diff --git a/README.rst b/README.rst index 894c9d7..9edd88a 100644 --- a/README.rst +++ b/README.rst @@ -39,8 +39,37 @@ necessary. Furthermore, all ``git`` submodules should be checked out: Spark and Hadoop should be installed and set up as runtime dependencies. -Usage ------ +Usage Overview +-------------- + +Functionalizer is an integral part of building a brain circuit. It will take the +connectome as established by + +- `appositionizer`_, in the form of detailed morphologies being in close proximity, or +- `connectome-manipulator`_, which will approximate connectivity following probabilistic + rules, + +and transform then in any of the following filtering steps: + +- trim appositions according to simple touch rules +- trim appositions to follow biological distributions, parametrized in connection rules +- add synaptic properties to convert any apposition into a proper synapse + +If the input format is binary from `appositionizer`_, one may use ``touch2parquet`` from +`parquet-converters`_ to convert into Parquet that may be read by Functionalizer. +All circuit inputs need to be defined in a ``circuit_config.json`` according to the +`SONATA extension`_, containing pointers to nodes in `nodes.h5` and morphologies. +A ``recipe.json``, defined in the same SONATA extension, is used to supply the parameters +needed for filters. + +The output of Functionalizer should be converted to SONATA-conform HDF5 via ``parquet2hdf5`` +from `parquet-converters`_. + +.. image:: docs/source/_static/circuit_building.png + :alt: A diagram showing the relations of circuit building software + +CLI Usage +--------- Basic usage follows the pattern:: @@ -59,6 +88,9 @@ from the Swiss government's ETH Board of the Swiss Federal Institutes of Technol Copyright (c) 2017-2024 Blue Brain Project/EPFL .. _SONATA extension: https://sonata-extension.readthedocs.io +.. _appositionizer: https://github.com/BlueBrain/appositionizer +.. _connectome-manipulator: https://github.com/BlueBrain/connectome-manipulator +.. _parquet-converters: https://github.com/BlueBrain/parquet-converters .. |license| image:: https://img.shields.io/pypi/l/functionalizer :target: https://github.com/BlueBrain/functionalizer/blob/master/LICENSE.txt diff --git a/docs/source/_static/circuit_building.png b/docs/source/_static/circuit_building.png new file mode 100644 index 0000000..c9dea2e Binary files /dev/null and b/docs/source/_static/circuit_building.png differ diff --git a/pyproject.toml b/pyproject.toml index 9ecc122..d922c00 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -28,7 +28,7 @@ dependencies = [ "jprops", "morphio", "mpi4py", - "libsonata", + "libsonata<=0.1.28", "numpy<2", "packaging", "pandas",