Morphology part 2. (#860)
* Add new "embedded morphology" `em_morphology`, constructed from a `morphology`, that: caches derived information such as terminal points, locations of sample points, branch lengths; provides services for canonicalizing locations and interpolation; and is used for the realisation of regions and locsets (see below). * Add simple DSL for describing locsets and regions, which are abstract descriptions of sets of locations and regions on morphologies, together with a set of operations. * Add a new class `label_dict` that associates names with regions and locsets. * Extend `cable_cell` to hold a `label_dict` argument, which is used by a new method `paint` for associating mechanisms with regions. Fixes #845.
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- arbor/CMakeLists.txt 6 additions, 1 deletionarbor/CMakeLists.txt
- arbor/cable_cell.cpp 52 additions, 12 deletionsarbor/cable_cell.cpp
- arbor/fvm_layout.cpp 4 additions, 4 deletionsarbor/fvm_layout.cpp
- arbor/fvm_layout.hpp 3 additions, 3 deletionsarbor/fvm_layout.hpp
- arbor/fvm_lowered_cell_impl.hpp 3 additions, 3 deletionsarbor/fvm_lowered_cell_impl.hpp
- arbor/include/arbor/cable_cell.hpp 30 additions, 28 deletionsarbor/include/arbor/cable_cell.hpp
- arbor/include/arbor/morph/label_dict.hpp 32 additions, 0 deletionsarbor/include/arbor/morph/label_dict.hpp
- arbor/include/arbor/morph/locset.hpp 122 additions, 0 deletionsarbor/include/arbor/morph/locset.hpp
- arbor/include/arbor/morph/morphology.hpp 15 additions, 33 deletionsarbor/include/arbor/morph/morphology.hpp
- arbor/include/arbor/morph/primitives.hpp 47 additions, 0 deletionsarbor/include/arbor/morph/primitives.hpp
- arbor/include/arbor/morph/region.hpp 129 additions, 0 deletionsarbor/include/arbor/morph/region.hpp
- arbor/morph/em_morphology.cpp 144 additions, 0 deletionsarbor/morph/em_morphology.cpp
- arbor/morph/em_morphology.hpp 39 additions, 0 deletionsarbor/morph/em_morphology.hpp
- arbor/morph/label_dict.cpp 76 additions, 0 deletionsarbor/morph/label_dict.cpp
- arbor/morph/locset.cpp 247 additions, 0 deletionsarbor/morph/locset.cpp
- arbor/morph/mbranch.cpp 29 additions, 0 deletionsarbor/morph/mbranch.cpp
- arbor/morph/mbranch.hpp 38 additions, 0 deletionsarbor/morph/mbranch.hpp
- arbor/morph/morphology.cpp 70 additions, 27 deletionsarbor/morph/morphology.cpp
- arbor/morph/primitives.cpp 40 additions, 3 deletionsarbor/morph/primitives.cpp
- arbor/morph/region.cpp 303 additions, 0 deletionsarbor/morph/region.cpp
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