9.3. Basic Array Manipulation

Arrays are sequences of numerical data, with each element having the same underlying data type – integers, real (floating point) numbers, or complex numbers. Of course, arrays are very important for scientific data, and the majority of data you will be manipulating with Larch will be in the form of arrays. Larch depends on the numpy library for providing basic array data types and the methods for fast manipulation of array data. These arrays can be multi-dimensional, have their dimensionality change dynamically, an can be sliced (subsets of elements taken). Many built-in functions will act on the whole array, generally element-by-element, in a highly efficient way, greatly reducing the need to “loop over” elements.

This section introduces the creation, basic manipulation, and key properties of arrays. The discussion here is not exhaustive, but is intended to get you far enough along to be able to manipulate arrays sufficiently for most needs. The numpy documentation is quite extensive and well-written, and should be consulted for more details.

9.3.1. Functions for creating arrays

There are a handful of builtin functions for creating arrays from scratch. These are listed in Table of Array Creation Functions In addition, when dealing with data stored in files, reading the files (see Reading and Writing Data) with Larch will create arrys for you. Like lists, arrays are mutable. That is, elements of arrays can be changed without changing the rest of the array.

Table of Array Creation Functions. These functions can all be used to create arrays in Larch.

Function Name	description	example
array	array from list	arr = array([1,2,3])
arange	indices 0, N-1	arr = arange(10)
zeros	fill with N zeros	arr = zeros(10)
ones	fill with N ones	arr = ones(10)
linspace	fill with bounds and N	arr = linspace(0, 1, 11)
eye	2-d identity matrix	arr = eye(3)
meshgrid	2-d mesh arrays	mx, my = meshgrid(x, y)

Some examples of using these functions are needed:

larch> i = arange(10)
larch> i
array([0, 1, 2, 3, 4, 5, 6, 7, 8, 9])
larch> f = arange(10, dtype=float)
larch> f
array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9.])
larch> c = arange(10, dtype=complex)
larch> c
array([ 0.+0.j,  1.+0.j,  2.+0.j,  3.+0.j,  4.+0.j,  5.+0.j,  6.+0.j,
        7.+0.j,  8.+0.j,  9.+0.j])
larch> i3 = eye(3)
larch> i3
array([[ 1.,  0.,  0.],
       [ 0.,  1.,  0.],
       [ 0.,  0.,  1.]])

Here, the dtype argument sets the data type for the array members. For example, float means a double precision floating point representation of a real number and complex means double precision complex floating point. The Table of Array Data types below lists the available data types that can be passed as a dtype argument.

The linspace() function is particularly useful for creating arrays, as it takes a starting value, ending value, and number of points between these:

larch> s = linspace(0, 10, 21)
larch> s
array([  0. ,   0.5,   1. ,   1.5,   2. ,   2.5,   3. ,   3.5,   4. ,
         4.5,   5. ,   5.5,   6. ,   6.5,   7. ,   7.5,   8. ,   8.5,
         9. ,   9.5,  10. ])

Several variants are possible. For more information, consult the numpy tutorials, or use the online help system within Larch (which will print out the documentation string from the underlying numpy function):

larch> help(linspace)

    Return evenly spaced numbers over a specified interval.

    Returns `num` evenly spaced samples, calculated over the
    interval [`start`, `stop` ].

    The endpoint of the interval can optionally be excluded.


    Parameters
    ----------
    start : scalar
        The starting value of the sequence.
    stop : scalar
        The end value of the sequence, unless `endpoint` is set to False.
        In that case, the sequence consists of all but the last of ``num + 1``
        evenly spaced samples, so that `stop` is excluded.  Note that the step
        size changes when `endpoint` is False.
    num : int, optional
        Number of samples to generate. Default is 50.
    endpoint : bool, optional
        If True, `stop` is the last sample. Otherwise, it is not included.
        Default is True.
    retstep : bool, optional
        If True, return (`samples`, `step`), where `step` is the spacing
        between samples.

    ....

The eye() function creates a 2 dimensional square array (or, possibly matrix, though that term can connote additional meaning that a square array does not necessarily have) with values of 1 for the diagonal elements, and 0 elsewhere.

