sstamer23 commented 4 days ago

FAQ check

[X] Yes, I checked the FAQ and my question has not been addressed.

Instrument

NIRSpec (Stages 1-3)

What happened?

So I'm trying to fix my window for this new data I've received, and I'm getting the following error. I saw the discussion in #685 and was able to get that error to go away by refining my window further, but now I'm getting this one.

Error traceback output

Starting Stage 3 Reduction

Input directory: /Users/sarahstamer/Desktop/Grad/2024-2025/Research/LTT-9779b_Eureka_Analysis/Data/NRS2Calints/ Found 7 data file(s) ending in calints.fits Output directory: /Users/sarahstamer/Desktop/Grad/2024-2025/Research/LTT-9779b_Eureka_Analysis/Data/Stage3/S3_2024-11-22_nirspec_fs_template_run21/ap6_bg7/ Using ap=6, bg=7, expand=1 Copying S3 control file Starting file 1 of 7 Reading file 1... Masking NaNs/infs in data arrays... FLUX has 411673 NaNs/infs, which is 2.25% of all pixels. ERR has 411673 NaNs/infs, which is 2.25% of all pixels. V0 has 411673 NaNs/infs, which is 2.25% of all pixels. Locating source position... Traceback (most recent call last): File "/Users/sarahstamer/Desktop/Grad/2024-2025/Research/LTT-9779b_Eureka_Analysis/DataAnalysis/Code/run_eureka.py", line 28, in spec, meta = s3.reduce(eventlabel, ecf_path=ecf_path) File "/opt/miniconda3/envs/eureka/lib/python3.10/site-packages/eureka-1.1.dev0+gf09c39a8.d20241108-py3.10.egg/eureka/S3_data_reduction/s3_reduce.py", line 350, in reduce File "/opt/miniconda3/envs/eureka/lib/python3.10/site-packages/eureka-1.1.dev0+gf09c39a8.d20241108-py3.10.egg/eureka/S3_data_reduction/source_pos.py", line 101, in source_pos_wrapper File "/opt/miniconda3/envs/eureka/lib/python3.10/site-packages/eureka-1.1.dev0+gf09c39a8.d20241108-py3.10.egg/eureka/S3_data_reduction/source_pos.py", line 162, in source_pos File "/opt/miniconda3/envs/eureka/lib/python3.10/site-packages/eureka-1.1.dev0+gf09c39a8.d20241108-py3.10.egg/eureka/S3_data_reduction/source_pos.py", line 413, in source_pos_gauss File "/opt/miniconda3/envs/eureka/lib/python3.10/site-packages/scipy/optimize/_minpack_py.py", line 832, in curve_fit raise TypeError(f"The number of func parameters={n} must not" TypeError: The number of func parameters=4 must not exceed the number of data points=3

What operating system are you using?

MacOS Sequoia 15.1

What version of Python are you running?

Python 3.10.14

What Python packages do you have installed?

packages in environment at /opt/miniconda3/envs/eureka:

