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[Bug]: Type Error in Stage 5 Lightcurve Fitting #708

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lheinke opened this issue Oct 29, 2024 · 3 comments
Open
2 tasks done

[Bug]: Type Error in Stage 5 Lightcurve Fitting #708

lheinke opened this issue Oct 29, 2024 · 3 comments
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@taylorbell57 @meganmansfield @sebastian-zieba @evamariaa
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bug Something isn't working LC Fit MIRI

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@lheinke
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lheinke commented Oct 29, 2024

FAQ check

  • Yes, I checked the FAQ and my question has not been addressed.

Instrument

Light curve fitting (Stages 4-6)

What happened?

I have encountered the type error below when trying to fit MIRI LRS transit lightcurves with Eureka! Stages 1-4 were reduced using Eureka! as well. My naive first guess would be that the parameters from the EPF file are not parsed correctly for some reason.

Error traceback output

WARNING: There are 4 metadata save files in the folder: /home/lheinke/JWST/Reduction/Stage4/
  Using the metadata file inside: /home/lheinke/JWST/Reduction/Stage4/S4_2024-10-29_jwst_run3/ap5_bg11/
  and will consider aperture ranges listed there. If this metadata file is not a part
  of the run you intended, please provide a more precise folder for the metadata file.
Finished loading parameters from /home/lheinke/JWST/Reduction/Stage4/S4_2024-10-29_jwst_run3/ap5_bg11//S4_jwst_ap5_bg11_LCData.h5

Starting Stage 5: Light Curve Fitting

Input directory: /home/lheinke/JWST/Reduction/Stage4/S4_2024-10-29_jwst_run3/ap5_bg11/
Output directory: /home/lheinke/JWST/Reduction/Stage5/S5_2024-10-29_jwst_run12/ap5_bg11/
Copying S5 control file
Copying S5 parameter control file

Starting Fit of White-light Light Curve

=========================
Starting dynesty fit.
<class 'numpy.str_'> <class 'numpy.float64'> <class 'numpy.float64'>
Traceback (most recent call last):
  File "/home/lheinke/JWST/Reduction/run_eureka.py", line 29, in <module>
    meta = s5.fitlc(eventlabel, ecf_path=ecf_path)
  File "/home/lheinke/.local/envs/eureka_1.0/lib/python3.10/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 289, in fitlc
    meta, params = fit_channel(meta, time, flux, 0, flux_err,
  File "/home/lheinke/.local/envs/eureka_1.0/lib/python3.10/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 964, in fit_channel
    lc_model.fit(model, meta, log, fitter='dynesty')
  File "/home/lheinke/.local/envs/eureka_1.0/lib/python3.10/site-packages/eureka/S5_lightcurve_fitting/lightcurve.py", line 181, in fit
    fit_model = self.fitter_func(self, model, meta, log, **kwargs)
  File "/home/lheinke/.local/envs/eureka_1.0/lib/python3.10/site-packages/eureka/S5_lightcurve_fitting/fitters.py", line 856, in dynestyfitter
    start_lnprob = lnprob(freepars, lc, model, prior1, prior2, priortype,
  File "/home/lheinke/.local/envs/eureka_1.0/lib/python3.10/site-packages/eureka/S5_lightcurve_fitting/likelihood.py", line 205, in lnprob
    lp = lnprior(theta, prior1, prior2, priortype, freenames)
  File "/home/lheinke/.local/envs/eureka_1.0/lib/python3.10/site-packages/eureka/S5_lightcurve_fitting/likelihood.py", line 137, in lnprior
    if (priortype[i] == 'U' and np.logical_or(theta[i] < prior1[i],
TypeError: '>' not supported between instances of 'numpy.ndarray' and 'numpy.str_'

What operating system are you using?

Ubuntu 20.04.6 LTS

What version of Python are you running?

Python 3.10.14

What Python packages do you have installed?

# Name                    Version                   Build  Channel
_libgcc_mutex             0.1                 conda_forge    conda-forge
_openmp_mutex             4.5                       2_gnu    conda-forge
alabaster                 1.0.0                    pypi_0    pypi
asciitree                 0.3.3                    pypi_0    pypi
asdf                      3.5.0                    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                   1.0.5                    pypi_0    pypi
astraeus                  0.3                      pypi_0    pypi
astropy                   6.1.4                    pypi_0    pypi
astropy-healpix           1.0.3                    pypi_0    pypi
astropy-iers-data         0.2024.10.28.0.34.7          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                     24.2.0                   pypi_0    pypi
babel                     2.16.0                   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                1.4.2                    pypi_0    pypi
bzip2                     1.0.8                h4bc722e_7    conda-forge
ca-certificates           2024.8.30            hbcca054_0    conda-forge
ccdproc                   2.4.2                    pypi_0    pypi
celerite2                 0.3.2                    pypi_0    pypi
certifi                   2024.8.30                pypi_0    pypi
cffi                      1.17.1                   pypi_0    pypi
cftime                    1.6.4.post1              pypi_0    pypi
charset-normalizer        3.4.0                    pypi_0    pypi
click                     8.1.7                    pypi_0    pypi
cloudpickle               3.1.0                    pypi_0    pypi
contourpy                 1.3.0                    pypi_0    pypi
corner                    2.2.2                    pypi_0    pypi
crds                      11.18.4                  pypi_0    pypi
cryptography              43.0.3                   pypi_0    pypi
cycler                    0.12.1                   pypi_0    pypi
dask                      2024.10.0                pypi_0    pypi
decorator                 5.1.1                    pypi_0    pypi
dill                      0.3.9                    pypi_0    pypi
docutils                  0.21.2                   pypi_0    pypi
drizzle                   2.0.0                    pypi_0    pypi
dynesty                   2.1.4                    pypi_0    pypi
emcee                     3.1.6                    pypi_0    pypi
eureka                    1.0                      pypi_0    pypi
exceptiongroup            1.2.2                    pypi_0    pypi
executing                 2.1.0                    pypi_0    pypi
exotic-ld                 3.2.0                    pypi_0    pypi
fasteners                 0.19                     pypi_0    pypi
filelock                  3.16.1                   pypi_0    pypi
fleck                     1.1.2                    pypi_0    pypi
fonttools                 4.54.1                   pypi_0    pypi
fsspec                    2024.10.0                pypi_0    pypi
future                    1.0.0                    pypi_0    pypi
george                    0.4.3                    pypi_0    pypi
gwcs                      0.21.0                   pypi_0    pypi
h5netcdf                  1.4.0                    pypi_0    pypi
h5py                      3.12.1                   pypi_0    pypi
html5lib                  1.1                      pypi_0    pypi
idna                      3.10                     pypi_0    pypi
imageio                   2.36.0                   pypi_0    pypi
imagesize                 1.4.1                    pypi_0    pypi
importlib-metadata        8.5.0                    pypi_0    pypi
iniconfig                 2.0.0                    pypi_0    pypi
ipython                   8.29.0                   pypi_0    pypi
jaraco-classes            3.4.0                    pypi_0    pypi
jaraco-context            6.0.1                    pypi_0    pypi
jaraco-functools          4.1.0                    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 2024.10.1                pypi_0    pypi
jwst                      1.15.1                   pypi_0    pypi
keyring                   25.5.0                   pypi_0    pypi
kiwisolver                1.4.7                    pypi_0    pypi
lazy-loader               0.4                      pypi_0    pypi
ld_impl_linux-64          2.43                 h712a8e2_2    conda-forge
libffi                    3.4.2                h7f98852_5    conda-forge
libgcc                    14.2.0               h77fa898_1    conda-forge
libgcc-ng                 14.2.0               h69a702a_1    conda-forge
libgomp                   14.2.0               h77fa898_1    conda-forge
libnsl                    2.0.1                hd590300_0    conda-forge
libsqlite                 3.47.0               hadc24fc_0    conda-forge
libuuid                   2.38.1               h0b41bf4_0    conda-forge
libxcrypt                 4.4.36               hd590300_1    conda-forge
libzlib                   1.3.1                hb9d3cd8_2    conda-forge
lmfit                     1.3.2                    pypi_0    pypi
locket                    1.0.0                    pypi_0    pypi
markupsafe                3.0.2                    pypi_0    pypi
matplotlib                3.9.2                    pypi_0    pypi
matplotlib-inline         0.1.7                    pypi_0    pypi
mc3                       3.2.0                    pypi_0    pypi
more-itertools            10.5.0                   pypi_0    pypi
ncurses                   6.5                  he02047a_1    conda-forge
netcdf4                   1.6.5                    pypi_0    pypi
networkx                  3.4.2                    pypi_0    pypi
numcodecs                 0.13.1                   pypi_0    pypi
numpy                     1.24.4                   pypi_0    pypi
numpydoc                  1.8.0                    pypi_0    pypi
opencv-python-headless    4.10.0.84                pypi_0    pypi
openssl                   3.3.2                hb9d3cd8_0    conda-forge
packaging                 24.1                     pypi_0    pypi
pandas                    2.2.3                    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                 2.0.2                    pypi_0    pypi
pillow                    11.0.0                   pypi_0    pypi
pip                       24.2               pyh8b19718_1    conda-forge
pluggy                    1.5.0                    pypi_0    pypi
poppy                     1.1.1                    pypi_0    pypi
prompt-toolkit            3.0.48                   pypi_0    pypi
psutil                    6.1.0                    pypi_0    pypi
ptyprocess                0.7.0                    pypi_0    pypi
pure-eval                 0.2.3                    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                 3.2.0                    pypi_0    pypi
pysynphot                 2.0.0                    pypi_0    pypi
pytest                    8.3.3                    pypi_0    pypi
python                    3.10.14         hd12c33a_0_cpython    conda-forge
python-dateutil           2.9.0.post0              pypi_0    pypi
pytz                      2024.2                   pypi_0    pypi
pyvo                      1.5.3                    pypi_0    pypi
pyyaml                    6.0.2                    pypi_0    pypi
readline                  8.2                  h8228510_1    conda-forge
referencing               0.35.1                   pypi_0    pypi
reproject                 0.14.0                   pypi_0    pypi
requests                  2.32.3                   pypi_0    pypi
rpds-py                   0.20.0                   pypi_0    pypi
scikit-image              0.24.0                   pypi_0    pypi
scipy                     1.14.1                   pypi_0    pypi
secretstorage             3.3.3                    pypi_0    pypi
semantic-version          2.10.0                   pypi_0    pypi
setuptools                75.1.0             pyhd8ed1ab_0    conda-forge
setuptools-scm            8.1.0                    pypi_0    pypi
shapely                   2.0.6                    pypi_0    pypi
six                       1.16.0                   pypi_0    pypi
snowballstemmer           2.2.0                    pypi_0    pypi
soupsieve                 2.6                      pypi_0    pypi
spherical-geometry        1.3.2                    pypi_0    pypi
sphinx                    8.1.3                    pypi_0    pypi
sphinxcontrib-applehelp   2.0.0                    pypi_0    pypi
sphinxcontrib-devhelp     2.0.0                    pypi_0    pypi
sphinxcontrib-htmlhelp    2.1.0                    pypi_0    pypi
sphinxcontrib-jsmath      1.0.1                    pypi_0    pypi
sphinxcontrib-qthelp      2.0.0                    pypi_0    pypi
sphinxcontrib-serializinghtml 2.0.0                    pypi_0    pypi
stack-data                0.6.3                    pypi_0    pypi
stcal                     1.7.3                    pypi_0    pypi
stdatamodels              2.0.0                    pypi_0    pypi
stpipe                    0.6.0                    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
synphot                   1.4.0                    pypi_0    pypi
tabulate                  0.9.0                    pypi_0    pypi
tifffile                  2024.9.20                pypi_0    pypi
tk                        8.6.13          noxft_h4845f30_101    conda-forge
tomli                     2.0.2                    pypi_0    pypi
toolz                     1.0.0                    pypi_0    pypi
tornado                   6.4.1                    pypi_0    pypi
tqdm                      4.66.6                   pypi_0    pypi
traitlets                 5.14.3                   pypi_0    pypi
tweakwcs                  0.8.9                    pypi_0    pypi
typing-extensions         4.12.2                   pypi_0    pypi
tzdata                    2024.2                   pypi_0    pypi
uncertainties             3.2.2                    pypi_0    pypi
urllib3                   2.2.3                    pypi_0    pypi
wcwidth                   0.2.13                   pypi_0    pypi
webencodings              0.5.1                    pypi_0    pypi
wheel                     0.44.0             pyhd8ed1ab_0    conda-forge
wiimatch                  0.3.2                    pypi_0    pypi
xarray                    2024.10.0                pypi_0    pypi
xz                        5.2.6                h166bdaf_0    conda-forge
zarr                      2.18.3                   pypi_0    pypi
zipp                      3.20.2                   pypi_0    pypi

