Installation
============

The intended use of this pipeline is through the use of `Singularity <https://docs.sylabs.io/guides/3.7/user-guide/index.html>`_
or `Docker <https://docs.docker.com/get-started/>`_ image.

.. note::
   If you are an independent researcher working on a Windows machine or a Mac,
   :ref:`option2-docker` is recommended.

.. _option1-singularity:

Option 1: Singularity
---------------------
If you are new to it, start by installing Singularity following this
`instructions <https://docs.sylabs.io/guides/3.7/user-guide/quick_start.html#quick-installation-steps>`_ .

Then use the following command to pull the docker image as a singularity: ::
        
        singularity pull docker:://inclab/hbcd_motion_postproc:<version_num>

where version_num denotes the specific version of the container. All available
versions of the container can be found `here <https://hub.docker.com/r/inclab/hbcd_motion_postproc/tags>`_.
If you are unsure of which version to use, use the tag:``latest``.

The full usage details can be seen under the :ref:`usage` section, but
the basic command to run the container using Singularity is as follows: ::

        bids_dir=/path/to/bids_dir
        output_dir=/path/to/output_dir
        container=/path/to/container
        analysis_level=participant

        singularity run -B $bids_dir:/bids \
        -B $output_dir:/out \
        $container /bids /out $analysis_level

where the following folder hierarchy is assumed in this case: ::

        bids_dir/
        |-- participants.tsv
        |-- participants.json
        |-- sub-<label>/
        |   |-- sub-<label>_sessions.tsv
        |   |-- sub-<label>_sessions.json
        |   |-- ses-<label>/
        |   |   |-- motion/
        |   |   |-- sub-<label>_ses-<label>_scans.tsv
        |   |   |-- sub-<label>_ses-<label>_scans.json

.. _option2-docker:

Option 2: Docker
----------------
Again, if you are new, start by getting Docker Desktop using
this `link <https://docs.docker.com/get-started/introduction/get-docker-desktop/>`_ .

If you are a Mac user, refer this `website <https://docs.cse.lehigh.edu/determine-mac-architecture/>`_ to
determine the architecture of your machine (Apple silicon vs. Intel chip).

After installing Docker Desktop, run the application. This will launch the
Docker Daemon and you will be able to use the ``docker pull`` command 
described at the top of this page.

Use the following command to pull the docker image. Again, if unsure of the version to use,
use the tag: ``latest``. ::

        docker pull inclab/hbcd_motion_postproc:<version_num>

Building the image from the scratch
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
The image can be built using the Dockerfile found in the `repository <https://github.com/Infant-Neuromotor-Control-Lab/hbcd_motion_postproc>`_.

Running the container using Docker is similar to doing so with Singularity. Here is the basic command::

        bids_dir=/path/to/bids_dir
        output_dir=/path/to/output_dir
        analysis_level=participant

        docker run -it -v $bids_dir:/bids_dir \
        inclab/hbcd_motion_postproc:<version_num> \
        /bids_dir /output_dir $analysis_level

Both *bids_dir* and *output_dir* should be provided as *absolute paths*

(ex. "/Users/user1/Documents/DATA", "/home/user1/Documents/DATA" or "C:/Documents/DATA")