Here is my attempt to perform an FFT on a random signal with 2 tones in which I applied zero padding AFTER windowing.

(I did not apply zero padding before windowing because that would suggest that the zeros are part of the original signal which is not correct.)

The signal amplitude is around 3.5 but the FFT amplitudes are off significantly. I cannot seem to get the correct FFT amplitudes.

What am I missing?

enter image description here

    import numpy as np
    import matplotlib.pyplot as plt
    # Set the sampling frequency
    fs = 20000  # Hz
    # Generate a random time signal with 2 pure sine tones
    t = np.linspace(0, 1, int(fs))
    x = np.sin(2*np.pi*500*t) + np.sin(2*np.pi*900*t) + np.random.randn(len(t))*0.5
    # Compute the FFT of the signal
    X = np.fft.fft(x)
    # Compute the frequency vector
    freqs = np.fft.fftfreq(len(x), 1/fs)
    # Apply a window function to reduce spectral leakage
    window = np.hanning(len(x))
    x_windowed = x * window
    # make signal periodic by finding the next power of 2
    n_fft = 2 ** int(np.ceil(np.log2(len(t))))
    # pad the signal with zeros
    x_windowed_padded = np.pad(x_windowed, (0,  n_fft - len(t)), mode='constant')
    X_windowed_padded = np.fft.fft(x_windowed_padded)
    freqs_padded = np.fft.fftfreq(len(x_windowed_padded), 1/fs)
    # Plot the results
    fig, ax = plt.subplots(2, 2, figsize=(10, 6))
    ax[0, 0].plot(t, x)
    ax[0, 0].set_xlabel('Time (s)')
    ax[0, 0].set_ylabel('Amplitude')
    ax[0, 0].set_title('Original Signal')
    ax[0, 1].plot(freqs[:len(freqs)//2], np.abs(X)[:len(X)//2])
    ax[0, 1].set_xlabel('Frequency (Hz)')
    ax[0, 1].set_ylabel('Amplitude')
    ax[0, 1].set_title('FFT of Original Signal')
    ax[1, 0].plot(t, x_windowed)
    ax[1, 0].set_xlabel('Time (s)')
    ax[1, 0].set_ylabel('Amplitude')
    ax[1, 0].set_title('Windowed Signal')
    ax[1, 1].plot(freqs_padded[:len(freqs_padded)//2], 
    ax[1, 1].set_xlabel('Frequency (Hz)')
    ax[1, 1].set_ylabel('Amplitude')
    ax[1, 1].set_title('FFT of Windowed and Padded Signal')
  • $\begingroup$ Would you care to elaborate a little bit on what exactly your problem is? The amplitudes are off but by how much? Do you have any images to show the issue? $\endgroup$
    – ZaellixA
    Commented Mar 29, 2023 at 19:20
  • $\begingroup$ @ZaellixA: I added a picture. Shouldnt the fft amplitude be somewhat similar to that of the original signal.? $\endgroup$ Commented Mar 29, 2023 at 19:28
  • 2
    $\begingroup$ No, this is not the case. @Jdip has provided a nice answer with some code corrections too. I suggest you try that first. Furthermore, you could (and should if you ask me) have another look at the theory of DFT (and possibly the Fourier Transform and Fourier Series too). $\endgroup$
    – ZaellixA
    Commented Mar 29, 2023 at 20:42
  • $\begingroup$ @ZaellixA: do you have some recommended book for reading? thanks $\endgroup$ Commented Mar 30, 2023 at 7:24
  • 2
    $\begingroup$ Well, I have used "Digital Signal Processing - Principles, Algorithms and Applications" by Proakis & Manolakis (relevant chapters are 4, 7 and 8) as well as "The Scientist and Engineer's Guide to Digital Signal Processing" by Steven W. Smith (relevant chapters are 8, 9, 10, 11 and 12) [free online: dspguide.com/pdfbook.htm ]. I am sure other people could also provide more references. You should, at least briefly, look at those textbooks and decide which suits your "study style" the most. $\endgroup$
    – ZaellixA
    Commented Mar 30, 2023 at 10:36

2 Answers 2


If you want to see the original amplitudes in your DFT magnitude plot, you need to apply correct scaling:

Scale the results by $\sum_{k}{w_k}$, $w_k$ being the window, and multiply by $2$ to account for the contributions of data on the negative side of the spectrum that you are not plotting (as @OverLordGoldDragon correctly pointed out, this is a simplification, refer to his answer).

