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  1. Sep 07, 2020
  2. Aug 31, 2020
    • Sam Yates's avatar
      Extend place_pwlin interface for multivalued. (#1124) · 57415f0b
      Sam Yates authored
      * Add `equal_range()` method to `pw_elements`.
      * Simplify `embed_pwlin`, `place_pwlin` implementations, in particular the handling of zero-length branches.
      * Scale segment positions in `embed_pwlin` by divding by branch_length, instead of multiplying by the reciprocal, as the latter is a false economy after all the caveats that need to be checked to preserve ordering and bounds.
      * Add new method `place_pwlin::all_at()`, which gives all the points that correspond to a single `mlocation`.
      * Add new method `place_pwlin::all_segments()`, providing the set of segments and/or partial-segments that correspond to an extent.
      * Add new method `place_pwlin::segments()`, which provides a minimal set of segments and/or partial-segments that map onto an extent.
      * Extend unit tests to suit.
      
      Fixes #1116 and #1068.
  3. Aug 27, 2020
    • Benjamin Cumming's avatar
      Pydoc (#1122) · 23a24b5a
      Benjamin Cumming authored
      This PR adds a bunch of high-level docs for concepts related to single cell models.
        * morphologies
        * labels (region and locset expressions)
        * mechanisms
        * cable cells
      
      It adds some python scripts to the `doc` path, which are called during documentation building to generate images of cell morphologies, regions and locsets that are generated in a separate script that uses the Arbor Python API.
      
      The docs are not complete: the cable cell and mechanism docs are unfinished, and the tutorial section needs to build on these concepts to give more detailed step by step examples.
    • Sam Yates's avatar
      Merge pull request #1123 from halfflat/feature/stitch-morphology · 135e91ac
      Sam Yates authored
      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...
    • Sam Yates's avatar
      Retrieve probe metadata from simulator object. (#1101) · 3cc73f1e
      Sam Yates authored
      * Add `get_probe_metadata` method to `simulator` that forwards probe metadata queries to appropriate cell group, via new interface method in cell group base class.
      * Replace `gid_to_local_` map in simulator implementation with a map that takes gid to local cell index _and_ local cell group index.
      * Move scheduler association map mutex into the cell group where it is being used (i.e. `mc_cell_group`).
      * Add generic (`visit`-able) interface to specifc fvm-probe types for accessing metadata via `any_ptr`.
      * Implement (override) `get_probe_metadata` method for `mc_cell_group`.
      * Use new cv policy API for LFP example discretization.
      * Use new probe metadata API to simplify LFP example sampler callback.
      * Add `on_components` locset expression that gives points a relative distance from the head of each component of a region.
      * Simplify implementation of thingification of `ls::boundary`.
      
      Fixes #1079 
  4. Aug 26, 2020
  5. Aug 20, 2020
    • Nora Abi Akar's avatar
      Expose `time` to the mechanisms (#1113) · 57394539
      Nora Abi Akar authored
      The `vec_t_` time vector is already available to the mechanisms, but not exposed. It is indexed by `cell_index` instead of directly by the `node_index` (`vec_t[vec_ci_[node_index_[i]]]`). This kind of indexing was previously unavailble. It has not been added to the printers. 
      This PR also includes some cleanup in the vectorized code printer. 
      
      Address #1109
  6. Aug 13, 2020
  7. Aug 10, 2020
  8. Aug 06, 2020
  9. Aug 05, 2020
  10. Jul 28, 2020
  11. Jul 24, 2020
  12. Jul 23, 2020
    • Harmen Stoppels's avatar
      Set the status on the commit from the PR (#1099) · 4d328ee0
      Harmen Stoppels authored
      This is copied from DLA Future. It should set the CI status on the commit from the PR instead of just on the Bors commit. This way the gitlab CI status also appears in the checks section below the PR.
    • Nora Abi Akar's avatar
      Fix python examples (#1096) · 5933b6f1
      Nora Abi Akar authored
      Fix a Python example that was out of date.
    • thorstenhater's avatar
      Gpu/restrict all the things (#1026) · 5ace929e
      thorstenhater authored
      Make all pointer arguments to kernels `__restrict__` to avoid unnecessary loads.
      
