FIX: Traverse BIDS hierarchy to find masks, bvals, and bvecs

AFQ/api.py

@@ -279,10 +279,13 @@ def __init__(self,
             The parameters for segmentation.
             Default: use the default behavior of the seg.Segmentation object.
         tracking_params: dict, optional
-            The parameters for tracking.
-            Default: use the default behavior of the aft.track function.
-            Seed mask and seed threshold, if not specified, are replaced
-            with scalar masks from scalar[0] thresholded to 0.2.
+            The parameters for tracking. Default: use the default behavior of
+            the aft.track function. Seed mask and seed threshold, if not
+            specified, are replaced with scalar masks from scalar[0]
+            thresholded to 0.2. The ``seed_mask`` and ``stop_mask`` items of
+            this dict may be ``AFQ.mask.MaskFile`` instances. If ``tracker``
+            is set to "pft" then ``stop_mask`` should be an instance of
+            ``AFQ.mask.PFTMask``.
         clean_params: dict, optional
             The parameters for cleaning.
             Default: use the default behavior of the seg.clean_bundle
@@ -509,11 +512,17 @@ def __init__(self,
                 if session is not None:
                     results_dir = op.join(results_dir, 'ses-' + session)
 
-                dwi_files = bids_layout.get(subject=subject, session=session,
-                                            extension='nii.gz',
-                                            return_type='filename',
-                                            scope=dmriprep,
-                                            **bids_filters)
+                dwi_bids_filters = {
+                    "subject": subject,
+                    "session": session,
+                    "return_type": "filename",
+                    "scope": dmriprep,
+                    "datatype": "dwi",
+                    "extension": "nii.gz",
+                    "suffix": "dwi",
+                }
+                dwi_bids_filters.update(bids_filters)
+                dwi_files = bids_layout.get(**dwi_bids_filters)
 
                 if (not len(dwi_files)):
                     self.logger.warning(
@@ -522,21 +531,23 @@ def __init__(self,
                     continue
 
                 results_dir_list.append(results_dir)
-
                 os.makedirs(results_dir_list[-1], exist_ok=True)
-                dwi_file_list.append(dwi_files[0])
-                bvec_file_list.append(
-                    bids_layout.get(subject=subject, session=session,
-                                    extension=['bvec', 'bvecs'],
-                                    return_type='filename',
-                                    scope=dmriprep,
-                                    **bids_filters)[0])
-                bval_file_list.append(
-                    bids_layout.get(subject=subject, session=session,
-                                    extension=['bval', 'bvals'],
-                                    return_type='filename',
-                                    scope=dmriprep,
-                                    **bids_filters)[0])
+
+                dwi_data_file = dwi_files[0]
+                dwi_file_list.append(dwi_data_file)
+
+                # For bvals and bvecs, use ``get_bval()`` and ``get_bvec()`` to
+                # walk up the file tree and inherit the closest bval and bvec
+                # files. Maintain input ``bids_filters`` in case user wants to
+                # specify acquisition labels, but pop suffix since it is
+                # already specified inside ``get_bvec()`` and ``get_bval()``
+                suffix = bids_filters.pop("suffix", None)
+                bvec_file_list.append(bids_layout.get_bvec(dwi_data_file,
+                                                           **bids_filters))
+                bval_file_list.append(bids_layout.get_bval(dwi_data_file,
+                                                           **bids_filters))
+                if suffix is not None:
+                    bids_filters["suffix"] = suffix
 
                 if custom_tractography_bids_filters is not None:
                     custom_tract_list.append(
@@ -554,28 +565,38 @@ def __init__(self,
 
                 if isinstance(self.reg_subject, dict):
                     reg_subject_list.append(
-                        bids_layout.get(subject=subject, session=session,
-                                        return_type='filename',
-                                        **self.reg_subject)[0])
+                        bids_layout.get_nearest(
+                            dwi_data_file,
+                            **self.reg_subject,
+                            session=session,
+                            subject=subject,
+                            full_search=True,
+                            strict=True,
+                            ignore_strict_entities=["session"]
+                        )
+                    )
                 else:
                     reg_subject_list.append(None)
 
                 if check_mask_methods(self.tracking_params["seed_mask"]):
                     self.tracking_params["seed_mask"].find_path(
                         bids_layout,
+                        dwi_data_file,
                         subject,
                         session
                     )
 
                 if check_mask_methods(self.tracking_params["stop_mask"]):
                     self.tracking_params["stop_mask"].find_path(
                         bids_layout,
+                        dwi_data_file,
                         subject,
                         session
                     )
 
                 self.brain_mask_definition.find_path(
                     bids_layout,
+                    dwi_data_file,
                     subject,
                     session
                 )