The function meshgrid() can be used to build a mesh of values from two one dimensional arrays. That is:

larch> x = array([0, 1, 2, 3, 4])
larch> y = array([-1, 0.5, 0, 0.5, 1])
larch> mx, my = meshgrid(x, y)
larch> print mx
array([[0, 1, 2, 3, 4],
       [0, 1, 2, 3, 4],
       [0, 1, 2, 3, 4],
       [0, 1, 2, 3, 4],
       [0, 1, 2, 3, 4]])
larch> print my
array([[-1. , -1. , -1. , -1. , -1. ],
       [-0.5, -0.5, -0.5, -0.5, -0.5],
       [ 0. ,  0. ,  0. ,  0. ,  0. ],
       [ 0.5,  0.5,  0.5,  0.5,  0.5],
       [ 1. ,  1. ,  1. ,  1. ,  1. ]])

That is, the values of each mx and my contain the coordinates of a two-dimensional mesh or map of the input x and y values.

9.3.2. The array dtype – datatype

Arrays are sequences of numbers stored in memory to make access to the elements of the arrays fast and memory use efficient. As mentioned above, each array will use one of several storage conventions depending on what type of data is needed for the elements. Basically, this dictates how many bytes to use and whether these values are meant to hold integers, real floating points, or complex floating point numbers. This information is encapsulated in the arrays dtype. It can be one of several values, listed in the

Table of Array Data types. Each array has exactly one of these create arrays in Larch. The dtype can be used in any of the array creation functions using the dtype keyword argument (e.g, dtype=float32).

dtype	description
bool	boolean (True or False)
int8	signed 8-bit integer (-128 to 127)
int16	signed 16-bit integer (-32768 to 32767)
int32	signed 32-bit integer (-2**31 to 2**31-1)
int64	signed 64-bit integer (-2**63 to 2**63-1)
uint8	unsigned 8-bit integer (0 to 255)
uint16	unsigned 16-bit integer (0 to 65535)
uint32	unsigned 32-bit integer (0 to 2**32)
uint64	unsigned 64-integer (0 to 2**64)
float32	single precision float
float64 or float	double precision float
complex64	single precision complex two float32s
complex128 or complex	double precision complex, two float64s.

9.3.3. Basic array manipulation

Arrays can either be used as a single object, or individual or ranges of elements can be extracted from them. Usually, mathematical operations and functions done to arrays are applied element-by-element. For example:

larch>  x = arange(5)
larch> print x
[0 1 2 3 4]
larch> print 2*x+1
[1 3 5 7 9]

and so on for all of the basic mathematical operators. To add to arrays of equal lengths together is also easy:

larch>  y = array([10, 12, 14, 16, 18])
larch> print y - 3*x
[10  9  8  7  6]

If the arrays are not of equal length, an exception is raised. In that case, you can take a sub-set of the larger array to match the size of the smaller one.

Boolean operators also apply to each element, so that:

larch> print y > 13
[False False  True  True  True]

The any() and all() functions (in the tables below) can be used to determine if any or all of the Boolean values are True.

You can extract single elements from arrays with brackets, just as for lists:

larch> print y[2]
14
larch> print (y-3*x)[2]
7

which leads us to the next section.

9.3.4. Slicing and extracting sub-arrays

An important aspect of arrays is that they can be treated as a single entity. That is, sin(x) operates on each element of x. But sometimes it is necessary to get a particular element from an array or work on only a selected part of an array. To do these, one takes a sub-set of the array – a slice. For extracting contiguous portions of 1-dimension arrays, this is pretty straightforward, using the range of indices needed for the slice between square brackets [ and ]. For example:

larch> arr = linspace(0, 2, 21)
larch> print arr
[ 0.   0.1  0.2  0.3  0.4  0.5  0.6  0.7  0.8  0.9  1.   1.1  1.2  1.3  1.4
  1.5  1.6  1.7  1.8  1.9  2. ]
larch> print arr[20]
2.0
larch> print arr[15]
1.5
larch> print arr[10:15]
[ 1.   1.1  1.2  1.3  1.4]

The general syntax for a slice is pretty complicated, but the simplest cases are straightforward. As with lists, arr[i] selects value at index i (counting from 0). Similarly, arr[i:j] selects elements starting at i and ending at (but not including – see the example above) j. If i is omitted, it is taken as 0 (the first element), and if j is omitted, it defaults to the last element of the array. In addition, if i and/or j are negative, they count from the end of the array:

larch> print arr[:-8]
[ 0.   0.1  0.2  0.3  0.4  0.5  0.6  0.7  0.8  0.9  1.   1.1  1.2]
larch> print arr[-2:]
[ 1.9  2.]

