.. title:: Overview

The MUSE 1.6.2 pipeline
###################################

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

Standard recipes
----------------
:data:`muse_bias`
   Combine several separate bias images into one master bias file.

:data:`muse_dark`
   Combine several separate dark images into one master dark file and locate hot pixels.

:data:`muse_flat`
   Combine several separate flat images into one master flat file, trace slice locations, and locate dark pixels.

:data:`muse_wavecal`
   Detect arc emission lines and determine the wavelength solution for each slice.

:data:`muse_geometry`
   Compute relative location of the slices within the field of view and measure the instrumental PSF on the detectors.

:data:`muse_create_sky`
   Create night sky model from selected pixels of an exposure of empty sky.

:data:`muse_standard`
   Create a flux response curve from a standard star exposure.

:data:`muse_astrometry`
   Compute an astrometric solution.

:data:`muse_scibasic`
   Remove the instrumental signature from the data of each CCD and convert them from an image into a pixel table.

:data:`muse_scipost`
   Prepare reduced and combined science products.

:data:`muse_exp_combine`
   Combine several exposures into one datacube.

Additional recipes
--------------------
:data:`muse_ampl`
   Determine the instrumental throughput from exposures taken with the pico-amplifier / photo diode readings.

:data:`muse_exp_align`
   Create a coordinate offset table to be used to align exposures during exposure combination.

:data:`muse_lingain`
   Compute the gain and a model of the residual non-linearity for each detector quadrant

:data:`muse_lsf`
   Compute the LSF

:data:`muse_qi_mask`
   Create image masks for use with the quick image reconstruction.

:data:`muse_scipost_apply_astrometry`
   Calibrate astrometry for MUSE pixel tables.

:data:`muse_scipost_calibrate_flux`
   Calibrate flux for MUSE pixel tables.

:data:`muse_scipost_combine_pixtables`
   Combine MUSE pixel tables, either from different IFUs, or from different exposures, or both.

:data:`muse_scipost_correct_dar`
   Apply DAR correction for MUSE pixel tables.

:data:`muse_scipost_correct_rv`
   Apply RV correction for MUSE pixel tables.

:data:`muse_scipost_make_cube`
   Make a MUSE cube from a MUSE pixel table.

:data:`muse_scipost_subtract_sky`
   Subtract night sky model.

:data:`muse_scipost_subtract_sky_simple`
   Subtract night sky spectrum.

:data:`muse_twilight`
   Combine several twilight skyflats into one cube, compute correction factors for each IFU, and create a smooth 3D illumination correction.

.. toctree::
   :hidden:

   muse_bias
   muse_dark
   muse_flat
   muse_wavecal
   muse_geometry
   muse_create_sky
   muse_standard
   muse_astrometry
   muse_scibasic
   muse_scipost
   muse_exp_combine
   muse_ampl
   muse_exp_align
   muse_lingain
   muse_lsf
   muse_qi_mask
   muse_scipost_apply_astrometry
   muse_scipost_calibrate_flux
   muse_scipost_combine_pixtables
   muse_scipost_correct_dar
   muse_scipost_correct_rv
   muse_scipost_make_cube
   muse_scipost_subtract_sky
   muse_scipost_subtract_sky_simple
   muse_twilight

.. seealso::

     * The `MUSE Pipeline User Manual 
       <ftp://ftp.eso.org/pub/dfs/pipelines/muse/muse-pipeline-cookbook-1.6.2.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 MUSE
pipeline recipes package, please, first refer to the list of known problems
and limitations in the pipeline manual of the current MUSE pipeline
release.

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

 * the MUSE 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.
