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kevin218 / Eureka

Eureka! is a data reduction and analysis pipeline intended for time-series observations with JWST and HST.
https://eurekadocs.readthedocs.io/
MIT License
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ModuleNotFoundError: No module named 'astraeus.xarrayIO' #319

Closed jovian-explorer closed 2 years ago

jovian-explorer commented 2 years ago

Instrument

NIRSpec

What happened?

(base) keshav@dev:~/Eureka/demos/JWST$ python3 run_eureka.py

Error traceback output

(base) keshav@dev:~/Eureka/demos/JWST$ python3 run_eureka.py Traceback (most recent call last): File "/home/keshav/Eureka/demos/JWST/run_eureka.py", line 3, in import eureka.lib.plots File "/home/keshav/Eureka/demos/JWST/../../eureka/init.py", line 20, in from . import S3_data_reduction File "/home/keshav/Eureka/demos/JWST/../../eureka/S3_data_reduction/init.py", line 5, in from . import miri File "/home/keshav/Eureka/demos/JWST/../../eureka/S3_data_reduction/miri.py", line 4, in import astraeus.xarrayIO as xrio ModuleNotFoundError: No module named 'astraeus.xarrayIO'

What operating system are you using?

linux ubuntu 20.04

What version of Python are you running?

No response

What Python packages do you have installed?

(base) keshav@dev:~/Eureka/demos/JWST$ conda list

packages in environment at /home/keshav/miniconda3:

#

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
asdf 2.11.1 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 astropy 5.0.4 pypi_0 pypi astropy-healpix 0.6 pypi_0 pypi astroscrappy 1.1.0 pypi_0 pypi attrs 21.4.0 pypi_0 pypi bayesicfitting 3.0.1 pypi_0 pypi brotlipy 0.7.0 py39h27cfd23_1003
ca-certificates 2021.10.26 h06a4308_2
ccdproc 2.3.1 pypi_0 pypi certifi 2021.10.8 py39h06a4308_2
cffi 1.15.0 py39hd667e15_1
charset-normalizer 2.0.4 pyhd3eb1b0_0
conda 4.11.0 py39h06a4308_0
conda-content-trust 0.1.1 pyhd3eb1b0_0
conda-package-handling 1.7.3 py39h27cfd23_1
crds 11.14.0 pypi_0 pypi cryptography 36.0.0 py39h9ce1e76_0
cycler 0.11.0 pypi_0 pypi drizzle 1.13.4 pypi_0 pypi filelock 3.6.0 pypi_0 pypi fonttools 4.33.3 pypi_0 pypi future 0.18.2 pypi_0 pypi gwcs 0.18.1 pypi_0 pypi h5py 3.6.0 pypi_0 pypi idna 3.3 pyhd3eb1b0_0
imageio 2.19.1 pypi_0 pypi jmespath 1.0.0 pypi_0 pypi jsonschema 4.5.1 pypi_0 pypi jwst 1.5.0 pypi_0 pypi kiwisolver 1.4.2 pypi_0 pypi ld_impl_linux-64 2.35.1 h7274673_9
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgomp 9.3.0 h5101ec6_17
libstdcxx-ng 9.3.0 hd4cf53a_17
lxml 4.8.0 pypi_0 pypi matplotlib 3.5.2 pypi_0 pypi ncurses 6.3 h7f8727e_2
networkx 2.8 pypi_0 pypi numpy 1.22.3 pypi_0 pypi openssl 1.1.1m h7f8727e_0
packaging 21.3 pypi_0 pypi parsley 1.3 pypi_0 pypi photutils 1.4.0 pypi_0 pypi pillow 9.1.0 pypi_0 pypi pip 21.2.4 py39h06a4308_0
poppy 1.0.2 pypi_0 pypi psutil 5.9.0 pypi_0 pypi pycosat 0.6.3 py39h27cfd23_0
pycparser 2.21 pyhd3eb1b0_0
pyerfa 2.0.0.1 pypi_0 pypi pyopenssl 21.0.0 pyhd3eb1b0_1
pyparsing 3.0.9 pypi_0 pypi pyrsistent 0.18.1 pypi_0 pypi pysocks 1.7.1 py39h06a4308_0
python 3.9.7 h12debd9_1
python-dateutil 2.8.2 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 2.27.1 pyhd3eb1b0_0
ruamel_yaml 0.15.100 py39h27cfd23_0
scikit-image 0.19.2 pypi_0 pypi scipy 1.8.0 pypi_0 pypi semantic-version 2.9.0 pypi_0 pypi setuptools 58.0.4 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_0
spherical-geometry 1.2.22 pypi_0 pypi sqlite 3.37.0 hc218d9a_0
stcal 0.6.4 pypi_0 pypi stdatamodels 0.4.2 pypi_0 pypi stpipe 0.3.3 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 tifffile 2022.5.4 pypi_0 pypi tk 8.6.11 h1ccaba5_0
tqdm 4.62.3 pyhd3eb1b0_1
tweakwcs 0.7.4 pypi_0 pypi tzdata 2021e hda174b7_0
urllib3 1.26.7 pyhd3eb1b0_0
wheel 0.37.1 pyhd3eb1b0_0
xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
zlib 1.2.11 h7f8727e_4

Code of Conduct

kevin218 commented 2 years ago

First try: pip install git+https://github.com/kevin218/Astraeus@main Otherwise, try: pip install git+https://github.com/kevin218/Astraeus@0.1 Let me know which one worked for you.

