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Update general documentation files #398

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Update general documentation files
Jul 2, 2026
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Revert index.rst and glossary.rst - depend on DEM content not yet in …
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20 changes: 10 additions & 10 deletions docs/about_xrt.rst
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Expand Up @@ -8,8 +8,8 @@ Hinode
======

.. image:: _static/images/hinode_satellite.png
:alt: Hinode Satellite
:align: center
:alt: Hinode Satellite
:align: center

Hinode is a joint mission involving the space agencies of Japan, the United States, Europe, and the United Kingdom.
It is depicted in the *illustration shown above*.
Expand All @@ -25,9 +25,9 @@ The X-Ray Telescope
===================

.. image:: _static/images/XRT_composite_image_full_disk_14February2015.png
:alt: XRT Composite Image
:align: center
:scale: 50%
:alt: XRT Composite Image
:align: center
:scale: 50%

The X-Ray Telescope (XRT), depicted as a long linear black tube on the Hinode spacecraft is a crucial instrument for observing the solar corona's most intense regions, with temperatures ranging from 1,000,000 to 10,000,000 Kelvin.
The image below is a synoptic composite from February 14, 2015, created using the Al-Mesh/Be-Thin/Al-Med filters.
Expand All @@ -36,7 +36,7 @@ For a comprehensive overview of XRT's mission and capabilities, please visit the

.. tip::

Visit the `XRT Picture of the Week`_ and the `Hinode-XRT YouTube`_ page for captivating visual content showcasing the XRT's solar observations.
Visit the `XRT Picture of the Week`_ and the `Hinode-XRT YouTube`_ page for captivating visual content showcasing the XRT's solar observations.

XRT uses two sequentially positioned filter wheels, as shown in the diagram below, where each wheel houses a variety of filters.
By rotating these wheels, scientists can select different filters to study the Sun in different wavelengths, thereby enhancing the resolution and quality of solar images.
Expand Down Expand Up @@ -73,8 +73,8 @@ The existing filters are structured as follows:
The process is the same for all XRT filter channels.

.. image:: _static/images/XRT_filter_wheels_Sun_View_Diagram.png
:alt: Diagram of the XRT Filter Wheels
:align: center
:alt: Diagram of the XRT Filter Wheels
:align: center

Data Products
*************
Expand All @@ -99,8 +99,8 @@ The XRT software was originally created in the Interactive Data Language (IDL).

.. note::

Please note that the `SolarSoft XRT Analysis Guide`_ does not serve as a guide for using XRTpy.
It focuses solely on the analysis of XRT data using the IDL software.
Please note that the `SolarSoft XRT Analysis Guide`_ does not serve as a guide for using XRTpy.
It focuses solely on the analysis of XRT data using the IDL software.

.. _Hinode-XRT YouTube: https://www.youtube.com/user/xrtpow
.. _Interactive Data Language: https://www.l3harrisgeospatial.com/Software-Technology/IDL
Expand Down
44 changes: 19 additions & 25 deletions docs/getting_started.rst
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Expand Up @@ -7,7 +7,7 @@ on board the Hinode spacecraft. This page is intended for new users of XRTpy. Fo
please refer to the `SolarSoft XRT Analysis Guide`_.

XRTpy Objects
*************
-------------

XRTpy currently provides access to the following core classes:

Expand All @@ -24,41 +24,41 @@ It also includes functionality to:
Visit our Examples page for step-by-step Jupyter notebook guides on how to use each feature.

Channel
-------
^^^^^^^

The ``Channel`` class describes the configuration of a specific XRT filter channel. It includes details for the Charge-Coupled Device (CCD),
Entrance Filter, Focal Plane Filters, Geometry, and Mirrors.

Effective Area
--------------
^^^^^^^^^^^^^^

XRTpy calculates the effective area for each XRT filter channel, accounting for time-dependent contamination on the CCD. For more details,
refer to the `SolarSoft XRT Analysis Guide`_.

Temperature Response
--------------------
^^^^^^^^^^^^^^^^^^^^

XRTpy calculates the temperature response of XRT filter channels using the CHIANTI_ atomic database (version 10.0) and coronal abundances
(:cite:t:`feldman:1992`). This produces a response function as a function of temperature, using an assumed emission model
(:cite:t:`narukage:2011`, :cite:t:`narukage:2014`).

Deriving Temperature and Emission Measure
-----------------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The ``temperature_from_filter_ratio`` function allows you to derive plasma temperature and emission measure from a pair of XRT images using the filter-ratio method. This mirrors the logic in the SolarSoft IDL routine of the same name. A usage example is available in the Examples section.

Image Deconvolution with the PSF
--------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

The ``deconvolve`` function applies image deconvolution using the instrument's Point Spread Function (PSF) to sharpen XRT images. This is especially useful for recovering detail around bright or sharp solar structures.

Light Leak Correction
---------------------
^^^^^^^^^^^^^^^^^^^^^

The ``remove_lightleak`` function subtracts visible stray light from XRT synoptic composite images. This correction improves the quality of long-term coronal evolution studies. See our Examples section for how to use this function.

Abundance Model Options
-----------------------
^^^^^^^^^^^^^^^^^^^^^^^

By default, XRTpy uses CHIANTI coronal abundances (:cite:t:`feldman:1992`). You may also choose:

Expand All @@ -83,12 +83,12 @@ You may also pass the ``abundance_model`` keyword to ``temperature_from_filter_r


Tools
*****
-----

The ``xrtpy.response.tools`` module includes helpful utility functions to streamline workflows. It includes the following:

Generate Temperature Responses
------------------------------
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

Use the ``generate_temperature_responses`` tool to compute the temperature response for one or more filters — including combinations like ``"Al-poly/Ti-poly"`` — with a single command.

Expand Down Expand Up @@ -117,16 +117,16 @@ This function returns a list of ``TemperatureResponseFundamental`` objects, one
.. code-block:: text

Filter: Al-poly
Temperatures: [100000. 112201.9 125892.516] K
Response: [8.34e-31 1.07e-30 1.53e-30] cm5 DN / (pix s)
Temperatures: [100000. 112201.9 125892.516] K
Response: [8.34e-31 1.07e-30 1.53e-30] cm5 DN / (pix s)

Filter: Be-thick
Temperatures: [100000. 112201.9 125892.516] K
Response: [0.00e+00 1.73e-94 2.43e-84] cm5 DN / (pix s)
Temperatures: [100000. 112201.9 125892.516] K
Response: [0.00e+00 1.73e-94 2.43e-84] cm5 DN / (pix s)

Filter: Al-poly/Ti-poly
Temperatures: [100000. 112201.9 125892.516] K
Response: [5.34e-34 7.24e-34 1.11e-33] cm5 DN / (pix s)
Temperatures: [100000. 112201.9 125892.516] K
Response: [5.34e-34 7.24e-34 1.11e-33] cm5 DN / (pix s)

Each response object has the following attributes:

Expand All @@ -138,7 +138,7 @@ This tool is useful on its own, but it also serves as a foundation for upcoming


Data Products
*************
-------------

XRT data products are available through the XRT website. These include:

Expand All @@ -148,7 +148,7 @@ XRT data products are available through the XRT website. These include:
For more information, visit the `XRT data products`_ page.

Double Filter Combinations
**************************
--------------------------

XRTpy now supports double filter combinations such as ``"Al-poly/Ti-poly"`` in both the :obj:`EffectiveAreaFundamental <xrtpy.response.EffectiveAreaFundamental>` and :obj:`TemperatureResponseFundamental <xrtpy.response.TemperatureResponseFundamental>` classes.

Expand Down Expand Up @@ -178,7 +178,7 @@ The following combinations are currently supported:


X-Ray Filter Channels
*********************
---------------------

XRT uses two filter wheels to configure the imaging filter channel. Each wheel includes several filters and an open slot:

Expand All @@ -204,12 +204,6 @@ Filter Wheel 2:

Filter names in XRTpy are passed as strings like ``'Ti-poly'``.

References
**********

Velasquez, J., Murphy, N., Reeves, K. K., Slavin, J., Weber, M., & Barnes, W. (2024).
*XRTpy: A Hinode-X-Ray Telescope Python Package*. JOSS, 9(100), 6396.
https://doi.org/10.21105/joss.06396

.. _CHIANTI: https://www.chiantidatabase.org/chianti_database_history.html
.. _SolarSoft XRT Analysis Guide: https://xrt.cfa.harvard.edu/resources/documents/XAG/XAG.pdf
Expand Down
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