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export_to_neuroml2 does not export non-integer fractionAlong value #22

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JustasB opened this issue Mar 1, 2016 · 0 comments
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S: needs info Needs more information to be acted on T: bug Type: bug

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@JustasB
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JustasB commented Mar 1, 2016

export_to_neuroml2 function results in cell nml files that do not specify the fractionAlong value when segments in neuron are not connected at segment ends.

There is a comment generated in the resulting NML file (example below). However, this comment is replaced with fractionAlong="1" if the file is read with the pynml.read_neuroml2_file function and saved.

<!-- Section: Granule[0].priden2[0] (segmentGroup: priden2_0) which has 2 3D points, so 1 segment(s)-->
      <segment id="3" name = "Seg0_priden2_0">  <!-- Connected at ****0.8**** on parent section: Granule[0].priden  -->
        <parent segment="0"/>
        <proximal x="0" y="0" z="0" diameter="0.4"/>
        <distal x="0" y="250" z="0" diameter="0.4"/>
      </segment>

There is no other warnings to the user otherwise.

I understand this is probably related to NeuroML/org.neuroml.export#46

I suggest one of the following changes:

  1. Warn the user during the function call that fractionAlong value will not be exported
  2. Include the value anyway, but warn the user that jnml will not support exporting the non-integer value
  3. During export, split the parent segment at the non-integer fractionAlong value into separate segments. If the parent has multiple child segments, this may require multiple splits.
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Labels
S: needs info Needs more information to be acted on T: bug Type: bug
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