#

Name Version Build Channel

aesara-theano-fallback 0.1.0 pypi_0 pypi alabaster 1.0.0 pypi_0 pypi appnope 0.1.4 pyhd8ed1ab_0 conda-forge arviz 0.20.0 pypi_0 pypi asciitree 0.3.3 pypi_0 pypi asdf 3.4.0 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 1.0.2 pypi_0 pypi astraeus 0.3 pypi_0 pypi astropy 6.1.2 pypi_0 pypi astropy-healpix 1.0.3 pypi_0 pypi astropy-iers-data 0.2024.8.19.0.32.16 pypi_0 pypi astroquery 0.4.7 pypi_0 pypi astroscrappy 1.2.0 pypi_0 pypi asttokens 2.4.1 pyhd8ed1ab_0 conda-forge 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 1.4.0 pypi_0 pypi bzip2 1.0.8 h6c40b1e_6
ca-certificates 2024.8.30 h8857fd0_0 conda-forge cachetools 5.5.0 pypi_0 pypi ccdproc 2.4.2 pypi_0 pypi celerite 0.4.3 pypi_0 pypi celerite2 0.3.2 pypi_0 pypi certifi 2024.7.4 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 comm 0.2.2 pyhd8ed1ab_0 conda-forge contourpy 1.2.1 pypi_0 pypi corner 2.2.2 pypi_0 pypi crds 11.18.1 pypi_0 pypi cycler 0.12.1 pypi_0 pypi dask 2024.8.1 pypi_0 pypi debugpy 1.8.6 py310h53e7c6a_0 conda-forge decorator 5.1.1 pyhd8ed1ab_0 conda-forge dill 0.3.8 pypi_0 pypi docutils 0.21.2 pypi_0 pypi drizzle 1.15.3 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 pyhd8ed1ab_0 conda-forge executing 2.0.1 pypi_0 pypi exoplanet 0.6.0 pypi_0 pypi exotic-ld 3.2.0 pypi_0 pypi fasteners 0.19 pypi_0 pypi fastprogress 1.0.3 pypi_0 pypi filelock 3.15.4 pypi_0 pypi fleck 1.1.2 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 0.4.3 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 2.35.1 pypi_0 pypi imagesize 1.4.1 pypi_0 pypi importlib-metadata 8.4.0 pypi_0 pypi iniconfig 2.0.0 pypi_0 pypi ipykernel 6.29.5 pyh57ce528_0 conda-forge ipython 8.26.0 pypi_0 pypi jaraco-classes 3.4.0 pypi_0 pypi jaraco-context 6.0.1 pypi_0 pypi jaraco-functools 4.0.2 pypi_0 pypi jedi 0.19.1 pyhd8ed1ab_0 conda-forge 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 jupyter_client 8.6.3 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 pyh31011fe_1 conda-forge jwst 1.15.1 pypi_0 pypi keyring 25.3.0 pypi_0 pypi kiwisolver 1.4.5 pypi_0 pypi krb5 1.21.3 h37d8d59_0 conda-forge lazy-loader 0.4 pypi_0 pypi libcxx 19.1.0 hf95d169_0 conda-forge libedit 3.1.20191231 h0678c8f_2 conda-forge libffi 3.4.4 hecd8cb5_1
libsodium 1.0.20 hfdf4475_0 conda-forge lmfit 1.3.2 pypi_0 pypi locket 1.0.0 pypi_0 pypi markupsafe 2.1.5 pypi_0 pypi matplotlib 3.9.2 pypi_0 pypi matplotlib-inline 0.1.7 pyhd8ed1ab_0 conda-forge mc3 3.2.0 pypi_0 pypi more-itertools 10.4.0 pypi_0 pypi ncurses 6.4 hcec6c5f_0
nest-asyncio 1.6.0 pyhd8ed1ab_0 conda-forge netcdf4 1.6.5 pypi_0 pypi networkx 3.3 pypi_0 pypi numcodecs 0.13.0 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 hd23fc13_0 conda-forge packaging 24.1 pyhd8ed1ab_0 conda-forge pandas 2.2.2 pypi_0 pypi parsley 1.3 pypi_0 pypi parso 0.8.4 pyhd8ed1ab_0 conda-forge partd 1.4.2 pypi_0 pypi patsy 0.5.6 pypi_0 pypi pexpect 4.9.0 pyhd8ed1ab_0 conda-forge photutils 1.13.0 pypi_0 pypi pickleshare 0.7.5 py_1003 conda-forge pillow 10.4.0 pypi_0 pypi pip 24.2 py310hecd8cb5_0
platformdirs 4.3.6 pyhd8ed1ab_0 conda-forge pluggy 1.5.0 pypi_0 pypi poppy 1.1.1 pypi_0 pypi prompt-toolkit 3.0.47 pyha770c72_0 conda-forge psutil 6.0.0 py310h837254d_1 conda-forge ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge pure_eval 0.2.3 pyhd8ed1ab_0 conda-forge pyerfa 2.0.1.4 pypi_0 pypi pygments 2.18.0 pyhd8ed1ab_0 conda-forge pymc3 3.11.4 pypi_0 pypi pymc3-ext 0.1.1 pypi_0 pypi pyparsing 3.1.2 pypi_0 pypi pysynphot 2.0.0 pypi_0 pypi pytest 8.3.2 pypi_0 pypi python 3.10.14 h5ee71fb_1
python-dateutil 2.9.0.post0 pypi_0 pypi python_abi 3.10 2_cp310 conda-forge pytz 2024.1 pypi_0 pypi pyvo 1.5.2 pypi_0 pypi pyyaml 6.0.2 pypi_0 pypi pyzmq 26.2.0 py310hfe2c05e_2 conda-forge readline 8.2 hca72f7f_0
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 1.9.3 pypi_0 pypi semantic-version 2.10.0 pypi_0 pypi semver 3.0.2 pypi_0 pypi setuptools 72.1.0 py310hecd8cb5_0
setuptools-scm 8.1.0 pypi_0 pypi shapely 2.0.6 pypi_0 pypi six 1.16.0 pyh6c4a22f_0 conda-forge snowballstemmer 2.2.0 pypi_0 pypi soupsieve 2.6 pypi_0 pypi spherical-geometry 1.3.2 pypi_0 pypi sphinx 8.0.2 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 sqlite 3.45.3 h6c40b1e_0
stack-data 0.6.3 pypi_0 pypi stack_data 0.6.2 pyhd8ed1ab_0 conda-forge 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 2024.8.10 pypi_0 pypi tk 8.6.14 h4d00af3_0
tomli 2.0.1 pypi_0 pypi toolz 0.12.1 pypi_0 pypi tornado 6.4.1 py310h837254d_1 conda-forge tqdm 4.66.5 pypi_0 pypi traitlets 5.14.3 pyhd8ed1ab_0 conda-forge tweakwcs 0.8.8 pypi_0 pypi typing_extensions 4.12.2 pyha770c72_0 conda-forge tzdata 2024.1 pypi_0 pypi uncertainties 3.2.2 pypi_0 pypi urllib3 2.2.2 pypi_0 pypi wcwidth 0.2.13 pyhd8ed1ab_0 conda-forge webencodings 0.5.1 pypi_0 pypi wheel 0.43.0 py310hecd8cb5_0
wiimatch 0.3.2 pypi_0 pypi xarray 2024.7.0 pypi_0 pypi xarray-einstats 0.8.0 pypi_0 pypi xz 5.4.6 h6c40b1e_1
zarr 2.18.2 pypi_0 pypi zeromq 4.3.5 hb33e954_5 conda-forge zipp 3.20.0 pypi_0 pypi zlib 1.2.13 h4b97444_1

Code of Conduct

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sstamer23 commented 4 days ago

Actually, made one number change on my window and now it's running, I'll reopen if I run into any further issues

sstamer23 commented 4 days ago

Never mind, it's back but with a new semaphore warning?

The above exception was the direct cause of the following exception: Traceback (most recent call last): File "/Users/sarahstamer/Desktop/Grad/2024-2025/Research/LTT-9779b_Eureka_Analysis/DataAnalysis/Code/run_eureka.py", line 28, in spec, meta = s3.reduce(eventlabel, ecf_path=ecf_path) File "/opt/miniconda3/envs/eureka/lib/python3.10/site-packages/eureka-1.1.dev0+gf09c39a8.d20241108-py3.10.egg/eureka/S3_data_reduction/s3_reduce.py", line 418, in reduce File "/opt/miniconda3/envs/eureka/lib/python3.10/site-packages/eureka-1.1.dev0+gf09c39a8.d20241108-py3.10.egg/eureka/S3_data_reduction/source_pos.py", line 89, in source_pos_wrapper File "/opt/miniconda3/envs/eureka/lib/python3.10/multiprocessing/pool.py", line 774, in get raise self._value TypeError: The number of func parameters=4 must not exceed the number of data points=3 /opt/miniconda3/envs/eureka/lib/python3.10/multiprocessing/resource_tracker.py:224: UserWarning: resource_tracker: There appear to be 9 leaked semaphore objects to clean up at shutdown warnings.warn('resource_tracker: There appear to be %d '

kevin218 commented 4 days ago

What aperture size are you using (spec_hw)? The source pos routine can fail if it is too small.

sstamer23 commented 4 days ago

That's set to 6 for me

sstamer23 commented 4 days ago

I think I got it fixed, just needed to do a complete update of Eureka.

kevin218 / Eureka

[Bug]: S3 Window Refinement leading to TypeError #725

FAQ check

Instrument

What happened?

Error traceback output

What operating system are you using?

What version of Python are you running?

What Python packages do you have installed?

packages in environment at /opt/miniconda3/envs/eureka:

Name Version Build Channel

Code of Conduct