Fetch BIDS information from schema (#34)

* Generate BIDS entity information from schema

* Sort BIDS entities according to schema

* Apply suggestions from code review

Co-authored-by: Chris Markiewicz <[email protected]>

* Revert test changes for run type int

* Run black

* Self

* typing

---------

Co-authored-by: Chris Markiewicz <[email protected]>

bids2table/entities.py

@@ -4,29 +4,37 @@
 
 import re
 import warnings
-from dataclasses import asdict, dataclass, field, fields
+from dataclasses import asdict, dataclass, field, fields, make_dataclass
 from functools import lru_cache
 from pathlib import Path
 from types import MappingProxyType
-from typing import Any, Callable, Dict, Iterable, List, Optional, Union
+from typing import Any, Callable, Dict, Iterable, List, Optional, Tuple, Union
 
+import bidsschematools.schema
 import pandas as pd
 from elbow.typing import StrOrPath
-from typing_extensions import get_args, get_origin
-
-BIDS_DATATYPES = (
-    "anat",
-    "beh",
-    "dwi",
-    "eeg",
-    "fmap",
-    "func",
-    "ieeg",
-    "meg",
-    "micr",
-    "perf",
-    "pet",
-)
+from typing_extensions import Self, get_args, get_origin
+
+_bids_schema_path: Optional[str] = None
+
+
+def set_bids_schema_path(path: Optional[str]):
+    """
+    Set the path to the BIDS schema.
+    """
+    global _bids_schema_path
+    _bids_schema_path = path
+
+
+def _get_bids_schema() -> Any:
+    """
+    Get the BIDS schema.
+    """
+    global _bids_schema_path
+    return bidsschematools.schema.load_schema(schema_path=_bids_schema_path)
+
+
+BIDS_DATATYPES = tuple(o.value for o in _get_bids_schema().objects.datatypes.values())
 
 
 def bids_field(
@@ -58,7 +66,7 @@ def bids_field(
 
 
 @dataclass
-class BIDSEntities:
+class _BIDSEntitiesBase:
     """
     A dataclass representing known BIDS entities.
 
@@ -72,52 +80,7 @@ class BIDSEntities:
 
     sub: str = bids_field(name="subject", display_name="Subject", required=True)
     ses: Optional[str] = bids_field(name="session", display_name="Session")
-    sample: Optional[str] = bids_field(name="sample", display_name="Sample")
-    task: Optional[str] = bids_field(name="task", display_name="Task")
-    acq: Optional[str] = bids_field(name="acquisition", display_name="Acquisition")
-    ce: Optional[str] = bids_field(
-        name="ceagent", display_name="Contrast Enhancing Agent"
-    )
-    trc: Optional[str] = bids_field(name="tracer", display_name="Tracer")
-    stain: Optional[str] = bids_field(name="stain", display_name="Stain")
-    rec: Optional[str] = bids_field(
-        name="reconstruction", display_name="Reconstruction"
-    )
-    dir: Optional[str] = bids_field(
-        name="direction", display_name="Phase-Encoding Direction"
-    )
-    run: Optional[int] = bids_field(name="run", display_name="Run")
-    mod: Optional[str] = bids_field(
-        name="modality", display_name="Corresponding Modality"
-    )
-    echo: Optional[int] = bids_field(name="echo", display_name="Echo")
-    flip: Optional[int] = bids_field(name="flip", display_name="Flip Angle")
-    inv: Optional[int] = bids_field(name="inversion", display_name="Inversion Time")
-    mt: Optional[str] = bids_field(
-        name="mtransfer",
-        display_name="Magnetization Transfer",
-        allowed_values={"on", "off"},
-    )
-    part: Optional[str] = bids_field(
-        name="part",
-        display_name="Part",
-        allowed_values={"mag", "phase", "real", "imag"},
-    )
-    proc: Optional[str] = bids_field(
-        name="processing", display_name="Processed (on device)"
-    )
-    hemi: Optional[str] = bids_field(
-        name="hemisphere", display_name="Hemisphere", allowed_values={"L", "R"}
-    )
-    space: Optional[str] = bids_field(name="space", display_name="Space")
-    split: Optional[int] = bids_field(name="split", display_name="Split")
-    recording: Optional[str] = bids_field(name="recording", display_name="Recording")
-    chunk: Optional[int] = bids_field(name="chunk", display_name="Chunk")
-    atlas: Optional[str] = bids_field(name="atlas", display_name="Atlas")
-    res: Optional[str] = bids_field(name="resolution", display_name="Resolution")
-    den: Optional[str] = bids_field(name="density", display_name="Density")
-    label: Optional[str] = bids_field(name="label", display_name="Label")
-    desc: Optional[str] = bids_field(name="description", display_name="Description")
+
     datatype: Optional[str] = bids_field(
         name="datatype", display_name="Data type", allowed_values=BIDS_DATATYPES
     )
@@ -248,7 +211,7 @@ def to_path(
 
