Running NICRED
==============

.. index:: quickstart, running

Quickstart
**********

Running NICRED can be as simple as executing the following command in a terminal::
	
	nicred.py run_name input_data_directory

Where ``run_name`` is the name of the dataset (e.g. A1689_NIC3) and ``input_data_directory`` is the path to the uncalibrated data directory.

.. index:: uncalibrated, data, mast

Getting NICMOS Data
*******************

The NICRED pipeline requires the full set of uncalibrated data products 
and best reference files for each observation in the input image set. These files 
can be readily obtained through the MAST_ HST archive. When
requesting data from MAST_ you need to specify:
	
	* Science Files Requested: **Uncalibrated** 
	* Reference Files: **Best Reference Files**

.. image:: _static/mast.png
	:align: center

.. _MAST: http://archive.stsci.edu/hst/search.php

.. index:: options

Optional Commands
*****************

For most image sets NICRED can be run in the default configuration with no additional interaction 
required. If the default settings are insufficient for processing a particular data 
set, there are a number of run-time options which may be applied to help improve 
the reductions:

	* Modules can be run manually step-by-step allowing for the inspection of the output at each step.
	* Modules can be skipped.
	* A pipeline run can be stopped, restarted or rerun at any stage of the reduction after the initial setup.
	* An external reference image can be used to improve the internal alignment of the reduced NICMOS frames.


Here's a listing of the NICRED command line options::

	Usage: nicred.py run_name raw_in_dir

	Options:
	  --version             show program's version number and exit
	  -h, --help            show this help message and exit
	  --setup               run setup only
	  --undopuft            run undopuft only
	  --calped              run calped only
	  --saaclean            run saaclean only
	  --medsub              run medsub only
	  --flatten             run flatten only
	  --nonlincor           run nonlincor only
	  --applymask           interrupt processing to manually run masking tools
	  --align               run align only
	  --weightmap           run weightmap only
	  --mdrizzle            run mdrizzle only
	  -a ALIGNREF, --alignref=ALIGNREF
	                        external reference image used for alignment
	  -n MODULE, --rerun=MODULE
	                        rerun nicred from MODULE on
	  -r, --restart         restart nicred
	  -s SKIP, --skip=SKIP  Skip running module/s
	  -t TARGNAME, --targname=TARGNAME
	                        run nicred only on images with name TARGNAME on
	  --pedsub              Use pedsub instead of pedsky
	  --pixel_scale=PIXEL_SCALE
	                        pixel scale (in arcsec/pixel) for final drizzled
	                        images (default=0.1)
	  --pixel_frac=PIXEL_FRAC
	                        pixel fraction for final drizzled images (default=0.7)
	  --drz_kernel=KERNEL   drizzel kernel for final drizzled images
	                        (default=square)
	  --noskysub            turn off multidrizzle sky subtraction
	  --brightobj           take several actions to better cope with bright

	                        objects

.. index:: mask, masking, applymask

Applying User Defined Masks
***************************

Run NICRED with the ``--applymask`` option. NICRED will stop processing after the ``nonlincor`` module and give
instructions on how to run the masking tools on your data.

.. _troubleshooting:

Troubleshooting
***************

As we stated previously, NICRED was developed primarily for reducing imaging data of extragalactic sources. 
Here are some tips for reducing other types of data:

*Add tips here*