Extracting the cell+lems files in the attached zip:
TestCell.zip
Then converting to neuron:
jnml Mitral_0_0.cell.nml_TestBed.xml -neuron
Results in a Mitral_0_0.hoc file that contains the following function, which is used for positioning cells in NML network files:
proc position() { local i
forsec all {
for i = 0, n3d()-1 {
pt3dchange(i, $1+x3d(i), $2+y3d(i), $3+z3d(i), diam3d(i))
}
}
x = $1 y = $2 z = $3
}
Then running the following python code:
from neuron import h,gui
h.load_file('Mitral_0_0.hoc')
mc = h.Mitral_0_0()
h.x3d(0,sec=mc.soma) # Returns x pos as 0 -- as expected
mc.position(1,1,1) # x,yz, should be translated by 1
h.x3d(0,sec=mc.soma) # Problem: returns 20.0 - expected 1.0
Similar problem with y & z, and for other sections.
I get this with latest dev jnml and NEURON 7.4 or 7.5.