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Waves Phenomena/Fourier Methods

Workshop 18

Fast Fourier Transforms using Python

Reminder: Use matplotlib and numpy Python modules for plotting and numerical calculations respectively. Start your program with the following statement:

In [30]:
import matplotlib.pyplot as plt import numpy as np

Recap and introduction

A Fourier transform (FT) is used to calculate the frequency components present in a signal that varies in time or the spatial frequencies present in an image that varies in space. In the lectures the Fourier transform and the inverse Fourier transform have been defined as F(ω)=12π+f(t)eiωtdt,f(t)=12π+F(ω)eiωtdω. \begin{array}{rl} F(\omega) &= \frac{1}{\sqrt{2\pi}} \int_{-\infty}^{+\infty} f(t) e^{-i\omega t} {\rm d} t \,, \\ f(t) &= \frac{1}{\sqrt{2\pi}} \int_{-\infty}^{+\infty} F(\omega) e^{i\omega t} {\rm d} \omega \,. \end{array} The inverse FT takes the FT and recovers the original function.

We saw in Fourier 9 that for a signal that has a finite number of points sampled at discrete, evenly spaced intervals, we instead have the Discrete Fourier Transform (DFT) and its inverse transform Fk=n=0N1fnei2πnk/N   for 0kN1,fn=1Nk=0N1Fkei2πnk/N  for 0nN1. \begin{array}{rl} F_k &= \sum_{n=0}^{N-1} f_n e^{-i 2\pi n k /N} \ \ \ \mathrm{ for } \ 0 \le k \le N-1 \,, \\ f_n &= \frac{1}{N} \sum_{k=0}^{N-1} F_k e^{ i 2\pi n k /N} \ \ \mathrm{for} \ 0 \le n \le N-1 \,. \end{array}

If you have NN data points, fnf_{n}, separated by Δt\Delta t, between t=0t=0 and (N1)Δt(N-1)\Delta t (i.e. t=nΔtt=n \Delta t with n=0,...,N1n=0,...,N-1) the discrete Fourier transform has NN data points, FkF_{k}, corresponding to frequencies ω=kΔω\omega= k \Delta \omega with k=0,...,N1k=0,...,N-1 and Δω=2π/(NΔt)\Delta \omega=2 \pi/(N \Delta t). The Nyquist frequency is defined as ωc=π/Δt\omega_{c}= \pi/\Delta t, and has k=kc=N/2k=k_{\rm c}= N/2. It determines the maximum frequency that you can detect in your signal.

The indices of a numpy array must start at 0, so the first data point f0f_0 is represented by the variable f[1]. Similarly the zero frequency component of the DFT F0F_0 is the variable F[0]. Therefore the definitions of the DFT and inverse DFT in terms of numpy arrays become

F[k]=n=0N1f(n)np.exp(1j2πkn/N),f[n]=1/Nk=0N1F[k]np.exp(1j2πkn/N). \begin{array}{rl} { \tt F[k]} &= { \tt \sum_{n=0}^{N-1} f(n)* np. exp(-1j*2*\pi*k*n/N)} \,, \\ { \tt f[n]} &= { \tt 1/N*\sum_{k=0}^{N-1} F[k]* np.exp(1j*2*\pi*k*n/N)} \,. \end{array}

In Python's numpy array F[0:N] the element F[0] contains the zero-frequency term. Then F[1:N/2] contains the positive-frequency terms, and F[(N/2+1):] contains the negative-frequency terms, in order of decreasingly negative frequency. For an even number of input points N, F[N/2] represents both positive and negative Nyquist frequency. For an odd number of input points N, F[(N-1)/2] contains the largest positive frequency, while F[(N+1)/2] contains the largest negative frequency.

The DFT will almost always be complex. Therefore we usually need to plot the modulus or the modulus squared of the DFT (which is often referred to as the power spectrum).