jovian-explorer commented 2 years ago

thanks, this worked. new errror though,

Traceback (most recent call last): File "/home/keshav/Eureka/demos/JWST/run_eureka.py", line 3, in import eureka.lib.plots File "/home/keshav/Eureka/demos/JWST/../../eureka/init.py", line 20, in from . import S3_data_reduction File "/home/keshav/Eureka/demos/JWST/../../eureka/S3_data_reduction/init.py", line 8, in from . import niriss File "/home/keshav/Eureka/demos/JWST/../../eureka/S3_data_reduction/niriss.py", line 26, in import pyximport ModuleNotFoundError: No module named 'pyximport

jovian-explorer commented 2 years ago

Is there some way to check what else is missing or is this the only way? one at a time I mean

jovian-explorer commented 2 years ago

First try: pip install git+https://github.com/kevin218/Astraeus@main Otherwise, try: pip install git+https://github.com/kevin218/Astraeus@0.1 Let me know which one worked for you.

first one worked perfectly for me

kevin218 commented 2 years ago

Check from the command line to see if import cython works. If it's found but doesn't import, it may be an indication of paths being wrong someplace. If cython isn't found, go back to ReadTheDocs to make sure you've installed Eureka! correctly.

jovian-explorer commented 2 years ago

(base) keshav@dev:~/Eureka/demos/JWST$ import cython import-im6.q16: attempt to perform an operation not allowed by the security policy `PS' @ error/constitute.c/IsCoderAuthorized/408.

kevin218 commented 2 years ago

I should note that we're in the middle of making major changes (including having stable releases and moving future changes to a development branch), so the main branch is a bit of a mess this week.

jovian-explorer commented 2 years ago

Welp shit. I needed to run the entire pipeline for NIRSpec to show to my project guide by 18th. I hope you guys are done before that

kevin218 commented 2 years ago

You can always revert back to an older version of Eureka! With that said, NIRSpec should work on the current version in main.

jovian-explorer commented 2 years ago

I was using that only. the one I had installed during the ERS workshop. But somehow it wasn't working for some reason. I thought it would be better to update to a newer version and not go through the hassle of sorting out errors in the older version. Now I realise how wrong I was.

kevin218 commented 2 years ago

(base) keshav@dev:~/Eureka/demos/JWST$ import cython import-im6.q16: attempt to perform an operation not allowed by the security policy `PS' @ error/constitute.c/IsCoderAuthorized/408.

It would help to open a python session first.

jovian-explorer commented 2 years ago

Check from the command line to see if import cython works. If it's found but doesn't import, it may be an indication of paths being wrong someplace. If cython isn't found, go back to ReadTheDocs to make sure you've installed Eureka! correctly.

It is working okay

jovian-explorer commented 2 years ago

Okay what now? :no_mouth:

taylorbell57 commented 2 years ago

I'm away from my computer this morning, but I can help troubleshoot in a few hours when I get back if you're still having issues. My first recommendation would be to install from scratch (make a new conda environment, and follow the instructions on the readthedocs page). Those instructions work well for me on Mac and Ubuntu.

jovian-explorer commented 2 years ago

this is the from scratch installation. Should I try it from scratch again? :no_mouth:

taylorbell57 commented 2 years ago

When did you last try starting from scratch? This morning or a long time ago?

jovian-explorer commented 2 years ago

this morning

taylorbell57 commented 2 years ago

Because if you'd started from scratch and followed the readthedocs instructions you wouldn't have needed to manually install Astraeus, so I think you haven't started from scratch in a while

taylorbell57 commented 2 years ago

Ah, but then you did git pull afterwards? Then do try starting from scratch again

jovian-explorer commented 2 years ago

i'll try again tomorrow then I guess

jovian-explorer commented 2 years ago

okay will do. Will let you know in this thread itself.

jovian-explorer commented 2 years ago

I have reinstalled everything. This time, the libraries are all okay I guess. Some other issue this time. I think with the files I am using themselves.

jovian-explorer commented 2 years ago

(base) keshav@dev:~/Data/JWST-Sim/NIRSpec$ python3 run_eureka.py WARNING: Unable to find an output metadata file from Eureka!'s S2 in the folder: "/home/keshav/Data/JWST-Sim/NIRSpec/Stage1/" Assuming this S2 data was produced by the JWST pipeline instead.

Starting Stage 2 Reduction Input directory: /home/keshav/Data/JWST-Sim/NIRSpec/Stage1/ Output directory: /home/keshav/Data/JWST-Sim/NIRSpec/Stage2/S2_2022-05-13_wasp39b_run6/ Copying S2 control file

