Saving the pyramidal model gives this error. When plotted has a diam...

[mattions]

In [2]: NEURON: lambda_f error: 0 diameter for 3d point 0 of soma.
 near line 0
 {forall SectionList[9].append()}
                                 ^
        execerror("lambda_f error:", "0 diameter for 3d point 0 of soma.")
      ModelViewSeclistAnalysis[0].lambda_f(100)
    ModelViewSeclistAnalysis[0].mk_nseg()
  ModelViewSeclistAnalysis[0].mkdisplay(TreeViewItem[5])
and others
oc_restore_code tobj_count=1 should be 0
ERROR: An unexpected error occurred while tokenizing input
The following traceback may be corrupted or invalid
The error message is: ('EOF in multi-line statement', (29, 0))

---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)

/home/mattions/Work/model/MSN/Neuronvisio/src/neuronvisio/controls.pyc in save_hdf(self)
    148             self.path_to_hdf = str(filename) # It will go with python 3
    149             if self.path_to_hdf != None:
--> 150                 self.manager.save_to_hdf(self.path_to_hdf)
    151                 msg = "Saved hdf file: %s" % self.path_to_hdf
    152                 self.ui.statusbar.showMessage(msg, 3500)

/home/mattions/Work/model/MSN/Neuronvisio/src/neuronvisio/manager.pyc in save_to_hdf(self, filename)
    299 
    300         # Saving the vecRef

--> 301         self._save_geom(h5f)
    302         res = h5f.createGroup('/', self.results_root)
    303         for group in self.refs:

/home/mattions/Work/model/MSN/Neuronvisio/src/neuronvisio/manager.pyc in _save_geom(self, h5file_holder)
    279 
    280         h.load_file('mview.hoc')
--> 281         modelView = h.ModelView(0)
    282         modelXml = h.ModelViewXML(modelView)
    283         tmp_file = 'temp.xml'

RuntimeError: hoc error

[mattions]

@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.

[pgleeson]

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?

[mattions]

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