Numerical techniques have been developed to calculate discrete Fourier transforms. The most commonly used algorithm is known as the Fast Fourier Transform or FFT. Here we will be using the FFT without studying its inner workings[^1]. Python's numpy.fft module has procedures for optimising the way it does the calculations depending on the size of the data sample. The original FFT algorithm was designed to work when the number of data points is equal to an integer power of 2. Conventional wisdom therefore states that, in order for the FFT to be calculated quickly, you should use a number of data points that is an integer power of 2. Very efficient FFT solvers have since been developed for powers of 3, 5 and 7. If the number of data points is a prime number, however, the calculation will be rather slow! If you are going to be doing a lot of FFTs (for instance in project work) you should search for the most efficient value of NN by direct timing (i.e. varying NN and seeing how long your code takes to run).

[^1]: If you're interested in how it works, see Appendix 5.A of the Fourier summary notes or the chapter on FFTs in the "Numerical methods in ..." series of textbooks by Press et al.

The numpy's FFT

The FFT of a vector x can be calculated simply using the numpy's function fft.fft:

import numpy as np y = np.fft.fft(x) y = np.fft.fft(x,n) y = np.fft.fft(x,n, axis=1)

The vector y is the discrete Fourier transform of the vector x, computed using a fast Fourier transform algorithm. If x is a matrix then y is the FFT of each column of the matrix. If a second parameter, n, is specified then y is the n-point FFT, which means that n data points are used to calculate the transform. If len(x)<n then np.fft.fft pads x with trailing zeros to reach a length of n. If len(x)>n then the data is truncated to use only the first n points. If x is a multidimensional array, the paramater axis specifies the dimension along which the FFT is applied.

The inverse Fourier transform can be calculated using np.fft.ifft which syntax is identical to that of np.fft.fft.

y = np.fft.ifft(x) y = np.fft.ifft(x,n) y = np.fft.ifft(x,n, axis=1)

Question 1

i) Generate 0.6s0.6 \, {\rm s} of a signal which is equal to the sum of two sinusoids with frequencies 50Hz50 \, {\rm Hz} and 120Hz120 \, {\rm Hz} , sampled at a rate 1000Hz1000 \, {\rm Hz}. Plot the first fifty points of the signal using plt.step.

In [6]:
import numpy as np import matplotlib.pyplot as plt duration = 0.6 dt=0.001 timestamps=np.arange(0, duration, dt) freq1=50 freq2=120 sin1=np.sin(2*np.pi*freq1*timestamps) sin2=np.sin(2*np.pi*freq2*timestamps) sintot=sin1+sin2 plt.plot(timestamps, sintot)
[<matplotlib.lines.Line2D at 0x7fae65b82910>]

ii) Calculate the 512 point FFT of this signal and plot the real part of the FFT versus array index. Notice that (as discussed in "Recap and Introduction" ) the data is symmetric about the halfway point. All the useful frequency components are stored in the first 256 points. The last 256 points are a mirror image caused by the finite sampling frequency.

In [8]:
N=512 y=sintot Ft=np.fft.fft(y, N) RFt=np.real(Ft) plt.figure(2,figsize=(8,6)) ax2=plt.axes() vec=np.arange(0,512) plt.plot(vec,RFt) plt.title('real part of FFT against index')
Text(0.5, 1.0, 'real part of FFT against index')

iii) The power spectrum is a measurement of the energy at each frequency. If Y is the Fourier transform, then the power spectrum is defined as

Pyy = np.real(Y*np.conj(Y)/N)

where np.conj(Y) is the complex conjugate of Y and N is the number of frequencies (which is equal to the number of data samples). Note that for plotting result of array multiplication should be recast as an array of real numbers.

We're going to plot the first 256 points of the power spectrum as a function of frequency. The spacing of the angular frequencies making up the Fourier transform is Δω=2π/(NΔt)\Delta \omega = 2 \pi/(N \Delta t). The spacing of the frequencies, ff, is therefore Δf=1/(NΔt)\Delta f = 1/(N \Delta t ). Δt\Delta t, the spacing of the data points, is equal to the inverse of the sampling rate, which in this case is 1000Hz1000 \, {\rm Hz}. Therefore we want:

rate=1000 N=512 f = rate*np.arange(0,256,1)/N; plt.plot(f, Pyy[0:256]);

You should see that the power spectrum peaks at the input frequencies (50Hz50 \, {\rm Hz} and 120Hz120 \, {\rm Hz}).

