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SectionList iteration no longer changes CAS. #6

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merged 1 commit into from
May 20, 2022
Merged

SectionList iteration no longer changes CAS. #6

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15 changes: 8 additions & 7 deletions PyPNS/axonClass.py
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Original file line number Diff line number Diff line change
Expand Up @@ -119,7 +119,7 @@ def collect_geometry_neuron(self):

#loop over all segments
for sec in self.allseclist:
n3d = int(h.n3d())
n3d = int(sec.n3d())
nseg = sec.nseg
gsen2 = 1./2/nseg
if n3d > 0:
Expand All @@ -129,10 +129,10 @@ def collect_geometry_neuron(self):
y = np.zeros(n3d)
z = np.zeros(n3d)
for i in range(n3d):
L[i] = h.arc3d(i)
x[i] = h.x3d(i)
y[i] = h.y3d(i)
z[i] = h.z3d(i)
L[i] = sec.arc3d(i)
x[i] = sec.x3d(i)
y[i] = sec.y3d(i)
z[i] = sec.z3d(i)
#normalize as seg.x [0, 1]
L /= sec.L

Expand All @@ -157,7 +157,7 @@ def collect_geometry_neuron(self):

#fill in values area, diam, length
for i, seg in enumerate(sec):
areavec[counter] = h.area(seg.x)
areavec[counter] = seg.area()
diamvec[counter] = seg.diam
lengthvec[counter] = sec.L/nseg
counter += 1
Expand Down Expand Up @@ -1107,4 +1107,5 @@ def delete_neuron_object(self):
self.nodes = None
self.FLUTs = None
self.MYSAs = None
self.STINs = None
self.STINs = None