Merge pull request #42 from oesteban/fix/32

ENH: First implementation of loading and applying ITK displacements fields

Author: mgxd

nitransforms/io/itk.py

@@ -1,6 +1,8 @@
 """Read/write ITK transforms."""
+import warnings
 import numpy as np
 from scipy.io import savemat as _save_mat
+from nibabel.loadsave import load as loadimg
 from nibabel.affines import from_matvec
 from .base import BaseLinearTransformList, LinearParameters, _read_mat, TransformFileError
 
@@ -245,3 +247,37 @@ def from_string(cls, string):
             _self.xforms.append(cls._inner_type.from_string(
                 '#%s' % xfm))
         return _self
+
+
+class ITKDisplacementsField:
+    """A data structure representing displacements fields."""
+
+    @classmethod
+    def from_filename(cls, filename):
+        """Import a displacements field from a NIfTI file."""
+        imgobj = loadimg(str(filename))
+        return cls.from_image(imgobj)
+
+    @classmethod
+    def from_image(cls, imgobj):
+        """Import a displacements field from a NIfTI file."""
+        _hdr = imgobj.header.copy()
+        _shape = _hdr.get_data_shape()
+
+        if (
+            len(_shape) != 5 or
+            _shape[-2] != 1 or
+            not _shape[-1] in (2, 3)
+        ):
+            raise TransformFileError(
+                'Displacements field "%s" does not come from ITK.' %
+                imgobj.file_map['image'].filename)
+
+        if _hdr.get_intent()[0] != 'vector':
+            warnings.warn('Incorrect intent identified.')
+            _hdr.set_intent('vector')
+
+        _field = np.squeeze(np.asanyarray(imgobj.dataobj))
+        _field[..., (0, 1)] *= -1.0
+
+        return imgobj.__class__(_field, imgobj.affine, _hdr)

nitransforms/nonlinear.py

@@ -22,19 +22,17 @@ class DisplacementsFieldTransform(TransformBase):
 
     def __init__(self, field, reference=None):
         """Create a dense deformation field transform."""
-        super(DisplacementsFieldTransform, self).__init__()
+        super().__init__()
         self._field = np.asanyarray(field.dataobj)
 
         ndim = self._field.ndim - 1
-        if len(self._field.shape[:-1]) != ndim:
+        if self._field.shape[-1] != ndim:
             raise ValueError(
-                'Number of components of the deformation field does '
-                'not match the number of dimensions')
+                'The number of components of the displacements (%d) does not '
+                'the number of dimensions (%d)' % (self._field.shape[-1], ndim))
 
-        if reference is None:
-            reference = field.__class__(np.zeros(self._field.shape[:-1]),
-                                        field.affine, field.header)
-        self.reference = reference
+        self.reference = field.__class__(np.zeros(self._field.shape[:-1]),
+                                         field.affine, field.header)
 
     def map(self, x, inverse=False, index=0):
         r"""

nitransforms/tests/test_nonlinear.py

@@ -8,7 +8,9 @@
 
 import numpy as np
 import nibabel as nb
+from ..io.base import TransformFileError
 from ..nonlinear import DisplacementsFieldTransform
+from ..io.itk import ITKDisplacementsField
 
