Simple Aperture Photometry: Gaussian1D fitting for radial profile by pllim · Pull Request #1409 · spacetelescope/jdaviz

pllim · 2022-06-22T19:26:07Z

Description

This pull request is to enable Gaussian1D fitting for radial profile in the Simple Aperture Photometry plugin.

(Screenshots a bit outdated, but you get the idea.)

TODO

See why multiple fits are shown.
Display fitted FWHM in GUI?
Want re-centering of raw radial profile data?
Fix mean at zero before fitting Gaussian1D. See imexamine - FWHM values in radial plot imexam#165 and fixes for #165, #238, #210, #205 imexam#241
Have Curve of Growth recenter too like Radial Profile.

Checklist for package maintainer(s)

This checklist is meant to remind the package maintainer(s) who will review this pull request of some common things to look for. This list is not exhaustive.

Are two approvals required? Branch protection rule does not check for the second approval. If a second approval is not necessary, please apply the trivial label.
Do the proposed changes actually accomplish desired goals? Also manually run the affected example notebooks, if necessary.
Do the proposed changes follow the STScI Style Guides?
Are tests added/updated as required? If so, do they follow the STScI Style Guides?
Are docs added/updated as required? If so, do they follow the STScI Style Guides?
Did the CI pass? If not, are the failures related?
Is a change log needed? If yes, is it added to CHANGES.rst?
Is a milestone set?
After merge, any internal documentations need updating (e.g., JIRA, Innerspace)? 🐱

codecov · 2022-06-22T19:39:08Z

Codecov Report

Merging #1409 (03f0e5f) into main (5d0511f) will increase coverage by 0.03%.
The diff coverage is 94.33%.

@@            Coverage Diff             @@
##             main    #1409      +/-   ##
==========================================
+ Coverage   85.13%   85.16%   +0.03%     
==========================================
  Files          91       91              
  Lines        8321     8359      +38     
==========================================
+ Hits         7084     7119      +35     
- Misses       1237     1240       +3

Impacted Files	Coverage Δ
...imviz/plugins/aper_phot_simple/aper_phot_simple.py	`92.19% <94.33%> (-0.02%)`	⬇️

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larrybradley · 2022-06-28T17:34:26Z

I don't see the fitted Gaussian1D parameters. The main use case for the fitting is to get an estimate of the FWHM of the Gaussian fit.

Also, when I use the fit on the "Raw Radial Profile" there seems to be 2 magenta lines (2 fits)?

pllim · 2022-06-28T18:02:38Z

I don't see the fitted Gaussian1D parameters

You get the fitted model via API.

So, are you saying you want the fitted FWHM to be displayed under GUI results?

pllim · 2022-06-28T18:03:14Z

2 magenta lines (2 fits)

Looks like the previous plot didn't clear properly? I'll investigate.

larrybradley · 2022-06-28T18:04:39Z

So, are you saying you want the fitted FWHM to be displayed under GUI results?

Yes. All of the fitted Gaussian parameters.

pllim · 2022-06-28T18:12:01Z

All of the fitted Gaussian parameters

x_mean would be pretty useless, no? It will be zero-ish.

larrybradley · 2022-06-28T18:44:09Z

x_mean would be pretty useless, no? It will be zero-ish.

It's not because no-recentering is happening. I think we should recenter, in which case the mean would be useless.

pllim · 2022-06-28T20:10:26Z

By re-centering, do you mean moving the Subset to new center, or just in the number crunching?

larrybradley · 2022-06-28T20:21:30Z

Number crunching, not moving the Subset. I expected the radial profile to always be centered on the source centroid. It would be very hard to manually position the Subset to be centered at the source centroid.

pllim · 2022-06-28T22:29:20Z

Re: #1409 (comment) -- turns out the data points were unsorted, not related to plot clearing. FYI.

pllim · 2022-06-28T23:16:51Z

I think I addressed most of the review comments but am waiting to hear back from @larrybradley about recentering.

pllim · 2022-06-28T23:20:02Z

                else:
                    tmp.append({'function': key, 'result': str(x)})
+            # Also display fit results
+            if fit_model is not None and isinstance(fit_model, Gaussian1D):


The isinstance check is future-proofing because it is just a matter of time before someone asks for Moffat.

pllim · 2022-06-29T18:05:32Z

@larrybradley , I think I have addressed all your comments. Please re-review. Thanks!

kecnry · 2022-06-29T18:11:46Z

+to the radial profile, the last fitted model can be obtained by as follows.
+See :ref:`astropy:astropy-modeling` on how to manipulate the model::
+
+    my_gaussian1d = imviz.app.fitted_models['phot_radial_profile']


can this conflict with anything else? We don't have the model fitting plugin for imviz, so probably won't be a problem unless we every include aperture photometry in a viz that does include model fitting, right?

