Formatting fix, support for myelinated section in Arbor cable cell (c…

…ommented out)
BlueBrain · Jul 28, 2022 · c0af192 · c0af192
1 parent e88168f
commit c0af192
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Showing 2 changed files with 8 additions and 8 deletions.
diff --git a/bluepyopt/ephys/models.py b/bluepyopt/ephys/models.py
@@ -334,13 +334,12 @@ def _create_sim_desc(self, param_values,
                                      radius=0.5 * section.diam,
                                      tag=morphologies._arb_tags['axon'])
                                 for section in self.icell.axon]
-                # TODO: if there is a myelinated section,
-                # append to replace_axon
-                #   dict(nseg=5,
-                #        length=1000,
-                #        radius=?,
-                #        tag=morphologies._arb_tags['myelin'])
-                # Where is the myelinated section instantiated, though?
+                # Requires safe iteration over myelin section
+                # replace_axon += [dict(nseg=section.nseg,
+                #                      length=section.L,
+                #                      radius=0.5 * section.diam,
+                #                      tag=morphologies._arb_tags['myelin'])
+                #                 for section in self.icell.myelin]
             else:
                 replace_axon = None
         else:

diff --git a/bluepyopt/ephys/morphologies.py b/bluepyopt/ephys/morphologies.py
@@ -343,7 +343,8 @@ def replace_axon(morphology, replacement=None):
                          ' of radii %s.', str(ar_radius))
 
         if replacement is not None:
-            ar_seg_scaling = numpy.cumsum([0] + [r['length'] for r in replacement])
+            ar_seg_scaling = numpy.cumsum([0] +
+                                          [r['length'] for r in replacement])
         else:
             ar_seg_scaling = numpy.cumsum([0, 30, 30])
         ar_seg_scaling /= numpy.linalg.norm(ar_dist_center - ar_prox_center)