**Introduction**

This tutorial provides a gentle, hands-on introduction to the Python programming language, and the Numpy library for scientific computing.

**What is expected of you:**

- Work through this at your own leisure before the Indaba.
- Fill out the form at the end to let us know you were able to complete this before the Indaba.

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 both on the Python programming language and on the use of Python for scientific computing.

Some of you may have previous knowledge in Matlab, in which case we also recommend the numpy for Matlab users page (https://docs.scipy.org/doc/numpy-dev/user/numpy-for-matlab-users.html).

In this tutorial, we will cover:

- Basic Python: Basic data types (Containers, Lists, Dictionaries, Sets, Tuples), Functions, Classes
- Numpy: Arrays, Array indexing, Datatypes, Array math, Broadcasting
- Matplotlib: Plotting, Subplots, Images
- IPython: Creating notebooks, Typical workflows

Python is a 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:

**NOTE**: In IPython, you can execute the code in a cell by clicking inside the cell and pressing both **Shift+Enter** at the same time.

```
In [1]:
```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])

```
```

There are currently two different supported versions of Python, 2.7 and 3.4. Somewhat confusingly, Python 3.0 introduced many backwards-incompatible changes to the language, so code written for 2.7 may not work under 3.4 and vice versa. For this class all code will use Python 2.7.

You can check your Python version at the command line by running `python --version`

.

Integers and floats work as you would expect from other languages:

```
In [3]:
```x = 3
print x, type(x)

```
```

```
In [4]:
```print x + 1 # Addition;
print x - 1 # Subtraction;
print x * 2 # Multiplication;
print x ** 2 # Exponentiation;

```
```

```
In [5]:
```x += 1
print x # Prints "4"
x *= 2
print x # Prints "8"

```
```

```
In [6]:
```y = 2.5
print type(y) # Prints "<type 'float'>"
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 increment (x++) or decrement (x--) operators.

Python also has built-in types for long integers and complex numbers; you can find all of the details in the documentation.

`&&`

, `||`

, etc.):

```
In [7]:
```t, f = True, False
print type(t) # Prints "<type 'bool'>"

```
```

Now we let's look at the operations:

```
In [8]:
```print t and f # Logical AND;
print t or f # Logical OR;
print not t # Logical NOT;
print t != f # Logical XOR;

```
```

```
In [9]:
```hello = 'hello' # String literals can use single quotes
world = "world" # or double quotes; it does not matter.
print hello, len(hello)

```
```

```
In [10]:
```hw = hello + ' ' + world # String concatenation
print hw # prints "hello world"

```
```

```
In [11]:
```hw12 = '%s %s %d' % (hello, world, 12) # sprintf style string formatting
print hw12 # prints "hello world 12"

```
```

String objects have a bunch of useful methods; for example:

```
In [12]:
```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 " hello"
print s.center(7) # Center a string, padding with spaces; prints " hello "
print s.replace('l', '(ell)') # Replace all instances of one substring with another;
# prints "he(ell)(ell)o"
print ' world '.strip() # Strip leading and trailing whitespace; prints "world"

```
```

You can find a list of all string methods in the documentation.

Python includes several built-in container types: lists, dictionaries, sets, and tuples.

```
In [13]:
```xs = [3, 1, 2] # Create a list
print xs, xs[2]
print xs[-1] # Negative indices count from the end of the list; prints "2"

```
```

```
In [14]:
```xs[2] = 'foo' # Lists can contain elements of different types
print xs

```
```

```
In [0]:
```xs.append('bar') # Add a new element to the end of the list
print xs

```
```

```
In [0]:
```x = xs.pop() # Remove and return the last element of the list
print x, xs

```
```