 TESTS_BORDER_TOLERANCE = 0.05
 APPLY_NONLINEAR_CMD = {
@@ -19,34 +21,88 @@
 }
 
 
+@pytest.mark.parametrize('size', [(20, 20, 20), (20, 20, 20, 3)])
+def test_itk_disp_load(size):
+    """Checks field sizes."""
+    with pytest.raises(TransformFileError):
+        ITKDisplacementsField.from_image(
+            nb.Nifti1Image(np.zeros(size), None, None))
+
+
+@pytest.mark.parametrize('size', [(20, 20, 20), (20, 20, 20, 1, 3)])
+def test_displacements_bad_sizes(size):
+    """Checks field sizes."""
+    with pytest.raises(ValueError):
+        DisplacementsFieldTransform(
+            nb.Nifti1Image(np.zeros(size), None, None))
+
+
+def test_itk_disp_load_intent():
+    """Checks whether the NIfTI intent is fixed."""
+    with pytest.warns(UserWarning):
+        field = ITKDisplacementsField.from_image(
+            nb.Nifti1Image(np.zeros((20, 20, 20, 1, 3)), None, None))
+
+    assert field.header.get_intent()[0] == 'vector'
+
+
+@pytest.mark.parametrize('image_orientation', ['RAS', 'LAS', 'LPS', 'oblique'])
 @pytest.mark.parametrize('sw_tool', ['itk'])
-def test_displacements_field(tmp_path, data_path, sw_tool):
+@pytest.mark.parametrize('axis', [0, 1, 2, (0, 1), (1, 2), (0, 1, 2)])
+def test_displacements_field1(tmp_path, get_testdata, image_orientation, sw_tool, axis):
+    """Check a translation-only field on one or more axes, different image orientations."""
     os.chdir(str(tmp_path))
-    img_fname = str(data_path / 'tpl-OASIS30ANTs_T1w.nii.gz')
-    xfm_fname = str(
-        data_path / 'ds-005_sub-01_from-OASIS_to-T1_warp.nii.gz')
-    ants_warp = nb.load(xfm_fname)
-    hdr = ants_warp.header.copy()
+    nii = get_testdata[image_orientation]
+    nii.to_filename('reference.nii.gz')
+    fieldmap = np.zeros((*nii.shape[:3], 1, 3), dtype='float32')
+    fieldmap[..., axis] = -10.0
+
+    _hdr = nii.header.copy()
+    _hdr.set_intent('vector')
+    _hdr.set_data_dtype('float32')
 
-    # fieldmap = np.squeeze(np.asanyarray(ants_warp.dataobj))
     xfm_fname = 'warp.nii.gz'
-    nii = nb.load(img_fname)
-    fieldmap = np.zeros((*nii.shape[:3], 1, 3))
-    fieldmap[..., 2] = -10.0
-    # fieldmap = np.flip(np.flip(fieldmap, 1), 0)
-    ants_warp = nb.Nifti1Image(fieldmap, nii.affine, hdr)
-    ants_warp.to_filename(xfm_fname)
-    fieldmap = np.squeeze(np.asanyarray(ants_warp.dataobj))
-    field = nb.Nifti1Image(
-        fieldmap,
-        ants_warp.affine, ants_warp.header
-    )
-
-    xfm = DisplacementsFieldTransform(field)
+    field = nb.Nifti1Image(fieldmap, nii.affine, _hdr)
+    field.to_filename(xfm_fname)
+
+    xfm = DisplacementsFieldTransform(
+        ITKDisplacementsField.from_image(field))
 
     # Then apply the transform and cross-check with software
     cmd = APPLY_NONLINEAR_CMD[sw_tool](
         transform=os.path.abspath(xfm_fname),
+        reference=tmp_path / 'reference.nii.gz',
+        moving=tmp_path / 'reference.nii.gz')
+
+    # skip test if command is not available on host
+    exe = cmd.split(" ", 1)[0]
+    if not shutil.which(exe):
+        pytest.skip("Command {} not found on host".format(exe))
+
+    exit_code = check_call([cmd], shell=True)
+    assert exit_code == 0
+    sw_moved = nb.load('resampled.nii.gz')
+
+    nt_moved = xfm.apply(nii, order=0)
+    nt_moved.to_filename('nt_resampled.nii.gz')
+    diff = sw_moved.get_fdata() - nt_moved.get_fdata()
+    # A certain tolerance is necessary because of resampling at borders
+    assert (np.abs(diff) > 1e-3).sum() / diff.size < TESTS_BORDER_TOLERANCE
+
+
+@pytest.mark.parametrize('sw_tool', ['itk'])
+def test_displacements_field2(tmp_path, data_path, sw_tool):
+    """Check a translation-only field on one or more axes, different image orientations."""
+    os.chdir(str(tmp_path))
+    img_fname = data_path / 'tpl-OASIS30ANTs_T1w.nii.gz'
+    xfm_fname = data_path / 'ds-005_sub-01_from-OASIS_to-T1_warp.nii.gz'
+
+    xfm = DisplacementsFieldTransform(
+        ITKDisplacementsField.from_filename(xfm_fname))
+
+    # Then apply the transform and cross-check with software
+    cmd = APPLY_NONLINEAR_CMD[sw_tool](
+        transform=xfm_fname,
         reference=img_fname,
         moving=img_fname)