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JP-251: Optimal extraction support for MIRI LRS #8967

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JP-251: Optimal extraction support for MIRI LRS #8967

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Commits on Dec 4, 2024

  1. Start extract1d refactor

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  2. Add test for custom extraction with polynomial limits

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  3. Fix log message f-string

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  4. Deduplicate extraction interface

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  5. Remove image reference type

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  6. Separate IFU from slit extraction

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  7. Remove NIRISS SOSS references from slit extraction code

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  8. Remove unnecessary middleman function; condense input type checking

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  9. Add helper functions for special extraction modes

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  10. Clean up messages

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  11. First version incorporating new extraction engine 

    Co-authored-by: Timothy D Brandt <timothy.d.brandt@gmail.com>
Co-authored-by: Timothy Brandt <tbrandt@astarlas2024.stsci.edu>
    @melanieclarke @t-brandt
    3 people committed Dec 4, 2024
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  12. Fix extraction limit defaults and partial pixel weights

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  13. Npixels is sum of weights instead of sum of pixels with non-zero weight

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  14. Move profile and wavelength calculations out of integration loop

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  15. Tidying up

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  16. Update unit tests for new extract1d

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  17. Add left/right limit handling, fix partial pixel weights

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  18. Make polynomial coefficient definition backward compatible

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  19. Clean up aperture definition, fix edge cases

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  20. Coverage tests for step interface

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  21. Move aperture correction setup outside integration loop

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  22. Return separate values from locn_from_wcs function

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  23. Rename 'boxcar' extraction to 'box'

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  24. Set up for future optimal extraction

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  25. Tidy up code organization, add docstrings

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  26. Code style fixes

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  27. Make sure background values are finite: they default to 0, not NaN

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  28. More general check for unresampled nirspec data

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  29. More robust file saving for containers

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  30. Add option to save spatial profile

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  31. Add check for negative values in profile

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  32. Add option to save scene model

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  33. Fix scene model default

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  34. Minor fixes for optimal extraction support

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  35. Add check for missing variances

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  36. Adding unit tests for extraction

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  37. Add temporary fix for background fit test

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  38. Coverage tests for extract1d

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  39. Better npixels estimate for optimal extraction; fix background fit test

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  40. More unit tests for extract_1d coverage

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  41. Fix npixels for non-uniform weights

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  42. More coverage tests

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  43. More unit tests for extract

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  44. Tests for extract_one_slit

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  45. Add change log fragment

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  46. Make some parameters for create_extraction keywords instead of args

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  47. Test coverage for create_extraction and run_extract1d

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  48. Reformat change note

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  49. Update docs for extract1d

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  50. Add more API docs for extraction tools

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  51. Make change notes fit on one line

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  52. Minor docs clarifications

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  53. First version of PSF extraction, contains hacks 

    Co-authored-by: jemorrison <morrison@as.arizona.edu>
    @melanieclarke @jemorrison
    melanieclarke and jemorrison committed Dec 4, 2024
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  54. Fix default locations for psf profile

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  55. Turn off aperture correction for optimal extraction

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  56. Add options for modeling a negative nod trace

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  57. Keep 0s in profile and scene model

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  58. Don't default optimal extraction to background subtraction

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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  59. Fix for ref names in extract params default

    @melanieclarke
    melanieclarke committed Dec 4, 2024
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