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توضیحات

NWB conversion scripts, functions, and classes for an the Ahrens lab.

ویژگی	مقدار
سیستم عامل	-
نام فایل	ahrens-lab-to-nwb-1.0.0
نام	ahrens-lab-to-nwb
نسخه کتابخانه	1.0.0
نگهدارنده	[]
ایمیل نگهدارنده	[]
نویسنده	CatalystNeuro
ایمیل نویسنده	-
آدرس صفحه اصلی	https://github.com/catalystneuro/ahrens-lab-to-nwb
آدرس اینترنتی	https://pypi.org/project/ahrens-lab-to-nwb/
مجوز	-

# ahrens-lab-to-nwb NWB conversion scripts for the [Ahrens lab](https://www.janelia.org/lab/ahrens-lab) data to the [Neurodata Without Borders](https://nwb-overview.readthedocs.io/) data format. ## Clone and install To run the conversion some basic machinery is needed: **python, git and pip**. For most users, we recommend you to install `conda` ([installation instructions](https://docs.conda.io/en/latest/miniconda.html)) as it contains all the required machinery in a single and simple install. If your system is windows you might also need to install `git` ([installation instructions](https://github.com/git-guides/install-git)) 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-env ``` This create a [conda environment](https://docs.conda.io/projects/conda/en/latest/user-guide/concepts/environments.html) which 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 in [editable mode](https://pip.pypa.io/en/stable/cli/pip_install/#editable-installs) ## Repository structure Each conversion is organized in a directory of its own in the `src` directory: 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__.py For example, for the conversion `yu_mu_cell_2019` you can find a directory located in `src/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 the `NWBConverter` class 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 conversion To 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.txt ``` You 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 ```

نیازمندی

مقدار	نام
-	neuroconv
-	nwbwidgets
==0.2.0	ndx-events

زبان مورد نیاز

مقدار	نام
>=3.7	Python

نحوه نصب

نصب پکیج whl ahrens-lab-to-nwb-1.0.0:

pip install ahrens-lab-to-nwb-1.0.0.whl

نصب پکیج tar.gz ahrens-lab-to-nwb-1.0.0:

pip install ahrens-lab-to-nwb-1.0.0.tar.gz