Chapter 1. Getting Started with NumPy

Let's get started. We will install NumPy and related software on different operating sytems and have a look at some simple code that uses NumPy. As mentioned in the Preface, SciPy is closely related to NumPy, so you will see the name SciPy appearing throughout the chapter. At the end of this chapter, you will find pointers on how to find additional information online if you get stuck or are uncertain about the best way to solve problems.

In this chapter, we shall learn the following skills:

Installing Python, SciPy, Matplotlib, IPython, and NumPy on Windows, Linux, and Macintosh
Writing simple NumPy code
Adding arrays
Making use of online resources and help

Python

NumPy is based on Python, so it is required to have Python installed. On some operating systems, Python is already installed. You, however, need to check whether the Python version is compatible with the NumPy version you want to install. There are many implementations of Python, including commercial implementations and distributions. In this book, we will focus on the standard CPython implementation, which is guaranteed to be compatible with NumPy.

NumPy has binary installers for Windows, various Linux distributions, and Mac OS X. There is also a source distribution, if you prefer that. You need to have Python 2.4.x or above installed on your system. Python 2.7.6 is currently the best Python version to have because most scientific Python libraries support it.

Installing NumPy, Matplotlib, SciPy, and IPython on Windows

Installing NumPy on Windows is a necessary but, fortunately, straightforward task that we will cover in detail. You only need to download an installer, and a wizard will guide you through the installation steps. It is recommended that Matplotlib, SciPy, and IPython be installed. However, this is not required to enjoy this book. The actions we will take are as follows:

Download a NumPy installer for Windows from the SourceForge website at http://sourceforge.net/projects/numpy/files/.
Choose the appropriate version. In this example, we chose numpy-1.8.0-win32-superpack-python2.7.exe.
Open the EXE installer by double-clicking on it.
Now, we can see a description of NumPy and its features, as shown in the previous screenshot. Click on the Next button.
If you have Python installed, it should automatically be detected. If it is not detected, maybe your path settings are wrong. At the end of this chapter, resources are listed in case you have problems installing NumPy.
In this example, Python 2.7 was found. Click on the Next button if Python is found, otherwise, click on the Cancel button and install Python (NumPy cannot be installed without Python). Click on the Next button. This is the point of no return. Well, kind of, but it is best to make sure that you are installing to the proper directory and so on and so forth. Now the real installation starts. This may take a while.
Install SciPy and Matplotlib with the Enthought distribution at http://www.enthought.com/products/epd.php.
Note
The situation around installers is rapidly evolving. Other alternatives exist in various stage of maturity (see http://www.scipy.org/install.html). It might be necessary to put the msvcp71.dll file in your C:\Windows\system32 directory. You can get it at http://www.dll-files.com/dllindex/dll-files.shtml?msvcp71. A Windows IPython installer is available on the IPython website (see http://ipython.scipy.org/Wiki/IpythonOnWindows).

Installing NumPy, Matplotlib, SciPy, and IPython on Linux

Installing NumPy and related recommended software on Linux depends on the distribution you have. We will discuss how you would install NumPy from the command line although you could probably use graphical installers; it depends on your distribution (distro). The commands to install Matplotlib, SciPy, and IPython are the same—only the package names are different. Installing Matplotlib, SciPy, and IPython is recommended, but optional.

Most Linux distributions have NumPy packages. We will go through the necessary steps for some of the popular Linux distros:

Run the following instructions from the command line for installing NumPy on Red Hat:
```
yum install python-numpy
```
To install NumPy on Mandriva, run the following command-line instruction:
```
urpmi python-numpy
```
To install NumPy on Gentoo, run the following command-line instruction:
```
sudo emerge numpy
```
To install NumPy on Debian or Ubuntu, we need to type the following:
```
sudo apt-get install python-numpy
```

The following table gives an overview of the Linux distributions and corresponding package names for NumPy, SciPy, Matplotlib, and IPython:

Linux distribution	NumPy	SciPy	Matplotlib	IPython
Arch Linux	`python-numpy`	`python-scipy`	`python-matplotlib`	`ipython`
Debian	`python-numpy`	`python-scipy`	`python-matplotlib`	`ipython`
Fedora	`numpy`	`python-scipy`	`python-matplotlib`	`ipython`
Gentoo	`dev-python/numpy`	`scipy`	`matplotlib`	`ipython`
OpenSUSE	`python-numpy, python-numpy-devel`	`python-scipy`	`python-matplotlib`	`ipython`
Slackware	`numpy`	`scipy`	`matplotlib`	`ipython`

Installing NumPy, Matplotlib, and SciPy on Mac OS X

You can install NumPy, Matplotlib, and SciPy on the Mac with a graphical installer or from the command line with a port manager, such as MacPorts or Fink, depending on your preference.

