In klapaukh/hangler: Fourier shape analysis as per Hangle

knitr::opts_chunk$set(fig.width=5, fig.height=5) 

We are going to run through an example of using hangler to analyse a simple closed curve shape.

First we need to generate our data set. This is equivalent to a human digitising a curve. We come out with only a set of xy coordinates sampled along the shape.

library(hangler)

theta = seq(0,2*pi, 0.01)

radius = 6

wiggle = 7

x = (sin(theta*wiggle) + radius) * cos(theta)
y = (sin(theta*wiggle) + radius) * sin(theta)

rm(theta)
rm(wiggle)
rm(radius)

We can now plot it and see our apeture.

plot(x,y,col="black")
lines(c(x,x[1]),c(y,y[1]),col="blue")

We now get the tangets.

tangents = computeTangents(x,y)

Now we can plot the tangents and notice that the tangent curve we get is nice and continuous.

plot(tangents)
lines(tangents,col="blue")

We can turn them back into a shape and see that they give the original.

with(tangentsToXY(tangents), {
   plot(x, y,col=rainbow(length(tangents))); 
   lines(x,y)
})

At this point we need to resample the tangent curve. This is because FFT requires evenly spaced points, but we cannot be certain that our digitisation / landmark capture is even along the curve length. We will resample the default number of points.

newTangents = resampleTangents(x,y, tangents)

We can now plot our new tangents to make sure they are the same as the old ones.

plot(newTangents)
lines(newTangents,col="blue")

That done, we now need to remove the normal shift associated with a unit circle. Hangle characterises shape by deviation from unit circle rather than directly.

newTangents = flattenTangents(newTangents)

Now we can plot the results to make sure they look sensible (like a wave).

plot(newTangents)
lines(newTangents,col="blue")

From this point one we can get our coefficients by using R's inbuilt FFT.

coeffs = fft(newTangents)/length(newTangents)

We start by taking only the first 30 and now trying to reconstruct the original curve.

coeffs = coeffs[1:30]

We now want to go back from fft coefficients to fft parameters to go backwards.

backCoeffs = fftoToCoeffs(coeffs)

Now we can reconstruct the original curve.

reconstructedTangents = sapply(seq(0,2*pi,length.out=length(newTangents)),
      function(s) getTangentAtS(s,backCoeffs))

We can now look at the reconstructed tangents and compare them to the originals

plot(reconstructedTangents)
lines(reconstructedTangents,col="blue")

And now reconstruct the curve

with(tangentsToXY(reconstructedTangents), {
   plot(x, y,col=rainbow(length(newTangents))); 
   lines(x,y)
})

klapaukh/hangler documentation built on May 20, 2019, 11:04 a.m.