Merge pull request #305 from nipreps/docker/t1-t2-derivatives

ENH+RF: Allow precomputed derivatives in T1w or T2w space

Author: mgxd

nibabies/utils/bids.py

@@ -1,31 +1,134 @@
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """Utilities to handle BIDS inputs."""
+from __future__ import annotations
+
 import json
 import os
 import sys
+import typing as ty
 import warnings
-from dataclasses import dataclass, field
 from pathlib import Path
-from typing import IO, List, Literal, Optional, Union
 
+import nibabel as nb
+import numpy as np
+from bids.layout import BIDSLayout, Query
+
+_spec: dict = {
+    't1w_mask': {
+        'datatype': 'anat',
+        'desc': 'brain',
+        'space': 'T1w',
+        'suffix': 'mask',
+    },
+    't1w_aseg': {'datatype': 'anat', 'desc': 'aseg', 'space': 'T1w', 'suffix': 'dseg'},
+    't2w_mask': {
+        'datatype': 'anat',
+        'desc': 'brain',
+        'space': 'T2w',
+        'suffix': 'mask',
+    },
+    't2w_aseg': {
+        'datatype': 'anat',
+        'desc': 'aseg',
+        'space': 'T2w',
+        'suffix': 'dseg',
+    },
+}
+
+
+class Derivatives:
+    """
+    A container class for collecting and storing derivatives.
+
+    A specification (either dictionary or JSON file) can be used to customize derivatives and
+    queries.
+    To populate this class with derivatives, the `populate()` method must first be called.
+    """
 
-@dataclass
-class BOLDGrouping:
-    """This class is used to facilitate the grouping of BOLD series."""
+    def __getattribute__(self, attr):
+        """In cases where the spec may change, avoid errors."""
+        try:
+            return object.__getattribute__(self, attr)
+        except AttributeError:
+            return None
+
+    def __init__(self, bids_root: Path | str, spec: dict | Path | str | None = None, **args):
+        self.bids_root = Path(bids_root)
+        self.spec = _spec
+        if spec is not None:
+            if not isinstance(spec, dict):
+                spec: dict = json.loads(Path(spec).read_text())
+            self.spec = spec
+
+        self.names = set(self.spec.keys())
+        self.references = {name: None for name in self.names}
+        for name in self.names:
+            setattr(self, name, None)
+
+    def __repr__(self):
+        return '\n'.join([name for name in self.names if getattr(self, name)])
+
+    def __contains__(self, val: str):
+        return val in self.names
+
+    def __bool__(self):
+        return any(getattr(self, name) for name in self.names)
+
+    def populate(
+        self, deriv_path, subject_id: str, session_id: str | Query | None = Query.OPTIONAL
+    ) -> None:
+        """Query a derivatives directory and populate values and references based on the spec."""
+        layout = BIDSLayout(deriv_path, validate=False)
+        for name, query in self.spec.items():
+            items = layout.get(
+                subject=subject_id,
+                session=session_id,
+                extension=['.nii', '.nii.gz'],
+                **query,
+            )
+            if not items or len(items) > 1:
+                warnings.warn(f"Could not find {name}")
+                continue
+            item = items[0]
+
+            # Skip if derivative does not have valid metadata
+            metadata = item.get_metadata()
+            if not metadata or not (reference := metadata.get('SpatialReference')):
+                warnings.warn(f"No metadata found for {item}")
+                continue
+            if isinstance(reference, list):
+                if len(reference) > 1:
+                    warnings.warn(f"Multiple reference found: {reference}")
+                    continue
+                reference = reference[0]
+
+            reference = self.bids_root / reference
+            if not self.validate(item.path, str(reference)):
+                warnings.warn(f"Validation failed between: {item.path} and {reference}")
+                continue
+
+            setattr(self, name, Path(item.path))
+            self.references[name] = reference
 
-    session: Union[str, None]
-    pe_dir: str
-    readout: float
-    multiecho_id: str = None
-    files: List[IO] = field(default_factory=list)
+    @property
+    def mask(self) -> str | None:
+        return self.t1w_mask or self.t2w_mask
 
     @property
-    def name(self) -> str:
-        return f"{self.session}-{self.pe_dir}-{self.readout}-{self.multiecho_id}"
+    def aseg(self) -> str | None:
+        return self.t1w_aseg or self.t2w_aseg
 
-    def add_file(self, fl) -> None:
-        self.files.append(fl)
+    @staticmethod
+    def validate(derivative: str, reference: str, atol: float = 1e-5) -> bool:
+        anat = nb.load(reference)
+        expected_ort = nb.aff2axcodes(anat.affine)
+        img = nb.load(derivative)
+        if nb.aff2axcodes(img.affine) != expected_ort:
+            return False
+        if img.shape != anat.shape or not np.allclose(anat.affine, img.affine, atol=atol):
+            return False
+        return True
 
 
 def write_bidsignore(deriv_dir):
@@ -221,55 +324,11 @@ def validate_input_dir(exec_env, bids_dir, participant_label):
             print("bids-validator does not appear to be installed", file=sys.stderr)
 