Found 1 data file(s) ending in rateints.fits 2022-05-13 12:05:32,364 - stpipe.EurekaSpec2Pipeline - INFO - EurekaSpec2Pipeline instance created. 2022-05-13 12:05:32,365 - stpipe.EurekaSpec2Pipeline.bkg_subtract - INFO - BackgroundStep instance created. 2022-05-13 12:05:32,366 - stpipe.EurekaSpec2Pipeline.assign_wcs - INFO - AssignWcsStep instance created. 2022-05-13 12:05:32,366 - stpipe.EurekaSpec2Pipeline.imprint_subtract - INFO - ImprintStep instance created. 2022-05-13 12:05:32,367 - stpipe.EurekaSpec2Pipeline.msa_flagging - INFO - MSAFlagOpenStep instance created. 2022-05-13 12:05:32,367 - stpipe.EurekaSpec2Pipeline.extract_2d - INFO - Extract2dStep instance created. 2022-05-13 12:05:32,369 - stpipe.EurekaSpec2Pipeline.master_background - INFO - MasterBackgroundNrsSlitsStep instance created. 2022-05-13 12:05:32,370 - stpipe.EurekaSpec2Pipeline.master_background.flat_field - INFO - FlatFieldStep instance created. 2022-05-13 12:05:32,371 - stpipe.EurekaSpec2Pipeline.master_background.pathloss - INFO - PathLossStep instance created. 2022-05-13 12:05:32,371 - stpipe.EurekaSpec2Pipeline.master_background.barshadow - INFO - BarShadowStep instance created. 2022-05-13 12:05:32,372 - stpipe.EurekaSpec2Pipeline.master_background.photom - INFO - PhotomStep instance created. 2022-05-13 12:05:32,372 - stpipe.EurekaSpec2Pipeline.wavecorr - INFO - WavecorrStep instance created. 2022-05-13 12:05:32,373 - stpipe.EurekaSpec2Pipeline.flat_field - INFO - FlatFieldStep instance created. 2022-05-13 12:05:32,373 - stpipe.EurekaSpec2Pipeline.srctype - INFO - SourceTypeStep instance created. 2022-05-13 12:05:32,374 - stpipe.EurekaSpec2Pipeline.straylight - INFO - StraylightStep instance created. 2022-05-13 12:05:32,374 - stpipe.EurekaSpec2Pipeline.fringe - INFO - FringeStep instance created. 2022-05-13 12:05:32,375 - stpipe.EurekaSpec2Pipeline.pathloss - INFO - PathLossStep instance created. 2022-05-13 12:05:32,375 - stpipe.EurekaSpec2Pipeline.barshadow - INFO - BarShadowStep instance created. 2022-05-13 12:05:32,376 - stpipe.EurekaSpec2Pipeline.photom - INFO - PhotomStep instance created. 2022-05-13 12:05:32,377 - stpipe.EurekaSpec2Pipeline.resample_spec - INFO - ResampleSpecStep instance created. 2022-05-13 12:05:32,378 - stpipe.EurekaSpec2Pipeline.cube_build - INFO - CubeBuildStep instance created. 2022-05-13 12:05:32,378 - stpipe.EurekaSpec2Pipeline.extract_1d - INFO - Extract1dStep instance created. Starting file 1 of 1 Editing (in place) the waverange in the input file Traceback (most recent call last): File "/home/keshav/Data/JWST-Sim/NIRSpec/run_eureka.py", line 23, in s2_meta = s2.calibrateJWST(eventlabel, ecf_path=ecf_path) File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S2_calibrations/s2_calibrate.py", line 148, in calibrateJWST pipeline.run_eurekaS2(filename, meta, log) File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S2_calibrations/s2_calibrate.py", line 214, in run_eurekaS2 with datamodels.open(filename) as m: File "/home/keshav/miniconda3/lib/python3.9/site-packages/jwst/datamodels/util.py", line 198, in open model = new_class(init, kwargs) File "/home/keshav/miniconda3/lib/python3.9/site-packages/jwst/datamodels/cube.py", line 44, in init super(CubeModel, self).init(init=init, kwargs) File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/model_base.py", line 215, in init asdffile = fits_support.from_fits(init, self._schema, self._ctx, File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/fits_support.py", line 611, in from_fits known_keywords, known_datas = _load_from_schema( File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/fits_support.py", line 531, in _load_from_schema mschema.walk_schema(schema, callback) File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/schema.py", line 149, in walk_schema recurse(schema, [], None, ctx) File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/schema.py", line 137, in recurse recurse(val, path + [key], combiner, ctx) File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/schema.py", line 124, in recurse if callback(schema, path, combiner, ctx, recurse): File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/fits_support.py", line 509, in callback result = _fits_array_loader( File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/fits_support.py", line 461, in _fits_array_loader return from_fits_hdu(hdu, schema) File "/home/keshav/miniconda3/lib/python3.9/site-packages/stdatamodels/fits_support.py", line 640, in from_fits_hdu data = hdu.data File "/home/keshav/miniconda3/lib/python3.9/site-packages/astropy/utils/decorators.py", line 777, in get val = self.fget(obj) File "/home/keshav/miniconda3/lib/python3.9/site-packages/astropy/io/fits/hdu/image.py", line 235, in data data = self._get_scaled_image_data(self._data_offset, self.shape) File "/home/keshav/miniconda3/lib/python3.9/site-packages/astropy/io/fits/hdu/image.py", line 779, in _get_scaled_image_data raw_data = self._get_raw_data(shape, code, offset) File "/home/keshav/miniconda3/lib/python3.9/site-packages/astropy/io/fits/hdu/base.py", line 531, in _get_raw_data return self._file.readarray(offset=offset, dtype=code, shape=shape) File "/home/keshav/miniconda3/lib/python3.9/site-packages/astropy/io/fits/file.py", line 335, in readarray data.shape = shape ValueError: cannot reshape array of size 0 into shape (8192,32,512)

taylorbell57 commented 2 years ago

Glad to hear that reinstalling seems to have resolved the issue you were experiencing before! Can you copy-paste the outputs of conda list now, copy-paste the contents of your S2 ECF, and tell me which file you're trying to process so I can try and reproduce your new issue?

jovian-explorer commented 2 years ago

`(base) keshav@dev:~$ conda list

packages in environment at /home/keshav/miniconda3:

