Morphology generation with L-systems (#162)
Adds a stand-alone program for the generation of random morphologies form a L-system description. The algorithm is that of Burke (1992), with some of the extensions provided by Ascoli et al. (2001). Two sets of L-system parameters have been included, corresponding to alpha motoneurons and Purkinje cells, but there is certainly something wrong with the data for the latter, and more correct numbers will probably need to be synthesized from existing Purkinje cell morphological information. Documentation for `lmorpho` is incomplete, but the command line help (`--help`) goes some way to explain the usage. In order to get output, one must specify `--swc` or `--pvec` (or both) to emit SWC files or the structural parent vectors. Coarser discretization can be obtained with the `--segment` option. Some minor modifications have been included in other parts of the source repo: * Added copy constructor for `TextBuffer` in `modcc/textbuffer.hpp`, required to keep cl...
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- CMakeLists.txt 1 addition, 0 deletionsCMakeLists.txt
- cmake/CompilerOptions.cmake 9 additions, 8 deletionscmake/CompilerOptions.cmake
- lmorpho/CMakeLists.txt 5 additions, 0 deletionslmorpho/CMakeLists.txt
- lmorpho/README.md 115 additions, 0 deletionslmorpho/README.md
- lmorpho/lmorpho.cpp 115 additions, 0 deletionslmorpho/lmorpho.cpp
- lmorpho/lsys_models.cpp 131 additions, 0 deletionslmorpho/lsys_models.cpp
- lmorpho/lsys_models.hpp 9 additions, 0 deletionslmorpho/lsys_models.hpp
- lmorpho/lsystem.cpp 309 additions, 0 deletionslmorpho/lsystem.cpp
- lmorpho/lsystem.hpp 131 additions, 0 deletionslmorpho/lsystem.hpp
- lmorpho/morphio.cpp 179 additions, 0 deletionslmorpho/morphio.cpp
- lmorpho/morphio.hpp 93 additions, 0 deletionslmorpho/morphio.hpp
- lmorpho/morphology.cpp 62 additions, 0 deletionslmorpho/morphology.cpp
- lmorpho/morphology.hpp 31 additions, 0 deletionslmorpho/morphology.hpp
- modcc/textbuffer.hpp 7 additions, 0 deletionsmodcc/textbuffer.hpp
- src/math.hpp 118 additions, 0 deletionssrc/math.hpp
- src/tinyopt.hpp 47 additions, 16 deletionssrc/tinyopt.hpp
- tests/unit/test_math.cpp 145 additions, 0 deletionstests/unit/test_math.cpp
- tests/validation/validate.cpp 3 additions, 3 deletionstests/validation/validate.cpp
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