NumPy
Questions
Why use NumPy instead of pure python?
How to use basic NumPy?
What is vectorization?
Objectives
Understand the Numpy array object
Be able to use basic NumPy functionality
Understand enough of NumPy to seach for answers to the rest of your questions ;)
We expect most people to be able to do all the basic exercises here. It is probably quite easy for many people; we have advanced exercises at the end in that case.
So, we already know about python lists, and that we can put all kinds of things in there. But in scientific usage, lists are often not enough. They are slow and not very flexible.
What is an array?
For example, consider [1, 2.5, 'asdf', False, [1.5, True]]

this is a Python list but it has different types for every
element. When you do math on this, every element has to be handled separately.
NumPy is the most used library for scientific computing. Even if you are not using it directly, chances are high that some library uses it in the background. NumPy provides the highperformance multidimensional array object and tools to use it.
An array is a ‘grid’ of values, with all the same types. It is indexed by tuples of non negative indices and provides the framework for multiple dimensions. An array has:
dtype  data type. Arrays always contain one type
shape  shape of the data, for example
3×2
or3×2×500
or even500
(one dimensional) or[]
(zero dimensional).data
 raw data storage in memory. This can be passed to C or Fortran code for efficient calculations.
To test the performance of pure Python vs NumPy we can write in our jupyter notebook:
Create one list and one ‘empty’ list, to store the result in
a = list(range(10000))
b = [ 0 ] * 10000
In a new cell starting with %%timeit
, loop through the list a
and fill the second list b
with a
squared
%%timeit
for i in range(len(a)):
b[i] = a[i]**2
That looks and feels quite fast. But let’s take a look at how NumPy performs for the same task.
So for the NumPy example, create one array and one ‘empty’ array to store the result in
import numpy as np
a = np.arange(10000)
b = np.zeros(10000)
In a new cell starting with %%timeit
, fill b
with a
squared
%%timeit
b = a ** 2
We see that compared to working with numpy arrays, working with traditional python lists is actually slow.
Creating arrays
There are different ways of creating arrays (numpy.array()
, numpy.ndarray.shape
, numpy.ndarray.size
):
a = np.array([1,2,3]) # 1dimensional array (rank 1)
b = np.array([[1,2,3],[4,5,6]]) # 2dimensional array (rank 2)
b.shape # the shape (rows,columns)
b.size # number of elements
In addition to above ways of creating arrays, there are many other ways of creating arrays depending on content (numpy.zeros()
, numpy.ones()
, numpy.full()
, numpy.eye()
, numpy.arange()
, numpy.linspace()
):
np.zeros((2, 3)) # 2x3 array with all elements 0
np.ones((1,2)) # 1x2 array with all elements 1
np.full((2,2),7) # 2x2 array with all elements 7
np.eye(2) # 2x2 identity matrix
np.arange(10) # Evenly spaced values in an interval
np.linspace(0,9,10) # same as above, see exercise
c = np.ones((3,3))
d = np.ones((3, 2), 'bool') # 3x2 boolean array
Arrays can also be stored and read from a (.npy) file (numpy.save()
, numpy.load()
):
np.save('x.npy', a) # save the array a to a .npy file
x = np.load('x.npy') # load an array from a .npy file and store it in variable x
In many occasions (especially when something goes different than expected) it is useful to check and control the datatype of the array (numpy.ndarray.dtype
, numpy.ndarray.astype()
):
d.dtype # datatype of the array
d.astype('int') # change datatype from boolean to integer
In the last example, .astype('int')
, it will make a copy of the
array, and reallocate data  unless the dtype is exactly the same as
before. Understanding and minimizing copies is one of the most
important things to do for speed.
Exercises 1
Exercises: Numpy1
Datatypes Try out
np.arange(10)
andnp.linspace(0,9,10)
, what is the difference? Can you adjust one to do the same as the other?Datatypes Create a 3x2 array of random float numbers (check
numpy.random.random()
) between 0 and 1. Now change the arrays datatype to int (array.astype
). How does the array look like?Reshape Create a 3x2 array of random integer numbers between 0 and 10. Change the shape of the array (check
array.reshape
) in any way possible. What is not possible?NumPyI/O Save above array to .npy file (
numpy.save()
) and read it in again.
Solutions: Numpy1
Datatypes
np.arange(10)
results inarray([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
with dtype int64,while
np.linspace(0,9,10)
results inarray([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
with dtype float64.Both
np.linspace
andnp.arange
take dtype as an argument and can be adjusted to match each other in that way.
