Merge dev with main branch to add back in stellar variability and EXOTIC fixes #1244

rzellem · 2024-02-02T18:45:32Z

No description provided.

Closes #1229

…iable star. Closes 1164

… even if they don't match the filter of the observation if needed. Also, some QOL changes.

…etting correctly predicted results, but will continue comparing this version and the previous version on main 3.3.0.

…an floats.

…-enter comp stars and check for variability again. Closes #1094

…e results.

…s. Not entirely complete. Organized some code a bit for clarity.

…ernally.

…code.

…ng warning font if a variable star is detected as one of the user-entered comp stars.

Issue 1235: Changing fitting prior from a/Rs to inc

…so, fixed bug regarding how time is accessed from residual results.

…rtions of OOT data being masked, causing multiple sections to be appear.

… variability code. Also, reorganizing for clarity.

Issue 1229: Bug for removing variable stars

Issue 1164: Printing variable star name and coordinates

Issue 1240, 1094, 1067: Bringing back AID Uploads

jpl-jengelke · 2024-02-07T01:54:12Z

exotic/exotic.py

-def vsp_query(file, axis, obs_filter, img_scale, maglimit=14):
-    stars_count = 0
-    comp_stars = {}
+def vsp_query(file, axis, obs_filter, img_scale, user_comp_stars, maglimit=14):


Adding an arg here breaks the API. We may want to up the version by a major number (or to mid-minor, e.g. 3.5.x? to indicate that) or add it to the end of the method arguments.

Done in PR #1248

jpl-jengelke · 2024-02-07T01:56:02Z

exotic/exotic.py

            return True
        return False
    except Exception:
        return False


+def check_for_variable_stars(ra_wcs, dec_wcs, comp_ra_dec, comp_stars):
+    for i, comp_star in enumerate(comp_stars[:]):
+        ra = ra_wcs[int(comp_star[1])][int(comp_star[0])]


If those values don't exist then this method will throw an index exception. Are these exceptions handled by calling methods?

Point: defensive programming

jpl-jengelke · 2024-02-07T01:58:46Z

exotic/exotic.py

-def stellar_variability(ref_flux, lmfit, times, comp_stars, id, vsp_comp_stars, vsp_ind, best_comp, save, s_name):
-    ref_comp = {}
-    idx_list, vsp_params = [], []
+def stellar_variability(fit_lc_refs, fit_lc_best, comp_stars, vsp_comp_stars, vsp_ind, best_comp, save, s_name):


Should there be exception handling here? This comment would apply to other new methods, also.

Done in PR #1248

jpl-jengelke · 2024-02-07T01:59:59Z

exotic/exotic.py

@@ -1566,7 +1572,7 @@ def realTimeReduce(i, target_name, p_dict, info_dict, ax):
    ax.plot(timeList, norm_flux, 'bo')


-def fit_lightcurve(times, tFlux, cFlux, airmass, ld, pDict):
+def fit_lightcurve(times, jd_times, tFlux, cFlux, airmass, ld, pDict):


similar comment here re method signature. In this instance it could possibly impact CITISENS as I think this method is called. @pearsonkyle @tamimfatahi Comments?

Will at it to the end to resolve this issue. CITISENS won't have any impact if so.

Done in PR #1248

exotic/exotic.py

exotic/inputs.py

jpl-jengelke · 2024-02-07T02:16:38Z

exotic/inputs.py

@@ -507,8 +507,9 @@ def comparison_star_coords(comp_stars, rt_bool):
            all(isinstance(star, list) for star in comp_stars):
        comp_stars = [star for star in comp_stars if star != []]
    elif isinstance(comp_stars, str) and any(str.isdigit(x) for x in comp_stars):
-        comp_stars = ' '.join(re.sub('\D', ' ', comp_stars).split()).split(' ')
-        comp_stars = [[int(comp_stars[i]), int(comp_stars[i+1])] for i in range(0, len(comp_stars), 2)]
+        comp_stars = re.findall(r"[-+]?(?:\d*\.*\d+)", comp_stars)


In the non-capturing group, it seems to allow '.'. I was wondering if it was intentional to capture a group starting with a decimal. (Maybe \d+ or \d{1,3}?)