#

Name Version Build Channel

_libgcc_mutex 0.1 main
_openmp_mutex 4.5 1_gnu
alabaster 0.7.12 pypi_0 pypi asdf 2.10.1 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 0.9.26 pypi_0 pypi astraeus 0.1 pypi_0 pypi astropy 5.0.4 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 2.10.1 pypi_0 pypi backcall 0.2.0 pypi_0 pypi batman-package 2.4.8 pypi_0 pypi bayesicfitting 3.0.1 pypi_0 pypi beautifulsoup4 4.11.1 pypi_0 pypi bleach 5.0.0 pypi_0 pypi bokeh 2.4.2 pypi_0 pypi bottleneck 1.3.4 pypi_0 pypi brotlipy 0.7.0 py39h27cfd23_1003
ca-certificates 2021.10.26 h06a4308_2
ccdproc 2.3.1 pypi_0 pypi celerite 0.4.2 pypi_0 pypi certifi 2021.10.8 py39h06a4308_2
cffi 1.15.0 py39hd667e15_1
cftime 1.6.0 pypi_0 pypi charset-normalizer 2.0.4 pyhd3eb1b0_0
cloudpickle 2.0.0 pypi_0 pypi commonmark 0.9.1 pypi_0 pypi conda 4.11.0 py39h06a4308_0
conda-content-trust 0.1.1 pyhd3eb1b0_0
conda-package-handling 1.7.3 py39h27cfd23_1
corner 2.2.1 pypi_0 pypi crds 11.14.0 pypi_0 pypi cryptography 36.0.0 py39h9ce1e76_0
cycler 0.11.0 pypi_0 pypi cython 0.29.28 pypi_0 pypi dask 2022.5.0 pypi_0 pypi decorator 5.1.1 pypi_0 pypi defusedxml 0.7.1 pypi_0 pypi docutils 0.17.1 pypi_0 pypi drizzle 1.13.4 pypi_0 pypi dynesty 1.2.2 pypi_0 pypi emcee 3.1.2 pypi_0 pypi entrypoints 0.4 pypi_0 pypi eureka 0.0.1 pypi_0 pypi executing 0.8.3 pypi_0 pypi fastjsonschema 2.15.3 pypi_0 pypi filelock 3.6.0 pypi_0 pypi fonttools 4.33.3 pypi_0 pypi fsspec 2022.3.0 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 1.0.0 pypi_0 pypi h5py 3.1.0 pypi_0 pypi html5lib 1.1 pypi_0 pypi idna 3.3 pyhd3eb1b0_0
imageio 2.19.1 pypi_0 pypi imagesize 1.3.0 pypi_0 pypi importlib-metadata 4.11.3 pypi_0 pypi iniconfig 1.1.1 pypi_0 pypi ipython 8.3.0 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 1.0.0 pypi_0 pypi jsonschema 3.2.0 pypi_0 pypi jupyter-client 7.3.1 pypi_0 pypi jupyter-core 4.10.0 pypi_0 pypi jupyterlab-pygments 0.2.2 pypi_0 pypi jwst 1.3.3 pypi_0 pypi keyring 23.5.0 pypi_0 pypi kiwisolver 1.4.2 pypi_0 pypi ld_impl_linux-64 2.35.1 h7274673_9
libffi 3.3 he6710b0_2
libgcc-ng 9.3.0 h5101ec6_17
libgomp 9.3.0 h5101ec6_17
libstdcxx-ng 9.3.0 hd4cf53a_17
lmfit 1.0.3 pypi_0 pypi locket 1.0.0 pypi_0 pypi lxml 4.8.0 pypi_0 pypi markdown-it-py 2.1.0 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 mdit-py-plugins 0.3.0 pypi_0 pypi mdurl 0.1.1 pypi_0 pypi mistune 0.8.4 pypi_0 pypi myst-parser 0.17.2 pypi_0 pypi nbclient 0.6.3 pypi_0 pypi nbconvert 6.5.0 pypi_0 pypi nbformat 5.4.0 pypi_0 pypi nbsphinx 0.8.8 pypi_0 pypi ncurses 6.3 h7f8727e_2
nest-asyncio 1.5.5 pypi_0 pypi netcdf4 1.5.8 pypi_0 pypi networkx 2.8 pypi_0 pypi numpy 1.22.3 pypi_0 pypi numpydoc 1.3.1 pypi_0 pypi openssl 1.1.1m h7f8727e_0
packaging 21.3 pypi_0 pypi pandas 1.4.2 pypi_0 pypi pandocfilters 1.5.0 pypi_0 pypi parsley 1.3 pypi_0 pypi parso 0.8.3 pypi_0 pypi partd 1.2.0 pypi_0 pypi pexpect 4.8.0 pypi_0 pypi photutils 1.1.0 pypi_0 pypi pickleshare 0.7.5 pypi_0 pypi pillow 9.1.0 pypi_0 pypi pip 21.2.4 py39h06a4308_0
pluggy 1.0.0 pypi_0 pypi poppy 1.0.2 pypi_0 pypi prompt-toolkit 3.0.29 pypi_0 pypi psutil 5.9.0 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 pycosat 0.6.3 py39h27cfd23_0
pycparser 2.21 pyhd3eb1b0_0
pyerfa 2.0.0.1 pypi_0 pypi pygments 2.12.0 pypi_0 pypi pyopenssl 21.0.0 pyhd3eb1b0_1
pyparsing 3.0.9 pypi_0 pypi pyrsistent 0.18.1 pypi_0 pypi pysocks 1.7.1 py39h06a4308_0
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 pyzmq 22.3.0 pypi_0 pypi readline 8.1.2 h7f8727e_1
recommonmark 0.7.1 pypi_0 pypi reproject 0.8 pypi_0 pypi requests 2.27.1 pyhd3eb1b0_0
ruamel_yaml 0.15.100 py39h27cfd23_0
scikit-image 0.19.2 pypi_0 pypi scipy 1.8.0 pypi_0 pypi secretstorage 3.3.2 pypi_0 pypi semantic-version 2.9.0 pypi_0 pypi setuptools 58.0.4 py39h06a4308_0
six 1.16.0 pyhd3eb1b0_0
snowballstemmer 2.2.0 pypi_0 pypi soupsieve 2.3.2.post1 pypi_0 pypi spherical-geometry 1.2.22 pypi_0 pypi sphinx 4.5.0 pypi_0 pypi sphinx-rtd-theme 1.0.0 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 3.37.0 hc218d9a_0
stack-data 0.2.0 pypi_0 pypi stcal 0.6.4 pypi_0 pypi stdatamodels 0.2.4 pypi_0 pypi stpipe 0.3.3 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 0.4.1 pypi_0 pypi tifffile 2022.5.4 pypi_0 pypi tinycss2 1.1.1 pypi_0 pypi tk 8.6.11 h1ccaba5_0
tomli 2.0.1 pypi_0 pypi toolz 0.11.2 pypi_0 pypi tornado 6.1 pypi_0 pypi tqdm 4.62.3 pyhd3eb1b0_1
traitlets 5.2.0 pypi_0 pypi tweakwcs 0.7.4 pypi_0 pypi typing-extensions 4.2.0 pypi_0 pypi tzdata 2021e hda174b7_0
uncertainties 3.1.6 pypi_0 pypi urllib3 1.26.7 pyhd3eb1b0_0
wcwidth 0.2.5 pypi_0 pypi webencodings 0.5.1 pypi_0 pypi wheel 0.37.1 pyhd3eb1b0_0
xarray 2022.3.0 pypi_0 pypi xz 5.2.5 h7b6447c_0
yaml 0.2.5 h7b6447c_0
zipp 3.8.0 pypi_0 pypi zlib 1.2.11 h7f8727e_4
(base) keshav@dev:~$ `