Datatypes eg
a = np.random.random((3,2))
.a.astype('int')
results in an all zero array, not as maybe expected the rounded int (all numbers [0, 1) are cast to 0).Reshape eg
b = np.random.randint(0,10,(3,2))
.
b.reshape((6,1))
andb.reshape((2,3))
possible.It is not possible to reshape to shapes using more or less elements than
b.size = 6
, so for exampleb.reshape((12,1))
gives an error.
NumPyI/O
np.save('x.npy', b)
andx = np.load('x.npy')
Array maths and vectorization
Clearly, you can do math on arrays. Math in NumPy is very fast because it is implemented in C or Fortran  just like most other highlevel languages such as R, Matlab, etc do.
By default, basic arithmetic (+
, 
, *
, /
) in NumPy is
elementbyelement. That is, the operation is performed for each element in the
array without you having to write a loop. We say an operation is “vectorized”
when the looping over elements is carried out by NumPy internally, which uses
specialized CPU instructions for this that greatly outperform a regular Python
loop.
Note that unlike Matlab, where *
means matrix multiplication, NumPy uses
*
to perform elementbyelement multiplication and uses the @
symbol to
perform matrix multiplication:
a = np.array([[1,2],[3,4]])
b = np.array([[5,6],[7,8]])
# Addition
c = a + b
d = np.add(a,b)
# Matrix multiplication
e = a @ b
f = np.dot(a, b)
Other common mathematical operations include: 
(numpy.subtract
), *
(numpy.multiply
), /
(numpy.divide
), .T
(numpy.transpose()
), numpy.sqrt
, numpy.sum()
, numpy.mean()
, …
Exercises 2
Exercises: Numpy2
Matrix multiplication What is the difference between
numpy.multiply
andnumpy.dot()
? Try it.Axis What is the difference between
np.sum(axis=1)
vsnp.sum(axis=0)
on a twodimensional array? What if you leave out the axis parameter?
Solutions: Numpy2
Matrix multiplication
np.multiply
does elementwise multiplication on two arrays, whilenp.dot
enables matrix multiplication.Axis
axis=1
does the operation (here:np.sum
) over each row, while axis=0 does it over each column. If axis is left out, the sum of the full array is given.
Indexing and Slicing
See also
NumPy has many ways to extract values out of arrays:
You can select a single element
You can select rows or columns
You can select ranges where a condition is true.
Clever and efficient use of these operations is a key to NumPy’s speed: you should try to cleverly use these selectors (written in C) to extract data to be used with other NumPy functions written in C or Fortran. This will give you the benefits of Python with most of the speed of C.
a = np.arange(16).reshape(4, 4) # 4x4 matrix from 0 to 15
a[0] # first row
a[:,0] # first column
a[1:3,1:3] # middle 2x2 array
a[(0, 1), (1, 1)] # second element of first and second row as array
Boolean indexing on above created array:
idx = (a > 0) # creates boolean matrix of same size as a
a[idx] # array with matching values of above criterion
a[a > 0] # same as above in one line
Exercises 3
Exercise: Numpy3
a = np.eye(4)
b = a[:,0]
b[0] = 5
View vs copy Try out above code. How does
a
look like beforeb
has changed and after? How could it be avoided?
Solution: Numpy3
View vs copy The change in
b
has also changed the arraya
! This is becauseb
is merely a view of a part of arraya
. Both variables point to the same memory. Hence, if one is changed, the other one also changes. If you need to keep the original array as is, usenp.copy(a)
.
Types of operations
There are different types of standard operations in NumPy:
ufuncs, “universal functions”: These are elementbyelement functions with standardized arguments:
One, two, or three input arguments
For example,
a + b
is similar tonp.add(a, b)
but the ufunc has more control.out=
output argument, store output in this array (rather than make a new array)  saves copying data!See the full reference
They also do broadcasting (ref). Can you add a 1dimensional array of shape (3) to an 2dimensional array of shape (3, 2)? With broadcasting you can!
a = np.array([[1, 2, 3], [4, 5, 6]]) b = np.array([10, 10, 10]) a + b # array([[11, 12, 13], # [14, 15, 16]])
Broadcasting is smart and consistent about what it does, which I’m not clever enough to explain quickly here: the manual page on broadcasting. The basic idea is that it expands dimensions of the smaller array so that they are compatible in shape.
Array methods do something to one array:
Some of these are the same as ufuncs:
x = np.arange(12) x.shape = (3, 4) x # array([[ 0, 1, 2, 3], # [ 4, 5, 6, 7], # [ 8, 9, 10, 11]]) x.max() # 11 x.max(axis=0) # array([ 8, 9, 10, 11]) x.max(axis=1) # array([ 3, 7, 11])
Other functions: there are countless other functions covering linear algebra, scientific functions, etc.
