Eureka
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Published
20 hours ago •
kevin218
kevin218
[Bug]: Bug in stage 5 during dynesty fitting.
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Instrument
Light curve fitting (Stages 4-6)
What happened?
For my stage 5 I set for fit method dynesty and I got the error below, I choose dynesty because that's the method in the demo file, but, should I use this method?, or does it matter if I pick a different one, because I ran again stage 5 but with fit method as lsq, is that correct?, because my results with lsq looked decent.
Error traceback output
55643it [1:18:22, 11.18it/s, bound: 338 | nc: 30 | ncall: 1596070 | eff(%): 3.486 | loglstar: -inf < 1678.602 < inf | logz: 1621.999 +/- 0.235 | d
55643it [1:18:22, 11.83it/s, bound: 338 | nc: 30 | ncall: 1596070 | eff(%): 3.486 | loglstar: -inf < 1678.602 < inf | logz: 1621.999 +/- 0.235 | dlogz: 2.392 > 0.100]
Traceback (most recent call last):
File "/home/iaunam/Escritorio/Verano_2024/ECF_files_byme/run_eureka_wasp39_2.py", line 34, in <module>
meta = s5.fitlc(eventlabel, ecf_path=ecf_path)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 460, in fitlc
meta, params = fit_channel(meta, time, flux, channel,
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 856, in fit_channel
lc_model.fit(model, meta, log, fitter='dynesty')
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/lightcurve.py", line 179, in fit
fit_model = self.fitter_func(self, model, meta, log, **kwargs)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/fitters.py", line 817, in dynestyfitter
sampler.run_nested(dlogz=tol, print_progress=True) # output progress bar
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/dynesty/sampler.py", line 1025, in run_nested
for it, results in enumerate(
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/dynesty/sampler.py", line 848, in sample
u, v, logl, nc = self._new_point(loglstar_new)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/dynesty/sampler.py", line 439, in _new_point
self.update_bound_if_needed(loglstar, ncall=ncall)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/dynesty/sampler.py", line 327, in update_bound_if_needed
bound = self.update(subset=subset)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/dynesty/nestedsamplers.py", line 679, in update
self.mell.update(self.live_u[subset, :self.ncdim],
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/dynesty/bounding.py", line 580, in update
ells = _bounding_ellipsoids(points, firstell)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/dynesty/bounding.py", line 1414, in _bounding_ellipsoids
k2_res = kmeans2(points / scale,
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/scipy/cluster/vq.py", line 788, in kmeans2
label = vq(data, code_book)[0]
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/scipy/cluster/vq.py", line 200, in vq
obs = _asarray_validated(obs, check_finite=check_finite)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/scipy/_lib/_util.py", line 287, in _asarray_validated
a = toarray(a)
File "/home/iaunam/anaconda3/envs/eureka/lib/python3.9/site-packages/numpy/lib/function_base.py", line 628, in asarray_chkfinite
raise ValueError(
ValueError: array must not contain infs or NaNs
What operating system are you using?
Ubuntu 18.04.6 LTS
What version of Python are you running?
Python 3.9.7
What Python packages do you have installed?
