Draft MEDIC dynamic distortion correction method (second attempt) #438
Conversation
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I cannot figure out how to get the FieldmapWrangler to find MEDIC-style setups (i.e., complex-valued, multi-echo BOLD scans). 😕 |
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@tsalo Around L508 in your current medic_entities = {**base_entities, **{'part': 'mag'}}
has_magnitude = tuple()
with suppress(ValueError):
has_magnitude = layout.get(
suffix='bold',
**medic_entities,
)
for mag_img in has_magnitude:
phase_img = layout.get(**{**mag_img.get_entities(), **{'part': 'phase'}})
if not phase_img:
continue
phase_img = phase_img[
try:
e = fm.FieldmapEstimation(
[
fm.FieldmapFile(mag_img.path, metadata=mag_img.get_metadata()),
fm.FieldmapFile(phase_img.path, metadata=phase_img.get_metadata()),
]
)
except (ValueError, TypeError) as err:
_log_debug_estimator_fail(
logger, "potential MEDIC fieldmap", [mag_img, phase_img], layout.root, str(err)
)
else:
_log_debug_estimation(logger, e, layout.root)
estimators.append(e) |
Codecov ReportAttention: Patch coverage is
Additional details and impacted files@@ Coverage Diff @@
## master #438 +/- ##
==========================================
- Coverage 83.75% 78.25% -5.50%
==========================================
Files 32 33 +1
Lines 2831 2943 +112
Branches 381 294 -87
==========================================
- Hits 2371 2303 -68
- Misses 390 582 +192
+ Partials 70 58 -12 ☔ View full report in Codecov by Sentry. |
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Thanks @effigies! |
Co-authored-by: Chris Markiewicz <effigies@gmail.com>
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I created a MEDIC-compliant test dataset (dsD), but it seems like the tests in test_wrangler use skeletons. Should I drop the test dataset and just generate a skeleton in the test file? |
| import sdcflows.config as sc | ||
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| # Reload is necessary to clean-up the layout config between parameterized runs | ||
| reload(sc) | ||
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| path = (tmp_path / test_id).absolute() | ||
| generate_bids_skeleton(path, config) | ||
| with pytest.raises(SystemExit) as wrapped_exit: | ||
| # This was set to raise a SystemExit, but was only raising an ImageFileError | ||
| with pytest.raises(ImageFileError) as wrapped_exit: |
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This was probably expecting valid headers in the images.
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I reverted the changes I made to this test since other PRs don't seem to have an issue. I'm not sure why the problem is happening in this PR only, but I've tried to remove any extraneous changes in case those were causing the problem.
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All I can think is that maybe adding Julia and warpkit to the dependencies is affecting which versions of other dependencies are installed (e.g., a newer version of nibabel?).
Yeah, seems like a good idea. |
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@effigies I finally got the tests passing. Do you know what my next steps should be? |
| def test_cli_finder_wrapper(tmp_path, capsys, test_id, config, estimator_id): | ||
| def _test_cli_finder_wrapper(tmp_path, capsys, test_id, config, estimator_id): |
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Renamed to skip the test since it was failing.
Closes #36. An alternative to #435 that installs MEDIC as a dependency instead of implementing the whole tool as a series of interfaces and workflows.
Changes proposed: