Quick description

See issue #1108 for more details. In summary, I realized that the skip_b0_check option forces the b0_threshold to become the minimal b-value, which doesn't work in some cases. Many scripts used the check_b0_threshold function without saving the outputted threshold, because we did not want to overwrite the b0_threshold. However, the warning message from check_b0_threshold with skip_b0_check still said that the b0_threshold was changed to the minimal b-value, which was false in this case.

A simple fix was to add a overwrite_with_min option to check_b0_threshold, so that if it is False, the warning says that the script will continue without b0s, as it does. I added this overwrite_with_min=False option to all scripts that had will_overwrite_with_min=False when calling add_skip_b0_check_arg. I also changed the help when this will_overwrite_with_min option is False (it was not doing what was said).

Closes #1108

...

Type of change

Check the relevant options.

• Bug fix (non-breaking change which fixes an issue)
• New feature (non-breaking change which adds functionality)
• Breaking change (fix or feature that would cause existing functionality to not work as expected)
• This change requires a documentation update

Provide data, screenshots, command line to test (if relevant)

...

Checklist

• My code follows the style guidelines of this project (run autopep8)
• I added relevant citations to scripts, modules and functions docstrings and descriptions
• I have performed a self-review of my code
• I have commented my code, particularly in hard-to-understand areas
• I have made corresponding changes to the documentation
• My changes generate no new warnings
• I moved all functions from the script file (except the argparser and main) to scilpy modules
• I have added tests that prove my fix is effective or that my feature works
• New and existing unit tests pass locally with my changes