# packages in environment at /home/iaunam/anaconda3/envs/eureka:
#
# Name Version Build Channel
_libgcc_mutex 0.1 main
_openmp_mutex 5.1 1_gnu
alabaster 0.7.16 pypi_0 pypi
asciitree 0.3.3 pypi_0 pypi
asdf 3.2.0 pypi_0 pypi
asdf-astropy 0.6.1 pypi_0 pypi
asdf-coordinates-schemas 0.3.0 pypi_0 pypi
asdf-standard 1.1.1 pypi_0 pypi
asdf-transform-schemas 0.5.0 pypi_0 pypi
asdf-wcs-schemas 0.4.0 pypi_0 pypi
asteval 1.0.0 pypi_0 pypi
astraeus 0.3 pypi_0 pypi
astropy 6.0.1 pypi_0 pypi
astropy-healpix 1.0.3 pypi_0 pypi
astropy-iers-data 0.2024.7.8.0.31.19 pypi_0 pypi
astroquery 0.4.7 pypi_0 pypi
astroscrappy 1.2.0 pypi_0 pypi
asttokens 2.4.1 pypi_0 pypi
attrs 23.2.0 pypi_0 pypi
babel 2.15.0 pypi_0 pypi
backports-tarfile 1.2.0 pypi_0 pypi
batman-package 2.4.9 pypi_0 pypi
bayesicfitting 3.2.1 pypi_0 pypi
beautifulsoup4 4.12.3 pypi_0 pypi
bokeh 2.4.3 pypi_0 pypi
bottleneck 1.4.0 pypi_0 pypi
ca-certificates 2024.7.2 h06a4308_0
ccdproc 2.4.2 pypi_0 pypi
celerite 0.4.3 pypi_0 pypi
certifi 2024.7.4 pypi_0 pypi
cffi 1.16.0 pypi_0 pypi
cftime 1.6.4 pypi_0 pypi
charset-normalizer 3.3.2 pypi_0 pypi
click 8.1.7 pypi_0 pypi
cloudpickle 3.0.0 pypi_0 pypi
contourpy 1.2.1 pypi_0 pypi
corner 2.2.2 pypi_0 pypi
crds 11.17.26 pypi_0 pypi
cryptography 42.0.8 pypi_0 pypi
cycler 0.12.1 pypi_0 pypi
dask 2024.7.0 pypi_0 pypi
decorator 5.1.1 pypi_0 pypi
dill 0.3.8 pypi_0 pypi
docutils 0.21.2 pypi_0 pypi
drizzle 1.15.1 pypi_0 pypi
dynesty 2.1.4 pypi_0 pypi
emcee 3.1.6 pypi_0 pypi
eureka 0.10 pypi_0 pypi
exceptiongroup 1.2.1 pypi_0 pypi
executing 2.0.1 pypi_0 pypi
exotic-ld 3.2.0 pypi_0 pypi
fasteners 0.19 pypi_0 pypi
filelock 3.15.4 pypi_0 pypi
fonttools 4.53.1 pypi_0 pypi
fsspec 2024.6.1 pypi_0 pypi
future 1.0.0 pypi_0 pypi
george 0.4.2 pypi_0 pypi
gwcs 0.21.0 pypi_0 pypi
h5netcdf 1.3.0 pypi_0 pypi
h5py 3.11.0 pypi_0 pypi
html5lib 1.1 pypi_0 pypi
idna 3.7 pypi_0 pypi
imageio 2.34.2 pypi_0 pypi
imagesize 1.4.1 pypi_0 pypi
importlib-metadata 8.0.0 pypi_0 pypi
importlib-resources 6.4.0 pypi_0 pypi
iniconfig 2.0.0 pypi_0 pypi
intel-openmp 2021.4.0 h06a4308_3561
ipython 8.18.1 pypi_0 pypi
jaraco-classes 3.4.0 pypi_0 pypi
jaraco-context 5.3.0 pypi_0 pypi
jaraco-functools 4.0.1 pypi_0 pypi
jedi 0.19.1 pypi_0 pypi
jeepney 0.8.0 pypi_0 pypi
jinja2 3.1.4 pypi_0 pypi
jmespath 1.0.1 pypi_0 pypi
jsonschema 4.23.0 pypi_0 pypi
jsonschema-specifications 2023.12.1 pypi_0 pypi
jwst 1.11.4 pypi_0 pypi
keyring 25.2.1 pypi_0 pypi
kiwisolver 1.4.5 pypi_0 pypi
lazy-loader 0.4 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 1.3.1 pypi_0 pypi
locket 1.0.0 pypi_0 pypi
markupsafe 2.1.5 pypi_0 pypi
matplotlib 3.9.1 pypi_0 pypi
matplotlib-inline 0.1.7 pypi_0 pypi
