Replace internal pybids calls with installed pybids calls

aslprep/cli/parser.py

@@ -47,7 +47,7 @@ def _drop_sub(value):
         return value[4:] if value.startswith("sub-") else value
 
     def _filter_pybids_none_any(dct):
-        from aslprep.pybids import layout
+        from bids import layout
 
         return {k: layout.Query.ANY if v == "*" else v for k, v in dct.items()}
 

aslprep/config.py

@@ -391,7 +391,7 @@ def init(cls):
         if cls._layout is None:
             import re
 
-            from aslprep.pybids.layout import BIDSLayout
+            from bids.layout import BIDSLayout
 
             work_dir = cls.work_dir / "bids.db"
             work_dir.mkdir(exist_ok=True, parents=True)

aslprep/data/aslprep_bids_config.json

@@ -0,0 +1,45 @@
+{
+  "name": "aslprep",
+  "entities": [
+    {
+      "name": "datatype",
+      "pattern": "[/\\\\]+(anat|beh|dwi|eeg|figures|fmap|func|ieeg|meg|micr|perf|pet)[/\\\\]+"
+    },
+    {
+      "name": "cohort",
+      "pattern": "(?:^|_)cohort-([0-9]+)",
+      "dtype": "int"
+    },
+    {
+      "name": "measure",
+      "pattern": "(?:^|_)measure-([a-zA-Z0-9]+)"
+    }
+  ],
+  "default_path_patterns": [
+    "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_res-{res}][_desc-{desc}]_{suffix<dseg>}{extension<.nii|.nii.gz|.tsv|.json>|.nii.gz}",
+    "[space-{space}_]atlas-{atlas}[_cohort-{cohort}][_den-{den}][_desc-{desc}]_{suffix<dseg>}{extension<.dlabel.nii|.tsv|.json>|.dlabel.nii}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_mod-{modality}]_{suffix<defacemask>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<func>|func}/sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|sbref>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_dir-{direction}][_run-{run}]_{fmap<phasediff|magnitude[12]|phase[12]|fieldmap>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<fmap>|fmap}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}]_dir-{direction}[_run-{run}]_{fmap<epi>}{extension<.nii|.nii.gz|.json>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/[{datatype<func|meg|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/[{datatype<perf|beh>|perf|perf}/]sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<aslcontext>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/[{datatype<func|beh>|func}/]sub-{subject}[_ses-{session}]_task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.tsv.gz|.json>|.tsv.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<func|perf>|func}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<regressors|timeseries>|timeseries}{extension<.json|.tsv|.csv|>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_desc-{desc}]_{suffix<confounds>}{extension<.tsv|.json>|.tsv}",
+    "sub-{subject}[/ses-{session}]/{datatype<perf>|perf}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|cbf|basil|score|scrub|pvc|mask>}{extension<.nii|.nii.gz|.json|.csv|.tsv>|.nii.gz}",
+    "sub-{subject}[/ses-{session}]/{datatype<figures>|figures}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<asl|aslref|cbf|basil|score|scrub|pvc|mask>}{extension<.svg|.png|.html>|.svg}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio|dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
+    "sub-{subject}/{datatype<figures>}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}][_space-{space}][_atlas-{atlas}][_cohort-{cohort}][_desc-{desc}]_{suffix<dseg|mask|dwi|epiref|fieldmap>}{extension<.html|.svg|.png>}",
+    "sub-{subject}[/ses-{session}]/{datatype<anat>|anat}/sub-{subject}[_ses-{session}][_acq-{acquisition}][_ce-{ceagent}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+    "sub-{subject}[/ses-{session}]/{datatype<func|perf>|func}/sub-{subject}[_ses-{session}][_task-{task}][_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}]_from-{from}_to-{to}_mode-{mode<image|points>|image}_{suffix<xfm>|xfm}{extension<.txt|.h5>}",
+    "[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_]{suffix<T1w|T2w|T1rho|T1map|T2map|T2star|FLAIR|FLASH|PDmap|PD|PDT2|inplaneT[12]|angio>}{extension<.json>|.json}",
+    "[acq-{acquisition}_][ce-{ceagent}_][rec-{reconstruction}_][mod-{modality}_]{suffix<defacemask>}{extension<.json>|.json}",
+    "task-{task}[_acq-{acquisition}][_ce-{ceagent}][_dir-{direction}][_rec-{reconstruction}][_run-{run}][_echo-{echo}]_{suffix<bold|cbv|sbref>}{extension<.json>|.json}",
+    "[acq-{acquisition}_][dir-{direction}_][run-{run}_]{fmap<phasediff|magnitude[1-2]|phase[1-2]|fieldmap>}{extension<.json>|.json}",
+    "[acq-{acquisition}_][ce-{ceagent}_]dir-{direction}[_run-{run}]_{fmap<epi>}{extension<.json>|.json}",
+    "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<events>}{extension<.json>|.json}",
+    "task-{task}[_acq-{acquisition}][_rec-{reconstruction}][_run-{run}][_echo-{echo}][_recording-{recording}]_{suffix<physio|stim>}{extension<.json>}"
+  ]
+}

