dendrite subtypes handling #70
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arnaudon
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arnaudon
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eleftherioszisis
| for section in iter_sections(neuron): | ||
| if section.type == SectionType.axon: | ||
| extended_types[section.id] = "axon" | ||
| if section.type == SectionType.basal_dendrite: |
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| if section.type == SectionType.basal_dendrite: | |
| elif section.type == SectionType.basal_dendrite: |
| extended_types[section.id] = "axon" | ||
| if section.type == SectionType.basal_dendrite: | ||
| extended_types[section.id] = "basal" | ||
| if section.type == SectionType.apical_dendrite: |
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| if section.type == SectionType.apical_dendrite: | |
| elif section.type == SectionType.apical_dendrite: |
| for section in iter_sections(neuron): | ||
| if section.type == SectionType.basal_dendrite: | ||
| extended_types[section.id] = "basal" | ||
| if section.type == SectionType.axon: |
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| if section.type == SectionType.axon: | |
| elif section.type == SectionType.axon: |
| return neuron | ||
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| def _unset_subtypes(neuron, base_type): |
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What about using a mapping of base types? So it is possible to use several custom types at the same time.
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yes, I should rather use the REV_ mapping here, so we can revert only specific custom types
| def set_apical_subtypes(neuron, tuft_percent=20): | ||
| """Set apical subtypes to a morphology. | ||
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| WARNING: cannot save it to .asc file, use unset_subtype to revert |
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Maybe use the .. warning:: directive?
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And by the way why can't we save custom types? Is it a limitation of MorphIO?
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I didn't try all format, abut asc is based on neurites, which can have only specific names via morphio. I'm not sure with new code of @eleftherioszisis in neurom how this can be better handled
For various project, it is convenient to have a way to assign sub sectiontypes to morphologies, based on a particular point (apical point, or 'axon point'). This is an attempt to provide such a little tool via the SectionType.custom[number] of morphio.
One set the subtypes, then use the provided dict to access specific section via names (trunk, oblique) instead of custom[number], then can unset them to return to original morphology (for example after some manipulations, to be able to save it on disc).
It is a bit of a mix-up between neurom and morphio, I'm open to any suggestions to make this cleaner.