jovian-explorer commented 2 years ago

Eureka! Control File for Stage 2: Data Reduction

Stage 2 Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-2

suffix rateints # Data file suffix

Controls the cross-dispersion extraction

slit_y_low -1 # Use None to rely on the default parameters slit_y_high 50 # Use None to rely on the default parameters

Modify the existing file to change the dispersion extraction - FIX: DOES NOT WORK CURRENTLY

waverange_start 6e-08 # Use None to rely on the default parameters waverange_end 6e-06 # Use None to rely on the default parameters

Note: different instruments and modes will use different steps by default

skip_bkg_subtract True # Not run for TSO observations skip_imprint_subtract True # Not run for NIRSpec Fixed Slit skip_msa_flagging True # Not run for NIRSpec Fixed Slit skip_extract_2d False skip_srctype False skip_master_background True # Not run for NIRSpec Fixed Slit skip_wavecorr False skip_flat_field True # NOTE At the time the NIRSpec ERS Hackathon simulated data was created, this step did not work correctly and is by default turned off. skip_straylight True # Not run for NIRSpec Fixed Slit skip_fringe True # Not run for NIRSpec Fixed Slit skip_pathloss True # Not run for TSO observations skip_barshadow True # Not run for NIRSpec Fixed Slit skip_photom True # Recommended to skip to get better uncertainties out of Stage 3. skip_resample True # Not run for TSO observations skip_cube_build True # Not run for NIRSpec Fixed Slit skip_extract_1d False

Diagnostics

testing_S2 False hide_plots False # If True, plots will automatically be closed rather than popping up

Project directory

topdir /home/keshav/Data/JWST-Sim/NIRSpec

Directories relative to topdir

inputdir /Stage1 outputdir /Stage2

jovian-explorer commented 2 years ago

I think that the error was in the file I downloaded itself. with a tiny dataset I managed to run stage 4 as well. althought, stage 5 is giving some error.

Starting Stage 5: Light Curve Fitting

Finished loading parameters from /home/keshav/Data/JWST-Sim/NIRSpec/Stage4/S4_2022-05-14_wasp39b_run1/ap6_bg7/S4_wasp39b_ap6_bg7_LCData.h5 Input directory: /home/keshav/Data/JWST-Sim/NIRSpec/Stage4/S4_2022-05-14_wasp39b_run1/ap6_bg7/ Output directory: /home/keshav/Data/JWST-Sim/NIRSpec/Stage5/S5_2022-05-14_wasp39b_run1/ap6_bg7/ Copying S5 control file Copying S5 parameter control file Traceback (most recent call last): File "/home/keshav/Data/JWST-Sim/NIRSpec/run_eureka.py", line 29, in s5_meta = s5.fitlc(eventlabel, ecf_path=ecf_path, s4_meta=s4_meta) File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 119, in fitlc params.write(meta.outputdir) File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/lib/readEPF.py", line 383, in write with open(os.path.join(folder, self.filename), 'w') as file: AttributeError: 'Parameters' object has no attribute 'filename'

jovian-explorer commented 2 years ago

this is the eureka.py file I am running

`import sys, os sys.path.append(f'..{os.sep}..{os.sep}') import eureka.lib.plots import eureka.S1_detector_processing.s1_process as s1 import eureka.S2_calibrations.s2_calibrate as s2 import eureka.S3_data_reduction.s3_reduce as s3 import eureka.S4_generate_lightcurves.s4_genLC as s4 import eureka.S5_lightcurve_fitting.s5_fit as s5 import eureka.S6_planet_spectra.s6_spectra as s6

# Set up some parameters to make plots look nicer. You can set usetex=True if you have LaTeX installed

eureka.lib.plots.set_rc(style='eureka', usetex=False, filetype='.png')

# eventlabel = 'imaging_template'
# eventlabel = 'miri_lrs_template'
# eventlabel = 'nirspec_fs_template'

eventlabel = 'wasp39b' ecf_path = '.'+os.sep

if name == 'main':

s1_meta = s1.rampfitJWST(eventlabel, ecf_path=ecf_path)

s2_meta = s2.calibrateJWST(eventlabel, ecf_path=ecf_path)

s3_spec, s3_meta = s3.reduce(eventlabel, ecf_path=ecf_path, s2_meta=s2_meta)

s4_spec, s4_lc, s4_meta = s4.genlc(eventlabel, ecf_path=ecf_path, s3_meta=s3_meta)

s5_meta = s5.fitlc(eventlabel, ecf_path=ecf_path, s4_meta=s4_meta)

s6_meta = s6.plot_spectra(eventlabel, ecf_path=ecf_path, s5_meta=s5_meta)`
kevin218 commented 2 years ago

I wonder if the FITS file is corrupt? Have you tried running pytest on the NIRSpec Python file in the Tests directory? If that works, you may need to re-download your data.

jovian-explorer commented 2 years ago

The large one? it seems that way to me as well. I am downloading it again. The tiny one? not sure.

jovian-explorer commented 2 years ago

============================= test session starts ============================== platform linux -- Python 3.9.7, pytest-7.1.2, pluggy-1.0.0 rootdir: /home/keshav/Data/JWST-Sim/NIRSpec plugins: jwst-1.3.3, asdf-2.10.1 collected 1 item

test_NIRSpec.py

IMPORTANT: Make sure that any changes to the ecf files are included in demo ecf files and documentation (docs/source/ecf.rst)

NIRSpec S2-5 test: Killed

kevin218 commented 2 years ago

The fact that it says Killed suggests to me that you've hit a memory limit on your computer. This shouldn't happen unless you have lots of open files. Have you tried restarting your computer?

jovian-explorer commented 2 years ago

test_NIRSpec.py::test_NIRSpec /home/keshav/miniconda3/lib/python3.9/site-packages/astropy/io/fits/file.py:379: AstropyUserWarning: File may have been truncated: actual file length (25165824) is smaller than the expected size (33572160) warnings.warn('File may have been truncated: actual file length '

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html ================================================ short test summary info ================================================= FAILED test_NIRSpec.py::test_NIRSpec - AttributeError: 'Parameters' object has no attribute 'filename' ======================================== 1 failed, 1 warning in 139.44s (0:02:19) ======================================== Exception ignored in: <function CachingFileManager.del at 0x7fe85a002af0> Traceback (most recent call last): File "/home/keshav/miniconda3/lib/python3.9/site-packages/xarray/backends/file_manager.py", line 244, in del File "/home/keshav/miniconda3/lib/python3.9/site-packages/xarray/backends/file_manager.py", line 222, in close File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5netcdf/core.py", line 1125, in close File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5py/_hl/files.py", line 445, in close File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 275, in h5py.h5f.get_obj_ids File "h5py/h5i.pyx", line 46, in h5py.h5i.wrap_identifier ImportError: sys.meta_path is None, Python is likely shutting down Exception ignored in: <function File.close at 0x7fe85930f160> Traceback (most recent call last): File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5netcdf/core.py", line 1125, in close File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5py/_hl/files.py", line 445, in close File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 275, in h5py.h5f.get_obj_ids File "h5py/h5i.pyx", line 46, in h5py.h5i.wrap_identifier ImportError: sys.meta_path is None, Python is likely shutting down Exception ignored in: <function CachingFileManager.del at 0x7fe85a002af0> Traceback (most recent call last): File "/home/keshav/miniconda3/lib/python3.9/site-packages/xarray/backends/file_manager.py", line 244, in del File "/home/keshav/miniconda3/lib/python3.9/site-packages/xarray/backends/file_manager.py", line 222, in close File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5netcdf/core.py", line 1125, in close File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5py/_hl/files.py", line 445, in close File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 275, in h5py.h5f.get_obj_ids File "h5py/h5i.pyx", line 46, in h5py.h5i.wrap_identifier ImportError: sys.meta_path is None, Python is likely shutting down Exception ignored in: <function File.close at 0x7fe85930f160> Traceback (most recent call last): File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5netcdf/core.py", line 1125, in close File "/home/keshav/miniconda3/lib/python3.9/site-packages/h5py/_hl/files.py", line 445, in close File "h5py/_objects.pyx", line 54, in h5py._objects.with_phil.wrapper File "h5py/_objects.pyx", line 55, in h5py._objects.with_phil.wrapper File "h5py/h5f.pyx", line 275, in h5py.h5f.get_obj_ids File "h5py/h5i.pyx", line 46, in h5py.h5i.wrap_identifier ImportError: sys.meta_path is None, Python is likely shutting down

jovian-explorer commented 2 years ago

The fact that it says Killed suggests to me that you've hit a memory limit on your computer. This shouldn't happen unless you have lots of open files. Have you tried restarting your computer?

that was for the large dataset. The previous comment is for a tiny dataset I used.

kevin218 commented 2 years ago

Strange... I'm unable to reproduce your error while running pytest test_NIRSpec.py. Maybe Taylor can offer more help?

