How to find the groups of consecutive elements in a NumPy array

I have to cluster the consecutive elements from a NumPy array. Considering the following example

a = [ 0, 47, 48, 49, 50, 97, 98, 99]

The output should be a list of tuples as follows

[(0), (47, 48, 49, 50), (97, 98, 99)]

Here the difference is just one between the elements. It will be great if the difference can also be specified as a limit or a hardcoded number.

Answers:

Thank you for visiting the Q&A section on Magenaut. Please note that all the answers may not help you solve the issue immediately. So please treat them as advisements. If you found the post helpful (or not), leave a comment & I’ll get back to you as soon as possible.

Method 1

def consecutive(data, stepsize=1):
    return np.split(data, np.where(np.diff(data) != stepsize)[0]+1)

a = np.array([0, 47, 48, 49, 50, 97, 98, 99])
consecutive(a)

yields

[array([0]), array([47, 48, 49, 50]), array([97, 98, 99])]

Method 2

Here’s a lil func that might help:

def group_consecutives(vals, step=1):
    """Return list of consecutive lists of numbers from vals (number list)."""
    run = []
    result = [run]
    expect = None
    for v in vals:
        if (v == expect) or (expect is None):
            run.append(v)
        else:
            run = [v]
            result.append(run)
        expect = v + step
    return result

>>> group_consecutives(a)
[[0], [47, 48, 49, 50], [97, 98, 99]]
>>> group_consecutives(a, step=47)
[[0, 47], [48], [49], [50, 97], [98], [99]]

P.S. This is pure Python. For a NumPy solution, see unutbu’s answer.

Method 3

(a[1:]-a[:-1])==1 will produce a boolean array where False indicates breaks in the runs. You can also use the built-in numpy.grad.

Method 4

this is what I came up so far: not sure is 100% correct

import numpy as np
a = np.array([ 0, 47, 48, 49, 50, 97, 98, 99])
print np.split(a, np.cumsum( np.where(a[1:] - a[:-1] > 1) )+1)

returns:

>>>[array([0]), array([47, 48, 49, 50]), array([97, 98, 99])]

Method 5

Tested for one dimensional arrays

Get where diff isn’t one

diffs = numpy.diff(array) != 1

Get the indexes of diffs, grab the first dimension and add one to all because diff compares with the previous index

indexes = numpy.nonzero(diffs)[0] + 1

Split with the given indexes

groups = numpy.split(array, indexes)

Method 6

It turns out that instead of np.split, list comprehension is more performative. So the below function (almost like @unutbu’s consecutive function except it uses a list comprehension to split the array) is much faster:

def consecutive_w_list_comprehension(arr, stepsize=1):
    idx = np.r_[0, np.where(np.diff(arr) != stepsize)[0]+1, len(arr)]
    return [arr[i:j] for i,j in zip(idx, idx[1:])]

For example, for an array of length 100_000, consecutive_w_list_comprehension is over 4x faster:

arr = np.sort(np.random.choice(range(150000), size=100000, replace=False))

%timeit -n 100 consecutive(arr)
96.1 ms ± 1.22 ms per loop (mean ± std. dev. of 7 runs, 100 loops each)

%timeit -n 100 consecutive_w_list_comprehension(arr)
23.2 ms ± 858 µs per loop (mean ± std. dev. of 7 runs, 100 loops each)

In fact, this relationship holds up no matter the size of the array. The plot below shows the runtime difference between the answers on here.

Code used to produce the plot above:

import perfplot
import numpy as np

def consecutive(data, stepsize=1):
    return np.split(data, np.where(np.diff(data) != stepsize)[0]+1)

def consecutive_w_list_comprehension(arr, stepsize=1):
    idx = np.r_[0, np.where(np.diff(arr) != stepsize)[0]+1, len(arr)]
    return [arr[i:j] for i,j in zip(idx, idx[1:])]

def group_consecutives(vals, step=1):
    run = []
    result = [run]
    expect = None
    for v in vals:
        if (v == expect) or (expect is None):
            run.append(v)
        else:
            run = [v]
            result.append(run)
        expect = v + step
    return result


def JozeWs(array):
    diffs = np.diff(array) != 1
    indexes = np.nonzero(diffs)[0] + 1
    groups = np.split(array, indexes)
    return groups

perfplot.show(
    setup = lambda n: np.sort(np.random.choice(range(2*n), size=n, replace=False)),
    kernels = [consecutive, consecutive_w_list_comprehension, group_consecutives, JozeWs],
    labels = ['consecutive', 'consecutive_w_list_comprehension', 'group_consecutives', 'JozeWs'],
    n_range = [2 ** k for k in range(5, 22)],
    equality_check = lambda *lst: all((x==y).all() for x,y in zip(*lst)),
    xlabel = '~len(arr)'
)

Method 7

This sounds a little like homework, so if you dont mind I will suggest an approach

You can iterate over a list using

for i in range(len(a)):
    print a[i]

You could test the next element in the list meets some criteria like follows

if a[i] == a[i] + 1:
    print "it must be a consecutive run"

And you can store results seperately in

results = []

Beware – there is an index out of range error hidden in the above you will need to deal with

All methods was sourced from stackoverflow.com or stackexchange.com, is licensed under cc by-sa 2.5, cc by-sa 3.0 and cc by-sa 4.0