Note that to increase frequency resolution (i.e. to see high frequency variations) you need lots of points in the FFT, since the sampling frequency determines the maximum frequency that can be detected in the FFT.

In [ ]:

Question 2

i) Define and plot a vector that represents the light transmitted through a 1d slit (i.e. a top-hat aperture function). As mentioned above, it's a good idea to make NN, the number of samples which your vector contains, an integer power of 2.

In [11]:
)''' n=1
--------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-11-a05db1cc95be> in <module> 9 np.append(tophat, slit) 10 np.append(tophat, w) ---> 11 plt.plot(length, tophat) /usr/local/lib/python3.8/dist-packages/matplotlib/pyplot.py in plot(scalex, scaley, data, *args, **kwargs) 2838 @_copy_docstring_and_deprecators(Axes.plot) 2839 def plot(*args, scalex=True, scaley=True, data=None, **kwargs): -> 2840 return gca().plot( 2841 *args, scalex=scalex, scaley=scaley, 2842 **({"data": data} if data is not None else {}), **kwargs) /usr/local/lib/python3.8/dist-packages/matplotlib/axes/_axes.py in plot(self, scalex, scaley, data, *args, **kwargs) 1741 """ 1742 kwargs = cbook.normalize_kwargs(kwargs, mlines.Line2D) -> 1743 lines = [*self._get_lines(*args, data=data, **kwargs)] 1744 for line in lines: 1745 self.add_line(line) /usr/local/lib/python3.8/dist-packages/matplotlib/axes/_base.py in __call__(self, data, *args, **kwargs) 271 this += args[0], 272 args = args[1:] --> 273 yield from self._plot_args(this, kwargs) 274 275 def get_next_color(self): /usr/local/lib/python3.8/dist-packages/matplotlib/axes/_base.py in _plot_args(self, tup, kwargs) 397 398 if x.shape[0] != y.shape[0]: --> 399 raise ValueError(f"x and y must have same first dimension, but " 400 f"have shapes {x.shape} and {y.shape}") 401 if x.ndim > 2 or y.ndim > 2: ValueError: x and y must have same first dimension, but have shapes (2000,) and (990,)

ii) The Fraunhofer diffraction pattern is proportional to the square of the Fourier transform of the aperture function.

Use np.fft.fft to find the Fraunhofer diffraction pattern of your 1d slit and plot the result. It should be the square of a sinc(x)\text{sinc}(x) function centred at zero spatial frequency.

In this case we're taking the Fourier transform of a spatial function (rather than a function of time), therefore the Fourier transform is a function of wavenumber or spatial frequency, kk (rather than angular frequency, ω\omega). In this case if LL is the spatial length of the vector, then the FFT will have NN equally spaced spatial frequencies between k=0k=0 and k=2π(N1)/Lk=2 \pi (N-1)/L, where NN is the number of samples that your vector from part i) contains.

In [ ]:

iii) The command np.fft.fftshift reorganizes the FFT so that zero frequency is placed in the centre of the vector rather than the first element. Use np.fft.fftshift and make a plot with the sinc function centred properly.

You'll need to manually shift your vector of frequencies so that its centered at zero frequency too, i.e.:

kx = np.arange(0,n,1)*(2*np.pi)/L # spatial frequencies kxny = (n/2)*(2*np.pi)/L # Nyquist frequency kxs = kx - kxny # shifted frequencies

where L is the length of your original vector representing the light transmitted through a 1d slit.

In [ ]:

iv) Change the width of the top hat function and see how the width of the sinc function changes. You should find that a wider slit leads to a narrower sinc function.

In [ ]:

Convolution

We saw in Fourier 8 that mathematically the convolution of two functions f(x)f(x) and g(x)g(x) is defined as h(x)=f(x)g(xx)dx.h(x^{\prime}) = \int_{-\infty}^{\infty} f(x) g(x^{\prime}-x) {\rm d} x \,. This can be used to model the situation where an intrinsic signal is 'blurred' by some aspect of the measurement process. If the intrinsic signal is a set of delta functions, but the measuring instrument has a response that is gaussian, the result will be the sum of gaussians centred at the positions of the delta functions. The intuitive interpretation of convolution is that if one function is slid across the other, then at each position the convolution is the area under the product of the functions.

