Source code for niworkflows.interfaces.patches

# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
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# Copyright 2021 The NiPreps Developers <nipreps@gmail.com>
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"""Temporary patches."""

from random import randint
from time import sleep

from nipype.algorithms import confounds as nac
from nipype.interfaces import io as nio
from nipype.interfaces.base import File
from numpy.linalg.linalg import LinAlgError



[docs]
class RobustACompCor(nac.ACompCor):
    """
    Runs aCompCor several times if it suddenly fails with
    https://github.com/nipreps/fmriprep/issues/776

    """

    def _run_interface(self, runtime):
        failures = 0
        while True:
            try:
                runtime = super()._run_interface(runtime)
                break
            except LinAlgError:
                failures += 1
                if failures > 10:
                    raise
                start = (failures - 1) * 10
                sleep(randint(start + 4, start + 10))

        return runtime




[docs]
class RobustTCompCor(nac.TCompCor):
    """
    Runs tCompCor several times if it suddenly fails with
    https://github.com/nipreps/fmriprep/issues/940

    """

    def _run_interface(self, runtime):
        failures = 0
        while True:
            try:
                runtime = super()._run_interface(runtime)
                break
            except LinAlgError:
                failures += 1
                if failures > 10:
                    raise
                start = (failures - 1) * 10
                sleep(randint(start + 4, start + 10))

        return runtime



class _FSSourceOutputSpec(nio.FSSourceOutputSpec):
    T2 = File(desc='Intensity normalized whole-head volume', loc='mri')



[docs]
class FreeSurferSource(nio.FreeSurferSource):
    """
    Patch to allow grabbing the T2 volume, if available
    """

    output_spec = _FSSourceOutputSpec