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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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Lightcurve fitting #527

Closed amitmazz closed 1 year ago

amitmazz commented 1 year ago

Instrument

Light curve fitting (Stages 4-6)

What happened?

I don't think I am applying the Step-function model variables right. I am currently using the G395H data for wasp 39b. I am currently running the NRS2 files and using the guidelines of the paper 'Early Release Science of the exoplanet WASP-39b with JWST NIRSpec G395H'. But as it appears I am not getting a good lightcurve fit. Due to the tilting the fitting should be able to take that into account . Attaching my white lightcurve. my ecf files can be found here : https://github.com/amitmazz/Eureka_was39b_G395H.git

Error traceback output

fig5101_ch0_lc_emcee

What operating system are you using?

Ubuntu 20.04.6 LTS

What version of Python are you running?

python 3.9.16

What Python packages do you have installed?

_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
aesara-theano-fallback 0.1.0 pypi_0 pypi alabaster 0.7.13 pypi_0 pypi anyio 3.6.2 pypi_0 pypi argon2-cffi 21.3.0 pypi_0 pypi argon2-cffi-bindings 21.2.0 pypi_0 pypi arrow 1.2.3 pypi_0 pypi arviz 0.12.1 pypi_0 pypi asdf 2.14.4 pypi_0 pypi asdf-astropy 0.4.0 pypi_0 pypi asdf-coordinates-schemas 0.2.0 pypi_0 pypi asdf-standard 1.0.3 pypi_0 pypi asdf-transform-schemas 0.3.0 pypi_0 pypi asdf-unit-schemas 0.1.0 pypi_0 pypi asdf-wcs-schemas 0.1.1 pypi_0 pypi asteval 0.9.29 pypi_0 pypi astraeus 0.3 pypi_0 pypi astropy 5.2.2 pypi_0 pypi astropy-healpix 0.7 pypi_0 pypi astroquery 0.4.6 pypi_0 pypi astroscrappy 1.1.0 pypi_0 pypi asttokens 2.2.1 pypi_0 pypi attrs 22.2.0 pypi_0 pypi babel 2.12.1 pypi_0 pypi backcall 0.2.0 pypi_0 pypi batman-package 2.4.9 pypi_0 pypi bayesicfitting 3.1.1 pypi_0 pypi beautifulsoup4 4.12.0 pypi_0 pypi bleach 6.0.0 pypi_0 pypi bokeh 2.4.3 pypi_0 pypi bottleneck 1.3.7 pypi_0 pypi ca-certificates 2023.01.10 h06a4308_0
cachetools 5.3.0 pypi_0 pypi ccdproc 2.4.0 pypi_0 pypi celerite 0.4.2 pypi_0 pypi certifi 2022.5.18.1 pypi_0 pypi cffi 1.15.1 pypi_0 pypi cftime 1.6.2 pypi_0 pypi charset-normalizer 3.1.0 pypi_0 pypi cloudpickle 2.2.1 pypi_0 pypi codecov 2.1.12 pypi_0 pypi comm 0.1.3 pypi_0 pypi contourpy 1.0.7 pypi_0 pypi corner 2.2.1 pypi_0 pypi coverage 7.2.2 pypi_0 pypi crds 11.16.21 pypi_0 pypi cryptography 40.0.1 pypi_0 pypi cycler 0.11.0 pypi_0 pypi cython 0.29.34 pypi_0 pypi dask 2022.6.0 pypi_0 pypi debugpy 1.6.6 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi deprecat 2.1.1 pypi_0 pypi dill 0.3.6 pypi_0 pypi docutils 0.18.1 pypi_0 pypi drizzle 1.13.7 pypi_0 pypi dynesty 2.1.0 pypi_0 pypi emcee 3.1.4 pypi_0 pypi eureka 0.9.dev164+g8808897 pypi_0 pypi exceptiongroup 1.1.1 pypi_0 pypi executing 1.2.0 pypi_0 pypi exoplanet 0.5.3 pypi_0 pypi exoplanet-core 0.1.2 pypi_0 pypi exotic-ld 3.0.0 pypi_0 pypi fastjsonschema 2.16.3 pypi_0 pypi fastprogress 1.0.3 pypi_0 pypi filelock 3.10.7 pypi_0 pypi flake8 6.0.0 