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@lheinke lheinke added the bug Something isn't working label Oct 29, 2024
@taylorbell57
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Can you please copy-paste the contents of your EPF file into a comment on this Issue so that I can better evaluate what's going on?

@lheinke
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lheinke commented Oct 29, 2024

Sure, here you go:

# Stage 5 Fit Parameters Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-5-fit-parameters

# Name       Value         Free?          PriorPar1    PriorPar2    PriorType
# "Free?" can be free, fixed, white_free, white_fixed, shared, or independent
# PriorType can be U (Uniform), LU (Log Uniform), or N (Normal).
# If U/LU, PriorPar1 and PriorPar2 represent upper and lower limits of the parameter/log(the parameter).
# If N, PriorPar1 is the mean and PriorPar2 is the standard deviation of a Gaussian prior.
#-------------------------------------------------------------------------------------------------------
# ------------------
# ** Transit/eclipse parameters **
# ------------------

rp           0.13401        'free'         0            0.5          U

# ------------------
# ** Orbital parameters **
# ------------------

per          2.10345       'fixed'
t0           2410345.03146  'white_free'    2410345.03146   0.05         N
time_offset  0.0            'fixed'
inc          87.167         'white_free'    87.167          0.05         N
ars          9.086          'white_free'    9.086           0.1          N
ecc          0.0            'fixed'         0               1            U
w            90.            'fixed'         0               180          U

# t_secondary  0.25           'free'             0.25         0.05         N
# Rs           0.12           'fixed'

# ----------------------
# ** Sinusoid_pc Phase Curve Parameters **
# ----------------------
# AmpCos1      0.4           'free'         0            1            U
# AmpSin1      0.01          'free'         -1           1            U
# AmpCos2      0.01          'free'         -1           1            U
# AmpSin2      0.01          'free'         -1           1            U
# ----------------------
# ** POET_pc Phase Curve Parameters **
# ----------------------
# cos1_amp     0.4           'free'         0            1            U
# cos1_off     0.00          'free'         -180         180          U
# cos2_amp     0.1           'free'         0            1            U
# cos2_off     0.00          'free'         0            180          U
# ----------------------
# ** quasilambert_pc Phase Curve Parameters **
# ----------------------
# quasi_gamma  4             'free'         2            40           U
# quasi_offset 0             'free'         -90          90           U

# -------------------------
# ** Limb darkening parameters **
# For BATMAN, choose limb_dark from ['uniform', 'linear', 'quadratic', 'kipping2013', 'squareroot', 'logarithmic', 'exponential','3-parameter', '4-parameter']
# For POET, choose limb_dark from ['uniform', 'linear', 'quadratic', '4-parameter']
# When using generated limb-darkening coefficients from exotic-ld or spam, choose from ['linear', 'quadratic', '3-parameter', '4-parameter'] and set their state to 'fixed' or use `recenter_ld_prior`.
# -------------------------
limb_dark   'kipping2013'   'free' #'quadratic'   'white_free'
u1          0.2             'free'          0           1           U
u2          0.2             'free'          0           1           U

# -------------------------
# ** Stellar variability parameters **
# A modified Lorentzian model can be used to fit stellar flares
# A damped oscillator model can be used to fit quasi-periodic pulsations
# -------------------------
# lor_amp_lhs     0.03    'free'          0            0.1            U
# lor_amp_rhs     0.03    'free'          0            0.1            U
# lor_hwhm_lhs    0       'fixed'         0            0.1            U
# lor_hwhm_rhs    1e-5    'free'          0            0.1            U
# lor_t0          0.3163  'free'          0.3160       0.3166         U
# lor_power       0.7     'free'          0.1          2              U

# osc_amp         0.0003  'free'          0            0.01           U
# osc_amp_decay   1       'free'          0            20             U
# osc_per         0.03    'free'          0            0.1            U
# osc_per_decay   0.      'fixed'         0            10             U
# osc_t0          0.3163  'fixed'         0            1              U
# osc_t1          0.3163  'free'          0.3          0.4            U

# ------------------
# ** Star Spot parameters **
# Each spot needs rad, lat, lon. See docs for details!
# For fleck: can only have one spot contrast (spotcon), spotnpts is the number of temporal points to evaluate at (~200-500)
# For starry: assign one spotcon per spot (spotcon, spotcon1, etc), spotnpts is the ydeg of the star map (~30)
# ------------------
# spotstari    90       'fixed'
# spotrot      100      'fixed'
# spotnpts     300      'independent'

# spotcon      0.9      'free'          0         1       U  # Should be between 0 and 1
# spotrad      0.2      'free'          0         1       U  # Should be between 0 and 1
# spotlat      0        'free'          -90       90      U  # Should be between -90 and 90
# spotlon      0        'free'          -90       90      U  # Should be between -90 and 90 to be on observer-facing hemisphere

# spotcon1     0.95     'free'          0         1       U  # Only use for starry! fleck cannot have different contrasts for each spot
# spotrad1     0.1      'free'          0         1       U  # Should be between 0 and 1
# spotlat1     10       'free'          -90       90      U  # Should be between -90 and 90
# spotlon1     45       'free'          -90       90      U  # Should be between -90 and 90 to be on observer-facing hemisphere

# --------------------
# ** Systematic variables **
# Polynomial model variables (c0--c9 for 0th--3rd order polynomials in time); Fitting at least c0 is very strongly recommended!
# Exponential ramp model variables (r0--r1 for one exponential ramp, r2--r3 for a second exponential ramp)
# GP model parameters (A, m for the first kernel; A1, m1 for the second kernel; etc.) in log scale
# Step-function model variables (step# and steptime# for step-function model #; e.g. step0 and steptime0)
# Drift model variables (xpos, ypos, xwidth, ywidth)
# --------------------
c0          1.015           'free'          1           0.05        N
c1          0               'free'          0           0.01        N
# A           -15             'free'          -25         0           U
# m           -4              'free'          -7          0           U

# -----------
# ** White noise **
# Use scatter_mult to fit a multiplier to the expected noise level from Stage 3 (recommended)
# Use scatter_ppm to fit the noise level in ppm
# -----------
scatter_mult 1.1            'free'         0.8          10           U

@taylorbell57
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Ah, I believe the issue is that you have:

limb_dark   'kipping2013'   'free'

All 'free' parameters must be numerical values that the code will fit for - you should instead set this to be 'independent'.

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@taylorbell57 taylorbell57

@meganmansfield meganmansfield

@sebastian-zieba sebastian-zieba

@evamariaa evamariaa

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