AFQ/data.py

@@ -1706,8 +1706,8 @@ def organize_cfin_data(path=None):
         nib.save(t1_img, op.join(anat_folder, 'sub-01_ses-01_T1w.nii.gz'))
         dwi_img, gtab = dpd.read_cfin_dwi()
         nib.save(dwi_img, op.join(dwi_folder, 'sub-01_ses-01_dwi.nii.gz'))
-        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bvecs'), gtab.bvecs)
-        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bvals'), gtab.bvals)
+        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bvec'), gtab.bvecs)
+        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bval'), gtab.bvals)
 
     to_bids_description(
         bids_path,
@@ -1743,8 +1743,8 @@ def organize_stanford_data(path=None):
             └── sub-01
                 └── ses-01
                     └── dwi
-                        ├── sub-01_ses-01_dwi.bvals
-                        ├── sub-01_ses-01_dwi.bvecs
+                        ├── sub-01_ses-01_dwi.bval
+                        ├── sub-01_ses-01_dwi.bvec
                         └── sub-01_ses-01_dwi.nii.gz
 
     """
@@ -1785,8 +1785,8 @@ def organize_stanford_data(path=None):
 
         dwi_img, gtab = dpd.read_stanford_hardi()
         nib.save(dwi_img, op.join(dwi_folder, 'sub-01_ses-01_dwi.nii.gz'))
-        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bvecs'), gtab.bvecs)
-        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bvals'), gtab.bvals)
+        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bvec'), gtab.bvecs)
+        np.savetxt(op.join(dwi_folder, 'sub-01_ses-01_dwi.bval'), gtab.bvals)
     else:
         logger.info('Dataset is already in place. If you want to fetch it '
                     + 'again please first remove the folder '

AFQ/mask.py

@@ -159,15 +159,35 @@ def __init__(self, suffix, filters={}):
         self.filters = filters
         self.fnames = {}
 
-    def find_path(self, bids_layout, subject, session):
+    def find_path(self, bids_layout, from_path, subject, session):
         if session not in self.fnames:
             self.fnames[session] = {}
-        self.fnames[session][subject] = bids_layout.get(
-            subject=subject, session=session,
-            extension='.nii.gz',
-            return_type='filename',
+
+        nearest_mask = bids_layout.get_nearest(
+            from_path,
+            **self.filters,
+            extension=".nii.gz",
             suffix=self.suffix,
-            **self.filters)[0]
+            session=session,
+            subject=subject,
+            full_search=True,
+            strict=False,
+        )
+
+        self.fnames[session][subject] = nearest_mask
+        from_path_subject = bids_layout.parse_file_entities(from_path).get(
+            "subject", None
+        )
+        mask_subject = bids_layout.parse_file_entities(nearest_mask).get(
+            "subject", None
+        )
+        if from_path_subject != mask_subject:
+            raise ValueError(
+                f"Expected subject IDs to match for the retrieved mask file "
+                f"and the supplied `from_path` file. Got sub-{mask_subject} "
+                f"from mask file {nearest_mask} and sub-{from_path_subject} "
+                f"from `from_path` file {from_path}."
+            )
 
     def get_path_data_affine(self, afq_object, row):
         mask_file = self.fnames[row['ses']][row['subject']]
@@ -209,7 +229,7 @@ class FullMask(StrInstantiatesMixin):
     def __init__(self):
         pass
 
-    def find_path(self, bids_layout, subject, session):
+    def find_path(self, bids_layout, from_path, subject, session):
         pass
 
     def get_mask(self, afq_object, row):
@@ -234,7 +254,7 @@ class RoiMask(StrInstantiatesMixin):
     def __init__(self):
         pass
 
-    def find_path(self, bids_layout, subject, session):
+    def find_path(self, bids_layout, from_path, subject, session):
         pass
 
     def get_mask(self, afq_object, row):
@@ -286,7 +306,7 @@ class B0Mask(StrInstantiatesMixin):
     def __init__(self, median_otsu_kwargs={}):
         self.median_otsu_kwargs = median_otsu_kwargs
 
-    def find_path(self, bids_layout, subject, session):
+    def find_path(self, bids_layout, from_path, subject, session):
         pass
 
     def get_mask(self, afq_object, row):
@@ -448,7 +468,7 @@ def __init__(self, scalar):
         self.scalar = scalar
 
     # overrides MaskFile
-    def find_path(self, bids_layout, subject, session):
+    def find_path(self, bids_layout, from_path, subject, session):
         pass
 
     # overrides MaskFile
@@ -536,9 +556,9 @@ def __init__(self, WM_probseg, GM_probseg, CSF_probseg):
         """
         self.probsegs = (WM_probseg, GM_probseg, CSF_probseg)
 
