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JP-3576: Implement the Ramp Fitting Likelihood Algorithm #278

Merged
merged 63 commits into from
Sep 19, 2024
Merged

JP-3576: Implement the Ramp Fitting Likelihood Algorithm #278

merged 63 commits into from
Sep 19, 2024

Commits on Sep 12, 2024

  1. First pass at adding the maximum likelihood algorithm to ramp fitting.

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  2. Cleaning up test.

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  3. Updating likelihood code.

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  4. Updating test.

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  5. Updating comments and computing diffs2use mask for ramp segmentation.

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  6. Attempts at computing values for the ERR array.

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  7. Adding DQ flag computation for integrations. Adding testing to analyz… 

    …e differences between this algorithm and the OLS.
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  8. Began updating code to include the Poisson and read noise variance co… 

    …mputation.
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  9. Updating the likelihood algorithm to compute the Poisson and read noi… 

    …se variance.
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  10. Update tests and debugging functions.

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  11. Adding rate product computations.

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  12. Updating likelihood testing.

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  13. Correcting the computation of alpha_readnoise.

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  14. Making some style changes and adding an exception if the ngroups are … 

    …less than 2 groups, since the likelihood algorithm requires at least 2 groups per integration.
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  15. Adding gain to the computatios.

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  16. Changes during testing of readtime computations.

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  17. Updating testing and debugging functions for testing.

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  18. Updating likelhood algorithm initial countrate guess and differences … 

    …to use, as well as modifying the creation of read patterns, when missing.
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  19. Updating the likelihood tests and removing unnecessary print statements.

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  20. Refactoring the code.

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  21. Updating the algorithm to choose the likelihood algorithm based on a … 

    …minimum number of NGROUPS. This will need to work with the pipeline in order to make sure that if the likelihood algorithm runs the pipeline jump detect is not run and if the likelihood algorithm is not run, then the pipeline jump detect should run.
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  22. Updating the tests for the likelihood algorithm.

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  23. Removing unneeded comments.

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  24. Updating the description of ramp fitting to include the likelihood al… 

    …gorithm documentation.
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  25. Some minor editing. Noting where bad groups need to be identified. Up… 

    …dating the collapse from cube to image computations.
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  26. Updating some basic debugging tests.

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  27. Suppressing warnings.

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  28. Updating comments.

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  29. Updating the computation of which diffs to use during the likelihood … 

    …ramp fitting.
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  30. Debugging likelihood ramp fitting tests.

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  31. Updating the formatting, as well as identifying possible jump detecti… 

    …on flagging locations.
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  32. Fixed shape bug when using dark current and changed the name of a fun… 

    …ction to make it more verbose.
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  33. Adding jump detection flagging to the likelihood algorithm for ramp f… 

    …itting.
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  34. Adding test for proper flagging for the likelihood jump detection in … 

    …ramp fitting.
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  35. Removing skip for multi-pixel test.

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  36. Updating the jump detection test for the ramp fitting using the likel… 

    …ihood algorithm.
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  37. Removing debugging import from ramp fitting likelihood.

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  38. Updating the change log and cleaning up the code comments.

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  39. Updating link documents for ramp fitting likelihood algorithm descrip… 

    …tion.
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  40. Updating docstring based on code review.

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  41. Adding parameter to the RampData class to be used in the likelihood a… 

    …lgorithm.
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  42. Updating the likelihood algorithm based on code review.

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  43. Updating some comments and the usage of the readnoise array from CRDS.

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  44. Updating test due to change in read noise computation.

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  45. Updating comments.

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  46. Making updates based on code review.

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  47. Adding change log fragment for towncrier.

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  48. Removing pedestal related code.

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  49. Renaming file.

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  50. Changes made due to code review.

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  51. Updating due to code review.

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  52. Update due to code review.

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  53. Updating due to code review.

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  54. Testing short ramp that should be switched to OLS_C.

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  55. Updating code based on code review.

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  56. Updating documentation based on code review.

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  57. Updating docs for likelihood algorithm in ramp fitting.

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Commits on Sep 13, 2024

  1. Suppressing warnings in likelihood fit computations.

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Commits on Sep 18, 2024

  1. Updating the jump handling for the likelihood ramp fitting algorithm.

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  2. Updating the calculations collapsing the rateints product to the rate… 

    … product to account for NaN's.
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  3. Updating the likelihood algorithm description documentation.

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    kmacdonald-stsci committed Sep 18, 2024
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Commits on Sep 19, 2024

  1. Changing sum to nansum.

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  2. Updating the documentation for ramp fitting wrt the likelihood algori… 

    …thm.
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