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Finish QR2 updates (#17)
* Add Solid Angle Pixel Map description * Add cross links * Update for QR2 * Apply feedback from bsipocz review
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documentation/index.md

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@@ -10,6 +10,8 @@ This User Guide will evolve as the SPHEREx project delivers new data products an
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SPHEREx is a NASA Astrophysics Medium Explorer mission that launched in March 2025.
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During its planned two-year mission, SPHEREx will obtain 0.75-5 micron spectroscopy over the entire sky, with deeper data in the SPHEREx Deep Fields.
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IRSA began releasing SPHEREx Quick Release 2 (QR2) data on a weekly basis in October 2025.
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QR2 features substantially improved calibrations and supersedes QR1.
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SPHEREx data will be used to:
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* **constrain the physics of inflation** by measuring its imprints on the three-dimensional large-scale distribution of matter,

documentation/spherex_data_access.md

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(data-access)=
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# SPHEREx Data Access
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IRSA serves SPHEREx data from two locations: (1) on premises at IPAC; and (2) on the cloud via Amazon Web Services (AWS).
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* **Browsable Directories:** SPHEREx on-premises data products are laid out in directories that can be navigated with standard web browsers.
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These data products are mirrored on AWS.
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* **Application Program Interfaces:** IRSA provides program-friendly Application Program Interfaces (APIs) to access SPHEREx Spectral Image data.
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The on-prem and cloud-hosted Quick Release Spectral Images that have been released thus far are accessible via the [Simple Image Access V2 protocol](https://ivoa.net/documents/SIA/20151223/) defined by the International Virtual Observatory Alliance ([IVOA](https://ivoa.net)).
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The on-prem and cloud-hosted Quick Release 2 Spectral Images that have been released thus far are accessible via the [Simple Image Access V2 protocol](https://ivoa.net/documents/SIA/20151223/) defined by the International Virtual Observatory Alliance ([IVOA](https://ivoa.net)).
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Cutouts of the Spectral Image data held on-prem are available via IRSA's Cutout Service.
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* **Python Packages:** SPHEREx data at IRSA are accessible via the Python packages [pyvo](https://pyvo.readthedocs.io/en/latest/) and [astroquery](https://astroquery.readthedocs.io/en/latest/ipac/irsa/irsa.html).
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* **SPHEREx Data Explorer:** IRSA provides a web-based Graphical User Interface (GUI) that makes it easy to search for, visualize, and download SPHEREx data.
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## Browsable Directories
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SPHEREx on-prem data products are laid out in directories that can be navigated with standard web browsers.
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SPHEREx data products are laid out in directories that can be navigated with standard web browsers.
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This is convenient for users to get a quick sense of the types of data products that are available, to quickly download some examples by clicking through the directory tree, and to script bulk downloads using `wget` or `curl`.
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The root of the SPHEREx data quick release data directories is:
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https://irsa.ipac.caltech.edu/ibe/data/spherex/qr
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The root of the SPHEREx QR2 on-premises data directories is: [https://irsa.ipac.caltech.edu/ibe/data/spherex/qr2](https://irsa.ipac.caltech.edu/ibe/data/spherex/qr2).
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For QR1, replace '/qr2' with '/qr'.
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All of the data products are also available on the cloud via AWS.
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Please see our [instructions for accessing on-cloud SPHEREx data](https://irsa.ipac.caltech.edu/cloud_access/#spherex).
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:::{note}
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QR1 is superseded by QR2.
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The QR1 files will be available through January 2026 for reference.
