- Jun 29, 2021
-
-
thorstenhater authored
1. All s-exp parsing has migrated to `arborio` 2. CV policies can now be read from string as per #1334. This is needed for the GUI project. 2. No longer can `arb::locset` and `arb::region` be constructed from mere strings 2. We have `arborio::literals` to construct `region`s, `locset`s, and `cv_policy`s in the form of `_rg`, `_ls`, and `_cvp`. 3. The `_lab` suffix now constructs an object that converts to `named` morphologies, rather than a simple string. 4. Constructors of `region` and `locset` are now properly guarded 5. Consequently, a lot of missing inheritance from `region_tag` and `locset_tag` was retrofitted. Closes #1334 Closes #1419
-
- Jun 18, 2021
-
-
Nora Abi Akar authored
New structs and types: * `cell_tag_type` (std::string): for labelling placeable items on a cell. The label refers to a number of items placed on a locset, equal to the number of locations in a locset. The number of locations in not always known to the user, so the previous way of using indices for items was no longer sufficient. * `lid_selection_policy`: for allowing a user to select a single item from a group of items sharing a label. Currently only `round_robin` and `assert_univalent` are supported. * `cell_local_label_type` and `cell_global_label_type`: for identifying the target and source of a connection or gap_junction connection. * `cell_label_ranges`, and `cell_labels_and_gids`: for propagating information about the labelled items on the cell from the cell groups back to the simulation and communicator. * `label_resolution_map` and `resolver`: for selecting an item (and retaining state) from a labelled group of items on a...
-
- Apr 21, 2021
-
-
Sebastian Schmitt authored
-
- Mar 30, 2021
-
-
Nora Abi Akar authored
* Fix the regular schedule generated in `single_cell_model::run` * Adjust frequency of probes in python examples to the correct unit (KHz). Fixes #1457
-
- Feb 17, 2021
-
-
Nora Abi Akar authored
* add neuroML example * no test, because GH actions arbor is built without neuroML support
-
- Dec 18, 2020
-
-
Nora Abi Akar authored
* Add 2 new examples to `python/examples` and their corresponding tutorials in the docs. 1. `single_cell_detailed.py` : a slightly more complex example using `single_cell_model` 2. `single_cell_detailed_recipe.py`: equivalent to `single_cell_detailed.py` but using a recipe. * Change `load_swc`-> `load_swc_arbor` for consistency. * Run Sphinx with specified PYTHON_EXECUTABLE. * Set PYTHONPATH env var in doc/CMakeLists.txt, such that it propagates correctly, including locally. * Build pyarb BEFORE html such that docs build can import arbor in Github Actions script.
-
- Dec 14, 2020
-
-
Benjamin Cumming authored
Make the `cable_cell` interface read only by passing the decorations to its constructor in a new `decor` type. C++ library * Remove the paint/place/set_default interface from `cable_cell` * Create a `decor` type that: * stores lists of paintings and placings * stores a set of cable cell parameters * uses the `paint`, `place`, `set_default` interface that was deprecated from `cable_cell`. * Create `paintable`, `placeable` and `defaultable` variants that are sum types over the respective types that can be painted, placed and defaulted. * Remove the overloaded `cable_cell::paint`, `cable_cell::place`, `cable_cell::set_default` methods to single methods that consume the sum types. Unit Tests * Many small changes because many many tests use cable cell API. * There were no `cable_cell` unit tests! Not such a big deal, since cable_cell is tested implicitly in so many other tests * but I added cable_cell tests: not much at the moment but will quickly fill up as we work on reading, writing, etc. Python * Wrap the new decor type. * Update cable cell type to reflect read only API. * Wrap the cv_policy types and implement the same operator overloading.
-
- Nov 18, 2020
-
-
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.
