__init__.py

# emacs: -*- mode: python-mode; py-indent-offset: 4; indent-tabs-mode: nil -*-
# vi: set ft=python sts=4 ts=4 sw=4 et:
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
#
#   See COPYING file distributed along with the NiBabel package for the
#   copyright and license terms.
#
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##

import os

from .info import long_description as __doc__
from .pkg_info import __version__

__doc__ += """
Quickstart
==========

::

   import nibabel as nib

   img1 = nib.load('my_file.nii')
   img2 = nib.load('other_file.nii.gz')
   img3 = nib.load('spm_file.img')

   data = img1.get_fdata()
   affine = img1.affine

   print(img1)

   nib.save(img1, 'my_file_copy.nii.gz')

   new_image = nib.Nifti1Image(data, affine)
   nib.save(new_image, 'new_image.nii.gz')

For more detailed information see the :ref:`manual`.
"""

# module imports
from . import analyze as ana
from . import ecat, imagestats, mriutils
from . import nifti1 as ni1
from . import spm2analyze as spm2
from . import spm99analyze as spm99
from . import streamlines, viewers

# isort: split

# object imports
from .analyze import AnalyzeHeader, AnalyzeImage
from .arrayproxy import is_proxy
from .cifti2 import Cifti2Header, Cifti2Image
from .fileholders import FileHolder, FileHolderError
from .freesurfer import MGHImage
from .funcs import as_closest_canonical, concat_images, four_to_three, squeeze_image
from .gifti import GiftiImage
from .imageclasses import all_image_classes
from .loadsave import load, save
from .minc1 import Minc1Image
from .minc2 import Minc2Image
from .nifti1 import Nifti1Header, Nifti1Image, Nifti1Pair
from .nifti2 import Nifti2Header, Nifti2Image, Nifti2Pair
from .orientations import (
    OrientationError,
    aff2axcodes,
    apply_orientation,
    flip_axis,
    io_orientation,
)
from .spm2analyze import Spm2AnalyzeHeader, Spm2AnalyzeImage
from .spm99analyze import Spm99AnalyzeHeader, Spm99AnalyzeImage

# isort: split

from .pkg_info import get_pkg_info as _get_pkg_info


def get_info():
    return _get_pkg_info(os.path.dirname(__file__))


def test(
    label=None,
    verbose=1,
    extra_argv=None,
    doctests=False,
    coverage=False,
    raise_warnings=None,
    timer=False,
):
    """
    Run tests for nibabel using pytest

    The protocol mimics the ``numpy.testing.NoseTester.test()``.
    Not all features are currently implemented.

    Parameters
    ----------
    label : None
        Unused.
    verbose: int, optional
        Verbosity value for test outputs. Positive values increase verbosity, and
        negative values decrease it. Default is 1.
    extra_argv : list, optional
        List with any extra arguments to pass to pytest.
    doctests: bool, optional
        If True, run doctests in module. Default is False.
    coverage: bool, optional
        If True, report coverage of NumPy code. Default is False.
        (This requires the
        `coverage module <https://nedbatchelder.com/code/modules/coveragehtml>`_).
    raise_warnings : None
        Unused.
    timer : False
        Unused.

    Returns
    -------
    code : ExitCode
        Returns the result of running the tests as a ``pytest.ExitCode`` enum
    """
    import pytest

    args = []

    if label is not None:
        raise NotImplementedError('Labels cannot be set at present')

    verbose = int(verbose)
    if verbose > 0:
        args.append('-' + 'v' * verbose)
    elif verbose < 0:
        args.append('-' + 'q' * -verbose)

    if extra_argv:
        args.extend(extra_argv)
    if doctests:
        args.append('--doctest-modules')
    if coverage:
        args.extend(['--cov', 'nibabel'])
    if raise_warnings is not None:
        raise NotImplementedError('Warning filters are not implemented')
    if timer:
        raise NotImplementedError('Timing is not implemented')

    args.extend(['--pyargs', 'nibabel'])

    return pytest.main(args=args)


def bench(label=None, verbose=1, extra_argv=None):
    """
    Run benchmarks for nibabel using pytest

    The protocol mimics the ``numpy.testing.NoseTester.bench()``.
    Not all features are currently implemented.

    Parameters
    ----------
    label : None
        Unused.
    verbose: int, optional
        Verbosity value for test outputs. Positive values increase verbosity, and
        negative values decrease it. Default is 1.
    extra_argv : list, optional
        List with any extra arguments to pass to pytest.

    Returns
    -------
    code : ExitCode
        Returns the result of running the tests as a ``pytest.ExitCode`` enum
    """
    try:
        from importlib.resources import as_file, files
    except ImportError:
        from importlib_resources import as_file, files

    args = []
    if extra_argv is not None:
        args.extend(extra_argv)

    config_path = files('nibabel') / 'benchmarks/pytest.benchmark.ini'
    with as_file(config_path) as config:
        args.extend(['-c', str(config)])
        return test(label, verbose, extra_argv=args)