What might be Cubeviz but none of that is even planned right now. Ideas welcome though. I am just trying to hook into existing machinery instead of creating even more API.

larrybradley · 2022-06-29T18:34:44Z

@pllim The radial plot titles all still say "from Subset center". Those should now say "from Source centroid".

Also, I still don't see the output of the Gaussian1D fitted parameters. Where are those?

The plots look nice.

kecnry

seems to work well, and results clear from the table as would be expected when alternating between the different plot types.

larrybradley · 2022-06-29T18:36:57Z

@pllim To be clear, the fitted Gaussian1D parameters should be in a section separate from the ApertureStats calculated values.

instead of aperture center

[ci skip] Co-authored-by: Kyle Conroy <kyleconroy@gmail.com>

and fix plot titles

like imexam PR 241

pllim · 2022-06-30T22:58:02Z

+                    gs = Gaussian1D(amplitude=y_max, mean=0, stddev=std,
+                                    fixed={'mean': True, 'amplitude': True},
+                                    bounds={'amplitude': (y_max * 0.5, y_max)})


This is hopefully now similar to spacetelescope/imexam#241 (comment) .

@larrybradley , please test this PR branch on some real data and let me know if this works as you expected. Thanks!

larrybradley

Thanks, @pllim. This looks great.

The curve of growth plot title still says "from subset center" instead of "from source centroid."

pllim · 2022-07-01T16:43:28Z

@larrybradley , I didn't realize curve of growth was in scope too. I have pushed a commit for it. Please let me know if this is what you want. Thanks.

duytnguyendtn

Ran into a bug I think? When fitting for a subset works well as expected. But when I move the subset/redefine it on another star and click "Calculate", the chart doesn't update

duytnguyendtn · 2022-07-01T18:41:16Z

Video of the above bug:

ImvizExample.-.Jupyter.Notebook.-.Brave.2022-07-01.14-39-43.mp4

pllim · 2022-07-01T18:41:31Z

Ran into a bug I think?

Yes, looks like the plugin is not listening to subset edit events. It is using cached info that is outdated. But this bug is not related to this PR, so can we open a new issue for that instead? Also, I think this plugin was written before @kecnry wrote the template mixin stuff, so I wonder if this bug will naturally go away if we refactor the plugin to use Kyle's mixin classes.

pllim · 2022-07-01T18:42:48Z

Currently, to get around the bug, if you go to the "Aperture" dropdown and reselect the subset, it will update properly.

pllim · 2022-07-01T18:43:44Z

p.p.s. When I wrote this originally, I might not have even realized you can go back and edit a subset after you finalized it.

kecnry · 2022-07-01T18:54:26Z

Agreed this bug was not introduced here, so can probably be considered out of scope and filed as a separate bug.

But now that I did some digging, I'll report my findings here for when we do get back to it: aperture photometry does use the template mixin, but then also does its own caching which is why this is breaking. Since it is also using the change to subset to update defaults for things like the background annulus, we may want to think of ways to generalize that type of situation a little better. The quick-and-dirty fix would be to just trigger _subset_selected_changed on every SubsetUpdateMessage... but there's probably significant overhead there that can be avoided.

duytnguyendtn

With the other bug I mentioned earlier being out of scope, this looks good! My only other suggestion is the ability to turn OFF the centroiding? I wonder if there are use cases we can't think of here where the user might want the raw result? Having an option to disable the centroiding might be a good option to provide? It would also clarify explicitly that centroiding is happening, beyond just the title (which some users may skim over)

pllim · 2022-07-01T18:59:10Z

My only other suggestion is the ability to turn OFF the centroiding?

