Moves the test to the DiffusionGradientTable object

The method `reorient_rasb` is now attached to this object.

Author: arokem

dmriprep/interfaces/vectors.py

@@ -6,7 +6,9 @@
     SimpleInterface, BaseInterfaceInputSpec, TraitedSpec,
     File, traits, isdefined
 )
-from ..utils.vectors import DiffusionGradientTable, B0_THRESHOLD, BVEC_NORM_EPSILON
+from ..utils.vectors import (DiffusionGradientTable, B0_THRESHOLD,
+                             BVEC_NORM_EPSILON
+                             )
 
 
 class _CheckGradientTableInputSpec(BaseInterfaceInputSpec):
@@ -96,72 +98,4 @@ def _undefined(objekt, name, default=None):
     value = getattr(objekt, name)
     if not isdefined(value):
         return default
-    return value
-
-
-class _ReorientVectorsInputSpec(BaseInterfaceInputSpec):
-    dwi_file = File(exists=True)
-    rasb_file = File(exists=True)
-    affines = traits.List()
-    b0_threshold = traits.Float(B0_THRESHOLD, usedefault=True)
-
-
-class _ReorientVectorsOutputSpec(TraitedSpec):
-    out_rasb = File(exists=True)
-
-
-class ReorientVectors(SimpleInterface):
-    """
-    Reorient Vectors
-
-    Example
-    -------
-    >>> os.chdir(tmpdir)
-    >>> oldrasb = str(data_dir / 'dwi.tsv')
-    >>> oldrasb_mat = np.loadtxt(str(data_dir / 'dwi.tsv'), skiprows=1)
-    >>> # The simple case: all affines are identity
-    >>> affine_list = np.zeros((len(oldrasb_mat[:, 3][oldrasb_mat[:, 3] != 0]), 4, 4))
-    >>> for i in range(4):
-    >>>     affine_list[:, i, i] = 1
-    >>>     reor_vecs = ReorientVectors()
-    >>> reor_vecs = ReorientVectors()
-    >>> reor_vecs.inputs.affines = affine_list
-    >>> reor_vecs.inputs.in_rasb = oldrasb
-    >>> res = reor_vecs.run()
-    >>> out_rasb = res.outputs.out_rasb
-    >>> out_rasb_mat = np.loadtxt(out_rasb, skiprows=1)
-    >>> assert oldrasb_mat == out_rasb_mat
-    True
-    """
-
-    input_spec = _ReorientVectorsInputSpec
-    output_spec = _ReorientVectorsOutputSpec
-
-    def _run_interface(self, runtime):
-        from nipype.utils.filemanip import fname_presuffix
-
-        table = DiffusionGradientTable(
-            dwi_file=self.inputs.dwi_file,
-            rasb_file=self.inputs.rasb_file,
-            transforms=self.inputs.affines,
-        )
-        table.generate_vecval()
-        reor_table = table.reorient_rasb()
-
-        cwd = Path(runtime.cwd).absolute()
-        reor_rasb_file = fname_presuffix(
-            self.inputs.rasb_file,
-            use_ext=False,
-            suffix="_reoriented.tsv",
-            newpath=str(cwd),
-        )
-        np.savetxt(
-            str(reor_rasb_file),
-            reor_table,
-            delimiter="\t",
-            header="\t".join("RASB"),
-            fmt=["%.8f"] * 3 + ["%g"],
-        )
-
-        self._results["out_rasb"] = reor_rasb_file
-        return runtime
+    return value

dmriprep/utils/vectors.py

@@ -52,6 +52,25 @@ def __init__(
             then bvecs and bvals will be dismissed.
         b_scale : bool
             Whether b-values should be normalized.
+
+        Example
+        -------
+        >>> os.chdir(tmpdir)
+        >>> old_rasb = str(data_dir / 'dwi.tsv')
+        >>> old_rasb_mat = np.loadtxt(str(data_dir / 'dwi.tsv'), skiprows=1)
+        >>> check = DiffusionGradientTable(
+        ...     dwi_file=str(data_dir / 'dwi.nii.gz'),
+        ...     rasb_file=str(data_dir / 'dwi.tsv'))
+        >>> affines = np.zeros((old_rasb_mat.shape[0], 4, 4))
+        >>> aff_file_list = []
+        >>> for ii, aff in enumerate(affines):
+        ...     aff_file = f'aff_{ii}.npy'
+        ...     np.save(aff_file, aff)
+        ...     aff_file_list.append(aff_file)
+        >>> check._transforms = aff_file_list
+        >>> out_rasb_mat = check.reorient_rasb()
+        >>> assert np.allclose(old_rasb_mat, out_rasb_mat)
+        True
         """
         self._transforms = transforms
         self._b_scale = b_scale
@@ -164,14 +183,15 @@ def generate_rasb(self):
 
     def reorient_rasb(self):
         """Reorient the vectors based o a list of affine transforms."""
-        from dipy.core.gradients import gradient_table_from_bvals_bvecs, reorient_bvecs
+        from dipy.core.gradients import (gradient_table_from_bvals_bvecs,
+                                         reorient_bvecs)
 
         affines = self._transforms.copy()
         bvals = self._bvals
         bvecs = self._bvecs
 
-        # Verify that number of non-B0 volumes corresponds to the number of affines.
-        # If not, raise an error.
+        # Verify that number of non-B0 volumes corresponds to the number of
+        # affines. If not, try to fix it, or raise an error:
         if len(self._bvals[self._bvals >= self._b0_thres]) != len(affines):
             b0_indices = np.where(self._bvals <= self._b0_thres)[0].tolist()
             if len(self._bvals[self._bvals >= self._b0_thres]) < len(affines):
@@ -188,7 +208,8 @@ def reorient_rasb(self):
                 )
 
         # Build gradient table object
-        gt = gradient_table_from_bvals_bvecs(bvals, bvecs, b0_threshold=self._b0_thres)
+        gt = gradient_table_from_bvals_bvecs(bvals, bvecs,
+                                             b0_threshold=self._b0_thres)
 
         # Reorient table
         new_gt = reorient_bvecs(gt, [np.load(aff) for aff in affines])
@@ -238,7 +259,7 @@ def to_filename(self, filename, filetype="rasb"):
             np.savetxt("%s.bval" % filename, self.bvals, fmt="%.6f")
         else:
             raise ValueError('Unknown filetype "%s"' % filetype)
-        
+
 
 def normalize_gradients(bvecs, bvals, b0_threshold=B0_THRESHOLD,
                         bvec_norm_epsilon=BVEC_NORM_EPSILON, b_scale=True):