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kevin218 / Eureka

Eureka! is a data reduction and analysis pipeline intended for time-series observations with JWST.
https://eurekadocs.readthedocs.io/
MIT License
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[Bug]: Minor issue: add exotic-ld data download to quick start documentation #407

Closed MartianColonist closed 2 years ago

MartianColonist commented 2 years ago

FAQ check

Instrument

Light curve fitting (Stages 4-6)

What happened?

Following the quick start guide, Eureka! fails at Stage 4 due to missing exotic-ld 3D stellar grid data.

A quick fix would be to add an instruction to download these data (https://zenodo.org/record/6344946#.YtWpcNLMKEB) and modify 'exotic_ld_direc' in 'S4_wasp39b.ecf' to point to the folder.

I also had to do two more steps to get Stages 5 and 6 to work:

  1. In 'exotic_ld_direc/Sensitivity_files', I renamed 'JWST_NIRSpec_prism_throughput.csv' -> 'JWST_NIRSpec_Prism_throughput.csv'.
  2. In 'S5_fit_par_wasp39b.epf', I changed 'limb_dark' from 'kipping2013' -> 'quadratic'.

Then everything ran perfectly. Thanks for the great code!

Error traceback output

Starting Stage 4: Generate Light Curves

Input directory: /home/ryanmacdonald/code/Eureka/DataAnalysis/JWST/MyFirstEureka/Stage3/S3_2022-07-18_wasp39b_run1/ap6_bg7/ Output directory: /home/ryanmacdonald/code/Eureka/DataAnalysis/JWST/MyFirstEureka/Stage4/S4_2022-07-18_wasp39b_run1/ap6_bg7/ Copying S4 control file Loading S3 save file: /home/ryanmacdonald/code/Eureka/DataAnalysis/JWST/MyFirstEureka/Stage3/S3_2022-07-18_wasp39b_run1/ap6_bg7/S3_wasp39b_ap6_bg7_SpecData.h5 Finished loading parameters from /home/ryanmacdonald/code/Eureka/DataAnalysis/JWST/MyFirstEureka/Stage3/S3_2022-07-18_wasp39b_run1/ap6_bg7/S3_wasp39b_ap6_bg7_SpecData.h5 Stage 4 MAD = 5684.28 ppm Generating light curves Bandpass 0 = 1.500 - 3.000 MAD = 1531 ppm Bandpass 1 = 3.000 - 4.500 MAD = 1323 ppm Generating white-light light curve White-light Bandpass = 1.500 - 4.500 MAD = 1322 ppm Generating limb-darkening coefficients... Traceback (most recent call last): File "/home/ryanmacdonald/anaconda3/envs/eureka/lib/python3.9/site-packages/exotic_ld/ld_computation.py", line 195, in _match_3d_stellar_model sav = readsav(os.path.join(stellar_data_path, load_file)) File "/home/ryanmacdonald/anaconda3/envs/eureka/lib/python3.9/site-packages/scipy/io/_idl.py", line 738, in readsav f = open(file_name, 'rb') FileNotFoundError: [Errno 2] No such file or directory: '/home/User/exotic-ld_data/3DGrid/mmu_t60g40m00v05.flx'

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/ryanmacdonald/code/Eureka/demos/WASP-39b_DC/run_eureka.py", line 30, in s4_spec, s4_lc, s4_meta = s4.genlc(eventlabel, ecf_path=ecf_path, File "/home/ryanmacdonald/code/Eureka/src/eureka/S4_generate_lightcurves/s4_genLC.py", line 415, in genlc generate_LD.exotic_ld(meta, spec) File "/home/ryanmacdonald/code/Eureka/src/eureka/S4_generate_lightcurves/generate_LD.py", line 50, in exotic_ld sld = StellarLimbDarkening(meta.metallicity, meta.teff, meta.logg, File "/home/ryanmacdonald/anaconda3/envs/eureka/lib/python3.9/site-packages/exotic_ld/ld_computation.py", line 74, in init self._match_3d_stellar_model() File "/home/ryanmacdonald/anaconda3/envs/eureka/lib/python3.9/site-packages/exotic_ld/ld_computation.py", line 197, in _match_3d_stellar_model raise FileNotFoundError( FileNotFoundError: File mmu_t60g40m00v05.flx, corresponding to M_H=0.0, Teff=6000, and logg=4.0 does not exist in the stellar models. Please try a different combination of stellar parameters.

