The muse_flat recipe
===============================================================

.. data:: muse_flat

Synopsis
--------

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

Description
-----------

This recipe combines several separate flat-field images into one master flat-field file and traces the location of the slices on the CCD. The master flat contains the combined pixel values of the raw flat exposures, with respect to the image combination method used, normalized to the mean flux. The trace table contains polynomials defining the location of the slices on the CCD. Processing trims the raw data and records the overscan statistics, subtracts the bias (taking account of the overscan, if --overscan is not "none"), and optionally, the dark from each raw input image, converts them from adu to count, scales them according to their exposure time, and combines the exposures using input parameters. To trace the position of the slices on the CCD, their edges are located using a threshold method. The edge detection is repeated at given intervals thereby tracing the central position (the mean of both edges) and width of each slit vertically across the CCD. Deviant positions of detections on CCD rows can be detected and excluded before fitting a polynomial to all positions measured for one slice. The polynomial parameters for each slice are saved in the output trace table. Finally, the area between the now known slice edges is searched for dark (and bright) pixels, using statistics in each row of the master flat.


Constructor
-----------

.. method:: cpl.Recipe("muse_flat")
   :noindex:

   Create an object for the recipe muse_flat.

::

   import cpl
   muse_flat = cpl.Recipe("muse_flat")

Parameters
----------

.. py:attribute:: muse_flat.param.nifu

    IFU to handle. If set to 0, all IFUs are processed serially. If set to  -1, all IFUs are processed in parallel. (int; default: 0) [default=0].
.. py:attribute:: muse_flat.param.overscan

    If this is "none", stop when detecting discrepant overscan levels (see  ovscsigma), for "offset" it assumes that the mean overscan level  represents the real offset in the bias levels of the exposures  involved, and adjusts the data accordingly; for "vpoly", a polynomial  is fit to the vertical overscan and subtracted from the whole  quadrant. (str; default: 'vpoly') [default="vpoly"].
.. py:attribute:: muse_flat.param.ovscreject

    This influences how values are rejected when computing overscan  statistics. Either no rejection at all ("none"), rejection using the  DCR algorithm ("dcr"), or rejection using an iterative constant fit  ("fit"). (str; default: 'dcr') [default="dcr"].
.. py:attribute:: muse_flat.param.ovscsigma

    If the deviation of mean overscan levels between a raw input image and  the reference image is higher than |ovscsigma x stdev|, stop the  processing. If overscan="vpoly", this is used as sigma rejection level  for the iterative polynomial fit (the level comparison is then done  afterwards with |100 x stdev| to guard against incompatible settings).  Has no effect for overscan="offset". (float; default: 30.0) [default=30.0].
.. py:attribute:: muse_flat.param.ovscignore

    The number of pixels of the overscan adjacent to the data section of  the CCD that are ignored when computing statistics or fits. (int;  default: 3) [default=3].
.. py:attribute:: muse_flat.param.combine

    Type of combination to use (str; default: 'sigclip') [default="sigclip"].
.. py:attribute:: muse_flat.param.nlow

    Number of minimum pixels to reject with minmax (int; default: 1) [default=1].
.. py:attribute:: muse_flat.param.nhigh

    Number of maximum pixels to reject with minmax (int; default: 1) [default=1].
.. py:attribute:: muse_flat.param.nkeep

    Number of pixels to keep with minmax (int; default: 1) [default=1].
.. py:attribute:: muse_flat.param.lsigma

    Low sigma for pixel rejection with sigclip (float; default: 3.0) [default=3.0].
.. py:attribute:: muse_flat.param.hsigma

    High sigma for pixel rejection with sigclip (float; default: 3.0) [default=3.0].
.. py:attribute:: muse_flat.param.scale

    Scale the individual images to a common exposure time before combining  them. (bool; default: True) [default=True].
.. py:attribute:: muse_flat.param.normalize

    Normalize the master flat to the average flux (bool; default: True) [default=True].
.. py:attribute:: muse_flat.param.trace

    Trace the position of the slices on the master flat (bool; default:  True) [default=True].
.. py:attribute:: muse_flat.param.nsum

    Number of lines over which to average when tracing (int; default: 32) [default=32].
.. py:attribute:: muse_flat.param.order

    Order of polynomial fit to the trace (int; default: 5) [default=5].
.. py:attribute:: muse_flat.param.edgefrac

    Fractional change required to identify edge when tracing (float;  default: 0.5) [default=0.5].
.. py:attribute:: muse_flat.param.losigmabadpix

    Low sigma to find dark pixels in the master flat (float; default: 5.0) [default=5.0].
.. py:attribute:: muse_flat.param.hisigmabadpix

    High sigma to find bright pixels in the master flat (float; default:  5.0) [default=5.0].
.. py:attribute:: muse_flat.param.samples

    Create a table containing all tracing sample points. (bool; default:  False) [default=False].
.. py:attribute:: muse_flat.param.merge

    Merge output products from different IFUs into a common file. (bool;  default: False) [default=False].


The following code snippet shows the default settings for the available 
parameters.

::

   import cpl
   muse_flat = cpl.Recipe("muse_flat")

   muse_flat.param.nifu = 0
   muse_flat.param.overscan = "vpoly"
   muse_flat.param.ovscreject = "dcr"
   muse_flat.param.ovscsigma = 30.0
   muse_flat.param.ovscignore = 3
   muse_flat.param.combine = "sigclip"
   muse_flat.param.nlow = 1
   muse_flat.param.nhigh = 1
   muse_flat.param.nkeep = 1
   muse_flat.param.lsigma = 3.0
   muse_flat.param.hsigma = 3.0
   muse_flat.param.scale = True
   muse_flat.param.normalize = True
   muse_flat.param.trace = True
   muse_flat.param.nsum = 32
   muse_flat.param.order = 5
   muse_flat.param.edgefrac = 0.5
   muse_flat.param.losigmabadpix = 5.0
   muse_flat.param.hisigmabadpix = 5.0
   muse_flat.param.samples = False
   muse_flat.param.merge = False


You may also set or overwrite some or all parameters by the recipe 
parameter `param`, as shown in the following example:

::

   import cpl
   muse_flat = cpl.Recipe("muse_flat")
   [...]
   res = muse_flat( ..., param = {"nifu":0, "overscan":"vpoly"})


.. seealso:: `cpl.Recipe <https://packages.python.org/python-cpl/recipe.html>`_
   for more information about the recipe object.

Bug reports
-----------

Please report any problems to `Peter Weilbacher (based on Joris Gerssen's draft) <usd-help@eso.org>`_. Alternatively, you may 
send a report to the `ESO User Support Department <usd-help@eso.org>`_.

Copyright
---------

This file is part of the MUSE Instrument Pipeline
Copyright (C) 2005, 2018 European Southern Observatory

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation; either version 2 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program; if not, write to the Free Software
Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, 
MA  02111-1307  USA

.. codeauthor:: Peter Weilbacher (based on Joris Gerssen's draft) <usd-help@eso.org>
