Python and Jupyter notebooks: part 02
Contents
Python and Jupyter notebooks: part 02#
Last revised: 07-Aug-2022 by Dick Furnstahl [furnstahl.1@osu.edu]
In this notebook we continue the tour of Python and Jupyter notebooks started in Jupyter_Python_intro_01.ipynb.
Numpy linear algebra#
Having used numpy arrrays to describe vectors, we are now ready to try out matrices. We can define a \(3 \times 3 \) real matrix A as
import numpy as np
A = np.log(np.array([ [4.0, 7.0, 8.0], [3.0, 10.0, 11.0], [4.0, 5.0, 7.0] ]))
print(A)
If we use the shape attribute we would get \((3, 3)\) as output, that is verifying that our matrix is a \(3\times 3\) matrix.
A.shape
We can slice the matrix and print for example the first column (Python organized matrix elements in a row-major order, see below) as
A = np.log(np.array([ [4.0, 7.0, 8.0], [3.0, 10.0, 11.0], [4.0, 5.0, 7.0] ]))
# print the first column, row-major order and elements start with 0
print(A[:,0])
We can continue this was by printing out other columns or rows. The example here prints out the second row
A = np.log(np.array([ [4.0, 7.0, 8.0], [3.0, 10.0, 11.0], [4.0, 5.0, 7.0] ]))
# print the first column, row-major order and elements start with 0
print(A[1,:])
Numpy contains many other functionalities that allow us to slice, subdivide etc etc arrays. We strongly recommend that you look up the Numpy website for more details. Useful functions when defining a matrix are the np.zeros function which declares a matrix of a given dimension and sets all elements to zero
n = 5
# define a matrix of dimension 10 x 10 and set all elements to zero
A = np.zeros( (n, n) )
print(A)
n = 5
# define a matrix of dimension 10 x 10 and set all elements to one
A = np.ones( (n, n) )
print(A)
or as uniformly distributed random numbers on \([0,1]\)
n = 4
# define a matrix of dimension 10 x 10 and set all elements to random numbers with x \in [0, 1]
A = np.random.rand(n, n)
print(A)
The transpose of this matrix
A.T
The dot product of two matrices can be computed with the @ operator (which is preferred to the numpy.dot function). Note that it is not the same as the arithmetic \(*\) operation that performs elementwise multiplication.
A = np.array([ [1., 2., 3.], [4., 5., 6.], [7., 8., 9.] ])
print('matrix A:')
print(A)
print('\nThe dot product of A with A:') # \n here inserts a blank line ('newline')
print(A @ A)
print('\nElement-wise product of A with A:')
print(A * A)
The inverse of this matrix \(A^{-1}\) can be computed using the numpy.linalg module
n = 4
# define a matrix of dimension 10 x 10 and set all elements to random numbers with x \in [0, 1]
A = np.random.rand(n, n)
Ainv = np.linalg.inv(A)
print(Ainv)
The dot product of a matrix by its inverse returns the identity matrix (with small floating-point errors; note their size). Verify that this is true:
print(A @ Ainv)
How would you check \(A^{-1} A\)?
The eigenvalues and eigenvectors of a matrix can be computed with the eig function (note that j is the notation for \(\sqrt{-1}\))
eigenvalues, eigenvectors = np.linalg.eig(A)
print('The eigenvalues are:\n',eigenvalues)
print('\nThe eigenvectors are:\n',eigenvectors)
Aside: List comprehensions#
In the plotting examples in the next section we use for loops to iterate through parameters or plots because it is familiar to anyone who has done programming. In Python, however, it is often preferred to use a different construction called a list comprehension. Here is a quick comparison of using for loop and using a list comprehension, followed by some representative further examples of list comprehensions. You can find much more information and other examples in the online Python documentation and other sources. (The examples here are from [https://hackernoon.com/list-comprehension-in-python-8895a785550b].)
numbers = [1, 2, 3, 4]
squares = []
for n in numbers: # standard for loop
squares.append(n**2)
print(squares) # Output: [1, 4, 9, 16]
numbers = [1, 2, 3, 4]
squares = [n**2 for n in numbers] # this is a "list comprehension"
print(squares) # Output: [1, 4, 9, 16]
You can see how much cleaner the list comprehension is!
# Find common numbers from two lists using list comprehension
list_a = [1, 2, 3, 4]
list_b = [2, 3, 4, 5]
common_num = [a for a in list_a for b in list_b if a == b]
print(common_num) # Output: [2, 3, 4]
# Return numbers from the list which are not equal as a tuple:
list_a = [1, 2, 3]
list_b = [2, 7]
different_num = [(a, b) for a in list_a for b in list_b if a != b]
print(different_num) # Output: [(1, 2), (1, 7), (2, 7), (3, 2), (3, 7)]
# Iterate over strings
list_a = ["Hello", "World", "In", "Python"]
small_list_a = [str.lower() for str in list_a]
print(small_list_a) # Output: ['hello', 'world', 'in', 'python']
# Making a list of lists
list_a = [1, 2, 3]
square_cube_list = [ [a**2, a**3] for a in list_a]
print(square_cube_list) # Output: [[1, 1], [4, 8], [9, 27]]
# Using an if statement to make a list of unequal pairs of numbers
[(x, y) for x in [1,2,3] for y in [3,1,4] if x != y]
# Output: [(1, 3), (1, 4), (2, 3), (2, 1), (2, 4), (3, 1), (3, 4)]
Iterating through a list of parameters to draw multiple lines on a plot#
Suppose we have a function of \(x\) that also depends on a parameter (call it \(r\)). We want to plot the function vs. \(x\) for multiple values of \(r\), either on the same plot or on separate plots. We can do this with a lot of cutting-and-pasting, but how can we do it based on a list of \(r\) values, which we can easily modify?
