Tentative_Numpy_Tutorial.txt

Prerequisites

Before reading this tutorial you should know a bit of Python. If you would like
to refresh your memory, take a look at the Python tutorial.  If you wish to
work the examples in this tutorial, you must also have some software installed
on your computer. Minimally: 
    Python
    NumPy

These you may find useful:

ipython is an enhanced interactive Python shell which is very convenient for
exploring NumPy's features matplotlib will enable you to plot graphics SciPy
provides a lot of scientific routines that work on top of NumPy

The Basics

NumPy's main object is the homogeneous multidimensional array. It is a table of
elements (usually numbers), all of the same type, indexed by a tuple of
positive integers. In Numpy dimensions are called axes. The number of axes is
rank.

For example, the coordinates of a point in 3D space [1, 2, 1] is an array of
rank 1, because it has one axis. That axis has a length of 3. In example
pictured below, the array has rank 2 (it is 2-dimensional). The first dimension
(axis) has a length of 2, the second dimension has a length of 3.

[[ 1., 0., 0.],
 [ 0., 1., 2.]]

Numpy's array class is called ndarray. It is also known by the alias array.
Note that numpy.array is not the same as the Standard Python Library class
array.array, which only handles one-dimensional arrays and offers less
functionality. The more important attributes of an ndarray object are:
ndarray.ndim

the number of axes (dimensions) of the array. In the Python world, the number
of dimensions is referred to as rank.  ndarray.shape

the dimensions of the array. This is a tuple of integers indicating the size of
the array in each dimension. For a matrix with n rows and m columns, shape will
be (n,m). The length of the shape tuple is therefore the rank, or number of
dimensions, ndim.  ndarray.size

the total number of elements of the array. This is equal to the product of the
elements of shape.  ndarray.dtype

an object describing the type of the elements in the array. One can create or
specify dtype's using standard Python types. Additionally NumPy provides types
of its own. numpy.int32, numpy.int16, and numpy.float64 are some examples.
ndarray.itemsize

the size in bytes of each element of the array. For example, an array of
elements of type float64 has itemsize 8 (=64/8), while one of type complex32
has itemsize 4 (=32/8). It is equivalent to ndarray.dtype.itemsize.
ndarray.data

the buffer containing the actual elements of the array. Normally, we won't need
to use this attribute because we will access the elements in an array using
indexing facilities.

An example
>>> from numpy  import *
>>> a = arange(15).reshape(3, 5)
>>> a
array([[ 0,  1,  2,  3,  4],
       [ 5,  6,  7,  8,  9],
       [10, 11, 12, 13, 14]])
>>> a.shape
(3, 5)
>>> a.ndim
2
>>> a.dtype.name
'int32'
>>> a.itemsize
4
>>> a.size
15
>>> type(a)
numpy.ndarray
>>> b = array([6, 7, 8])
>>> b
array([6, 7, 8])
>>> type(b)
numpy.ndarray

Array Creation
===== ========

There are several ways to create arrays.

For example, you can create an array from a regular Python list or tuple using
the array function. The type of the resulting array is deduced from the type of
the elements in the sequences.

>>> from numpy  import *
>>> a = array( [2,3,4] )
>>> a
array([2, 3, 4])
>>> a.dtype
dtype('int32')
>>> b = array([1.2, 3.5, 5.1])
>>> b.dtype
dtype('float64')

A frequent error consists in calling array with multiple numeric arguments,
rather than providing a single list of numbers as an argument.

>>> a = array(1,2,3,4)    # WRONG

>>> a = array([1,2,3,4])  # RIGHT

array transforms sequences of sequences into two-dimensional arrays, sequences
of sequences of sequences into three-dimensional arrays, and so on.

>>> b = array( [ (1.5,2,3), (4,5,6) ] )
>>> b
array([[ 1.5,  2. ,  3. ],
       [ 4. ,  5. ,  6. ]])

The type of the array can also be explicitly specified at creation time:

>>> c = array( [ [1,2], [3,4] ], dtype=complex )
>>> c
array([[ 1.+0.j,  2.+0.j],
       [ 3.+0.j,  4.+0.j]])

Often, the elements of an array are originally unknown, but its size is known.
Hence, NumPy offers several functions to create arrays with initial placeholder
content. These minimize the necessity of growing arrays, an expensive
operation.  The function zeros creates an array full of zeros, the function
ones creates an array full of ones, and the function empty creates an array
whose initial content is random and depends on the state of the memory. By
default, the dtype of the created array is float64.

>>> zeros( (3,4) )
array([[0.,  0.,  0.,  0.],
       [0.,  0.,  0.,  0.],
       [0.,  0.,  0.,  0.]])
>>> ones( (2,3,4), dtype=int16 )                # dtype can also be specified
array([[[ 1, 1, 1, 1],
        [ 1, 1, 1, 1],
        [ 1, 1, 1, 1]],
       [[ 1, 1, 1, 1],
        [ 1, 1, 1, 1],
        [ 1, 1, 1, 1]]], dtype=int16)
>>> empty( (2,3) )
array([[  3.73603959e-262,   6.02658058e-154,   6.55490914e-260],
       [  5.30498948e-313,   3.14673309e-307,   1.00000000e+000]])

To create sequences of numbers, NumPy provides a function analogous to range
that returns arrays instead of lists

>>> arange( 10, 30, 5 )
array([10, 15, 20, 25])
>>> arange( 0, 2, 0.3 )                 # it accepts float arguments
array([ 0. ,  0.3,  0.6,  0.9,  1.2,  1.5,  1.8])

