fix: remove mentions to fieldmap for now

Author: oesteban

src/nifreeze/data/dmri.py

@@ -43,11 +43,7 @@ class DWI(BaseDataset):
     """Data representation structure for dMRI data."""
 
     bzero = attr.ib(default=None, repr=_data_repr, eq=attr.cmp_using(eq=_cmp))
-    """
-    A *b=0* reference map, preferably obtained by some smart averaging.
-    If the :math:`B_0` fieldmap is set, this *b=0* reference map should also
-    be unwarped.
-    """
+    """A *b=0* reference map, preferably obtained by some smart averaging."""
     gradients = attr.ib(default=None, repr=_data_repr, eq=attr.cmp_using(eq=_cmp))
     """A 2D numpy array of the gradient table (4xN)."""
     eddy_xfms = attr.ib(default=None)
@@ -254,7 +250,7 @@ def load(
     -------
     dwi : DWI
         A DWI object containing the loaded data, gradient table, and optional
-        b-zero volume, brainmask, or fieldmap.
+        b-zero volume, and brainmask.
 
     Raises
     ------

src/nifreeze/estimator.py

@@ -181,7 +181,6 @@ def estimate(
                             data.affine,
                             data.dataobj.shape[:3],
                             data_test[1][3],
-                            data.fieldmap,
                             i_iter,
                             i,
                             ptmp_dir,

src/nifreeze/registration/ants.py

@@ -409,7 +409,6 @@ def _run_registration(
     affine: np.ndarray,
     shape: tuple[int, int, int],
     bval: int,
-    fieldmap: nb.spatialimages.SpatialImage,
     i_iter: int,
     vol_idx: int,
     dirname: Path,
@@ -435,8 +434,6 @@ def _run_registration(
         Shape of the DWI frame.
     bval : :obj:`int`
         b-value of the corresponding DWI volume.
-    fieldmap : :class:`~nibabel.spatialimages.SpatialImage`
-        Fieldmap.
     i_iter : :obj:`int`
         Iteration number.
     vol_idx : :obj:`int`
@@ -473,13 +470,7 @@ def _run_registration(
 
     if em_affines is not None and np.any(em_affines[vol_idx, ...]):
         reference = namedtuple("ImageGrid", ("shape", "affine"))(shape=shape, affine=affine)
-
-        # create a nitransforms object
-        if fieldmap:
-            # compose fieldmap into transform
-            raise NotImplementedError
-        else:
-            initial_xform = Affine(matrix=em_affines[vol_idx], reference=reference)
+        initial_xform = Affine(matrix=em_affines[vol_idx], reference=reference)
         mat_file = dirname / f"init_{i_iter}_{vol_idx:05d}.mat"
         initial_xform.to_filename(mat_file, fmt="itk")
         registration.inputs.initial_moving_transform = str(mat_file)

test/test_data_dmri.py

@@ -49,15 +49,13 @@ def _create_dwi_random_dataobj():
     brainmask_dataobj = rng.random(vol_size, dtype="float32")
     b0_dataobj = rng.random(vol_size, dtype="float32")
     gradients = np.vstack([bvecs, bvals[np.newaxis, :]], dtype="float32")
-    fieldmap_dataobj = rng.random(vol_size, dtype="float32")
 
     return (
         dwi_dataobj,
         affine,
         brainmask_dataobj,
         b0_dataobj,
         gradients,
-        fieldmap_dataobj,
         b0_thres,
     )
 
@@ -67,42 +65,36 @@ def _create_dwi_random_data(
     affine,
     brainmask_dataobj,
     b0_dataobj,
-    fieldmap_dataobj,
 ):
     dwi = nb.Nifti1Image(dwi_dataobj, affine)
     brainmask = nb.Nifti1Image(brainmask_dataobj, affine)
     b0 = nb.Nifti1Image(b0_dataobj, affine)
-    fieldmap = nb.Nifti1Image(fieldmap_dataobj, affine)
 
-    return dwi, brainmask, b0, fieldmap
+    return dwi, brainmask, b0
 
 
 def _serialize_dwi_data(
     dwi,
     brainmask,
     b0,
     gradients,
-    fieldmap,
     _tmp_path,
 ):
     dwi_fname = _tmp_path / "dwi.nii.gz"
     brainmask_fname = _tmp_path / "brainmask.nii.gz"
     b0_fname = _tmp_path / "b0.nii.gz"
     gradients_fname = _tmp_path / "gradients.txt"
-    fieldmap_fname = _tmp_path / "fieldmap.nii.gz"
 
     nb.save(dwi, dwi_fname)
     nb.save(brainmask, brainmask_fname)
     nb.save(b0, b0_fname)
     np.savetxt(gradients_fname, gradients.T)
-    nb.save(fieldmap, fieldmap_fname)
 
     return (
         dwi_fname,
         brainmask_fname,
         b0_fname,
         gradients_fname,
-        fieldmap_fname,
     )
 
 
@@ -153,30 +145,26 @@ def test_equality_operator(tmp_path):
         brainmask_dataobj,
         b0_dataobj,
         gradients,
-        fieldmap_dataobj,
         b0_thres,
     ) = _create_dwi_random_dataobj()
 
-    dwi, brainmask, b0, fieldmap = _create_dwi_random_data(
+    dwi, brainmask, b0 = _create_dwi_random_data(
         dwi_dataobj,
         affine,
         brainmask_dataobj,
         b0_dataobj,
-        fieldmap_dataobj,
     )
 
     (
         dwi_fname,
         brainmask_fname,
         b0_fname,
         gradients_fname,
-        fieldmap_fname,
     ) = _serialize_dwi_data(
         dwi,
         brainmask,
         b0,
         gradients,
-        fieldmap,
         tmp_path,
     )