Enable modeling of starspots with both Fleck and Starry #627

erinmmay · 2024-02-27T15:48:50Z

Exactly what the title says - Adds fleck for starspot modeling, modifies starry code to allow starspots (not recommended, very slow...). Adds a plot to show starspots for fleck. This addresses #605

taylorbell57 · 2024-03-01T19:11:27Z

@erinmmay, once this PR is ready for review, please mark it as such near the bottom of the page and request a review from Kevin and/or I.

erinmmay · 2024-05-01T19:13:48Z

Resolved conflicts and set fleck's "fast" option as the default (assumes stellar rotation is much longer than transit time and spots are stationary. user still has option to supply stellar rotation and calculate in "slow" mode). Pulling down the new version of the branch with conflicts resolved to test and then will remove "draft" status so it can be reviewed

erinmmay · 2024-05-14T17:04:24Z

I'm removing the draft status from this to expedite the process so it can be reviewed now, but I still have a couple tests to run (e.g. making sure this works with dynesty) before it should be merged

kevin218

Here is some preliminary feedback on this PR.

kevin218 · 2024-05-15T19:46:37Z

demos/JWST/S5_fit_par_template.epf

+# spotstari    90       'fixed'         90    	  1       N
+# spotrot      10       'fixed'		      10		    1		    N
+# spotnpts     100      'independent
+# spotcon0     0.9			'free'			    0		      1		    U
+# spotrad0     0.2			'free'          0    	    360     U
+# spotlat0     0			  'free'          -90    	  90      U
+# spotlon0     0			  'free'          -180    	180     U
+# spotcon1     0.1			'free'			    0		      1		    U
+# spotrad1	   0.2		  'free'          0    	    1       U
+# spotlat1	   0		    'free'          -90    	  90      U
+# spotlon1	   0			  'free'          -180    	180     U


Can you align the columns so that they are easier to read?

kevin218 · 2024-05-15T20:09:45Z

docs/source/ecf.rst

+
+   - Star Spot Parameters
+      - ``spotstari`` - The stellar inclination in degrees.
+      - ``spotrot`` - The stellar rotation rate in days. For fleck, only assign if you'd like to run in slow mode! (In slow mode the star rotates and spots move appropriately. Otherwise Eureka! will use fleck's slow mode which assumes the stellar rotation is >> transit time and spots are stationary)


"Otherwise Eureka! will use fleck's fast mode, which..."

kevin218 · 2024-05-15T20:20:09Z

src/eureka/S5_lightcurve_fitting/plots_s5.py

+            setattr(bm_params, attr, model.parameters.dict[attr][0])
+    bm_params.u = uarray
+
+    fig = plt.figure(1000, figsize=(8, 6))


I suggest using figure number 5306. The general numbering scheme is 5XXX for Stage 5, X3XX for isplots >=3, and the last two digits for the actual figure number (01 - 05 are already taken).

kevin218 · 2024-05-15T20:20:21Z

src/eureka/S5_lightcurve_fitting/plots_s5.py

+    star.plot(spotlon[:, None]*unit.deg, spotlat[:, None]*unit.deg, 
+              spotrad[:, None], star_inc*unit.deg, 
+              planet=bm_params, time=0)
+    fname = (f'figs{os.sep}fig1000_fleck_star_{fitter}')


kevin218 · 2024-05-15T20:20:53Z

src/eureka/S5_lightcurve_fitting/fitters.py

@@ -434,6 +438,10 @@ def emceefitter(lc, model, meta, log, **kwargs):
    # Plot fit
    if meta.isplots_S5 >= 1:
        plots.plot_fit(lc, model, meta, fitter='emcee')
+
+    # Plot star spots
+    if 'fleck_tr' in meta.run_myfuncs and meta.isplots_S5:


meta.isplots_S5 >= 3

kevin218 · 2024-05-15T20:20:59Z

src/eureka/S5_lightcurve_fitting/fitters.py

@@ -900,6 +908,10 @@ def dynestyfitter(lc, model, meta, log, **kwargs):
    if meta.isplots_S5 >= 1:
        plots.plot_fit(lc, model, meta, fitter='dynesty')

