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71 viewsPython Numpy Tutorial by Justin Johnson
Python Numpy Tutorial by Justin Johnson
Uploaded by
Levema SiraCopyright
© © All Rights Reserved
Available Formats
Download as PDF or read online on Scribd
/ 27
sizaz021 Python Numpy Tutorial with Jupyter and Colab)
[esveeaTa) olutional Neural Networks for Visual Recognition
Python Numpy Tutorial (with Jupyter and Colab)
EE
This tutorial was originally contributed by Justin Johnson
We will use the Python programming language for all assignments in this course, Python is a
great general-purpose programming language on its own, but with the help of a few popular
libraries (numpy, scipy, matplotlib) it becomes a powerful environment for scientific
computing,
We expect that many of you will have some experience with Python and numpy; for the rest of
you, this section will serve as a quick crash course on both the Python programming language
and its use for scientific computing. We'll also introduce notebooks, which are a very
convenient way of tinkering with Python code. Some of you may have previous knowledge in a
different language, in which case we also recommend referencing: NumPy for Matlab users,
Python for R users, and/or Python for SAS users.
Table of Contents
+ Jupyter and Colab Notebooks
* Python
© Python versions
© Basic data types
© Containers
= Lists
* Dictionaries
= Sets
* Tuples
© Functions
© Classes
* Numpy
© Arrays
© Array indexing
© Datatypes
© Array math Back to Top
hitpsies281n github iolpytnor-rumpy:tutoriai#mumpy-math wer siaeiz0a1 Python Numay Tora (th Jupyter and Colas)
© Broadcasting
© Numpy Documentation
+ sciPy
© Image operations
© MATLAB files
© Distance between points
+ Matplotlib
© Plotting
© Subplots
© Images
Jupyter and Colab Notebooks
Before we dive into Python, we'd like to briefly talk about notebooks, A Jupyter notebook lets
you write and execute Python code /ocaily in your web browser. Jupyter notebooks make it
very easy to tinker with code and execute it in bits and pieces; for this reason they are widely
used in scientific computing. Colab on the other hand is Google's flavor of Jupyter notebooks
that is particularly suited for machine learning and data analysis and that runs entirely in the
cloud. Colab is basically Jupyter notebook on steroids: it's free, requires no setup, comes
preinstalled with many packages, is easy to share with the world, and benefits from free
access to hardware accelerators like GPUs and TPUs (with some caveats)
Run Tutorial in Colab (recommended). If you wish to run this tutorial entirely in Colab, click the
Open in Colab badge at the very top of this page
Run Tutorial in Jupyter Notebook. If you wish to run the notebook locally with Jupyter, make
sure your virtual environment is installed correctly (as per the setup instructions), activate it,
then run pip install notebook to install Jupyter notebook. Next, open the notebook and
download it to a directory of your choice by right-clicking on the page and selecting save
Page As .Then cd to that directory andrun jupyter notebook
Back to Top
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08 = merase x4
© > © © locanosssesanee © ome
Csupyter Co
This should automatically launch a notebook server at http://localhost:8888.. If
everything worked correctly, you should see a screen like this, showing all available notebooks
in the current directory. Click jupyter-notebook-tutorial.ipynb and follow the
instructions in the notebook. Otherwise, you can continue reading the tutorial with code
snippets below.
Python
Python is @ high-level, dynamically typed multiparadigm programming language. Python code
is often said to be almost like pseudocode, since it allows you to express very powerful ideas
in very few lines of code while being very readable. As an example, here is an implementation
of the classic quicksort algorithm in Python:
def quicksort(arr):
if len(arr) <= 1:
return arr
pivot = arr[len(arr) // 2]
left [x for x in arr if x < pivot]
middle = [x for x in arr if x == pivot]
right = [x for x in arr if x > pivot]
return quicksort(left) + middle + quicksort (right)
print (quicksort([3,6,8,10,1,2,1]))
# Prints "[1, 1, 2, 3, 6, 8, 10]
Back to Top
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Python versions
As of Janurary 1, 2020, Python has officially dropped support for python2 . For this class all
code will use Python 3.7. Ensure you have gone through the setup instructions and correctly
installed a python3 virtual environment before proceeding with this tutorial. You can double-
check your Python version at the command line after activating your environment by running
python --version
Basic data types
Like most languages, Python has a number of basic types including integers, floats, booleans,
and strings, These data types behave in ways that are familiar from other programming
languages.
