.. title:: Overview

The KMOS 1.3.5 pipeline
###################################

These pages describe the python interface for the KMOS pipeline recipes.

Standard recipes
----------------
:data:`kmos_dark`
   Create master dark frame & bad pixel mask

:data:`kmos_flat`
   Create master flatfield frame and badpixel map

:data:`kmos_wave_cal`
   Create a wavelength calibration frame

:data:`kmos_illumination`
   Create a frame to correct spatial non-uniformity of flatfield

:data:`kmo_std_star`
   Create the telluric correction frame.

:data:`kmo_sci_red`
   Reconstruct obj/sky-pairs individually and combine them afterwards

Additional recipes
--------------------
:data:`kmo_fits_strip`
   Strip noise, rotator and/or empty extensions from a processed KMOS fits frame

:data:`kmo_combine`
   Combine reconstructed cubes

:data:`kmo_illumination_flat`
   Alternative to kmo_illumination based on flatfield frames.

:data:`kmo_make_image`
   Collapse a cube to create a spatial image

:data:`kmo_sky_mask`
   Create a mask of spatial pixels that indicates which pixels can be considered as sky.

:data:`kmo_reconstruct`
   Performs the cube reconstruction using different interpolation methods.

:data:`kmo_rotate`
   Rotate a cube spatially

:data:`kmo_fit_profile`
   Fit spectral line profiles as well as spatial profiles with a simple function - for example to measure resolution or find the centre of a source

:data:`kmo_copy`
   Copy a section of a cube to another cube, image or spectrum

:data:`kmo_fits_stack`
   Creates KMOS conform fits-files

:data:`kmo_extract_spec`
   Extract a spectrum from a cube.

:data:`kmo_noise_map`
   Generate a noise map from a raw frame

:data:`kmo_fits_check`
   Check contents of a KMOS fits-file

:data:`kmo_multi_reconstruct`
   Reconstruct and combine obj/sky-pairs in one step.

:data:`kmos_gen_reflines`
   Create REFLINES calibration file

:data:`kmo_sky_tweak`
   Removal of OH sky lines

:data:`kmo_arithmetic`
   Perform basic arithmetic on cubes

:data:`kmo_shift`
   Shift a cube spatially

:data:`kmo_stats`
   Perform basic statistics on a KMOS-conform fits-file

.. toctree::
   :hidden:

   kmos_dark
   kmos_flat
   kmos_wave_cal
   kmos_illumination
   kmo_std_star
   kmo_sci_red
   kmo_fits_strip
   kmo_combine
   kmo_illumination_flat
   kmo_make_image
   kmo_sky_mask
   kmo_reconstruct
   kmo_rotate
   kmo_fit_profile
   kmo_copy
   kmo_fits_stack
   kmo_extract_spec
   kmo_noise_map
   kmo_fits_check
   kmo_multi_reconstruct
   kmos_gen_reflines
   kmo_sky_tweak
   kmo_arithmetic
   kmo_shift
   kmo_stats

.. seealso::

     * The `KMOS Pipeline User Manual 
       <ftp://ftp.eso.org/pub/dfs/pipelines/kmos/kmos-pipeline-manual-2.9.pdf>`_ in PDF format,

     * an `overview <http://www.eso.org/sci/software/pipelines/>`_
       over the existing ESO pipelines,

     * the `python-cpl <http://packages.python.org/python-cpl>`_ package.
    
Bug reports
===========

If you experience an unexpected behavior of any component of the KMOS
pipeline recipes package, please, first refer to the list of known problems
and limitations in the pipeline manual of the current KMOS pipeline
release.

For any other issues or requests, please, send a report to the `ESO User
Support Department <usd-help@eso.org>`_, describing:

 * the KMOS pipeline version,
 * the version of your OS and C compiler,
 * the exact sequence of actions that were performed before the problem occurred,
 * what were precisely the symptoms and the possible error message(s),
 * whether the problem is repeatable.