+    # Plot star spots
+    if 'fleck_tr' in meta.run_myfuncs and meta.isplots_S5:


meta.isplots_S5 >= 3

kevin218 · 2024-05-15T20:21:05Z

src/eureka/S5_lightcurve_fitting/fitters.py

@@ -1012,6 +1024,10 @@ def lmfitter(lc, model, meta, log, **kwargs):
    if meta.isplots_S5 >= 1:
        plots.plot_fit(lc, model, meta, fitter='lmfitter')

+    # Plot star spots
+    if 'fleck_tr' in meta.run_myfuncs and meta.isplots_S5:


meta.isplots_S5 >= 3

kevin218 · 2024-05-15T20:23:54Z

src/eureka/S5_lightcurve_fitting/s5_fit.py

@@ -647,6 +647,24 @@ def fit_channel(meta, time, flux, chan, flux_err, eventlabel, params,
                                         nints=lc_model.nints,
                                         num_planets=meta.num_planets)
        modellist.append(t_eclipse)
+    if 'fleck_tr' in meta.run_myfuncs:


Make sure to add fleck_tr as an option on line run_myfuncs in the file demos/JWST/S5_template.ecf.

kevin218 · 2024-05-16T20:39:19Z

src/eureka/S5_lightcurve_fitting/models/FleckModel.py

+            # something that should be a horrible fit
+            if not ((0 < bm_params.per) and (0 < bm_params.inc < 90) and
+                    (1 < bm_params.a) and (0 <= bm_params.ecc < 1) and
+                    (0 <= bm_params.w <= 360)):


We recently removed the constraint on omega (see BatmanModels.py). You should check for other differences in BatmanModels.py

erinmmay · 2024-05-25T18:59:34Z

addressed comments and updated FleckModel.py to use new PlanetParams class. Fully tested with emcee and dynesty.

erinmmay added 6 commits February 27, 2024 10:13

initial commit of fleck/starry starspot models

0b4fb5b

adding params to epf template, docs

8aa829d

fixing things

29c32a7

fixing things part2

c50766f

fixing things part3

6aedf18

adding fleck to yml, quick fix to fleck model

9891a0c

taylorbell57 added enhancement New feature or request LC Fit labels Mar 1, 2024

taylorbell57 added this to In progress in Stage 5: Light Curve Fitting via automation Mar 1, 2024

taylorbell57 added this to In progress in Road to v1.1 via automation Mar 1, 2024

erinmmay and others added 2 commits May 1, 2024 14:50

sets fleck's slow option as the default for faster lc calculations

2099338

Merge branch 'main' into starspots

4a32714

erinmmay marked this pull request as ready for review May 14, 2024 17:05

erinmmay requested a review from kevin218 May 14, 2024 17:05

kevin218 requested a review from taylorbell57 May 15, 2024 19:45

Stage 5: Light Curve Fitting automation moved this from In progress to Pending Review May 16, 2024

kevin218 requested changes May 16, 2024

View reviewed changes

Road to v1.1 automation moved this from In progress to Review in progress May 16, 2024

addressing comments, updating fleck_tr to use new planetparams class

040a769

addressing formatting

5bca077

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Enable modeling of starspots with both Fleck and Starry #627

Enable modeling of starspots with both Fleck and Starry #627

erinmmay commented Feb 27, 2024 •

edited

taylorbell57 commented Mar 1, 2024

erinmmay commented May 1, 2024

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edited

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erinmmay commented May 25, 2024

Enable modeling of starspots with both Fleck and Starry #627

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Enable modeling of starspots with both Fleck and Starry #627

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erinmmay commented Feb 27, 2024 • edited

taylorbell57 commented Mar 1, 2024

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erinmmay commented May 25, 2024

erinmmay commented Feb 27, 2024 •

edited

kevin218 left a comment •

edited