Note

We can get a NumPy installer from the SourceForge website at http://sourceforge.net/projects/numpy/files/. Similar files exist for Matplotlib and SciPy. Just change numpy in the previous URL to scipy or matplotlib. IPython didn't have a GUI installer at the time of writing. Download the appropriate DMG file as shown in the following screenshot; usually the latest one is the best. Another alternative is the SciPy Superpack (https://github.com/fonnesbeck/ScipySuperpack). Whichever option you choose, it is important to make sure that updates which impact the system Python library don't negatively influence the already installed software by not building against the Python library provided by Apple.

We will install NumPy with a GUI installer using the following steps:

Open the DMG file as shown in the following screenshot (in this example, numpy-1.8.0-py2.7-python.org-macosx10.6.dmg):
Double-click on the icon of the opened box, that is, the one having a subscript that ends with .mpkg. We will be presented with the welcome screen of the installer.
Click on the Continue button to go to the Read Me screen, where we will be presented with a short description of NumPy, as shown in the following screenshot:
Click on the Continue button to go to the License screen.
Read the license, click on the Continue button, and then on the Accept button, when prompted to accept the license. Continue through the next screens and click on the Finish button at the end.

Alternatively, we can install NumPy, SciPy, Matplotlib, and IPython through the MacPorts route or with Fink. The following installation steps install all these packages. We only need NumPy for the tutorials in this book, so please omit the packages you are not interested in.

To install with MacPorts, type the following command:

sudo port install py-numpy py-scipy py-matplotlib py-ipython

Fink also has packages for NumPy: scipy-core-py24, scipy-core-py25, and scipy-core-py26. The SciPy packages are: scipy-py24, scipy-py25, and scipy-py26. We can install NumPy and the other recommended packages that we will be using in this book for Python 2.6 with the following command:
```
fink install scipy-core-py26 scipy-py26 matplotlib-py26
```

Building from source

As a last resort or if we want to have the latest code, we can build from source. In practice it shouldn't be that hard although, depending on your operating system, you might run into problems. As operating systems and related software are rapidly evolving, the best you can do is search online or ask for help. In this chapter, we give pointers on good places to look for help.

The steps to install NumPy from source are straightforward and given here. We can retrieve the source code for NumPy with .git as follows:

git clone git://github.com/numpy/numpy.git numpy

Install on /usr/local with the following command:

python setup.py build
sudo python setup.py install --prefix=/usr/local

To build, we need a C compiler such as GCC and the Python header files in the python-dev or python-devel package.

NumPy arrays

After going through the installation of NumPy, it's time to have a look at NumPy arrays. NumPy arrays are more efficient than Python lists when it comes to numerical operations. NumPy arrays are in fact specialized objects with extensive optimizations. NumPy code requires less explicit loops than the equivalent Python code. This is based on vectorization.

If we go back to high school mathematics, then we should remember the concepts of scalars and vectors. The number 2 for instance is a scalar. When we add 2 and 2, we are performing scalar addition. We can form a vector out of a group of scalars. In Python programming terms, we will then have a one-dimensional array. This concept can of course be extended to higher dimensions. Performing an operation on two arrays such as addition can be reduced to a group of scalar operations. In straight Python, we will do that with loops going through each element in the first array and adding it to the corresponding element in the second array. However, this is more verbose than the way it is done in mathematics. In mathematics, we treat the addition of two vectors as a single operation. That's the way NumPy arrays do it too and there are certain optimizations using low-level C routines, which make these basic operations more efficient. We will cover NumPy arrays in more detail in the next chapter.

Adding arrays

Imagine that we want to add two vectors called a and b. A vector is used here in the mathematical sense, which means a one-dimensional array. We will learn in Chapter 4, Simple Predictive Analytics with NumPy, about specialized NumPy arrays that represent matrices. The vector a holds the squares of integers 0 to n, for instance. If n is equal to 3, then a contains 0, 1, or 4. The vector b holds the cubes of integers 0 to n, so if n is equal to 3, then the vector b is equal to 0, 1, or 8. How would you do that using plain Python? After we come up with a solution, we will compare it with the NumPy equivalent.

The following function solves the vector addition problem using pure Python without NumPy:

def pythonsum(n):
   a = range(n)
   b = range(n)
   c = []

   for i in range(len(a)):
       a[i] = i ** 2
       b[i] = i ** 3
       c.append(a[i] + b[i])

   return c

The following is a function that achieves the same with NumPy:

def numpysum(n):
  a = numpy.arange(n) ** 2
  b = numpy.arange(n) ** 3
  c = a + b
  return c

Notice that numpysum() does not need a for loop. Also, we used the arange function from NumPy, which creates a NumPy array for us with integers 0 to n. The arange function was imported; that is why it is prefixed with numpy.

