Пример #1
0
 def test_reorder(self):
     (vox_array, 
      affine, 
      aff_trans, 
      ornt_trans) = dcmstack.reorder_voxels(self.vox_array, 
                                            self.affine, 
                                            'PRS')
     ok_(np.all(vox_array == np.array([[[[4, 5], 
                                         [6, 7]],
                                        [[12, 13], 
                                         [14,15]]
                                       ],
                                       [[[0, 1], 
                                         [2, 3]],
                                        [[8, 9], 
                                         [10, 11]]
                                       ]
                                      ]
                                     )
               )
        )
     ok_(np.allclose(affine, 
                     np.array([[0,1,0,0],
                               [-1,0,0,1],
                               [0,0,1,0],
                               [0,0,0,1]])
                    )
        )
Пример #2
0
 def test_reorder(self):
     (vox_array,
      affine,
      aff_trans,
      ornt_trans) = dcmstack.reorder_voxels(self.vox_array,
                                            self.affine,
                                            'PRS')
     ok_(np.all(vox_array == np.array([[[[4, 5],
                                         [6, 7]],
                                        [[12, 13],
                                         [14,15]]
                                       ],
                                       [[[0, 1],
                                         [2, 3]],
                                        [[8, 9],
                                         [10, 11]]
                                       ]
                                      ]
                                     )
               )
        )
     ok_(np.allclose(affine,
                     np.array([[0,1,0,0],
                               [-1,0,0,1],
                               [0,0,1,0],
                               [0,0,0,1]])
                    )
        )
Пример #3
0
 def test_no_op(self):
     vox_order = [dcmstack.closest_ortho_pat_axis(self.affine[:3, idx])[0] for idx in range(3)]
     vox_order = "".join(vox_order)
     vox_array, affine, perm = dcmstack.reorder_voxels(self.vox_array, self.affine, vox_order)
     ok_((vox_array == self.vox_array).all())
     ok_((affine == self.affine).all())
     eq_(perm, (0, 1, 2))
     eq_(np.may_share_memory(affine, self.affine), False)
Пример #4
0
 def test_no_op(self):
     vox_order = ''.join(aff2axcodes(self.affine))
     (vox_array, affine, aff_trans,
      ornt_trans) = dcmstack.reorder_voxels(self.vox_array, self.affine,
                                            vox_order)
     ok_((vox_array == self.vox_array).all())
     ok_((affine == self.affine).all())
     ok_((aff_trans == np.eye(4)).all())
     ok_(np.allclose(ornt_trans, [[0, 1], [1, 1], [2, 1]]))
     eq_(np.may_share_memory(affine, self.affine), False)
Пример #5
0
 def test_aniso_reorder(self):
     self.vox_array = self.vox_array.reshape(2, 4, 2)
     self.affine = np.eye(4)
     (vox_array, affine, aff_trans,
      ornt_trans) = dcmstack.reorder_voxels(self.vox_array, self.affine,
                                            'PLS')
     ok_(
         np.allclose(
             affine,
             np.array([[0, -1, 0, 1], [-1, 0, 0, 3], [0, 0, 1, 0],
                       [0, 0, 0, 1]])))
Пример #6
0
 def test_no_op(self):
     vox_order = [
         dcmstack.closest_ortho_pat_axis(self.affine[:3, idx])[0]
         for idx in range(3)
     ]
     vox_order = ''.join(vox_order)
     vox_array, affine, perm = dcmstack.reorder_voxels(
         self.vox_array, self.affine, vox_order)
     ok_((vox_array == self.vox_array).all())
     ok_((affine == self.affine).all())
     eq_(perm, (0, 1, 2))
     eq_(np.may_share_memory(affine, self.affine), False)
Пример #7
0
 def test_no_op(self):
     vox_order = ''.join(aff2axcodes(self.affine))
     (vox_array, 
      affine, 
      aff_trans, 
      ornt_trans) = dcmstack.reorder_voxels(self.vox_array, 
                                            self.affine, 
                                            vox_order)
     ok_((vox_array == self.vox_array).all())
     ok_((affine == self.affine).all())
     ok_((aff_trans == np.eye(4)).all())
     ok_(np.allclose(ornt_trans, [[0, 1], [1, 1], [2, 1]]))
     eq_(np.may_share_memory(affine, self.affine), False)
Пример #8
0
 def test_aniso_reorder(self):
     self.vox_array = self.vox_array.reshape(2, 4, 2)
     self.affine = np.eye(4)
     (vox_array, 
      affine, 
      aff_trans, 
      ornt_trans) = dcmstack.reorder_voxels(self.vox_array, 
                                            self.affine, 
                                            'PLS')
     ok_(np.allclose(affine, 
                     np.array([[0,-1,0,1],
                               [-1,0,0,3],
                               [0,0,1,0],
                               [0,0,0,1]])
                    )
        )
Пример #9
0
    def reorder_voxels(imagedata, qto_xyz, voxel_order):
        """
        Reorder voxel data to the specified voxel_order.

        Does not directly manipulate imagedata or qto_xyz.
        Returns manipulated copies of imagedata and qto_xyz.

        Parameters
        ----------
        imagedata : np.array
            single np.array of image data
        qto_xyz : np.matrix, 4x4
            patient space
        voxel_order : str, 3 char
            3 character voxel order string, such as 'LPS' or 'RAI'

        """
        log.debug('reorienting to voxel order %s' % voxel_order)
        new_data, new_qto_xyz, _, _ = dcmstack.reorder_voxels(imagedata, qto_xyz, voxel_order)
        return new_data, new_qto_xyz
Пример #10
0
    def reorder_voxels(imagedata, qto_xyz, voxel_order):
        """
        Reorder voxel data to the specified voxel_order.

        Does not directly manipulate imagedata or qto_xyz.
        Returns manipulated copies of imagedata and qto_xyz.

        Parameters
        ----------
        imagedata : np.array
            single np.array of image data
        qto_xyz : np.matrix, 4x4
            patient space
        voxel_order : str, 3 char
            3 character voxel order string, such as 'LPS' or 'RAI'

        """
        log.debug('reorienting to voxel order %s' % voxel_order)
        new_data, new_qto_xyz, _, _ = dcmstack.reorder_voxels(
            imagedata, qto_xyz, voxel_order)
        return new_data, new_qto_xyz