ENH: Add NaN failure mode to CompCor interfaces #2819
Merged
Conversation
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Codecov Report
@@ Coverage Diff @@
## master #2819 +/- ##
==========================================
- Coverage 67.48% 67.47% -0.01%
==========================================
Files 341 341
Lines 43343 43351 +8
Branches 5375 5377 +2
==========================================
+ Hits 29248 29250 +2
- Misses 13396 13402 +6
Partials 699 699
Continue to review full report at Codecov.
|
yarikoptic
added a commit
to yarikoptic/nipype
that referenced
this pull request
Jan 11, 2019
1.1.7 (December 17, 2018) * FIX: Copy node list before generating a flat graph (nipy#2828) * FIX: Update pytest req'd version to 3.6 (nipy#2827) * FIX: Set ResourceMonitor.fname to an absolute path (nipy#2824) * FIX: Order of SPM.NewSegment channel_info boolean tuple is (Field, Corrected) (nipy#2817) * FIX: Indices were swapped for memory and cpu profile data (nipy#2816) * FIX: ``status_callback`` not called with ``stop_on_first_crash`` (nipy#2810) * FIX: Change undefined ScriptError on LFS plugin to IOError (nipy#2803) * ENH: Add NaN failure mode to CompCor interfaces (nipy#2819) * ENH: Enable cnr_maps and residuals outputs for FSL eddy (nipy#2750) * ENH: Improve ``str2bool`` + doctests (nipy#2807) * TST: Improve py.test configuration of doctests (nipy#2802) * DOC: Update DOI badge to point to all versions (nipy#2804) * MAINT: Offload interfaces with help formatting (nipy#2797) * MAINT: Reduce minimal code redundancy in filemanip.get_dependencies (nipy#2782) * MAINT: Delayed imports to reduce import time (nipy#2809) ...
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Summary
Following discussion in nipreps/fmriprep#1433, having CompCor interfaces gracefully handle failure states by returning NaN arrays of the appropriate size is preferable to crashing the pipeline.
This PR adds a
failure_modeinput to the interface, which defaults to'error'and maintains the current behavior. Iffailure_mode == 'nan', then exceptions are not raised, and columns of NaNs are returned.List of changes proposed in this PR (pull-request)
failure_modeinput to CompCor interfacesfailure_mode == 'nan', return columns of NaNs instead of raising exceptionsAcknowledgment