TEST: Add smoke-tests for bold_fit_wf (#3152)

Turns out testing's a good idea. Starting out doing something similar to
nipreps/smriprep#390. Will try to expand the smoke tests upward to
`workflows.bold.base` and `workflows.base`.

Author: effigies

fmriprep/workflows/bold/base.py

@@ -192,21 +192,6 @@ def init_bold_wf(
         mem_gb["largemem"],
     )
 
-    functional_cache = {}
-    if config.execution.derivatives:
-        from fmriprep.utils.bids import collect_derivatives, extract_entities
-
-        entities = extract_entities(bold_series)
-
-        for deriv_dir in config.execution.derivatives:
-            functional_cache.update(
-                collect_derivatives(
-                    derivatives_dir=deriv_dir,
-                    entities=entities,
-                    fieldmap_id=fieldmap_id,
-                )
-            )
-
     workflow = Workflow(name=_get_wf_name(bold_file, "bold"))
     workflow.__postdesc__ = """\
 All resamplings can be performed with *a single interpolation
@@ -266,7 +251,7 @@ def init_bold_wf(
 
     bold_fit_wf = init_bold_fit_wf(
         bold_series=bold_series,
-        precomputed=functional_cache,
+        precomputed=precomputed,
         fieldmap_id=fieldmap_id,
         omp_nthreads=omp_nthreads,
     )

fmriprep/workflows/bold/fit.py

@@ -287,7 +287,9 @@ def init_bold_fit_wf(
         name="hmcref_buffer",
     )
     fmapref_buffer = pe.Node(niu.Function(function=_select_ref), name="fmapref_buffer")
-    hmc_buffer = pe.Node(niu.IdentityInterface(fields=["hmc_xforms"]), name="hmc_buffer")
+    hmc_buffer = pe.Node(
+        niu.IdentityInterface(fields=["hmc_xforms", "movpar_file", "rmsd_file"]), name="hmc_buffer"
+    )
     fmapreg_buffer = pe.Node(
         niu.IdentityInterface(fields=["boldref2fmap_xfm"]), name="fmapreg_buffer"
     )

fmriprep/workflows/bold/registration.py

@@ -582,8 +582,8 @@ def init_fsl_bbr_wf(
     )
 
     FSLDIR = os.getenv('FSLDIR')
-    if FSLDIR:
-        flt_bbr.inputs.schedule = op.join(FSLDIR, 'etc/flirtsch/bbr.sch')
+    if FSLDIR and os.path.exists(schedule := op.join(FSLDIR, 'etc/flirtsch/bbr.sch')):
+        flt_bbr.inputs.schedule = schedule
     else:
         # Should mostly be hit while building docs
         LOGGER.warning("FSLDIR unset - using packaged BBR schedule")

fmriprep/workflows/bold/tests/test_base.py

@@ -0,0 +1,77 @@
+from pathlib import Path
+
+import nibabel as nb
+import numpy as np
+import pytest
+from nipype.pipeline.engine.utils import generate_expanded_graph
+from niworkflows.utils.testing import generate_bids_skeleton
+
+from .... import config
+from ...tests import mock_config
+from ...tests.test_base import BASE_LAYOUT
+from ..base import init_bold_wf
+
+
+@pytest.fixture(scope="module", autouse=True)
+def _quiet_logger():
+    import logging
+
+    logger = logging.getLogger("nipype.workflow")
+    old_level = logger.getEffectiveLevel()
+    logger.setLevel(logging.ERROR)
+    yield
+    logger.setLevel(old_level)
+
+
+@pytest.fixture(scope="module")
+def bids_root(tmp_path_factory):
+    base = tmp_path_factory.mktemp("boldbase")
+    bids_dir = base / "bids"
+    generate_bids_skeleton(bids_dir, BASE_LAYOUT)
+    yield bids_dir
+
+
+@pytest.mark.parametrize("task", ["rest", "nback"])
+@pytest.mark.parametrize("fieldmap_id", ["phasediff", None])
+@pytest.mark.parametrize("freesurfer", [False, True])
+@pytest.mark.parametrize("level", ["minimal", "resampling", "full"])
+def test_bold_wf(
+    bids_root: Path,
+    tmp_path: Path,
+    task: str,
+    fieldmap_id: str | None,
+    freesurfer: bool,
+    level: str,
+):
+    """Test as many combinations of precomputed files and input
+    configurations as possible."""
+    output_dir = tmp_path / 'output'
+    output_dir.mkdir()
+
+    img = nb.Nifti1Image(np.zeros((10, 10, 10, 10)), np.eye(4))
+
+    if task == 'rest':
+        bold_series = [
+            str(bids_root / 'sub-01' / 'func' / 'sub-01_task-rest_run-1_bold.nii.gz'),
+        ]
+    elif task == 'nback':
+        bold_series = [
+            str(bids_root / 'sub-01' / 'func' / f'sub-01_task-nback_echo-{i}_bold.nii.gz')
+            for i in range(1, 4)
+        ]
+
+    # The workflow will attempt to read file headers
+    for path in bold_series:
+        img.to_filename(path)
+
+    with mock_config(bids_dir=bids_root):
+        config.workflow.level = level
+        config.workflow.run_reconall = freesurfer
+        wf = init_bold_wf(
+            bold_series=bold_series,
+            fieldmap_id=fieldmap_id,
+            precomputed={},
+        )
+
+    flatgraph = wf._create_flat_graph()
+    generate_expanded_graph(flatgraph)

