Standard deviation from center of mass along Numpy array axis - python

I am trying to find a well-performing way to calculate the standard deviation from the center of mass/gravity along an axis of a Numpy array.
In formula this is (sorry for the misalignment):
The best I could come up with is this:
def weighted_com(A, axis, weights):
average = np.average(A, axis=axis, weights=weights)
return average * weights.sum() / A.sum(axis=axis).astype(float)
def weighted_std(A, axis):
weights = np.arange(A.shape[axis])
w1com2 = weighted_com(A, axis, weights)**2
w2com1 = weighted_com(A, axis, weights**2)
return np.sqrt(w2com1 - w1com2)
In weighted_com, I need to correct the normalization from sum of weights to sum of values (which is an ugly workaround, I guess). weighted_std is probably fine.
To avoid the XY problem, I still ask for what I actually want, (a better weighted_std) instead of a better version of my weighted_com.
The .astype(float) is a safety measure as I'll apply this to histograms containing ints, which caused problems due to integer division when not in Python 3 or when from __future__ import division is not active.

You want to take the mean, variance and standard deviation of the vector [1, 2, 3, ..., n] — where n is the dimension of the input matrix A along the axis of interest —, with weights given by the matrix A itself.
For concreteness, say you want to consider these center-of-mass statistics along the vertical axis (axis=0) — this is what corresponds to the formulas you wrote. For a fixed column j, you would do
n = A.shape[0]
r = np.arange(1, n+1)
mu = np.average(r, weights=A[:,j])
var = np.average(r**2, weights=A[:,j]) - mu**2
std = np.sqrt(var)
In order to put all of the computations for the different columns together, you have to stack together a bunch of copies of r (one per column) to form a matrix (that I have called R in the code below). With a bit of care, you can make things work for both axis=0 and axis=1.
import numpy as np
def com_stats(A, axis=0):
A = A.astype(float) # if you are worried about int vs. float
n = A.shape[axis]
m = A.shape[(axis-1)%2]
r = np.arange(1, n+1)
R = np.vstack([r] * m)
if axis == 0:
R = R.T
mu = np.average(R, axis=axis, weights=A)
var = np.average(R**2, axis=axis, weights=A) - mu**2
std = np.sqrt(var)
return mu, var, std
For example,
A = np.array([[1, 1, 0], [1, 2, 1], [1, 1, 1]])
print(A)
# [[1 1 0]
# [1 2 1]
# [1 1 1]]
print(com_stats(A))
# (array([ 2. , 2. , 2.5]), # centre-of-mass mean by column
# array([ 0.66666667, 0.5 , 0.25 ]), # centre-of-mass variance by column
# array([ 0.81649658, 0.70710678, 0.5 ])) # centre-of-mass std by column
EDIT:
One can avoid creating in-memory copies of r to build R by using numpy.lib.stride_tricks: swap the line
R = np.vstack([r] * m)
above with
from numpy.lib.stride_tricks import as_strided
R = as_strided(r, strides=(0, r.itemsize), shape=(m, n))
The resulting R is a (strided) ndarray whose underlying array is the same as r's — absolutely no copying of any values occurs.
from numpy.lib.stride_tricks import as_strided
FMT = '''\
Shape: {}
Strides: {}
Position in memory: {}
Size in memory (bytes): {}
'''
def find_base_nbytes(obj):
if obj.base is not None:
return find_base_nbytes(obj.base)
return obj.nbytes
def stats(obj):
return FMT.format(obj.shape,
obj.strides,
obj.__array_interface__['data'][0],
find_base_nbytes(obj))
n=10
m=1000
r = np.arange(1, n+1)
R = np.vstack([r] * m)
S = as_strided(r, strides=(0, r.itemsize), shape=(m, n))
print(stats(r))
print(stats(R))
print(stats(S))
Output:
Shape: (10,)
Strides: (8,)
Position in memory: 4299744576
Size in memory (bytes): 80
Shape: (1000, 10)
Strides: (80, 8)
Position in memory: 4304464384
Size in memory (bytes): 80000
Shape: (1000, 10)
Strides: (0, 8)
Position in memory: 4299744576
Size in memory (bytes): 80
Credit to this SO answer and this one for explanations on how to get the memory address and size of the underlying array of a strided ndarray.

