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Add shim CLI and sequencer #296

Merged
merged 117 commits into from Jan 26, 2022
Merged

Add shim CLI and sequencer #296

merged 117 commits into from Jan 26, 2022

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po09i
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@po09i po09i commented Aug 25, 2021

Description

Adds the ability to shim using the sequencer through st_b0shim. More precisely, the PR adds:

  • st_b0shim CLI
  • st_b0shim argument to use the sequencer (st_b0shim static, st_b0shim realtime, st_b0shim gradient_realtime)
  • st_b0shim argument to define slices (st_b0shim define_slices) (Removed)
  • Ability to define the slices using the "--slices" and "--slice-factor" options
  • Define coil names in the constraints when defining a Coil
  • Displays the R2 score of the linear fit in debug mode for rt sequencer
  • Ability to output shim coefficients in different file formats
    • For realtime, available file formats: slicewise-ch, chronological-ch, eva
    • This allows for custom coils and scanner coils.
  • Function to convert from physical CS to Gradient CS

To test

Run the tests in test/cli/test_cli_b0shim

Related

Fixes #101
Related to #297

@po09i po09i added feature Introduces a new functionality Epic General collection of features that will be sub-divided labels Aug 25, 2021
@po09i po09i self-assigned this Aug 25, 2021
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@gaspardcereza gaspardcereza left a comment

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Tested it locally and it works just fine. I went through the code and didn't spot any mistake/typo. LGTM !

@po09i po09i merged commit c146f89 into master Jan 26, 2022
@po09i po09i deleted the ad/sequencer-cli branch January 26, 2022 03:43
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Create an API and a CLI for realtime_zshimming sequencer and optimizer
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