Numbers: Integers and floats work as you would expect from other languages:
x=3
print(type(x)) # Prints “"
print (x) # Prints "3"
print(x +1) # Addition; prints
print(x - 1) # Subtraction; prints
print(x * 2) # Multiplication; prints "6"
print(x ** 2)
Exponentiation; prints "9"
x4e1
print(x) # Prints "4"
x 2 2
print(x) # Prints “s"
y=2.5
print(type(y)) # Prints “"
print(y, y +1, y * 2, y ** 2) # Prints "2.5 3.5 5.0 6.25"
Note that unlike many languages, Python does not have unary inerernent ( x++ ) or decrement
(e- ) operators.
Python also has builtin types for complex numbers; you can find all of the details in the
documentation
Booleans: Python implements all of the usual operators for Boolean logic, but uses English
words rather than symbols ( &&, || , etc.)
t = True
f = False
Back to Top
nts ""
print(type(t)) # P,
hitpsies281n github iolpytnor-rumpy-tutoria#numpy-math 427 5128/2021 Python Numpy Tutorial with Jupyter and Colab)
print(t and #) #
print(t or f) # Logical oR; prints “True”
#
Logical AND; prints “False
print(not t)
print(t != f)
Logical NOT; prints “False”
Logical XOR; prints “True”
Strings: Python has great support for strings:
hello = ‘hello’ —# String Literals can use single quotes
world = “world” # or double quotes; it does not matter.
print(hello) # Prints “hello”
print(len(hello)) # String Length; prints "5"
hw = hello + ' '
print(hw) # prints “hello world”
hwi2 = '%s %s Xd‘ % (hello, world, 12) # sprintf style string formatting
print(hwi2) # prints "hello world 12"
+ world # String concatenation
String objects have a bunch of useful methods; for example
s = “hello”
print(s.capitalize()) # Capitalize a string; prints "Hello"
print(s.upper()) # Convert a string to uppercase; prints "HELLO"
print(s.rjust(7)) # Right-justify a string, padding with spaces; prints
print(s.center(7)) # Center a string, padding with spaces; prints " hell
print(s.replace('l', ‘(ell)')) # Replace all instances of one substring wit
# prints “he(ell)(elL)o"
print(' world ‘.strip()) # Strip Leading and trailing whitespace; prints
You can find a list of all string methods in the documentation.
Containers
Python includes several builtin container types: lists, dictionaries, sets, and tuples.
Lists
A list is the Python equivalent of an array, but is resizeable and can contain elements of
different types:
xs =[3, 1, 2] # Create a List
print(xs, xs[2]) # Prints "[3, 1, 2] 2 Back to Top
print(xs[-1]) # Negative indices count from the end of the List "BRINE
hitpsies281n github iolpytnor-rumpy-tutoria#numpy-math ser svzerae21 Python Numpy Tutoral (wih Jupyer and Colb)
xs[2] = ‘foo! # Lists can contain elements of different types
print (xs) Prints "[3, 1, ‘foo']"
xs.append('bar') # Add a new element to the end of the List
print (xs) # Prints "[3, 1, ‘foo’, ‘bar']”
x = xs.pop() # Remove and return the Last element of the List
print(x, xs) # Prints “bar [3, 1, 'foo']”
As usual, you can find all the gory details about lists in the documentation.
Slicing: In addition to accessing list elements one at a time, Python provides concise syntax to
access sublists; this is known as slicing.
ums = list(range(5)) # range is a built-in function that creates a List
print (nuns) # Prints “[@, 1, 2, 3, 4]"
print (nums[2:4]) # Get a slice from index 2 to 4 (exclusive); print
print (nums[2:]) # Get a slice from index 2 to the end; prints “[2,
print (nums[:2]) # Get a slice from the start to index 2 (exclusive
print (nums[:]) # Get a slice of the whole List; prints "[@, 1, 2,
print (nums[:-1]) # Slice indices can be negative; prints "[@, 1, 2,
nums[2:4] = [8, 9] # Assign a new sublist to a slice
print (nuns) # Prints "[0, 1, 8 9, 4]
We will see slicing again in the context of numpy arrays
Loops: You can loop over the elements of a list like this:
animals = [‘cat', ‘dog’, ‘monkey"]
for animal in animals:
print(animal)
