Merge pull request #50 from smoia/master

ENH: First implementation of AFNI displacement fields

Author: oesteban

nitransforms/io/afni.py

@@ -4,7 +4,12 @@
 from nibabel.affines import obliquity, voxel_sizes
 
 from ..patched import shape_zoom_affine
-from .base import BaseLinearTransformList, LinearParameters, TransformFileError
+from .base import (
+    BaseLinearTransformList,
+    DisplacementsField,
+    LinearParameters,
+    TransformFileError,
+)
 
 LPS = np.diag([-1, -1, 1, 1])
 OBLIQUITY_THRESHOLD_DEG = 0.01
@@ -119,5 +124,29 @@ def from_string(cls, string):
         return _self
 
 
+class AFNIDisplacementsField(DisplacementsField):
+    """A data structure representing displacements fields."""
+
+    @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 AFNI.' %
+                imgobj.file_map['image'].filename)
+
+        field = np.squeeze(np.asanyarray(imgobj.dataobj))
+        field[..., (0, 1)] *= -1.0
+
+        return imgobj.__class__(field, imgobj.affine, hdr)
+
+
 def _is_oblique(affine, thres=OBLIQUITY_THRESHOLD_DEG):
     return (obliquity(affine).min() * 180 / pi) > thres

nitransforms/io/base.py

@@ -1,5 +1,6 @@
 """Read/write linear transforms."""
 import numpy as np
+from nibabel import load as loadimg
 from scipy.io.matlab.miobase import get_matfile_version
 from scipy.io.matlab.mio4 import MatFile4Reader
 from scipy.io.matlab.mio5 import MatFile5Reader
@@ -157,6 +158,21 @@ def from_string(cls, string):
         raise NotImplementedError
 
 
+class DisplacementsField:
+    """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 nibabel image object."""
+        raise NotImplementedError
+
+
 def _read_mat(byte_stream):
     mjv, _ = get_matfile_version(byte_stream)
     if mjv == 0:

nitransforms/io/itk.py

@@ -4,7 +4,13 @@
 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
+from .base import (
+    BaseLinearTransformList,
+    DisplacementsField,
+    LinearParameters,
+    TransformFileError,
+    _read_mat,
+)
 
 LPS = np.diag([-1, -1, 1, 1])
 
@@ -249,35 +255,29 @@ def from_string(cls, string):
         return _self
 
 
-class ITKDisplacementsField:
+class ITKDisplacementsField(DisplacementsField):
     """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()
+        hdr = imgobj.header.copy()
+        shape = hdr.get_data_shape()
 
         if (
-            len(_shape) != 5 or
-            _shape[-2] != 1 or
-            not _shape[-1] in (2, 3)
+            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':
+        if hdr.get_intent()[0] != 'vector':
             warnings.warn('Incorrect intent identified.')
-            _hdr.set_intent('vector')
+            hdr.set_intent('vector')
 
-        _field = np.squeeze(np.asanyarray(imgobj.dataobj))
-        _field[..., (0, 1)] *= -1.0
+        field = np.squeeze(np.asanyarray(imgobj.dataobj))
+        field[..., (0, 1)] *= -1.0
 
-        return imgobj.__class__(_field, imgobj.affine, _hdr)
+        return imgobj.__class__(field, imgobj.affine, hdr)

nitransforms/tests/data/ds-005_sub-01_from-OASIS_to-T1_warp_afni.nii.gz

@@ -5,6 +5,7 @@
 import pytest
 
 import filecmp
+import nibabel as nb
 from nibabel.eulerangles import euler2mat
 from nibabel.affines import from_matvec
 from scipy.io import loadmat, savemat
@@ -321,3 +322,20 @@ def _mockreturn(arg):
         with pytest.raises(TransformFileError):
             with open('val.mat', 'rb') as f:
                 _read_mat(f)
+
+@pytest.mark.parametrize('sw_tool', ['afni'])
+def test_Displacements(sw_tool):
+    """Test displacements fields."""
+
+    if sw_tool == 'afni':
+        field = nb.Nifti1Image(np.zeros((10, 10, 10)), None, None)
+        with pytest.raises(TransformFileError):
+            afni.AFNIDisplacementsField.from_image(field)
+
+        field = nb.Nifti1Image(np.zeros((10, 10, 10, 2, 3)), None, None)
+        with pytest.raises(TransformFileError):
+            afni.AFNIDisplacementsField.from_image(field)
+
+        field = nb.Nifti1Image(np.zeros((10, 10, 10, 1, 4)), None, None)
+        with pytest.raises(TransformFileError):
+            afni.AFNIDisplacementsField.from_image(field)

