spacetelescope · jemorrison · Oct 21, 2021 · Oct 6, 2021 · Oct 8, 2021 · Oct 8, 2021
diff --git a/docs/jwst/package_index.rst b/docs/jwst/package_index.rst
@@ -51,6 +51,7 @@ Package Index
    refpix/index.rst
    resample/index.rst
    reset/index.rst
+   residual_fringe/index.rst
    rscd/index.rst
    saturation/index.rst
    skymatch/index.rst

diff --git a/docs/jwst/references_general/fringefreq_format.inc b/docs/jwst/references_general/fringefreq_format.inc
@@ -0,0 +1,51 @@
++-------------------+--------------+-----------+---------------+
+| Table             | Column       | Data type | Units         |
++===================+==============+===========+===============+
+| RFC_FREQ_SHORT    | SLICE        | double    | N/A           |
++                   +--------------+-----------+---------------+
+|                   | FFREQ        | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | DFFREQ       | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | MIN_NFRIGES  | int       | N/A           |
++                   +--------------+-----------+---------------+
+|                   | MAX_NFRINGES | int       | N/A           |
++                   +--------------+-----------+---------------+
+|                   | MIN_SNR      | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | PGRAM_RES    | double    | cm\ :sup:`-1` |
++-------------------+--------------+-----------+---------------+
+| FRC_FREQ_MEDIUM   | SLICE        | double    | N/A           |
++                   +--------------+-----------+---------------+
+|                   | FFREQ        | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | DFFREQ       | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | MIN_NFRIGES  | int       | N/A           |
++                   +--------------+-----------+---------------+
+|                   | MAX_NFRINGES | int       | N/A           |
++                   +--------------+-----------+---------------+
+|                   | MIN_SNR      | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | PGRAM_RES    | double    | cm\ :sup:`-1` |
++-------------------+--------------+-----------+---------------+
+| RFC_FREQ_LONG     | SLICE        | double    | N/A           |
++                   +--------------+-----------+---------------+
+|                   | FFREQ        | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | DFFREQ       | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | MIN_NFRIGES  | int       | N/A           |
++                   +--------------+-----------+---------------+
+|                   | MAX_NFRINGES | int       | N/A           |
++                   +--------------+-----------+---------------+
+|                   | MIN_SNR      | double    | cm\ :sup:`-1` |
++                   +--------------+-----------+---------------+
+|                   | PGRAM_RES    | double    | cm\ :sup:`-1` |
++-------------------+--------------+-----------+---------------+
+| MAX_AMP           | WAVELENGTH   | double    | micron        |
++                   +--------------+-----------+---------------+
+|                   | AMPLITUDE    | double    | N/A           |
++-------------------+--------------+-----------+---------------+
+
+
diff --git a/docs/jwst/references_general/fringefreq_reffile.inc b/docs/jwst/references_general/fringefreq_reffile.inc
@@ -0,0 +1,61 @@
+.. _fringefreq_reffile:
+
+FRINGEFREQ reference file
+-------------------------
+
+:REFTYPE: FRINGEFREQ
+:Data models: `~jwst.datamodels.FringeFreqModel`
+
+The FRINGEFREQ reference files contain parameter values used to correct MIRI MRS images
+for  residual fringes that remain  after applying the fringe flat.
+
+.. include:: ../references_general/fringefreq_selection.inc
+
+.. include:: ../includes/standard_keywords.inc
+
+Type Specific Keywords for FRINGEFREQ
++++++++++++++++++++++++++++++++++++++
+In addition to the standard reference file keywords listed above,
+the following keywords are *required* in FRINGEFREQ reference files,
+because they are used as CRDS selectors
+(see :ref:`fringefreq_selectors`):
+
+=========  ==============================
+Keyword    Data Model Name
+=========  ==============================
+DETECTOR   model.meta.instrument.detector
+EXP_TYPE   model.meta.exposure.type
+=========  ==============================
+
+Reference File Format
+++++++++++++++++++++++++++
+The FRINGEFREQ reference files are FITS format, with  4  BINTABLE extensions.
+The FITS primary data array is assumed to be empty.
+The format and content of the FRINGEFREQ reference file is
+
+===================  ========  ===========  
+EXTNAME              XTENSION  Dimensions   
+===================  ========  ===========  
+RFC_FREQ_SHORT       BINTABLE  TFIELDS = 7  
+RFC_FREQ_MEDIUM      BINTABLE  TFIELDS = 7  
+RFC_FREQ_LONG        BINTABLE  TFIELDS = 7  
+MAX_AMP              BINTABLE  TFIELDS = 2  
+===================  ========  ===========  
+
+The formats of the individual table extensions are listed below.
+
+.. include:: ../references_general/fringefreq_format.inc
+
+These reference files contain tables for each MIRI band giving the
+fringe frequencies and other parameters for each band to fit and remove residual fringes. 
+
+
+The reference table descriptions:
+
+- **RFC_FREQ_SHORT** table contains the fringe frequences and parameters for the SHORT band.
+- **RFC_FREQ_MEDIUM** table contains the fringe frequences and parameters for the MEDIUM band.
