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src/n/i/nipy-0.3.0/nipy/core/reference/spaces.py   nipy(Download)
from nibabel.affines import from_matvec
from ...fixes.nibabel import io_orientation
from .coordinate_system import CoordSysMaker, is_coordsys, is_coordsys_maker
        raise AxesError('First 3 output axes must be X, Y, Z')
    # Check equivalent input axes
    ornt = io_orientation(affine)
    if set(ornt[:3, 0]) != set((0, 1, 2)):
        raise AxesError('First 3 input axes must correspond to X, Y, Z')

src/n/i/nipy-0.3.0/nipy/core/reference/coordinate_map.py   nipy(Download)
from nibabel.affines import to_matvec, from_matvec
from ...fixes.nibabel import io_orientation
from .coordinate_system import(CoordinateSystem,
    affine = coordmap.affine
    affine = _fix0(affine) if fix0 else affine
    ornts = io_orientation(affine)
    ornts = [None if np.isnan(R) else int(R) for R in ornts[:, 0]]
    if in2out:

src/n/i/nipy-0.3.0/nipy/core/image/image_spaces.py   nipy(Download)
import numpy as np
from ...fixes.nibabel import io_orientation
from ..image.image import Image
    reo_img = img.reordered_reference(order)
    # Which input axes correspond?
    ornt = io_orientation(reo_img.coordmap.affine)
    current_in_order = ornt[:,0]
    # Set nan to inf to make np.argsort work for old numpy versions

src/n/i/nipy-0.3.0/nipy/algorithms/registration/groupwise_registration.py   nipy(Download)
from nibabel.affines import apply_affine
from ...fixes.nibabel import io_orientation
from ...core.image.image_spaces import (make_xyz_image,
        # guess the slice axis and direction (z-axis)
        if slice_info == None:
            orient = io_orientation(self.affine)
            self.slice_axis = int(np.where(orient[:, 0] == 2)[0])
            self.slice_direction = int(orient[self.slice_axis, 1])

src/n/i/nipy-0.3.0/nipy/algorithms/registration/tests/test_fmri_realign4d.py   nipy(Download)
from .... import load_image
from ....testing import funcfile
from ....fixes.nibabel import io_orientation
from ..groupwise_registration import Image4d, resample4d, FmriRealign4d
    runs = [im, im]
    orient = io_orientation(im.affine)
    slice_axis = int(np.where(orient[:, 0] == 2)[0])
    R1 = FmriRealign4d(runs, tr=2., slice_order='ascending')