antsRegistrationSyNQuick (continuation of #1392) #2347
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@djarecka anymore additions or is this ready? |
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| # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT | |||
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I didn't remove it manually. I mentioned in #2349 that since we have a non-auto test, this test has been removed by make specs. What happen when you run make specs?
small changes in FSSourceInputSpec (fixes nipy#2116)
[MAINT] Cleanup EngineBase
* 'master' of github.com:nipy/nipype: fix error type remove install_aliases sty fix tests refactoring tests update changes [MAINT] Cleanup engine/base
* origin/master: (139 commits) fix error type remove install_aliases sty fix tests refactoring tests update changes [MAINT] Cleanup engine/base STY: Add newline pep formatting Revert "after make specs" address review and add changelog MAINT: Adjust test names to placate make specs Fix 3dFWHMx outputs fix: composemultitransform doctest sty: fix examples sty: fix styles in updated interfaces sty: cleanup tools folder sty: add yapf to extras installs fix: specs ...
| desc="A prefix that is prepended to all output files") | ||
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| # todo ANTSCommandInputSpec already has this, but I can't figure out how to set it without defining it again | ||
| num_threads = traits.Int(default_value=1, desc='Number of threads (default = 1)', argstr='-n %d') |
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you should check if the script checks for the environment variables that is set by the base class instead of this argument. if so the underlying commands in the script will use it.
but since this script has an explicit flag for threads, you should over-ride the base class.
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@satra - don't understand how this should be changed. Should num_threads be in RegistrationSynQuickInputSpec (as it is now), or over-ride somewhere else?
In this script the default value is -n 1, so that's why probably the author of changes used `default_value=1.
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it should be in:
RegistrationSynQuickInputSpec(as it is now)
since the script explicitly overrides this: https://github.com/ANTsX/ANTs/blob/master/Scripts/antsRegistrationSyNQuick.sh#L388
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| class RegistrationSynQuick(ANTSCommand): | ||
| """ | ||
| Examples |
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you can just use some of the ants registration examples here in much simplified form.
RF: Update and factor mount table parsing
bug for datagrabber
[WIP] COV: Ignore tests in calculating coverage
CI: Add doctests to pytest script
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something went wrong, will open a new pr |
continuing #1392
not sure where to find a good description of RegistrationSyNQuick, here I can find only a few usage examples.