aslprep/interfaces/bids.py

@@ -1,13 +1,35 @@
 """Adapted interfaces from Niworkflows."""
-from aslprep.niworkflows.interfaces.bids import (
-    DerivativesDataSink as BaseDerivativesDataSink,
-)
+from json import loads
+from pathlib import Path
+
+from bids.layout import Config
+from nipype import logging
+from niworkflows.interfaces.bids import DerivativesDataSink as BaseDerivativesDataSink
+from pkg_resources import resource_filename as pkgrf
+
+# NOTE: Modified for aslprep's purposes
+aslprep_spec = loads(Path(pkgrf("aslprep", "data/aslprep_bids_config.json")).read_text())
+bids_config = Config.load("bids")
+deriv_config = Config.load("derivatives")
+
+aslprep_entities = {v["name"]: v["pattern"] for v in aslprep_spec["entities"]}
+merged_entities = {**bids_config.entities, **deriv_config.entities}
+merged_entities = {k: v.pattern for k, v in merged_entities.items()}
+merged_entities = {**merged_entities, **aslprep_entities}
+merged_entities = [{"name": k, "pattern": v} for k, v in merged_entities.items()]
+config_entities = frozenset({e["name"] for e in merged_entities})
+
+LOGGER = logging.getLogger("nipype.interface")
 
 
 class DerivativesDataSink(BaseDerivativesDataSink):
     """Store derivative files.
 
-    A child class of the niworkflows DerivativesDataSink, using aslprep's output directory.
+    A child class of the niworkflows DerivativesDataSink, using aslprep's configuration files.
     """
 
     out_path_base = "aslprep"
+    _allowed_entities = set(config_entities)
+    _config_entities = config_entities
+    _config_entities_dict = merged_entities
+    _file_patterns = aslprep_spec["default_path_patterns"]

aslprep/niworkflows/interfaces/bids.py

@@ -10,9 +10,9 @@
 
 import nibabel as nb
 import numpy as np
-from ...pybids.layout import parse_file_entities
-from ...pybids.layout.writing import build_path
-from ...pybids.utils import listify
+from bids.layout import parse_file_entities
+from bids.layout.writing import build_path
+from bids.utils import listify
 
 from nipype import logging
 from nipype.interfaces.base import (

aslprep/niworkflows/reports/core.py

@@ -11,7 +11,7 @@
 from itertools import compress
 from collections import defaultdict
 from pkg_resources import resource_filename as pkgrf
-from ...pybids.layout import BIDSLayout, add_config_paths
+from bids.layout import BIDSLayout, add_config_paths
 import jinja2
 from nipype.utils.filemanip import copyfile
 
@@ -65,7 +65,7 @@ class Reportlet(Element):
 
     >>> from pkg_resources import resource_filename
     >>> from shutil import copytree
-    >>> from aslprep.pybids.layout import BIDSLayout
+    >>> from bids.layout import BIDSLayout
     >>> test_data_path = resource_filename('niworkflows', 'data/tests/work')
     >>> testdir = Path(tmpdir)
     >>> data_dir = copytree(test_data_path, str(testdir / 'work'))
@@ -217,7 +217,7 @@ class Report:
 
     >>> from pkg_resources import resource_filename
     >>> from shutil import copytree
-    >>> from aslprep.pybids.layout import BIDSLayout
+    >>> from bids.layout import BIDSLayout
     >>> test_data_path = resource_filename('niworkflows', 'data/tests/work')
     >>> testdir = Path(tmpdir)
     >>> data_dir = copytree(test_data_path, str(testdir / 'work'))

aslprep/niworkflows/reports/tests/test_core.py

@@ -8,8 +8,8 @@
 from yaml import safe_load as load
 
 import matplotlib.pyplot as plt
-from aslprep.pybids.layout.writing import build_path
-from aslprep.pybids.layout import BIDSLayout
+from bids.layout.writing import build_path
+from bids.layout import BIDSLayout
 
 import pytest
 

aslprep/niworkflows/utils/bids.py

@@ -11,7 +11,7 @@
 import json
 import re
 import warnings
-from ...pybids import BIDSLayout
+from bids import BIDSLayout
 from packaging.version import Version