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:::
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The public data products are organized into subdirectories based on the following organizational scheme:
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* **Absolute Gain Matrix:** `abs_gain_matrix/cal-agm-v[Version]-[Processing Date]/[Detector]/`
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* **Exposure-Averaged Point Spread Functions (PSFs):** `average_psf/cal-psf-v[Version]-[Processing Date]/[Detector]/`
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* **Dark Current:** `dark/cal-drk-v[Version]-[Processing Date]/[Detector]/`
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* **Nonfunctional Pixels:** `nonfunc/base-[Processing Date]/[Detector]/`
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* **Nonlinearity Parameters:** `nonlinear_pars/base-[Processing Date]/[Detector]/`
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* **Read Noise Parameters:** `readnoise_pars/base-[Processing Date]/[Detector]/`
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* **Solid Angle Pixel Map:** `solid_angle_pixel_map/cal-sapm-v[Version]-[Processing Date]/`
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* **Spectral WCS:** `spectral_wcs/base-[Processing Date]/[Detector]/`
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* **Solid Angle Pixel Map:** `solid_angle_pixel_map/cal-sapm-v[Version]-[Processing Date]/[Detector]/`
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* **Spectral WCS:** `spectral_wcs/cal-wcs-v[Version]-[Processing Date]/[Detector]/` (QR2) or `spectral_wcs/base-[Processing Date]/[Detector]/` (QR1)
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The content of each subdirectory is described in greater detail in the Data Products section of this user guide and in the [SPHEREx Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/SPHEREx_Expsupp_QR.pdf).
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All of the data products listed above are also available on the cloud via AWS.
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Please see our [instructions for accesssing cloud-hosted SPHEREx data](https://irsa.ipac.caltech.edu/cloud_access/).
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The content of each subdirectory and the filename formats are described in greater detail in the {ref}`Data Products <data-products>` section of this user guide and in the [SPHEREx Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/SPHEREx_Expsupp_QR.pdf).
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## Application Program Interfaces (APIs)
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:::{note}
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SPHEREx data are ingested on a weekly basis.
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Due to the nature of the ingestion process, new SPHEREx data will first be available in the browsable directories and in the SPHEREx Data Explorer GUI.
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Availability via SIA2 and Python libraries like Astroquery and PyVO will lag on the order of a day.
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Due to the nature of the ingestion process, new SPHEREx data will first be available in the browsable directories, the SPHEREx Data Explorer GUI, and certain TAP queries (see the [cutouts notebook](https://caltech-ipac.github.io/irsa-tutorials/spherex-cutouts/) for a TAP example).
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Availability via SIA2 will lag on the order of a day.
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IRSA's generic SIA2 endpoint is:
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Users must add a `COLLECTION` parameter to this endpoint to specify which dataset to search.
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There are three SPHEREx-related SIA2 collections:
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* SPHEREx Quick Release Spectral Image MEFs that are part of the SPHEREx **Wide Survey** can be accessed with: `COLLECTION=spherex_qr`.
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Use this collection if you are interested in more uniform coverage across the entire sky and want to ignore the additional coverage in the deep fields.
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* SPHEREx QR2 Spectral Image MEFs that are part of the SPHEREx **Wide Survey** can be accessed with: `COLLECTION=spherex_qr2`.
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Use this collection if you are interested in more uniform coverage across the entire sky and want to ignore the additional coverage in the deep fields.
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* SPHEREx Quick Release Spectral Image MEFs that are part of the SPHEREx **Deep Survey** can be accessed with: `COLLECTION=spherex_qr_deep`.
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* SPHEREx QR2 Spectral Image MEFs that are part of the SPHEREx **Deep Survey** can be accessed with: `COLLECTION=spherex_qr2_deep`.
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* SPHEREx Quick Release **Calibration files** can be accessed with: `COLLECTION=spherex_qr_cal`.
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* SPHEREx QR2 **Calibration files** can be accessed with: `COLLECTION=spherex_qr2_cal`.
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You can use `wget` or `curl` to submit SIA2 queries from the command line.
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For example:
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* `wget -O example1.html "https://irsa.ipac.caltech.edu/SIA?COLLECTION=spherex_qr&POS=circle+127.69444+-39.17760+0.01&RESPONSEFORMAT=HTML"`
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* `wget -O example1.html "https://irsa.ipac.caltech.edu/SIA?COLLECTION=spherex_qr2&POS=circle+127.69444+-39.17760+0.01&RESPONSEFORMAT=HTML"`
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See the section on Python packages to learn how to use Python wrappers around IRSA’s SIA2 service.