With discrete data the convolution becomes a sum: h(k)=jf(j)g(kj), h(k) = \sum_j f(j) g(k-j), where the sum extends over all valid indices.

drawing

The diagram schematically shows the process of convolving three delta-functions (solid lines) with a gaussian (the dotted line). The left column shows the two functions and the right column their convolution. The top panels show the gaussian positioned at the leftmost offset, where just one point overlaps. As the gaussian is moved to the right more points overlap, so the sum extends over the points between the o and the x. When the gaussian passes over the delta-functions, the convolution is large. Elsewhere it is small. The last point is when the gaussian is at the furthest right, with just one point overlapping. You can see from this that the convolved array is bigger than the individual arrays. If the original arrays have N points, then the convolved array will have 2*N-1 points. In practice we are usually interested in the central N points of the convolved array.

The Python function to convolve two functions is np.convolve . This function requires a vector for ff and another for gg, and returns a vector hh which has elements h[k].

Question 3

i) Generate and plot 10s10 \, {\rm s} of a signal sampled at 100Hz100 \, {\rm Hz} so that the signal is zero everywhere, except for three points at time t=2.5,5.0t=2.5, 5.0 and 7.5s7.5 \, {\rm s} which are set to 11. This is the numerical equivalent to three delta-functions.

Also generate a gaussian with σ=0.1s\sigma = 0.1 \, {\rm s} for tt between 5s-5 \, {\rm s} and +5s+5 \, {\rm s} using the same time steps.

In [ ]:
t=10s dt=0.01 f=np.zeros((t*dt)) f[np.array([250,500,750])]=1 s=0.1 g=np.exp((-t1**2)/(2*s**2))

ii) Use the np.convolve function to calculate the convolution of the delta-function signal and the gaussian. The np.convolve function does the entire set of summations for all values of kk in one go, and returns an array containing the convolved function hh. Plot the convolution.

In [ ]:
convf=np.covolve(f) plt.plot(f, convf)

Convolution Theorem

The convolution theorem says that the Fourier transform of the convolution of ff and gg is the product of the Fourier transforms of ff and gg. For discrete FTs FT[h]=FT[f]FT[g]FT[h] = FT[f] FT[g] and so h=IFT[FT[f]FT[g]]h = IFT[ FT[f] FT[g]] .

Calculating FTs and IFTs is quicker than calculating a convolution directly. Therefore we can use the convolution theorem (and np.fft.fft and np.fft.ifft to efficiently calculate a convolution.

Question 4

i) Use np.fft.fft and np.fft.ifft to calculate the convolution of the delta-function signal and gaussian from Question 3, and compare with the result you found in Question 3 using np.convolve .

Remember that np.fft.fft returns an array with the zero frequency component of the FT as the first element. The np.convolve function returns an array with the zero frequency component in the middle. Therefore to compare your results you'll need to use the np.fft.fftshift command as in Question 2iii).

In [ ]:

Two dimensional Fourier Transforms

In the previous sections you calculated some 1d Fourier transforms by generating 1d vectors of data and using the np.fft.fft command. In this section we will extend this to 2d data. The command to calculate a 2d FFT is np.fft.fft2 , and for the 2d inverse transform np.fft.fft2 .

work in exactly the same way as np.fft.fft and np.fft.ifft, but on a two-dimensional matrix rather than a vector.

There are also Fourier transform commands for data that is in three or more dimensional arrays. The commands are np.fft.fftn and np.fft.ifftn where n the number of dimensions.

Question 5

i) Create a 2d matrix that represents the intensity of light passing through a square aperture, and calculate the resulting Fraunhofer diffraction pattern (c.f. Question 2).

ii) Plot the intensity of the diffraction pattern using plt.imshow. You can show low level detail as well as the main peak by plotting the logarithm of one plus the intensity.

In [15]:
n=1024 L=2 x=np.linspace(-L/2, L/2, n) y=np.linspace(-L/2, L/2, n) [xx, yy]=np.meshgrid(x,y) a=0.018 light=np.where((np.abs(xx)<a) & (np.abs(yy)<a),1,0) plt.plot(xx, yy, light)
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