'''Functions to set, check, and log random seed'''
import os
import random
from logging import getLogger
import numpy as np
from nipype.interfaces.ants.registration import Registration
from nipype.interfaces.ants.segmentation import Atropos
from nipype.interfaces.freesurfer.preprocess import ApplyVolTransform, ReconAll
from nipype.interfaces.fsl.maths import MathsCommand
from nipype.interfaces.fsl.utils import ImageMaths
from CPAC.registration.utils import hardcoded_reg
from CPAC.utils.interfaces.ants import AI
from CPAC.utils.monitoring.custom_logging import set_up_logger
_seed = {'seed': None}
def random_random_seed():
'''Returns a random postive integer up to 2147483647
Parameters
----------
None
Returns
-------
random_seed : int
Examples
--------
>>> 0 < random_random_seed() <= np.iinfo(np.int32).max
True
'''
return random.randint(1, np.iinfo(np.int32).max)
def random_seed():
'''Function to access current random seed
Parameters
----------
None
Returns
-------
seed : int or None
'''
if _seed['seed'] == 'random':
_seed['seed'] = random_random_seed()
return _seed['seed']
[docs]def random_seed_flags():
'''Function to return dictionary of flags with current random seed.
Parameters
----------
None
Returns
-------
dict of {'functions': {function: function}, 'interfaces': {list or tuple}}
Developer note: sequence matters here! Only the first match
will be applied!
In the 'functions' sub-dictionary, each key should be a function
used in a :py:class:`CPAC.utils.interfaces.function.Function`,
and each value should be a function that takes a single
parameter (a function) to apply to the key-function such that,
once the value-function is applied, the random seed is applied
when the key-function is run.
In the 'interfaces' sub-dictionary, each key should be an
:py:class:`nipype.interfaces.base.core.Interface`, and each
value should be either a list of strings to add to the
interface's flags/args or a tuple of (list of strings to add to,
list of strings to remove from) the interface's flags/args.
Examples
--------
>>> list(random_seed_flags().keys())
['functions', 'interfaces']
>>> all([isinstance(random_seed_flags()[key], dict) for key in [
... 'functions', 'interfaces']])
True
>>> rs = set_up_random_state('random')
>>> list(random_seed_flags().keys())
['functions', 'interfaces']
>>> all([isinstance(random_seed_flags()[key], dict) for key in [
... 'functions', 'interfaces']])
True
'''
seed = random_seed()
if seed is None:
return {'functions': {}, 'interfaces': {}}
return {
'functions': {
# function: lambda function to apply to function source
hardcoded_reg: lambda fn_string: fn_string.replace(
'regcmd = ["antsRegistration"]',
f'regcmd = ["antsRegistration", "--random-seed", \"{seed}\"]'
)
},
'interfaces': {
# interface: [flags to apply]
# OR
# interface: ([flags to apply], [flags to remove])
#
# ANTs
# NOTE: Atropos gives the option "Initialize internal random number
# generator with a random seed. Otherwise, initialize with a
# constant seed number," so for Atropos nodes, the built-in
# Atropos constant seed is used if a seed is specified for
# C-PAC
AI: _reusable_flags()['ANTs'],
Registration: _reusable_flags()['ANTs'],
Atropos: (['--use-random-seed 0'],
[flag for one in ['', ' 1'] for flag in
[f'--use-random-seed{one}', f'-r{one}']]),
# FreeSurfer
ReconAll: ['-norandomness', f'-rng-seed {seed}'],
ApplyVolTransform: _reusable_flags()['FSL'],
# FSL
ImageMaths: _reusable_flags()['FSL'],
MathsCommand: _reusable_flags()['FSL']
}
}
def _reusable_flags():
seed = random_seed()
return {
'ANTs': [f'--random-seed {seed}'],
'FSL': [f'-seed {seed}']
}
def set_up_random_state(seed):
'''Set global random seed
Parameters
----------
seed : int, 'random', or None
Returns
-------
seed: int or None
Examples
--------
>>> isinstance(set_up_random_state('random'), int)
True
>>> set_up_random_state('rando')
Traceback (most recent call last):
ValueError: Valid random seeds are positive integers up to 2147483647, "random", or None, not rando
>>> set_up_random_state(100)
100
>>> set_up_random_state(0)
Traceback (most recent call last):
ValueError: Valid random seeds are positive integers up to 2147483647, "random", or None, not 0
>>> set_up_random_state(None)
''' # noqa: E501 # pylint: disable=line-too-long
if seed is not None:
if seed == 'random':
seed = random_random_seed()
if (seed != 'random' and not (
isinstance(seed, int) and
(0 < int(seed) <= np.iinfo(np.int32).max)
)):
raise ValueError('Valid random seeds are positive integers up to '
f'2147483647, "random", or None, not {seed}')
try:
_seed['seed'] = int(seed)
except (TypeError, ValueError):
_seed['seed'] = seed
return random_seed()
def set_up_random_state_logger(log_dir):
'''Prepare C-PAC for logging random seed use.
Parameters
----------
log_dir : str
'''
set_up_logger('random', level='info', log_dir=log_dir)
getLogger('random').info('seed: %s', random_seed())
