[ENH] Update config to support microscopy, qMRI, PET, ASL #840
Conversation
Remi-Gau
requested review from
effigies,
tsalo,
mariehbourget,
HenkMutsaerts and
agahkarakuzu
and removed request for
effigies
Codecov Report
@@ Coverage Diff @@
## master #840 +/- ##
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+ Coverage 85.96% 86.13% +0.17%
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Files 35 35
Lines 3932 3932
Branches 1018 1018
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+ Hits 3380 3387 +7
+ Misses 359 353 -6
+ Partials 193 192 -1
Continue to review full report at Codecov.
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| @pytest.mark.xfail(reason="missing derivatives description: https://github.com/bids-standard/bids-examples/issues/310") | ||
| @pytest.mark.parametrize( | ||
| "dataset, nb_files", | ||
| [ | ||
| ("qmri_mpm", 125), | ||
| ], | ||
| ) | ||
| def test_layout_on_examples_with_derivatives(dataset, nb_files): | ||
| ds = join(get_test_data_path(), "bids-examples", dataset) | ||
| layout = BIDSLayout(ds, derivatives=True) | ||
| files = layout.get() | ||
| assert len(files) == nb_files |
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Setting aside this test as an expected failure.
@agahkarakuzu you were right "some" failures are due to invalid derivatives in the qMRI bids-examples.
I checked and simply adding a valid dataset descritpion will fix this one.
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@Remi-Gau the error is related to dropping a new data directory into the Python source tree. I would suggest instead of doing this, that we create a git submodule in the project root, look for it in |
oh that's the pythonic way to say this? Noted. :-p
mostly clear but let's chat about all this tomorrow during our bids maintainers meeting because I have other questions about this PR that could benefit from a video call. |
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for the record here is an example of what I get for "micr_SPIM" ds = join(get_test_data_path(), "bids-examples", "micr_SPIM")
layout = BIDSLayout(ds)
files = layout.get(return_type="file")
print(files)
['/home/remi/github/pybids/bids/tests/data/bids-examples/micr_SPIM/dataset_description.json',
'/home/remi/github/pybids/bids/tests/data/bids-examples/micr_SPIM/participants.json',
'/home/remi/github/pybids/bids/tests/data/bids-examples/micr_SPIM/participants.tsv',
'/home/remi/github/pybids/bids/tests/data/bids-examples/micr_SPIM/README'] |
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Thank you @Remi-Gau for looking into this!
I tested the indexation of microscopy datasets with the BIDSlayout and everything is working great for me.
I was wondering if it would be possible to add the samples.tsv file to the get_collections function at the "dataset" level At the moment, the "dataset" level seems to only index metadata from participants.tsv.
For example on micr_SPIM with:
subj_df = layout.get_collections(level='dataset', merge=True).to_df()
subj_df
I get the following from participant.tsv, but samples.tsv metadata is not present:
Co-authored-by: mariehbourget <[email protected]>
Co-authored-by: mariehbourget <[email protected]>
… update_config
I suggest moving this to a different issue and fix it in a different PR |
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This is good for a final review for me. Tests are still failing locally but that's a me problem. |
closes #807
should cover both new entities and default path patterns
most of this was done by reading from the bids schema and relying on elbow grease and patience to do the rest.
Cannot wait for #818 to be done so I never have to do this by hand ever again but in the mean time: here we go.
Has not been properly tested yet: