Book Image

Python: End-to-end Data Analysis

By : Ivan Idris, Luiz Felipe Martins, Martin Czygan, Phuong Vo.T.H, Magnus Vilhelm Persson
Book Image

Python: End-to-end Data Analysis

By: Ivan Idris, Luiz Felipe Martins, Martin Czygan, Phuong Vo.T.H, Magnus Vilhelm Persson

Overview of this book

Data analysis is the process of applying logical and analytical reasoning to study each component of data present in the system. Python is a multi-domain, high-level, programming language that offers a range of tools and libraries suitable for all purposes, it has slowly evolved as one of the primary languages for data science. Have you ever imagined becoming an expert at effectively approaching data analysis problems, solving them, and extracting all of the available information from your data? If yes, look no further, this is the course you need! In this course, we will get you started with Python data analysis by introducing the basics of data analysis and supported Python libraries such as matplotlib, NumPy, and pandas. Create visualizations by choosing color maps, different shapes, sizes, and palettes then delve into statistical data analysis using distribution algorithms and correlations. You’ll then find your way around different data and numerical problems, get to grips with Spark and HDFS, and set up migration scripts for web mining. You’ll be able to quickly and accurately perform hands-on sorting, reduction, and subsequent analysis, and fully appreciate how data analysis methods can support business decision-making. Finally, you will delve into advanced techniques such as performing regression, quantifying cause and effect using Bayesian methods, and discovering how to use Python’s tools for supervised machine learning. The course provides you with highly practical content explaining data analysis with Python, from the following Packt books: 1. Getting Started with Python Data Analysis. 2. Python Data Analysis Cookbook. 3. Mastering Python Data Analysis. By the end of this course, you will have all the knowledge you need to analyze your data with varying complexity levels, and turn it into actionable insights.
Table of Contents (6 chapters)

NumPy is the fundamental package supported for presenting and computing data with high performance in Python. It provides some interesting features as follows:

NumPy is a good starting package for you to get familiar with arrays and array-oriented computing in data analysis. Also, it is the basic step to learn other, more effective tools such as Pandas, which we will see in the next chapter. We will be using NumPy version 1.9.1.

An array can be used to contain values of a data object in an experiment or simulation step, pixels of an image, or a signal recorded by a measurement device. For example, the latitude of the Eiffel Tower, Paris is 48.858598 and the longitude is 2.294495. It can be presented in a NumPy array object as p:

This is a manual construction of an array using the np.array function. The standard convention to import NumPy is as follows:

You can, of course, put from numpy import * in your code to avoid having to write np. However, you should be careful with this habit because of the potential code conflicts (further information on code conventions can be found in the Python Style Guide, also known as PEP8, at

There are two requirements of a NumPy array: a fixed size at creation and a uniform, fixed data type, with a fixed size in memory. The following functions help you to get information on the p matrix:

>>> p.ndim    # getting dimension of array p
>>> p.shape   # getting size of each array dimension
>>> len(p)    # getting dimension length of array p
>>> p.dtype    # getting data type of array p

There are five basic numerical types including Booleans (bool), integers (int), unsigned integers (uint), floating point (float), and complex. They indicate how many bits are needed to represent elements of an array in memory. Besides that, NumPy also has some types, such as intc and intp, that have different bit sizes depending on the platform.

See the following table for a listing of NumPy's supported data types:


Type code


Range of value



Boolean stored as a byte




Similar to C int (int32 or int 64)




Integer used for indexing (same as C size_t)


int8, uint8

i1, u1

Signed and unsigned 8-bit integer types

int8: (-128 to 127)

uint8: (0 to 255)

int16, uint16

i2, u2

Signed and unsigned 16-bit integer types

int16: (-32768 to 32767)

uint16: (0 to 65535)

int32, uint32

I4, u4

Signed and unsigned 32-bit integer types

int32: (-2147483648 to 2147483647

uint32: (0 to 4294967295)

int64, uinit64

i8, u8

Signed and unsigned 64-bit integer types

Int64: (-9223372036854775808 to 9223372036854775807)

uint64: (0 to 18446744073709551615)



Half precision float: sign bit, 5 bits exponent, and 10b bits mantissa



f4 / f

Single precision float: sign bit, 8 bits exponent, and 23 bits mantissa



f8 / d

Double precision float: sign bit, 11 bits exponent, and 52 bits mantissa


complex64, complex128, complex256

c8, c16, c32

Complex numbers represented by two 32-bit, 64-bit, and 128-bit floats




Python object type




Fixed-length string type

Declare a string dtype with length 10, using S10



Fixed-length Unicode type

Similar to string_ example, we have 'U10'

We can easily convert or cast an array from one dtype to another using the astype method:

There are various functions provided to create an array object. They are very useful for us to create and store data in a multidimensional array in different situations.

Now, in the following table we will summarize some of NumPy's common functions and their use by examples for array creation:




empty, empty_like

Create a new array of the given shape and type, without initializing elements

>>> np.empty([3,2], dtype=np.float64)
array([[0., 0.], [0., 0.], [0., 0.]])
>>> a = np.array([[1, 2], [4, 3]])
>>> np.empty_like(a)
array([[0, 0], [0, 0]])

eye, identity

Create a NxN identity matrix with ones on the diagonal and zero elsewhere

>>> np.eye(2,
array([[1, 0], [0, 1]])

ones, ones_like

Create a new array with the given shape and type, filled with 1s for all elements

>>> np.ones(5)
array([1., 1., 1., 1., 1.])
>>> np.ones(4,
array([1, 1, 1, 1])
>>> x = np.array([[0,1,2], [3,4,5]])
>>> np.ones_like(x)
array([[1, 1, 1],[1, 1, 1]])

zeros, zeros_like

This is similar to ones, ones_like, but initializing elements with 0s instead

>>> np.zeros(5)
array([0., 0., 0., 0-, 0.])
>>> np.zeros(4,
array([0, 0, 0, 0])
>>> x = np.array([[0, 1, 2], [3, 4, 5]])
>>> np.zeros_like(x)
array([[0, 0, 0],[0, 0, 0]])


Create an array with even spaced values in a given interval

>>> np.arange(2, 5)
array([2, 3, 4])
>>> np.arange(4, 12, 5)
array([4, 9])

full, full_like

Create a new array with the given shape and type, filled with a selected value

>>> np.full((2,2), 3,
array([[3, 3], [3, 3]])
>>> x = np.ones(3)
>>> np.full_like(x, 2)
array([2., 2., 2.])


Create an array from the existing data

>>> np.array([[1.1, 2.2, 3.3], [4.4, 5.5, 6.6]])
array([1.1, 2.2, 3.3], [4.4, 5.5, 6.6]])


Convert the input to an array

>>> a = [3.14, 2.46]
>>> np.asarray(a)
array([3.14, 2.46])


Return an array copy of the given object

>>> a = np.array([[1, 2], [3, 4]])
>>> np.copy(a)
array([[1, 2], [3, 4]])


Create 1-D array from a string or text

>>> np.fromstring('3.14 2.17', dtype=np.float, sep=' ')
array([3.14, 2.17])

Many helpful array functions are supported in NumPy for analyzing data. We will list some part of them that are common in use. Firstly, the transposing function is another kind of reshaping form that returns a view on the original data array without copying anything:

In general, we have the swapaxes method that takes a pair of axis numbers and returns a view on the data, without making a copy:

The transposing function is used to do matrix computations; for example, computing the inner matrix product XT.X using

Sorting data in an array is also an important demand in processing data. Let's take a look at some sorting functions and their use:

See the following table for a listing of array functions:




sin, cos, tan, cosh, sinh, tanh, arcos, arctan, deg2rad

Trigonometric and hyperbolic functions

>>> a = np.array([0.,30., 45.])
>>> np.sin(a * np.pi / 180)
array([0., 0.5, 0.7071678])

around, round, rint, fix, floor, ceil, trunc

Rounding elements of an array to the given or nearest number

>>> a = np.array([0.34, 1.65])
>>> np.round(a)
array([0., 2.])

sqrt, square, exp, expm1, exp2, log, log10, log1p, logaddexp

Computing the exponents and logarithms of an array

>>> np.exp(np.array([2.25, 3.16]))
array([9.4877, 23.5705])

add, negative, multiply, devide, power, substract, mod, modf, remainder

Set of arithmetic functions on arrays

>>> a = np.arange(6)
>>> x1 = a.reshape(2,3)
>>> x2 = np.arange(3)
>>> np.multiply(x1, x2)

greater, greater_equal, less, less_equal, equal, not_equal

Perform elementwise comparison: >, >=, <, <=, ==, !=

>>> np.greater(x1, x2)
array([[False, False, False], [True, True, True]], dtype = bool)

With the NumPy package, we can easily solve many kinds of data processing tasks without writing complex loops. It is very helpful for us to control our code as well as the performance of the program. In this part, we want to introduce some mathematical and statistical functions.

See the following table for a listing of mathematical and statistical functions:





Calculate the sum of all the elements in an array or along the axis

>>> a = np.array([[2,4], [3,5]])
>>> np.sum(a, axis=0)
array([5, 9])


Compute the product of array elements over the given axis

>>>, axis=1)
array([8, 15])


Calculate the discrete difference along the given axis

>>> np.diff(a, axis=0)


Return the gradient of an array

>>> np.gradient(a)
[array([[1., 1.], [1., 1.]]), array([[2., 2.], [2., 2.]])]


Return the cross product of two arrays

>>> b = np.array([[1,2], [3,4]])
>>> np.cross(a,b)
array([0, -3])

std, var

Return standard deviation and variance of arrays

>>> np.std(a)
>>> np.var(a)


Calculate arithmetic mean of an array

>>> np.mean(a)


Return elements, either from x or y, that satisfy a condition

>>> np.where([[True, True], [False, True]], [[1,2],[3,4]], [[5,6],[7,8]])
array([[1,2], [7, 4]])


Return the sorted unique values in an array

>>> id = np.array(['a', 'b', 'c', 'c', 'd'])
>>> np.unique(id)
array(['a', 'b', 'c', 'd'], dtype='|S1')


Compute the sorted and common elements in two arrays

>>> a = np.array(['a', 'b', 'a', 'c', 'd', 'c'])
>>> b = np.array(['a', 'xyz', 'klm', 'd'])
>>> np.intersect1d(a,b)
array(['a', 'd'], dtype='|S3')

Loading and saving data

We can also save and load data to and from a disk, either in text or binary format, by using different supported functions in NumPy package. Saving an array

Arrays are Loading an array

We have two

Linear algebra is a branch of mathematics concerned with vector spaces and the mappings between those spaces. NumPy has a package called linalg that supports powerful linear algebra functions. We can use these functions to find eigenvalues and eigenvectors or to perform singular value decomposition:

The function is implemented using the geev Lapack routines that compute the eigenvalues and eigenvectors of general square matrices.