Related

Building N-th order Markovian transition matrix from a given sequence

I am trying to create a function which can transform a given input sequence to a transition matrix of the requested order. I found an implementation for the first-order Markovian transition matrix.
Now, I want to be able to come up with a solution which can calculate 2nd and 3rd order transition matrices.
Example of the 1st order matrix implementation:
import numpy as np
# sequence with 3 states -> 0, 1, 2
a = [0, 1, 0, 0, 0, 2, 2, 1, 1, 1, 0, 0, 0, 0, 0, 1, 2, 2, 2, 0, 0, 2]
def transition_matrix_first_order(seq):
M = np.full((3, 3), fill_value = 1/3, dtype= np.float64)
for (i,j) in zip(seq, seq[1:]):
M[i, j] += 1
M = M / M.sum(axis = 1, keepdims = True)
return M
print(transition_matrix_first_order(a))
Which gives me this:
[[0.61111111 0.19444444 0.19444444]
[0.38888889 0.38888889 0.22222222]
[0.22222222 0.22222222 0.55555556]]
When making a 2nd order matrix, it should have unique_state_count ** order rows and unique_state_count columns. In the example above, I have 3 unique states, so the matrix will have 9x3 structure.
Desirable function sample:
cal_tr_matrix(seq, unique_state_count, order)
I think you have a slight misunderstanding about the Markov chains and their transition matrices.
First of all, the estimated transition matrix your function produces is unfortunately not correct. Why? Let's refresh.
A discrete Markov chain in discrete time with N different states has a transition matrix P of size N x N, where a (i, j) element is P(X_1=j|X_0=i), i.e. the probability of transition from state i to state j in a single time step.
Now a transition matrix of order n, denoted P^{n}is once again a matrix of size N x N where a (i, j) element is P(X_n=j|X_0=i), i.e. the probability of transition from state i to state j in n time steps.
A wonderful result says: P^{n} = P^n, i.e. taking n powers of single-step transition matrix gives you the n-step transition matrix.
Now with this recap, all that is needed is to estimate P from the given sequence, then to estimate P^{n} one can just use the already estimated P and take a n-th power of the matrix. So how to estimate the matrix P? Well if we denote N_{ij} the number of observations of transition from state i to state j and N_{i*} the number of observations being in state i, then P_{ij} = N_{ij} / N_{i*}.
Overall here in Python:
import numpy as np
def transition_matrix(arr, n=1):
""""
Computes the transition matrix from Markov chain sequence of order `n`.
:param arr: Discrete Markov chain state sequence in discrete time with states in 0, ..., N
:param n: Transition order
"""
M = np.zeros(shape=(max(arr) + 1, max(arr) + 1))
for (i, j) in zip(arr, arr[1:]):
M[i, j] += 1
T = (M.T / M.sum(axis=1)).T
return np.linalg.matrix_power(T, n)
transition_matrix(arr=a, n=1)
>>> array([[0.63636364, 0.18181818, 0.18181818],
>>> [0.4 , 0.4 , 0.2 ],
>>> [0.2 , 0.2 , 0.6 ]])
transition_matrix(arr=a, n=2)
>>> array([[0.51404959, 0.22479339, 0.26115702],
>>> [0.45454545, 0.27272727, 0.27272727],
>>> [0.32727273, 0.23636364, 0.43636364]])
transition_matrix(arr=a, n=3)
>>> array([[0.46927122, 0.23561232, 0.29511645],
>>> [0.45289256, 0.24628099, 0.30082645],
>>> [0.39008264, 0.24132231, 0.36859504]])
Interesting thing, when you set the order n to a fairly high number, the higher and higher powers of the P matrix seem to converge to some very specific values. That's known as stationary/invariant distribution of the Markov chain and it gives a very good indication of how the chain behaves over a long period of time/transitions. Also:
P = transition_matrix(a, 1)
P111 = transition_matrix(a, 111)
print(P)
print(P111.dot(P))
EDIT: Now to the tweaked solution based on your comment, I'd suggest to have higher dimensional matrices for higher orders instead of exploding the number of rows. One way would be like this:
def cal_tr_matrix(arr, order):
_shape = (max(arr) + 1,) * (order + 1)
M = np.zeros(_shape)
for _ind in zip(*[arr[_x:] for _x in range(order + 1)]):
M[_ind] += 1
return M
res1 = cal_tr_matrix(a, 1)
res2 = cal_tr_matrix(a, 2)
Now the element res1[i, j] says how many times transition i->j happened, while the element res2[i, j, k] says how many times transition i->j->k happened.

