Merge pull request #103 from oesteban/fix/doctests-broken

FIX: Revise vector tests broken when addressing other issues

Author: oesteban

dmriprep/interfaces/vectors.py

@@ -68,7 +68,7 @@ def _run_interface(self, runtime):
         rasb_file = _undefined(self.inputs, 'in_rasb')
 
         table = DiffusionGradientTable(
-            self.inputs.dwi_file,
+            dwi_file=self.inputs.dwi_file,
             bvecs=_undefined(self.inputs, 'in_bvec'),
             bvals=_undefined(self.inputs, 'in_bval'),
             rasb_file=rasb_file,

dmriprep/utils/tests/test_vectors.py

@@ -46,12 +46,14 @@ def test_corruption(tmpdir, dipy_test_data, monkeypatch):
     bval_no_b0[0] = 51
     with pytest.raises(ValueError):
         dgt = v.DiffusionGradientTable(dwi_file=dipy_test_data['dwi_file'],
-                                       bvals=bval_no_b0, bvecs=bvecs)
+                                       bvals=bval_no_b0, bvecs=bvecs,
+                                       raise_inconsistent=True)
     bvec_no_b0 = bvecs.copy()
     bvec_no_b0[0] = np.array([1.0, 0.0, 0.0])
     with pytest.raises(ValueError):
         dgt = v.DiffusionGradientTable(dwi_file=dipy_test_data['dwi_file'],
-                                       bvals=bvals, bvecs=bvec_no_b0)
+                                       bvals=bvals, bvecs=bvec_no_b0,
+                                       raise_inconsistent=True)
 
     # Corrupt b0 b-val
     bval_odd_b0 = bvals.copy()

dmriprep/utils/vectors.py

@@ -15,44 +15,57 @@ class DiffusionGradientTable:
 
     __slots__ = [
         "_affine",
-        "_gradients",
+        "_b0_thres",
         "_b_scale",
-        "_bvecs",
         "_bvals",
+        "_bvec_norm_epsilon",
+        "_bvecs",
+        "_gradients",
         "_normalized",
+        "_raise_inconsistent",
         "_transforms",
-        "_b0_thres",
-        "_bvec_norm_epsilon",
     ]
 
     def __init__(
         self,
-        dwi_file=None,
-        bvecs=None,
+        b0_threshold=B0_THRESHOLD,
+        b_scale=True,
         bvals=None,
+        bvec_norm_epsilon=BVEC_NORM_EPSILON,
+        bvecs=None,
+        dwi_file=None,
+        raise_inconsistent=False,
         rasb_file=None,
-        b_scale=True,
         transforms=None,
-        b0_threshold=B0_THRESHOLD,
-        bvec_norm_epsilon=BVEC_NORM_EPSILON,
     ):
         """
         Create a new table of diffusion gradients.
 
         Parameters
         ----------
-        dwi_file : str or os.pathlike or nibabel.spatialimage
-            File path to the diffusion-weighted image series to which the
-            bvecs/bvals correspond.
+        b0_threshold : :obj:`float`
+            The upper threshold to consider a low-b shell as :math:`b=0`.
+        b_scale : :obj:`bool`
+            Automatically scale the *b*-values with the norm of the corresponding
+            *b*-vectors before the latter are normalized.
         bvals : str or os.pathlike or numpy.ndarray
             File path of the b-values.
+        b_vec_norm_epsilon : :obj:`float`
+            The minimum difference in the norm of two *b*-vectors to consider them different.
         bvecs : str or os.pathlike or numpy.ndarray
             File path of the b-vectors.
+        dwi_file : str or os.pathlike or nibabel.spatialimage
+            File path to the diffusion-weighted image series to which the
+            bvecs/bvals correspond.
+        raise_inconsistent : :obj:`bool`
+            If ``True``, a :obj:`ValueError` is raised when discrepancies are found between the
+            :math:`b=0` lists calculated from the *b*-vectors and *b*-values, respectively.
+            If ``False``, inconsistencies will be mended (if possible).
         rasb_file : str or os.pathlike
             File path to a RAS-B gradient table. If rasb_file is provided,
             then bvecs and bvals will be dismissed.
-        b_scale : bool
-            Whether b-values should be normalized.
+        transforms : :obj:`list` of :obj:`numpy.ndarray`
+            A list of affine transforms to rotate the list of vectors.
 
         Example
         -------
@@ -75,16 +88,18 @@ def __init__(
         >>> out_rasb_mat = check.reorient_rasb()
         >>> np.allclose(old_rasb_mat, out_rasb_mat)
         True
+
         """
-        self._transforms = transforms
-        self._b_scale = b_scale
+        self._affine = None
         self._b0_thres = b0_threshold
-        self._bvec_norm_epsilon = bvec_norm_epsilon
-        self._gradients = None
+        self._b_scale = b_scale
         self._bvals = None
+        self._bvec_norm_epsilon = bvec_norm_epsilon
         self._bvecs = None
-        self._affine = None
+        self._gradients = None
         self._normalized = False
+        self._raise_inconsistent = raise_inconsistent
+        self._transforms = transforms
 
         if dwi_file is not None:
             self.affine = dwi_file
@@ -175,6 +190,7 @@ def normalize(self):
             b0_threshold=self._b0_thres,
             bvec_norm_epsilon=self._bvec_norm_epsilon,
             b_scale=self._b_scale,
+            raise_error=self._raise_inconsistent,
         )
         self._normalized = True
 
@@ -295,7 +311,7 @@ def normalize_gradients(bvecs, bvals, b0_threshold=B0_THRESHOLD,
     --------
     >>> bvecs = np.vstack((np.zeros(3), 2.0 * np.eye(3), -0.8 * np.eye(3), np.ones(3)))
     >>> bvals = np.array([1000] * bvecs.shape[0])
-    >>> normalize_gradients(bvecs, bvals, 50)  # doctest: +IGNORE_EXCEPTION_DETAIL
+    >>> normalize_gradients(bvecs, bvals, 50, raise_error=True)
     Traceback (most recent call last):
     ValueError:
 

setup.cfg

@@ -111,7 +111,7 @@ exclude =
 [tool:pytest]
 norecursedirs = .* _*
 addopts = -vx --doctest-modules
-doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE
+doctest_optionflags = ALLOW_UNICODE NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL
 env =
     PYTHONHASHSEED=0
 filterwarnings =