Another common problem is solving linear systems such as Ax = b with A as a matrix and x and b as vectors. The problem can be solved easily using the numpy.linalg.solve function:

The following table will summarise some commonly used functions in the numpy.linalg package:





Calculate the dot product of two arrays

>>> a = np.array([[1, 0],[0, 1]])
>>> b = np.array( [[4, 1],[2, 2]])
array([[4, 1],[2, 2]])

inner, outer

Calculate the inner and outer product of two arrays

>>> a = np.array([1, 1, 1])
>>> b = np.array([3, 5, 1])
>>> np.inner(a,b)


Find a matrix or vector norm

>>> a = np.arange(3)
>>> np.linalg.norm(a)


Compute the determinant of an array

>>> a = np.array([[1,2],[3,4]])
>>> np.linalg.det(a)


Compute the inverse of a matrix

>>> a = np.array([[1,2],[3,4]])
>>> np.linalg.inv(a)
array([[-2., 1.],[1.5, -0.5]])


Calculate the QR decomposition

>>> a = np.array([[1,2],[3,4]])
>>> np.linalg.qr(a)
(array([[0.316, 0.948], [0.948, 0.316]]), array([[ 3.162, 4.427], [ 0., 0.632]]))


Compute the condition number of a matrix

>>> a = np.array([[1,3],[2,4]])
>>> np.linalg.cond(a)


Compute the sum of the diagonal element

>>> np.trace(np.arange(6)).

An important part of any simulation is the ability to generate random numbers. For this purpose, NumPy provides various routines in the submodule random. It uses a particular algorithm, called the Mersenne Twister, to generate pseudorandom numbers.

First, we need to define a seed that makes the random numbers predictable. When the value is reset, the same numbers will appear every time. If we do not assign the seed, NumPy automatically selects a random seed value based on the system's random number generator device or on the clock:

An array of random numbers in the [0.0, 1.0] interval can be generated as follows:

If we want to generate random integers in the half-open interval [min, max], we can user the randint(min, max, length) function:

NumPy also provides for many other distributions, including the Beta, bionomial, chi-square, Dirichlet, exponential, F, Gamma, geometric, or Gumbel.

The following table will list some distribution functions and give examples for generating random numbers:





Draw samples from a binomial distribution (n: number of trials, p: probability)

>>> n, p = 100, 0.2
>>> np.random.binomial(n, p, 3)
array([17, 14, 23])


Draw samples using a Dirichlet distribution

>>> np.random.dirichlet(alpha=(2,3), size=3)
array([[0.519, 0.480], [0.639, 0.36],
 [0.838, 0.161]])


Draw samples from a Poisson distribution

>>> np.random.poisson(lam=2, size= 2)


Draw samples using a normal Gaussian distribution

>>> np.random.normal
(loc=2.5, scale=0.3, size=3)
array([2.4436, 2.849, 2.741)


Draw samples using a uniform distribution

>>> np.random.uniform(
low=0.5, high=2.5, size=3)
array([1.38, 1.04, 2.19[)

We can also use the random number generation to shuffle items in a list. Sometimes this is useful when we want to sort a list in a random order:

The following figure shows two distributions, binomial and poisson , side by side with various parameters (the visualization was created with matplotlib, which will be covered in Chapter 4, Data Visualization):

NumPy random numbers

In this chapter, we covered a lot of information related to the NumPy package, especially commonly used functions that are very helpful to process and analyze data in ndarray. Firstly, we learned the properties and data type of ndarray in the NumPy package. Secondly, we focused on how to create and manipulate an ndarray in different ways, such as conversion from other structures, reading an array from disk, or just generating a new array with given values. Thirdly, we studied how to access and control the value of each element in ndarray by using indexing and slicing.

Then, we are getting familiar with some common functions and operations on ndarray.

And finally, we continue with some advance functions that are related to statistic, linear algebra and sampling data. Those functions play important role in data analysis.

However, while NumPy by itself does not provide very much high-level data analytical functionality, having an understanding of it will help you use tools such as Pandas much more effectively. This tool will be discussed in the next chapter.

Practice exercises

Exercise 1: Using an array creation function, let's try to create arrays variable in the following situations:

Exercise 2: What is the difference between, b) and (a*b)?

Exercise 3: Consider the vector [1, 2, 3, 4, 5] building a new vector with four consecutive zeros interleaved between each value.

Exercise 4: Taking the data example file chapter2-data.txt, which includes information on a system log, solves the following tasks: