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  1. Nov 01, 2022
    • Thorsten Hater's avatar
      Make LIF cells probeable. (#2021) · 3106ff78
      Thorsten Hater authored
      * Functionality
        * Add probes to LIF cells.
      * Docs
        * Remove errorneous statement(s) about LIF cells (there never was an E_reset...)
        * Move probing chapter one level up (concepts/cable_cells -> concepts)
      * Tests
        * Add tests for LIF probes
  2. Sep 20, 2022
  3. Nov 18, 2020
    • Sam Yates's avatar
      Expose diverse probes in Python API. (#1225) · 1bfe96bc
      Sam Yates authored
      Major changes in Python library and documentation:
      
      * Add global state (immutable after initialization) for the Python module that
        manages the mapping between probe metadata types and the method by which the
        corresponding [sample data can be collected and presented as Python objects.
        This is necessary for decoupling the implementation of the simulation wrapper
        from that of the various cable cell probe types.
      
      * Wrap each of the C++ cable cell probe types with a Python function that
        returns a `probe_info` object.
      
      * Add code for converting and accumulating C++ probe metadata and sample
        data, registered in the module global state against the metadata type info.
      
      * Make the `arbor.simulator` object responsible for recording all spike and
        sample data, with corresponding new methods.
      
      * Use NumPy arrays and structured datatypes for returning spike and
        sample data.
      
      * Place Python schedule proxies under an abstract interface so that consumers
        of the proxies can be made generic over schedule types.
      
      * Add unit tests for the `arbor.simulator` class and its new functionality,
        including distributed spike collection.
      
      * Rework all Python API documentation concerning probes, sampling, and spike
        recording; add information on newly exposed cable cell probe addresses.
      
      * Add new python example `single_cell_recipe.py` which is a generic recipe
        version of `single_cell_model.py`.
      
      * Adjust other code in the wrapper and examples to accommodate these changes.
      
      Minor changes in Python library:
      
      * Add equality tests for `arbor.location` and `arbor.cable` Python classes.
      
      * Use the `py::` namespace shorthand more often in the Python wrapping sources.
      
      * Add an implicit conversion for a pair of numbers to `arbor.cell_member`, so
        that e.g. probe ids can be specified simply as `(gid, index)`.
      
      * Add an implicit conversion from a tuple to `arbor.mpoint` so that a
        morphological point can be specified simply as `(x, y, z, radius)`.
      
      * Modify the interface to `arbor.regular_schedule` so that the overloads
        correspond more closely to the C++ API. In particular,
        `arbor.regular_schedule(dt)` now describes a schedule with times 0, dt, 2*dt,
        etc.
      
      Minor changes in C++ library:
      
      * Change test in FVM lowered cell implementation and exception message for
        `bad_source_description`: assert number of detectors is exactly the number
        of sources promised by the recipe.
      
      * Add comment describing `probe_metadata` object in `sampling.hpp` which
        asserts that the type and value of probe-specific metadata completely
        determines the correct interpretation of sampled data provided to a callback.