Merge pull request #1123 from halfflat/feature/stitch-morphology
New PR post master rollback; squashed and rebased, but reprises #1111. * Add (forward) ordered forest implementation, tests. * Add `segment` region expression; to ease implementation, `msegment` now also knows its own id. * Add `stitch_builder` and `stitched_morphology`. A stitch corresponds to a labelled, linearly-interpolated segment which can be attached at any point along a parent stitch. A `stitched_morphology` takes a `stitch_builder` object and constructs a segment tree and morphology, and provides a dictionary of stitch labels to segment indices and region expressions. * Add `import` method for `label_dict`, so that the label dictionary returned by `stitched_morphology` can be merged with an existing dictionary. * Add section on stitch builder etc. to cable cell docs. * Update cable cell docs to remove out of date info and to provide some context. * Describe ordered forest datastructure and interface in a long comment at the...
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- arbor/CMakeLists.txt 1 addition, 0 deletionsarbor/CMakeLists.txt
- arbor/include/arbor/morph/embed_pwlin.hpp 11 additions, 8 deletionsarbor/include/arbor/morph/embed_pwlin.hpp
- arbor/include/arbor/morph/label_dict.hpp 1 addition, 0 deletionsarbor/include/arbor/morph/label_dict.hpp
- arbor/include/arbor/morph/morphexcept.hpp 21 additions, 0 deletionsarbor/include/arbor/morph/morphexcept.hpp
- arbor/include/arbor/morph/morphology.hpp 1 addition, 1 deletionarbor/include/arbor/morph/morphology.hpp
- arbor/include/arbor/morph/primitives.hpp 1 addition, 1 deletionarbor/include/arbor/morph/primitives.hpp
- arbor/include/arbor/morph/region.hpp 3 additions, 0 deletionsarbor/include/arbor/morph/region.hpp
- arbor/include/arbor/morph/stitch.hpp 93 additions, 0 deletionsarbor/include/arbor/morph/stitch.hpp
- arbor/morph/embed_pwlin.cpp 16 additions, 7 deletionsarbor/morph/embed_pwlin.cpp
- arbor/morph/label_dict.cpp 9 additions, 0 deletionsarbor/morph/label_dict.cpp
- arbor/morph/locset.cpp 1 addition, 1 deletionarbor/morph/locset.cpp
- arbor/morph/morphexcept.cpp 27 additions, 6 deletionsarbor/morph/morphexcept.cpp
- arbor/morph/primitives.cpp 1 addition, 5 deletionsarbor/morph/primitives.cpp
- arbor/morph/region.cpp 34 additions, 24 deletionsarbor/morph/region.cpp
- arbor/morph/segment_tree.cpp 1 addition, 1 deletionarbor/morph/segment_tree.cpp
- arbor/morph/stitch.cpp 214 additions, 0 deletionsarbor/morph/stitch.cpp
- arbor/util/ordered_forest.hpp 668 additions, 0 deletionsarbor/util/ordered_forest.hpp
- doc/cpp_cable_cell.rst 160 additions, 44 deletionsdoc/cpp_cable_cell.rst
- test/unit/CMakeLists.txt 2 additions, 0 deletionstest/unit/CMakeLists.txt
- test/unit/test_morph_embedding.cpp 31 additions, 45 deletionstest/unit/test_morph_embedding.cpp
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