import numpy as np
import matplotlib.pyplot as plt
import seaborn; seaborn.set() # for plot formatting
def sine_map(r, x):
"""Sine map function: f_r(x) = r sin(pi x)
"""
return r * np.sin(np.pi * x)
Suppose the \(r\) values initially of interest are 0.3, 0.5, 0.8, and 0.9. First the multiple copy approach:
x_pts = np.linspace(0,1, num=101, endpoint=True)
fig = plt.figure()
ax = fig.add_subplot(1,1,1)
ax.set_aspect(1)
ax.plot(x_pts, x_pts, color='black') # black y=x line
ax.plot(x_pts, sine_map(0.3, x_pts), label='$r = 0.3$')
ax.plot(x_pts, sine_map(0.5, x_pts), label='$r = 0.5$')
ax.plot(x_pts, sine_map(0.8, x_pts), label='$r = 0.8$')
ax.plot(x_pts, sine_map(0.9, x_pts), label='$r = 0.9$')
ax.legend()
ax.set_xlabel(r'$x$')
ax.set_ylabel(r'$f(x)$')
ax.set_title('sine map')
fig.tight_layout()
This certainly works, but making changes is awkward and prone to error because we have to find where to change (or add another) \(r\) but we might not remember to change it correctly everywhere.
With minor changes we have a much better implementation (try modifying the list of \(r\) values):
r_list = [0.3, 0.5, 0.8, 0.9] # this could also be a numpy array
x_pts = np.linspace(0,1, num=101, endpoint=True)
fig = plt.figure()
ax = fig.add_subplot(1,1,1)
ax.set_aspect(1)
ax.plot(x_pts, x_pts, color='black') # black y=x line
# Step through the list. r is a dummy variable.
# Note the use of an f-string and LaTeX by putting rf in front of the label.
for r in r_list:
ax.plot(x_pts, sine_map(r, x_pts), label=rf'$r = {r:.1f}$')
ax.legend()
ax.set_xlabel(r'$x$')
ax.set_ylabel(r'$f(x)$')
ax.set_title('sine map')
fig.tight_layout()
def plot_sine_map(r):
x_pts = np.linspace(0,1, num=101, endpoint=True)
fig = plt.figure()
ax = fig.add_subplot(1,1,1)
ax.set_aspect(1)
ax.plot(x_pts, x_pts, color='black') # black y=x line
# Step through the list. r is a dummy variable.
# Note the use of an f-string and LaTeX by putting rf in front of the label.
for r in r_list:
ax.plot(x_pts, sine_map(r, x_pts), label=rf'$r = {r:.1f}$')
ax.legend()
ax.set_xlabel(r'$x$')
ax.set_ylabel(r'$f(x)$')
ax.set_title('sine map')
fig.tight_layout()
Now suppose we want each the different \(r\) values to be plotted on separate graphs? We could make multiple copies of the single plot. Instead, lets make a function to do any single plot and call it for each \(r\) in the list.
r_list = [0.3, 0.5, 0.8, 0.9] # this could also be a numpy array
def plot_sine_map(r):
x_pts = np.linspace(0,1, num=101, endpoint=True)
fig = plt.figure()
ax = fig.add_subplot(1,1,1)
ax.set_aspect(1)
ax.plot(x_pts, x_pts, color='black') # black y=x line
# Note the use of an f-string and LaTeX by putting rf in front of the label.
ax.plot(x_pts, sine_map(r, x_pts), label=rf'$r = {r:.1f}$')
ax.legend()
ax.set_xlabel(r'$x$')
ax.set_ylabel(r'$f(x)$')
ax.set_title(rf'sine map for $r = {r:.1f}$')
fig.tight_layout()
# Step through the list. r is a dummy variable.
for r in r_list:
plot_sine_map(r)
What if instead of distinct plots we wanted subplots of the same figure? Then create the figure and subplot axes outside of the function and have the function return the modified axis object.
r_list = [0.3, 0.5, 0.8, 0.9] # this could also be a numpy array
def plot_sine_map(r, ax_passed):
x_pts = np.linspace(0,1, num=101, endpoint=True)
ax_passed.set_aspect(1)
ax_passed.plot(x_pts, x_pts, color='black') # black y=x line
# Note the use of an f-string and LaTeX by putting rf in front of the label.
ax_passed.plot(x_pts, sine_map(r, x_pts), label=rf'$r = {r:.1f}$')
ax_passed.legend()
ax_passed.set_xlabel(r'$x$')
ax_passed.set_ylabel(r'$f(x)$')
ax_passed.set_title(rf'sine map for $r = {r:.1f}$')
return ax_passed
fig = plt.figure(figsize=(8, 8))
# Step through the list. r is a dummy variable.
rows = 2
cols = 2
for index, r in enumerate(r_list):
ax = fig.add_subplot(rows, cols, index+1)
ax = plot_sine_map(r, ax)
fig.tight_layout()