diff --git a/README.md b/README.md index afc281401136ab4e564c1a24e72669cb32c87f90..14d8e30e482cd0d5a1760c6a345b1a908d9296f6 100644 --- a/README.md +++ b/README.md @@ -39,7 +39,7 @@ A description of the requirements for the code can be found at the end of this R -------------------------------------------------------------------------------- -### Preparations +### Preparations To start using the framework, the user has to define a few environment variables in a new file called `config.py`. The file `config_template.py` lists the required @@ -100,7 +100,7 @@ Note that it can sometimes be necessary to execute `snakemake --touch` to avoid The files `run_example_downscaled.py` and `run_example_fullscale.py` provide examples. A simple simulation can be run in the following way: -1. Define custom parameters. +1. Define custom parameters. See `multi_area_model/default_params.py` for a full list of parameters. All parameters can be customized. 2. Instantiate the model class together with a simulation class instance. @@ -127,6 +127,29 @@ The procedure is similar to a simple simulation: Be aware that, depending on the chosen parameters and initial conditions, the network can enter a high-activity state, which slows down the simulation drastically and can cost a significant amount of computing resources. +## Extracting connectivity & neuron numbers + +First, the model class has to be instantiated: + +1. Define custom parameters. + See `multi_area_model/default_params.py` for a full list of parameters. All parameters can be customized. + +2. Instantiate the model class. + + from multiarea_model import MultiAreaModel + M = MultiAreaModel(custom_params) + +The connectivity and neuron numbers are stored in the attributes of the model class. +Neuron numbers are stored in `M.N` as a dictionary (or in `M.N_vec` as an array), +indegrees in `M.K` as a dictionary (or in `M.K_matrix` as an array). To extract e.g. +the neuron numbers into a yaml file execute + + import yaml + with open('neuron_numbers.yaml', 'w') as f: + yaml.dump(M.N, f, default_flow_style=False) + +Alternatively, you can have a look at the data with `print(M.N)`. + ## Simulation modes The multi-area model can be run in different modes. @@ -236,5 +259,5 @@ Grants SFB936/A1,Z1 and TRR169/A2) and computing time granted by the JARA-HPC Ver- gabegremium and provided on the JARA-HPC Partition part of the supercomputer JUQUEEN (Jülich Supercomputing Centre 2015) at Forschungszentrum Jülich (VSR Computation Time Grant JINB33), and Priority -Program 2041 (SPP 2041) "Computational Connectomics" of the German Research +Program 2041 (SPP 2041) "Computational Connectomics" of the German Research Foundation (DFG). diff --git a/framework_sketch.png b/framework_sketch.png index b10d5acbbf327e5d7dd2a4aba481174fb983ed61..e76b3e6f516d033520054356a24c9eee8d2e5a2d 100644 Binary files a/framework_sketch.png and b/framework_sketch.png differ