kai.reduce.calib
================

.. py:module:: kai.reduce.calib


Attributes
----------

.. autoapisummary::

   kai.reduce.calib.module_dir


Functions
---------

.. autoapisummary::

   kai.reduce.calib.makedark
   kai.reduce.calib.makeflat
   kai.reduce.calib.makemask
   kai.reduce.calib.make_instrument_mask
   kai.reduce.calib.analyzeDarkCalib


Module Contents
---------------

.. py:data:: module_dir

.. py:function:: makedark(files, output, raw_dir=None, instrument=instruments.default_inst)

   
   Make dark image for imaging data. Makes a calib/ directory
   and stores all output there. All output and temporary files
   will be created in a darks/ subdirectory.


   :Parameters:

       **files** : list of int
           Integer list of the files. Does not require padded zeros.

       **output** : str
           Output file name. Include the .fits extension.

       **raw_dir** : str, optional
           Directory where raw files are stored. By default,
           assumes that raw files are stored in '../raw'

       **instrument** : instruments object, optional
           Instrument of data. Default is `instruments.default_inst`














   ..
       !! processed by numpydoc !!

.. py:function:: makeflat(onFiles, offFiles, output, dark_frame=None, normalizeFirst=False, raw_dir=None, instrument=instruments.default_inst)

   
   Make flat field image for imaging data. Makes a calib/ directory
   and stores all output there. All output and temporary files
   will be created in a flats/ subdirectory.

   If only twilight flats were taken (as in 05jullgs), use these flats as
   the onFiles, and use 0,0 for offFiles. So the reduce.py file should look
   something like this: onFiles = range(22, 26+1) and offFiles = range(0,0)
   The flat will then be made by doing a median combine using just the
   twilight flats.

   :Parameters:

       **onFiles** : list of int
           Integer list of lamps ON files. Does not require padded zeros.

       **offFiles** : list of int
           Integer list of lamps OFF files. Does not require padded zeros.

       **output** : str
           Output file name. Include the .fits extension.

       **dark_frame** : str, default=None
           File name for the dark frame in order to carry out dark correction.
           If not provided, dark frame is not subtracted and a warning is thrown.
           Assumes dark file is located under ./calib/darks/

       **normalizeFirst** : bool, default=False
           If the individual flats should be normalized first,
           such as in the case of twilight flats.

       **raw_dir** : str, optional
           Directory where raw files are stored. By default,
           assumes that raw files are stored in '../raw'

       **instrument** : instruments object, optional
           Instrument of data. Default is `instruments.default_inst`














   ..
       !! processed by numpydoc !!

.. py:function:: makemask(dark, flat, output, instrument=instruments.default_inst)

   
   Make bad pixel mask for imaging data. Makes a calib/ directory
   and stores all output there. All output and temporary files
   will be created in a masks/ subdirectory.


   :Parameters:

       **dark** : str
           The filename of the dark file (must be in the
           calib/darks/ directory). This is used to
           construct a hot pixel mask. Use a long (t>20sec) exposure dark.

       **flat** : str
           The filename of a flat file  (must be in the
           calib/flats/ directory). This is used to
           construct a dead pixel mask. The flat should be normalized.

       **output** : str
           The output file name. This will be created in the masks/
           subdirectory.

       **instrument** : instruments object, optional
           Instrument of data. Default is `instruments.default_inst`














   ..
       !! processed by numpydoc !!

.. py:function:: make_instrument_mask(dark, flat, outDir, instrument=instruments.default_inst)

   
   Make the static bad pixel mask for the instrument. This only needs to be
   run once. This creates a file called nirc2mask.fits or osiris_img_mask.fits
   which is subsequently used throughout the pipeline. The dark should be a long
   integration dark.


   :Parameters:

       **dark** : str
           The full absolute path to a medianed dark file. This is
           used to construct a hot pixel mask (4 sigma detection thresh).

       **flat** : str
           The full absolute path to a medianed flat file. This is
           used to construct a dead pixel mask.

       **outDir** : str
           full path to output directory with '/' at the end.

       **instrument** : instruments object, optional
           Instrument of data. Default is `instruments.default_inst`














   ..
       !! processed by numpydoc !!

.. py:function:: analyzeDarkCalib(firstFrame, skipcombo=False)

   
   Reduce data from the dark_calib script that should be run once
   a summer in order to test the dark current and readnoise.

   This should be run in the reduce/calib/ directory for a particular
   run.















   ..
       !! processed by numpydoc !!