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Beam splitting off-axis zone plate analysis

Merged Loïc Le Guyader requested to merge boz into master
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This adds the beam splitting off-axis zone plate analysis code to the toolbox:

  • determination of correction parameters are shown in a notebook documentation
  • correction parameters and parameters used in their determination are all saved in one single JSON file for reproducibility
  • analysis of actual data using these correction parameters is shown in a second notebook documentation
Edited by Loïc Le Guyader

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  • added 1 commit

    • bba3ab0b - Adds alpha parametrized correction cost in fitting non-linearities to prevent divergence

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  • Loïc Le Guyader added 4 commits

    added 4 commits

    • 024f6704 - Inspect dark plot histograms and compute mask
    • f8c6b255 - Make rois based on int to be saved by json
    • 3041e51f - Separate calculating plane field from plotting plane field
    • c087c221 - Adds fitting with callback and plot function

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  • added 1 commit

    • 99520bb9 - Adds analysis parameters class

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  • added 1 commit

    • 7566d31d - Adds cleared notebook doc for boz parameter extraction

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  • Loïc Le Guyader added 3 commits

    added 3 commits

    • 6dc4d38e - Adds find rois from parameters
    • 22b52016 - small XAS fixes
    • 776cf26a - Adds second BOZ notebook part with XAS calculation

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  • Author Maintainer

    Alright, with these last commits we have a complete functioning example. There is 2 notebooks in the documentation. The first part details extraction of analysis parameters such as bad pixel mask, rois, flat field correction and non linearity correction. This is all saved in a single json file, including the parameters used in all the steps so that:

    1. everything can be reproduced
    2. the small json file could be uploaded on the online cluster for online analysis

    The second notebook uses this extracted parameters and applies them to a recorded spectra. It also shows what can change, for example rois might need to be different, meaning the flat field correction needs to be recalculated.

    @carinanc I will present this on Monday at the SCS Moonshot meeting so we can start discussing how we want to do the online analysis.

  • Loïc Le Guyader resolved all discussions

    resolved all discussions

  • added 1 commit

    • a017b028 - Cyclic shift of data for plane field fitting with rois of different size

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  • added 1 commit

    • 4b4399d4 - Loads data persistently once

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  • Author Maintainer

    I think this can be merge now.

  • Loïc Le Guyader unmarked as a Work In Progress

    unmarked as a Work In Progress

  • Loïc Le Guyader changed the description

    changed the description

  • Author Maintainer

    TODO for me:

    • write documentation to all functions
    • in the notebook part II, compute and plot the spectra with no correction, only flat field correction and both flat field and non-linearity correction
    Edited by Loïc Le Guyader
  • Loïc Le Guyader assigned to @teichman and unassigned @lleguy

    assigned to @teichman and unassigned @lleguy

  • Loïc Le Guyader
  • Loïc Le Guyader added 3 commits

    added 3 commits

    • a1d95847 - Adds more documentation
    • c8806091 - Adds XAS spectra comparison with and without correction
    • 591a7737 - Fixes and cleanup

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  • Martin Teichmann
  • Martin Teichmann
  • Loïc Le Guyader assigned to @lleguy and unassigned @teichman

    assigned to @lleguy and unassigned @teichman

  • added 1 commit

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  • Loïc Le Guyader resolved all discussions

    resolved all discussions

  • mentioned in commit d18c870c

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