# Prints "cat", “dog”, "monkey", each on its own Line.
If you want access to the index of each element within the body of a loop, use the builtin
enumerate function’
animals = ['cat', ‘dog’, ‘monkey']
for idx, animal in enumerate(animals):
print('#%d: %s' % (idx + 1, animal))
# Prints "#1: cat", "#2: dog", "#3: monkey", each on its own Line
List comprehensions: When programming, frequently we want to transform one Back to Top
into another. As a simple example, consider the following code that compusce -oquure
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numbers;
nums = [2, 1, 2, 3, 4]
squares = []
for x in nums:
squares.append(x ** 2)
print(squares) # Prints [0, 1, 4, 9, 16]
You can make this code simpler using a list comprehension:
nums = [@, 1, 2, 3, 4]
squares = [x ** 2 for x in nums]
print(squares) # Prints [@, 1, 4, 9, 16]
List comprehensions can also contain conditions:
nums = [8, 1, 2, 3, 4]
even_squares = [x ** 2 for x in nums if x % 2
print(even_squares) # Prints "[0, 4, 16]"
Dictionaries
A dictionary stores (key, value) pairs, similar toa Map in Java or an object in Javascript. You
can use it like this:
d= (‘cat': ‘cute’, ‘dog’: ‘furry'} # Create a new dictionary with some dat
print(d[‘cat']) # Get an entry from a dictionary; prints "cute"
print(‘cat' ind) # Check if a dictionary has a given key; prints “True”
d[‘fish'] = ‘wet' # Set an entry in a dictionary
print (d[ ‘fish’ ]) # Prints “wet”
# print(d['monkey’J) # KeyError: ‘monkey’ not a key of d
print(d.get('monkey’, ‘N/A')) # Get an element with a default; prints
print(d.get("fish’, ‘N/A')) # Get an element with a default; prints "
del d['fish"] # Remove an element from a dictionary
print(d.get('fish', 'N/A')) # "fish" is no Longer a key; prints "N/A"
You can find all you need to know about dictionaries in the cocumentation.
Loops: It is easy to iterate over the keys in a dictionary: Beck to Top
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d= (‘person': 2, ‘cat': 4, ‘spider’: 8}
for animal in
legs = d[animal]
print('A %s has %d legs’ % (animal, legs))
# Prints "A person has 2 Legs", “A cat has 4 Legs", "A spider has 8 Legs”
If you want access to keys and their corresponding values, use the items method:
d= {‘person': 2, ‘cat': 4, ‘spider’: 8}
for animal, legs in d.items():
print('A %s has %d legs’ % (animal, legs))
# Prints "A person has 2 Legs", "A cat has 4 Legs", "A spider has 8 Legs”
Dictionary comprehensions: These are sirnilar to list comprehensions, but allow you to easily
construct dictionaries. For example:
nums = [@, 1, 2, 3, 4]
even_num_to_square = {x: x ** 2 for x in nums if x % 2
print(even_num_to_square) # Prints "{@: 9, 2: 4, 4: 16)"
Sets
A set is an unordered collection of distinct elements. As a simple example, consider the
following:
animals = {‘cat', ‘dog’}
print(‘cat’ in animals) # Check if an element is in a set; prints "True"
print('fish' in animals) # prints "False
animals .add(' fish") # Add an element to a set
print(‘fish’ in animals) # Prints “True”
print (en(animals)) # Number of elements in a set; prints "3"
animals .add(‘ cat") # Adding an element that is already in the set doe
print (1en(animals)) # Prints "3"
animals.remove(' cat’) # Remove an element from a set
print (len(animals) ) # Prints "2"
As usual, everything you want to know about sets can be found in the documentation
Loops: Iterating over a set has the same syntax as iterating over a list; however S Back to Top
unordered, you cannot make assumptions about the order in which you visit the-erernents or
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the set
animals = {'cat', ‘dog’, ‘fish'}
for idx, animal in enumerate(animals):
print(‘#%d: %s' % (idx + 1, animal))
# Prints “#1: fish", "#2: dog", “#3: cat”
Set comprehensions: Like lists and dictionaries, we can easily construct sets using set
comprehensions:
from math import sqrt
nums = {int(sqrt(x)) for x in range(3e)}
print(nums) # Prints "{@, 1, 2, 3, 4, 5}"
Tuples
A tuple is an (immutable) ordered list of values. A tuple is in many ways similar to a list; one of
the most important differences is that tuples can be used as keys in dictionaries and as
elements of sets, while lists cannot. Here is a trivial example:
d= {(x, x #1): x for x dn range(1@)} # Create a dictionary with tuple key
t= (5, 6) # Create a tuple
print(type(t)) # Prints ""
print(d[t]) # Prints "5"
print(d[(, 2)]) # Prints "2
The documentation has more information about tuples.
