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  1. Mar 09, 2017
    • Sam Yates's avatar
      Morphologies in miniapp (#178) · f91d0b3c
      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.
      f91d0b3c
    • Sam Yates's avatar
      Add flat morphology representation to `nestmc` lib. (#176) · 88dfb499
      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.
      88dfb499