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Improve HedwigZARRImages performance in CZI flow #477

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@blowekamp blowekamp commented Jun 25, 2024

In the generate_czi_imageset subflow, allow the dask array computations in HedwigZARRImage to reuse Prefect's Dask task scheduler with all the workers for the node.

Depends on niaid/tomojs-pytools#108 and #479

Changes

  • List of changes
  • Breaking changes
  • Changes to configurations

This PR doesn't introduce any:

  • Binary files
  • Temporary files, auto-generated files
  • Secret keys
  • Local debugging print statements
  • Unwanted comments (e.g: # Gets user from environment for code os.environ['user'] )

This PR contains valid:

  • tests

In the generate_czi_imageset subflow, allow the dask array
computations in HedwigZARRImage to reuse Prefect's Dask task
scheduler with all the workers for the node.
@blowekamp blowekamp force-pushed the use_pytools_compute_args branch from 4f6c588 to 6db4e00 Compare June 25, 2024 14:29
@blowekamp blowekamp changed the title Improve HedwigZARRImages performanve in CZI flow Improve HedwigZARRImages performance in CZI flow Jun 27, 2024
@blowekamp blowekamp marked this pull request as ready for review November 5, 2024 14:10
@philipmac
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There was an update to pytools which changed the default to use a restricted number of local dask threads. This above PR, allows this prefect task to use all threads.

@blowekamp blowekamp requested a review from philipmac November 5, 2024 14:36
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