When arange is used with floating point arguments, it is generally not possible
to predict the number of elements obtained, due to the finite floating point
precision. For this reason, it is usually better to use the function linspace
that receives as an argument the number of elements that we want, instead of
the step:

>>> linspace( 0, 2, 9 )                 # 9 numbers from 0 to 2
array([ 0.  ,  0.25,  0.5 ,  0.75,  1.  ,  1.25,  1.5 ,  1.75,  2.  ])
>>> x = linspace( 0, 2*pi, 100 )        # useful to evaluate function at lots of points
>>> f = sin(x)

See also: array, zeros, zeros_like, ones, ones_like, empty, empty_like, arange,
linspace, rand, randn, fromfunction, fromfile

Printing Arrays

When you print an array, NumPy displays it in a similar way to nested lists,
but with the following layout: the last axis is printed from left to right, the
second-to-last is printed from top to bottom, the rest are also printed from
top to bottom, with each slice separated from the next by an empty line.
One-dimensional arrays are then printed as rows, bidimensionals as matrices and
tridimensionals as lists of matrices.

>>> a = arange(6)                         # 1d array
>>> print a
[0 1 2 3 4 5]
>>>
>>> b = arange(12).reshape(4,3)           # 2d array
>>> print b
[[ 0  1  2]
 [ 3  4  5]
 [ 6  7  8]
 [ 9 10 11]]
>>>
>>> c = arange(24).reshape(2,3,4)         # 3d array
>>> print c
[[[ 0  1  2  3]
  [ 4  5  6  7]
  [ 8  9 10 11]]

 [[12 13 14 15]
  [16 17 18 19]
  [20 21 22 23]]]

See below to get more details on reshape.  If an array is too large to be
printed, NumPy automatically skips the central part of the array and only
prints the corners:

>>> print arange(10000)
[   0    1    2 ..., 9997 9998 9999]
>>>
>>> print arange(10000).reshape(100,100)
[[   0    1    2 ...,   97   98   99]
 [ 100  101  102 ...,  197  198  199]
 [ 200  201  202 ...,  297  298  299]
 ...,
 [9700 9701 9702 ..., 9797 9798 9799]
 [9800 9801 9802 ..., 9897 9898 9899]
 [9900 9901 9902 ..., 9997 9998 9999]]

To disable this behaviour and force NumPy to print the entire array, you can
change the printing options using set_printoptions.

>>> set_printoptions(threshold='nan')

Basic Operations
===== ==========

Arithmetic operators on arrays apply elementwise. A new array is created and
filled with the result.

>>> a = array( [20,30,40,50] )
>>> b = arange( 4 )
>>> b
array([0, 1, 2, 3])
>>> c = a-b
>>> c
array([20, 29, 38, 47])
>>> b**2
array([0, 1, 4, 9])
>>> 10*sin(a)
array([ 9.12945251, -9.88031624,  7.4511316 , -2.62374854])
>>> a<35
array([True, True, False, False], dtype=bool)

Unlike in many matrix languages, the product operator * operates elementwise in
NumPy arrays. The matrix product can be performed using the dot function or
creating matrix objects ( see matrix section of this tutorial ).

>>> A = array( [[1,1],
...             [0,1]] )
>>> B = array( [[2,0],
...             [3,4]] )
>>> A*B                         # elementwise product
array([[2, 0],
       [0, 4]])
>>> dot(A,B)                    # matrix product
array([[5, 4],
       [3, 4]])

Some operations, such as += and *=, act in place to modify an existing array
rather than create a new one.

>>> a = ones((2,3), dtype=int)
>>> b = random.random((2,3))
>>> a *= 3
>>> a
array([[3, 3, 3],
       [3, 3, 3]])
>>> b += a
>>> b
array([[ 3.69092703,  3.8324276 ,  3.0114541 ],
       [ 3.18679111,  3.3039349 ,  3.37600289]])
>>> a += b                                  # b is converted to integer type
>>> a
array([[6, 6, 6],
       [6, 6, 6]])

When operating with arrays of different types, the type of the resulting array
corresponds to the more general or precise one (a behavior known as upcasting).

>>> a = ones(3, dtype=int32)
>>> b = linspace(0,pi,3)
>>> b.dtype.name
'float64'
>>> c = a+b
>>> c
array([ 1.        ,  2.57079633,  4.14159265])
>>> c.dtype.name
'float64'
>>> d = exp(c*1j)
>>> d
array([ 0.54030231+0.84147098j, -0.84147098+0.54030231j,
       -0.54030231-0.84147098j])
>>> d.dtype.name
'complex128'

Many unary operations, such as computing the sum of all the elements in the
array, are implemented as methods of the ndarray class.

>>> a = random.random((2,3))
>>> a
array([[ 0.6903007 ,  0.39168346,  0.16524769],
       [ 0.48819875,  0.77188505,  0.94792155]])
>>> a.sum()
3.4552372100521485
>>> a.min()
0.16524768654743593
>>> a.max()
0.9479215542670073

By default, these operations apply to the array as though it were a list of
numbers, regardless of its shape. However, by specifying the axis parameter you
can apply an operation along the specified axis of an array:

>>> b = arange(12).reshape(3,4)
>>> b
array([[ 0,  1,  2,  3],
       [ 4,  5,  6,  7],
       [ 8,  9, 10, 11]])
>>>
>>> b.sum(axis=0)                            # sum of each column
array([12, 15, 18, 21])
>>>
>>> b.min(axis=1)                            # min of each row
array([0, 4, 8])
>>>
>>> b.cumsum(axis=1)                         # cumulative sum along each row
array([[ 0,  1,  3,  6],
       [ 4,  9, 15, 22],
       [ 8, 17, 27, 38]])

Universal Functions
========= =========

NumPy provides familiar mathematical functions such as sin, cos, and exp. In
NumPy, these are called "universal functions"(ufunc). Within NumPy, these
functions operate elementwise on an array, producing an array as output.