Softmax function of a numpy array by row

I am trying to apply a softmax function to a numpy array. But I am not getting the desired results. This is the code I have tried:
import numpy as np
x = np.array([[1001,1002],[3,4]])
softmax = np.exp(x - np.max(x))/(np.sum(np.exp(x - np.max(x)))
print softmax
I think the x - np.max(x) code is not subtracting the max of each row. The max needs to be subtracted from x to prevent very large numbers.
This is supposed to output
np.array([
[0.26894142, 0.73105858],
[0.26894142, 0.73105858]])
But I am getting:
np.array([
[0.26894142, 0.73105858],
[0, 0]])
A convenient way to keep the axes that are consumed by "reduce" operations such as max or sum is the keepdims keyword:
mx = np.max(x, axis=-1, keepdims=True)
mx
# array([[1002],
# [ 4]])
x - mx
# array([[-1, 0],
# [-1, 0]])
numerator = np.exp(x - mx)
denominator = np.sum(numerator, axis=-1, keepdims=True)
denominator
# array([[ 1.36787944],
# [ 1.36787944]])
numerator/denominator
# array([[ 0.26894142, 0.73105858],
[ 0.26894142, 0.73105858]])
My 5-liner (which uses scipy logsumexp for the tricky bits):
def softmax(a, axis=None):
"""
Computes exp(a)/sumexp(a); relies on scipy logsumexp implementation.
:param a: ndarray/tensor
:param axis: axis to sum over; default (None) sums over everything
"""
from scipy.special import logsumexp
lse = logsumexp(a, axis=axis) # this reduces along axis
if axis is not None:
lse = np.expand_dims(lse, axis) # restore that axis for subtraction
return np.exp(a - lse)
You may have to use from scipy.misc import logsumexp if you have an older scipy version.
EDIT. As of version 1.2.0, scipy includes softmax as a special function:
https://scipy.github.io/devdocs/generated/scipy.special.softmax.html
I wrote a very general softmax function operating over an arbitrary axis, including the tricky max subtraction bit. The function is below, and I wrote a blog post about it here.
def softmax(X, theta = 1.0, axis = None):
"""
Compute the softmax of each element along an axis of X.
Parameters
----------
X: ND-Array. Probably should be floats.
theta (optional): float parameter, used as a multiplier
prior to exponentiation. Default = 1.0
axis (optional): axis to compute values along. Default is the
first non-singleton axis.
Returns an array the same size as X. The result will sum to 1
along the specified axis.
"""
# make X at least 2d
y = np.atleast_2d(X)
# find axis
if axis is None:
axis = next(j[0] for j in enumerate(y.shape) if j[1] > 1)
# multiply y against the theta parameter,
y = y * float(theta)
# subtract the max for numerical stability
y = y - np.expand_dims(np.max(y, axis = axis), axis)
# exponentiate y
y = np.exp(y)
# take the sum along the specified axis
ax_sum = np.expand_dims(np.sum(y, axis = axis), axis)
# finally: divide elementwise
p = y / ax_sum
# flatten if X was 1D
if len(X.shape) == 1: p = p.flatten()
return p
The x - np.max(x) code is not doing row-wise subtraction.
Let's do it step-wise. First we will make a 'maxes' array by tiling or making a copy of the column:
maxes = np.tile(np.max(x,1), (2,1)).T
This will create a 2X2 matrix which will correspond to the maxes for each row by making a duplicate column(tile). After this you can do:
x = np.exp(x - maxes)/(np.sum(np.exp(x - maxes), axis = 1))
You should get your result with this. The axis = 1 is for the row-wise softmax you mentioned in the heading of your answer. Hope this helps.
How about this?
For taking max along the rows just specify the argument as axis=1 and then convert the result as a column vector(but a 2D array actually) using np.newaxis/None.
In [40]: x
Out[40]:
array([[1001, 1002],
[ 3, 4]])
In [41]: z = x - np.max(x, axis=1)[:, np.newaxis]
In [42]: z
Out[42]:
array([[-1, 0],
[-1, 0]])
In [44]: softmax = np.exp(z) / np.sum(np.exp(z), axis=1)[:, np.newaxis]
In [45]: softmax
Out[45]:
array([[ 0.26894142, 0.73105858],
[ 0.26894142, 0.73105858]])
In the last step, again when you take sum just specify the argument axis=1 to sum it along the rows.

