Lecture7 Revised

7
Lecture
Numerical Computing in Python
Tuesday, October 20, 2009
Numerical Computing in Python: Review of the Basics

Weve already seen how python can be used to compute some fairly basic mathematics.
And that the math module provides some additional functionality.
Numerical Computing in Python: Review of the Basics

Weve already seen how python can be used to compute some fairly basic mathematics.
And that the math module provides some additional functionality.
Today were going to talk about python modules that extend its standard numerical computing
abilities.
from numpy import *

NumPy provides fast numerical computing methods
for Python.

from numpy import *

for Python.
Multi-dimensional arrays
Standard matrix/array operations
Sophisticated random number functionality
Access to the fortran-based LINPACK numerical linear algebra software library
Ability to integrate Fortran & C/C++ code
from numpy import *

for Python.
Multi-dimensional arrays
Standard matrix/array operations
Sophisticated random number functionality
Access to the fortran-based LINPACK numerical linear algebra software library
Ability to integrate Fortran & C/C++ code
NumPy can also be used as an efficient multi-dimensional container, and has three
fundamental objects:
[1] the ndarray itself
[2] the data-type objects describing the layout
of a single fixed-size element of the array.
[3] the array-scalar Python object that is
returned when a single element is accessed.
from numpy import *

NumPy is primarily used for array functionality:
Create array like a nested list
from numpy import *

Obtain dimensions of a (rows, columns)
from numpy import *

Obtain dimensions of a (rows, columns)
Array slicing is a natural extension of list slicing
from numpy import *

Vectors, matrices, and tensors are all arrays.
vector:
matrix:
tensor:
[1, 2, 3]
[[1, 2, 3],
[4, 5, 6]]
[[[1, 2, 3], [4, 5, 6]],
[[1, 2, 3], [4, 5, 6]]]
from numpy import *

Vectors, matrices, and tensors are all arrays.
vector:
matrix:
tensor:
[1, 2, 3]
[[1, 2, 3],
[4, 5, 6]]
[[[1, 2, 3], [4, 5, 6]],
[[1, 2, 3], [4, 5, 6]]]
...but why would we want our data in an array, rather than something else?
from numpy import *

Main Advantage: a single command can be used to perform basic math operations.
This can substantially increase the efficiency of your code.
NumPy arrays have

several attributes:
dot(a, b)
Matrix product of a and b
More in the linalg submodule...
from numpy import *

In addition to normal slicing, there are several other array methods for item selection
& manipulation
an order for the indices

that would lead to sorting
from numpy import *
abbreviated command summary

Random numbers
abbreviated summary of array methods
Random numbers
Two solutions:
>>> import random
>>> import numpy.random
One often needs to generate

random numbers in scientific
scripting.
Random numbers
Two solutions:
>>> import random
One often needs to generate

random numbers in scientific
scripting.
We already saw that the
random module can do this.
Random numbers
Two solutions:
>>> import random
Random numbers
Two solutions:
The random module within NumPy

Provides vectorized drawing of random
numbers, in addition to a variety of
additional methods.
Random numbers
Two solutions:
The random module within NumPy

Provides vectorized drawing of random
numbers, in addition to a variety of
additional methods.
The NumPy random module allows

us to take advantage of powerful
array methods!
Random numbers
Watch out for namespace collision!
from scipy import *

SciPy provides a variety of scientific tools, and is built to specifically work with
NumPy arrays
from scipy import linalg

SciPys linalg submodule provides most of the matrix algebra-related operations youll
want.
In linear algebra, one frequently needs to solve systems of equations taking

the form
Xb = y
using a procedure called Gaussian Elimination. This becomes very
straightforward with our Python library extensions. For example, if
we could determine the values in b by
from scipy import linalg

SciPys linalg submodule provides most of the matrix algebra-related operations youll
want.
linalg.inv(a)
linalg.pinv(a)
linalg.svd(a)
Returns the inverse of matrix a

Returns the pseudoinverse of singular matrix a
Returns U, s, V--results from singular value decomposition
Compute the inverse

