[FIX] fix cross_midline when R/L axis not first orientation

AFQ/recognition/other_bundles.py

@@ -1,9 +1,11 @@
 import numpy as np
+import logging
 
 import dipy.tracking.utils as dtu
 import dipy.tracking.streamline as dts
 
 from scipy.spatial.distance import cdist
+logger = logging.getLogger('AFQ')
 
 
 def clean_by_other_density_map(this_bundle_sls, other_bundle_sls,
@@ -98,6 +100,10 @@ def clean_relative_to_other_core(core, this_fgarray, other_fgarray, affine):
     >>> cleaned_streamlines = [s for i, s in enumerate(streamlines1) 
     ...                        if cleaned_core_idx[i]]
     """
+    if len(other_fgarray) == 0:
+        logger.warning("Cleaning relative to core skipped, no core found.")
+        return np.ones(this_fgarray.shape[0], dtype=np.bool8)
+
     if core == 'anterior':
         core_axis, core_direc = 1, -1
     elif core == 'posterior':

AFQ/recognition/preprocess.py

@@ -1,4 +1,5 @@
 import numpy as np
+import nibabel as nib
 import pimms
 from time import time
 import logging
@@ -55,9 +56,16 @@ def crosses(fgarray, img):
     zero_coord = np.dot(np.linalg.inv(img.affine),
                         np.array([0, 0, 0, 1]))
 
+    orientation = nib.orientations.aff2axcodes(img.affine)
+    lr_axis = 0
+    for idx, axis_label in enumerate(orientation):
+        if axis_label in ['L', 'R']:
+            lr_axis = idx
+            break
+
     return np.logical_and(
-        np.any(fgarray[:, :, 0] > zero_coord[0], axis=1),
-        np.any(fgarray[:, :, 0] < zero_coord[0], axis=1))
+        np.any(fgarray[:, :, lr_axis] > zero_coord[lr_axis], axis=1),
+        np.any(fgarray[:, :, lr_axis] < zero_coord[lr_axis], axis=1))
 
 
 # Things that can be calculated for multiple bundles at once