numpy ND array: take index'ed elements along a certain axis (ND choose)

I obtain indices along a certain axis. For example like this with 2D and axis=-1 :
>>> axis = -1
>>> a = rand(5, 3) - 0.5; a
array([[ 0.49970414, -0.14251437, 0.2881351 ],
[ 0.3280437 , 0.33766112, 0.4263927 ],
[ 0.37377502, 0.05392274, -0.4647834 ],
[-0.09461463, -0.25347861, -0.29381079],
[-0.09642799, 0.15729681, 0.06048399]])
>>> axisinds = a.__abs__().argmax(axis); axisinds
array([0, 2, 2, 2, 1])
Now how can I reduce the array by 1 dimension by taking the indexed elements along that axis?
For 2D and axis=-1 it could be done like this (in order to get the absolute max'es of each row the example array):
>>> a[arange(len(axisinds)), axisinds]
array([ 0.49970414, 0.4263927 , -0.4647834 , -0.29381079, 0.15729681])
But this is very special and limited to 1 or 0 result dimensions.
How for any ndim and axis ?
Now I found a simple solution myself:
def choose_axis(inds, a, axis=-1):
return np.choose(inds, np.rollaxis(a, axis))
>>> choose_axis(axisinds, a, -1)
array([ 0.49970414, 0.4263927 , -0.4647834 , -0.29381079, 0.15729681])
Edit: However this approach turned out to be limited to max 31 elements in the axis direction (32bit?) - because of the (undocumented) limitation of np.choose. In many cases this is ok.
Yet this is an
Unlimited method:
def choose_axis(inds, a, axis=-1):
# handles any number & size of dimensions, and any axis
if (axis + 1) % a.ndim: # move axis to last dim
a = np.moveaxis(a, axis, -1) # = np.rollaxis(a, axis, a.ndim)
shape = a.shape
a = a.reshape(-1, shape[-1]) # 2D
a = a[np.arange(inds.size), inds.ravel()] # effective reduction
return a.reshape(shape[:-1])
Thus an ND absolute min example can be done like:
def absminND(a, axis=-1):
inds = a.__abs__().argmin(axis)
if axis is None:
return a.ravel()[inds]
return choose_axis(inds, a)

Compute pairwise distance in a batch without replicating tensor in Tensorflow?

