[MRG] Make cell morphology plots reflect actual cell size

hnn_core/cell.py

@@ -208,6 +208,10 @@ def __repr__(self):
     def L(self):
         return self._L
 
+    @L.setter
+    def L(self, value):
+        self._L = value
+
     @property
     def diam(self):
         return self._diam
@@ -216,6 +220,10 @@ def diam(self):
     def end_pts(self):
         return self._end_pts
 
+    @end_pts.setter
+    def end_pts(self, value):
+        self._end_pts = value
+
 
 class Cell:
     """Create a cell object.
@@ -640,3 +648,20 @@ def plot_morphology(self, ax=None, cell_types=None, show=True):
             The matplotlib 3D axis handle.
         """
         return plot_cell_morphology(self, ax=ax, show=show)
+
+    def update_end_pts(self):
+        """"Create cell and copy coordinates to Section.end_pts"""
+        self._create_sections(self.sections, self.topology)
+        section_names = list(self.sections.keys())
+
+        for name in section_names:
+            nrn_pts = self._nrn_sections[name].psection()['morphology'][
+                'pts3d']
+
+            del self._nrn_sections[name]
+
+            x0, y0, z0 = nrn_pts[0][0], nrn_pts[0][1], nrn_pts[0][2]
+            x1, y1, z1 = nrn_pts[1][0], nrn_pts[1][1], nrn_pts[1][2]
+            self.sections[name]._end_pts = [[x0, y0, z0], [x1, y1, z1]]
+
+        self._nrn_sections = dict()

hnn_core/tests/test_cell.py

@@ -1,5 +1,6 @@
 import pytest
 import pickle
+import numpy as np
 
 import matplotlib
 
@@ -79,6 +80,15 @@ def test_cell():
     with pytest.raises(ValueError, match='sec_name_apical must be an'):
         cell.build(sec_name_apical='blah')
 
+    # Test length modification
+    sec_name = 'soma'
+    new_L = 5.0
+    cell.sections[sec_name].L = new_L
+    cell.update_end_pts()
+    new_pts = np.array(cell.sections[sec_name].end_pts)
+    new_dist = np.linalg.norm(new_pts[0, :] - new_pts[1, :])
+    np.isclose(new_L, new_dist)
+
 
 def test_artificial_cell():
     """Test artificial cell object."""