Package: ahrens-lab-to-nwb
ahrens-lab-to-nwbNWB conversion scripts for theAhrens labdata to theNeurodata Without Bordersdata format.Clone and installTo run the conversion some basic machinery is needed:python, git and pip. For most users, we recommend you to installconda(installation instructions) as it contains all the required machinery in a single and simple install. If your system is windows you might also need to installgit(installation instructions) to interact with this repository.From a terminal (note that conda should install one in your system) you can do the following:git clone https://github.com/catalystneuro/ahrens-lab-to-nwb
cd ahrens-lab-to-nwb
conda env create --file make_env.yml
conda activate ahrens-lab-to-nwb-envThis create aconda environmentwhich isolates the conversion from your system. We recommend that you run all your conversion related tasks and analysis from that environment to minimize the intereference of this code with your own system.Alternatively, if you want to avoid conda altogether (for example if you use another virtual environment tool) you can install the repository with the following commands using only pip:git clone https://github.com/catalystneuro/ahrens-lab-to-nwb
cd ahrens-lab-to-nwb
pip install -e .Note:
both of the methods above install the repository ineditable modeRepository structureEach conversion is organized in a directory of its own in thesrcdirectory:ahrens-lab-to-nwb/
├── LICENSE
├── make_env.yml
├── pyproject.toml
├── README.md
├── requirements.txt
├── setup.py
└── src
    ├── ahrens_lab_to_nwb
    │   ├── conversion_directory_1
    │   └── yu_mu_cell_2019`
    │       ├── yu_mu_cell_2019behaviorinterface.py
    │       ├── yu_mu_cell_2019_convert_script.py
    │       ├── yu_mu_cell_2019_metadata.yml
    │       ├── yu_mu_cell_2019nwbconverter.py
    │       ├── yu_mu_cell_2019_requirements.txt
    │       ├── yu_mu_cell_2019_notes.md

    │       └── __init__.py
    │   ├── conversion_directory_b

    └── __init__.pyFor example, for the conversionyu_mu_cell_2019you can find a directory located insrc/ahrens-lab-to-nwb/yu_mu_cell_2019. Inside each conversion directory you can find the following files:yu_mu_cell_2019_convert_script.py: this is the cemtral script that you must run in order to perform the full conversion.yu_mu_cell_2019_requirements.txt: dependencies specific to this conversion specifically.yu_mu_cell_2019_metadata.yml: metadata in yaml format for this specific conversion.yu_mu_cell_2019behaviorinterface.py: the behavior interface. Usually ad-hoc for each conversion.yu_mu_cell_2019nwbconverter.py: the place where theNWBConverterclass is defined.yu_mu_cell_2019_notes.md: notes and comments concerning this specific conversion.The directory might contain other files that are necessary for the conversion but those are the central ones.Running a specific conversionTo run a specific conversion, you might need to install first some conversion specific dependencies that are located in each conversion directory:pip install -r src/ahrens_lab_to_nwb/yu_mu_cell_2019/yu_mu_cell_2019_requirements.txtYou can run a specific conversion with the following command:python src/ahrens_lab_to_nwb/yu_mu_cell_2019/yu_mu_cell_2019_conversion_script.py