 
-def collect_precomputed_derivatives(layout, subject_id, derivatives_filters=None):
-    """
-    Query and collect precomputed derivatives.
-
-    This function is used to determine which workflow steps can be skipped,
-    based on the files found.
-    """
-
-    deriv_queries = {
-        'anat_mask': {
-            'datatype': 'anat',
-            'desc': 'brain',
-            'space': 'orig',
-            'suffix': 'mask',
-        },
-        'anat_aseg': {
-            'datatype': 'anat',
-            'desc': 'aseg',
-            'space': 'orig',
-            'suffix': 'dseg',
-        },
-    }
-    if derivatives_filters is not None:
-        deriv_queries.update(derivatives_filters)
-
-    derivatives = {}
-    for deriv, query in deriv_queries.items():
-        res = layout.get(
-            scope='derivatives',
-            subject=subject_id,
-            extension=['.nii', '.nii.gz'],
-            return_type="filename",
-            **query,
-        )
-        if not res:
-            continue
-        if len(res) > 1:  # Some queries may want multiple results
-            raise Exception(
-                f"When searching for <{deriv}>, found multiple results: {[f.path for f in res]}"
-            )
-        derivatives[deriv] = res[0]
-    return derivatives
-
-
 def parse_bids_for_age_months(
-    bids_root: Union[str, Path],
+    bids_root: str | Path,
     subject_id: str,
-    session_id: Optional[str] = None,
-) -> Optional[int]:
+    session_id: str | None = None,
+) -> int | None:
     """
     Given a BIDS root, query the BIDS metadata files for participant age, in months.
 
@@ -295,8 +354,8 @@ def parse_bids_for_age_months(
 
 
 def _get_age_from_tsv(
-    bids_tsv: Path, level: Literal['session', 'participant'], key: str
-) -> Optional[int]:
+    bids_tsv: Path, level: ty.Literal['session', 'participant'], key: str
+) -> int | None:
     import pandas as pd
 
     df = pd.read_csv(str(bids_tsv), sep='\t')

nibabies/utils/tests/__init__.py

@@ -0,0 +1,113 @@
+from __future__ import annotations
+
+import json
+import typing as ty
+from pathlib import Path
+
+import pytest
+
+from nibabies.utils import bids
+
+
+def _create_nifti(filename: str) -> str:
+    import nibabel as nb
+    import numpy as np
+
+    data = np.zeros((4, 4, 4), dtype='int8')
+    nb.Nifti1Image(data, np.eye(4)).to_filename(filename)
+    return filename
+
+
+def _create_bids_dir(root_path: Path):
+    if not root_path.exists():
+        root_path.mkdir()
+    anat_dir = root_path / 'sub-01' / 'anat'
+    anat_dir.mkdir(parents=True)
+    _create_nifti(str(anat_dir / 'sub-01_T1w.nii.gz'))
+    _create_nifti(str(anat_dir / 'sub-01_T2w.nii.gz'))
+
+
+def _create_bids_derivs(
+    root_path: Path,
+    *,
+    t1w_mask: bool = False,
+    t1w_aseg: bool = False,
+    t2w_mask: bool = False,
+    t2w_aseg: bool = False,
+):
+    if not root_path.exists():
+        root_path.mkdir()
+    (root_path / 'dataset_description.json').write_text(
+        json.dumps(
+            {'Name': 'Derivatives Test', 'BIDSVersion': '1.8.0', 'DatasetType': 'derivative'}
+        )
+    )
+    anat_dir = root_path / 'sub-01' / 'anat'
+    anat_dir.mkdir(parents=True)
+
+    def _create_deriv(name: str, modality: ty.Literal['t1w', 't2w']):
+        if modality == 't1w':
+            reference = 'sub-01/anat/sub-01_T1w.nii.gz'
+        elif modality == 't2w':
+            reference = 'sub-01/anat/sub-01_T2w.nii.gz'
+
+        _create_nifti(str((anat_dir / name).with_suffix('.nii.gz')))
+        (anat_dir / name).with_suffix('.json').write_text(
+            json.dumps({'SpatialReference': reference})
+        )
+
+    if t1w_mask:
+        _create_deriv('sub-01_space-T1w_desc-brain_mask', 't1w')
+    if t1w_aseg:
+        _create_deriv('sub-01_space-T1w_desc-aseg_dseg', 't1w')
+    if t2w_mask:
+        _create_deriv('sub-01_space-T2w_desc-brain_mask', 't2w')
+    if t2w_aseg:
+        _create_deriv('sub-01_space-T2w_desc-aseg_dseg', 't2w')
+
+
+@pytest.mark.parametrize(
+    't1w_mask,t1w_aseg,t2w_mask,t2w_aseg,mask,aseg',
+    [
+        (True, True, False, False, 't1w_mask', 't1w_aseg'),
+        (True, True, True, True, 't1w_mask', 't1w_aseg'),
+        (False, False, True, True, 't2w_mask', 't2w_aseg'),
+        (True, False, False, True, 't1w_mask', 't2w_aseg'),
+        (False, False, False, False, None, None),
+    ],
+)
+def test_derivatives(
+    tmp_path: Path,
+    t1w_mask: bool,
+    t1w_aseg: bool,
+    t2w_mask: bool,
+    t2w_aseg: bool,
+    mask: str | None,
+    aseg: str | None,
+):
+    bids_dir = tmp_path / 'bids'
+    _create_bids_dir(bids_dir)
+    deriv_dir = tmp_path / 'derivatives'
+    _create_bids_derivs(
+        deriv_dir, t1w_mask=t1w_mask, t1w_aseg=t1w_aseg, t2w_mask=t2w_mask, t2w_aseg=t2w_aseg
+    )
+
+    derivatives = bids.Derivatives(bids_dir)
+    assert derivatives.mask is None
+    assert derivatives.t1w_mask is None
+    assert derivatives.t2w_mask is None
+    assert derivatives.aseg is None
+    assert derivatives.t1w_aseg is None
+    assert derivatives.t2w_aseg is None
+
+    derivatives.populate(deriv_dir, subject_id='01')
+    if mask:
+        assert derivatives.mask == getattr(derivatives, mask)
+        assert derivatives.references[mask]
+    else:
+        assert derivatives.mask is None
+    if aseg:
+        assert derivatives.aseg == getattr(derivatives, aseg)
+        assert derivatives.references[aseg]
+    else:
+        assert derivatives.aseg == None