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[ENH] Update config to support microscopy, qMRI, PET, ASL (#840)
* add Pipfile to gitingore
* add missing datatypes to config
* add microscopy entities to config
* add draft path patterns microscopy and qMRI
* clean up and refactor
* add extension micr
* add suffixes micr
* add photo files for micr
* add parametric parts of qMRI
* add PET tracer entity to config
* add path patterns for PET
* add path patterns for ASL
* refactor some patterns
* add patterns for json files in root of dataset
* update bids nodot config and use {suffix<>} everywhere
* add tracer entity to no dot config
* fix entity order in filename pattern for no dot config
* fix typo
* remove problematic path pattern
* readd sample entity to micr filename pattern in root of dataset
* sample is actually required for micr
* update test layout on bids-example
* Update bids/layout/config/bids.json
Co-authored-by: Chris Markiewicz <[email protected]>
* Update bids/layout/config/bids.json
Co-authored-by: Chris Markiewicz <[email protected]>
* fix separator position for session
* add more bids example layout tests and flag MPM as xfail
* flag qmri_qsm as failure expected too
* make xfail strict to detect tests when they start passing
* Update bids/layout/config/bids.json
Co-authored-by: mariehbourget <[email protected]>
* Update bids/layout/config/bids.json
Co-authored-by: mariehbourget <[email protected]>
* fix more typos
* use bids-example submodule and fixture for testing
* remove makefile recipe for bids-examles
* MNT: Restore makefile
Co-authored-by: Chris Markiewicz <[email protected]>
Co-authored-by: mariehbourget <[email protected]>
Co-authored-by: Christopher J. Markiewicz <[email protected]>- Loading branch information
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| """ Tests runs layout on bids examples and make sure all files are caught""" | ||
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|
||
| """ TODO | ||
| - add more 'vanilla' datasets | ||
| - missing files in micr? | ||
| """ | ||
|
|
||
| from os.path import join | ||
|
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||
| import pytest | ||
|
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| from bids.layout import BIDSLayout | ||
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| # Values for the number of file got from a: | ||
| # | ||
| # find ds_name -type f | wc -l | ||
| # | ||
|
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| @pytest.mark.parametrize( | ||
| "dataset, nb_files", | ||
| [ | ||
| ("qmri_irt1", 15), | ||
| ("qmri_mese", 73), | ||
| ("qmri_mp2rage", 14), | ||
| ("qmri_mp2rageme", 28), | ||
| ("qmri_mtsat", 23), | ||
| ("qmri_sa2rage", 9), | ||
| ("qmri_vfa", 17), | ||
| ], | ||
| ) | ||
| def test_layout_on_examples_with_derivatives(dataset, nb_files, bids_examples): | ||
| ds = join(bids_examples, dataset) | ||
| layout = BIDSLayout(ds, derivatives=True) | ||
| files = layout.get() | ||
| assert len(files) == nb_files | ||
|
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||
|
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| @pytest.mark.parametrize( | ||
| "dataset, nb_files", | ||
| [ | ||
| ("micr_SEM", 12), | ||
| ("micr_SPIM", 22), | ||
| ("asl001", 8), | ||
| ("asl002", 10), | ||
| ("asl003", 10), | ||
| ("asl004", 12), | ||
| ("asl005", 10), | ||
| ("pet001", 12), | ||
| ("pet002", 20), | ||
| ("pet003", 9), | ||
| ("pet004", 10), | ||
| ("pet005", 14), | ||
| ("qmri_megre", 18), | ||
| ("qmri_tb1tfl", 6), | ||
| ], | ||
| ) | ||
| def test_layout_on_examples_no_derivatives(dataset, nb_files, bids_examples): | ||
| ds = join(bids_examples, dataset) | ||
| layout = BIDSLayout(ds) | ||
| files = layout.get() | ||
| assert len(files) == nb_files | ||
|
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||
|
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| @pytest.mark.parametrize( | ||
| "dataset, nb_files", | ||
| [ | ||
| pytest.param( | ||
| "qmri_qsm", | ||
| 8, | ||
| marks=pytest.mark.xfail(strict=True, | ||
| reason="https://github.com/bids-standard/bids-examples/issues/311" | ||
| ), | ||
| ), | ||
| pytest.param( | ||
| "qmri_mpm", | ||
| 125, | ||
| marks=pytest.mark.xfail(strict=True, | ||
| reason="https://github.com/bids-standard/bids-examples/issues/310" | ||
| ), | ||
| ), | ||
| ], | ||
| ) | ||
| def test_layout_on_examples_invalid_ds_description(dataset, nb_files, bids_examples): | ||
| ds = join(bids_examples, dataset) | ||
| layout = BIDSLayout(ds, derivatives=True) | ||
| files = layout.get() | ||
| assert len(files) == nb_files |