOfColorBands should be = 3.
[rows, columns, numberOfColorBands] = size(rgbImage);
% Display the original color image.
subplot(2, 2, 1);
imshow(rgbImage);
title('Original Color Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Enlarge figure to full screen.
set(gcf, 'Units', 'Normalized', 'Outerposition', [0, 0, 1, 1]);
% Take the red channel
grayImage = rgbImage(:,:, 1);
subplot(2, 2, 2);
imshow(grayImage);
axis on;
title('Red Channel Image', 'FontSize', fontSize, 'Interpreter', 'None');
% Threshold the image
binaryImage = grayImage < 127;
subplot(2, 2, 3);
imshow(binaryImage, []);
title('Binary Image', 'FontSize', fontSize, 'Interpreter', 'None');
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binaryImage = ~bwareafilt(binaryImage, 8);
subplot(2, 2, 4);
imshow(binaryImage, []);
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title(caption, 'FontSize', fontSize, 'Interpreter', 'None');

Best Answer

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