Skip to content

fix: topup when out_base is a path #928

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom
Merged
merged 2 commits into from
Oct 8, 2014
Merged

fix: topup when out_base is a path #928

merged 2 commits into from
Oct 8, 2014

Conversation

satra
Copy link
Member

@satra satra commented Sep 23, 2014

@oesteban
Copy link
Contributor

I'm checking that this command line would work fine:

topup --config=b02b0.cnf --datain=/media/data/fsl_course_data/fdt1/subj1_preproc/acqparams.txt --imain=/media/data/fsl_course_data/fdt1/subj1_preproc/pre_baked/topup_input.nii.gz --out=base --iout=topup_input_corrected.nii.gz --fout=topup_input_field.nii.gz --logout=topup_input_topup.log

but I fear that the actual outputs will be base_topup_input_corrected.nii.gz, etc. In that case, it would work and the interface still would crash in _list_outputs.

That's why I modified the base interface to allow name_source be an input that is a name_source itself.

@oesteban
Copy link
Contributor

This is ok. The --out argument is not prepended in --fout nor --iout. It should be fine.

Still of interest to deal correctly with inputs with 2 or more levels of name source implemented in #927 .

@satra
Merge remote-tracking branch 'upstream/master' into fix/topup
0c06170 
* upstream/master: (82 commits)
  tiny typo
  another attempt at fixing bash conditionals
  fixed bash conditionals
  added no dep install version. we'll be testing on both.
  Added xor option in Camino connectivity for robustness
  Conmat test function
  Added more connectivity matrix options in Camino interface
  Fixed tests.
  remove deb packages installation
  added apt caching
  fix: d3 change.
  switched to six.string_types for string type checks
  added external package: 'six'
  Mention AddNoise in the changelog
  Remove d3.min.js dependency
  Log cleanup
  Fixed tests
  Update README.rst
  Update links_names.txt
  Update index.rst
  ...
@coveralls
Copy link

Coverage Status

Coverage increased (+0.0%) when pulling 0c06170 on satra:fix/topup into 9fef6d4 on nipy:master.

satra added a commit that referenced this pull request Oct 8, 2014
@satra
Merge pull request #928 from satra/fix/topup
efa7d39 
fix: topup when out_base is a path
@satra satra merged commit efa7d39 into nipy:master Oct 8, 2014
@satra satra deleted the fix/topup branch October 8, 2014 00:46
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Reviewers
No reviews
Assignees
No one assigned
Labels
None yet
Projects
None yet
Milestone
No milestone
Development

Successfully merging this pull request may close these issues.
4 participants
@satra @oesteban @coveralls @rfdougherty