Difference between revisions of "Python/NumPy"

Revision as of 18:27, 30 March 2017

This article will list quick examples and tips on using the Python modules SciPy and NumPy.

Be sure to first:

import numpy
import scipy

Constructing arrays

• construct an n-dimensional array from a Python list (all elements of list must be of same length)

numpy.array(alist)
## E.g.:
a = numpy.array([[1,2,3],[4,5,6]])
b = numpy.array([i*i for i in range(100) if i%2==1])
c = b.tolist()   # convert array back to Python list

• construct an n-dimensional array of the specified shape, filled with zeros of the specified dtype

numpy.zeros(shape, dtype=float)
## E.g.:
a = numpy.zeros(100)               # a 100-element array of float zeros
b = numpy.zeros((2,8), int)        # a 2x8 array of int zeros
c = numpy.zeros((N,M,L), complex)  # a NxMxL array of complex zeros

• construct an n-dimensional array of the specified shape, filled with ones of the specified dtype

numpy.ones(shape, dtype=float)
## E.g.:
a = numpy.ones(10, int)            # a 10-element array of int ones
b = numpy.pi * numpy.ones((5,5))   # a useful way to fill up an array with a specified value

numpy.eye(shape, dtype=float)
## E.g.:
id = numpy.eye(10,10, int)                         # 10x10 identity matrix (1's on diagonal)
offdiag = numpy.eye(10,10,1)+numpy.eye(10,10,-1)   # off diagonal elements = 1

numpy.transpose(a)
## E.g.:
b = numpy.transpose(a)                # reverse dimensions of a (even for dim > 2)
b = a.T                               # equivalent to numpy.transpose(a)
c = numpy.swapaxes(a, axis1, axis2)   # swap specified axes

numpy.arange
numpy.linspace

• like Python range, but with (potentially) real-valued arrays

a = numpy.arange(start, stop, increment)

• create array of equally-spaced points based on specified number of points

b = numpy.linspace(start, stop, num_elements)

Random array constructors in numpy.random

• 100x100 array of floats uniform on [0.,1.)

a = numpy.random.random((100,100))

• 100 random ints uniform on [0, 10), i.e., not including the upper bound 10

b = numpy.random.randint(0,10, (100,))

• zero-mean, unit-variance Gaussian random numbers in a 5x5x5 array

c = numpy.random.standard_normal((5,5,5))

Indexing arrays

• Multidimensional indexing

elem = a[i,j,k]   # equiv. to a[i][j][k] but presumably more efficient

• "Negative" indexing (wrap around the end of the array)

last_elem = a[-1]   # the last element of the array

• Arrays as indices

i = numpy.array([0,1,2,1])                    # array of indices for the first axis
j = numpy.array([1,2,3,4])                    # array of indices for the second axis
a[i,j]                                        # return array([a[0,1], a[1,2], a[2,3], a[1,4]])
b = numpy.array([True, False, True, False])
a[b]                                          # return array([a[0], a[2]]) since only b[0] and b[2] are True

Slicing arrays (extracting subsections)

• Slice a defined subblock:

section = a[10:20, 30:40]   # 10x10 subblock starting at [10,30]

• Grab everything up to the beginning/end of the array:

asection = a[10:, 30:]   # missing stop index implies until end of array
bsection = b[:10, :30]   # missing start index implies until start of array

• Grab an entire column(s)

x = a[:, 0]   # get everything in the 0th column (missing start and stop)
y = a[:, 1]   # get everything in the 1st column

• Slice off the tail end of an array

tail = a[-10:]                   # grab the last 10 elements of the array
slab = b[:, -10:]                # grab a slab of width 10 off the "side" of the array
interior = c[1:-1, 1:-1, 1:-1]   # slice out everything but the outer shell

Element-wise functions on arrays

Arithmetic operations

• add a and b element-wise (must be same shape)

c = a + b

• multiply e and f element-wise (NOT matrix multiplication)

d = e * f

• negate every element of h

g = -h

• swap 0's and 1's in binary array x

y = (x+1)%2

• return boolean array indicating which elements are > 0.0

z = w > 0.0

• 50 equally-spaced-in-log points between 1.e-06 and 1.0e-01

logspace = 10.**numpy.linspace(-6.0, -1.0, 50)

Trigonometric operations

• sin of every element of x

y = numpy.sin(x)

• conversion from list to array as part of function application

w = numpy.sin([i*i for i in range(100) if i%2==1])

• perform exp(i * theta) where i = sqrt(-1) = 0.+1.j

z = numpy.exp((0.+1.j) * theta)

Summation of arrays

Simple sums

• sum all elements in a, returning a scalar

s  = numpy.sum(a)

• sum elements along specified axis (=0), returning an array of remaining shape

s0 = numpy.sum(a, axis=0)
a  = numpy.ones((10,20,30))
s0 = numpy.sum(a, axis=0)   # s0 has shape (20,30)

Averaging, etc.

