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src/n/i/nipy-0.3.0/nipy/algorithms/registration/groupwise_registration.py   nipy(Download)
import numpy as np
 
from nibabel.affines import apply_affine
 
from ...fixes.nibabel import io_orientation
def scanner_coords(xyz, affine, from_world, to_world):
    Tv = np.dot(from_world, np.dot(affine, to_world))
    XYZ = apply_affine(Tv, xyz)
    return XYZ[:, 0], XYZ[:, 1], XYZ[:, 2]
 

src/n/i/nipy-0.3.0/nipy/algorithms/registration/affine.py   nipy(Download)
import scipy.linalg as spl
 
from nibabel.affines import apply_affine
 
from ...externals.transforms3d.quaternions import mat2quat, quat2axangle
    def apply(self, xyz):
        return apply_affine(self.as_affine(), xyz)
 
    def _get_param(self):
        param = self._vec12 / self._precond

src/n/i/nipy-0.3.0/nipy/labs/statistical_mapping.py   nipy(Download)
# Use the nibabel image object
from nibabel import Nifti1Image as Image
from nibabel.affines import apply_affine
 
from ..algorithms.graph.field import field_from_graph_and_data
        pval = sp_stats.norm.sf(zscore)
        # Replace array indices with real coordinates
        c['maxima'] = apply_affine(zimg.get_affine(), xyz_th[maxima])
        c['zscore'] = zscore
        c['pvalue'] = pval

src/n/i/nipy-0.3.0/nipy/algorithms/registration/tests/test_chain_transforms.py   nipy(Download)
import numpy.linalg as npl
 
from nibabel.affines import apply_affine
 
from ..chain_transform import ChainTransform
    # Check apply gives expected result
    assert_array_equal(ct.apply(POINTS),
                       apply_affine(AFF2, POINTS))
    # Check that result is changed by setting params
    assert_array_equal(ct.param, aff2_obj.param)
    tmp = np.dot(AFF2, AFF1)
    assert_array_almost_equal(ct.apply(POINTS),
                       apply_affine(np.dot(AFF2, AFF1), POINTS))
    # Check that result is changed by setting params
    assert_array_almost_equal(ct.param, aff2_obj.param)
    ct.param = np.zeros((12,))
    assert_array_almost_equal(ct.apply(POINTS), apply_affine(AFF1, POINTS))
    ct = ChainTransform(aff2_obj, pre=AFF1_OBJ, post=AFF3_OBJ)
    assert_array_almost_equal(ct.apply(POINTS),
                       apply_affine(np.dot(AFF3, np.dot(AFF2, AFF1)), POINTS))
    # Check that result is changed by setting params
    assert_array_equal(ct.param, aff2_obj.param)