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JP-3755: Remove unused options and add unit tests to SOSS extraction algorithm #9000

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JP-3755: Remove unused options and add unit tests to SOSS extraction algorithm #9000

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a1a6ca3
added unit tests for wv_map_bounds and arange_2d
emolter Oct 25, 2024
1842f84
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Oct 25, 2024
fbd4521
simplify oversample_grid and write tests
emolter Oct 25, 2024
7cb20b1
fixed edge case where extrapolate_grid could run forever, added unit …
emolter Oct 25, 2024
8a4759b
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Oct 28, 2024
a69282a
replace legacy scipy interp1d with make_interp_spline
emolter Oct 28, 2024
2dc62d3
add unit tests to get_soss_grid and helpers
emolter Oct 28, 2024
4197b38
remove unused soss utilities
emolter Oct 28, 2024
5f70c9c
combine BaseOverlap class with ExtractionEngine
emolter Oct 29, 2024
33712be
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Oct 29, 2024
c4de667
make data, err required for ExtractionEngine calls, remove them as en…
emolter Oct 30, 2024
8e2766c
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Oct 31, 2024
5f3610f
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Oct 31, 2024
324b3ff
made functions private, removed some unused optionals
emolter Nov 1, 2024
65e3b0a
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 5, 2024
333d817
added fixes and unit tests to WebbKernel
emolter Nov 6, 2024
6be6310
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 6, 2024
d736f8e
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 8, 2024
20ea48e
fix some failing unit tests
emolter Nov 11, 2024
a85d542
remove unused options and simplify call structure of Tikhonov and Tik…
emolter Nov 13, 2024
a6e448b
simplify indexing in get_w
emolter Nov 21, 2024
93c3eab
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 21, 2024
0a54415
some style fixes
emolter Nov 21, 2024
0894291
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 21, 2024
0e976b8
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 21, 2024
402f34d
tracking down bug
emolter Nov 22, 2024
2e20b6f
bugfix for kernels
emolter Nov 22, 2024
53e6349
trying to fix results is nan bug
emolter Nov 22, 2024
056424b
still trying to bugfix mask
emolter Nov 22, 2024
da9c2e2
add note
emolter Nov 22, 2024
6968a3e
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 25, 2024
b80b6fb
adding tests of engine
emolter Nov 26, 2024
7d99e53
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 26, 2024
7742e62
add more tests to extraction engine
emolter Nov 26, 2024
824a916
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 26, 2024
b0e587c
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Nov 27, 2024
53607a6
more unit tests for extraction engine methods
emolter Nov 27, 2024
bed22ac
more unit tests of extraction engine
emolter Nov 29, 2024
cddde89
toy model for tests is round-tripping successfully now
emolter Dec 2, 2024
b13909a
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 3, 2024
d98cf94
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 3, 2024
85e7fb9
move utils tests into atoca main
emolter Dec 4, 2024
f42a74e
split fixtures into conftest, add more tests of kernels
emolter Dec 4, 2024
1797037
ruff check according to stcal rules
emolter Dec 4, 2024
432e38f
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 4, 2024
4d6a71c
starting tests for box extract
emolter Dec 5, 2024
81ffd52
added unit tests for boxextract functions
emolter Dec 6, 2024
1aacac1
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 6, 2024
4fceb78
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 9, 2024
ba52f91
added test coverage for pastasoss helper functions
emolter Dec 10, 2024
22e111d
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 10, 2024
1359e05
added unit tests for soss_syscor functions
emolter Dec 10, 2024
3ae226d
added test for estim_flux_first_order
emolter Dec 11, 2024
9bb45ab
Added unit tests and supporting fixtures for model_image testing
emolter Dec 12, 2024
8c2b093
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 12, 2024
43a77d4
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 16, 2024
74b5719
small start to docs
emolter Dec 16, 2024
b661cb2
Merge branch 'main' of https://github.com/spacetelescope/jwst into JP…
emolter Dec 17, 2024
e0c8883
fixed a few typos during self review
emolter Dec 17, 2024
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6 changes: 6 additions & 0 deletions docs/jwst/extract_1d/description.rst
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Expand Up @@ -383,3 +383,9 @@ the data must be given. The steps to run this correction outside the pipeline ar
flux_cor = rf1d(flux, wave, channel=4)

where `flux` is the extracted spectral data, and the data are from channel 4 for this example.

Extraction for NIRISS SOSS Data
-------------------------------
For NIRISS SOSS data, the two spectral orders overlap slightly, so a specialized extraction
algorithm known as ATOCA (Algorithm to Treat Order ContAmination) is used...
Link paper
1,264 changes: 281 additions & 983 deletions jwst/extract_1d/soss_extract/atoca.py
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