>>> B = arange(3)
>>> B
array([0, 1, 2])
>>> exp(B)
array([ 1.        ,  2.71828183,  7.3890561 ])
>>> sqrt(B)
array([ 0.        ,  1.        ,  1.41421356])
>>> C = array([2., -1., 4.])
>>> add(B, C)
array([ 2.,  0.,  6.])

See also: all, alltrue, any, apply along axis, argmax, argmin, argsort,
average, bincount, ceil, clip, conj, conjugate, corrcoef, cov, cross, cumprod,
cumsum, diff, dot, floor, inner, inv, lexsort, max, maximum, mean, median, min,
minimum, nonzero, outer, prod, re, round, sometrue, sort, std, sum, trace,
transpose, var, vdot, vectorize, where Indexing, Slicing and Iterating

One-dimensional arrays can be indexed, sliced and iterated over, much like
lists and other Python sequences.

>>> a = arange(10)**3
>>> a
array([  0,   1,   8,  27,  64, 125, 216, 343, 512, 729])
>>> a[2]
8
>>> a[2:5]
array([ 8, 27, 64])
>>> a[:6:2] = -1000    # equivalent to a[0:6:2] = -1000; from start to position
                       # 6, exclusive, set every 2nd element to -1000
>>> a
array([-1000,     1, -1000,    27, -1000,   125,   216,   343,   512,   729])
>>> a[ : :-1]                                 # reversed a
array([  729,   512,   343,   216,   125, -1000,    27, -1000,     1, -1000])
>>> for i in a:
...         print i**(1/3.),
...
nan 1.0 nan 3.0 nan 5.0 6.0 7.0 8.0 9.0

Multidimensional arrays can have one index per axis. These indices are given in
a tuple separated by commas:

>>> def f(x,y):
...         return 10*x+y
...
>>> b = fromfunction(f,(5,4),dtype=int)
>>> b
array([[ 0,  1,  2,  3],
       [10, 11, 12, 13],
       [20, 21, 22, 23],
       [30, 31, 32, 33],
       [40, 41, 42, 43]])
>>> b[2,3]
23
>>> b[0:5, 1]                       # each row in the second column of b
array([ 1, 11, 21, 31, 41])
>>> b[ : ,1]                        # equivalent to the previous example
array([ 1, 11, 21, 31, 41])
>>> b[1:3, : ]                      # each column in the second and third row of b
array([[10, 11, 12, 13],
       [20, 21, 22, 23]])

When fewer indices are provided than the number of axes, the missing indices
are considered complete slices:

>>> b[-1]                                  # the last row. Equivalent to b[-1,:]
array([40, 41, 42, 43])

The expression within brackets in b[i] is treated as an i followed by as many
instances of : as needed to represent the remaining axes. NumPy also allows you
to write this using dots as b[i,...].  The dots (...) represent as many colons
as needed to produce a complete indexing tuple. For example, if x is a rank 5
array (i.e., it has 5 axes), then

x[1,2,...] is equivalent to x[1,2,:,:,:],
x[...,3] to x[:,:,:,:,3] and
x[4,...,5,:] to x[4,:,:,5,:].

>>> c = array( [ [[  0,  1,  2],          # a 3D array (two stacked 2D arrays)
...               [ 10, 12, 13]],
...
...              [[100,101,102],
...               [110,112,113]] ] )
>>> c.shape
(2, 2, 3)
>>> c[1,...]                                   # same as c[1,:,:] or c[1]
array([[100, 101, 102],
       [110, 112, 113]])
>>> c[...,2]                                   # same as c[:,:,2]
array([[  2,  13],
       [102, 113]])
Iterating over multidimensional arrays is done with respect to the first axis:
>>> for row in b:
...         print row
...
[0 1 2 3]
[10 11 12 13]
[20 21 22 23]
[30 31 32 33]
[40 41 42 43]

However, if one wants to perform an operation on each element in the array, one
can use the flat attribute which is an iterator over all the elements of the
array:

>>> for element in b.flat:
...         print element,
...
0 1 2 3 10 11 12 13 20 21 22 23 30 31 32 33 40 41 42 43
See also
[], ..., newaxis, ndenumerate, indices, index exp
Shape Manipulation
Changing the shape of an array
An array has a shape given by the number of elements along each axis:
>>> a = floor(10*random.random((3,4)))
>>> a
array([[ 7.,  5.,  9.,  3.],
       [ 7.,  2.,  7.,  8.],
       [ 6.,  8.,  3.,  2.]])
>>> a.shape
(3, 4)
The shape of an array can be changed with various commands:
>>> a.ravel() # flatten the array
array([ 7.,  5.,  9.,  3.,  7.,  2.,  7.,  8.,  6.,  8.,  3.,  2.])
>>> a.shape = (6, 2)
>>> a.transpose()
array([[ 7.,  9.,  7.,  7.,  6.,  3.],
       [ 5.,  3.,  2.,  8.,  8.,  2.]])