Singular Value Decomposition
Matrix multiplication is
included in the NumPy module
import xlrd
Sometimes we need to get data

out of/into excel directly.
The xlrd & xlwt modules provide
this functionality. Both have to
be downloaded from their web
sites and installed.
http://www.python-excel.org/
On macintosh, youll have to

install it manually from the zip or
tar.gz source file:
Computery:~
Computery:~
Computery:~
Computery:~
(for .zip, just unzip
and do this line)
ambertk$
ambertk$
ambertk$
ambertk$
cd Desktop
gunzip xlrd-0.7.1.tar.gz
tar -xvf xlrd-0.7.1.tar
python xlrd-0.7.1/setup.py install
import xlrd
Lets say we
needed to
work with
an .xls
spreadsheet
like this
one...
import xlrd
xlrd example
denotes a unicode string
get information about a specific sheet
get data from a specific sheet
Scenario.
Projecting from three dimensions to two is one type of linear transformation. We can
use a 2x3 matrix P whose columns dictate where the transformed x, y, and z will be
located in two dimensions (u, v).
Kerl, 2009
Scenario.
Projecting from three dimensions to two is one type of linear transformation. We can
use a 2x3 matrix P whose columns dictate where the transformed x, y, and z will be
located in two dimensions (u, v).
Lets say we have a 50 x 3 excel file containing a set of x, y, z coordinates that we

want to map to two dimensions, and write to a
tab-delimited text file.
Kerl, 2009
Scenario.
Kerl, 2009
Scenario--better code
Kerl, 2009
misc.
Others that may interest you...

biopython (http://piopython.org)
Bioinformatics et al.
scipy (http://www.scipy.org)
Symbolic mathematics--integration
FFT
matplotlib (http://matplotlib.sourceforge.net/)
Interactive 2D plotting
MATLAB-like interface
SymPy (http://code.google.com/p/sympy/)
Computer Algebra System written in Python
mlpy (https://mlpy.fbk.eu/)
General-purpose machine learning using numpy arrays
rpy2 (http://rpy.sourceforge.net/rpy2.html)
python-R interfacing (well talk about this one on Friday...)

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7

Numerical Computing in Python

Tuesday, October 20, 2009

Numerical Computing in Python: Review of the Basics

And that the math module provides some additional functionality.

Tuesday, October 20, 2009

Numerical Computing in Python: Review of the Basics

And that the math module provides some additional functionality.

Tuesday, October 20, 2009

from numpy import *

Tuesday, October 20, 2009

from numpy import *

Tuesday, October 20, 2009

from numpy import *

Tuesday, October 20, 2009

from numpy import *

Tuesday, October 20, 2009

from numpy import *

Tuesday, October 20, 2009

from numpy import *

Array slicing is a natural extension of list slicing

Tuesday, October 20, 2009

from numpy import *

Tuesday, October 20, 2009

from numpy import *

Tuesday, October 20, 2009

from numpy import *

This can substantially increase the efficiency of your code.

NumPy arrays have

Tuesday, October 20, 2009

from numpy import *

an order for the indices

Tuesday, October 20, 2009

from numpy import *

abbreviated command summary

abbreviated summary of array methods

Tuesday, October 20, 2009

Tuesday, October 20, 2009

One often needs to generate

One often needs to generate

Tuesday, October 20, 2009

Tuesday, October 20, 2009

Tuesday, October 20, 2009

The random module within NumPy

The random module within NumPy

The NumPy random module allows

Tuesday, October 20, 2009

Watch out for namespace collision!

Tuesday, October 20, 2009

from scipy import *

Tuesday, October 20, 2009

from scipy import linalg

In linear algebra, one frequently needs to solve systems of equations taking

we could determine the values in b by

Tuesday, October 20, 2009

from scipy import linalg

Returns the inverse of matrix a

Compute the inverse

Tuesday, October 20, 2009

Sometimes we need to get data

On macintosh, youll have to

Tuesday, October 20, 2009

denotes a unicode string

get information about a specific sheet