Add test flip and swap axis

scilpy/gradients/bvec_bval_tools.py

@@ -28,7 +28,6 @@ def is_normalized_bvecs(bvecs):
     -------
     True/False
     """
-
     bvecs_norm = np.linalg.norm(bvecs, axis=1)
     return np.all(np.logical_or(np.abs(bvecs_norm - 1) < 1e-3,
                                 bvecs_norm == 0))
@@ -48,7 +47,7 @@ def normalize_bvecs(bvecs):
     bvecs : (N, 3)
        normalized b-vectors
     """
-
+    bvecs = bvecs.copy()  # Avoid in-place modification.
     bvecs_norm = np.linalg.norm(bvecs, axis=1)
     idx = bvecs_norm != 0
     bvecs[idx] /= bvecs_norm[idx, None]
@@ -217,19 +216,22 @@ def flip_gradient_sampling(bvecs, axes, sampling_type):
     Parameters
     ----------
     bvecs: np.ndarray
-        Loaded bvecs. In the case 'mrtrix' the bvecs actually also contain the
-        bvals.
+        bvecs loaded directly, not re-formatted. Careful! Must respect the
+        format (not verified here).
     axes: list of int
-        List of axes to flip (e.g. [0, 1])
+        List of axes to flip (e.g. [0, 1]). See str_to_axis_index.
     sampling_type: str
-        Either 'mrtrix' or 'fsl'.
+        Either 'mrtrix': bvecs are of shape (N, 4) or
+               'fsl': bvecs are of shape (3, N)
 
     Returns
     -------
     bvecs: np.array
         The final bvecs.
     """
     assert sampling_type in ['mrtrix', 'fsl']
+
+    bvecs = bvecs.copy()  # Avoid in-place modification.
     if sampling_type == 'mrtrix':
         for axis in axes:
             bvecs[:, axis] *= -1
@@ -246,12 +248,13 @@ def swap_gradient_axis(bvecs, final_order, sampling_type):
     Parameters
     ----------
     bvecs: np.array
-        Loaded bvecs. In the case 'mrtrix' the bvecs actually also contain the
-        bvals.
+        bvecs loaded directly, not re-formatted. Careful! Must respect the
+        format (not verified here).
     final_order: new order
         Final order (ex, 2 1 0)
     sampling_type: str
-        Either 'mrtrix' or 'fsl'.
+        Either 'mrtrix': bvecs are of shape (N, 4) or
+               'fsl': bvecs are of shape (3, N)
 
     Returns
     -------

scilpy/gradients/tests/test_bvec_bval_tools.py

@@ -3,11 +3,13 @@
 
 from scilpy.gradients.bvec_bval_tools import (
     check_b0_threshold, is_normalized_bvecs, normalize_bvecs,
-    round_bvals_to_shell, identify_shells)
+    round_bvals_to_shell, identify_shells, str_to_axis_index, flip_gradient_sampling,
+    swap_gradient_axis)
 
 bvecs = np.asarray([[1.0, 1.0, 1.0],
                     [1.0, 0.0, 1.0],
-                    [0.0, 1.0, 0.0]])
+                    [0.0, 1.0, 0.0],
+                    [8.0, 1.0, 1.0]])
 
 
 def test_is_normalized_bvecs():
@@ -63,17 +65,26 @@ def _subtest_identify_shells(bvals, threshold,
 
 def test_str_to_axis_index():
     # Very simple, nothing to do
-    pass
+    assert str_to_axis_index('x') == 0
 
 
 def test_flip_gradient_sampling():
-    # toDo
-    pass
+    fsl_bvecs = bvecs.T
+    b = flip_gradient_sampling(fsl_bvecs, axes=[0], sampling_type='fsl')
+    assert np.array_equal(b, np.asarray([[-1.0, 1.0, 1.0],
+                                         [-1.0, 0.0, 1.0],
+                                         [-0.0, 1.0, 0.0],
+                                         [-8.0, 1.0, 1.0]]).T)
 
 
 def test_swap_gradient_axis():
-    # toDo
-    pass
+    fsl_bvecs = bvecs.T
+    final_order = [1, 0, 2]
+    b = swap_gradient_axis(fsl_bvecs, final_order, sampling_type='fsl')
+    assert np.array_equal(b, np.asarray([[1.0, 1.0, 1.0],
+                                         [0.0, 1.0, 1.0],
+                                         [1.0, 0.0, 0.0],
+                                         [1.0, 8.0, 1.0]]).T)
 
 
 def test_round_bvals_to_shell():

scripts/scil_gradients_modify_axes.py

@@ -83,14 +83,24 @@ def main():
     if len(np.unique(swapped_order)) != 3:
         parser.error("final_order should contain the three axis.")
 
+    # Could use io.gradients method, but we don't have a bvals file here, only
+    # treating with the bvecs. Loading directly.
     bvecs = np.loadtxt(args.in_gradient_sampling_file)
     if ext_in == '.bvec':
-        # Supposing FSL format
+        # Supposing FSL format: Per columns
+        if bvecs.shape[0] != 3:
+            parser.error("b-vectors format for a .b file should be FSL, "
+                         "and contain 3 lines (x, y, z), but got {}"
+                         .format(bvecs.shape[0]))
         bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'fsl')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'fsl')
         np.savetxt(args.out_gradient_sampling_file, bvecs, "%.8f")
     else:  # ext == '.b':
         # Supposing mrtrix format
+        if bvecs.shape[1] != 4:
+            parser.error("b-vectors format for a .b file should be mrtrix, "
+                         "and contain 4 columns (x, y, z, bval), but got {}"
+                         .format(bvecs.shape[1]))
         bvecs = flip_gradient_sampling(bvecs, axes_to_flip, 'mrtrix')
         bvecs = swap_gradient_axis(bvecs, swapped_order, 'mrtrix')
         np.savetxt(args.out_gradient_sampling_file, bvecs,