As usual, you can find all the gory details about lists in the documentation.

```
In [15]:
```nums = range(5) # range is a built-in function that creates a list of integers
print nums # Prints "[0, 1, 2, 3, 4]"
print nums[2:4] # Get a slice from index 2 to 4 (exclusive); prints "[2, 3]"
print nums[2:] # Get a slice from index 2 to the end; prints "[2, 3, 4]"
print nums[:2] # Get a slice from the start to index 2 (exclusive); prints "[0, 1]"
print nums[:] # Get a slice of the whole list; prints "[0, 1, 2, 3, 4]"
print nums[:-1] # Slice indices can be negative; prints "[0, 1, 2, 3]"
nums[2:4] = [8, 9] # Assign a new sublist to a slice
print nums # Prints "[0, 1, 8, 8, 4]"

```
```

You can loop over the elements of a list like this:

```
In [16]:
```animals = ['cat', 'dog', 'monkey']
for animal in animals:
print animal

```
```

`enumerate`

function:

```
In [17]:
```animals = ['cat', 'dog', 'monkey']
for idx, animal in enumerate(animals):
print '#%d: %s' % (idx + 1, animal)

```
```

```
In [0]:
```nums = [0, 1, 2, 3, 4]
squares = []
for x in nums:
squares.append(x ** 2)
print squares

```
```

You can make this code simpler using a list comprehension:

```
In [18]:
```nums = [0, 1, 2, 3, 4]
squares = [x ** 2 for x in nums]
print squares

```
```

List comprehensions can also contain conditions:

```
In [0]:
```nums = [0, 1, 2, 3, 4]
even_squares = [x ** 2 for x in nums if x % 2 == 0]
print even_squares

```
```

`Map`

in Java or an object in Javascript. You can use it like this:

```
In [0]:
```d = {'cat': 'cute', 'dog': 'furry'} # Create a new dictionary with some data
print d['cat'] # Get an entry from a dictionary; prints "cute"
print 'cat' in d # Check if a dictionary has a given key; prints "True"

```
```

```
In [0]:
```d['fish'] = 'wet' # Set an entry in a dictionary
print d['fish'] # Prints "wet"

```
```

```
In [0]:
```print d['monkey'] # KeyError: 'monkey' not a key of d

```
```

```
In [0]:
```print d.get('monkey', 'N/A') # Get an element with a default; prints "N/A"
print d.get('fish', 'N/A') # Get an element with a default; prints "wet"

```
```

```
In [0]:
```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 documentation.

It is easy to iterate over the keys in a dictionary:

```
In [19]:
```d = {'person': 2, 'cat': 4, 'spider': 8}
for animal in d:
legs = d[animal]
print 'A %s has %d legs' % (animal, legs)

```
```

If you want access to keys and their corresponding values, use the iteritems method:

```
In [20]:
```d = {'person': 2, 'cat': 4, 'spider': 8}
for animal, legs in d.iteritems():
print 'A %s has %d legs' % (animal, legs)

```
```

```
In [0]:
```nums = [0, 1, 2, 3, 4]
even_num_to_square = {x: x ** 2 for x in nums if x % 2 == 0}
print even_num_to_square

```
```

A set is an unordered collection of distinct elements. As a simple example, consider the following:

```
In [0]:
```animals = {'cat', 'dog'}
print 'cat' in animals # Check if an element is in a set; prints "True"
print 'fish' in animals # prints "False"

```
```

```
In [0]:
```animals.add('fish') # Add an element to a set
print 'fish' in animals
print len(animals) # Number of elements in a set;

```
```

```
In [0]:
```animals.add('cat') # Adding an element that is already in the set does nothing
print len(animals)
animals.remove('cat') # Remove an element from a set
print len(animals)

```
```

*Loops*: Iterating over a set has the same syntax as iterating over a list; however since sets are unordered, you cannot make assumptions about the order in which you visit the elements of the set:

```
In [0]:
```animals = {'cat', 'dog', 'fish'}
for idx, animal in enumerate(animals):
print '#%d: %s' % (idx + 1, animal)
# Prints "#1: fish", "#2: dog", "#3: cat"

```
```

```
In [0]:
```from math import sqrt
print {int(sqrt(x)) for x in range(30)}

```
```

```
In [0]:
```d = {(x, x + 1): x for x in range(10)} # Create a dictionary with tuple keys
t = (5, 6) # Create a tuple
print type(t)
print d[t]
print d[(1, 2)]

```
```

```
In [0]:
```t[0] = 1

```
```

