ENH: Make default native resolution explicit #494

mgxd · 2020-04-03T19:57:28Z

Sets the default value of volumetric references resolution to native.

Originally discussed in #457 (comment), looks it is needed.

Addresses nipreps/fmriprep#2060 ~~nipreps/fmriprep#2000~~

pull-assistant · 2020-04-03T19:57:30Z

Best reviewed: commit by commit

Optimal code review plan

ENH: Make default native resolution explicit

enh: strip native resolution identifier from derivatives

ENH: avoid setting nonstandard references resolutions

Merge branch 'master' of github.com:nipreps/niworkflows into fix/defau...

DOC: add space usage to docstring

doc: insert urls to discussions [skip ci]

Powered by Pull Assistant. Last update e0f04ec ... f59e306. Read the comment docs.

codecov · 2020-04-03T20:45:58Z

Codecov Report

Merging #494 into master will increase coverage by 0.07%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master     #494      +/-   ##
==========================================
+ Coverage   62.86%   62.94%   +0.07%     
==========================================
  Files          42       42              
  Lines        5098     5098              
  Branches      742      740       -2     
==========================================
+ Hits         3205     3209       +4     
+ Misses       1739     1735       -4     
  Partials      154      154

Flag	Coverage Δ
#documentation	`33.67% <0.00%> (-0.03%)`	⬇️
#masks	`?`
#reportlettests	`100.00% <ø> (ø)`
#travis	`57.89% <100.00%> (+0.03%)`	⬆️
#unittests	`45.78% <100.00%> (+0.04%)`	⬆️

Impacted Files	Coverage Δ
niworkflows/interfaces/bids.py	`90.33% <100.00%> (+0.07%)`	⬆️
niworkflows/utils/spaces.py	`89.50% <100.00%> (+0.11%)`	⬆️
niworkflows/interfaces/images.py	`55.82% <0.00%> (+0.14%)`	⬆️
niworkflows/viz/utils.py	`80.06% <0.00%> (+0.24%)`	⬆️
niworkflows/interfaces/mni.py	`42.52% <0.00%> (+0.24%)`	⬆️
niworkflows/utils/bids.py	`77.17% <0.00%> (+0.82%)`	⬆️

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mgxd · 2020-04-03T21:06:17Z

With this change applied, the default BOLD outputs will now have the "res-native" identifier included in filenames.

I'm inclined to edit DerivativesDataSink to ignore this identifier, but open to any thoughts/concerns (cc @oesteban @effigies)

…ult-refs-native

effigies · 2020-04-06T19:43:50Z

This looks fine, but I'm missing where it changes anything but filenames.

mgxd · 2020-04-06T19:49:14Z

niworkflows/utils/spaces.py

+            if (
+                val not in NONSTANDARD_REFERENCES
+                and not val.split(':')[0].startswith('fs')
+                and ":res-" not in val
+                and ":resolution-" not in val
+            ):
+                # by default, explicitly set volumetric resolution to native
+                val = ":".join((val, "res-native"))


@effigies res-native is already handled correctly, so this change just appends it to the output spaces by default if no resolution is specified

oesteban

Sorry, I realize I have been pretty unclear on this one. When I said IMHO, spaces set via the --output-spaces option should always fill a res-native if no resolution modifier is specified I didn't mean that ReferenceSpace should have always a res-native. In other words, I would leave the responsibility of setting the res-native when resolution is missing to the cli module of fMRIPrep.

This solution has a lot of potential side-effects. Have you tested it locally?

oesteban · 2020-04-07T04:57:39Z

I'm inclined to edit DerivativesDataSink to ignore this identifier, but open to any thoughts/concerns

Check #334

mgxd · 2020-04-07T13:24:21Z

@oesteban actually this shouldn't have much side effects, since the only timeOutputReferencesAction is used is in the CLI for the user requested output spaces - the way we add internal spaces shouldn't be affected.

Check #334

that looks useful, but don't see how we can leverage it here - res-native isn't included in the source file, but rather in the provided space.

oesteban

Okay, I see your points. I'm most concerned about whether we are already sticking the res- entity into the space input of the DataSinks. If so, then I think it is time to give them (the DataSinks) the love they deserve.

Also, I'm not convinced we should always drop the res-native bit. If there are other resolutions we might as well keep it. DYT?

This case is not similar to space, for which there is indeed one space matching the original image (and therefore, since there's no change on the property, it should not be added to the filename).

oesteban · 2020-04-07T14:45:20Z

niworkflows/interfaces/bids.py

+        if self.inputs.space and '_res-native' in self.inputs.space:
+            # strip native tag
+            self.inputs.space = self.inputs.space.split('_')[0]
+


Can't we just drop the resolution entity in the connection? Or the resolution entity is currently crammed into the space input in fMRIPrep and you are working around that hacky solution (honestly, I can't remember)?

the resolution is appended to the space input, a hack we implemented to allow multiple resolutions of the same template

oesteban · 2020-04-07T14:48:42Z

niworkflows/utils/spaces.py

@@ -660,10 +660,14 @@ def __call__(self, parser, namespace, values, option_string=None):
            spaces.checkpoint()
        for val in values:
            val = val.rstrip(":")
-            # Should we support some sort of explicit "default" resolution?
-            # https://github.com/nipreps/niworkflows/pull/457#discussion_r375510227


Can we keep this reference and add a reference to this PR as comments?

mgxd · 2020-04-07T15:03:38Z

Also, I'm not convinced we should always drop the res-native bit. If there are other resolutions we might as well keep it. DYT?

I went back and forth here - ultimately I went with the route of least changes to the documentation. Do we want to make this explicit now (its been implicit for a long time) at the cost of renaming the expected output files?

If we have other resolutions, those others will have the res- fields included. It seems off to produce different filenames based on how many output spaces were requested

oesteban · 2020-04-07T16:14:07Z

I'm also bouncing back and forth on this one. WDYT @effigies ?

effigies · 2020-04-07T16:43:59Z

I would lean toward keeping it invisible.

res/den are only required to distinguish from another file. The goal of BIDS is not to put all relevant metadata in the file name but to help people quickly distinguish files. All other resolutions will have a res-* entity, so that seems fine.

mgxd · 2020-04-07T17:17:15Z

great, thanks for the reviews!

ENH: Make default native resolution explicit

e0f04ec

mgxd requested a review from oesteban April 3, 2020 19:57

mgxd added 2 commits April 5, 2020 23:43

enh: strip native resolution identifier from derivatives

a3edc3d

ENH: avoid setting nonstandard references resolutions

73f4dc1

mgxd force-pushed the master branch from c52180f to 1977707 Compare April 6, 2020 15:58

Merge branch 'master' of github.com:nipreps/niworkflows into fix/defa…

be05b4e

…ult-refs-native

mgxd force-pushed the fix/default-refs-native branch from bbcb1ca to be05b4e Compare April 6, 2020 16:04

DOC: add space usage to docstring

d830e55

mgxd force-pushed the fix/default-refs-native branch from 8f7df56 to d830e55 Compare April 6, 2020 18:11

mgxd commented Apr 6, 2020

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oesteban reviewed Apr 7, 2020

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oesteban approved these changes Apr 7, 2020

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doc: insert urls to discussions [skip ci]

f59e306

mgxd merged commit d109e99 into nipreps:master Apr 7, 2020

mgxd deleted the fix/default-refs-native branch April 7, 2020 17:17

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ENH: Make default native resolution explicit #494

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ENH: Make default native resolution explicit #494

ENH: Make default native resolution explicit #494

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