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JP-3913: Add sirskernel to refpix reference types #9261

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JP-3913: Add sirskernel to refpix reference types #9261

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e32189c
Add sirskernel to reference types
melanieclarke Mar 10, 2025
ffc942c
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melanieclarke Mar 10, 2025
f8a3ee8
Add SIRSKERNEL docs
melanieclarke Mar 10, 2025
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1 change: 1 addition & 0 deletions changes/9261.refpix.rst
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@@ -0,0 +1 @@
Add 'sirskernel' to the reference types for the step, so that 'override_sirskernel' is available as a step parameter.
4 changes: 4 additions & 0 deletions docs/jwst/references_general/references_general.rst
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Expand Up @@ -149,6 +149,8 @@ documentation on each reference file.
| | :ref:`READNOISE <readnoise_reffile>` |
+-------------------------------------------------------+--------------------------------------------------+
| :ref:`refpix <refpix_step>` | :ref:`REFPIX <refpix_reffile>` |
+ +--------------------------------------------------+
| | :ref:`SIRSKERNEL <sirskernel_reffile>` |
+-------------------------------------------------------+--------------------------------------------------+
| :ref:`reset <reset_step>` | :ref:`RESET <reset_reffile>` |
+-------------------------------------------------------+--------------------------------------------------+
Expand Down Expand Up @@ -282,6 +284,8 @@ documentation on each reference file.
+--------------------------------------------------+-------------------------------------------------------+
| :ref:`SFLAT <sflat_reffile>` | :ref:`flatfield <flatfield_step>` |
+--------------------------------------------------+-------------------------------------------------------+
| :ref:`SIRSKERNEL <sirskernel_reffile>` | :ref:`refpix <refpix_step>` |
+--------------------------------------------------+-------------------------------------------------------+
| :ref:`SPECWCS <specwcs_reffile>` | :ref:`assign_wcs <assign_wcs_step>` |
+--------------------------------------------------+-------------------------------------------------------+
| :ref:`SUPERBIAS <superbias_reffile>` | :ref:`superbias <superbias_step>` |
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25 changes: 25 additions & 0 deletions docs/jwst/references_general/sirskernel_reffile.inc
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.. _sirskernel_reffile:

SIRSKERNEL Reference File
-------------------------

:REFTYPE: SIRSKERNEL
:Data model: `~jwst.datamodels.SIRSKernelModel`

The SIRSKERNEL reference file contains Fourier coefficients for an
optimized convolution kernel, used for correcting 1/f noise from
detector reference pixels.

.. include:: ../includes/standard_keywords.inc

Reference File Format
+++++++++++++++++++++
SIRSKERNEL reference files are in ASDF format. They contain a dictionary with
keys corresponding to lower-case detector names. Each detector entry contains
two arrays, `gamma` and `zeta`, which contain the complex Fourier coefficients
required to apply the Simple Improved Reference Subtraction (SIRS) algorithm
for reference pixel correction.

The first dimension of the array holds the sector index (amplifier output,
4 per detector). The second dimension matches the height of the sector, plus one.
The data type for both arrays is `complex64`.
9 changes: 6 additions & 3 deletions docs/jwst/refpix/reference_files.rst
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Reference Files
===============

The ``refpix`` step uses a REFPIX reference file, but only when
The ``refpix`` step uses a REFPIX reference file when
processing NIRSpec exposures that have been acquired using an IRS2
readout pattern. No other instruments or exposure modes require a
reference file for this step.
readout pattern.

For other full-frame NIR instruments and modes, when the optional SIRS algorithm
is selected, the ``refpix`` step uses a SIRSKERNEL reference file.

.. include:: ../references_general/refpix_reffile.inc
.. include:: ../references_general/sirskernel_reffile.inc
2 changes: 1 addition & 1 deletion jwst/refpix/refpix_step.py
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Expand Up @@ -31,7 +31,7 @@ class RefPixStep(Step):
halfwidth = integer(default=30) # Half-width of convolution kernel to build
""" # noqa: E501

reference_file_types = ['refpix']
reference_file_types = ['refpix', 'sirskernel']

def process(self, step_input):

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