pypi_0 pypi fonttools 4.39.3 pypi_0 pypi fqdn 1.5.1 pypi_0 pypi fsspec 2023.3.0 pypi_0 pypi future 0.18.3 pypi_0 pypi george 0.4.0 pypi_0 pypi gwcs 0.18.3 pypi_0 pypi h5netcdf 1.1.0 pypi_0 pypi h5py 3.1.0 pypi_0 pypi html5lib 1.1 pypi_0 pypi idna 3.4 pypi_0 pypi image-registration 0.2.7.dev16+g24e5018 pypi_0 pypi imageio 2.27.0 pypi_0 pypi imagesize 1.4.1 pypi_0 pypi importlib-metadata 6.1.0 pypi_0 pypi importlib-resources 5.12.0 pypi_0 pypi iniconfig 2.0.0 pypi_0 pypi intel-openmp 2021.4.0 h06a4308_3561
ipykernel 6.22.0 pypi_0 pypi ipython 8.12.0 pypi_0 pypi ipython-genutils 0.2.0 pypi_0 pypi ipywidgets 8.0.6 pypi_0 pypi isoduration 20.11.0 pypi_0 pypi jaraco-classes 3.2.3 pypi_0 pypi jedi 0.18.2 pypi_0 pypi jeepney 0.8.0 pypi_0 pypi jinja2 3.1.2 pypi_0 pypi jmespath 1.0.1 pypi_0 pypi jsonpointer 2.3 pypi_0 pypi jsonschema 4.9.1 pypi_0 pypi jupyter 1.0.0 pypi_0 pypi jupyter-client 8.1.0 pypi_0 pypi jupyter-console 6.6.3 pypi_0 pypi jupyter-core 5.3.0 pypi_0 pypi jupyter-events 0.6.3 pypi_0 pypi jupyter-server 2.5.0 pypi_0 pypi jupyter-server-terminals 0.4.4 pypi_0 pypi jupyterlab-pygments 0.2.2 pypi_0 pypi jupyterlab-widgets 3.0.7 pypi_0 pypi jwst 1.8.2 pypi_0 pypi keyring 23.13.1 pypi_0 pypi kiwisolver 1.4.4 pypi_0 pypi lazy-loader 0.2 pypi_0 pypi ld_impl_linux-64 2.38 h1181459_1
libffi 3.4.2 h6a678d5_6
libgcc-ng 11.2.0 h1234567_1
libgomp 11.2.0 h1234567_1
libstdcxx-ng 11.2.0 h1234567_1
lmfit 1.1.0 pypi_0 pypi locket 1.0.0 pypi_0 pypi lxml 4.9.2 pypi_0 pypi markdown-it-py 2.2.0 pypi_0 pypi markupsafe 2.1.2 pypi_0 pypi matplotlib 3.7.1 pypi_0 pypi matplotlib-inline 0.1.6 pypi_0 pypi mccabe 0.7.0 pypi_0 pypi mdit-py-plugins 0.3.5 pypi_0 pypi mdurl 0.1.2 pypi_0 pypi mistune 2.0.5 pypi_0 pypi mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
more-itertools 9.1.0 pypi_0 pypi myst-parser 1.0.0 pypi_0 pypi nbclassic 0.5.4 pypi_0 pypi nbclient 0.7.3 pypi_0 pypi nbconvert 7.3.0 pypi_0 pypi nbformat 5.8.0 pypi_0 pypi nbsphinx 0.9.1 pypi_0 pypi ncurses 6.4 h6a678d5_0
nest-asyncio 1.5.6 pypi_0 pypi netcdf4 1.6.3 pypi_0 pypi networkx 3.0 pypi_0 pypi notebook 6.5.3 pypi_0 pypi notebook-shim 0.2.2 pypi_0 pypi numpy 1.21.6 pypi_0 pypi numpydoc 1.5.0 pypi_0 pypi opencv-python 4.7.0.72 pypi_0 pypi openssl 1.1.1t h7f8727e_0
packaging 23.0 pypi_0 pypi pandas 1.5.3 pypi_0 pypi pandocfilters 1.5.0 pypi_0 pypi parsley 1.3 pypi_0 pypi parso 0.8.3 pypi_0 pypi partd 1.3.0 pypi_0 pypi patsy 0.5.3 pypi_0 pypi pexpect 4.8.0 pypi_0 pypi photutils 1.6.0 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pillow 9.5.0 pypi_0 pypi pip 23.0.1 py39h06a4308_0
platformdirs 3.2.0 pypi_0 pypi pluggy 1.0.0 pypi_0 pypi poppy 1.0.3 pypi_0 pypi prometheus-client 0.16.0 pypi_0 pypi prompt-toolkit 3.0.38 pypi_0 pypi psutil 5.9.4 pypi_0 pypi ptyprocess 0.7.0 pypi_0 pypi pure-eval 0.2.2 pypi_0 pypi pycodestyle 2.10.0 pypi_0 pypi pycparser 2.21 pypi_0 pypi pyerfa 2.0.0.3 pypi_0 pypi pyflakes 3.0.1 pypi_0 pypi pygments 2.14.0 pypi_0 pypi pymc3 3.11.5 pypi_0 pypi pymc3-ext 0.1.1 pypi_0 pypi pyparsing 3.0.9 pypi_0 pypi pyrsistent 0.19.3 pypi_0 pypi pysynphot 2.0.0 pypi_0 pypi pytest 7.2.2 pypi_0 pypi pytest-cov 4.0.0 pypi_0 pypi pytest-doctestplus 0.12.1 pypi_0 pypi python 3.9.16 h7a1cb2a_2