A slice can take a third argument k – the stride – which allows selection of every k elements. That is:

larch> print arr[1:6:2]
[ 0.1  0.3  0.5]
larch> print arr[::2]
[ 0.   0.2  0.4  0.6  0.8  1.   1.2  1.4  1.6  1.8  2. ]

If k is negative, it starts from the end of the array:

larch> print arr[::-3]
[2.   1.7  1.4  1.1  0.8  0.5  0.2]

For mult-dimensional arrays, slices can be made for each dimension, with slices separated by commas. If no slice is given, the whole array along that dimension is used. Thus:

larch> x = arange(30).reshape((6, 5)
larch> print x
[[ 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]]
larch> print x[2]  # third row
[10 11 12 13 14]
larch> print x[:,1]  # second column
[ 1  6 11 16 21 26]
larch> print x[:3,2:5]
[[ 2  3  4]
 [ 7  8  9]
 [12 13 14]]

Note that multi-dimensional arrays use a layout like C and unlike Fortran by default. In addition to the comma-based syntax shown above to extract different dimensions or use brackets around each dimension:

larch> print x[1][:4]  # second row, first 4 columns
[5 6 7 8]
larch> print x[1,:4]   # same
[5 6 7 8]

In general, the syntax for a slice is then arr[i1:j1,:k1, i2:j2:k2, ...] with default values for i of 0, for j of the length of the array, and for k of 1.

9.3.5. Array attributes and methods

Arrays have several useful attributes and methods. As mentioned above, each array has a dtype attribute describing how its data is mapped in memory. In addition, each has a size attribute giving the number of elements, a ndim giving the number of dimensions, and shape giving the a tuple with the length along each dimension. The dimensionality and shape of a multi-dimensional array can be specified by setting the value of shape to the desired value:

larch> x = arange(12, dtype=float)
larch> x
array([0., 1., 2., 3., 4., 5., 6., 7., 8., 9., 11., 12.])
larch> x.shape = (2, 6)
larch> x
array([[ 0.,  1.,  2.,  3.,  4.,  5.],
       [ 6.,  7.,  8.,  9., 10., 11.]])

Table of Array Attribute and Methods. Those ending with parentheses (()) are methods, that act on the array. Most of the attributes and the vast majority of methods return a value based on the array contents, leaving the array unchanged. The attributes and methods marked read/write operate in place, changing the array.

attribute	description	notes
dtype	data type	read only
size	number of elements (int)	read only
ndim	number of dimensions (int)	read only
shape	length along each dimension (tuple)	read/write
real	real part of array	read/write
imag	imaginary part of array	read/write
resize()	grow/shrink array to specified size	read/write
conjugate()	conjugate of array
all()	boolean: if all values are True	(non-zero)
any()	boolean: if any value is True	(non-zero)
min()	minimum value of array elements
max()	maximum value of array elements
mean()	mean value of array elements
std()	standard deviation of array elements
prod()	product of array elements
sum()	sum of array elements
argmin()	index of first minimum value
argmax()	index of first maximum value
argsort()	array of indices for sorted array	(min to max)
cumprod()	array of cumulative product of elements
cumsum()	array of cumulative sum of elements
astype()	array re-cast as a different dtype
round()	array of rounded elements
diagonal()	array of diagonal elements
trace()	sum of diagonal elements()
transpose()	transpose of array
flatten()	array “flattened” to 1-dimension
tolist()	list containing array elements
reshape()	array reshaped to specified shape tuple

9.3.6. Mathematical functions for arrays

Many of the basic mathemetical functions in larch automatically work on arrays element-by-element. For example, sqrt() returns the square-root of a single value or for each element in an array:

larch> print sqrt(3)
1.73205080757
larch> x = arange(10)
larch> print sqrt(x)
[ 0.          1.          1.41421356  1.73205081  2.          2.23606798
  2.44948974  2.64575131  2.82842712  3.        ]

The numpy library provides the underlying functions, and they are much faster than looping over elements of the array:

larch> for el in x:  # this is much slower than sqrt(x)!!
.....>     print el, sqrt(el)
.....> endfor
0 0.0
1 1.0
2 1.41421356237
3 1.73205080757
4 2.0
5 2.2360679775
6 2.44948974278
7 2.64575131106
8 2.82842712475
9 3.0

There are a large number of general purpose mathematical functions available in larch – the _math group contains over 500 items on startup. A partial list is given in the The Table of Array-aware Mathematical functions below. What’s more, many more are available by importing them from the scipy library.