Now comes the fun part. Remember that it is mentioned in the Preface that NumPy is faster when it comes to array operations. How much faster is Numpy, though? The following program will show us by measuring the elapsed time in microseconds, for the numpysum and pythonsum functions. It also prints the last two elements of the vector sum. Let's check that we get the same answers when using Python and NumPy:

#!/usr/bin/env/python

import sys
from datetime import datetime
import numpy as np

"""
 This program demonstrates vector addition the Python way.
 Run from the command line as follows
     
  python vectorsum.py n
 
 where n is an integer that specifies the size of the vectors.

 The first vector to be added contains the squares of 0 up to n.
 The second vector contains the cubes of 0 up to n.
 The program prints the last 2 elements of the sum and the elapsed time.
"""

def numpysum(n):
   a = np.arange(n) ** 2
   b = np.arange(n) ** 3
   c = a + b

   return c

def pythonsum(n):
   a = range(n)
   b = range(n)
   c = []

   for i in range(len(a)):
       a[i] = i ** 2
       b[i] = i ** 3
       c.append(a[i] + b[i])

   return c
   
size = int(sys.argv[1])

start = datetime.now()
c = pythonsum(size)
delta = datetime.now() - start
print "The last 2 elements of the sum", c[-2:]
print "PythonSum elapsed time in microseconds", delta.microseconds

start = datetime.now()
c = numpysum(size)
delta = datetime.now() - start
print "The last 2 elements of the sum", c[-2:]
print "NumPySum elapsed time in microseconds", delta.microseconds

The output of the program for the 1000, 2000, and 3000 vector elements is as follows:

$ python vectorsum.py 1000
The last 2 elements of the sum [995007996, 998001000]
PythonSum elapsed time in microseconds 707
The last 2 elements of the sum [995007996 998001000]
NumPySum elapsed time in microseconds 171
$ python vectorsum.py 2000
The last 2 elements of the sum [7980015996, 7992002000]
PythonSum elapsed time in microseconds 1420
The last 2 elements of the sum [7980015996 7992002000]
NumPySum elapsed time in microseconds 168
$ python vectorsum.py 4000
The last 2 elements of the sum [63920031996, 63968004000]
PythonSum elapsed time in microseconds 2829
The last 2 elements of the sum [63920031996 63968004000]
NumPySum elapsed time in microseconds 274

Tip

Downloading the example code

You can download the example code files for all Packt books you have purchased from your account at http://www.PacktPub.com. If you purchased this book elsewhere, you can visit http://www.PacktPub.com/support and register to have the files e-mailed directly to you.

Clearly, NumPy is much faster than the equivalent normal Python code. One thing is certain: we get the same results whether we are using NumPy or not. However, the result that is printed differs in representation. Notice that the result from the numpysum function does not have any commas. How come? Obviously we are not dealing with a Python list, but with a NumPy array. It was mentioned in the Preface that NumPy arrays are specialized data structures for numerical data. We will learn more about NumPy arrays in Chapter 2, NumPy Basics.

Online resources and help

The main documentation website for NumPy and SciPy is at http://docs.scipy.org/doc/. On this web page, we can browse the NumPy reference at http://docs.scipy.org/doc/numpy/reference/ and the user guide, as well as several tutorials.

NumPy has a wiki with lots of documentation at http://docs.scipy.org/numpy/Front%20Page/.

The NumPy and SciPy forum can be found at http://ask.scipy.org/en.

The popular Stack Overflow software development forum has hundreds of questions tagged as numpy. To view them, go to http://stackoverflow.com/questions/tagged/numpy.

If you are really stuck with a problem or you want to be kept informed of NumPy's development, you can subscribe to the NumPy discussion mailing list. The e-mail address is <numpy-discussion@scipy.org>. The number of e-mails per day is not too high, and there is almost no spam to speak of. Most importantly, developers actively involved with NumPy also answer questions asked on the discussion group. The complete list can be found at http://www.scipy.org/Mailing_Lists.

For IRC users, there is an IRC channel on irc://irc.freenode.net. The channel is called #scipy, but you can also ask NumPy questions since SciPy users also have knowledge of NumPy, as SciPy is based on NumPy. There are at least 50 members on the SciPy channel at all times.

Summary

In this chapter, we installed NumPy and other recommended software that we will be using in some tutorials. We got a vector addition program working and convinced ourselves that NumPy has superior performance. In addition, we explored the available NumPy documentation and online resources.

In the next chapter, we will take a look under the hood and explore some fundamental concepts, including arrays and data types.

Learning NumPy Array: Supercharge your scientific Python computations by understanding how to use the NumPy library effectively

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