+- **RFC_FREQ_LONG** table contains the fringe frequences and parameters for the LONG band.
+- **MAX_AMP** table contains a wavelength dependent maximum amplitude which is use for feature identification and fit rejection. 
+
+
+
diff --git a/docs/jwst/references_general/fringefreq_selection.inc b/docs/jwst/references_general/fringefreq_selection.inc
@@ -0,0 +1,13 @@
+.. _fringefreq_selectors:
+
+Reference Selection Keywords for FRINGEFREQ
++++++++++++++++++++++++++++++++++++++++++++
+CRDS selects appropriate FRINGEFREQ reference file based on the following keywords.
+FRINGEFREQ is not applicable for instruments not in the table.
+
+========== ================================================
+Instrument Keywords                               
+========== ================================================
+MIRI       INSTRUME, EXP_TYPE, DETECTOR, DATE-OBS, TIME-OBS 
+========== ================================================
+
diff --git a/docs/jwst/residual_fringe/arguments.rst b/docs/jwst/residual_fringe/arguments.rst
@@ -0,0 +1,6 @@
+.. _resid_fringe_arguments:
+
+Step Arguments
+==============
+
+The residual fringe step has no step-specific arguments.
diff --git a/docs/jwst/residual_fringe/index.rst b/docs/jwst/residual_fringe/index.rst
@@ -0,0 +1,14 @@
+.. _residual_fringe_step:
+
+===============
+Residual Fringe
+===============
+
+.. toctree::
+   :maxdepth: 2
+
+   main.rst
+   arguments.rst
+   reference_files.rst
+
+.. automodapi:: jwst.residual_fringe.residual_fringe_step
diff --git a/docs/jwst/residual_fringe/main.rst b/docs/jwst/residual_fringe/main.rst
@@ -0,0 +1,55 @@
+Description
+===========
+
+The JWST pipeline contains two steps devoted to the removal of fringes on MIRI MRS images.
+The first correction is applied in the ``fringe_step`` in the :ref:`calwebb_spec2 <calwebb_spec2>` pipeline
+and  consists in dividing
+detector-level data by a fringe-flat and is described in the :ref:`fringe <fringe_step>` step.
+Applying the fringe flat should eliminate fringes from spectra of spatially extended sources, however
+residual fringes can remain. For spatially unresolved (point) sources or extended sources with structure,
+applying the fringe flat will undoubtedly leave residual fringes since these produce different fringe patterns
+on the detector than accounted for by the fringe flat. The second step for fringe removal is the
+``residual_fringe_step``. At this time this step can only be run offline; it is not part of the default pipeline.
+After thorough testing and possible updates after commissioning,
+it will be determined if this step should be run as part of  :ref:`calwebb_spec3 <calwebb_spec3>` pipeline.
+To run this offline it is best if it is applied  after the ``mrs_imatch_step``, but before the ``cube_build_step``.
+
+
+
+The ``residual_fringe`` step can accept several different forms of input data, including:
+
+  - a single file containing a 2-D IFU image
+
+  - a data model (IFUImageModel) containing a 2-D IFU image
+
+  - an association table (in json format) containing a list of input files
+
+  - a model container with several 2-D IFU data models
+
+
+Assumptions
+-----------
+This step only works on MIRI MRS data.
+It is assumed that the calwebb_spec2 pipeline has been run on the data. In addition, the detection of residual fringes
+are  better determined if the ``mrs_imatch``  step has also been applied to the data.
+
+
+
+Fringe Background Information
+-----------------------------
+As is typical for spectrometers, the MIRI MRS detectors are affected by fringes.  These are periodic gain modulations caused by
+standing waves between parallel surfaces in the optical path, acting as a slow-finesse Fabry-Pérot etalons. In the MRS,
+the principal fringe sources are the detector layers. A detailed  detailed discussion on these fringe components
+can be found in Argyriou, I., Wells, M., Glasse, A., et al. 2020, A&A, 641, A150 and
+Wells, M., Pel, J.-W., Glasse, A., et al. 2015, PASP, 127, 646.
+
+
+The primary MRS fringe, observed in all MRS bands, is caused by the etalons between the anti-reflection coating
+and lower layers, encompassing the detector substrate and the infrared-active layer. Since the thickness of the substrate
+is not the same in the SW and LW detectors, the fringe frequency will differ in the two detectors. Up to 16 microns, this
+fringe is produced by the anti-reflection coating and  pixel metalization etalons, whereas above 16 microns it is
+produced by the anti-reflection coating and  bottom contact etalon, resulting in a different fringe frequency.
+The information in the fringe frequency
+reference file  is used to determine, for each MRS band, the frequencies to fit to this main fringe component.
+The residual fringes are corrected for by fitting and removing sinusoidal gain to the detector level data.
+
diff --git a/docs/jwst/residual_fringe/reference_files.rst b/docs/jwst/residual_fringe/reference_files.rst
@@ -0,0 +1,8 @@
+Reference Files
+===============
+
+The ``residual_fringe`` step uses the FRINGEFREQ reference file. 
+
+
+.. include:: ../references_general/fringefreq_reffile.inc
+