I think this may be a little safer: '\d*.?\d+'. (limits to single decimal or none)

Done in PR #1248

exotic/output_files.py

jpl-jengelke · 2024-02-07T02:19:59Z

exotic/output_files.py

-class VSPOutputFiles:
-    def __init__(self, fit, p_dict, i_dict, vsp_params):
+class AIDOutputFiles:
+    def __init__(self, fit, p_dict, i_dict, auid, chart_id, vsp_params):


Method signature changes ...

Name change sounds appropriate. Options are to increase major version but that's a bit dramatic. If we version up to 3.5.0 then it indicates itself a semi-major change. So, set version up to 3.5.0.

Done in PR #1248

rzellem · 2024-03-21T18:56:44Z

@jpl-jengelke and @tamimfatahi - please let me know when you're ready for me to approve this PR

…tries, updated linear fitter on how it checks for given labels, modified exotic.py for to take into account API handling. Version bump to 3.5.0 to indicate minor/major release of method signature changes

rzellem · 2024-03-26T00:20:38Z

@jpl-jengelke and @tamimfatahi - please let me know when you're ready for me to approve this PR

(astropy already supports, so just need extension)

Add support for fpack based extensions

…ssue_1240

Solving develop branch issues

tamimfatahi and others added 30 commits December 1, 2023 13:55

Replacing a/Rs with inc as prior for fitting.

e0a38b3

Changed variable name for cohesiveness. Closes #1235

29cb874

Duplicated list to avoid errors when removing variable stars from list.

a861437

Closes #1229

Printing star name as well as coordinates if VSX deems it to be a var…

d331fff

…iable star. Closes 1164

Redoing logic for VSP api so that we can always grab comparison stars…

a6ee0a0

… even if they don't match the filter of the observation if needed. Also, some QOL changes.

Committing changes to reorganize logic for the jd times change. Not g…

ba42bf9

…etting correctly predicted results, but will continue comparing this version and the previous version on main 3.3.0.

Changing plot time units from BJD_TDB to JD

33afa68

Making the entered coordinates for the target stars be ints rather th…

bc45ebc

…an floats.

Fixing bug that when no comp stars are left, we prompt the user to re…

362e237

…-enter comp stars and check for variability again. Closes #1094

Replacing key of transit section with airmass instead.

2a1f465

saving current correct progress for mag calculations

f784952

Target magnitude calculations are in tolerance of error, verifying th…

b1ea617

…e results.

Updating variable name for clarity.

2a03159

Adding in partial changes to handle data that consists of OOT portion…

c9326d5

…s. Not entirely complete. Organized some code a bit for clarity.

Reorganizing photometric routine. Still some coding left to organize.

24c1c62

Fixing rest of organization for photometric routine.

d0956d7

Fixing errors and organizing a bit more.

6a7fe9c

Account for JD times when fitting lightcurve due to masks created int…

07c699f

…ernally.

Made JD times optional in lc_fitter and reorganized post-photometric …

184f2c6

…code.

renaming time conversion function

6a5e628

Fixing OOT bug and renamed variables for clarity.

b4a6720

Removing dependencies on multiple variables such as jd_times and addi…

788999a

…ng warning font if a variable star is detected as one of the user-entered comp stars.

Merge pull request #1236 from rzellem/issue_1235

dbb1533

Issue 1235: Changing fitting prior from a/Rs to inc

Fixed output file for AID to reference dictionary for filter type. Al…

f881612

…so, fixed bug regarding how time is accessed from residual results.

Merge branch 'develop' into issue_1229

4a0598b

Fixing bug that causes more than two magnitude calculations due to po…

3a24089

…rtions of OOT data being masked, causing multiple sections to be appear.

Fixing error regarding truncating data from reference star in stellar…

ba2d3fe

… variability code. Also, reorganizing for clarity.

Merge pull request #1237 from rzellem/issue_1229

64d5247

Issue 1229: Bug for removing variable stars

Merge branch 'develop' into issue_1164

5ef1080

Merge pull request #1238 from rzellem/issue_1164

c356a89

Issue 1164: Printing variable star name and coordinates

tamimfatahi and others added 4 commits January 22, 2024 15:26

Fixing target and comp star flux plots.

