Convert an automatic registration into an option #1068
Merged
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Make registering a SpectrumList reader for any `data_loader` that reads Spectrum1D objects optional, per the TODO in `specutils/io/registers.py`.
tbowers7
requested review from
eteq,
rosteen,
nmearl and
keflavich
as code owners
Codecov ReportAll modified and coverable lines are covered by tests ✅
Additional details and impacted files@@ Coverage Diff @@
## main #1068 +/- ##
=======================================
Coverage 70.72% 70.72%
=======================================
Files 64 64
Lines 4485 4485
=======================================
Hits 3172 3172
Misses 1313 1313 ☔ View full report in Codecov by Sentry. |
tbowers7
added a commit
to pypeit/PypeIt
that referenced
this pull request
Jun 23, 2023
When users try to ingest a `spec1d` file into a Spectrum1D object, the current scheme ends badly with an obscure error message like: ``` OSError: Could not identify column containing the wavelength, frequency or energy ``` Because PypeIt `spec1d` files may have multiple extensions, by convention we load these into SpectrumList objects in specutils, even if there is only a single spectrum. This commit catches the case when a user tries to load a `spec1d` file into a Spectrum1D object. Previously, such an attempt ended up with specutils loading in the `spec1d` file as a tabular FITS format, then didn't know what to do about the spectral axis (leading to the above obscure error). This commit specifically includes a loader for `spec1d` files into Spectrum1D objects, but emits a sensible error message in this case rather than trying to actually load the file. As it happens, in order to properly do this, I needed to make an adjustment in specutils itself. A PR has been submitted (astropy/specutils#1068), but this commit should not be considered as a PypeIt PR until the specutils change has incorporated into an official release. At that time, the specutils optional dependency will need to have a minimum version specified. So... this commit will quietly sit in a branch until specutils makes its move. modified: pypeit/specutils/pypeit_loaders.py
|
This looks good to me, but I would call the option |
PR comment; change option to `autogenerate_spectrumlist`.
tbowers7
added a commit
to pypeit/PypeIt
that referenced
this pull request
Jul 31, 2023
When users try to ingest a `spec1d` file into a Spectrum1D object, the current scheme ends badly with an obscure error message like: ``` OSError: Could not identify column containing the wavelength, frequency or energy ``` Because PypeIt `spec1d` files may have multiple extensions, by convention we load these into SpectrumList objects in specutils, even if there is only a single spectrum. This commit catches the case when a user tries to load a `spec1d` file into a Spectrum1D object. Previously, such an attempt ended up with specutils loading in the `spec1d` file as a tabular FITS format, then didn't know what to do about the spectral axis (leading to the above obscure error). This commit specifically includes a loader for `spec1d` files into Spectrum1D objects, but emits a sensible error message in this case rather than trying to actually load the file. As it happens, in order to properly do this, I needed to make an adjustment in specutils itself. A PR has been submitted (astropy/specutils#1068), but this commit should not be considered as a PypeIt PR until the specutils change has incorporated into an official release. At that time, the specutils optional dependency will need to have a minimum version specified. So... this commit will quietly sit in a branch until specutils makes its move. modified: pypeit/specutils/pypeit_loaders.py
rosteen
approved these changes
Jul 31, 2023
rosteen
pushed a commit
to rosteen/specutils
that referenced
this pull request
Aug 15, 2023
* Convert an automatic registration into an option Make registering a SpectrumList reader for any `data_loader` that reads Spectrum1D objects optional, per the TODO in `specutils/io/registers.py`. * Option name change PR comment; change option to `autogenerate_spectrumlist`.
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Per the TODO suggestion in the code, this PR makes registering a SpectrumList reader for any
data_loaderthat reads Spectrum1D objects optional (rather than automatic) via a boolean input flag. The default behavior is identical to the existing code, but the new flag allows users to opt out in situations where such registration causes errors.