fmriprep/workflows/bold/tests/test_fit.py

@@ -0,0 +1,172 @@
+from pathlib import Path
+
+import nibabel as nb
+import numpy as np
+import pytest
+from nipype.pipeline.engine.utils import generate_expanded_graph
+from niworkflows.utils.testing import generate_bids_skeleton
+
+from .... import config
+from ...tests import mock_config
+from ...tests.test_base import BASE_LAYOUT
+from ..fit import init_bold_fit_wf, init_bold_native_wf
+
+
+@pytest.fixture(scope="module", autouse=True)
+def _quiet_logger():
+    import logging
+
+    logger = logging.getLogger("nipype.workflow")
+    old_level = logger.getEffectiveLevel()
+    logger.setLevel(logging.ERROR)
+    yield
+    logger.setLevel(old_level)
+
+
+@pytest.fixture(scope="module")
+def bids_root(tmp_path_factory):
+    base = tmp_path_factory.mktemp("boldfit")
+    bids_dir = base / "bids"
+    generate_bids_skeleton(bids_dir, BASE_LAYOUT)
+    yield bids_dir
+
+
+def _make_params(
+    have_hmcref: bool = True,
+    have_coregref: bool = True,
+    have_hmc_xfms: bool = True,
+    have_boldref2fmap_xfm: bool = True,
+    have_boldref2anat_xfm: bool = True,
+):
+    return (
+        have_hmcref,
+        have_coregref,
+        have_hmc_xfms,
+        have_boldref2anat_xfm,
+        have_boldref2fmap_xfm,
+    )
+
+
+@pytest.mark.parametrize("task", ["rest", "nback"])
+@pytest.mark.parametrize("fieldmap_id", ["phasediff", None])
+@pytest.mark.parametrize(
+    (
+        'have_hmcref',
+        'have_coregref',
+        'have_hmc_xfms',
+        'have_boldref2fmap_xfm',
+        'have_boldref2anat_xfm',
+    ),
+    [
+        (True, True, True, True, True),
+        (False, False, False, False, False),
+        _make_params(have_hmcref=False),
+        _make_params(have_hmc_xfms=False),
+        _make_params(have_coregref=False),
+        _make_params(have_coregref=False, have_boldref2fmap_xfm=False),
+        _make_params(have_boldref2anat_xfm=False),
+    ],
+)
+def test_bold_fit_precomputes(
+    bids_root: Path,
+    tmp_path: Path,
+    task: str,
+    fieldmap_id: str | None,
+    have_hmcref: bool,
+    have_coregref: bool,
+    have_hmc_xfms: bool,
+    have_boldref2fmap_xfm: bool,
+    have_boldref2anat_xfm: bool,
+):
+    """Test as many combinations of precomputed files and input
+    configurations as possible."""
+    output_dir = tmp_path / 'output'
+    output_dir.mkdir()
+
+    img = nb.Nifti1Image(np.zeros((10, 10, 10, 10)), np.eye(4))
+
+    if task == 'rest':
+        bold_series = [
+            str(bids_root / 'sub-01' / 'func' / 'sub-01_task-rest_run-1_bold.nii.gz'),
+        ]
+    elif task == 'nback':
+        bold_series = [
+            str(bids_root / 'sub-01' / 'func' / f'sub-01_task-nback_echo-{i}_bold.nii.gz')
+            for i in range(1, 4)
+        ]
+
+    # The workflow will attempt to read file headers
+    for path in bold_series:
+        img.to_filename(path)
+
+    dummy_nifti = str(tmp_path / 'dummy.nii')
+    dummy_affine = str(tmp_path / 'dummy.txt')
