parfor 2020.8.1

A package to mimic the use of parfor as done in Matlab.

Parfor

Used to parallelize for-loops using parfor in Matlab? This package allows you to do the same in python. Take any normal serial but parallelizable for-loop and execute it in parallel using easy syntax. Don't worry about the technical details of using the multiprocessing module, race conditions, queues, parfor handles all that.

Tested on linux on python 2.7 and 3.8

Usage

Parfor decorates a functions and returns the result of that function evaluated for each iteration of an iterator.

Requires

tqdm, dill

Limitations

Some objects cannot be passed and or used in child processes. Such objects include objects relying on java-bridge. Examples include reader objects from the python-bioformats package.

Required arguments:

fun:      function taking arguments: iteration from  iterable, other arguments defined in args & kwargs
iterable: iterable from which an item is given to fun as a first argument

Optional arguments:

args:   tuple with other unnamed arguments to fun
kwargs: dict with other named arguments to fun
length: give the length of the iterator in cases where len(iterator) results in an error
desc:   string with description of the progress bar
bar:    bool enable progress bar
pbar:   bool enable buffer indicator bar
nP:     number of workers, default: number of cpu's/3
serial: switch to serial if number of tasks less than serial, default: 4
debug:  if an error occurs in an iteration, return the erorr instead of retrying in the main process

Output

list with results from applying the decorated function to each iteration of the iterator
specified as the first argument to the function

Examples

Normal serial for loop

<<
from time import sleep
a = 3
fun = []
for i in range(10):
    sleep(1)
    fun.append(a*i**2)
print(fun)

>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]

Using parfor on the same loop

<<
from time import sleep
from parfor import parfor
@parfor(range(10), (3,))
def fun(i, a):
    sleep(1)
    return a*i**2
print(fun)

>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]

<<
@parfor(range(10), (3,), bar=False)
def fun(i, a):
    sleep(1)
    return a*i**2
print(fun)

>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]

If you hate decorators not returning a function

pmap maps an iterator to a function like map does, but in parallel

<<
from parfor import pmap
from time import sleep
def fun(i, a):
    sleep(1)
    return a*i**2
print(pmap(fun, range(10), (3,)))

>> [0, 3, 12, 27, 48, 75, 108, 147, 192, 243]     

Using generators

If iterators like lists and tuples are too big for the memory, use generators instead. Since generators don't have a predefined length, give parfor the length as an argument (optional).

<<
import numpy as np
c = (im for im in imagereader)
@parfor(c, length=len(imagereader))
def fun(im):
    return np.mean(im)

>> [list with means of the images]

Extra's

Pmap

The function parfor decorates, use it like map.

Chunks

Split a long iterator in bite-sized chunks to parallelize

Parpool

More low-level accessibility to parallel execution. Submit tasks and request the result at any time, (although necessarily submit first, then request a specific task), use different functions and function arguments for different tasks.

Tqdmm

Meter bar, inherited from tqdm, used for displaying buffers.