Functions
Python functions are defined using the def keyword. For example:
def sign(x):
if x > 0:
return ‘positive’
elif x <
return ‘negative’
else:
return ‘zero’
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for x in [-1, 9, 1]:
print (sign(x))
# Prints “negative”, “zero”, “positive”
We will often define functions to take optional keyword arguments, like this:
def hello(name, loud="aise)
if loud:
print('HELLO, %s!' % name.upper())
else:
print(‘Hello, %s' % name)
hello('Bob') # Prints "Hello, Bob”
hello('Fred', loud=True) # Prints “HELLO, FRED!"
There is a lot more information about Python functions in the documentation.
Classes
The syntax for defining classes in Python is straightforward
class Greeter(object):
# Constructor
def _init_ (self, name):
self.name = name # Create an instance variable
# Instance method
def greet(self, loud=False):
if loud:
print(‘HELLO, %s!' % self.name.upper())
else:
print(‘Hello, %s' % self.name)
g = Greeter(‘Fred') # Construct an instance of the Greeter class
g-greet() # Call an instance method; prints “Hello, Fred”
gB-greet(loud=True) # Call an instance method; prints "HELLO, FRED!"
You can read a lot more about Python classes in the documentation.
Back to Top
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Numpy
Numpy is the core library for scientific computing in Python. It provides a high-performance
multidimensional array object, and tools for working with these arrays. If you are already
familiar with MATLAB, you might find this tutorial useful to get started with Numpy.
Arrays
Anumpy array is a grid of values, all of the same type, and is indexed by a tuple of nonnegative
integers. The number of dimensions is the rank of the array; the shape of an array is a tuple of
integers giving the size of the array along each dimension.
We can initialize numpy arrays from nested Python lists, and access elements using square
brackets:
import numpy as np
a = np.array([1, 2, 3]) # Create a rank 1 array
print (type(a)) # Prints “"
print (a. shape) # Prints "(3,)"
print(a(o], a{1], a[2]) # Prints "1 2 3"
af] = 5 # Change an element of the array
print(a) # Prints "[5, 2, 3]”
b = np.array([[1,2,3],[4,5,6]]) # Create a rank 2 array
print(b. shape) # Prints "(2, 3)"
print(b[9, 2], b[@, 1], b[1, @]) # Prints "12 4"
Numpy also provides many functions to create arrays’
import numpy as np
a = np.zeros((2,2)) # Create an array of all zeros
print(a) # Prints "[[ @. @.]
# [0 0]
b = np.ones((1,2)) # Create an array of all ones
print (b) # Prints "[[ 4. 1.]]
€ = np.full((2,2), 7) # Create a constant array
print(c) # Prints “[[ 7. 7.]
# [7 7.]]"
Back to Top
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d= np.eye(2) # Create a 2x2 identity matrix
print(d) # Prints "[[ 1. @.]
# [@. 1.)]"
@ = np.random.random((2,2)) # Create an array filled with random values
print(e) # Might print "[[ @.91940167 0.08143941]
@.68744134 0, 87236687]]"
You can read about other methods of array creation in the documentation.
Array indexing
Numpy offers several ways to index into arrays.