I want to compute the pairwise square distance of a batch of feature in Tensorflow. I have a simple implementation using + and * operations by
tiling the original tensor :
def pairwise_l2_norm2(x, y, scope=None):
with tf.op_scope([x, y], scope, 'pairwise_l2_norm2'):
size_x = tf.shape(x)[0]
size_y = tf.shape(y)[0]
xx = tf.expand_dims(x, -1)
xx = tf.tile(xx, tf.pack([1, 1, size_y]))
yy = tf.expand_dims(y, -1)
yy = tf.tile(yy, tf.pack([1, 1, size_x]))
yy = tf.transpose(yy, perm=[2, 1, 0])
diff = tf.sub(xx, yy)
square_diff = tf.square(diff)
square_dist = tf.reduce_sum(square_diff, 1)
return square_dist
This function takes as input two matrices of size (m,d) and (n,d) and compute the squared distance between each row vector. The output is a matrix of size (m,n) with element 'd_ij = dist(x_i, y_j)'.
The problem is that I have a large batch and high dim features 'm, n, d' replicating the tensor consume a lot of memory.
I'm looking for another way to implement this without increasing the memory usage and just only store the final distance tensor. Kind of double looping the original tensor.
You can use some linear algebra to turn it into matrix ops. Note that what you need matrix D where a[i] is the ith row of your original matrix and
D[i,j] = (a[i]-a[j])(a[i]-a[j])'
You can rewrite that into
D[i,j] = r[i] - 2 a[i]a[j]' + r[j]
Where r[i] is squared norm of ith row of the original matrix.
In a system that supports standard broadcasting rules you can treat r as a column vector and write D as
D = r - 2 A A' + r'
In TensorFlow you could write this as
A = tf.constant([[1, 1], [2, 2], [3, 3]])
r = tf.reduce_sum(A*A, 1)
# turn r into column vector
r = tf.reshape(r, [-1, 1])
D = r - 2*tf.matmul(A, tf.transpose(A)) + tf.transpose(r)
sess = tf.Session()
sess.run(D)
result
array([[0, 2, 8],
[2, 0, 2],
[8, 2, 0]], dtype=int32)
Using squared_difference:
def squared_dist(A):
expanded_a = tf.expand_dims(A, 1)
expanded_b = tf.expand_dims(A, 0)
distances = tf.reduce_sum(tf.squared_difference(expanded_a, expanded_b), 2)
return distances
One thing I noticed is that this solution using tf.squared_difference gives me out of memory (OOM) for very large vectors, while the approach by #YaroslavBulatov doesn't. So, I think decomposing the operation yields a smaller memory footprint (which I thought squared_difference would handle better under the hood).
Here is a more general solution for two tensors of coordinates A and B:
def squared_dist(A, B):
assert A.shape.as_list() == B.shape.as_list()
row_norms_A = tf.reduce_sum(tf.square(A), axis=1)
row_norms_A = tf.reshape(row_norms_A, [-1, 1]) # Column vector.
row_norms_B = tf.reduce_sum(tf.square(B), axis=1)
row_norms_B = tf.reshape(row_norms_B, [1, -1]) # Row vector.
return row_norms_A - 2 * tf.matmul(A, tf.transpose(B)) + row_norms_B
Note that this is the square distance. If you want to change this to the Euclidean distance, perform a tf.sqrt on the result. If you want to do that, don't forget to add a small constant to compensate for the floating point instabilities: dist = tf.sqrt(squared_dist(A, B) + 1e-6).
If you want compute other method , then change the order of the tf modules.
def compute_euclidean_distance(x, y):
size_x = x.shape.dims[0]
size_y = y.shape.dims[0]
for i in range(size_x):
tile_one = tf.reshape(tf.tile(x[i], [size_y]), [size_y, -1])
eu_one = tf.expand_dims(tf.sqrt(tf.reduce_sum(tf.pow(tf.subtract(tile_one, y), 2), axis=1)), axis=0)
if i == 0:
d = eu_one
else:
d = tf.concat([d, eu_one], axis=0)
return d

Partial convolution / correlation with numpy [duplicate]