The order of the elements in the array resulting from ravel() is normally
"C-style", that is, the rightmost index "changes the fastest", so the element
after a[0,0] is a[0,1]. If the array is reshaped to some other shape, again the
array is treated as "C-style". Numpy normally creates arrays stored in this
order, so ravel() will usually not need to copy its argument, but if the array
was made by taking slices of another array or created with unusual options, it
may need to be copied. The functions ravel() and reshape() can also be
instructed, using an optional argument, to use FORTRAN-style arrays, in which
the leftmost index changes the fastest.  The reshape function returns its
argument with a modified shape, whereas the resize method modifies the array
itself:

>>> a
array([[ 7.,  5.],
       [ 9.,  3.],
       [ 7.,  2.],
       [ 7.,  8.],
       [ 6.,  8.],
       [ 3.,  2.]])
>>> a.resize((2,6))
>>> a
array([[ 7.,  5.,  9.,  3.,  7.,  2.],
       [ 7.,  8.,  6.,  8.,  3.,  2.]])

If a dimension is given as -1 in a reshaping operation, the other dimensions
are automatically calculated:

>>> a.reshape(3,-1)
array([[ 7.,  5.,  9.,  3.],
       [ 7.,  2.,  7.,  8.],
       [ 6.,  8.,  3.,  2.]])

See also:: shape example, reshape example, resize example, ravel example

Stacking together different arrays
Several arrays can be stacked together along different axes:

>>> a = floor(10*random.random((2,2)))
>>> a
array([[ 1.,  1.],
       [ 5.,  8.]])
>>> b = floor(10*random.random((2,2)))
>>> b
array([[ 3.,  3.],
       [ 6.,  0.]])
>>> vstack((a,b))
array([[ 1.,  1.],
       [ 5.,  8.],
       [ 3.,  3.],
       [ 6.,  0.]])
>>> hstack((a,b))
array([[ 1.,  1.,  3.,  3.],
       [ 5.,  8.,  6.,  0.]])

The function column_stack stacks 1D arrays as columns into a 2D array. It is
equivalent to vstack only for 1D arrays:

>>> column_stack((a,b))   # With 2D arrays
array([[ 1.,  1.,  3.,  3.],
       [ 5.,  8.,  6.,  0.]])
>>> a=array([4.,2.])
>>> b=array([2.,8.])
>>> a[:,newaxis]  # This allows to have a 2D columns vector
array([[ 4.],
       [ 2.]])
>>> column_stack((a[:,newaxis],b[:,newaxis]))
array([[ 4.,  2.],
       [ 2.,  8.]])
>>> vstack((a[:,newaxis],b[:,newaxis])) # The behavior of vstack is different
array([[ 4.],
       [ 2.],
       [ 2.],
       [ 8.]])

The function row_stack, on the other hand, stacks 1D arrays as rows into a 2D
array.  For arrays of with more than two dimensions, hstack stacks along their
second axes, vstack stacks along their first axes, and concatenate allows for
an optional arguments giving the number of the axis along which the
concatenation should happen.  Note In complex cases, r_[] and c_[] are useful
for creating arrays by stacking numbers along one axis. They allow the use of
range literals (":") :

>>> r_[1:4,0,4]
array([1, 2, 3, 0, 4])

When used with arrays as arguments, r_[] and c_[] are similar to vstack and
hstack in their default behavior, but allow for an optional argument giving the
number of the axis along which to concatenate.

See also: hstack example, vstack exammple, column_stack example, row_stack
example, concatenate example, c_ example, r_ example Splitting one array into
several smaller ones Using hsplit, you can split an array along its horizontal
axis, either by specifying the number of equally shaped arrays to return, or by
specifying the columns after which the division should occur:

>>> a = floor(10*random.random((2,12)))
>>> a
array([[ 8.,  8.,  3.,  9.,  0.,  4.,  3.,  0.,  0.,  6.,  4.,  4.],
       [ 0.,  3.,  2.,  9.,  6.,  0.,  4.,  5.,  7.,  5.,  1.,  4.]])
>>> hsplit(a,3)   # Split a into 3
[array([[ 8.,  8.,  3.,  9.],
       [ 0.,  3.,  2.,  9.]]), array([[ 0.,  4.,  3.,  0.],
       [ 6.,  0.,  4.,  5.]]), array([[ 0.,  6.,  4.,  4.],
       [ 7.,  5.,  1.,  4.]])]
>>> hsplit(a,(3,4))   # Split a after the third and the fourth column
[array([[ 8.,  8.,  3.],
       [ 0.,  3.,  2.]]), array([[ 9.],
       [ 9.]]), array([[ 0.,  4.,  3.,  0.,  0.,  6.,  4.,  4.],
       [ 6.,  0.,  4.,  5.,  7.,  5.,  1.,  4.]])]

vsplit splits along the vertical axis, and array split allows one to specify
along which axis to split.

Copies and Views

When operating and manipulating arrays, their data is sometimes copied into a
new array and sometimes not. This is often a source of confusion for beginners.
There are three cases:

No Copy at All
Simple assignments make no copy of array objects or of their data.

>>> a = arange(12)
>>> b = a            # no new object is created
>>> b is a           # a and b are two names for the same ndarray object
True
>>> b.shape = 3,4    # changes the shape of a
>>> a.shape
(3, 4)
Python passes mutable objects as references, so function calls make no copy.
>>> def f(x):
...     print id(x)
...
>>> id(a)                           # id is a unique identifier of an object
148293216
>>> f(a)
148293216

View or Shallow Copy

Different array objects can share the same data. The view method creates a new
array object that looks at the same data.

