Open mattions opened 14 years ago
@pgleeson does NeuroMl (1.8) exporter accept diameter 0? Because I can't save the Pyramidal neuron that comes as an example, due to diameter 0 in the soma.
execerror("lambda_f error:", "0 diameter for 3d point 0 of soma.")
I've checked soma has 0 ad diam in one point.
Believe this issue is nothing to do with NeuroML. It seems to be an internal check in Neuron before it gets to export the cell. Maybe throw up a dialog box when you get this error asking if the use wants to use 0.01 for zero diam segments, and insert this before exporting?
This is a bug in NEURON I guess.
I don't think changing the data would be a good idea, and I think we should report this.
consider this test
from neuron import h
for i in range(int(h.n3d())):
msg = "Index %s, x3d: %s, y3d: %s, z3d: %s, diam3d: %s" %( i,
h.x3d(i),
h.y3d(i),
h.z3d(i),
h.diam3d(i)
)
print msg
this produces:
In [16]: run test_soma_diam3d.py
Index 0, x3d: -161.5, y3d: -17.0, z3d: -8.0, diam3d: 0.0
Index 1, x3d: -161.0, y3d: -18.375, z3d: -8.0, diam3d: 5.25
Index 2, x3d: -161.0, y3d: -19.375, z3d: -8.0, diam3d: 7.25
Index 3, x3d: -159.5, y3d: -18.25, z3d: -8.0, diam3d: 12.5
Index 4, x3d: -159.0, y3d: -18.2140007019, z3d: -8.0, diam3d: 13.5710000992
Index 5, x3d: -158.5, y3d: -19.1790008545, z3d: -8.0, diam3d: 16.642999649
Index 6, x3d: -156.0, y3d: -18.1669998169, z3d: -7.79169988632, diam3d: 20.3379993439
Index 7, x3d: -155.0, y3d: -17.5830001831, z3d: -7.70830011368, diam3d: 22.1739997864
Index 8, x3d: -152.5, y3d: -17.7220001221, z3d: -7.5, diam3d: 23.5769996643
Index 9, x3d: -150.5, y3d: -17.25, z3d: -7.5, diam3d: 23.5209999084
Index 10, x3d: -148.5, y3d: -16.7000007629, z3d: -8.0, diam3d: 21.6000003815
Index 11, x3d: -148.0, y3d: -16.611000061, z3d: -8.0, diam3d: 21.2220001221
Index 12, x3d: -146.5, y3d: -17.9440002441, z3d: -8.0, diam3d: 16.888999939
Index 13, x3d: -145.0, y3d: -19.5279998779, z3d: -8.0, diam3d: 12.0559997559
Index 14, x3d: -144.0, y3d: -20.5830001831, z3d: -8.0, diam3d: 8.83329963684
Index 15, x3d: -144.0, y3d: -19.3330001831, z3d: -8.0, diam3d: 6.33330011368
Index 16, x3d: -143.5, y3d: -17.5, z3d: -8.0, diam3d: 0.0
In index 0 and 16 the diam3d is reported to be 0, while the programmer reference state that diam3d should be always positive http://www.neuron.yale.edu/neuron/static/docs/help/neuron/neuron/geometry.html#diam3d
I guess this has to be flagged on the neuron forum and we will see from there