FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable #2739
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nipype/interfaces/camino/convert.py
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| @@ -463,7 +463,8 @@ def _get_actual_outputroot(self, outputroot): | |||
| def _list_outputs(self): | |||
| outputs = self.output_spec().get() | |||
| outputs['proc'] = os.path.abspath(self._gen_outfilename()) | |||
| outputs['outputroot_files'] = self.outputroot_files | |||
| if isdefined(self.inputs.outputroot): | |||
| outputs['outputroot_files'] = self.outputroot_files | |||
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I think there's a slightly bigger bug, which is that self.outputroot_files is not defined until the interface is run, and then only sometimes. I would instead make sure that it is defined at __init__:
def __init__(self, *args, **kwargs):
super(ProcStreamlines, self).__init__(*args, **kwargs)
self.outputroot_files = []This way _list_outputs() will not raise an exception either before or after the interface is run, and whether self.inputs.outputroot is defined or not. For OutputMultiPaths, [] is equivalent to Undefined, so this change can be reverted, as well.
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Hi @cni-md. Do you have a few minutes to finish this one off? |
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@effigies not this month. |
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When you do get back to this, please merge master to fix tests. |
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Just a heads up: We're looking to make the next release on Nov 26, if you want to try to get this in this month. |
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Hi, just a reminder that the 1.1.8 release is targeted for January 28. Please let us know if you'd like to try to finish this up for that release. |
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@effigies Ups, I had to work on other projects first. I am not able to finish it til monday 28th. Let's keep it for 1.1.9 |
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@cni-md Thanks for the response! I'll push to 1.1.9. |
Codecov Report
@@ Coverage Diff @@
## master #2739 +/- ##
==========================================
- Coverage 67.49% 67.12% -0.37%
==========================================
Files 342 342
Lines 43559 43562 +3
Branches 5422 5422
==========================================
- Hits 29399 29240 -159
- Misses 13458 13575 +117
- Partials 702 747 +45
Continue to review full report at Codecov.
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effigies
changed the title
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LGTM, thanks. |
1.1.9 (February 25, 2019) Full changelog: https://github.com/nipy/nipype/milestone/30?closed=1 * FIX: Make positional arguments to LaplacianThickness require previous argument (nipy#2848) * FIX: Import math and csv modules for bids_gen_info (nipy#2881) * FIX: Ensure outputs can be listed in camino.ProcStreamlines by defining instance variable (nipy#2739) * ENH: Allow afni.MaskTool to take multiple input files (nipy#2892) * ENH: Add flags dictionary input to spm.Level1Design (nipy#2861) * ENH: Threshold stddev once only in TSNR (nipy#2883) * ENH: Add workbench.CiftiSmooth interface (nipy#2871) * DOC: Replace initialism typo in comment with intended phrase (nipy#2875) * DOC: Fix typos in ANTs Registration input documentation (nipy#2869) * tag '1.1.9': (34 commits) MNT: Update changelog MNT: Add Katherine Bottenhorn, Paul Mihai to Zenodo MNT: Add kchawla-pi to Zenodo, update mailmap and ordering add to zenodo MNT: Update zenodo ordering Update .zenodo.json afni utils.py - masktool - InputMultiPath for in_file argument MNT: Update .zenodo ordering MNT: Add Oliver Contier name to .zenodo.json Update nipype/interfaces/spm/model.py ENH: Add zenodo updating script MNT: Update mailmap to avoid renames in script MNT: Update .mailmap, .zenodo.json MNT: Version 1.1.9 DOC: 1.1.9 changelog ENH: minor - compute non degenerate stddev map once BF: regenerated test_auto_LaplacianThickness using wonderfully long running tools/checkspecs.py TEST: Thorough test of LaplacianThickness requirement cascade FIX: Requires error text was backwards import math and csv modules for bids_gen_info ...
Summary
Camino procstreamlines can be used without -outputroot to filter streamlines. The function _list_outputs insits on a definition of outputroot_files in contrast to _run_interface.
Acknowledgment