Rewrite SWC reader code. (#1127)
* Simplify scanning of SWC records. * `parse_swc` now retains metadata read from SWC comments. * `parse_swc` is given two modes, relaxed and strict. Strict mode enforces contiguous record numbering and rejects SWC that looks like it has a single-point soma. * Subtype `swc_error` according to error mode. * Remove `point` class and corresponding unit tests. * Add a RAII stream formatting flag saver, used in SWC record output operator. * Replace included 1-point soma SWC example with a regular SWC from NeuroMorpho.
Showing
- ATTRIBUTIONS.md 18 additions, 1 deletionATTRIBUTIONS.md
- arbor/include/arbor/cable_cell.hpp 0 additions, 1 deletionarbor/include/arbor/cable_cell.hpp
- arbor/include/arbor/cable_cell_param.hpp 1 addition, 0 deletionsarbor/include/arbor/cable_cell_param.hpp
- arbor/include/arbor/morph/segment_tree.hpp 0 additions, 4 deletionsarbor/include/arbor/morph/segment_tree.hpp
- arbor/include/arbor/point.hpp 0 additions, 76 deletionsarbor/include/arbor/point.hpp
- arbor/include/arbor/swcio.hpp 96 additions, 60 deletionsarbor/include/arbor/swcio.hpp
- arbor/io/save_ios.hpp 24 additions, 0 deletionsarbor/io/save_ios.hpp
- arbor/morph/morphology.cpp 1 addition, 0 deletionsarbor/morph/morphology.cpp
- arbor/morph/region.cpp 1 addition, 0 deletionsarbor/morph/region.cpp
- arbor/morph/segment_tree.cpp 0 additions, 35 deletionsarbor/morph/segment_tree.cpp
- arbor/swcio.cpp 142 additions, 154 deletionsarbor/swcio.cpp
- example/single/example.swc 0 additions, 1062 deletionsexample/single/example.swc
- example/single/single.cpp 1 addition, 1 deletionexample/single/single.cpp
- python/morphology.cpp 5 additions, 7 deletionspython/morphology.cpp
- test/ubench/fvm_discretize.cpp 9 additions, 9 deletionstest/ubench/fvm_discretize.cpp
- test/ubench/mech_vec.cpp 30 additions, 29 deletionstest/ubench/mech_vec.cpp
- test/unit/CMakeLists.txt 0 additions, 1 deletiontest/unit/CMakeLists.txt
- test/unit/swc/example.swc 0 additions, 1062 deletionstest/unit/swc/example.swc
- test/unit/swc/pyramidal.swc 5813 additions, 0 deletionstest/unit/swc/pyramidal.swc
- test/unit/test_morphology.cpp 9 additions, 8 deletionstest/unit/test_morphology.cpp
Please register or sign in to comment