ENH: Add optional session filter when collecting data

[mgxd]

A slight alteration to provide session level control.

[mgxd]

@effigies looks like using Query.ANY is filtering out the files...is this a pybids bug?

(Pdb) layout.get(
                return_type="file",
                subject=participant_label,
                session=session_id,
                extension=[".nii", ".nii.gz"], **queries['fmap'])
[]
(Pdb) session_id
<Query.ANY: 2>
(Pdb) layout.get(
                return_type="file",
                subject=participant_label,
                extension=[".nii", ".nii.gz"], **queries['fmap'])
['/Users/mathiasg/code/niworkflows/../nibabies/testdata/roo/sub-01/fmap/sub-01_dir-AP_epi.nii.gz', '/Users/mathiasg/code/niworkflows/../nibabies/testdata/roo/sub-01/fmap/sub-01_dir-PA_epi.nii.gz']

[mgxd]

Actually, I think this is expected

• Query.NONE: The named entity must not be defined.
• Query.ANY: the named entity must be defined, but can have any
  value.

Perhaps there needs to be another value for Query that mimics ANY, but allows undefined entities as well.

[effigies]

Oh damn.

     filters : dict
        Any optional key/values to filter the entities on.
        Keys are entity names, values are regexes to filter on. For
        example, passing filters={'subject': 'sub-[12]'} would return
        only files that match the first two subjects. In addition to
        ordinary data types, the following enums are defined (in the
        Query class):
            * Query.NONE: The named entity must not be defined.
            * Query.ANY: the named entity must be defined, but can have any
                value.

I guess we don't currently have a query enum that would do what I was thinking. I guess we need to revert to what you had, but let's open an issue on PyBIDS to allow a query that means it can be present or absent (maybe Query.OPTIONAL?).

[oesteban]

As per the new docstring, session_id can be None. If so, it would be better to make the value replacement the latest possible, rather than the default parameter.

[oesteban]

Suggested change

	session_id=Query.ANY,
	session_id=None,

[oesteban]

let's open an issue on PyBIDS to allow a query that means it can be present or absent (maybe Query.OPTIONAL?).

Perhaps Query.EITHER (somewhat closer to enthought traits)?

[effigies]

bids-standard/pybids#809

[oesteban]

OMG you guys are fast :)

[codecov-commenter]

Codecov Report

Merging #678 (22ddb99) into master (3d10143) will decrease coverage by 1.76%.
The diff coverage is 0.00%.

❗ Current head 22ddb99 differs from pull request most recent head 620ce08. Consider uploading reports for the commit 620ce08 to get more accurate results

@@            Coverage Diff             @@
##           master     #678      +/-   ##
==========================================
- Coverage   49.14%   47.38%   -1.77%     
==========================================
  Files          49       45       -4     
  Lines        5858     5605     -253     
  Branches      834      808      -26     
==========================================
- Hits         2879     2656     -223     
+ Misses       2871     2854      -17     
+ Partials      108       95      -13     

Flag	Coverage Δ
reportlettests	∅ <ø> (∅)
unittests	47.38% <0.00%> (-1.77%)	⬇️

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Impacted Files	Coverage Δ
niworkflows/utils/bids.py	72.81% <0.00%> (-2.19%)	⬇️
niworkflows/viz/plots.py	5.94% <0.00%> (-16.19%)	⬇️
niworkflows/interfaces/confounds.py	22.92% <0.00%> (ø)
niworkflows/testing.py
niworkflows/utils/timeseries.py
niworkflows/utils/testing.py
niworkflows/interfaces/morphology.py
niworkflows/interfaces/bids.py	96.77% <0.00%> (+0.55%)	⬆️
niworkflows/interfaces/freesurfer.py	49.21% <0.00%> (+0.78%)	⬆️
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[effigies]

Looks good.