Python functions are defined using the `def`

keyword. For example:

```
In [0]:
```def sign(x):
if x > 0:
return 'positive'
elif x < 0:
return 'negative'
else:
return 'zero'
for x in [-1, 0, 1]:
print sign(x)

```
```

We will often define functions to take optional keyword arguments, like this:

```
In [0]:
```def hello(name, loud=False):
if loud:
print 'HELLO, %s' % name.upper()
else:
print 'Hello, %s!' % name
hello('Bob')
hello('Fred', loud=True)

```
```

The syntax for defining classes in Python is straightforward:

```
In [0]:
```class Greeter:
# 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"
g.greet(loud=True) # Call an instance method; prints "HELLO, FRED!"

```
```

To use Numpy, we first need to import the `numpy`

package:

```
In [0]:
```import numpy as np

We can initialize numpy arrays from nested Python lists, and access elements using square brackets:

```
In [4]:
```a = np.array([1, 2, 3]) # Create a rank 1 array
print type(a), a.shape, a[0], a[1], a[2]
a[0] = 5 # Change an element of the array
print a

```
```

```
In [5]:
```b = np.array([[1,2,3],[4,5,6]]) # Create a rank 2 array
print b

```
```

```
In [6]:
```print b.shape
print b[0, 0], b[0, 1], b[1, 0]

```
```

Numpy also provides many functions to create arrays:

```
In [7]:
```a = np.zeros((2,2)) # Create an array of all zeros
print a

```
```

```
In [0]:
```b = np.ones((1,2)) # Create an array of all ones
print b

```
```

```
In [0]:
```c = np.full((2,2), 7) # Create a constant array
print c

```
```

```
In [0]:
```d = np.eye(2) # Create a 2x2 identity matrix
print d

```
```

```
In [0]:
```e = np.random.random((2,2)) # Create an array filled with random values
print e

```
```

Numpy offers several ways to index into arrays.

```
In [0]:
```import numpy as np
# Create the following rank 2 array with shape (3, 4)
# [[ 1 2 3 4]
# [ 5 6 7 8]
# [ 9 10 11 12]]
a = np.array([[1,2,3,4], [5,6,7,8], [9,10,11,12]])
# 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]
print b

```
```

A slice of an array is a view into the same data, so modifying it will modify the original array.

```
In [0]:
```print a[0, 1]
b[0, 0] = 77 # b[0, 0] is the same piece of data as a[0, 1]
print a[0, 1]

```
```

```
In [0]:
```# Create the following rank 2 array with shape (3, 4)
a = np.array([[1,2,3,4], [5,6,7,8], [9,10,11,12]])
print a

```
```

```
In [0]:
```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
row_r3 = a[[1], :] # Rank 2 view of the second row of a
print row_r1, row_r1.shape
print row_r2, row_r2.shape
print row_r3, row_r3.shape

```
```

```
In [0]:
```# We can make the same distinction when accessing columns of an array:
col_r1 = a[:, 1]
col_r2 = a[:, 1:2]
print col_r1, col_r1.shape
print
print col_r2, col_r2.shape

```
```

```
In [0]:
```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[[0, 1, 2], [0, 1, 0]]
# The above example of integer array indexing is equivalent to this:
print np.array([a[0, 0], a[1, 1], a[2, 0]])

```
```

```
In [0]:
```# When using integer array indexing, you can reuse the same
# element from the source array:
print a[[0, 0], [1, 1]]
# Equivalent to the previous integer array indexing example
print np.array([a[0, 1], a[0, 1]])

```
```

```
In [0]:
```# Create a new array from which we will select elements
a = np.array([[1,2,3], [4,5,6], [7,8,9], [10, 11, 12]])
print a

```
```

```
In [0]:
```# Create an array of indices
b = np.array([0, 2, 0, 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]"

```
```

```
In [0]:
```# Mutate one element from each row of a using the indices in b
a[np.arange(4), b] += 10
print a

```
```

```
In [0]:
```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

```
```

```
In [0]:
```# We use boolean array indexing to construct a rank 1 array
# consisting of the elements of a corresponding to the True values
# of bool_idx
print a[bool_idx]
# We can do all of the above in a single concise statement:
print a[a > 2]

```
```

```
In [0]:
```x = np.array([1, 2]) # Let numpy choose the datatype
y = np.array([1.0, 2.0]) # Let numpy choose the datatype
z = np.array([1, 2], dtype=np.int64) # Force a particular datatype
print x.dtype, y.dtype, z.dtype

```
```