In the first case, your window is effectively rectangular ("no windowing"), so $\sum_{k}{w_k} = \sum_{k}{1}$ is just the length of the input signal.
In the second, just use np.sum to sum the hamming window:

ax[0, 1].plot(freqs[:len(freqs)//2], 2*np.abs(X)[:len(X)//2]/len(x))
ax[1, 1].plot(freqs_padded[:len(freqs_padded)//2], 

Alternatively, you can scale using the window mean (which is 1 for the first case). You’ll get the same magnitude for both, but not they won’t match the original amplitudes of course.

  • $\begingroup$ @OverLordGoldDragon but the OP is using fft, not rfft… does your comment still hold? $\endgroup$
    – Jdip
    Commented Mar 30, 2023 at 16:13
  • $\begingroup$ This is a fair answer if it acknowledges the DC/Nyquist simplification and addresses/clarifies my remark. $\endgroup$ Commented Apr 2, 2023 at 11:14
  • 1
    $\begingroup$ Edited accordingly $\endgroup$
    – Jdip
    Commented Apr 2, 2023 at 18:07
  • $\begingroup$ I celebrated a bit early - what I don't follow is "x2 since plot only positive". Adding negatives to the plot wouldn't change this. Maybe you mean something else but I don't know what it is. It's x2 due to analyticity scaling for real-valued signals (Hilbert). "Simplification" appears to understate the issue. $\endgroup$ Commented Apr 4, 2023 at 8:47
  • 1
    $\begingroup$ That is much better, and I think it better edited in, but I leave it to you. $\endgroup$ Commented Apr 4, 2023 at 16:05
  • Real-valued x: double non-DC and non-Nyquist bins
  • Complex-valued x: sum magnitudes of non-DC and non-Nyquist bins
  • Both: divide by sum(window)

This'll work well with simple examples of just sines. The real-valued case supposes you wish to read off signal's amplitudes from a plot of DFT, but in this case it's best to not show negative frequencies as it's duplicative (and hence in a sense incorrect).

In complex-valued case it'll be peak amplitude, since A.M. is likely. For a general complex signal, it's best to interpret positive and negative frequencies separately, as they're about as distinct as different frequencies - some visuals. In general time-frequency analysis should be favored - see e.g. STFT Amplitude Extraction.

Adapted to your code:

N = len(x)
M = len(X_windowed_padded)
X[1:N//2] *= 2
X_windowed_padded[1:M//2] *= 2
X /= N
X_windowed_padded /= sum(window)
freqs[N//2] *= -1
freqs_padded[M//2] *= -1

# ...
ax[0, 1].plot(freqs[:N//2 + 1], np.abs(X)[:N//2 + 1])
# ...
ax[1, 1].plot(freqs_padded[:M//2 + 1], np.abs(X_windowed_padded)[:M//2 + 1])

The *= -1 is to not confuse the plot, since by library convention Nyquist is negative.

enter image description here

Other remarks

No guarantees: the simple "window then FFT" won't work 100% of the time even with pure sines. Full list of conditions in this post ("Criteria demos").

Windowing order: doesn't matter. What may matter is how it's written in code - if hanning is longer, that's changing the window itself, not just the order of windowing.

Window mean: never actually do this for amplitude, energy, or power calculations. It implies every point of the window is weighed equally, which is false. If a formula says mean, it just happens to coincide with mean of window, when really the division by constant is cancelling something else. (So in this sense it can be "mean")

Code excerpt 1:

# make signal periodic by finding the next power of 2
n_fft = 2 ** int(np.ceil(np.log2(len(t))))
# pad the signal with zeros

"make the signal periodic" no. It's interpolating the spectrum.

Code excerpt 2:

ax[0, 1].plot(freqs[:len(freqs)//2], np.abs(X)[:len(X)//2])

That's missing Nyquist --> len(freqs)//2 + 1.

  • $\begingroup$ Thanks for the tips. Does the use of one window not capture the complete timehistory? Ie, would some sort of overlapping windows be required? $\endgroup$ Commented Apr 3, 2023 at 17:26
  • $\begingroup$ @shoggananna Yes, one window, in a sense, doesn't capture any time history: the time dimension is collapsed. $\endgroup$ Commented Apr 4, 2023 at 8:35

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