mkl 2021.4.0 h06a4308_640
mkl-service 2.4.0 py39h7f8727e_0
more-itertools 10.3.0 pypi_0 pypi
ncurses 6.4 h6a678d5_0
netcdf4 1.7.1.post1 pypi_0 pypi
networkx 3.2.1 pypi_0 pypi
numcodecs 0.12.1 pypi_0 pypi
numpy 1.24.4 pypi_0 pypi
numpydoc 1.7.0 pypi_0 pypi
opencv-python-headless 4.10.0.84 pypi_0 pypi
openssl 1.1.1w h7f8727e_0
packaging 24.1 pypi_0 pypi
pandas 2.2.2 pypi_0 pypi
parsley 1.3 pypi_0 pypi
parso 0.8.4 pypi_0 pypi
partd 1.4.2 pypi_0 pypi
pexpect 4.9.0 pypi_0 pypi
photutils 1.11.0 pypi_0 pypi
pillow 10.4.0 pypi_0 pypi
pip 24.0 py39h06a4308_0
pluggy 1.5.0 pypi_0 pypi
poppy 1.1.1 pypi_0 pypi
prompt-toolkit 3.0.47 pypi_0 pypi
psutil 6.0.0 pypi_0 pypi
ptyprocess 0.7.0 pypi_0 pypi
pure-eval 0.2.2 pypi_0 pypi
pycparser 2.22 pypi_0 pypi
pyerfa 2.0.1.4 pypi_0 pypi
pygments 2.18.0 pypi_0 pypi
pyparsing 3.1.2 pypi_0 pypi
pysynphot 2.0.0 pypi_0 pypi
pytest 8.2.2 pypi_0 pypi
python 3.9.7 h12debd9_1
python-dateutil 2.9.0.post0 pypi_0 pypi
pytz 2024.1 pypi_0 pypi
pyvo 1.5.2 pypi_0 pypi
pyyaml 6.0.1 pypi_0 pypi
readline 8.2 h5eee18b_0
referencing 0.35.1 pypi_0 pypi
reproject 0.13.0 pypi_0 pypi
requests 2.32.3 pypi_0 pypi
rpds-py 0.19.0 pypi_0 pypi
scikit-image 0.24.0 pypi_0 pypi
scipy 1.9.3 pypi_0 pypi
secretstorage 3.3.3 pypi_0 pypi
semantic-version 2.10.0 pypi_0 pypi
setuptools 69.5.1 py39h06a4308_0
setuptools-scm 8.1.0 pypi_0 pypi
six 1.16.0 pyhd3eb1b0_1
snowballstemmer 2.2.0 pypi_0 pypi
soupsieve 2.5 pypi_0 pypi
spherical-geometry 1.3.2 pypi_0 pypi
sphinx 7.3.7 pypi_0 pypi
sphinxcontrib-applehelp 1.0.8 pypi_0 pypi
sphinxcontrib-devhelp 1.0.6 pypi_0 pypi
sphinxcontrib-htmlhelp 2.0.5 pypi_0 pypi
sphinxcontrib-jsmath 1.0.1 pypi_0 pypi
sphinxcontrib-qthelp 1.0.7 pypi_0 pypi
sphinxcontrib-serializinghtml 1.1.10 pypi_0 pypi
sqlite 3.45.3 h5eee18b_0
stack-data 0.6.3 pypi_0 pypi
stcal 1.4.4 pypi_0 pypi
stdatamodels 1.7.2 pypi_0 pypi
stpipe 0.5.1 pypi_0 pypi
stsci-image 2.3.9 pypi_0 pypi
stsci-imagestats 1.8.3 pypi_0 pypi
stsci-stimage 0.2.9 pypi_0 pypi
svo-filters 0.4.4 pypi_0 pypi
tabulate 0.9.0 pypi_0 pypi
tifffile 2024.7.2 pypi_0 pypi
tk 8.6.14 h39e8969_0
tomli 2.0.1 pypi_0 pypi
toolz 0.12.1 pypi_0 pypi
tornado 6.4.1 pypi_0 pypi
tqdm 4.66.4 pypi_0 pypi
traitlets 5.14.3 pypi_0 pypi
tweakwcs 0.8.7 pypi_0 pypi
typing-extensions 4.12.2 pypi_0 pypi
tzdata 2024.1 pypi_0 pypi
uncertainties 3.2.2 pypi_0 pypi
urllib3 2.2.2 pypi_0 pypi
wcwidth 0.2.13 pypi_0 pypi
webencodings 0.5.1 pypi_0 pypi
wheel 0.43.0 py39h06a4308_0
wiimatch 0.3.2 pypi_0 pypi
xarray 2024.6.0 pypi_0 pypi
xz 5.4.6 h5eee18b_1
zarr 2.18.2 pypi_0 pypi
zipp 3.19.2 pypi_0 pypi
zlib 1.2.13 h5eee18b_1
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