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Various tools for de-streaking #196

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Various tools for de-streaking #196

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Commits on Jul 19, 2024

  1. Import first version from FIJI (works decently well)

    @minnerbe
    minnerbe committed Jul 19, 2024
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  2. Save part of de-streaking parameters 

    Those are the parameters that are worth keeping after some experimental
tests
    @minnerbe
    minnerbe committed Jul 19, 2024
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  3. Pull masking into a separate method

    @minnerbe
    minnerbe committed Jul 19, 2024
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  4. Refactor mask creation

    @minnerbe
    minnerbe committed Jul 19, 2024
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  5. Separate actual from test code

    @minnerbe
    minnerbe committed Jul 19, 2024
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  6. Refactor test code

    @minnerbe
    minnerbe committed Jul 19, 2024
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  7. Adapt inpainting code from hotknife repo

    @minnerbe
    minnerbe committed Jul 19, 2024
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Commits on Jul 22, 2024

  1. Make inpainting work for first example

    @minnerbe
    minnerbe committed Jul 22, 2024
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Commits on Aug 8, 2024

  1. Add StreakFinderParameters

    @minnerbe
    minnerbe committed Aug 8, 2024
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Commits on Aug 9, 2024

  1. Add preliminary version of streak statistics client

    @minnerbe
    minnerbe committed Aug 9, 2024
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  2. Add method to store masks

    @minnerbe
    minnerbe committed Aug 9, 2024
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  3. Refactor StreakStatisticsClient

    @minnerbe
    minnerbe committed Aug 9, 2024
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  4. Split test code from other code

    @minnerbe
    minnerbe committed Aug 9, 2024
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  5. Improve logging and slightly change parameters

    @minnerbe
    minnerbe committed Aug 9, 2024
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Commits on Sep 25, 2024

  1. Create outline for streak statistics client

    @minnerbe
    minnerbe committed Sep 25, 2024
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  2. Add spark parallelization skeleton

    @minnerbe
    minnerbe committed Sep 25, 2024
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Commits on Sep 26, 2024

  1. First version of full code (still throws an error)

    @minnerbe
    minnerbe committed Sep 26, 2024
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  2. Fix a few bugs and refactor

    @minnerbe
    minnerbe committed Sep 26, 2024
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  3. Make blurring optional

    @minnerbe
    minnerbe committed Sep 26, 2024
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Commits on Sep 27, 2024

  1. Add zRange parameters to only process a layer range

    @minnerbe
    minnerbe committed Sep 27, 2024
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  2. Also store run parameters

    @minnerbe
    minnerbe committed Sep 27, 2024
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  3. Optimize streak mask

    @minnerbe
    minnerbe committed Sep 27, 2024
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  4. Use StreakFinderParameters in StreakStatisticsClient

    @minnerbe
    minnerbe committed Sep 27, 2024
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  5. Account for inverted interpretation of mask

    @minnerbe
    minnerbe committed Sep 27, 2024
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  6. Refactor spark parallelization (pull tile specs on workers)

    @minnerbe
    minnerbe committed Sep 27, 2024
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  7. Remove an unecessary broadcast wrapper

    @minnerbe
    minnerbe committed Sep 27, 2024
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Commits on Sep 29, 2024

  1. Fix more inverse mask problems

    @minnerbe
    minnerbe committed Sep 29, 2024
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Commits on Oct 1, 2024

  1. Fix integer overflow in streak statistics

    @minnerbe
    minnerbe committed Oct 1, 2024
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  2. Move Inpainter from test to src module

    @minnerbe
    minnerbe committed Oct 1, 2024
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  3. Add very preliminary version of inpainting client

    @minnerbe
    minnerbe committed Oct 1, 2024
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Commits on Oct 2, 2024

  1. Factor the ray direction strategy out of Inpainter

    @minnerbe
    minnerbe committed Oct 2, 2024
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  2. Move inpainting code to its own package

    @minnerbe
    minnerbe committed Oct 2, 2024
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  3. Rename RayDirectionStrategy -> DirectionalStatistic

    @minnerbe
    minnerbe committed Oct 2, 2024
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  4. Add anisotropic ray casting

    @minnerbe
    minnerbe committed Oct 2, 2024
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Commits on Oct 3, 2024

  1. Delete client superseded by newer spark-client

    @minnerbe
    minnerbe committed Oct 3, 2024
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  2. Move and rename InpaintingClient (was used for testing only)

    @minnerbe
    minnerbe committed Oct 3, 2024
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  3. Fix minor typos

    @minnerbe
    minnerbe committed Oct 3, 2024
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Commits on Oct 10, 2024

  1. Handle the case where there's no data in a cell

    @minnerbe
    minnerbe committed Oct 10, 2024
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  2. Limit chunk size in z

    @minnerbe
    minnerbe committed Oct 10, 2024
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  3. Fix chunking

    @minnerbe
    minnerbe committed Oct 10, 2024
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  4. Really fix chunk size

    @minnerbe
    minnerbe committed Oct 10, 2024
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Commits on Oct 11, 2024

  1. Add stack resolution to metadata

    @minnerbe
    minnerbe committed Oct 11, 2024
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  2. Additionally store layer bounding boxes

    @minnerbe
    minnerbe committed Oct 11, 2024
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Commits on Oct 18, 2024

  1. Make DirectionalStatistic work for 3D

    @minnerbe
    minnerbe committed Oct 18, 2024
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Commits on Oct 29, 2024

  1. Add 3D directional statistic

    @minnerbe
    minnerbe committed Oct 29, 2024
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Commits on Oct 30, 2024

  1. Add prototype for inpainting job for Celegans dataset

    @minnerbe
    minnerbe committed Oct 30, 2024
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