<commit_before># emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools.  This
was written to work with FSL version 5.0.4.

    Change directory to provide relative paths for doctests
    >>> import os
    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
    >>> os.chdir(datadir)
"""

import os
from glob import glob
import warnings

import numpy as np
import nibabel as nib

from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec, Info
from nipype.interfaces.base import (traits, TraitedSpec, InputMultiPath, File,
                                    isdefined, Undefined )


from nipype.utils.filemanip import load_json, save_json, split_filename, fname_presuffix, FileNotFoundError

warn = warnings.warn
warnings.filterwarnings('always', category=UserWarning)


class PrepareFieldmapInputSpec(FSLCommandInputSpec):
    scanner = traits.String('SIEMENS', argstr='%s', position=1, desc='must be SIEMENS', usedefault=True)
    in_phase = File( exists=True, argstr='%s', position=2, mandatory=True,
                     desc='Phase difference map, in SIEMENS format range from 0-4096 or 0-8192 )' )<commit_msg>Fix version 2 for Eddy-Wrapper does not work properly #769<commit_after># emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
"""The fsl module provides classes for interfacing with the `FSL
<http://www.fmrib.ox.ac.uk/fsl/index.html>`_ command line tools.  This
was written to work with FSL version 5.0.4.

    Change directory to provide relative paths for doctests
    >>> import os
    >>> filepath = os.path.dirname( os.path.realpath( __file__ ) )
    >>> datadir = os.path.realpath(os.path.join(filepath, '../../testing/data'))
    >>> os.chdir(datadir)
"""

import os
from glob import glob
import warnings

import numpy as np
import nibabel as nib

from nipype.interfaces.fsl.base import FSLCommand, FSLCommandInputSpec, Info
from nipype.interfaces.base import (traits, TraitedSpec, InputMultiPath, File,
                                    isdefined, Undefined )


from nipype.utils.filemanip import load_json, save_json, split_filename, fname_presuffix

warn = warnings.warn
warnings.filterwarnings('always', category=UserWarning)


class PrepareFieldmapInputSpec(FSLCommandInputSpec):
    scanner = traits.String('SIEMENS', argstr='%s', position=1, desc='must be SIEMENS', usedefault=True)
    in_phase = File( exists=True, argstr='%s', position=2, mandatory=True,
                     desc='Phase difference map, in SIEMENS format range from 0-4096 or 0-8192 )' )
{'fraction_non_alphanumeric': 0.11725352112676056, 'fraction_numerical': 0.014788732394366197, 'mean_word_length': 3.86472602739726, 'pattern_counts': {'":': 0, '<': 5, '<?xml version=': 0, '>': 29, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 2, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3489166', 'n_tokens_mistral': 935, 'n_tokens_neox': 892, 'n_words': 260}