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Ensuring NEURON 3d() functions target the correct section. #149

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Ensuring NEURON 3d() functions target the correct section. #149

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14 changes: 7 additions & 7 deletions bmtk/simulator/bionet/default_setters/cell_models.py
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Original file line number Diff line number Diff line change
Expand Up @@ -354,20 +354,20 @@ def fix_axon_allactive_directed(hobj):

def get_axon_direction(hobj):
for sec in hobj.somatic:
n3d = int(h.n3d()) # get number of n3d points in each section
soma_end = np.asarray([h.x3d(n3d - 1), h.y3d(n3d - 1), h.z3d(n3d - 1)])
n3d = int(h.n3d(sec=sec)) # get number of n3d points in each section
soma_end = np.asarray([h.x3d(n3d - 1, sec=sec), h.y3d(n3d - 1, sec=sec), h.z3d(n3d - 1, sec=sec)])
mid_point = int(n3d / 2)
soma_mid = np.asarray([h.x3d(mid_point), h.y3d(mid_point), h.z3d(mid_point)])
soma_mid = np.asarray([h.x3d(mid_point, sec=sec), h.y3d(mid_point, sec=sec), h.z3d(mid_point, sec=sec)])

for sec in hobj.all:
section_name = sec.name().split(".")[1][:4]
if section_name == 'axon':
n3d = int(h.n3d()) # get number of n3d points in each section
n3d = int(h.n3d(sec=sec)) # get number of n3d points in each section
axon_p3d = np.zeros((n3d, 3)) # to hold locations of 3D morphology for the current section
for i in range(n3d):
axon_p3d[i, 0] = h.x3d(i)
axon_p3d[i, 1] = h.y3d(i) # shift coordinates such to place soma at the origin.
axon_p3d[i, 2] = h.z3d(i)
axon_p3d[i, 0] = h.x3d(i, sec=sec)
axon_p3d[i, 1] = h.y3d(i, sec=sec) # shift coordinates such to place soma at the origin.
axon_p3d[i, 2] = h.z3d(i, sec=sec)

# Add soma coordinates to the list
p3d = np.concatenate(([soma_mid], axon_p3d), axis=0)
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14 changes: 7 additions & 7 deletions bmtk/simulator/bionet/morphology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -49,7 +49,7 @@ def get_soma_pos(self):
n3dsoma = 0
r3dsoma = np.zeros(3)
for sec in self.hobj.soma:
n3d = int(h.n3d()) # get number of n3d points in each section
n3d = int(h.n3d(sec=sec)) # get number of n3d points in each section
r3d = np.zeros((3, n3d)) # to hold locations of 3D morphology for the current section
n3dsoma += n3d

Expand All @@ -75,17 +75,17 @@ def calc_seg_coords(self):
d1 = np.zeros(self.nseg)

for sec in self.hobj.all:
n3d = int(h.n3d()) # get number of n3d points in each section
n3d = int(h.n3d(sec=sec)) # get number of n3d points in each section
p3d = np.zeros((3, n3d)) # to hold locations of 3D morphology for the current section
l3d = np.zeros(n3d) # to hold locations of 3D morphology for the current section
diam3d = np.zeros(n3d) # to diameters

for i in range(n3d):
p3d[0, i] = h.x3d(i) - p3dsoma[0]
p3d[1, i] = h.y3d(i) - p3dsoma[1] # shift coordinates such to place soma at the origin.
p3d[2, i] = h.z3d(i) - p3dsoma[2]
diam3d[i] = h.diam3d(i)
l3d[i] = h.arc3d(i)
p3d[0, i] = h.x3d(i, sec=sec) - p3dsoma[0]
p3d[1, i] = h.y3d(i, sec=sec) - p3dsoma[1] # shift coordinates such to place soma at the origin.
p3d[2, i] = h.z3d(i, sec=sec) - p3dsoma[2]
diam3d[i] = h.diam3d(i, sec=sec)
l3d[i] = h.arc3d(i, sec=sec)

l3d /= sec.L # normalize
nseg = sec.nseg
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