Using Scripts 
==============

We use scripts to use the functionalities offered by ``cytocalc``. Scripts provide an interface for using ``cytocalc`` while maintaining a relatively
stable 'core' functions. System specific information (file structure, folder names etc.)
are handled using the scripts, which hence change more often than code in the ``src``
folder (eg: function for computing network radius) which doesn't have to be modified a lot.

The ``scripts`` directory provides a few pre-made scripts for some common systems.
These are intended to be used as a starting point for :doc:`creating more complex scripts.
</creating_scripts>`

Example
--------

Suppose we would like to measure the Mean Squared Displacement of brownian particles 
using the ``diffusing_bead_msd.py`` script. The simulation details which the script has
been designed for are as follows:

- Initialize *N* beads, non interacting

- Run the simulation for *T* time

- Use ``reportF`` to produce report files in ``<directory>``

To run the script, we must first ensure that the ``cytocalc`` is available in the current
python environment. This can be done by switching to the virtual environment created during
:doc:`installation`.

.. code-block:: sh

   $ source $CYTOCALCPATH/.venv/bin/activate

where ``$CYTOCALCPATH`` is the path to the local ``Cytocalc`` repository. We can now run the script
with the directory location as the argument.

.. code-block:: sh

   (.venv) $ $CYTOCALCPATH/scripts/diffusing_bead_msd.py <directory>

.. image:: /plots/diffusing_bead_msd.png
   :width: 400
   :align: center
   :alt: MSD plot showing a linear trend, expected from brownian diffusion