-
- Nov 17, 2020
-
-
Nora Abi Akar authored
* Return `arb::morphology` from `load_swc_xxx` methods for consistency with the NeuroML interface. * Fix unit tests. * Fix documentation
-
- Nov 10, 2020
-
-
Sebastian Schmitt authored
-
Sebastian Schmitt authored
Speed up plotting in seaborn.relplot by disabling calculation of confidence intervals
-
- Oct 09, 2020
-
-
Nora Abi Akar authored
* Add some log messages in python examples * Add python examples to CI
-
- Oct 05, 2020
-
-
Brent Huisman authored
* Python examples: Updated to use region expressions (quotes) * Python examples: Uniform plotting * Python examples: Removed tutorial directory (example roughly matches python/example/single_cell_model.py) * Python examples: Rewrote flat_cell_builder() to segment_tree()
-
- Sep 29, 2020
-
-
Nora Abi Akar authored
* Update `dryrun` to generate some spikes again, add a voltage printer. * Fix `ring.py` recipe. * Fix labels in `single_cell_builder.py` and `single_cell_swc.py`.
-
- Sep 22, 2020
-
-
Benjamin Cumming authored
* Move label and s-expr parsing code and unit tests from Python to arbor C++ library. * Update `locset` and `region` constructors that take string arguments to parse strings as s-expressions or "quoted" labels. * Modify the input stream modifier used to parse asc files to use a lookup table for substitutions, renamed it transmogrifier. * Replace `hopefully` type implemented in python headers with an `arb::util::expected`. * Add `ARBDEV_COLOR` CMake option that forces gcc and clang to always output color output. * Allow arbitrary strings in labels in region and locset expressions. * Add `parse_region_expression` and `parse_locset_expression` functions alongside the existing `parse_label_expression` function for use when a region or locset is expected. These calls will promote a quoted string `"label"` to `(region "label")` or `(locset "label")` respectively. * Add user-defined string literals for labels so that the C++ interface can use `"soma"_lab` instead of awkward escaping `"\"soma\""`. * Simplify Python wrapper code.
-
- Jul 23, 2020
-
-
Nora Abi Akar authored
Fix a Python example that was out of date.
-
- Jul 13, 2020
-
-
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.
-
- Feb 19, 2020
-
-
Benjamin Cumming authored
Add `cable_cell::concrete_region(region)` method that returns a the cable segments in a region. This is required by the Arbor GUI #953 so that it can illustrate regions (and locsets) defined by users on a concrete cell morphology. Note that the `concrete_region` and `concrete_locset` interfaces will need to be extended with random number seed information when we add full support for that, but shouldn't need to be replaced or changed otherwise. Fixes #960.
-
- Feb 11, 2020
-
-
Benjamin Cumming authored
Use locset names to set probe sites in single cell model. 1. Extend C++ cable_cell interface to provide a concrete list of locations associated with a locset on the cell. 2. Extend Python single_cell_model to allow placement of probes on locsets. 3. Remove "debug" output in Python ring example. The single cell model maintains a trace callback for each probe location, and needs to know the explicit locations before starting the simulation. The first step is required to enumerate and record the locations associated with a locset when attaching probes. Open issues: 1. The extension to `cable_cell` won't sufficiently support locsets that rely on random number generators with global seeds (it would require passing additional meta data required to fully instantiate the locset) 2. Enhancing the probe recipe interface to be able to associate one `probe_id` with all locations in a locset (the number of which is not specified at the time the `probe_id` is created) would support the interface implemented for the `single_cell_model`. Note: The richer interface on the C++ side will be implemented in time (see #957).
-
- Feb 04, 2020
-
-
Benjamin Cumming authored
A big update that wraps over 90% of the public C++ API, with enough functionality to let Python users to perform useful modelling. Key features - wrapping of cable cell functionality - user-defined explicit compartmentalisation not supported - `single_cell_model` abstraction unique to the Python wrapper that simplifies developing and testing single cell models - one-dimensional cell builder for Python wrapper that simplfies building cells that - in and of itself limited in scope, but a very useful example of mapping a richer morphology builder onto `sample_tree`s. - parsing of region and location expressions from strings - implements a generic s-expression parser that we can use for other purposes later
-