Workarounds for fractionAlong != (0 or 1)?

[JustasB]

I have a NEURON model where the segments are connected at non 0 or 1 parent locations, resulting in NML that uses e.g. fractionAlong="0.8" or "0.517...". When I use jnml to convert LEMS file to neuron, it results in the following error:

Cannot yet handle fractionAlong being neither 0 or 1

If I set the fractionAlong to 0 or 1, it introduces small errors in the voltage during simulation.

My example NML is:

            <segment id="1" name="Seg0_priden">
                <parent fractionAlong="1" segment="0"/>
                <proximal y="-3.005222e+00" x="4.340876e+00" z="6.010444e+00" diameter="5.000000e-01"/>
                <distal y="-7.102542e+01" x="1.025923e+02" z="1.420508e+02" diameter="5.000000e-01"/>
            </segment>
            <segment id="2" name="Seg0_priden2_0">
                <parent ****fractionAlong="0.8"**** segment="1"/>
                <proximal y="-3.005222e+00" x="4.340876e+00" z="6.010444e+00" diameter="4.000000e-01"/>
                <distal y="-9.691841e+01" x="1.399933e+02" z="1.938368e+02" diameter="4.000000e-01"/>
            </segment>

Is the best workaround for this issue to split the parent segment into two segments along the non-integer fraction of the parent segment's length? If so, I'll include this in the error message text and submit a pull-request.

@pgleeson

[pgleeson]

@JustasB there is a quick fix for this (implemented locally here) if the parent segmentGroup/section has only one segment in it (i.e. use the fraction along the segment as fraction along the segmentGroup). Is this the case for you?

[JustasB]

@pgleeson Yes, just one segment is in the parent segment.

[pgleeson]

I've just committed a fix for this (with just one segment in the parent segment) on the dveelopment branch. Rebuild jNeuroML from source on the development branches and you should have the fix.