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(access-spectral-image-cutouts)=
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### Cutouts of SPHEREx Spectral Image MEFs
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If you have identified the access URL for an on-premises Spectral Image MEF using SIA2 as described above, you can request a cutout of this MEF by appending a query string containing the center and size parameters. The parameters are described in more detail here:
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`https://irsa.ipac.caltech.edu/ibe/cutouts.html`
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If you have identified the access URL for an on-premises Spectral Image MEF using SIA2 as described above, you can request a cutout of this MEF by appending a query string containing the center and size parameters.
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The parameters are described in more detail at [https://irsa.ipac.caltech.edu/ibe/cutouts.html](https://irsa.ipac.caltech.edu/ibe/cutouts.html).
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**Example:**
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`curl -o cutout.fits "https://irsa.ipac.caltech.edu/ibe/data/spherex/qr/level2/2025W19_2B/l2b-v11-2025-163/3/level2_2025W19_2B_0073_2D3_spx_l2b-v11-2025-163.fits?center=156.09328159,-41.64466331&size=0.1"`
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`curl -o cutout.fits "https://irsa.ipac.caltech.edu/ibe/data/spherex/qr2/level2/2025W19_2B/l2b-v20-2025-247/3/level2_2025W19_2B_0073_2D3_spx_l2b-v20-2025-247.fits?center=156.09328159,-41.64466331&size=0.1"`
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This cutout service is also invoked by the SPHEREx Data Collection Explorer Spectral Image Search when users select the cutout option upon download.
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This cutout service can also be invoked via Python, as illustrated in the Python Tutorial notebook titled [Download a collection of SPHEREx Spectral Image cutouts as a multi-extension FITS file](https://caltech-ipac.github.io/irsa-tutorials/spherex-cutouts/).
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Information on how to work with the PSF extension in these cutouts is documented in the [Data Products section](https://caltech-ipac.github.io/spherex-archive-documentation/spherex-data-products#cutouts-of-spectral-image-mefs) of this User Guide and demonstrated in the Python Tutorial notebook titled [Understanding and Extracting the PSF Extension in a SPHEREx Cutout](https://caltech-ipac.github.io/irsa-tutorials/spherex-psf/).
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Information on how to work with the PSF extension in these cutouts is documented in the {ref}`products-spectral-image-cutouts` of this User Guide and demonstrated in the Python Tutorial notebook titled [Understanding and Extracting the PSF Extension in a SPHEREx Cutout](https://caltech-ipac.github.io/irsa-tutorials/spherex-psf/).
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## Python packages: PyVO & Astroquery
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The notebook titled [Download a collection of SPHEREx Spectral Image cutouts as a multi-extension FITS file](https://caltech-ipac.github.io/irsa-tutorials/spherex-cutouts/#id-5-query-irsa-for-a-list-of-cutouts-that-satisfy-the-criteria-specified-above) demonstrates how to use the PyVO library to execute an IVOA Table Access Protocol (TAP) query for SPHEREx spectral images that cover the specified coordinates and match the specified bandpass.
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Due to the nature of the ingestion process, new SPHEREx data will first be available in the browsable directories and in the SPHEREx Data Explorer GUI.
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Availability via SIA2 and Python libraries like Astroquery and PyVO will lag on the order of a day.
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Due to the nature of the ingestion process, new SPHEREx data will first be available in the browsable directories, the SPHEREx Data Explorer GUI, and certain TAP queries (see the [cutouts notebook](https://caltech-ipac.github.io/irsa-tutorials/spherex-cutouts/) for a TAP example).
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Availability via SIA2 will lag on the order of a day.
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## SPHEREx Data Explorer Web Application

documentation/spherex_data_products.md

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(data-products)=
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# SPHEREx Data Products
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IRSA began releasing SPHEREx Spectral Image data on a weekly basis in July 2025 (Quick Release 1; QR1).
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In October 2025, IRSA began distributing SPHEREx Spectral Image data processed with substantially improved calibrations.