>>> c = a.view()
>>> c is a
False
>>> c.base is a                        # c is a view of the data owned by a
True
>>> c.flags.owndata
False
>>>
>>> c.shape = 2,6                      # a's shape doesn't change
>>> a.shape
(3, 4)
>>> c[0,4] = 1234                      # a's data changes
>>> a
array([[   0,    1,    2,    3],
       [1234,    5,    6,    7],
       [   8,    9,   10,   11]])
Slicing an array returns a view of it:
>>> s = a[ : , 1:3]     # spaces added for clarity; could also be written "s = a[:,1:3]"
>>> s[:] = 10           # s[:] is a view of s. Note the difference between s=10 and s[:]=10
>>> a
array([[   0,   10,   10,    3],
       [1234,   10,   10,    7],
       [   8,   10,   10,   11]])

Deep Copy

The copy method makes a complete copy of the array and its data.

>>> d = a.copy()                          # a new array object with new data is created
>>> d is a
False
>>> d.base is a                           # d doesn't share anything with a
False
>>> d[0,0] = 9999
>>> a
array([[   0,   10,   10,    3],
       [1234,   10,   10,    7],
       [   8,   10,   10,   11]])

Functions and Methods Overview

Here is a list of NumPy functions and methods names ordered in some categories.
The names link to the Numpy Example List so that you can see the functions in
action.

Array Creation

arange, array, copy, empty, empty_like, eye, fromfile, fromfunction, identity,
linspace, logspace, mgrid, ogrid, ones, ones_like, r , zeros, zeros_like

Conversions

astype, atleast 1d, atleast 2d, atleast 3d, mat

Manipulations

array split, column stack, concatenate, diagonal, dsplit, dstack, hsplit,
hstack, item, newaxis, ravel, repeat, reshape, resize, squeeze, swapaxes, take,
transpose, vsplit, vstack

Questions

all, any, nonzero, where

Ordering

argmax, argmin, argsort, max, min, ptp, searchsorted, sort

Operations

choose, compress, cumprod, cumsum, inner, fill, imag, prod, put, putmask, real,
sum

Basic Statistics
cov, mean, std, var

Basic Linear Algebra
cross, dot, outer, svd, vdot

Less Basic

Broadcasting rules

Broadcasting allows universal functions to deal in a meaningful way with inputs
that do not have exactly the same shape.  The first rule of broadcasting is
that if all input arrays do not have the same number of dimensions, a "1" will
be repeatedly prepended to the shapes of the smaller arrays until all the
arrays have the same number of dimensions.  The second rule of broadcasting
ensures that arrays with a size of 1 along a particular dimension act as if
they had the size of the array with the largest shape along that dimension. The
value of the array element is assumed to be the same along that dimension for
the "broadcast" array.  After application of the broadcasting rules, the sizes
of all arrays must match. More details can be found in this documentation.

Fancy indexing and index tricks

NumPy offers more indexing facilities than regular Python sequences. In
addition to indexing by integers and slices, as we saw before, arrays can be
indexed by arrays of integers and arrays of booleans.

Indexing with Arrays of Indices

>>> a = arange(12)**2                          # the first 12 square numbers
>>> i = array( [ 1,1,3,8,5 ] )                 # an array of indices
>>> a[i]                                       # the elements of a at the positions i
array([ 1,  1,  9, 64, 25])
>>>
>>> j = array( [ [ 3, 4], [ 9, 7 ] ] )         # a bidimensional array of indices
>>> a[j]                                       # the same shape as j
array([[ 9, 16],
       [81, 49]])

When the indexed array a is multidimensional, a single array of indices refers
to the first dimension of a. The following example shows this behavior by
converting an image of labels into a color image using a palette.

>>> palette = array( [ [0,0,0],                # black
...                    [255,0,0],              # red
...                    [0,255,0],              # green
...                    [0,0,255],              # blue
...                    [255,255,255] ] )       # white
>>> image = array( [ [ 0, 1, 2, 0 ],           # each value corresponds to a color in the palette
...                  [ 0, 3, 4, 0 ]  ] )
>>> palette[image]                            # the (2,4,3) color image
array([[[  0,   0,   0],
        [255,   0,   0],
        [  0, 255,   0],
        [  0,   0,   0]],
       [[  0,   0,   0],
        [  0,   0, 255],
        [255, 255, 255],
        [  0,   0,   0]]])

We can also give indexes for more than one dimension. The arrays of indices for
each dimension must have the same shape.

>>> a = arange(12).reshape(3,4)
>>> a
array([[ 0,  1,  2,  3],
       [ 4,  5,  6,  7],
       [ 8,  9, 10, 11]])
>>> i = array( [ [0,1],                        # indices for the first dim of a
...              [1,2] ] )
>>> j = array( [ [2,1],                        # indices for the second dim
...              [3,3] ] )
>>>
>>> a[i,j]                                     # i and j must have equal shape
array([[ 2,  5],
       [ 7, 11]])
>>>
>>> a[i,2]
array([[ 2,  6],
       [ 6, 10]])
>>>
>>> a[:,j]                                     # i.e., a[ : , j]
array([[[ 2,  1],
        [ 3,  3]],
       [[ 6,  5],
        [ 7,  7]],
       [[10,  9],
        [11, 11]]])

Naturally, we can put i and j in a sequence (say a list) and then do the
indexing with the list.

>>> l = [i,j]
>>> a[l]                                       # equivalent to a[i,j]
array([[ 2,  5],
       [ 7, 11]])

However, we can not do this by putting i and j into an array, because this
array will be interpreted as indexing the first dimension of a.

