Modsdocs1 #2044

opkuhn · 2025-12-19T18:20:09Z

The modsdocs1 branch stems from pypeit/develop and adds a doc/tutorials/mods_howto.rst and associated figures in doc/figures/mods/

It walks the user through reduction of the lbt_mods1b_proc/dual_grating_longslit_qso and lbt_mods1r_proc/dual_grating_longslit_qso datasets, up to the telluric correction.

There were some questions about the flux calibration and telluric correction. The qso was observed at airmass 1.96 and the standard star at airmass 1.35, so the flux calibration is sensitive to methods used for treating extinction -- whether an extinction file is used or the extinction is inferred from a telluric model. Using UVIS and an extinction file seemed to provide the best match of the blue and red channel spectra, and good agreement with results from IRAF, but when the telluric correction is made with pypeit_tellfit, then the blue- and red-channel fluxes no longer match in the spectral region of overlap, so this step has not been added to the documentation.

There are still questions, but the basic setup and run could still be useful for MODS users.

kbwestfall

These docs are great! Thanks for adding this detail. I have a few minor suggestions for your consideration. The main one is to add the doc to the list of tutorials and make sure that the docs compile without any warnings. Thanks!

kbwestfall · 2026-01-05T23:12:31Z

doc/tutorials/mods_howto.rst

@@ -0,0 +1,589 @@
+.. include:: ../include/links.rst
+
+.. _mods_howto:


You should add this to the list of instrument-specific tutorials in tutorials/tutorials.rst. I.e., in that list add: LBT MODS <mods_howto>.

Also, make sure that the docs build correctly by running make htmlonly in the doc/ directory.

I added this to the list in tutorials.rst.

kbwestfall · 2026-01-05T23:16:48Z

doc/tutorials/mods_howto.rst

+flux calibration, coaddition of the extracted 1D spectra and correction of telluric 
+absorption. 
+
+There are two sets of MODS spectrograph classes: (1) the original ones (mods1b, mods1r, mods2b


Instead of, e.g., mods1b, I would use the full pypeit spectrograph names (lbt_mods1b and lbt_mods1b_proc, etc).

kbwestfall · 2026-01-05T23:34:18Z

doc/tutorials/mods_howto.rst

+
+   The proc classes work in ADUs and not electrons (the conversion gain, which is ~2 e-/ADU, is not applied), 
+   so snr_thresh = 10/sqrt(2) will find sources above 10-sigma.
+


I would add a comment here just noting that this is what the top of the pypeit file would look like with the options discussed above.

I've added the sentence: "The box below, which shows the top of the pypeit file used to reduce the sample dataset, illustrates the use of the user-defined parameters mentioned in item 3 above."

kbwestfall · 2026-01-05T23:35:57Z

doc/tutorials/mods_howto.rst

+--------------------
+
+The pipeline has been run for binned spectra which have been pre-processed by modsCCDRed.
+Please contact the developers if there are issues.


You might point people specifically to the Users Slack or to submit a GitHub issue.

I added these references/links.

kbwestfall · 2026-01-05T23:39:01Z

doc/tutorials/mods_howto.rst

+Wavelengths
+++++++++++
+
+To check the quality of the wavelength calibration, open the QA/MF_A.html file and view the Arc_1D_Fit_A_DETO1.html to insure that the lines have been identified and the RMS is low, ideally < 0.1 pixel, or run :ref:`pypeit_chk_wavecalib`.


I would point people directly to the PNG files. We have been bad about maintaining the html output files; e.g., there are many PNGs that aren't included in the html.

I replaced the reference to the MF_A.html file with one to the appropriate PNG file.

kbwestfall · 2026-01-05T23:40:49Z

doc/tutorials/mods_howto.rst

+
+.. figure:: ../figures/mods/mods1b_identify.png
+
+Remember, the default calibration is in vacuum wavelengths. The line lists provided on the `LBTO Sciops MODS webpages <https://scienceops.lbto.org/mods/>`__ have been converted to vacuum wavelengths for use by pypeit. 


You might highlight this in a .. important:: box.

I put the following in an "important" box, trying to clarify the difference between these and the standard lists already in pypeit and that these lists are used by default for MODS reductions in pypeit. Hopefully it is clear. After-the-fact, I don't think they make much difference, but it is cleaner just to use the lines which have been identified in the arc spectra.

"Remember, the default calibration is in vacuum wavelengths. The line lists provided on the LBTO Sciops MODS webpages <https://scienceops.lbto.org/mods/>__, which contain air wavelengths for lines positively identified
in MODS comparison lamp spectra, have been regenerated from NIST in vacuum wavelengths and are part of the default instrument-specific parameters for the lbt_mods#c and lbt_mods#c_proc classes in pypeit."

kbwestfall · 2026-01-05T23:44:02Z

doc/tutorials/mods_howto.rst

+
+   spec = specobjs.SpecObjs.from_fitsfile(spec1dfits)
+   plt.plot(spec[0]['BOX_WAVE'],spec[0]['BOX_COUNTS']
+   plt.plot(spec[0]['OPT_WAVE'],spec[0]['OPT_COUNTS']


You need a closing parenthesis on this line and the one above.

I fixed this.

debora-pe

Thanks for this!

Merge 'develop'

opkuhn added 2 commits December 19, 2025 10:42

first draft of mods_howto

26ae858

noted that tellfit section is still being worked on

2c7c470

kbwestfall changed the base branch from release to develop December 19, 2025 18:28

Merge branch 'develop' into modsdocs1

2d57989

kbwestfall approved these changes Jan 5, 2026

View reviewed changes

kbwestfall requested a review from debora-pe January 5, 2026 23:52

kbwestfall added this to the v2.0.0 milestone Jan 6, 2026

debora-pe approved these changes Jan 8, 2026

View reviewed changes

opkuhn added 4 commits January 10, 2026 20:16

changes suggested by KBW made

a5512d8

Merge branch 'modsdocs1' of github.com:opkuhn/PypeIt into modsdocs1

28b6cf2

Merge remote-tracking branch 'upstream/develop' into modsdocs1

6ab8c57

Merge 'develop'

minor updates to the changes in response to KBW's comments.

26848be

		@@ -0,0 +1,589 @@
		.. include:: ../include/links.rst

		.. _mods_howto:


		The proc classes work in ADUs and not electrons (the conversion gain, which is ~2 e-/ADU, is not applied),
		so snr_thresh = 10/sqrt(2) will find sources above 10-sigma.


		.. figure:: ../figures/mods/mods1b_identify.png

		Remember, the default calibration is in vacuum wavelengths. The line lists provided on the `LBTO Sciops MODS webpages <https://scienceops.lbto.org/mods/>`__ have been converted to vacuum wavelengths for use by pypeit.

Modsdocs1 #2044

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Modsdocs1 #2044

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opkuhn commented Dec 19, 2025

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