- Mar 09, 2017
-
-
Sam Yates authored
Fix morphology section ctor bug. Add morphology pools for miniapp from which morphologies are drawn in the recipe. Add command-line options to expose above. Add option --report-compartments to (slowly) check the min, mean, and max number of compartments in the generated cells across the simulation. Use morphology::add_section to do all the heavy lifting; no need to make section_geometry objects by hand, unless you really, really want to.
-
Sam Yates authored
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 'natural' discretization in morphology to determine number of compartments in built cell. Update test_swcio.cpp to accommodate new API.
-