      The effect on the busyring benchmark (swapped pas -> hh) with 8192 cells on a V100 GPU (time for model-run in seconds): 
      ```
      |----------+-------|
      | Baseline | After |
      |----------+-------|
      |    2.347 | 2.268 |
      |    2.345 | 2.262 |
      |    2.321 | 2.276 |
      |    2.323 | 2.267 |
      |    2.330 | 2.249 |
      |----------+-------|
      |    2.321 | 2.249 |
      |----------+-------|
      ```
  13. Jul 21, 2020
  14. Jul 13, 2020
    • Benjamin Cumming's avatar
      flexible cable-based cable_cell representation (#1083) · 9dc8969c
      Benjamin Cumming authored
      * Remove spherical root/soma from morphology representations and logic.
      * Replace `sample_tree` with `segment_tree`, which represents sample points in pairs and allows the representation of detached branches and cable segments.
      * Remove sample point properties and predicates.
      * Remove `cv_policy_flag::single_root_cv` as somata with a single attached dendrite will have a representation in the morphology of a single branch.
      * Remove `arb::math::{volume/area}_sphere`, which are no longer being used.
      * Remove spherical root special cases from `embed_pwlin` and `place_pwlin` objects.
      * Add textual representation of `mnpos` in morphology exception text.
      * Rename `sample_tree_from_swc` to `segement_tree_from_swc` and remove any special casing for one point somata.
      * Remove `msample` and `mbranch` types.
      * Update unit tests and python wrapper to reflect the changes.
    • thorstenhater's avatar
      Python/allen catalogue (#1074) · 6151e173
      thorstenhater authored
      * Add import method for mechanism catalogues, allowing mechanisms from a second catalogue to be incorporated with a prefix, together with Python interface.
      * Expose `global_allen_catalogue`.
      * Extend unit tests to cover mechanism catalogue import and check for name collision error cases.
  15. Jul 08, 2020
  16. Jul 07, 2020
  17. Jul 02, 2020
    • Sam Yates's avatar
      Allow CV policies to be composed over subregions. (#1078) · 2e90a382
      Sam Yates authored
      * Move `cv_policy` classes to new source files.
      * Remove `cv_policy_flag::single_root_cv`.
      * Allow all supplied `cv_policy` makers to be restricted a domain specified by a region: the policy is then applied per component, with the boundary points of the completion of the components included.
      * Expose `cv_policy` domain in public interface.
      * Add `components` function for splitting an extent into disconnected components. Add comment describing what is meant by connected in this context.
      * Rename `super` region function to `complete`.
      * Add region expression functions `complement` and `difference`.
      * Add new locset expression function `boundary` which returns the extrmal points of each component of a region.
      * Add new locset expression `cboundary` which returns the extremal points of the completion of each component of the region, which is what we need to close off CVs generated by region-restricted CV policies.
      * Add locset expression `supp...
  18. Jun 25, 2020
    • Nora Abi Akar's avatar
      Refactor simd API and add SVE backend (#1044) · 7fe3141d
      Nora Abi Akar authored
      * Add new API for the SIMD library that is compatible with the ARM 'sizeless' SVE vectors. Language restrictions prevent the use of the operator overload interface used up to this point for SIMD.
      * Add `indirect_expressions` and `indirect_indexed_expressions` for describing memory reads/writes. `where_expressions` control masked access to simd vectors.
      * Implement the SVE SIMD back-end in accordance with the alternate SIMD API.
      * Retrieve vector width information from compiled mechanisms.
      * Use alternate SIMD API in modcc-generated mechanisms.
      * Add assertion in generated mechanism code that checks runtime vector width compatibility.
      
      Fixess #1021. 
    • Sam Yates's avatar
      Add LFP example/demo. (#1073) · 0c374140
      Sam Yates authored
      * Add C++ analogue to simple NEURON demo provided by LFPy project under example/lfp.
      * Add plot script for rending example output to match that from NEURON demo.
  19. Jun 24, 2020
    • thorstenhater's avatar
      Performance/copy to swap (#1027) · a316dd87
      thorstenhater authored
      Remove a redundant copy in favor of a swap operation for a gain in performance;
      especially on GPU since copies are synchronous. Similarly, instead of solving the 
      linear system into an intermediate array, write output directly into the target.
      