>>> s = array( [i,j] )
>>> a[s]                                       # not what we want
Traceback (most recent call last):
  File "<stdin>", line 1, in ?
IndexError: index (3) out of range (0<=index<=2) in dimension 0
>>>
>>> a[tuple(s)]                                # same as a[i,j]
array([[ 2,  5],
       [ 7, 11]])

Another common use of indexing with arrays is the search of the maximum value
of time-dependent series :

>>> time = linspace(20, 145, 5)                 # time scale
>>> data = sin(arange(20)).reshape(5,4)         # 4 time-dependent series
>>> time
array([  20.  ,   51.25,   82.5 ,  113.75,  145.  ])
>>> data
array([[ 0.        ,  0.84147098,  0.90929743,  0.14112001],
       [-0.7568025 , -0.95892427, -0.2794155 ,  0.6569866 ],
       [ 0.98935825,  0.41211849, -0.54402111, -0.99999021],
       [-0.53657292,  0.42016704,  0.99060736,  0.65028784],
       [-0.28790332, -0.96139749, -0.75098725,  0.14987721]])
>>>
>>> ind = data.argmax(axis=0)        # index of the maxima for each series
>>> ind
array([2, 0, 3, 1])
>>>
>>> time_max = time[ ind]            # times corresponding to the maxima
>>>
>>> data_max = data[ind, xrange(data.shape[1])] # => data[ind[0],0], data[ind[1],1]...
>>>
>>> time_max
array([  82.5 ,   20.  ,  113.75,   51.25])
>>> data_max
array([ 0.98935825,  0.84147098,  0.99060736,  0.6569866 ])
>>>
>>> all(data_max == data.max(axis=0))
True
You can also use indexing with arrays as a target to assign to:
>>> a = arange(5)
>>> a
array([0, 1, 2, 3, 4])
>>> a[[1,3,4]] = 0
>>> a
array([0, 0, 2, 0, 0])

However, when the list of indices contains repetitions, the assignment is done
several times, leaving behind the last value:

>>> a = arange(5)
>>> a[[0,0,2]]=[1,2,3]
>>> a
array([2, 1, 3, 3, 4])

This is reasonable enough, but watch out if you want to use Python's +=
construct, as it may not do what you expect:

>>> a = arange(5)
>>> a[[0,0,2]]+=1
>>> a
array([1, 1, 3, 3, 4])

Even though 0 occurs twice in the list of indices, the 0th element is only
incremented once. This is because Python requires "a+=1" to be equivalent to
"a=a+1".

Indexing with Boolean Arrays

When we index arrays with arrays of (integer) indices we are providing the list
of indices to pick. With boolean indices the approach is different; we
explicitly choose which items in the array we want and which ones we don't.
The most natural way one can think of for boolean indexing is to use boolean
arrays that have the same shape as the original array:

>>> a = arange(12).reshape(3,4)
>>> b = a > 4
>>> b                                          # b is a boolean with a's shape
array([[False, False, False, False],
       [False, True, True, True],
       [True, True, True, True]], dtype=bool)
>>> a[b]                                       # 1d array with the selected elements
array([ 5,  6,  7,  8,  9, 10, 11])
This property can be very useful in assignments:
>>> a[b] = 0                                   # All elements of 'a' higher than 4 become 0
>>> a
array([[0, 1, 2, 3],
       [4, 0, 0, 0],
       [0, 0, 0, 0]])

You can look at the Mandelbrot set example to see how to use boolean indexing
to generate an image of the Mandelbrot set.  The second way of indexing with
booleans is more similar to integer indexing; for each dimension of the array
we give a 1D boolean array selecting the slices we want.

>>> a = arange(12).reshape(3,4)
>>> b1 = array([False,True,True])             # first dim selection
>>> b2 = array([True,False,True,False])       # second dim selection
>>>
>>> a[b1,:]                                   # selecting rows
array([[ 4,  5,  6,  7],
       [ 8,  9, 10, 11]])
>>>
>>> a[b1]                                     # same thing
array([[ 4,  5,  6,  7],
       [ 8,  9, 10, 11]])
>>>
>>> a[:,b2]                                   # selecting columns
array([[ 0,  2],
       [ 4,  6],
       [ 8, 10]])
>>>
>>> a[b1,b2]                                  # a weird thing to do
array([ 4, 10])

Note that the length of the 1D boolean array must coincide with the length of
the dimension (or axis) you want to slice. In the previous example, b1 is a
1-rank array with length 3 (the number of rows in a), and b2 (of length 4) is
suitable to index the 2nd rank (columns) of a.

The ix_() function

The ix_ function can be used to combine different vectors so as to obtain the
result for each n-uplet. For example, if you want to compute all the a+b*c for
all the triplets taken from each of the vectors a, b and c:

>>> a = array([2,3,4,5])
>>> b = array([8,5,4])
>>> c = array([5,4,6,8,3])
>>> ax,bx,cx = ix_(a,b,c)
>>> ax
array([[[2]],

