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Template morphology glialcell#256
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jacquemi-bbp wants to merge 26 commits intoBlueBrain:masterfrom
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Some tests are passing.
-add src/ttree.cpp cleans code by moving functions that do not relate to Morphology immutable from morphology.cpp to ttree.cpp
and most tests
- All enable tests success
…ection Type: GlialSectionType
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wizmer
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Mar 19, 2021
include/morphio/mut/morphology.h
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| If recursive == true, all descendent will be appended as well | ||
| **/ | ||
| std::shared_ptr<Section> appendRootSection(const morphio::Section&, bool recursive = false); | ||
| std::shared_ptr<Section> appendRootSection(const morphio::Node<CellFamily::NEURON>&, |
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Suggested change
| std::shared_ptr<Section> appendRootSection(const morphio::Node<CellFamily::NEURON>&, | |
| std::shared_ptr<Section> appendRootSection(const morphio::NeuronalSection&, |
is equivalent.
I think it would be good to take the habit of no longer using the old alias Section or even Node<CellFamily::NEURON but the new NeuronalSection.
This will make MorphIO less neuron centric.
include/morphio/ttree.tpp
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| /* | ||
| template <typename Node, typename CRTP, typename Mut> | ||
| const CellFamily& TTree<Node, CRTP, Mut>::cellFamily() const { | ||
| return _properties->cellFamily(); | ||
| } | ||
| */ |
| struct CellFamily { | ||
| struct NEURON { | ||
| using Type = SectionType; | ||
| static constexpr int value = 0; |
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Those values must correspond to the values of the cell family in the spec.
https://bbpteam.epfl.ch/documentation/projects/Morphology%20Documentation/latest/h5v1.html
Maybe you can add a comment about it in the code.
setup.py
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| cfg = 'Debug' if self.debug else 'Release' | ||
| # cfg = 'Debug' if self.debug else 'Release' | ||
| cfg = 'Debug' |
- Remove dead code - Use alias NeuralSection instead of Node<CellFamily::NEURON> - Use alias GlialSection instead of Node<CellFamily::GLIA>
…bp/MorphIO into template_morphology_glialcell
This was referenced May 10, 2021
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This PR is the first one of a series that will implement Dendritic spine Specifications for morphio h5 format. We (@wizmer and @jacquemi-bbp ) decided to not produce too large PULL REQUEST to facilitate the work of reviewers
This PR templatizes immutable Morphology.
The mutable Morphology will be templatized in a next PR
Spine Class will be only implemented in a next next PR
Immutable Morphology becomes a TTree template class:
Two TTree instantiation are created:
Immutable Section becomes Node template class:
Two Node instantiation are created:
enum CellFamily replaced by struct CellFamily (that contains static constexpr to identify Cell type)