Update bids.py

PennLINC · Nov 1, 2024 · 84109c4 · 84109c4
1 parent 1004366
commit 84109c4
Showing 1 changed file with 25 additions and 7 deletions.
diff --git a/aslprep/interfaces/bids.py b/aslprep/interfaces/bids.py
@@ -37,34 +37,54 @@ class _BIDSDataGrabberInputSpec(BaseInterfaceInputSpec):
 class _BIDSDataGrabberOutputSpec(TraitedSpec):
     out_dict = traits.Dict(desc='output data structure')
     fmap = OutputMultiObject(desc='output fieldmaps')
-    asl = OutputMultiObject(desc='output ASL images')
+    bold = OutputMultiObject(desc='output functional images')
     sbref = OutputMultiObject(desc='output sbrefs')
     t1w = OutputMultiObject(desc='output T1w images')
     roi = OutputMultiObject(desc='output ROI images')
     t2w = OutputMultiObject(desc='output T2w images')
     flair = OutputMultiObject(desc='output FLAIR images')
+    pet = OutputMultiObject(desc='output PET images')
+    dwi = OutputMultiObject(desc='output DWI images')
+    asl = OutputMultiObject(desc='output ASL images')
 
 
 class BIDSDataGrabber(SimpleInterface):
-    """Collect files from a BIDS directory structure."""
+    """Collect files from a BIDS directory structure.
+
+    .. testsetup::
+
+        >>> data_dir_canary()
+
+    >>> bids_src = BIDSDataGrabber(anat_only=False)
+    >>> bids_src.inputs.subject_data = bids_collect_data(
+    ...     str(datadir / 'ds114'), '01', bids_validate=False)[0]
+    >>> bids_src.inputs.subject_id = '01'
+    >>> res = bids_src.run()
+    >>> res.outputs.t1w  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    ['.../ds114/sub-01/ses-retest/anat/sub-01_ses-retest_T1w.nii.gz',
+     '.../ds114/sub-01/ses-test/anat/sub-01_ses-test_T1w.nii.gz']
+
+    """
 
     input_spec = _BIDSDataGrabberInputSpec
     output_spec = _BIDSDataGrabberOutputSpec
     _require_funcs = True
 
     def __init__(self, *args, **kwargs):
         anat_only = kwargs.pop('anat_only')
+        anat_derivatives = kwargs.pop('anat_derivatives', None)
         super().__init__(*args, **kwargs)
         if anat_only is not None:
             self._require_funcs = not anat_only
+        self._require_t1w = 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 not bids_dict['t1w']:
+        if self._require_t1w and not bids_dict['t1w']:
             raise FileNotFoundError(
                 f'No T1w images found for subject sub-{self.inputs.subject_id}'
             )
@@ -74,12 +94,10 @@ def _run_interface(self, runtime):
                 f'No ASL images found for subject sub-{self.inputs.subject_id}'
             )
 
-        for imtype in ['t2w', 'flair', 'fmap', 'sbref', 'roi', 'asl']:
+        for imtype in ['bold', 't2w', 'flair', 'fmap', 'sbref', 'roi', 'pet', 'asl']:
             if not bids_dict[imtype]:
                 config.loggers.interface.info(
-                    'No "%s" images found for sub-%s',
-                    imtype,
-                    self.inputs.subject_id,
+                    'No "%s" images found for sub-%s', imtype, self.inputs.subject_id
                 )
 
         return runtime