0e6b038

Check if if numpy array is None bug

c9184d9

Removing second labels incorrect check for None on numpy array bug,

cc5842f

Merge pull request #1242 from rzellem/issue_1240

e27ef87

Issue 1240, 1094, 1067: Bringing back AID Uploads

rzellem requested review from pearsonkyle, tamimfatahi and jpl-jengelke February 2, 2024 18:45

rzellem assigned tamimfatahi Feb 2, 2024

tamimfatahi previously approved these changes Feb 2, 2024

View reviewed changes

jpl-jengelke requested changes Feb 7, 2024

View reviewed changes

jpl-jengelke changed the title ~~Merge dev with main branch to add back in stellar variability and EXOTIC fixes~~ DRAFT Merge dev with main branch to add back in stellar variability and EXOTIC fixes Mar 21, 2024

jpl-jengelke marked this pull request as draft March 21, 2024 05:38

tamimfatahi added 2 commits March 22, 2024 12:08

Merge branch 'main' into issue_1240

ada115b

Changed regular expression for both the target and comparison star en…

3e9da11

…tries, updated linear fitter on how it checks for given labels, modified exotic.py for to take into account API handling. Version bump to 3.5.0 to indicate minor/major release of method signature changes

tamimfatahi and others added 4 commits March 26, 2024 07:55

implementing exception handling to stellar variability code

634d337

Updating regular expression

80080ba

Add support for fpack based extensions

00c974d

(astropy already supports, so just need extension)

Merge pull request #1251 from mikeprimm/addFZ

aa13f7d

Add support for fpack based extensions

rzellem dismissed tamimfatahi’s stale review via aa13f7d April 4, 2024 22:19

pearsonkyle and others added 6 commits April 10, 2024 14:59

updates to joint fitter for circular orbit

d7c4af9

Merge branch 'issue_1240' of https://github.com/rzellem/EXOTIC into i…

9e59b09

…ssue_1240

Adding legend to RV plot

fcfa4d3

changed default location of legend from upper left to best

932a43f

Changed output of transit duration's sig figs

774050f

Merge pull request #1248 from rzellem/issue_1240

9782776

Solving develop branch issues

tamimfatahi marked this pull request as ready for review April 25, 2024 20:19

tamimfatahi changed the title ~~DRAFT Merge dev with main branch to add back in stellar variability and EXOTIC fixes~~ Merge dev with main branch to add back in stellar variability and EXOTIC fixes May 16, 2024

tamimfatahi mentioned this pull request May 16, 2024

Fix for AAVSO comp additions - particularly when one matches target star #1253

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Merge dev with main branch to add back in stellar variability and EXOTIC fixes #1244

Merge dev with main branch to add back in stellar variability and EXOTIC fixes #1244

rzellem commented Feb 2, 2024

jpl-jengelke Feb 7, 2024 •

edited

tamimfatahi Mar 26, 2024

jpl-jengelke Feb 7, 2024

jpl-jengelke Mar 21, 2024

jpl-jengelke Feb 7, 2024

tamimfatahi Mar 26, 2024

jpl-jengelke Feb 7, 2024

tamimfatahi Mar 21, 2024

tamimfatahi Mar 26, 2024

jpl-jengelke Feb 7, 2024

jpl-jengelke Mar 21, 2024 •

edited

tamimfatahi Mar 26, 2024

jpl-jengelke Feb 7, 2024

jpl-jengelke Mar 21, 2024

tamimfatahi Mar 26, 2024

rzellem commented Mar 21, 2024

rzellem commented Mar 26, 2024

Merge dev with main branch to add back in stellar variability and EXOTIC fixes #1244

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Merge dev with main branch to add back in stellar variability and EXOTIC fixes #1244

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rzellem commented Feb 2, 2024

jpl-jengelke Feb 7, 2024 • edited

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jpl-jengelke Mar 21, 2024 • edited

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rzellem commented Mar 21, 2024

rzellem commented Mar 26, 2024

jpl-jengelke Feb 7, 2024 •

edited

jpl-jengelke Mar 21, 2024 •

edited