python-dateutil 2.8.2 pypi_0 pypi python-json-logger 2.0.7 pypi_0 pypi pytz 2023.3 pypi_0 pypi pyvo 1.4.1 pypi_0 pypi pywavelets 1.4.1 pypi_0 pypi pyyaml 6.0 pypi_0 pypi pyzmq 25.0.2 pypi_0 pypi qtconsole 5.4.2 pypi_0 pypi qtpy 2.3.1 pypi_0 pypi readline 8.2 h5eee18b_0
reproject 0.10.0 pypi_0 pypi requests 2.28.2 pypi_0 pypi rfc3339-validator 0.1.4 pypi_0 pypi rfc3986-validator 0.1.1 pypi_0 pypi scikit-image 0.19.3 pypi_0 pypi scipy 1.7.3 pypi_0 pypi secretstorage 3.3.3 pypi_0 pypi semantic-version 2.10.0 pypi_0 pypi semver 3.0.0 pypi_0 pypi send2trash 1.8.0 pypi_0 pypi setuptools 65.6.3 py39h06a4308_0
setuptools-scm 7.1.0 pypi_0 pypi six 1.16.0 pyhd3eb1b0_1
sniffio 1.3.0 pypi_0 pypi snowballstemmer 2.2.0 pypi_0 pypi soupsieve 2.4 pypi_0 pypi spherical-geometry 1.2.23 pypi_0 pypi sphinx 6.1.3 pypi_0 pypi sphinx-automodapi 0.15.0 pypi_0 pypi sphinx-rtd-theme 1.2.0 pypi_0 pypi sphinxcontrib-applehelp 1.0.4 pypi_0 pypi sphinxcontrib-devhelp 1.0.2 pypi_0 pypi sphinxcontrib-htmlhelp 2.0.1 pypi_0 pypi sphinxcontrib-jquery 4.1 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 3.41.1 h5eee18b_0
stack-data 0.6.2 pypi_0 pypi starry 1.2.0 pypi_0 pypi stcal 1.2.2 pypi_0 pypi stdatamodels 0.4.5 pypi_0 pypi stpipe 0.4.6 pypi_0 pypi stsci-image 2.3.5 pypi_0 pypi stsci-imagestats 1.6.3 pypi_0 pypi stsci-stimage 0.2.6 pypi_0 pypi svo-filters 0.4.4 pypi_0 pypi terminado 0.17.1 pypi_0 pypi theano-pymc 1.1.2 pypi_0 pypi tifffile 2023.3.21 pypi_0 pypi tinycss2 1.2.1 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 4.65.0 pypi_0 pypi traitlets 5.9.0 pypi_0 pypi tweakwcs 0.8.1 pypi_0 pypi typing-extensions 4.5.0 pypi_0 pypi tzdata 2023c h04d1e81_0
uncertainties 3.1.7 pypi_0 pypi uri-template 1.2.0 pypi_0 pypi urllib3 1.26.15 pypi_0 pypi wcwidth 0.2.6 pypi_0 pypi webcolors 1.13 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi websocket-client 1.5.1 pypi_0 pypi wheel 0.38.4 py39h06a4308_0
widgetsnbextension 4.0.7 pypi_0 pypi wiimatch 0.3.1 pypi_0 pypi wrapt 1.15.0 pypi_0 pypi xarray 2023.3.0 pypi_0 pypi xarray-einstats 0.5.1 pypi_0 pypi xz 5.2.10 h5eee18b_1
zipp 3.15.0 pypi_0 pypi zlib 1.2.13 h5eee18b_0

Code of Conduct

jbrande commented 1 year ago

The step function systematic needs to be specified in your S5_nirspec_fs_template.ecf. Currently you have run_myfuncs set to [batman_tr,polynomial], but it should be [batman_tr,polynomial,step], so that Eureka! knows to actually fit for the step function.

taylorbell57 commented 1 year ago

In addition to that, your step0 will be in the same units as your lightcurve, so 0.5--1.50 is much too large a number. I would use a Normal prior (N instead of U), and give it something like 3000 +/- 3000 ppm which would be specified as:

step0       0.003       'free'      0.003   0.003   N
taylorbell57 commented 1 year ago

As this does not appear to be a bug with the code but rather a user error, I am now closing this issue.