     def with_update(
         self, entitities: Optional[Dict[str, Any]] = None, **kwargs
-    ) -> "BIDSEntities":
+    ) -> Self:
         """
         Create a new instance with updated entities.
         """
@@ -257,7 +220,39 @@ def with_update(
             data.update(entitities)
         if kwargs:
             data.update(kwargs)
-        return BIDSEntities.from_dict(data)
+        return self.__class__.from_dict(data)
+
+
+def make_bids_field(
+    entity_schema: Dict[str, Any],
+) -> Tuple[str, Any, Any]:
+    """
+    BIDS entity dataclass field.
+    """
+    metadata = {
+        "name": entity_schema["name"],
+        "display_name": entity_schema["display_name"],
+        "allowed_values": entity_schema.get("enum"),
+    }
+    type_ = {"index": int}.get(entity_schema["format"], str)
+    field_ = field(default=None, metadata=metadata)
+    return entity_schema["name"], Optional[type_], field_
+
+
+_sorted_entities = [
+    _get_bids_schema().objects.entities[field_name]
+    for field_name in _get_bids_schema().rules.entities
+]
+BIDSEntities: Any = make_dataclass(
+    "BIDSEntities",
+    [
+        make_bids_field(dict(f))
+        for f in _sorted_entities
+        if f.name not in {f.name for f in fields(_BIDSEntitiesBase)}
+    ],
+    bases=(_BIDSEntitiesBase,),
+)
+del _sorted_entities
 
 
 def _get_type(alias: Any) -> type:

pyproject.toml

@@ -27,6 +27,8 @@ dependencies = [
     "elbow",
     "nibabel",
     "pandas",
+    "bidsschematools",
+    "typing_extensions",
 ]
 dynamic = ["version"]
 

tests/test_bids2table.py

@@ -4,6 +4,7 @@
 import pytest
 
 from bids2table import bids2table
+from bids2table.entities import ENTITY_NAMES_TO_KEYS
 
 BIDS_EXAMPLES = Path(__file__).parent.parent / "bids-examples"
 
@@ -35,7 +36,7 @@ def test_bids2table(tmp_path: Path, persistent: bool, with_meta: bool):
     tab = bids2table(
         root=root, with_meta=with_meta, persistent=persistent, index_path=index_path
     )
-    assert tab.shape == (128, 40)
+    assert tab.shape == (128, len(ENTITY_NAMES_TO_KEYS) + 8)
 
     if not with_meta:
         assert tab.loc[0, "meta__json"] is None

tests/test_main.py

@@ -7,6 +7,7 @@
 import pytest
 
 from bids2table import __main__ as cli
+from bids2table.entities import ENTITY_NAMES_TO_KEYS
 
 BIDS_EXAMPLES = Path(__file__).parent.parent / "bids-examples"
 
@@ -37,7 +38,7 @@ def test_main(tmp_path: Path):
         cli.main()
 
     df = pd.read_parquet(output)
-    assert df.shape == (128, 40)
+    assert df.shape == (128, len(ENTITY_NAMES_TO_KEYS) + 8)
 
 
 if __name__ == "__main__":

tests/test_table.py

@@ -6,6 +6,7 @@
 
 from bids2table import bids2table
 from bids2table.table import (
+    ENTITY_NAMES_TO_KEYS,
     BIDSTable,
     flat_to_multi_columns,
     join_bids_path,
@@ -32,13 +33,13 @@ def tab_no_meta() -> BIDSTable:
 
 
 def test_table(tab: BIDSTable):
-    assert tab.shape == (128, 40)
+    assert tab.shape == (128, len(ENTITY_NAMES_TO_KEYS) + 8)
 
     groups = tab.nested.columns.unique(0).tolist()
     assert groups == ["ds", "ent", "meta", "finfo"]
 
     assert tab.ds.shape == (128, 4)
-    assert tab.ent.shape == (128, 32)
+    assert tab.ent.shape == (128, len(ENTITY_NAMES_TO_KEYS))
     assert tab.meta.shape == (128, 1)
     assert tab.flat_meta.shape == (128, 2)
     assert tab.finfo.shape == (128, 3)
@@ -231,7 +232,7 @@ def test_join_bids_path(
     expected: str,
 ):
     path = join_bids_path(entities, prefix=prefix, valid_only=valid_only)
-    assert str(path) == expected
+    assert Path(path).as_posix() == expected
 
 
 if __name__ == "__main__":