Exercises 4
Exercises: Numpy4
Inplace addition: Create an array, add it to itself using a ufunc.
Inplace addition (advanced): Create an array of
dtype='float'
, and an array ofdtype='int'
. Try to use the int array is the output argument of the first two arrays.Output arguments and timing Repeat the initial
b = a ** 2
example using the output arguments and time it. Can you make it even faster using the output argument?
Solution: Numpy4
inplace addition:
x = np.array([1, 2, 3]) id(x) # get the memoryID of x np.add(x, x, x) # Third argument is output array np.add(x, x, x) print(x) id(x) # get the memoryID of x #  notice it is the same
You note that
np.add()
has a third argument that is the output array (same asout=
), and the function returns that same array.Output arguments and timing In this case, on my computer, it was actually slower (this is due to it being such a small array!):
a = np.arange(10000) b = np.zeros(10000)
%%timeit numpy.square(a, out=b)
This is a good example of why you always need to time things before deciding what is best.
Linear algebra and other advanced math
In general, you use arrays
(ndimensions), not matrixes
(specialized 2dimensional) in NumPy.
Internally, NumPy doesn’t invent its own math routines: it relies on BLAS and LAPACK to do this kind of math  the same as many other languages.
Scipy has even more functions
Many other libraries use NumPy arrays as the standard data structure: they take data in this format, and return it similarly. Thus, all the other packages you may want to use are compatible
If you need to write your own fast code in C, NumPy arrays can be used to pass data. This is known as extending Python.
Additional exercises
Numpy5
If you have extra time, try these out. These are advanced and optional, and will not be done in most courses.
Reverse a vector. Given a vector, reverse it such that the last element becomes the first, e.g.
[1, 2, 3]
=>[3, 2, 1]
Create a 2D array with zeros on the borders and 1 inside.
Create a random array with elements [0, 1), then add 10 to all elements in the range [0.2, 0.7).
What is
np.round(0.5)
? What isnp.round(1.5)
? Why?In addition to
np.round
, explorenumpy.ceil
,numpy.floor
,numpy.trunc
. In particular, take note of how they behave with negative numbers.Recall the identity \(\sin^2(x) + \cos^2(x) = 1\). Create a random 4x4 array with values in the range [0, 10). Now test the equality with
numpy.equal
. What result do you get withnumpy.allclose()
instead ofnp.equal
?Create a 1D array with 10 random elements. Sort it.
What’s the difference between
np_array.sort()
andnp.sort(np_array)
?For the random array in question 8, instead of sorting it, perform an indirect sort. That is, return the list of indices which would index the array in sorted order.
Create a 4x4 array of zeros, and another 4x4 array of ones. Next combine them into a single 8x4 array with the content of the zeros array on top and the ones on the bottom. Finally, do the same, but create a 4x8 array with the zeros on the left and the ones on the right.
NumPy functionality Create two 2D arrays and do matrix multiplication first manually (for loop), then using the np.dot function. Use %%timeit to compare execution times. What is happening?
Solution Numpy5
One solution is:
a = np.array([1, 2, 3]) a[::1]
One solution is:
b = np.ones((10,10)) b[:,[0, 1]]=0 b[[0, 1],:]=0
A possible solution is:
x = np.random.rand(100) y = x + 10*(x >= 0.2)*(x < 0.7)
For values exactly halfway between rounded decimal values, NumPy rounds to the nearest even value.
Let’s test those functions with few negative and positive values:
a = np.array([3.3, 2.5, 1.5, 0.75, 0.5, 0.5, 0.75, 1.5, 2.5, 3]) np.round(a) np.ceil(a) np.floor(a) np.trun(a)
One solution is:
x = 10*np.random.rand(4,4) oo = np.ones((4,4)) s2c2 = np.square(np.sin(x))+np.square(np.cos(x)) np.equal(oo,s2c2) np.allclose(oo,s2c2)
Sorting the array itself, without copying it:
x = np.random.rand(10) x.sort()
NumPy.sort() returns a sorted copy of an array.
np.argsort(x)
One solution is:
z = np.zeros((4,4)) o = np.ones((4,4)) np.concatenate((z,o)) np.concatenate((z,o),axis=1)
Using numpy without numpy functionality (np.dot) in this case, is still slow.
See also
Keypoints
NumPy is a powerful library every scientist using python should know about, since many other libraries also use it internally.
Be aware of some NumPy specific peculiarities