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This new processing, referred to as QR2, includes reprocessed versions of all Spectral Image data acquired since the start of the mission.
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Future quick releases will also use the QR2 pipeline.
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IRSA will continue to provide access to QR1 data for reference.
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IRSA will continue to provide access to QR1 data through January 2026 for reference.
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However, QR2 supersedes QR1 and will be the default returned in the SPHEREx Data Explorer and by all IRSA program-friendly APIs.
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## Main Science Data Product: Spectral Image Multi-Extension FITS Files (MEF)
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The main Quick Release data product is the Level 2 Spectral Image MEF,as described in Section 2.1 of the [Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/SPHEREx_Expsupp_QR.pdf).
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The main Quick Release data product is the Level 2 Spectral Image MEF, as described in Section 2.1 of the [Explanatory Supplement](https://irsa.ipac.caltech.edu/data/SPHEREx/docs/SPHEREx_Expsupp_QR.pdf).
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There are 6 Spectral MEFs (one for each detector) for each sky pointing.
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*Filename Format:*
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- `level2_[Observation ID]D[Detector]_spx_l2b_v[Version]_[Processing Date].fits`
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(products-spectral-image-cutouts)=
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## Cutouts of Spectral Image MEFs
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IRSA's Cutout Service provides spatial subsets of the SPHEREx Spectral Image MEFs.
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Information on how to use the Cutout Service is provided in the [Data Access](https://caltech-ipac.github.io/spherex-archive-documentation/spherex-data-access#cutouts-of-spherex-spectral-image-mefs) section of this User Guide.
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Information on how to use the Cutout Service is provided in the {ref}`access-spectral-image-cutouts` section of this User Guide.
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The cutout MEFs returned from this service contain the same HDUs as the original Spectral Images (IMAGE, FLAGS, VARIANCE, ZODI, PSF, WCS-WAVE). However, the IMAGE, FLAGS, VARIANCE, AND ZODI HDUs have been modified to include only those pixels within the specified cutout size.
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The spatially-varying PSF is represented as an image cube with 121 planes.
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Each plane is a 101x101 pixel image representing a PSF for a different region of the detector. Users interested in performing photometry on a cutout using the information in the cutout PSF HDU will need to understand how to find the most applicable PSF cube plane for each pixel in the cutout.
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The basic steps are described below, and a [Python notebook tutorial](https://caltech-ipac.github.io/irsa-tutorials/) is provided to help users get started with a simple implementation.
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The basic steps are described below, and a [Python notebook tutorial](https://caltech-ipac.github.io/irsa-tutorials/spherex-psf/) is provided to help users get started with a simple implementation.
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1. Determine the 0-based pixel coordinates of the position of interest in the IMAGE HDU of the cutout.
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2. Determine the 0-based pixel coordinates of the position of interest in the IMAGE HDU of the original Spectral Image.
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```
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xpix_orig = 1 + xpix_cutout - CRPIX1A
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```
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xpix_orig = 1 + xpix_cutout - CRPIX1A
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ypix_orig = 1 + ypix_cutout - CRPIX2A
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```
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## Additional Product: Solid Angle Pixel Map
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The Solid Angle Pixel Map products are ~16 MB FITS image files (one per detector) with dimensions 2,040 x 2,040.
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Pixel values measure the solid angle in units of squared arcsec.
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*Filename Format:*
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- `solid_angle_pixel_map_D[Detector]_spx_cal-sapm-v[Version]-[Processing Date].fits`
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*Example:*
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- `solid_angle_pixel_map_D4_spx_cal-sapm-v2-2025-164.fits`
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## Additional Product: Spectral WCS
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- QR2: `spectral_wcs_D[Detector]_spx_cal-wcs-v[Version]-[Processing Date].fits`
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- QR1: `spectral_wcs_D[Detector]_spx_base-[Processing Date].fits`
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- QR2: `spectral_wcs_D1_spx_cal-wcs-v4-2025-254.fits`
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- QR1: `spectral_wcs_D1_spx_base-2025-158.fits`

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