Slicing: Similar to Python lists, numpy arrays can be sliced. Since arrays may be
multidirnensional, you must specify a slice for each dimension of the array:
import numpy as np
# Create the following rank 2 array with shape (3, 4)
[[1 2 3 4]
[5 67 8]
[ 9 10 11 12]
= np.array([[1,2,3,4], [5,6,7,8], [9,10,11,12]])
wea
# Use slicing to pull out the subarray consisting of the first 2 rows
# and columns 1 and 2; b is the following array of shape (2, 2):
# [[2 3]
# [6 7]]
b = a[:2, 1:3]
# A slice of an array is a view into the same data, so modifying it
# will modify the original array.
print(a[2, 1]) # Prints "2"
ble, @] = 77 —# b[@, 0] is the same piece of data as af, 1]
print(a[2, 1]) # Prints "77"
You can also mix integer indexing with slice indexing, However, doing so will yield an array of
lower rank than the original array. Note that this is quite different from the way that MATLAB
handles array slicing
import nunpy as np Back to Top
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Create the following rank 2 array with shape (3, 4)
[[1 2 3 4]
[5 67 8]
[ 9 19 11 12]]
= np.array([[1,2,3,4], [5,6,7,8], [9,10,11,12]])
vee aH
Two ways of accessing the data in the middle row of the array.
Mixing integer indexing with slices yields an array of Lower rank,
while using only slices yields an array of the same rank as the
original array:
row_r1 = a[1, :] | # Rank 1 view of the second row of a
row_r2 = a[1:2, :] # Rank 2 view of the second row of a
print(row_r1, row_ri.shape) # Prints "[5 6 7 8] (4,)"
print(row_r2, row_r2.shape) # Prints "[[5 6 7 8]] (1, 4)"
#
#
#
#
# We can make the same distinction when accessing columns of an array:
col_r1 = a[:, 1]
col_r2 = a[:, 1:2]
print(col_ri, col_r1.shape) # Prints “[ 2 6 19] (3,)"
print(col_r2, col_r2.shape) # Prints "[[ 2]
# [ 6]
* [10] (3, 1)"
Integer array indexing: When you index into numpy arrays using slicing, the resulting array
view will always be a subarray of the original array. In contrast, integer array indexing allows
you to construct arbitrary arrays using the data from another array. Here is an example:
import numpy as np
a = np.array([[1,2], [3, 4], [5, 6]])
# An example of integer array indexing.
# The returned array will have shape (3,) and
print(a[[2, 1, 2], [@, 1, @]]) # Prints "[1 4 5]"
# The above example of integer array indexing is equivalent to this:
print(np.array([al®, @], a[1, 1], a[2, @]])) # Prints "[1 4 5)"
# When using integer array indexing, you can reuse the same
# element from the source array:
print(a[[9, ®], [1, 1]]) # Prints “(2 2)”
# Equivalent to the previous integer array indexing example
print(np.array({a{®, 1], a[@, 1]])) # Prints "(2 2)"
Back to Top
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One useful trick with integer array indexing is selecting or mutating one element from each
row of a matrix:
import nunpy as np
# Create a new array from which we will select elements
a = np.array([[1,2,3], [45,6], [78,9], [10, 11, 12]])
print(a) # prints “array([[ 1, 2, 3],
# [4 5, 6],
# [7 8& 9],
# [1@, 11, 12]])"
# Create an array of indices
b = np.array([2, 2, @ 1])
# Select one element from each row of a using the indices in b
print(a[np.arange(4), b]) # Prints "[ 1 6 7 11)"
# Mutate one element from each row of a using the indices in b
a[np.arange(4), b] += 10
print(a) # prints “array([[11, 2, 3],
# [4, 5, 16],
# (17, 8 9],
# (18, 21, 12]])
Boolean array indexing: Boolean array indexing lets you pick out arbitrary elernents of an array.
Frequently this type of indexing is used to select the elements of an array that satisfy some
condition. Here is an example:
import numpy as np
a = np.array([[1,2], [3, 4], [5, 6]])
bool_idx = (a > 2) # Find the elements of a that are bigger than 2;
