The muse_ampl recipe
===============================================================

.. data:: muse_ampl

Synopsis
--------

Determine the instrumental throughput from exposures taken with the pico-amplifier / photo diode readings.

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

This recipe combines several separate amplifier images (flat-fields with special FITS headers containing pico amplifier measurements) into one master image file and computes the instrumental throughput per IFU (and slice). 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 them using input parameters. To compute the throughput the image is converted into a pixel table, the flux is then integrated over the given filter band, and the ratio of the expected flux (FITS header INS.AMPL2.CURR) to measured flux is taken, in the same units. If a geometry table was given as input, the relative area of the IFUs is taken into account when computing the flux per unit area. The resulting ratio is the instrument efficiency (throughput) and saved as QC parameters for the whole input image and per slice in the output pixel table.


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

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

   Create an object for the recipe muse_ampl.

::

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

Parameters
----------

.. py:attribute:: muse_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.param.combine

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

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

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

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

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

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

    Factor to describe the widening of the beam from the focal plane to  photo diode 2. (float; default: 1.1) [default=1.1].
.. py:attribute:: muse_ampl.param.temp

    Lamp temperature [K] used to create the black body function. (float;  default: 3200.0) [default=3200.0].
.. py:attribute:: muse_ampl.param.savemaster

    Save the processed and combined master image before any concolution is  done. (bool; default: False) [default=False].
.. py:attribute:: muse_ampl.param.savetable

    Save the table with all the processed pixel values. (bool; default:  False) [default=False].
.. py:attribute:: muse_ampl.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_ampl = cpl.Recipe("muse_ampl")

   muse_ampl.param.nifu = 0
   muse_ampl.param.overscan = "vpoly"
   muse_ampl.param.ovscreject = "dcr"
   muse_ampl.param.ovscsigma = 30.0
   muse_ampl.param.ovscignore = 3
   muse_ampl.param.combine = "sigclip"
   muse_ampl.param.nlow = 1
   muse_ampl.param.nhigh = 1
   muse_ampl.param.nkeep = 1
   muse_ampl.param.lsigma = 3.0
   muse_ampl.param.hsigma = 3.0
   muse_ampl.param.fbeam = 1.1
   muse_ampl.param.temp = 3200.0
   muse_ampl.param.savemaster = False
   muse_ampl.param.savetable = False
   muse_ampl.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_ampl = cpl.Recipe("muse_ampl")
   [...]
   res = muse_ampl( ..., 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 <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 <usd-help@eso.org>