You can read all about numpy datatypes in the documentation.

```
In [2]:
```x = np.array([[1,2],[3,4]], dtype=np.float64)
y = np.array([[5,6],[7,8]], dtype=np.float64)
# Elementwise sum; both produce the array
print x + y
print np.add(x, y)

```
```

```
In [0]:
```# Elementwise difference; both produce the array
print x - y
print np.subtract(x, y)

```
```

```
In [0]:
```# Elementwise product; both produce the array
print x * y
print np.multiply(x, y)

```
```

```
In [0]:
```# Elementwise division; both produce the array
# [[ 0.2 0.33333333]
# [ 0.42857143 0.5 ]]
print x / y
print np.divide(x, y)

```
```

```
In [0]:
```# Elementwise square root; produces the array
# [[ 1. 1.41421356]
# [ 1.73205081 2. ]]
print np.sqrt(x)

```
```

`*`

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:

```
In [0]:
```x = np.array([[1,2],[3,4]])
y = np.array([[5,6],[7,8]])
v = np.array([9,10])
w = np.array([11, 12])
# Inner product of vectors; both produce 219
print v.dot(w)
print np.dot(v, w)

```
```

```
In [0]:
```# Matrix / vector product; both produce the rank 1 array [29 67]
print x.dot(v)
print np.dot(x, v)

```
```

```
In [0]:
```# Matrix / matrix product; both produce the rank 2 array
# [[19 22]
# [43 50]]
print x.dot(y)
print np.dot(x, y)

```
```

`sum`

:

```
In [0]:
```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 list of mathematical functions provided by numpy in the documentation.

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:

```
In [0]:
```print x
print x.T

```
```

```
In [0]:
```v = np.array([[1,2,3]])
print v
print v.T

```
```

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 like this:

```
In [0]:
```# We will add the vector v to each row of the matrix x,
# storing the result in the matrix y
x = np.array([[1,2,3], [4,5,6], [7,8,9], [10, 11, 12]])
v = np.array([1, 0, 1])
y = np.empty_like(x) # Create an empty matrix with the same shape as x
# Add the vector v to each row of the matrix x with an explicit loop
for i in range(4):
y[i, :] = x[i, :] + v
print y

```
```

`x`

is very large, computing an explicit loop in Python could be slow. Note that adding the vector v to each row of the matrix `x`

is equivalent to forming a matrix `vv`

by stacking multiple copies of `v`

vertically, then performing elementwise summation of `x`

and `vv`

. We could implement this approach like this:

```
In [0]:
```vv = np.tile(v, (4, 1)) # Stack 4 copies of v on top of each other
print vv # Prints "[[1 0 1]
# [1 0 1]
# [1 0 1]
# [1 0 1]]"

```
```

```
In [0]:
```y = x + vv # Add x and vv elementwise
print y

```
```

```
In [0]:
```import numpy as np
# We will add the vector v to each row of the matrix x,
# storing the result in the matrix y
x = np.array([[1,2,3], [4,5,6], [7,8,9], [10, 11, 12]])
v = np.array([1, 0, 1])
y = x + v # Add v to each row of x using broadcasting
print y

```
```

The line `y = x + v`

works even though `x`

has shape `(4, 3)`

and `v`

has shape `(3,)`

due to broadcasting; this line works as if v actually had shape `(4, 3)`

, where each row was a copy of `v`

, and the sum was performed elementwise.