jovian-explorer commented 2 years ago

I am able to run upto stage 4 using a tiny dataset. stage 5 gives this error

Starting Stage 5: Light Curve Fitting

Finished loading parameters from /home/keshav/Data/JWST-Sim/NIRSpec/Stage4/S4_2022-05-16_wasp39b_run1/ap6_bg7/S4_wasp39b_ap6_bg7_LCData.h5 Input directory: /home/keshav/Data/JWST-Sim/NIRSpec/Stage4/S4_2022-05-16_wasp39b_run1/ap6_bg7/ Output directory: /home/keshav/Data/JWST-Sim/NIRSpec/Stage5/S5_2022-05-16_wasp39b_run1/ap6_bg7/ Copying S5 control file Copying S5 parameter control file Traceback (most recent call last): File "/home/keshav/Data/JWST-Sim/NIRSpec/run_eureka.py", line 29, in s5_meta = s5.fitlc(eventlabel, ecf_path=ecf_path, s4_meta=s4_meta) File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 119, in fitlc params.write(meta.outputdir) File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/lib/readEPF.py", line 383, in write with open(os.path.join(folder, self.filename), 'w') as file: AttributeError: 'Parameters' object has no attribute 'filename'

kevin218 commented 2 years ago

Can you share your ECF and EPF files?

jovian-explorer commented 2 years ago 
# Stage 5 Fit Parameters Documentation: https://eurekadocs.readthedocs.io/en/latest/ecf.html#stage-5-fit-parameters

#Name        Value         Free?          PriorPar1    PriorPar2    PriorType
# 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           0.173010       'free'         0.1         0.3          U
#fp           0.008         'free'         0            0.5          U
# ----------------------
# ** 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
# ------------------
# ** Orbital parameters **
# ------------------
per          4.055259       'free'         4.055259     1e-5         N
t0           0.5            'free'         0.4     0.6     U
time_offset  0              'independent'
inc          87.93          'free'         85       90        U
a            11.612         'free'         10         13         U
ecc          0.0            'fixed'        0            1            U
w            90.            'fixed'        0            180          U
# -------------------------
# ** Limb darkening parameters **
# Choose limb_dark from ['uniform', 'linear', 'quadratic', 'kipping2013', 'square-root', 'logarithmic', 'exponential', '4-parameter']
# -------------------------
limb_dark    'kipping2013'  'independent'
u1           0.5            'free'         0            1            U
u2           0.5            'free'         0            1            U
# --------------------
# ** Systematic variables **
# polynomial model variables (c0--c9 for 0th--3rd order polynomials in time); Fitting at least c0 is very strongly recommended!
# expramp model variables (r0--r2 for one exponential ramp, r3--r5 for a second exponential ramp)
# GP model parameters (A, WN, m1, m2) in log scale
# --------------------
c0           1              'free'         0.95         1.05         U
c1           0              'free'         -0.1         0.1          U
#A            -5            'free'         -20.         -5.          U
#WN           -15           'free'         -20.         -10.         U
#m1           -5            'free'         -10.         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
# Use WN parameter in GP model parameters to account for white noise in the GP model
# -----------
scatter_mult 1              'free'         1            0.1          N
jovian-explorer commented 2 years ago 
# Eureka! Control File for Stage 5: Lightcurve Fitting

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

ncpu            8 # The number of CPU threads to use when running emcee or dynesty in parallel

allapers        False                   # Run S5 on all of the apertures considered in S4? Otherwise will use newest output in the inputdir
rescale_err     False                   # Rescale uncertainties to have reduced chi-squared of unity
fit_par         ./S5_fit_par_template.epf   # What fitting epf do you want to use?
verbose         True                    # If True, more details will be printed about steps
fit_method      [dynesty]               #options are: lsq, emcee, dynesty (can list multiple types separated by commas)
run_myfuncs     [batman_tr,polynomial]  #options are: batman_tr, batman_ecl, sinusoid_pc, expramp, GP, and polynomial (can list multiple types separated by commas)

# Limb darkening controls (not yet implemented)
#fix_ld          False #use limb darkening file?
#ld_file         /path/to/limbdarkening/ld_outputfile.txt  #location of limb darkening file

# General fitter
old_fitparams   None # filename relative to topdir that points to a fitparams csv to resume where you left off (set to None to start from scratch)

#lsq
lsq_method      'Nelder-Mead' # The scipy.optimize.minimize optimization method to use
lsq_tol         1e-6    # The tolerance for the scipy.optimize.minimize optimization method
lsq_maxiter     None    # Maximum number of iterations to perform. Depending on the method each iteration may use several function evaluations. Set to None to use the default value

#mcmc
old_chain       None    # Output folder relative to topdir that contains an old emcee chain to resume where you left off (set to None to start from scratch)
lsq_first       True    # Initialize with an initial lsq call (can help shorten burn-in, but turn off if lsq fails). Only used if old_chain is None
run_nsteps      1000
run_nwalkers    200
run_nburn       500     # How many of run_nsteps should be discarded as burn-in steps

#dynesty
run_nlive       1024    # Must be > ndim * (ndim + 1) // 2
run_bound       'multi'
run_sample      'auto'
run_tol         0.1

#GP inputs
kernel_inputs   ['time'] #options: time
kernel_class    ['Matern32'] #options: ExpSquared, Matern32, Exp, RationalQuadratic for george, Matern32 for celerite (sums of kernels possible for george separated by commas)
GP_package      'celerite' #options: george, celerite