+    img.to_filename(dummy_nifti)
+    np.savetxt(dummy_affine, np.eye(4))
+
+    # Construct precomputed files
+    precomputed = {'transforms': {}}
+    if have_hmcref:
+        precomputed['hmc_boldref'] = dummy_nifti
+    if have_coregref:
+        precomputed['coreg_boldref'] = dummy_nifti
+    if have_hmc_xfms:
+        precomputed['transforms']['hmc'] = dummy_affine
+    if have_boldref2anat_xfm:
+        precomputed['transforms']['boldref2anat'] = dummy_affine
+    if have_boldref2fmap_xfm:
+        precomputed['transforms']['boldref2fmap'] = dummy_affine
+
+    with mock_config(bids_dir=bids_root):
+        wf = init_bold_fit_wf(
+            bold_series=bold_series,
+            precomputed=precomputed,
+            fieldmap_id=fieldmap_id,
+            omp_nthreads=1,
+        )
+
+    flatgraph = wf._create_flat_graph()
+    generate_expanded_graph(flatgraph)
+
+
+@pytest.mark.parametrize("task", ["rest", "nback"])
+@pytest.mark.parametrize("fieldmap_id", ["phasediff", None])
+@pytest.mark.parametrize("run_stc", [True, False])
+def test_bold_native_precomputes(
+    bids_root: Path,
+    tmp_path: Path,
+    task: str,
+    fieldmap_id: str | None,
+    run_stc: bool,
+):
+    """Test as many combinations of precomputed files and input
+    configurations as possible."""
+    output_dir = tmp_path / 'output'
+    output_dir.mkdir()
+
+    img = nb.Nifti1Image(np.zeros((10, 10, 10, 10)), np.eye(4))
+
+    if task == 'rest':
+        bold_series = [
+            str(bids_root / 'sub-01' / 'func' / 'sub-01_task-rest_run-1_bold.nii.gz'),
+        ]
+    elif task == 'nback':
+        bold_series = [
+            str(bids_root / 'sub-01' / 'func' / f'sub-01_task-nback_echo-{i}_bold.nii.gz')
+            for i in range(1, 4)
+        ]
+
+    # The workflow will attempt to read file headers
+    for path in bold_series:
+        img.to_filename(path)
+
+    with mock_config(bids_dir=bids_root):
+        config.workflow.ignore = ['slicetiming'] if not run_stc else []
+        wf = init_bold_native_wf(
+            bold_series=bold_series,
+            fieldmap_id=fieldmap_id,
+            omp_nthreads=1,
+        )
+
+    flatgraph = wf._create_flat_graph()
+    generate_expanded_graph(flatgraph)

fmriprep/workflows/tests/__init__.py

@@ -33,7 +33,7 @@
 
 
 @contextmanager
-def mock_config():
+def mock_config(bids_dir=None):
     """Create a mock config for documentation and testing purposes."""
     from ... import config
 
@@ -51,9 +51,13 @@ def mock_config():
     config.loggers.init()
     config.init_spaces()
 
+    bids_dir = bids_dir or data.load('tests/ds000005').absolute()
+
     config.execution.work_dir = Path(mkdtemp())
-    config.execution.bids_dir = data.load('tests/ds000005').absolute()
+    config.execution.bids_dir = bids_dir
     config.execution.fmriprep_dir = Path(mkdtemp())
+    config.execution.bids_database_dir = None
+    config.execution._layout = None
     config.execution.init()
 
     yield