I think this came up during one of the tag-ups. I am very hesitant to add more GUI to this plugin as it is already very crowded and Larry cannot think of a good reason why someone would not want centroiding.

duytnguyendtn · 2022-07-01T19:03:13Z

Perhaps I'm the minority here, in which case I'm happy to be outvoted, but I'll file my dissent here anyways :)

I'm generally a fan of providing additional functionality regardless of whether we can or cannot think of a good reason. It allows our tools to be more responsive to usecases we can't think of that are outside of our perspective; though I can understand the UI concerns, though I feel like a small crosshair icon (like for "aim assist" in FPS games) wouldn't be too obstructive in this case 🤷

pllim · 2022-07-01T19:09:31Z

Maybe centroiding toggle can be a new issue too? 😸

kecnry · 2022-07-01T19:18:01Z

I already briefly mentioned my thoughts on the switch on the call, but I'll add them here too in case we ever revisit. I think a switch serves two purposes:

allowing increased flexibility. I can imagine a case where you intentionally (maybe with the API) set the position of the subset to be off-centroid and want to see the profile as-is... although that may not be all that common. (My example was blended sources or background contamination that move the technical centroid away from the location you want).
self-documents the behavior. The presence of a switch and its descriptive text also tells the user that this re-centroiding will happen by default, without having to dig into the documentation. And I think it does so more effectively than a text blurb.

(But I'm fine with postponing that decision/implementation)

duytnguyendtn · 2022-07-01T19:21:51Z

@kecnry said it much more eloquently than i did, but yes 💯 agree

pllim · 2022-07-01T20:12:21Z

Since the original intent of this PR is approved twice, I am going to merge. I opened two follow up issues here:

Thanks for the thorough reviews!

pllim added the 💤 enhancement New feature or request label Jun 22, 2022

pllim added this to the 2.7 milestone Jun 22, 2022

github-actions Bot added documentation Explanation of code and concepts imviz labels Jun 22, 2022

pllim marked this pull request as ready for review June 22, 2022 19:44

pllim requested review from duytnguyendtn, javerbukh, kecnry, ojustino and rosteen as code owners June 22, 2022 19:44

pllim requested a review from larrybradley June 22, 2022 19:44

pllim force-pushed the fit-line-to-histogram branch from 106c6f1 to 99fd9df Compare June 28, 2022 23:15

pllim commented Jun 28, 2022

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pllim force-pushed the fit-line-to-histogram branch from 99fd9df to fac8623 Compare June 29, 2022 17:52

kecnry reviewed Jun 29, 2022

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kecnry approved these changes Jun 29, 2022

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Comment thread jdaviz/configs/imviz/plugins/aper_phot_simple/aper_phot_simple.vue Outdated

pllim and others added 5 commits June 30, 2022 18:30

Use centroid for radial profile

991455f

instead of aperture center

Future-proof Vue.js logic

3faa064

[ci skip] Co-authored-by: Kyle Conroy <kyleconroy@gmail.com>

Display fit results in its own section

a3ea64f

and fix plot titles

Update phot plugin doc

a48f801

Gaussian1D: Fix mean and bind amplitude

2da055a

like imexam PR 241

pllim force-pushed the fit-line-to-histogram branch from 5a372c7 to 2da055a Compare June 30, 2022 22:54

pllim mentioned this pull request Jun 30, 2022

fixes for #165, #238, #210, #205 spacetelescope/imexam#241

Open

pllim commented Jun 30, 2022

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larrybradley reviewed Jul 1, 2022

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Imviz phot curve of growth also from centroid

03f0e5f

duytnguyendtn reviewed Jul 1, 2022

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duytnguyendtn approved these changes Jul 1, 2022

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pllim mentioned this pull request Jul 1, 2022

Option to disable centroiding in Simple Aperture Photometry #1442

Closed

Jdaviz-Triage-Bot mentioned this pull request Jul 1, 2022

Simple Aperture Photometry: Recalculation breaks after Subset is edited #1443

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pllim merged commit 050b62d into spacetelescope:main Jul 1, 2022

pllim deleted the fit-line-to-histogram branch July 1, 2022 20:12

pllim mentioned this pull request Nov 2, 2022

large subset warnings in aperture photometry #1801

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pllim mentioned this pull request Nov 14, 2022

No more centroiding in Simple Aperture Photometry plugin #1841

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TODO

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