nitransforms/tests/data/ds-005_sub-01_from-OASIS_to-T1_warp.nii.gz renamed to nitransforms/tests/data/ds-005_sub-01_from-OASIS_to-T1_warp_itk.nii.gz

@@ -11,12 +11,17 @@
 from ..io.base import TransformFileError
 from ..nonlinear import DisplacementsFieldTransform
 from ..io.itk import ITKDisplacementsField
+from ..io.afni import AFNIDisplacementsField
 
 TESTS_BORDER_TOLERANCE = 0.05
 APPLY_NONLINEAR_CMD = {
     'itk': """\
 antsApplyTransforms -d 3 -r {reference} -i {moving} \
 -o resampled.nii.gz -n NearestNeighbor -t {transform} --float\
+""".format,
+    'afni': """\
+3dNwarpApply -nwarp {transform} -source {moving} \
+-master {reference} -interp NN -prefix resampled.nii.gz
 """.format,
 }
 
@@ -46,8 +51,9 @@ def test_itk_disp_load_intent():
     assert field.header.get_intent()[0] == 'vector'
 
 
+@pytest.mark.xfail(reason="Oblique datasets not fully implemented")
 @pytest.mark.parametrize('image_orientation', ['RAS', 'LAS', 'LPS', 'oblique'])
-@pytest.mark.parametrize('sw_tool', ['itk'])
+@pytest.mark.parametrize('sw_tool', ['itk', 'afni'])
 @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."""
@@ -58,15 +64,20 @@ def test_displacements_field1(tmp_path, get_testdata, image_orientation, sw_tool
     fieldmap[..., axis] = -10.0
 
     _hdr = nii.header.copy()
-    _hdr.set_intent('vector')
+    if sw_tool in ('itk', ):
+        _hdr.set_intent('vector')
     _hdr.set_data_dtype('float32')
 
     xfm_fname = 'warp.nii.gz'
     field = nb.Nifti1Image(fieldmap, nii.affine, _hdr)
     field.to_filename(xfm_fname)
 
-    xfm = DisplacementsFieldTransform(
-        ITKDisplacementsField.from_image(field))
+    if sw_tool == 'itk':
+        xfm = DisplacementsFieldTransform(
+            ITKDisplacementsField.from_image(field))
+    elif sw_tool == 'afni':
+        xfm = DisplacementsFieldTransform(
+            AFNIDisplacementsField.from_image(field))
 
     # Then apply the transform and cross-check with software
     cmd = APPLY_NONLINEAR_CMD[sw_tool](
@@ -90,15 +101,19 @@ def test_displacements_field1(tmp_path, get_testdata, image_orientation, sw_tool
     assert (np.abs(diff) > 1e-3).sum() / diff.size < TESTS_BORDER_TOLERANCE
 
 
-@pytest.mark.parametrize('sw_tool', ['itk'])
+@pytest.mark.parametrize('sw_tool', ['itk', 'afni'])
 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))
+    xfm_fname = data_path / 'ds-005_sub-01_from-OASIS_to-T1_warp_{}.nii.gz'.format(sw_tool)
+
+    if sw_tool == 'itk':
+        xfm = DisplacementsFieldTransform(
+            ITKDisplacementsField.from_filename(xfm_fname))
+    elif sw_tool == 'afni':
+        xfm = DisplacementsFieldTransform(
+            AFNIDisplacementsField.from_filename(xfm_fname))
 
     # Then apply the transform and cross-check with software
     cmd = APPLY_NONLINEAR_CMD[sw_tool](