       [[3]],

       [[4]],

       [[5]]])
>>> bx
array([[[8],
        [5],
        [4]]])
>>> cx
array([[[5, 4, 6, 8, 3]]])
>>> ax.shape, bx.shape, cx.shape
((4, 1, 1), (1, 3, 1), (1, 1, 5))
>>> result = ax+bx*cx
>>> result
array([[[42, 34, 50, 66, 26],
        [27, 22, 32, 42, 17],
        [22, 18, 26, 34, 14]],
       [[43, 35, 51, 67, 27],
        [28, 23, 33, 43, 18],
        [23, 19, 27, 35, 15]],
       [[44, 36, 52, 68, 28],
        [29, 24, 34, 44, 19],
        [24, 20, 28, 36, 16]],
       [[45, 37, 53, 69, 29],
        [30, 25, 35, 45, 20],
        [25, 21, 29, 37, 17]]])
>>> result[3,2,4]
17
>>> a[3]+b[2]*c[4]
17
You could also implement the reduce as follows:
def ufunc_reduce(ufct, *vectors):
    vs = ix_(*vectors)
    r = ufct.identity
    for v in vs:
        r = ufct(r,v)
    return r
and then use it as:
>>> ufunc_reduce(add,a,b,c)
array([[[15, 14, 16, 18, 13],
        [12, 11, 13, 15, 10],
        [11, 10, 12, 14,  9]],
       [[16, 15, 17, 19, 14],
        [13, 12, 14, 16, 11],
        [12, 11, 13, 15, 10]],
       [[17, 16, 18, 20, 15],
        [14, 13, 15, 17, 12],
        [13, 12, 14, 16, 11]],
       [[18, 17, 19, 21, 16],
        [15, 14, 16, 18, 13],
        [14, 13, 15, 17, 12]]])

The advantage of this version of reduce compared to the normal ufunc.reduce is
that it makes use of the Broadcasting Rules in order to avoid creating an
argument array the size of the output times the number of vectors.

Indexing with strings

See RecordArrays.

Linear Algebra
Work in progress. Basic linear algebra to be included here.

Simple Array Operations

See linalg.py in numpy folder for more.

>>> from numpy import *
>>> from numpy.linalg import *

>>> a = array([[1.0, 2.0], [3.0, 4.0]])
>>> print a
[[ 1.  2.]
 [ 3.  4.]]

>>> a.transpose()
array([[ 1.,  3.],
       [ 2.,  4.]])

>>> inv(a)
array([[-2. ,  1. ],
       [ 1.5, -0.5]])

>>> u = eye(2) # unit 2x2 matrix; "eye" represents "I"
>>> u
array([[ 1.,  0.],
       [ 0.,  1.]])
>>> j = array([[0.0, -1.0], [1.0, 0.0]])

>>> dot (j, j) # matrix product
array([[-1.,  0.],
       [ 0., -1.]])

>>> trace(u)  # trace
2.0

>>> y = array([[5.], [7.]])
>>> solve(a, y)
array([[-3.],
       [ 4.]])

>>> eig(j)
(array([ 0.+1.j,  0.-1.j]),
array([[ 0.70710678+0.j,  0.70710678+0.j],
       [ 0.00000000-0.70710678j,  0.00000000+0.70710678j]]))
Parameters:
    square matrix

Returns
    The eigenvalues, each repeated according to its multiplicity.

    The normalized (unit "length") eigenvectors, such that the
    column ``v[:,i]`` is the eigenvector corresponding to the
    eigenvalue ``w[i]`` .
The Matrix Class
Here is a short intro to the Matrix class.
>>> A = matrix('1.0 2.0; 3.0 4.0')
>>> A
[[ 1.  2.]
 [ 3.  4.]]
>>> type(A)  # file where class is defined
<class 'numpy.matrixlib.defmatrix.matrix'>

>>> A.T  # transpose
[[ 1.  3.]
 [ 2.  4.]]

>>> X = matrix('5.0 7.0')
>>> Y = X.T
>>> Y
[[5.]
 [7.]]

>>> print A*Y  # matrix multiplication
[[19.]
 [43.]]

>>> print A.I  # inverse
[[-2.   1. ]
 [ 1.5 -0.5]]

>>> solve(A, Y)  # solving linear equation
matrix([[-3.],
        [ 4.]])

Indexing: Comparing Matrices and 2D Arrays Note that there are some important
differences between NumPy arrays and matrices. NumPy provides two fundamental
objects: an N-dimensional array object and a universal function object. Other
objects are built on top of these. In particular, matrices are 2-dimensional
array objects that inherit from the NumPy array object. For both arrays and
matrices, indices must consist of a proper combination of one or more of the
following: integer scalars, ellipses, a list of integers or boolean values, a
tuple of integers or boolean values, and a 1-dimensional array of integer or
boolean values. A matrix can be used as an index for matrices, but commonly an
array, list, or other form is needed to accomplish a given task.  As usual in
Python, indexing is zero-based. Traditionally we represent a 2D array or matrix
as a rectangular array of rows and columns, where movement along axis 0 is
movement across rows, while movement along axis 1 is movement across columns.
Let's make an array and matrix to slice:

>>> A = arange(12)
>>> A
array([ 0,  1,  2,  3,  4,  5,  6,  7,  8,  9, 10, 11])
>>> A.shape = (3,4)
>>> M = mat(A.copy())
>>> print type(A),"  ",type(M)
<type 'numpy.ndarray'>    <class 'numpy.core.defmatrix.matrix'>
>>> print A
[[ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]]
>>> print M
[[ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]]

Now, let's take some simple slices. Basic slicing uses slice objects or
integers. For example, the evaluation of A[:] and M[:] will appear familiar
from Python indexing, however it is important to note that slicing NumPy arrays
does *not* make a copy of the data; slicing provides a new view of the same
data.