# Plotting controls
interp          False   # Should astrophysical model be interpolated (useful for uneven sampling like that from HST)

# Diagnostics
isplots_S5      5       # Generate few (1), some (3), or many (5) figures (Options: 1 - 5)
testing_S5      False   # Boolean, set True to only use the first spectral channel
testing_model   False   # Boolean, set True to only inject a model source of systematics
hide_plots      False   # If True, plots will automatically be closed rather than popping up

# Project directory
topdir          /home/keshav/Data/JWST-Sim/NIRSpec

# Directories relative to topdir
inputdir        /Stage4   # The folder containing the outputs from Eureka!'s S4 pipeline (will be overwritten if calling S4 and S5 sequentially)
outputdir       /Stage5
jovian-explorer commented 2 years ago

Stage 5 is finally running now. I will keep you posted. Also, is there some way to increase the speed of this stage?

jovian-explorer commented 2 years ago

It has hit an error (again)

Traceback (most recent call last):
  File "/home/keshav/Data/JWST-Sim/NIRSpec/run_eureka.py", line 29, in <module>
    s5_meta = s5.fitlc(eventlabel, ecf_path=ecf_path, s4_meta=s4_meta)
  File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 173, in fitlc
    meta = fit_channel(meta,time,flux,channel,flux_err,eventlabel,sharedp,params,log,longparamlist,time_units,paramtitles,chanrng)
  File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/s5_fit.py", line 257, in fit_channel
    lc_model.fit(model, meta, log, fitter='dynesty')
  File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/lightcurve.py", line 156, in fit
    fit_model = self.fitter_func(self, model, meta, log, **kwargs)
  File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/fitters.py", line 644, in dynestyfitter
    plots.plot_corner(samples, lc, meta, freenames, fitter='dynesty')
  File "/home/keshav/miniconda3/lib/python3.9/site-packages/eureka/S5_lightcurve_fitting/plots_s5.py", line 203, in plot_corner
    fig = corner.corner(samples, fig=fig, quantiles=[0.16, 0.5, 0.84], max_n_ticks=3,
  File "/home/keshav/miniconda3/lib/python3.9/site-packages/corner/corner.py", line 226, in corner
    return corner_impl(
  File "/home/keshav/miniconda3/lib/python3.9/site-packages/corner/core.py", line 121, in corner_impl
    raise ValueError(
ValueError: It looks like the parameter(s) in column(s) 9 have no dynamic range. Please provide a `range` argument.
taylorbell57 commented 2 years ago

Hi Keshav, we've covered multiple problems in this one issue, so it is a pretty hard for me to understand the status of all the different questions you've asked. In general, please try to open one issue for each specific problem you encounter and please try to provide as many details about what caused that problem when you first open that issue so that we can get to the bottom of the issue quicker. In general, please also make a concerted effort to troubleshoot the issue yourself and read the documentation for the most up-to-date recommendations.

I've enumerated below the problems that you've encountered below with my understanding of what might have caused them or the current status of that issue:

  1. ModuleNotFoundError: No module named 'astraeus.xarrayIO'
    • This was caused by updating the code but not updating the requirements.
    • This issue has been resolved for you.
  2. ModuleNotFoundError: No module named 'pyximport'
    • This was caused by updating the code but not updating the requirements.
    • This issue has been resolved for you.
  3. ValueError: cannot reshape array of size 0 into shape (8192,32,512) and AstropyUserWarning: File may have been truncated: actual file length (25165824) is smaller than the expected size (33572160)
    • To me it seems quite probable that your download of that file had been interrupted and/or the file had been corrupted. I do not believe that this is a bug related to Eureka.
    • I believe this issue still persists for you?
  4. NIRSpec S2-5 test: Killed
    • I'm not quite clear what you did to get this. Did you edit the ECF files in the test folder? To run the tests, you should just be doing pytest test_NIRSpec.py within the test folder (without having edited any of the ECF files or anything). The file should be plenty small and shouldn't overflow the RAM or anything.
    • I believe this issue still persists for you?
  5. AttributeError: 'Parameters' object has no attribute 'filename'
    • I believe you didn't update the fit_par setting in your Stage 5 ECF to point to the EPF file you'd made. I'm adding a bit of code so that this gets caught earlier on and gives a more helpful error message.
    • I believe you worked out this issue yourself.
  6. ValueError: It looks like the parameter(s) in column(s) 9 have no dynamic range. Please provide arangeargument.
    • This happens in general when a parameter cannot successfully be fit and all the values for one of the parameters in the chain are the same. This typically happens because the starting position is outside of the priors (for emcee) or because the priors are invalid (for dynesty). I recommend you look closely at all of your EPF settings and make sure they look correct. If the EPF and ECF you copy-pasted above are exactly what you ran, then I don't think you should have encountered that issue, but I don't have everything I'd need to reproduce your issue. If you are still encountering this issue, please open it in a separate issue and provide as many details as you can so that I can try to investigate the issue.
    • I believe this issue still persists for you?
  7. Also, is there some way to increase the speed of this stage (Stage 5)?
    • Setting ncpu equal to the number of threads available on your cpu (typically 2 times the number of cpu cores you have) is the best option available for now. You should try just running the lsq fitter if you're debugging things though as that runs far faster than the other fitters. Once you have that working, you can try dynesty or something else to get uncertainties. You can also set testing_S5 to True if you want to try dynesty or something for just a single wavelength and then look at the plots afterward to understand what went well or what went wrong
jovian-explorer commented 2 years ago

Okay yeah,this thread has been quite long. I'll open a new one with the last issue. Thanks.