Table of Array-aware Mathematical functions. More info on each of these can be found with the builtin help() function. The table is broken up by categories to make printing easier.

General Purpose Functions

function	description
all	all values are True
allclose	all values of 2 arrays are close
info	print information about array storage
fabs	absolute value of values
sqrt	square root of values
exp	exponential of values
expm1	exp(x) - 1 for values x
exp2	2**x for values x
ln / log	natural logarithm of values
log1p	log(x) + 1 for values x
log10	base-10 logarithm of values
log2	base-2 logarithm of values
mod	modulus of values
ldexp	x * 2**y for values x and y
fmin	element-wise minima of two arrays
fmax	element-wise maxima of two arrays
fmod	element-wise modulus of two arrays
frexp	split value into fractional and exponent

Trigonometry Functions

function	description
angle	phase angle for complex values
acos / arccos	inverse of cosine
asin / arcsin	inverse of sine
atan / arctan	inverse of tangent
atan2 / arctan2	inverse of tangent of ratio of two values
acosh / arccosh	inverse of hyperbolic cosine
asinh / arcsinh	inverse of hyperbolic sine
atanh / arctanh	inverse of hyperbolic tangent
cos	cosine
cosh	hyperbolic cosine
sin	sine
sinh	hyperbolic sine
tan	tangent
tanh	hyperbolic tangent
deg2rad	convert degrees to radians
rad2deg	convert radians to degrees
hypot	hypotenuse (distance) of two values

Array Manipulation and Re-shaping

function	description
append	append a value to an array
insert	insert a value into a specified location of an array
concatenate	Join a sequence of arrays together
tile	build array by repeating an array a number of times
repeat	repeat elements of an array a number of times
split	Split array into sub-arrays vertically (row)
hsplit	Split array into sub-arrays horizontally (column)
dsplit	Split array into sub-arrays along the 3rd axixpth (depth)
hstack	Stack arrays in sequence horizontally (column)
vstack	Stack arrays in sequence vertically (row )
dstack	Stack arrays in sequence along third dimension (depth)
take	take values at specified indices
choose	construct array from index array and a set of arrays
where	select array elements depending on an input condition

Statistical Functions

function	description
average	average value of an array, with optional weights
max	maximum value of an array
mean	mean value of an array
median	median value of an array
min	minimum value of an array
var	variance of an array
std	standard deviation of an array
trapz	integrate using composite trapezoidal rule
remainder	remainder of division (x1 - floor(x1 / x2) * x2)
percentile	returns the given percentile of array elements
ceil	ceiling values (round “up”) of input
floor	floor values (round “down”) of input
round	round values (away from 0) of input
clip	set upper/lower bounds on array values
digitize	indices of bins for binned values
bincount	number of occurrences of each value in array
histogram	build a histogram from an array
histogram2d	build a 2-d histogram from two arrays
convolve	discrete convolution of two 1-d arrays
correlate	cross-correlation of two 1-d arrays
cumprod	cumulative product
cumsum	cumulative sum

Multi-dimensional and Matrix Functions

function	description
tril	upper triagonal of an array
triu	lower triagonal of an array
diagonal	diagonal elements of an array
trace	sum of diagonal elements
dot	dot product of two arrays
inner	inner product of two arrays
outer	outer product of two arrays
kron	Kronecker product of two arrays
swapaxes	rotate axes of an array
transpose	transpose array
fliplr	Flip an array horizontally
flipud	Flip an array vertically
rot90	rotate an array 90 degrees counter clockwise

Array and Signal Processing

function	description
diff	finite difference of array elements
gradient	gradient of an array
interp	linear interpolation of 1-d arrays
poly	Evaluate a polynomial at a point
root	the roots of a polynomial
polyfit	least squares polynomial fit

Random number generation and other

function	description
random.random	randomly distributed reals, on [0, 1).
random.randint	array of random integers, over specified range
random.normal	normally distributed random numbers

Fourier transforms

function	description
fft.fft	Fourier transform of a 1-d array
fft.ifft	inverse Fourier transform of a 1-d array
fft.fft2	Fourier transform of a 2-d array
fft.ifft2	inverse Fourier transform of a 2-d array

Many other functions that work on arrays are available from numpy subpackages and from scipy.