# this returns a numpy array of Booleans of the same
# shape as a, where each slot of bool_idx tells
# whether that element of a is > 2.
print (bool_idx) # Prints "[[False False]
# [ True True]
# [ True True]]"
Back to Top
# We use boolean array indexing to construct a rank 1 array
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# consisting of the elements of a corresponding to the True values
# of bool_idx
print(a[bool_idx]) # Prints "[3 4 5 6]"
# We can do all of the above i
print(a[a > 2]) # Prints "
a single concise statement:
[3 45 6]
For brevity we have left out a lot of details about numpy array indexing; if you want to know
more you should read the documentation,
Datatypes
Every numpy array is a grid of elements of the same type. Numpy provides a large set of
numeric datatypes that you can use to construct arrays. Numpy tries to guess a datatype
when you create an array, but functions that construct arrays usually also include an optional
argument to explicitly specify the datatype. Here is an example:
import numpy as np
X = np.array([1, 2]) # Let numpy choose the datatype
print(x.dtype) # Prints "int6a”
xX = np.array([1.0, 2.0]) # Let numpy choose the datatype
print(x.dtype) # Prints “floatea”
X = np.array([1, 2], dtype=np.inté4) # Force a particular datatype
print (x.dtype) # Prints "intea”
You can read all about numpy datatypes in the documentation
Array math
Basic mathematical functions operate elernentwise on arrays, and are available both as
operator overloads and as functions in the numpy module:
import numpy as np
np.array([{[{1,2],[3,4]], dtypesnp.floate4)
np.array([[5,6],[7,8]], dtypesnp.floate4)
# ELementwise sum; both produce the array Back to Top
#[[ 6.0 8.0]
hitpsses231n github iolpytnor-numpytutrianumpy-math 127 svzerae21 Python Numpy Tutor with Jupyer and Cota)
# [10.0 12.6]]
print(x + y)
print(np.add(x, y))
# Elementwise difference; both produce the array
# [[-4.0 -4.0]
# [-4.0 -4.0]]
print(x - y)
print(np.subtract(x, y))
# Elementwise product; both produce the array
# [[ 5.0 12.6]
# [21.0 32.0]]
print(x * y)
print(np.multiply(x, y))
# Elementwise division; both produce the array
# [[ 0.2 0, 33333333]
# [ 0.42857143 0.5 1]
print(x / y)
print(np.divide(x, y))
# ELementwise square root; produces the array
#[[1 1.41421356]
# [ 1.73205081 2 W
print(np.sqrt(x))
Note that unlike MATLAB, * is elementwise multiplication, not matrix multiplication. We
instead use the dot function to compute inner products of vectors, to multiply a vector by a
matrix, and to multiply matrices, dot is available both as a function in the numpy module and
as an instance method of array objects:
import numpy as np
np-array({(1,2],[3.4]])
np.array([[5,6],[7.8]])
<
0
np.array([9,10])
np.array([11, 12])
# Inner product of vectors; both produce 219
print(v.dot(w))
print(np.dot(v, w))
# Matrix / vector product; both produce the rank 1 array [29 67] |_B@ck 0 Top
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print(x.dot(v))
print(np.dot(x, v))
# Matrix / matrix product; both produce the rank 2 array
# [[19 22]
# [43 50]]
print(x.dot(y))
print(np.dot(x, y))
Numpy provides many useful functions for performing computations on arrays; one of the
most useful is sum
import numpy as np
x = np.array([[1,2],[3,4]])
print(np.sum(x)) # Compute sum of aLl elements; prints "10"
print(np.sum(x, axis=0)) # Compute sum of each column; prints "[4 6]”
print(np.sum(x, axis=1)) # Compute sum of each row; prints "[3 7]"
You can find the full ist of mathematical functions provided by numpy in the docurnentation
Apart from computing mathematical functions using arrays, we frequently need to reshape or
otherwise manipulate data in arrays, The simplest example of this type of operation is
transposing a matrix; to transpose a matrix, simply use the T attribute of an array object:
import numpy as np
x = np.array([[1,2], [3,4]])
print(x) # Prints “[[1 2]
#
print(x.1) # Prints "[[1 3]
# [2 4]]"
# Note that taking the transpose of a rank 1 array does nothing
v = np.array([1,2,3])
print(v) # Prints “[1 2 3)"
print(v.t) # Prints “[1 2 3)"
Numpy provides many mote functions for manipulating arrays; you can see the full list in the
documentation.
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Broadcasting
Broadcasting is a powerful mechanism that allows numpy to work with arrays of different
shapes when performing arithmetic operations. Frequently we have a smaller array and a
larger array, and we want to use the smaller array multiple times to perform some operation
on the larger array
For example, suppose that we want to add a constant vector to each row of a matrix. We
could do it lke this:
import numpy as np
L add the vector v to each row of the matrix x,
storing the result in the matrix y
np-array([[1,2,3], [4,556], [7,89], [18 11, 12]])
np.array([1, @, 1])
np.empty_like(x) # Create an empty matrix with the same shape as x
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