Broadcasting two arrays together follows these rules:

- If the arrays do not have the same rank, prepend the shape of the lower rank array with 1s until both shapes have the same length.
- The two arrays are said to be compatible in a dimension if they have the same size in the dimension, or if one of the arrays has size 1 in that dimension.
- The arrays can be broadcast together if they are compatible in all dimensions.
- After broadcasting, each array behaves as if it had shape equal to the elementwise maximum of shapes of the two input arrays.
- In any dimension where one array had size 1 and the other array had size greater than 1, the first array behaves as if it were copied along that dimension

If this explanation does not make sense, try reading the explanation from the documentation or this explanation.

Functions that support broadcasting are known as universal functions. You can find the list of all universal functions in the documentation.

Here are some applications of broadcasting:

```
In [0]:
```# Compute outer product of vectors
v = np.array([1,2,3]) # v has shape (3,)
w = np.array([4,5]) # w has shape (2,)
# To compute an outer product, we first reshape v to be a column
# vector of shape (3, 1); we can then broadcast it against w to yield
# an output of shape (3, 2), which is the outer product of v and w:
print np.reshape(v, (3, 1)) * w

```
```

```
In [0]:
```# Add a vector to each row of a matrix
x = np.array([[1,2,3], [4,5,6]])
# x has shape (2, 3) and v has shape (3,) so they broadcast to (2, 3),
# giving the following matrix:
print x + v

```
```

```
In [0]:
```# Add a vector to each column of a matrix
# x has shape (2, 3) and w has shape (2,).
# If we transpose x then it has shape (3, 2) and can be broadcast
# against w to yield a result of shape (3, 2); transposing this result
# yields the final result of shape (2, 3) which is the matrix x with
# the vector w added to each column. Gives the following matrix:
print (x.T + w).T

```
```

```
In [0]:
```# Another solution is to reshape w to be a row vector of shape (2, 1);
# we can then broadcast it directly against x to produce the same
# output.
print x + np.reshape(w, (2, 1))

```
```

```
In [0]:
```# Multiply a matrix by a constant:
# x has shape (2, 3). Numpy treats scalars as arrays of shape ();
# these can be broadcast together to shape (2, 3), producing the
# following array:
print x * 2

```
```

`matplotlib.pyplot`

module, which provides a plotting system similar to that of MATLAB.

```
In [0]:
```import matplotlib.pyplot as plt

By running this special iPython command, we will be displaying plots inline:

```
In [0]:
```%matplotlib inline

`matplotlib`

is plot, which allows you to plot 2D data. Here is a simple example:

```
In [0]:
```# Compute the x and y coordinates for points on a sine curve
x = np.arange(0, 3 * np.pi, 0.1)
y = np.sin(x)
# Plot the points using matplotlib
plt.plot(x, y)

```
Out[0]:
```

```
In [0]:
```y_cos = np.cos(x)
# Plot the points using matplotlib
plt.plot(x, y_sin)
plt.plot(x, y_cos)
plt.xlabel('x axis label')
plt.ylabel('y axis label')
plt.title('Sine and Cosine')
plt.legend(['Sine', 'Cosine'])

```
Out[0]:
```

You can plot different things in the same figure using the subplot function. Here is an example:

```
In [0]:
```# Compute the x and y coordinates for points on sine and cosine curves
x = np.arange(0, 3 * np.pi, 0.1)
y_sin = np.sin(x)
y_cos = np.cos(x)
# Set up a subplot grid that has height 2 and width 1,
# and set the first such subplot as active.
plt.subplot(2, 1, 1)
# Make the first plot
plt.plot(x, y_sin)
plt.title('Sine')
# Set the second subplot as active, and make the second plot.
plt.subplot(2, 1, 2)
plt.plot(x, y_cos)
plt.title('Cosine')
# Show the figure.
plt.show()

```
```

You can read much more about the `subplot`

function in the documentation.

```
In [0]:
```

Please quickly fill out this form to let us know you've completed the pre-work! (Please use the email address you used to register for the DL Indaba.)

This tutorial is based on the adapted version by Volodymyr Kuleshov and Isaac Caswell, which was in turn adapted from the original `CS231n`

Python tutorial by Justin Johnson (http://cs231n.github.io/python-numpy-tutorial/).

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