What operating system are you using?

Ubuntu 20.04

What version of Python are you running?

Python 3.9.7

What Python packages do you have installed?

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
alabaster 0.7.12 pypi_0 pypi asdf 2.12.0 pypi_0 pypi asdf-astropy 0.2.1 pypi_0 pypi asdf-coordinates-schemas 0.1.0 pypi_0 pypi asdf-standard 1.0.2 pypi_0 pypi asdf-transform-schemas 0.2.2 pypi_0 pypi asdf-wcs-schemas 0.1.1 pypi_0 pypi asteval 0.9.27 pypi_0 pypi astraeus 0.2 pypi_0 pypi astropy 5.1 pypi_0 pypi astropy-healpix 0.6 pypi_0 pypi astroquery 0.4.6 pypi_0 pypi astroscrappy 1.1.0 pypi_0 pypi asttokens 2.0.5 pypi_0 pypi attrs 21.4.0 pypi_0 pypi babel 2.10.3 pypi_0 pypi backcall 0.2.0 pypi_0 pypi batman-package 2.4.9 pypi_0 pypi bayesicfitting 3.0.1 pypi_0 pypi beautifulsoup4 4.11.1 pypi_0 pypi bokeh 2.4.3 pypi_0 pypi bottleneck 1.3.5 pypi_0 pypi ca-certificates 2022.4.26 h06a4308_0
ccdproc 2.3.1 pypi_0 pypi celerite 0.4.2 pypi_0 pypi certifi 2022.6.15 py39h06a4308_0
cffi 1.15.1 pypi_0 pypi cftime 1.6.1 pypi_0 pypi charset-normalizer 2.1.0 pypi_0 pypi cloudpickle 2.1.0 pypi_0 pypi corner 2.2.1 pypi_0 pypi crds 11.16.5 pypi_0 pypi cryptography 37.0.4 pypi_0 pypi cycler 0.11.0 pypi_0 pypi cython 0.29.30 pypi_0 pypi dask 2022.6.0 pypi_0 pypi decorator 5.1.1 pypi_0 pypi docutils 0.18.1 pypi_0 pypi drizzle 1.13.4 pypi_0 pypi dynesty 1.2.3 pypi_0 pypi emcee 3.1.2 pypi_0 pypi eureka 0.3 dev_0 executing 0.8.3 pypi_0 pypi exotic-ld 2.0.0 pypi_0 pypi filelock 3.7.1 pypi_0 pypi fonttools 4.34.4 pypi_0 pypi fsspec 2022.5.0 pypi_0 pypi future 0.18.2 pypi_0 pypi george 0.4.0 pypi_0 pypi gwcs 0.18.1 pypi_0 pypi h5netcdf 1.0.1 pypi_0 pypi h5py 3.1.0 pypi_0 pypi html5lib 1.1 pypi_0 pypi idna 3.3 pypi_0 pypi imageio 2.19.5 pypi_0 pypi imagesize 1.4.1 pypi_0 pypi importlib-metadata 4.12.0 pypi_0 pypi iniconfig 1.1.1 pypi_0 pypi ipython 8.4.0 pypi_0 pypi jedi 0.18.1 pypi_0 pypi jeepney 0.8.0 pypi_0 pypi jinja2 3.1.2 pypi_0 pypi jmespath 1.0.1 pypi_0 pypi jsonschema 4.7.2 pypi_0 pypi jwst 1.6.0 pypi_0 pypi keyring 23.7.0 pypi_0 pypi kiwisolver 1.4.4 pypi_0 pypi ld_impl_linux-64 2.38 h1181459_1
libffi 3.3 he6710b0_2
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
lmfit 1.0.3 pypi_0 pypi locket 1.0.0 pypi_0 pypi lxml 4.9.1 pypi_0 pypi markupsafe 2.1.1 pypi_0 pypi matplotlib 3.5.2 pypi_0 pypi matplotlib-inline 0.1.3 pypi_0 pypi ncurses 6.3 h5eee18b_3
netcdf4 1.6.0 pypi_0 pypi networkx 2.8.4 pypi_0 pypi numpy 1.23.1 pypi_0 pypi numpydoc 1.4.0 pypi_0 pypi openssl 1.1.1q h7f8727e_0
