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Remove and refactor visualization references in APE 13 #106

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Sep 26, 2024
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Remove and refactor visualization references in APE 13 #106

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0f186db
initial removal of "specviz" references
weaverba137 Jun 14, 2024
038be9c
another implicit reference
weaverba137 Jun 14, 2024
17a9bf6
add some metadata
weaverba137 Jun 14, 2024
a77ce40
fix a typo
weaverba137 Jul 19, 2024
2dbcd51
mention renamed spectrum class
weaverba137 Jul 22, 2024
1eac03c
fix some typos
weaverba137 Sep 4, 2024
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64 changes: 24 additions & 40 deletions APE13.rst
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Expand Up @@ -11,14 +11,17 @@ type: Process, Standard Track

status: Accepted

revised-by:

* Benjamin Weaver - 2024 July 19 - Spectrum visualization is now out-of-scope.

Abstract
--------

The goal of this APE is to coordinate and plan the development of spectroscopic
software within the astropy project. The requirements for spectroscopic tools
include handling and reducing observations, different types of analysis, and
visualization of spectra. The goal of this APE is to provide a framework that
supporting IO on data files used in the community. The goal of this APE is to provide a framework that
different astronomy packages can use to coordinate the development of
spectroscopic tools. The idea is a set of foundational packages that can then
be extended to build other tools. As part of this coordination effort, this APE
Expand Down Expand Up @@ -108,7 +111,7 @@ The path forward
^^^^^^^^^^^^^^^^

This APE proposes a coordinated suite of packages for doing astronomical
spectroscopy in Python. It suggests a division of functionality into three
spectroscopy in Python. It suggests a division of functionality into two
packages, then specifies in detail the structure and API of the core spectral
object, `Spectrum1D`.

Expand All @@ -128,15 +131,15 @@ domain-specific classes are not defined in this APE; instead, the intent is for
`Spectrum1D` to provide a starting point for such efforts, which will then
develop as they are called for by the community.

The development outlined in this APE will consist of three packages:
The development outlined in this APE will consist of two packages:
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* `specutils <https://github.com/astropy/specutils)>`_. This will provide the
basic interface classes (including the `Spectrum1D` object), as well as
* `specutils <https://github.com/astropy/specutils>`_. This will provide the
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basic interface classes (including the `Spectrum1D` object, to be renamed `Spectrum` in specutils 2.0), as well as
*basic* analysis of spectroscopic data (which are enumerated in `Analysis
tools to be included in specutils`_ below). This package is the primary
focus of this APE.

* `specreduce`. This will provide a standard toolbox for reducing spectra,
* `specreduce <https://github.com/astropy/specreduce>`_. This will provide a standard toolbox for reducing spectra,
roughly akin to the IRAF “specred” functionality (although not necessarily
*all* of those tasks, nor in a one-to-one manner). Note that this should
*not* contain any instrument-specific code. Observatories or instruments are
Expand All @@ -145,23 +148,12 @@ The development outlined in this APE will consist of three packages:
This package will provide the tools to quickly be able to build specific
instrument pipelines.

* `specviz`. This package will provide 1D spectrum visualization capabilities,
but is scoped to be focused primarily on that, and not arbitrarily complex
spectrum visualization (e.g., data cubes). Note that, unlike the above two,
this package should *not* be considered a toolbox that other tools should be
derived from. While other packages are welcome to use it, it is meant to
provide a critical piece of functionality, while acknowledging that
visualization, GUI code, and even personal taste are variable enough that
there is room for a few other visualization packages in the ecosystem. It
will, however, have a plugin architecture that may allow users/developers to
add to it.

In addition to the packages described above, there are a wide range of more
domain-specific, experimental, or taste-specific packages that are likely to be
desired in the field of astronomical spectroscopy. These packages can be
developed as independent affiliated packages, and this APE encourages such
development. However, the intent is for such packages to not *duplicate*
behavior in the foundational three packages described above. Because of the
behavior in the foundational packages described above. Because of the
wide range of scientific use cases for spectra, it is understood that some
level of duplication between affiliated packages is expected. E.g., multiple
line-fitting packages may be reasonable because different science cases may be
Expand Down Expand Up @@ -420,29 +412,19 @@ This should *not* be taken as an exhaustive list, however. Additional
functionality that meets the above guidelines will be implemented or accepted
via PRs to `specutils` if of sufficient general interest.

The next steps: specreduce and specviz
--------------------------------------
This APE is not intended to specify the full details of the ``specviz`` and
``specreduce`` packages. They will develop separately following the
The next steps: specreduce
--------------------------
This APE is not intended to specify the full details of the
``specreduce`` package. It will develop separately following the
standard process for developing astropy packages, but this section
outlines *example* functionality expected for these packages.

``specreduce``:
outlines *example* functionality expected for this package:

* Methods for extracting a 1D spectrum from a 2D image of a dispersed spectrum, including boxcar and “optimal” extraction
* Wavelength calibration
* Removal of sky features
* Flux calibration of spectra
* Integration with (but *not* duplication of) 2D image-level reduction steps from packages like `ccdproc <https://github.com/astropy/ccdproc>`_

``specviz``:
* Display a spectrum
* Explore the spectra by zooming in on features or moving to different areas.
*
* Do analysis like line flux measurements (using algorithms provided in `specutils`) or line fitting
* Overlay spectral line lists (including redshift offsets if relevant)



Branches and pull requests
--------------------------
Expand All @@ -453,13 +435,11 @@ Implementation
--------------

`specutils <https://github.com/astropy/specutils>`_ already exists in its
github repository, and *part* of the `Spectrum1D` class in this APE has been
implemented there, but will need to be completed if this APE is accepted.
`specreduce <https://github.com/crawfordsm/specreduce>`_
also has an implementation, which can be adapted to use the framework described
here. Similarly, visualization via the `specviz
<https://github.com/spacetelescope/specviz>`_ package will do the same. Of
course, other packages for spectroscopic analysis exist, and hopefully will
github repository, and the `Spectrum1D` class in this APE has been
implemented there. Additional features are in development.
`specreduce <https://github.com/astropy/specreduce>`_
also has an implementation, which has been adapted to use the framework described
here. Of course, other packages for spectroscopic analysis exist, and hopefully will
also be adapted to this framework in due time.


Expand Down Expand Up @@ -498,3 +478,7 @@ Decision rationale
------------------
There were extensive discussions with multiple stakeholders undertaken in the process of putting together this APE and it appears as though concensus has been reached. This APE was accepted on Dec 18, 2017.

Previous versions of this APE
-----------------------------

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It might be good to briefly mention that the previous version included a vision for specvis and describe the rationale for removing it.

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Fair point, I'll try to get something added today.

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Actually, I'm going to give a bit of push-back first. This section is formatted identically to all other APEs that have a previous version. In other words, no other APE provides any discussion of the contents of the previous version. Presumably, the previous version is still readable in its entirety.

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I don't think any other revision did more than clarify. Though arguably that is the case here too. Anyway, it is no big deal, I think right now this is just ensuring the APE reflects reality, not a wish from the past, and that is fine! Happy to have this in as is too.

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Thanx. I'll leave this open in case others want to comment.

* 2017-12-12 [`DOI <https://doi.org/10.5281/zenodo.1117942>`_] [`GitHub <https://github.com/astropy/astropy-APEs/blob/b544e82ed1942045886c15acd4985ae3ed2ead6d/APE13.rst>`_]