-    def find_path(self, bids_layout, subject, session):
+    def find_path(self, bids_layout, from_path, subject, session):
         for probseg in self.probsegs:
-            probseg.find_path(bids_layout, subject, session)
+            probseg.find_path(bids_layout, from_path, subject, session)
 
     def get_mask(self, afq_object, row):
         probseg_imgs = []
@@ -547,7 +567,7 @@ def get_mask(self, afq_object, row):
             data, affine, meta = probseg.get_mask(afq_object, row)
             probseg_imgs.append(nib.Nifti1Image(data, affine))
             probseg_metas.append(meta)
-        return probseg_imgs, _, dict(sources=probseg_metas)
+        return probseg_imgs, None, dict(sources=probseg_metas)
 
 
 class CombinedMask(StrInstantiatesMixin, CombineMaskMixin):
@@ -581,9 +601,9 @@ def __init__(self, mask_list, combine="and"):
         CombineMaskMixin.__init__(self, combine)
         self.mask_list = mask_list
 
-    def find_path(self, bids_layout, subject, session):
+    def find_path(self, bids_layout, from_path, subject, session):
         for mask in self.mask_list:
-            mask.find_path(bids_layout, subject, session)
+            mask.find_path(bids_layout, from_path, subject, session)
 
     def get_mask(self, afq_object, row):
         self.mask_draft = None

AFQ/tests/test_api.py

@@ -71,11 +71,11 @@ def create_dummy_data(dmriprep_dir, subject, session=None):
 
     np.savetxt(
         op.join(
-            dmriprep_dir, data_dir, 'dwi', 'dwi.bvals'),
+            dmriprep_dir, data_dir, 'dwi', 'dwi.bval'),
         bvals)
     np.savetxt(
         op.join(
-            dmriprep_dir, data_dir, 'dwi', 'dwi.bvecs'),
+            dmriprep_dir, data_dir, 'dwi', 'dwi.bvec'),
         bvecs)
     nib.save(
         nib.Nifti1Image(data, aff),

AFQ/tests/test_mask.py

@@ -1,5 +1,7 @@
+import os.path as op
 import numpy as np
 import numpy.testing as npt
+import pytest
 
 from bids.layout import BIDSLayout
 
@@ -75,13 +77,30 @@ def test_resample_mask():
         mask_data.dtype)
 
 
-def test_find_path():
+@pytest.mark.parametrize("subject", ["01", "02"])
+@pytest.mark.parametrize("session", ["01", "02"])
+def test_find_path(subject, session):
     bids_dir = create_dummy_bids_path(2, 2)
-    print(bids_dir)
     bids_layout = BIDSLayout(bids_dir, derivatives=True)
 
+    test_dwi_path = bids_layout.get(
+        subject=subject, session=session, return_type="filename",
+        suffix="dwi", extension="nii.gz"
+    )[0]
+
     mask_file = MaskFile("seg", {'scope': 'synthetic'})
-    mask_file.find_path(bids_layout, '01', '01')
-    mask_file.find_path(bids_layout, '02', '01')
-    mask_file.find_path(bids_layout, '01', '02')
-    mask_file.find_path(bids_layout, '02', '02')
+    mask_file.find_path(bids_layout, test_dwi_path, subject, session)
+
+    assert mask_file.fnames[session][subject] == op.join(
+        bids_dir, "derivatives", "dmriprep", "sub-" + subject,
+        "ses-" + session, "anat", "seg.nii.gz"
+    )
+
+    other_sub = "01" if subject == "02" else "02"
+    with pytest.raises(ValueError):
+        mask_file.find_path(
+            bids_layout,
+            test_dwi_path,
+            subject=other_sub,
+            session=session,
+        )

AFQ/tractography.py

@@ -1,3 +1,4 @@
+from collections.abc import Iterable
 import numpy as np
 import nibabel as nib
 import dipy.reconst.shm as shm
@@ -166,11 +167,11 @@ def track(params_file, directions="det", max_angle=30., sphere=None,
                 "You are using PFT tracking, but did not provide a string ",
                 "'stop_threshold' input. ",
                 "Possible inputs are: 'CMC' or 'ACT'")
-        if not isinstance(stop_mask, tuple):
+        if not (isinstance(stop_mask, Iterable) and len(stop_mask) == 3):
             raise RuntimeError(
-                "You are using PFT tracking, but did not provide a tuple for",
-                "`stop_mask`",
-                "input. Expected a (pve_wm, pve_gm, pve_csf) tuple.")
+                "You are using PFT tracking, but did not provide a length "
+                "3 iterable for `stop_mask`. "
+                "Expected a (pve_wm, pve_gm, pve_csf) tuple.")
         pves = []
         pve_imgs = []
         vox_sizes = []

docs/source/usage/data.rst

@@ -41,6 +41,6 @@ data set in a directory called `stanford_hardi`::
     └── sub-01
         └── ses-01
             └── dwi
-                ├── sub-01_ses-01_dwi.bvals
-                ├── sub-01_ses-01_dwi.bvecs
+                ├── sub-01_ses-01_dwi.bval
+                ├── sub-01_ses-01_dwi.bvec
                 └── sub-01_ses-01_dwi.nii.gz