packaging 21.3 pypi_0 pypi pandas 1.4.3 pypi_0 pypi parsley 1.3 pypi_0 pypi parso 0.8.3 pypi_0 pypi partd 1.2.0 pypi_0 pypi pexpect 4.8.0 pypi_0 pypi photutils 1.5.0 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pillow 9.2.0 pypi_0 pypi pip 22.1.2 py39h06a4308_0
pluggy 1.0.0 pypi_0 pypi poppy 1.0.3 pypi_0 pypi prompt-toolkit 3.0.30 pypi_0 pypi psutil 5.9.1 pypi_0 pypi ptyprocess 0.7.0 pypi_0 pypi pure-eval 0.2.2 pypi_0 pypi py 1.11.0 pypi_0 pypi pycparser 2.21 pypi_0 pypi pyerfa 2.0.0.1 pypi_0 pypi pygments 2.12.0 pypi_0 pypi pyparsing 3.0.9 pypi_0 pypi pyrsistent 0.18.1 pypi_0 pypi pysynphot 2.0.0 pypi_0 pypi pytest 7.1.2 pypi_0 pypi python 3.9.7 h12debd9_1
python-dateutil 2.8.2 pypi_0 pypi pytz 2022.1 pypi_0 pypi pyvo 1.3 pypi_0 pypi pywavelets 1.3.0 pypi_0 pypi pyyaml 6.0 pypi_0 pypi readline 8.1.2 h7f8727e_1
reproject 0.8 pypi_0 pypi requests 2.28.1 pypi_0 pypi scikit-image 0.19.3 pypi_0 pypi scipy 1.8.1 pypi_0 pypi secretstorage 3.3.2 pypi_0 pypi semantic-version 2.10.0 pypi_0 pypi setuptools 61.2.0 py39h06a4308_0
six 1.16.0 pypi_0 pypi snowballstemmer 2.2.0 pypi_0 pypi soupsieve 2.3.2.post1 pypi_0 pypi spherical-geometry 1.2.22 pypi_0 pypi sphinx 5.0.2 pypi_0 pypi sphinxcontrib-applehelp 1.0.2 pypi_0 pypi sphinxcontrib-devhelp 1.0.2 pypi_0 pypi sphinxcontrib-htmlhelp 2.0.0 pypi_0 pypi sphinxcontrib-jsmath 1.0.1 pypi_0 pypi sphinxcontrib-qthelp 1.0.3 pypi_0 pypi sphinxcontrib-serializinghtml 1.1.5 pypi_0 pypi sqlite 3.38.5 hc218d9a_0
stack-data 0.3.0 pypi_0 pypi stcal 1.0.0 pypi_0 pypi stdatamodels 0.4.3 pypi_0 pypi stpipe 0.4.1 pypi_0 pypi stsci-image 2.3.5 pypi_0 pypi stsci-imagestats 1.6.3 pypi_0 pypi stsci-stimage 0.2.5 pypi_0 pypi svo-filters 0.4.3 pypi_0 pypi tifffile 2022.5.4 pypi_0 pypi tk 8.6.12 h1ccaba5_0
tomli 2.0.1 pypi_0 pypi toolz 0.12.0 pypi_0 pypi tornado 6.2 pypi_0 pypi tqdm 4.64.0 pypi_0 pypi traitlets 5.3.0 pypi_0 pypi tweakwcs 0.7.4 pypi_0 pypi typing-extensions 4.3.0 pypi_0 pypi tzdata 2022a hda174b7_0
uncertainties 3.1.7 pypi_0 pypi urllib3 1.26.10 pypi_0 pypi wcwidth 0.2.5 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi wheel 0.37.1 pyhd3eb1b0_0
wiimatch 0.2.1 pypi_0 pypi xarray 2022.3.0 pypi_0 pypi xz 5.2.5 h7f8727e_1
zipp 3.8.1 pypi_0 pypi zlib 1.2.12 h7f8727e_2

Code of Conduct

taylorbell57 commented 2 years ago

Ah yes, thanks for a reminder to add this - I knew it was missing, but had forgotten. Also note that you might want to change your limb darkening priors to either be fixed (if you want to use the exotic-ld values) or update the priors to span -1 to 1 or something like that (since quadratic limb darkening values can go negative) if you are just wanting to use the exotic-ld values as a starting point