SVD - Matrix transformation Python

Question

Trying to compute SVD in Python to find the most significant elements of a spectrum and created a matrix just containing the most significant parts.

In python I have:

u,s,v = linalg.svd(Pxx, full_matrices=True)

This gives 3 matrices back; where "s" contains the magnitudes that corresponds to u, v.

In order to construct a new matrix, containing all of the significant parts of the signal, I need to capture the highest values in "s" and match them with the columns in "u" and "v" and the resulting matrix should give me the most significant part of the data.

The problem is I don't know how I would do this in Python, for example, how do I find the highest numbers in "s" and select the columns in "u" and "v" in order to create a new matrix?

(I'm new to Python and numpy) so any help would be greatly appreciated

Edit:

import wave, struct, numpy as np, matplotlib.mlab as mlab, pylab as pl
from scipy import linalg, mat, dot;
def wavToArr(wavefile):
    w = wave.open(wavefile,"rb")
    p = w.getparams()
    s = w.readframes(p[3])
    w.close()
    sd = np.fromstring(s, np.int16)
    return sd,p

def wavToSpec(wavefile,log=False,norm=False):
    wavArr,wavParams = wavToArr(wavefile)
    print wavParams
    return  mlab.specgram(wavArr, NFFT=256,Fs=wavParams[2],detrend=mlab.detrend_mean,window=mlab.window_hanning,noverlap=128,sides='onesided',scale_by_freq=True)

wavArr,wavParams = wavToArr("wavBat1.wav")

Pxx, freqs, bins = wavToSpec("wavBat1.wav")
Pxx += 0.0001

U, s, Vh = linalg.svd(Pxx, full_matrices=True)
assert np.allclose(Pxx, np.dot(U, np.dot(np.diag(s), Vh)))

s[2:] = 0
new_a = np.dot(U, np.dot(np.diag(s), Vh))
print(new_a)

Answer 1

linalg.svd returns s in descending order. So to select the n highest numbers in s, you'd simply form

s[:n]

If you set the smaller values of s to zero,

s[n:] = 0

then matrix multiplication would take care of "selecting" the appropriate columns of U and V.

For example,

import numpy as np
LA = np.linalg

a = np.array([[1, 3, 4], [5, 6, 9], [1, 2, 3], [7, 6, 8]])
print(a)
# [[1 3 4]
#  [5 6 9]
#  [1 2 3]
#  [7 6 8]]
U, s, Vh = LA.svd(a, full_matrices=False)
assert np.allclose(a, np.dot(U, np.dot(np.diag(s), Vh)))

s[2:] = 0
new_a = np.dot(U, np.dot(np.diag(s), Vh))
print(new_a)
# [[ 1.02206755  2.77276308  4.14651336]
#  [ 4.9803474   6.20236935  8.86952026]
#  [ 0.99786077  2.02202837  2.98579698]
#  [ 7.01104783  5.88623677  8.07335002]]

---

Given the data here,

import numpy as np
import scipy.linalg as SL
import matplotlib.pyplot as plt

Pxx = np.genfromtxt('mBtasJLD.txt')
U, s, Vh = SL.svd(Pxx, full_matrices=False)
assert np.allclose(Pxx, np.dot(U, np.dot(np.diag(s), Vh)))

s[2:] = 0
new_a = np.dot(U, np.dot(np.diag(s), Vh))
print(new_a)
plt.plot(new_a)
plt.show()

produces