ENH: Add SpatialReference field to some outputs

.circleci/ds054_outputs.txt

@@ -24,6 +24,7 @@ smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_desc-brain_mask.json
 smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_desc-brain_mask.nii.gz
 smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_desc-preproc_T1w.json
 smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_desc-preproc_T1w.nii.gz
+smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_dseg.json
 smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_dseg.nii.gz
 smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_label-CSF_probseg.nii.gz
 smriprep/sub-100185/anat/sub-100185_space-MNI152Lin_label-GM_probseg.nii.gz
@@ -32,6 +33,7 @@ smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-brain_mask.js
 smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
 smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-preproc_T1w.json
 smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz
+smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_dseg.json
 smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_dseg.nii.gz
 smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_label-CSF_probseg.nii.gz
 smriprep/sub-100185/anat/sub-100185_space-MNI152NLin2009cAsym_label-GM_probseg.nii.gz

src/smriprep/interfaces/bids.py

@@ -0,0 +1,84 @@
+# emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
+# vi: set ft=python sts=4 ts=4 sw=4 et:
+#
+# Copyright The NiPreps Developers <nipreps@gmail.com>
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+#
+# We support and encourage derived works from this project, please read
+# about our expectations at
+#
+#     https://www.nipreps.org/community/licensing/
+#
+"""BIDS-related interfaces."""
+
+from pathlib import Path
+
+from bids.utils import listify
+from nipype.interfaces.base import (
+    DynamicTraitedSpec,
+    SimpleInterface,
+    TraitedSpec,
+    isdefined,
+    traits,
+)
+from nipype.interfaces.io import add_traits
+from nipype.interfaces.utility.base import _ravel
+
+from ..utils.bids import _find_nearest_path
+
+
+class _BIDSURIInputSpec(DynamicTraitedSpec):
+    dataset_links = traits.Dict(mandatory=True, desc='Dataset links')
+    out_dir = traits.Str(mandatory=True, desc='Output directory')
+
+
+class _BIDSURIOutputSpec(TraitedSpec):
+    out = traits.List(
+        traits.Str,
+        desc='BIDS URI(s) for file',
+    )
+
+
+class BIDSURI(SimpleInterface):
+    """Convert input filenames to BIDS URIs, based on links in the dataset.
+
+    This interface can combine multiple lists of inputs.
+    """
+
+    input_spec = _BIDSURIInputSpec
+    output_spec = _BIDSURIOutputSpec
+
+    def __init__(self, numinputs=0, **inputs):
+        super().__init__(**inputs)
+        self._numinputs = numinputs
+        if numinputs >= 1:
+            input_names = [f'in{i + 1}' for i in range(numinputs)]
+        else:
+            input_names = []
+        add_traits(self.inputs, input_names)
+
+    def _run_interface(self, runtime):
+        inputs = [getattr(self.inputs, f'in{i + 1}') for i in range(self._numinputs)]
+        in_files = listify(inputs)
+        in_files = _ravel(in_files)
+        # Remove undefined inputs
+        in_files = [f for f in in_files if isdefined(f)]
+        # Convert the dataset links to BIDS URI prefixes
+        updated_keys = {f'bids:{k}:': Path(v) for k, v in self.inputs.dataset_links.items()}
+        updated_keys['bids::'] = Path(self.inputs.out_dir)
+        # Convert the paths to BIDS URIs
+        out = [_find_nearest_path(updated_keys, f) for f in in_files]
+        self._results['out'] = out
+
+        return runtime

src/smriprep/utils/bids.py

@@ -197,3 +197,85 @@ def write_derivative_description(bids_dir, deriv_dir):
         desc['License'] = orig_desc['License']
 
     Path.write_text(deriv_dir / 'dataset_description.json', json.dumps(desc, indent=4))
+
+
+def _find_nearest_path(path_dict, input_path):
+    """Find the nearest relative path from an input path to a dictionary of paths.
+
+    If ``input_path`` is not relative to any of the paths in ``path_dict``,
+    the absolute path string is returned.
+
+    If ``input_path`` is already a BIDS-URI, then it will be returned unmodified.
+
+    Parameters
+    ----------
+    path_dict : dict of (str, Path)
+        A dictionary of paths.
+    input_path : Path
+        The input path to match.
+
+    Returns
+    -------
+    matching_path : str
+        The nearest relative path from the input path to a path in the dictionary.
+        This is either the concatenation of the associated key from ``path_dict``
+        and the relative path from the associated value from ``path_dict`` to ``input_path``,
+        or the absolute path to ``input_path`` if no matching path is found from ``path_dict``.
+
+    Examples
+    --------
+    >>> from pathlib import Path
+    >>> path_dict = {
+    ...     'bids::': Path('/data/derivatives/fmriprep'),
+    ...     'bids:raw:': Path('/data'),
+    ...     'bids:deriv-0:': Path('/data/derivatives/source-1'),
+    ... }
+    >>> input_path = Path('/data/derivatives/source-1/sub-01/func/sub-01_task-rest_bold.nii.gz')
+    >>> _find_nearest_path(path_dict, input_path)  # match to 'bids:deriv-0:'
+    'bids:deriv-0:sub-01/func/sub-01_task-rest_bold.nii.gz'
+    >>> input_path = Path('/out/sub-01/func/sub-01_task-rest_bold.nii.gz')
+    >>> _find_nearest_path(path_dict, input_path)  # no match- absolute path
+    '/out/sub-01/func/sub-01_task-rest_bold.nii.gz'
+    >>> input_path = Path('/data/sub-01/func/sub-01_task-rest_bold.nii.gz')
+    >>> _find_nearest_path(path_dict, input_path)  # match to 'bids:raw:'
+    'bids:raw:sub-01/func/sub-01_task-rest_bold.nii.gz'
+    >>> input_path = 'bids::sub-01/func/sub-01_task-rest_bold.nii.gz'
+    >>> _find_nearest_path(path_dict, input_path)  # already a BIDS-URI
+    'bids::sub-01/func/sub-01_task-rest_bold.nii.gz'
+    >>> input_path = 'https://example.com/sub-01/func/sub-01_task-rest_bold.nii.gz'
+    >>> _find_nearest_path(path_dict, input_path)  # already a URL
+    'https://example.com/sub-01/func/sub-01_task-rest_bold.nii.gz'
+    >>> path_dict['bids:tfl:'] = 'https://example.com'
+    >>> _find_nearest_path(path_dict, input_path)  # match to 'bids:tfl:'
+    'bids:tfl:sub-01/func/sub-01_task-rest_bold.nii.gz'
+    """
+    # Don't modify BIDS-URIs
+    if isinstance(input_path, str) and input_path.startswith('bids:'):
+        return input_path
+
+    # Only modify URLs if there's a URL in the path_dict
+    if isinstance(input_path, str) and input_path.startswith('http'):
+        remote_found = False
+        for path in path_dict.values():
+            if str(path).startswith('http'):
+                remote_found = True
+                break
+
+        if not remote_found:
+            return input_path
+
+    input_path = Path(input_path)
+    matching_path = None
+    for key, path in path_dict.items():
+        if input_path.is_relative_to(path):
+            relative_path = input_path.relative_to(path)
+            if (matching_path is None) or (len(relative_path.parts) < len(matching_path.parts)):
+                matching_key = key
+                matching_path = relative_path
+
+    if matching_path is None:
+        matching_path = str(input_path.absolute())
+    else:
+        matching_path = f'{matching_key}{matching_path}'
+
+    return matching_path