I am learning numpy/scipy, coming from a MATLAB background. The xcorr function in Matlab has an optional argument "maxlag" that limits the lag range from –maxlag to maxlag. This is very useful if you are looking at the cross-correlation between two very long time series but are only interested in the correlation within a certain time range. The performance increases are enormous considering that cross-correlation is incredibly expensive to compute.
In numpy/scipy it seems there are several options for computing cross-correlation. numpy.correlate, numpy.convolve, scipy.signal.fftconvolve. If someone wishes to explain the difference between these, I'd be happy to hear, but mainly what is troubling me is that none of them have a maxlag feature. This means that even if I only want to see correlations between two time series with lags between -100 and +100 ms, for example, it will still calculate the correlation for every lag between -20000 and +20000 ms (which is the length of the time series). This gives a 200x performance hit! Do I have to recode the cross-correlation function by hand to include this feature?
Here are a couple functions to compute auto- and cross-correlation with limited lags. The order of multiplication (and conjugation, in the complex case) was chosen to match the corresponding behavior of numpy.correlate.
import numpy as np
from numpy.lib.stride_tricks import as_strided
def _check_arg(x, xname):
x = np.asarray(x)
if x.ndim != 1:
raise ValueError('%s must be one-dimensional.' % xname)
return x
def autocorrelation(x, maxlag):
"""
Autocorrelation with a maximum number of lags.
`x` must be a one-dimensional numpy array.
This computes the same result as
numpy.correlate(x, x, mode='full')[len(x)-1:len(x)+maxlag]
The return value has length maxlag + 1.
"""
x = _check_arg(x, 'x')
p = np.pad(x.conj(), maxlag, mode='constant')
T = as_strided(p[maxlag:], shape=(maxlag+1, len(x) + maxlag),
strides=(-p.strides[0], p.strides[0]))
return T.dot(p[maxlag:].conj())
def crosscorrelation(x, y, maxlag):
"""
Cross correlation with a maximum number of lags.
`x` and `y` must be one-dimensional numpy arrays with the same length.
This computes the same result as
numpy.correlate(x, y, mode='full')[len(a)-maxlag-1:len(a)+maxlag]
The return vaue has length 2*maxlag + 1.
"""
x = _check_arg(x, 'x')
y = _check_arg(y, 'y')
py = np.pad(y.conj(), 2*maxlag, mode='constant')
T = as_strided(py[2*maxlag:], shape=(2*maxlag+1, len(y) + 2*maxlag),
strides=(-py.strides[0], py.strides[0]))
px = np.pad(x, maxlag, mode='constant')
return T.dot(px)
For example,
In [367]: x = np.array([2, 1.5, 0, 0, -1, 3, 2, -0.5])
In [368]: autocorrelation(x, 3)
Out[368]: array([ 20.5, 5. , -3.5, -1. ])
In [369]: np.correlate(x, x, mode='full')[7:11]
Out[369]: array([ 20.5, 5. , -3.5, -1. ])
In [370]: y = np.arange(8)
In [371]: crosscorrelation(x, y, 3)
Out[371]: array([ 5. , 23.5, 32. , 21. , 16. , 12.5, 9. ])
In [372]: np.correlate(x, y, mode='full')[4:11]
Out[372]: array([ 5. , 23.5, 32. , 21. , 16. , 12.5, 9. ])
(It will be nice to have such a feature in numpy itself.)
Until numpy implements the maxlag argument, you can use the function ucorrelate from the pycorrelate package. ucorrelate operates on numpy arrays and has a maxlag keyword. It implements the correlation from using a for-loop and optimizes the execution speed with numba.
Example - autocorrelation with 3 time lags:
import numpy as np
import pycorrelate as pyc
x = np.array([2, 1.5, 0, 0, -1, 3, 2, -0.5])
c = pyc.ucorrelate(x, x, maxlag=3)
c
Result:
Out[1]: array([20, 5, -3])
The pycorrelate documentation contains a notebook showing perfect match between pycorrelate.ucorrelate and numpy.correlate:
matplotlib.pyplot provides matlab like syntax for computating and plotting of cross correlation , auto correlation etc.
You can use xcorr which allows to define the maxlags parameter.
import matplotlib.pyplot as plt
import numpy as np
data = np.arange(0,2*np.pi,0.01)
y1 = np.sin(data)
y2 = np.cos(data)
coeff = plt.xcorr(y1,y2,maxlags=10)
print(*coeff)
[-10 -9 -8 -7 -6 -5 -4 -3 -2 -1 0 1 2 3 4 5 6 7
8 9 10] [ -9.81991753e-02 -8.85505028e-02 -7.88613080e-02 -6.91325329e-02
-5.93651264e-02 -4.95600447e-02 -3.97182508e-02 -2.98407146e-02
-1.99284126e-02 -9.98232812e-03 -3.45104289e-06 9.98555430e-03
1.99417667e-02 2.98641953e-02 3.97518558e-02 4.96037706e-02
5.94189688e-02 6.91964864e-02 7.89353663e-02 8.86346584e-02
9.82934198e-02] <matplotlib.collections.LineCollection object at 0x00000000074A9E80> Line2D(_line0)
