Speed up BIDSLayout.get(return_type='id', ...)

[adelavega]

Fixes #940

The issue is that BIDSFile.get_entities is somewhat slow, because it has to do a SQL query. A single query is fine, but in this instance its doing it times the number of files in the result (which with no other argument, is the total number of files indexed).

Instead, I use BIDSFile.entities, which is much faster, because its an association_proxy. Essentially, instead of doing a complex query that filters, it just pulls all the entities for every file.

This results in 36x speedup for get_subjects in my example dataset (660ms -> 18ms)

The crazy thing is this can be sped up even further, by doing a direct SQL query such as:

layout.session.query(models.Tag).filter_by(entity_name='subject').distinct().with_entities(models.Tag._value).all()

This only takes 2.14ms, which is over 300x faster.

The only issue is the latter query bypasses a lot of the Python logic built into pybids classes, which do somewhat important things such as formatting run ids as PaddedInt and ensuring the are returned in the correct type, so I was not able to use this implementation.

On the whole, this makes me think that a lot of things that are "slow with pybids" need not be so...

[codecov]

Codecov Report

Base: 86.32% // Head: 86.35% // Increases project coverage by +0.02% 🎉

Coverage data is based on head (39b9f8a) compared to base (1ba4f66).
Patch coverage: 100.00% of modified lines in pull request are covered.

Additional details and impacted files

@@            Coverage Diff             @@
##           master     #942      +/-   ##
==========================================
+ Coverage   86.32%   86.35%   +0.02%     
==========================================
  Files          35       35              
  Lines        4022     4023       +1     
  Branches      973      974       +1     
==========================================
+ Hits         3472     3474       +2     
  Misses        355      355              
+ Partials      195      194       -1     

Impacted Files	Coverage Δ
bids/layout/layout.py	88.10% <100.00%> (+0.18%)	⬆️
bids/layout/models.py	92.08% <100.00%> (+0.05%)	⬆️

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[effigies]

Looks entirely sensible. Coverage looks reasonable. I assume you've tested it with non-entities like get_RepetitionTimes()? Or, even better, we have tests that cover that case?

[adelavega]

I just tested it and it works, but I added an additional get_RepetitionTimes test to make sure (couldn't find an equivalent test elsewhere).

Will merge once tests pass.