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feat: preprocess with tiling #504

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merged 34 commits into from
Nov 26, 2024
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cpaniaguam
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@cpaniaguam cpaniaguam commented Nov 9, 2024

Orchestration function for preprocessing with tiling.

  • Add tests

Steps 1-12 out of about 17
@cpaniaguam cpaniaguam linked an issue Nov 9, 2024 that may be closed by this pull request
@cpaniaguam cpaniaguam requested a review from a team November 15, 2024 21:58
@cpaniaguam cpaniaguam marked this pull request as ready for review November 15, 2024 21:59
danielmwatkins
danielmwatkins previously approved these changes Nov 18, 2024
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Outlining the steps is helpful. Is there a way to easily turn the @info logging on and off if the user were to be running a batch of images?

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Is there a way to easily turn the @info logging on and off if the user were to be running a batch of images?

@danielmwatkins
Yes, that can be handled using a Logging configuration.

using Logging
global_logger(ConsoleLogger(stderr, Logging.Error))

This would only log Error and Fatal messages.

@cpaniaguam cpaniaguam force-pushed the 503-orchestrate-into-a-macro-function branch from ac1f891 to 727b154 Compare November 19, 2024 21:16
danielmwatkins
danielmwatkins previously approved these changes Nov 20, 2024
danielmwatkins
danielmwatkins previously approved these changes Nov 20, 2024
@cpaniaguam cpaniaguam requested review from danielmwatkins and a team November 20, 2024 18:14
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Just some questions for clarifications and adding k to the docstrings.

src/histogram_equalization.jl Show resolved Hide resolved
src/histogram_equalization.jl Show resolved Hide resolved
src/ice_masks.jl Show resolved Hide resolved
src/ice_masks.jl Show resolved Hide resolved
src/ice_masks.jl Show resolved Hide resolved
src/preprocess_tiling.jl Show resolved Hide resolved
src/watershed.jl Show resolved Hide resolved
cpaniaguam and others added 2 commits November 25, 2024 16:29
Co-authored-by: Timothy Divoll <timothy.divoll@gmail.com>
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This looks good, just one comment on the code.

One question: does anything need to change in the CLI to make this work, or will it just slot in?

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One question: does anything need to change in the CLI to make this work, or will it just slot in?

@hollandjg
This function processes one unit of input data in the same way preprocess does. It will need a wrapper that leverages it (like the namesake preprocess does.

@cpaniaguam cpaniaguam merged commit 8ad0ea8 into main Nov 26, 2024
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@cpaniaguam cpaniaguam deleted the 503-orchestrate-into-a-macro-function branch November 26, 2024 17:18
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orchestrate into a macro function
4 participants