• compute mean along the specified axis (over entire array if axis=None)

m = numpy.mean(a, axis)

• compute standard deviation along the specified axis (over entire array if axis=None)

s = numpy.std(a, axis)

Cumulative sums

• cumulatively sum over 0 axis, returning array with same shape as a

s0 = numpy.cumsum(a, axis=0)

• cumulatively sum over 0 axis, returning 1D array of length shape[0]*shape[1]*...*shape[dim-1]

s0 = numpy.cumsum(a)

NumPy for linear algebra

Basics

import numpy as np
L = [1,2,3]
A = np.array([1,2,3])
for e in L:
    print e
for e in A:
    print e
L.append(4)
L = L + [5]
L2 = []
for e in L:
    L2.append(e + e)
L2
A + A
A
2*A
2*L
L2 = []
for e in L:
    L2.append(e*e)
L2
A**2
np.sqrt(A)
np.log(A)
np.exp(A)
# Dot products
a = np.array([1,2])
b = np.array([2,1])
dot = 0
for e, f in zip(a, b):
    dot += e*f
dot
a*b
np.sum(a*b)
(a*b).sum()
np.dot(a, b)
a.dot(b)
b.dot(a)
a_magnitude = np.sqrt( (a*a).sum() )
a_magnitude
a_magnitude = np.linalg.norm(a)
a_magnitude
cos_angle = a.dot(b) / ( np.linalg.norm(a) * np.linalg.norm(b) )
cos_angle
angle = np.arccos(cos_angle)
angle
# radians
np.random.randn(10)
# matrix (2D array or a list of lists)
M = np.array([ [1,2], [3,4] ])
# row, col
L = [ [1,2], [3,4] ] # list of lists
L[0][0]
M[0][0]
M[0,0]
M2 = np.matrix([ [1,2], [3,4] ])
M2
A = np.array(M2)
A
# better to use arrays instead of matrices
A.T # transpose
# generating matrices to work with
Z = np.zeros(10)
Z = np.zeros((10, 10))
O = np.ones((10, 10))
R = np.random.random((10, 10))
G = np.random.randn(10,10) # Gaussian distribution; mean = 0, variance = 1
G.mean()
G.var()

• Matrix products
  • Matrix multiplication
  • Requirement: inner dimensions must match
  • If we have A of size (2,3) and B of size (3,3)
  • We can multiply AB (inner dimension is 3)
  • We cannot multiply BA (inner dimension is 3 / 2)

• Eigenvalues and eigenvectors
  • Two methods:
    1. eigenvalues, eigenvectors = np.eig(C)
    2. eigenvalues, eigenvectors = np.eigh(C)

    eigh is for symmetric and Hermitian matrices

    Symetric means A = A^T

    Hermitian means A = A^H, where A^H is the conjugate transpose of A

Misc

See: http://www.scipy.org/Numpy_Example_List_With_Doc

• return True if any element of a is True

numpy.any(a)

• return True if all elements of a are True

numpy.all(a)

• perform logical_and along given axis of a

numpy.alltrue(a, axis)

• append values to a along specified axis

numpy.append(a, values, axis)

• concatenate tuple of arrays along specified axis

numpy.concatenate((a1, a2, ...), axis)

• get min/max values of a along specified axis (global min/max if axis=None)

numpy.min(a, axis=None), numpy.max(a, axis=None)

• get indices of min/max of a along specified axis (global min/max if axis=None)

numpy.argmin(a, axis=None), numpy.argmax(a, axis=None)

• reshape a to newshape (must conserve total number of elements)

numpy.reshape(a, newshape)

• create matrix from 2D array a (matrices implement matrix multiplication rather than element-wise multiplication)

numpy.matrix(a)

• 1-dimensional, 2-dimensional, and d-dimensional histograms, respectively

numpy.histogram
numpy.histogram2d
numpy.histogramdd

• round elements of matrix a to specified number of decimals

numpy.round(a, decimals=0)

• return array of same shape as a, with -1 where a < 0, 0 where a = 0, and +1 where a > 0

numpy.sign(a)

• write a to specified file (fid), in either binary or ascii format depending on options

a.tofile(fid, sep="", format="%s")

• read array from specified file (binary or ascii)

numpy.fromfile(file=, dtype=float, count=-1, sep=)

• return sorted unique elements of array a

numpy.unique(a)

• return array with same shape as condition, where values from x are inserted in positions where condition is True, and values from y where condition is False

numpy.where(condition, x, y)