>>> print A[:]; print A[:].shape
[[ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]]
(3, 4)
>>> print M[:]; print M[:].shape
[[ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]]
(3, 4)

Now for something that differs from Python indexing: you may use
comma-separated indices to index along multiple axes at the same time.

>>> print A[:,1]; print A[:,1].shape
[1 5 9]
(3,)
>>> print M[:,1]; print M[:,1].shape
[[1]
 [5]
 [9]]
(3, 1)

Notice the difference in the last two results. Use of a single colon for the 2D
array produces a 1-dimensional array, while for a matrix it produces a
2-dimensional matrix. A slice of a matrix will always produce a matrix. For
example, a slice M[2,:] produces a matrix of shape (1,4). In contrast, a slice
of an array will always produce an array of the lowest possible dimension. For
example, if C were a 3-dimensional array, C[...,1] produces a 2D array while
C[1,:,1] produces a 1-dimensional array. From this point on, we will show
results only for the array slice if the results for the corresponding matrix
slice are identical.  Lets say that we wanted the 1st and 3rd column of an
array. One way is to slice using a list:

>>> A[:,[1,3]]
array([[ 1,  3],
       [ 5,  7],
       [ 9, 11]])
A slightly more complicated way is to use the take() method:
>>> A[:,].take([1,3],axis=1)
array([[ 1,  3],
       [ 5,  7],
       [ 9, 11]])
If we wanted to skip the first row, we could use:
>>> A[1:,].take([1,3],axis=1)
array([[ 5,  7],
       [ 9, 11]])

Or we could simply use A[1:,[1,3]]. Yet another way to slice the above is to use a cross product:

>>> A[ix_((1,2),(1,3))]
array([[ 5,  7],
       [ 9, 11]])
For the reader's convenience, here is our array again:
>>> print A
[[ 0  1  2  3]
 [ 4  5  6  7]
 [ 8  9 10 11]]

Now let's do something a bit more complicated. Lets say that we want to retain
all columns where the first row is greater than 1. One way is to create a
boolean index:

>>> A[0,:]>1
array([False, False, True, True], dtype=bool)
>>> A[:,A[0,:]>1]
array([[ 2,  3],
       [ 6,  7],
       [10, 11]])
Just what we wanted! But indexing the matrix is not so convenient.
>>> M[0,:]>1
matrix([[False, False, True, True]], dtype=bool)
>>> M[:,M[0,:]>1]
matrix([[2, 3]])

The problem of course is that slicing the matrix slice produced a matrix. But
matrices have a convenient 'A' attribute whose value is the array
representation, so we can just do this instead:

>>> M[:,M.A[0,:]>1]
matrix([[ 2,  3],
        [ 6,  7],
        [10, 11]])

If we wanted to conditionally slice the matrix in two directions, we must
adjust our strategy slightly. Instead of

>>> A[A[:,0]>2,A[0,:]>1]
array([ 6, 11])
>>> M[M.A[:,0]>2,M.A[0,:]>1]
matrix([[ 6, 11]])
we need to use the cross product 'ix_':
>>> A[numpy.ix_(A[:,0]>2,A[0,:]>1)]
array([[ 6,  7],
       [10, 11]])
>>> M[numpy.ix_(M.A[:,0]>2,M.A[0,:]>1)]
matrix([[ 6,  7],
        [10, 11]])

Tricks and Tips

Here we give a list of short and useful tips.  "Automatic" Reshaping To change
the dimensions of an array, you can omit one of the sizes which will then be
deduced automatically:

>>> a = arange(30)
>>> a.shape = 2,-1,3  # -1 means "whatever is needed"
>>> a.shape
(2, 5, 3)
>>> a
array([[[ 0,  1,  2],
        [ 3,  4,  5],
        [ 6,  7,  8],
        [ 9, 10, 11],
        [12, 13, 14]],
       [[15, 16, 17],
        [18, 19, 20],
        [21, 22, 23],
        [24, 25, 26],
        [27, 28, 29]]])

Vector Stacking

How do we construct a 2D array from a list of equally-sized row vectors? In
MATLAB this is quite easy: if x and y are two vectors of the same length you
only need do m=[x;y]. In NumPy this works via the functions column_stack,
dstack, hstack and vstack, depending on the dimension in which the stacking is
to be done. For example:

x = arange(0,10,2)                     # x=([0,2,4,6,8])
y = arange(5)                          # y=([0,1,2,3,4])
m = vstack([x,y])                      # m=([[0,2,4,6,8],
                                       #     [0,1,2,3,4]])
xy = hstack([x,y])                     # xy =([0,2,4,6,8,0,1,2,3,4])

The logic behind those functions in more than two dimensions can be strange.
See also NumPy for Matlab Users and add your new findings there. 

Histograms

The NumPy histogram function applied to an array returns a pair of vectors: the
histogram of the array and the vector of bins. Beware: matplotlib also has a
function to build histograms (called hist, as in Matlab) that differs from the
one in NumPy. The main difference is that pylab.hist plots the histogram
automatically, while numpy.histogram only generates the data.

import numpy
import pylab
# Build a vector of 10000 normal deviates with variance 0.5^2 and mean 2
mu, sigma = 2, 0.5
v = numpy.random.normal(mu,sigma,10000)
# Plot a normalized histogram with 50 bins
pylab.hist(v, bins=50, normed=1)       # matplotlib version (plot)
pylab.show()
# Compute the histogram with numpy and then plot it
(n, bins) = numpy.histogram(v, bins=50, normed=True)  # NumPy version (no plot)
pylab.plot(.5*(bins[1:]+bins[:-1]), n)
pylab.show()