bidsreader 0.1.0__tar.gz → 0.2.1__tar.gz

{bidsreader-0.1.0 → bidsreader-0.2.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bidsreader
-Version: 0.1.0
+Version: 0.2.1
 Summary: Data loader and file reader for the OpenBIDS format
 Author: Computational Memory Lab
 License-Expression: MIT

{bidsreader-0.1.0 → bidsreader-0.2.1}/bidsreader/__init__.py

@@ -8,8 +8,9 @@ from .filtering import (
 )
 from .convert import mne_epochs_to_ptsa, mne_raw_to_ptsa
 from .units import detect_unit, get_scale_factor, convert_unit
+from .public_helpers import get_data_index
 from collections import namedtuple
 
-__version__ = "0.1.0"
+__version__ = "0.2.1"
 version_info = namedtuple("VersionInfo", "major,minor,patch")(
     *__version__.split('.'))

{bidsreader-0.1.0 → bidsreader-0.2.1}/bidsreader/cmlbidsreader.py

@@ -183,7 +183,7 @@ class CMLBIDSReader(BaseReader):
             return json.load(f)
 
     @public_api
-    def load_raw(self, acquisition: Optional[str] = None) -> mne.io.BaseRaw:
+    def load_raw(self, acquisition: Optional[str] = None, extension: Optional[str] = None) -> mne.io.BaseRaw:
         self._require(self._get_needed_fields(), context="load_raw")
 
         acq = self._validate_acq(acquisition)
@@ -193,6 +193,15 @@ class CMLBIDSReader(BaseReader):
             bp_kwargs["acquisition"] = acq
         bp = self._bp(**bp_kwargs)
 
+        if extension is None:
+            for ext in (".bdf", ".edf", ".vhdr", ".set", ".nwb", ".fif"):
+                candidate = bp.copy().update(suffix=self.device, extension=ext).fpath
+                if candidate.exists():
+                    bp = bp.copy().update(suffix=self.device, extension=ext)
+                    break
+        else :
+            bp = bp.copy().update(suffix=self.device, extension=extension)
+
         with warnings.catch_warnings():
             warnings.filterwarnings(
                 "ignore",
@@ -222,9 +231,10 @@ class CMLBIDSReader(BaseReader):
         event_repeated: str = "merge",
         channels: Optional[Iterable[str]] = None,
         preload: bool = False,
+        extension: Optional[str] = None
     ) -> mne.Epochs:
         self._require(self._get_needed_fields(), context="load_epochs")
-        raw = self.load_raw(acquisition=acquisition)
+        raw = self.load_raw(acquisition=acquisition, extension=extension)
 
         all_events_raw, all_event_id = mne.events_from_annotations(raw)
 

bidsreader-0.2.1/bidsreader/public_helpers.py

@@ -0,0 +1,17 @@
+# imports
+import pandas as pd
+from pathlib import Path
+import re
+
+def get_data_index(root, task):
+    root = Path(root)
+    rows = []
+
+    pattern = re.compile(r"sub-(?P<sub>[^_]+)_ses-(?P<ses>[^_]+)_task-" + re.escape(task), re.IGNORECASE)
+
+    for f in root.rglob(f"*task-{task}*beh.tsv"):
+        m = pattern.search(f.name)
+        if m:
+            rows.append({"subject": m.group("sub"), "task": task, "session": m.group("ses")})
+
+    return pd.DataFrame(rows).drop_duplicates().sort_values(["subject", "session"]).reset_index(drop=True)

{bidsreader-0.1.0 → bidsreader-0.2.1}/bidsreader.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: bidsreader
-Version: 0.1.0
+Version: 0.2.1
 Summary: Data loader and file reader for the OpenBIDS format
 Author: Computational Memory Lab
 License-Expression: MIT

{bidsreader-0.1.0 → bidsreader-0.2.1}/bidsreader.egg-info/SOURCES.txt

@@ -12,6 +12,7 @@ bidsreader/convert.py
 bidsreader/exc.py
 bidsreader/filtering.py
 bidsreader/helpers.py
+bidsreader/public_helpers.py
 bidsreader/units.py
 bidsreader.egg-info/PKG-INFO
 bidsreader.egg-info/SOURCES.txt

{bidsreader-0.1.0 → bidsreader-0.2.1}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "bidsreader"
-version = "0.1.0"
+version = "0.2.1"
 description = "Data loader and file reader for the OpenBIDS format"
 readme = "README.md"
 license = "MIT"