Add flat morphology representation to `nestmc` lib. (#176)
This PR is a prelude to closer integration of the random morphology generation with the miniapp, with the first step being support for recipes that create cells from morphologies generated off-line. It aims to use nest::mc::morphology as the flat morphology-only representation that can be used to construct nest::mc::cell objects and which can exist as a target for SWC conversion and random morphology generation. Simplify swc io implementation: Avoid throwing exceptions in istream parsing and swc_record constructors — only throw when explicitly checking consistency, or when parsing a full sequence of records. Allow direct access to record members. Separate parsing considerations from canonicalization (renumbering, sorting) of a sequence of records. Move lmorpho morphology classes into src/ Add invariant check procedure for morphology. Make cells via swc -> morphology -> cell building, rather than direct swc -> cell. Allow option to use ...
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- lmorpho/CMakeLists.txt 1 addition, 1 deletionlmorpho/CMakeLists.txt
- lmorpho/lsystem.cpp 7 additions, 3 deletionslmorpho/lsystem.cpp
- lmorpho/lsystem.hpp 2 additions, 2 deletionslmorpho/lsystem.hpp
- lmorpho/morphio.cpp 7 additions, 5 deletionslmorpho/morphio.cpp
- lmorpho/morphio.hpp 3 additions, 3 deletionslmorpho/morphio.hpp
- lmorpho/morphology.hpp 0 additions, 31 deletionslmorpho/morphology.hpp
- miniapp/miniapp_recipes.cpp 4 additions, 3 deletionsminiapp/miniapp_recipes.cpp
- src/CMakeLists.txt 1 addition, 0 deletionssrc/CMakeLists.txt
- src/cell.cpp 45 additions, 0 deletionssrc/cell.cpp
- src/cell.hpp 7 additions, 0 deletionssrc/cell.hpp
- src/morphology.cpp 135 additions, 0 deletionssrc/morphology.cpp
- src/morphology.hpp 75 additions, 0 deletionssrc/morphology.hpp
- src/segment.hpp 15 additions, 21 deletionssrc/segment.hpp
- src/swcio.cpp 91 additions, 260 deletionssrc/swcio.cpp
- src/swcio.hpp 149 additions, 316 deletionssrc/swcio.hpp
- tests/test_common_cells.hpp 7 additions, 7 deletionstests/test_common_cells.hpp
- tests/unit/test_cell.cpp 11 additions, 11 deletionstests/unit/test_cell.cpp
- tests/unit/test_fvm_multi.cpp 3 additions, 3 deletionstests/unit/test_fvm_multi.cpp
- tests/unit/test_probe.cpp 1 addition, 1 deletiontests/unit/test_probe.cpp
- tests/unit/test_segment.cpp 10 additions, 10 deletionstests/unit/test_segment.cpp
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