src/smriprep/workflows/outputs.py

@@ -31,9 +31,14 @@
 from niworkflows.interfaces.nibabel import ApplyMask, GenerateSamplingReference
 from niworkflows.interfaces.space import SpaceDataSource
 from niworkflows.interfaces.utility import KeySelect
+from templateflow import api as tf
 
 from ..interfaces import DerivativesDataSink
-from ..interfaces.templateflow import TemplateFlowSelect, fetch_template_files
+from ..interfaces.bids import BIDSURI
+from ..interfaces.templateflow import (
+    TemplateFlowSelect,
+    fetch_template_files,
+)
 
 if ty.TYPE_CHECKING:
     from niworkflows.utils.spaces import SpatialReferences
@@ -929,6 +934,7 @@ def init_ds_anat_volumes_wf(
     *,
     bids_root: str,
     output_dir: str,
+    dataset_links: dict[str, str] | None = None,
     name='ds_anat_volumes_wf',
     tpm_labels=BIDS_TISSUE_ORDER,
 ) -> pe.Workflow:
@@ -957,6 +963,21 @@ def init_ds_anat_volumes_wf(
     raw_sources = pe.Node(niu.Function(function=_bids_relative), name='raw_sources')
     raw_sources.inputs.bids_root = bids_root
 
+    dataset_links = (dataset_links or {}).copy()
+    if 'bids' not in dataset_links:
+        dataset_links['bids'] = str(output_dir)
+    if 'templateflow' not in dataset_links:
+        dataset_links['templateflow'] = str(tf.TF_LAYOUT.root)
+
+    spatial_reference_uri = pe.Node(
+        BIDSURI(
+            numinputs=1,
+            dataset_links=dataset_links,
+            out_dir=str(output_dir),
+        ),
+        name='spatial_reference_uri',
+    )
+
     gen_ref = pe.Node(GenerateSamplingReference(), name='gen_ref', mem_gb=0.01)
 
     # Mask T1w preproc images
@@ -1017,9 +1038,11 @@ def init_ds_anat_volumes_wf(
     ds_std_tpms.inputs.label = tpm_labels
 
     workflow.connect([
+        (inputnode, spatial_reference_uri, [('ref_file', 'in1')]),
         (inputnode, gen_ref, [
             ('ref_file', 'fixed_image'),
             (('resolution', _is_native), 'keep_native'),
+            ('anat_preproc', 'moving_image'),
         ]),
         (inputnode, mask_anat, [
             ('anat_preproc', 'in_file'),
@@ -1029,11 +1052,14 @@ def init_ds_anat_volumes_wf(
         (inputnode, anat2std_mask, [('anat_mask', 'input_image')]),
         (inputnode, anat2std_dseg, [('anat_dseg', 'input_image')]),
         (inputnode, anat2std_tpms, [('anat_tpms', 'input_image')]),
-        (inputnode, gen_ref, [('anat_preproc', 'moving_image')]),
         (anat2std_t1w, ds_std_t1w, [('output_image', 'in_file')]),
+        (spatial_reference_uri, ds_std_t1w, [(('out', _pop), 'SpatialReference')]),
         (anat2std_mask, ds_std_mask, [('output_image', 'in_file')]),
+        (spatial_reference_uri, ds_std_mask, [(('out', _pop), 'SpatialReference')]),
         (anat2std_dseg, ds_std_dseg, [('output_image', 'in_file')]),
+        (spatial_reference_uri, ds_std_dseg, [(('out', _pop), 'SpatialReference')]),
         (anat2std_tpms, ds_std_tpms, [('output_image', 'in_file')]),
+        (spatial_reference_uri, ds_std_tpms, [(('out', _pop), 'SpatialReference')]),
     ])  # fmt:skip
 
     workflow.connect(