#Warren Weckesser's answer is the best as it leverages numpy to get performance savings (and not just call corr for each lag). Nonetheless, it returns the cross-product (eg the dot product between the inputs at various lags). To get the actual cross-correlation I modified his answer w/ an optional mode argument, which if set to 'corr' returns the cross-correlation as such:
def crosscorrelation(x, y, maxlag, mode='corr'):
"""
Cross correlation with a maximum number of lags.
`x` and `y` must be one-dimensional numpy arrays with the same length.
This computes the same result as
numpy.correlate(x, y, mode='full')[len(a)-maxlag-1:len(a)+maxlag]
The return vaue has length 2*maxlag + 1.
"""
py = np.pad(y.conj(), 2*maxlag, mode='constant')
T = as_strided(py[2*maxlag:], shape=(2*maxlag+1, len(y) + 2*maxlag),
strides=(-py.strides[0], py.strides[0]))
px = np.pad(x, maxlag, mode='constant')
if mode == 'dot': # get lagged dot product
return T.dot(px)
elif mode == 'corr': # gets Pearson correlation
return (T.dot(px)/px.size - (T.mean(axis=1)*px.mean())) / \
(np.std(T, axis=1) * np.std(px))
I encountered the same problem some time ago, I paid more attention to the efficiency of calculation.Refer to the source code of MATLAB's function xcorr.m, I made a simple one.
import numpy as np
from scipy import signal, fftpack
import math
import time
def nextpow2(x):
if x == 0:
y = 0
else:
y = math.ceil(math.log2(x))
return y
def xcorr(x, y, maxlag):
m = max(len(x), len(y))
mx1 = min(maxlag, m - 1)
ceilLog2 = nextpow2(2 * m - 1)
m2 = 2 ** ceilLog2
X = fftpack.fft(x, m2)
Y = fftpack.fft(y, m2)
c1 = np.real(fftpack.ifft(X * np.conj(Y)))
index1 = np.arange(1, mx1+1, 1) + (m2 - mx1 -1)
index2 = np.arange(1, mx1+2, 1) - 1
c = np.hstack((c1[index1], c1[index2]))
return c
if __name__ == "__main__":
s = time.clock()
a = [1, 2, 3, 4, 5]
b = [6, 7, 8, 9, 10]
c = xcorr(a, b, 3)
e = time.clock()
print(c)
print(e-c)
Take the results of a certain run as an exmple:
[ 29. 56. 90. 130. 110. 86. 59.]
0.0001745000000001884
comparing with MATLAB code:
clear;close all;clc
tic
a = [1, 2, 3, 4, 5];
b = [6, 7, 8, 9, 10];
c = xcorr(a, b, 3)
toc
29.0000 56.0000 90.0000 130.0000 110.0000 86.0000 59.0000
时间已过 0.000279 秒。
If anyone can give a strict mathematical derivation about this,that would be very helpful.
I think I have found a solution, as I was facing the same problem:
If you have two vectors x and y of any length N, and want a cross-correlation with a window of fixed len m, you can do:
x = <some_data>
y = <some_data>
# Trim your variables
x_short = x[window:]
y_short = y[window:]
# do two xcorrelations, lagging x and y respectively
left_xcorr = np.correlate(x, y_short) #defaults to 'valid'
right_xcorr = np.correlate(x_short, y) #defaults to 'valid'
# combine the xcorrelations
# note the first value of right_xcorr is the same as the last of left_xcorr
xcorr = np.concatenate(left_xcorr, right_xcorr[1:])
Remember you might need to normalise the variables if you want a bounded correlation
Here is another answer, sourced from here, seems faster on the margin than np.correlate and has the benefit of returning a normalised correlation:
def rolling_window(self, a, window):
shape = a.shape[:-1] + (a.shape[-1] - window + 1, window)
strides = a.strides + (a.strides[-1],)
return np.lib.stride_tricks.as_strided(a, shape=shape, strides=strides)
def xcorr(self, x,y):
N=len(x)
M=len(y)
meany=np.mean(y)
stdy=np.std(np.asarray(y))
tmp=self.rolling_window(np.asarray(x),M)
c=np.sum((y-meany)*(tmp-np.reshape(np.mean(tmp,-1),(N-M+1,1))),-1)/(M*np.std(tmp,-1)*stdy)
return c
as I answered here, https://stackoverflow.com/a/47897581/5122657
matplotlib.xcorr has the maxlags param. It is actually a wrapper of the numpy.correlate, so there is no performance saving. Nevertheless it gives exactly the same result given by Matlab's cross-correlation function. Below I edited the code from matplotlib so that it will return only the correlation. The reason is that if we use matplotlib.corr as it is, it will return the plot as well. The problem is, if we put complex data type as the arguments into it, we will get "casting complex to real datatype" warning when matplotlib tries to draw the plot.
<!-- language: python -->
import numpy as np
import matplotlib.pyplot as plt
def xcorr(x, y, maxlags=10):
Nx = len(x)
if Nx != len(y):
raise ValueError('x and y must be equal length')
c = np.correlate(x, y, mode=2)
if maxlags is None:
maxlags = Nx - 1
if maxlags >= Nx or maxlags < 1:
raise ValueError('maxlags must be None or strictly positive < %d' % Nx)
c = c[Nx - 1 - maxlags:Nx + maxlags]
return c

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