.. highlight:: bash
*************************
Data Analysis Quick Start
*************************

You can perform data analysis remotely, off-site, or at a beamline computer.
Accordingly, there are two parts to this guide.

Option 1: At the Beamline
-------------------------

#. Log in to your controls account. If this is your first time, execute this
   command to add a line to your ``.bashrc`` file.::

    echo "export PATH=/opt/conda/bin:\$PATH" >> ~/.bashrc
    source ~/.bashrc

#. Activate the ``analysis`` conda environment.::

    source activate analysis 

   This command makes the data collection software available by adding it
   your UNIX ``$PATH``.

#. Start IPython.::

    ipython

   or, alternatively, IPython notebook::

    ipython notebook

You are ready to work. See the
`dataportal documentation <https://nsls-ii.github.io/dataportal>`_
to look up scans and retrieve data. See the
`scikit-xray documentation <https://scikit-xray.github.io/scikit-xray>`_
for some Python tools for X-ray data analysis.

Option 2: Remotely
------------------

You need access to the BNL campus network, via a wired connection or VPN. You
also need a controls account. (Contact one of the NSLS-II sysadmins.)

#. Go to `https://notebook.nsls2.bnl.gov <https://notebook.nsls2.bnl.gov>`_.
   Remember, if you are not connected to the campus network, that link will not
   work.

#. You will be shown a login prompt. Enter your *controls* account and
   password.

   .. image:: _static/jupyterhub-login.png
      :align: center

#. Choose a beamline from drop-down menu at the top right of the page.

   .. image:: _static/jupyterhub-kernel-menu.png
      :align: center

This will open a new IPython notebook with all the software ready to use. It
has fast access to the beamline's data.   

   .. image:: _static/jupyterhub-blank-nb.png
      :align: center

You are ready to work. See the
`dataportal documentation <https://nsls-ii.github.io/dataportal>`_
to look up scans and retrieve data. See the
`scikit-xray documentation <https://scikit-xray.github.io/scikit-xray>`_
for some Python tools for X-ray data analysis.