      Here is the effect on the busyring benchmark (swapped pas -> hh) with 8192 cells on a
      V100 GPU (time for model-run in seconds).
      ```
      |----------+--------------------------------+------------------------------------|
      | Baseline | fvm_lowered_cell: copy -> swap | matrix: solve + copy -> solve_into |
      |----------+--------------------------------+------------------------------------|
      |    2.230 |                          2.199 |                              2.129 |
      |    2.231 |                          2.209 |                              2.132 |
      |    2.225 |                          2.209 |                              2.136 |
      |    2.227 |                          2.186 |                              2.130 |
      |    2.220 |   ...
    • thorstenhater's avatar
      Allen catalogue (#1071) · a9f0b2fa
      thorstenhater authored
      Add a new catalogue comprising optimised version of some of the mechanisms commonly used in models of the Allen Cell Types Database, eg http://celltypes.brain-map.org/mouse/experiment/electrophysiology/323535089.
      This made required extending modcc to some new NMODL features, as well as to expose some optimisations.
      
      In addition clean up the default catalogue by moving test mechanisms to their proper place in the unit tests.
    • Benjamin Cumming's avatar
      Pycat (#1072) · e0c14f34
      Benjamin Cumming authored
      Update core library:
      * support derivation of named mechanisms in catalogue from a string description of the parent.
      * fix bug in radois_ge region expression that was finding region_lt.
      * fix test for radius_ge region expression
      
      Add support for mechanism, global properties and catalogue shenanigans to python wrapper
  20. Jun 23, 2020
    • Sam Yates's avatar
      Fix event_generator constructor. (#1067) · c0b1ee06
      Sam Yates authored
      * Guard `event_generator` implicit constructor with type test.
      * Fix linking error from use of `empty_generator` by replacing pointers to `no_event` with nullptr.
      * Clarify `regular_generator` semantics in comment.
      * Add unit test for checking.
      
      Fixes #1066
  21. Jun 22, 2020
    • Sam Yates's avatar
      Add place_pwlin for morphology geometry queries. (#1062) · 58c4abef
      Sam Yates authored
      * Add new `isometry` class representing a direct Euclidean isometry comprising a rotation and translation. Translations are always taken with respect to absolute coordinates, but rotations are composed with respect to intrinsic coordinates.
      * Add new `place_pwlin` class, that takes a morphology and an isometry, and answers location queries: where in space does a particular `mlocation` lie?
      * Split out (some of) the common code between `place_pwlin` and `embed_pwlin`.
      * Add equality operator to `mpoint`.
      
      This functionality is added to aid the presentation of the local field potential example.
  22. Jun 16, 2020
  23. Jun 12, 2020
    • Sam Yates's avatar
      New recipe probe API (#1054) · 8d866593
      Sam Yates authored
      * Make recipe return probes as a vector.
      * Remove `probe_id` from `probe_info`.
      * Rename `fvm_probe_info` to `fvm_probe_data` (everything was being called info, and it was getting confusing).
      * Make `probe_association_map` specific to `mc_cell_group`/`fvm_lowered_cell`.
      * Change probe_association_map representation: unordered map for probe_id -> tag; unordered multimap for probe_id -> fvm_probe_data. This allows multiple probes to be associated with the same probe id.
      * Call sampler callback separately for each probe with the same probe_id.
      * Replace location-based probes with locset equivalents.
      * Add index for probes sharing a probe id.
      * Bundle all probe metadata (id, tag, index, probe-specific meta) into `probe_metadata` struct for passing to sampler callbacks.
      * Change simple_sampler to work on `trace_vector`, a vector of `trace_data`. The _i_th element is the data from probe with index i.
      * Consolidate hash composition and `std::hash` specialization code in new header.
      * Update python lib for new API.
      * Update tests and examples for new recipe, internal probe, and simple_sampler APIs.
      * Update docs to suit.
  24. Jun 04, 2020
  25. May 28, 2020