Merge pull request #951 from nipreps/update_bids_pet

ENH: Toggle requirement for any image type BIDSDataGrabber, add task filtering when collecting PET data

Author: mnoergaard

niworkflows/interfaces/bids.py

@@ -260,36 +260,42 @@ class BIDSDataGrabber(SimpleInterface):
 
     input_spec = _BIDSDataGrabberInputSpec
     output_spec = _BIDSDataGrabberOutputSpec
-    _require_funcs = True
 
-    def __init__(self, *args, **kwargs):
-        anat_only = kwargs.pop('anat_only', None)
-        anat_derivatives = kwargs.pop('anat_derivatives', None)
-        require_t1w = kwargs.pop('require_t1w', True)
+    _image_types = {'asl', 'bold', 'dwi', 'flair', 'fmap', 'pet', 'roi', 'sbref', 't1w', 't2w'}
+
+    def __init__(
+        self,
+        anat_only=False,
+        anat_derivatives=None,
+        *args,
+        **kwargs,
+    ):
+        default_required = {'t1w', 'bold'}
+
+        for imtype in self._image_types:
+            kwarg = f'require_{imtype}'
+            val = kwargs.pop(kwarg, True if imtype in default_required else False)
+            setattr(self, f'_{kwarg}', val)
+
+        self._require_t1w = self._require_t1w and anat_derivatives is None
+        if anat_only:
+            self._require_bold = False
+            self._require_pet = False
+
         super().__init__(*args, **kwargs)
-        if anat_only is not None:
-            self._require_funcs = not anat_only
-        self._require_t1w = require_t1w and anat_derivatives is None
 
     def _run_interface(self, runtime):
         bids_dict = self.inputs.subject_data
 
         self._results['out_dict'] = bids_dict
         self._results.update(bids_dict)
 
-        if self._require_t1w and not bids_dict['t1w']:
-            raise FileNotFoundError(
-                f'No T1w images found for subject sub-{self.inputs.subject_id}'
-            )
-
-        if self._require_funcs and not bids_dict['bold']:
-            raise FileNotFoundError(
-                f'No functional images found for subject sub-{self.inputs.subject_id}'
-            )
-
-        for imtype in ['bold', 't2w', 'flair', 'fmap', 'sbref', 'roi', 'pet', 'asl']:
+        for imtype in self._image_types:
             if not bids_dict[imtype]:
-                LOGGER.info('No "%s" images found for sub-%s', imtype, self.inputs.subject_id)
+                msg = f'No "{imtype}" images found for sub-{self.inputs.subject_id}'
+                if getattr(self, f'_require_{imtype}', False):  # only raise if image is required
+                    raise FileNotFoundError(msg)
+                LOGGER.info(msg)
 
         return runtime
 

niworkflows/interfaces/tests/test_bids.py

@@ -798,11 +798,61 @@ def test_fsdir_min_version(tmp_path, min_version):
 def test_BIDSDataGrabber():
     x = bintfs.BIDSDataGrabber(anat_only=True)
     assert x._require_t1w is True
-    assert x._require_funcs is False
+    assert x._require_bold is False
 
     x = bintfs.BIDSDataGrabber(anat_only=False, require_t1w=False)
     assert x._require_t1w is False
-    assert x._require_funcs is True
+    assert x._require_bold is True
 
     x = bintfs.BIDSDataGrabber(anat_derivatives='derivatives')
     assert x._require_t1w is False
+
+
+def test_require_bold_pet_behavior():
+    import pytest
+
+    from niworkflows.interfaces.bids import BIDSDataGrabber
+
+    subject_data_pet = {
+        't1w': ['t1.nii'],
+        'bold': [],
+        'pet': ['pet.nii'],
+        't2w': [],
+        'flair': [],
+        'fmap': [],
+        'sbref': [],
+        'roi': [],
+        'asl': [],
+        'dwi': [],
+    }
+
+    subject_data_bold = {
+        't1w': ['t1.nii'],
+        'bold': ['bold.nii'],
+        'pet': [],
+        't2w': [],
+        'flair': [],
+        'fmap': [],
+        'sbref': [],
+        'roi': [],
+        'asl': [],
+        'dwi': [],
+    }
+
+    # PET present, functional not required
+    grabber_pet = BIDSDataGrabber(
+        subject_data=subject_data_pet, subject_id='01', require_pet=True, require_bold=False
+    )
+    assert grabber_pet._require_bold is False
+    assert grabber_pet._require_pet is True
+    grabber_pet.run()  # Should succeed without bold data
+
+    # PET absent, functional required by default
+    grabber_func = BIDSDataGrabber(subject_data=subject_data_bold, subject_id='01')
+    assert grabber_func._require_bold is True
+    assert grabber_func.run().outputs.bold == 'bold.nii'
+
+    # Fail when bold is required but missing
+    grabber_fail = BIDSDataGrabber(subject_data=subject_data_pet, subject_id='01')
+    with pytest.raises(FileNotFoundError, match='No "bold" images found'):
+        grabber_fail.run()

niworkflows/utils/bids.py

@@ -34,7 +34,11 @@
 from packaging.version import Version
 
 DEFAULT_BIDS_QUERIES = {
-    'bold': {'datatype': 'func', 'suffix': 'bold', 'part': ['mag', None]},
+    'bold': {
+        'datatype': 'func',
+        'suffix': 'bold',
+        'part': ['mag', None],
+    },
     'dwi': {'suffix': 'dwi'},
     'flair': {'datatype': 'anat', 'suffix': 'FLAIR', 'part': ['mag', None]},
     'fmap': {'datatype': 'fmap'},
@@ -272,7 +276,7 @@ def collect_data(
                 del layout_get_kwargs[entity]
 
     if task:
-        queries['bold']['task'] = task
+        queries['bold']['task'] = queries['pet']['task'] = task
 
     if echo:
         queries['bold']['echo'] = echo