1
LECTURE 5:
NUMPY AND
MATPLOTLIB
Introduction to Scientific Python, CME 193
Feb. 6, 2014
Download exercises from:
web.stanford.edu/~ermartin/Teaching/CME193-Winter15
Eileen Martin
Some slides are from Sven Schmit’s Fall ‘14 slides
2
Overview
• Numpy: basic objects, methods, functions
• Numpy: linear algebra
• Numpy: random
• Matplotlib: 2D plots
• Matplotlib: 3D plots
• Scipy vs Numpy
• Discuss assignment 4
3
Numpy
• Fundamental package for working with N-dimensional
array objects (vector, matrix, tensor, …)
• corn has version 1.9.1, documentation:
http://docs.scipy.org/doc/numpy/index.html
• Numpy arrays are a fundamental data type for some other
packages to use
• Numpy has many specialized modules and functions:
numpy.linalg (Linear algebra) numpy.random (Random sampling)
numpy.fft (Discrete Fourier transform) sorting/searching/counting
math functions numpy.testing (unit test support)
4
Declaring a Numpy array
Each Numpy array has some attributes:
shape (a tuple of the size in each dimension), dtype (data type of
entries), size (total # of entries), ndim (# of dimensions), T (transpose)
Use these attributes to insert print statements into declaration.py
to figure out each object’s type, dimensions and entry data type:
import numpy as np
x0 = np.array([True,True,False])
x1 = np.array([2,1,4], np.int32)
x2 = np.array([[2,0,4],[3,2,7]])
x3 = np.empty([3,2])
x4 = np.empty_like(x2)
x5 = np.zeros(4, np.complex64)
x6 = np.arange(1,9,2.0)
x7 = np.diag([1, 2, 4])
x8 = np.linspace(0,np.pi,10)
http://docs.scipy.org/doc/numpy/reference/routines.array-creation.html
5
What can you do?
• Add two arrays
• Add all entries in one array
• Multiply two arrays (1D, 2D)
• Take the exponential of each element in an array
• Multiply an array by a scalar
• Get the minimum element of an array
• Print a few elements of an array
• Print a single column or row of an array
• Multiply two arrays via matrix multiplication
Solutions will be posted on website after class
6
Array broadcasting:
Automatically make copies of arrays to fill in length 1 dimensions
0 0 0 0 1 2 0 1 2
10 10 10 10 11 12
0 0 0 0 1 2 0 1 2
10 10 10 0 1 2 10 11 12
0 1 2 0 1 2
0
10 10 11 12
7
Iterating over an array
• Iteration over all elements of array:
for element in A.flat
• Iteration over multidimensional arrays is done on slices in
the first dimension:
for row in A
• Alternatively, could access entries through indices:
for i in range(A.shape[0]):
for j in range(A.shape[1]):
8
Reshaping an array
• Use reshape to modify the dimensions of an array while
leaving the total number of elements the same
A = np.arange(8)
A.reshape(2,4)
# gives [[0,1,2,3],[4,5,6,7]]
• Use resize to remove elements or append 0’s in place
(size can change under some circumstances*)
A.resize(2,3)
• Use resize to return a copy with removed elements or
repeated copies
b = resize(a,(2,4))
9
Overview
• Numpy: basic objects, methods, functions
• Numpy: linear algebra
• Numpy: random
• Matplotlib: 2D plots
• Matplotlib: 3D plots
• Scipy vs Numpy
• Discuss assignment 4
10
Numpy: Linear Algebra
name explanation
• The numpy.linalg module
dot(a,b) dot product of two arrays
has many matrix/vector
kron(a,b) Kronecker product
manipulation algorithms
(a subset of these is in the table) linalg.norm(x) matrix or vector norm
linalg.cond(x) condition number
linalg.solve(A,b) solve linear system Ax=b
linalg.inv(A) inverse of A
linalg.pinv(A) pseudo-inverse of A
linalg.eig(A) eigenvalues/vectors of
square A
linalg.eigvals(A) eigenvalues of general A
trace(A) trace (diagonal sum)
linalg.svd(A) singular value
decomposition
http://docs.scipy.org/doc/numpy/reference/routines.linalg.html
11
Linear algebra exercise: least squares
• In leastSquares.py, you are given a bunch of noisy data points
and you want to fit them with a line:
axi + b = yi
• This can be written in matrix format
• Solve for (a,b) so that
• Hint: Try using linalg.solve(X,y), linalg.pinv(X), or linalg.lstsq(X,y)
http://docs.scipy.org/doc/numpy/reference/routines.linalg.html
12
Overview
• Numpy: basic objects, methods, functions
• Numpy: linear algebra
• Numpy: random
• Matplotlib: 2D plots
• Matplotlib: 3D plots
• Scipy vs Numpy
• Discuss assignment 4
13
Numpy: Random
• In the linear regression exercise, those ‘measurements’
were actually generated by numpy.random
x = np.random.randn(50) # draw 50 numbers from the standard normal dist.
y = 3.5*x+2+np.random.randn(50)*0.3 # apply a linear transform and add noise
• If you run this, you’ll get different numbers each time, so
you might want to use np.random.seed(someObject)
to reproduce a random experiment
http://docs.scipy.org/doc/numpy/reference/routines.random.html
14
Numpy: Random
• The numpy.random module has many distributions
you can draw from (a very small subset of these is in the table)
name explanation
rand(n0,n1,…) ndarray of random values from uniform [0,1]
randn(n0,n1,…) random standard normal
randint(lo, [hi, size]) random integers [lo, hi)
shuffle(seq) shuffle sequence randomly
choice(seq,[size,replace,p]) sample k items from a 1D array with or
without replacement
chisquare(df,[size]) sample from Chi-squared distribution with df
degrees of freedom
exponential([scale,size]) sample from exponential distribution
http://docs.scipy.org/doc/numpy/reference/routines.random.html
15
Overview
• Numpy: basic objects, methods, functions
• Numpy: linear algebra
• Numpy: random
• Matplotlib: 2D plots
• Matplotlib: 3D plots
• Scipy vs Numpy
• Discuss assignment 4
16
Matplotlib: 2D plots
• Matplotlib is the 2D Python plotting library
• We’ll mostly use matplotlib.pyplot
• There are tons of options, so consult the documentation:
http://matplotlib.org/users/beginner.html
• matplotlib.pyplot can do many types of visualizations including:
• Histograms, bar charts (using hist)
• Error bars on plots, box plots (using boxplot, errorbar)
• Scatterplots (using scatter)
• Line plots (using plot)
• Contour maps (using contour or tricontour)
• Images (matrix to image) (using imshow)
• Stream plots which show derivatives at many locations (streamplot)
• Pie charts, polar charts (using pie, polar)
17
Matplotlib: First example
• Run the code in sin.py
• How do we show two curves on the same plot?
import numpy as np
import matplotlib.pyplot as plt
# array of evenly spaces points from 0 to pi
x = np.linspace(0,np.pi,100)
# calculate the sine of each of those points
y = np.sin(x)
# create a plot of the sine curve
plt.plot(x,y)
# actually show that plot
plt.show()
More examples: http://matplotlib.org/gallery.html
Documentation: http://matplotlib.org/api/pyplot_api.html
18
Back to the linear regression example
• Uncomment lines 28-32 and run the code to produce a
scatter plot
• At the end of the code create a plot that overlays the
scatter plot with a line plot showing your fit: ax+b = y
• As an extra challenge, try to color the markers of the data
points to reflect their distance from the line
19
Overview
• Numpy: basic objects, methods, functions
• Numpy: linear algebra
• Numpy: random
• Matplotlib: 2D plots
• Matplotlib: 3D plots
• Scipy vs Numpy
• Discuss assignment 4
20
Matplotlib: 3D plots
• To do 3D plotting, we’ll use mpl_toolkits.mplot3d
Axes3D class
• Documentation:
http://matplotlib.org/mpl_toolkits/mplot3d/tutorial.html#mplot3d-tutorial
• Can do:
• Line plots (use plot)
• Scatter plots (use scatter)
• Wireframe plots (use plot_wireframe)
• Surface plots (use plot_surface)
• Contours (use contour)
• Bar charts (use bar)
21
3D Plots: First example
• Run the code in sin3D.py
import numpy as np
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
# arrays of evenly spaces points from 0 to pi
x = np.linspace(0,np.pi,40)
y = np.linspace(0,np.pi*2,80)
x,y = np.meshgrid(x,y)
# calculate the product of sines for each point
z = np.sin(x)*np.sin(y)
# create a plot of the sine product
ax = plt.subplot(111, projection=‘3d’)
ax.plot_surface(x,y,z)
# actually show that plot
plt.show()
More examples: http://matplotlib.org/gallery.html
Documentation: http://matplotlib.org/mpl_toolkits/mplot3d/
22
Overview
• Numpy: basic objects, methods, functions
• Numpy: linear algebra
• Numpy: random
• Matplotlib: 2D plots
• Matplotlib: 3D plots
• Scipy vs Numpy
• Discuss assignment 4
23
Scipy vs. Numpy
• Scipy is a library that can work with Numpy arrays, but can
achieve better performance and has some more specialized
libraries
• linear algebra (scipy.linalg uses BLAS/LAPACK)
• statistics (scipy.stats has hypothesis tests, correlation analysis)
• optimization (scipy.optimize has multiple solvers, gradient checks,
simulated annealing)
• sparse matrices (scipy.sparse supports sparse linear algebra, graph
analysis, multiple sparse matrix formats)
• signal processing (scipy.signal has convolutions, wavelets, splines, filters)
http://docs.scipy.org/doc/scipy/reference/
24
Overview
• Numpy: basic objects, methods, functions
• Numpy: linear algebra
• Numpy: random
• Matplotlib: 2D plots
• Matplotlib: 3D plots
• Scipy vs Numpy
• Discuss assignment 4
25
Assignment 4 discussion
• Your questions on assignment 4?
• Tips for assignment 5:
• Online documentation is your friend. Don’t hesitate to use it!
• Stuck? test smaller, simpler statements in interactive mode
• Build test cases to verify correctness of your code (not every unit
test has to fit into the unittest module framework
• Talk to each other. Use the CourseWork Forums.
• Come to office hrs. Mon. 9:30-10:30, Wed. 3:15-4:15
