Merge branch 'main' into test_save

Author: christian-oreilly

.readthedocs.yaml

@@ -21,3 +21,4 @@ python:
       - requirements: requirements.txt
       - requirements: docs/requirements_doc.txt
       - requirements: requirements_testing.txt
+      - requirements: requirements_rtd.txt

pylossless/datasets/datasets.py

@@ -6,7 +6,7 @@
 import pylossless as ll
 
 
-def load_openneuro_bids(subject="pd6"):
+def load_openneuro_bids(subject="pd6", timeout=20):
     """Download and Load BIDS dataset ds002778 from OpenNeuro.
 
     Parameters
@@ -72,8 +72,14 @@ def load_openneuro_bids(subject="pd6"):
         root=bids_root,
     )
 
-    while not bids_path.fpath.with_suffix(".bdf").exists():
-        print(list(bids_path.fpath.glob("*")))
+    for _ in range(timeout):
+        if bids_path.fpath.with_suffix(".bdf").exists():
+            break
+        print("Waiting for .bdf files to be created. Current files available:",
+              list(bids_path.fpath.glob("*")))
         sleep(1)
+    else:
+        raise TimeoutError("OpenNeuro failed to create the .bdf files.")
+
     raw = mne_bids.read_raw_bids(bids_path, verbose="ERROR")
     return raw, config, bids_path

pylossless/flagging.py

@@ -17,8 +17,53 @@
 
 from .utils._utils import _icalabel_to_data_frame
 
+IC_LABELS = mne_icalabel.config.ICA_LABELS_TO_MNE
+CH_LABELS: dict[str, str] = {
+    "Noisy": "ch_sd",
+    "Bridged": "bridge",
+    "Uncorrelated": "low_r",
+    "Rank": "rank"
+}
+EPOCH_LABELS: dict[str, str] = {
+    "Noisy": "noisy",
+    "Noisy ICs": "noisy_ICs",
+    "Uncorrelated": "uncorrelated",
+}
+
+
+class _Flagged(dict):
+
+    def __init__(self, key_map, kind_str, ll, *args, **kwargs):
+        """Initialize class."""
+        super().__init__(*args, **kwargs)
+        self.ll = ll
+        self._key_map = key_map
+        self._kind_str = kind_str
+
+    @property
+    def valid_keys(self):
+        """Return the valid keys."""
+        return tuple(self._key_map.values())
+
+    def __repr__(self):
+        """Return a string representation."""
+        ret_str = f"Flagged {self._kind_str}s: |\n"
+        for key, val in self._key_map.items():
+            ret_str += f"  {key}: {self.get(val, None)}\n"
+        return ret_str
+
+    def __eq__(self, other):
+        for key in self.valid_keys:
+            if not np.array_equal(self.get(key, np.array([])),
+                                  other.get(key, np.array([]))):
+                return False
+        return True
+
+    def __ne__(self, other):
+        return not self == other
 
-class FlaggedChs(dict):
+
+class FlaggedChs(_Flagged):
     """Object for handling flagged channels in an instance of mne.io.Raw.
 
     Attributes
@@ -47,28 +92,17 @@ class FlaggedChs(dict):
     and methods for python dictionaries.
     """
 
-    def __init__(self, ll, *args, **kwargs):
+    def __init__(self, *args, **kwargs):
         """Initialize class."""
-        super().__init__(*args, **kwargs)
-        self.ll = ll
-
-    def __repr__(self):
-        """Return a string representation of the FlaggedChs object."""
-        return (
-            f"Flagged channels: |\n"
-            f"  Noisy: {self.get('ch_sd', None)}\n"
-            f"  Bridged: {self.get('bridge', None)}\n"
-            f"  Uncorrelated: {self.get('low_r', None)}\n"
-            f"  Rank: {self.get('rank', None)}\n"
-        )
+        super().__init__(CH_LABELS, "channel", *args, **kwargs)
 
     def add_flag_cat(self, kind, bad_ch_names, *args):
         """Store channel names that have been flagged by pipeline.
 
         Parameters
         ----------
         kind : str
-            Should be one of ``'outlier'``, ``'ch_sd'``, ``'low_r'``,
+            Should be one of ``'ch_sd'``, ``'low_r'``,
             ``'bridge'``, ``'rank'``.
         bad_ch_names : list | tuple
             Channel names. Will be the values corresponding to the ``kind``
@@ -140,7 +174,7 @@ def load_tsv(self, fname):
             self[label] = grp_df.ch_names.values
 
 
-class FlaggedEpochs(dict):
+class FlaggedEpochs(_Flagged):
     """Object for handling flagged Epochs in an instance of mne.Epochs.
 
     Methods
@@ -159,7 +193,7 @@ class FlaggedEpochs(dict):
     and methods for python dictionaries.
     """
 
-    def __init__(self, ll, *args, **kwargs):
+    def __init__(self, *args, **kwargs):
         """Initialize class.
 
         Parameters
@@ -171,9 +205,7 @@ def __init__(self, ll, *args, **kwargs):
         kwargs : dict
             keyword arguments accepted by python's dictionary class.
         """
-        super().__init__(*args, **kwargs)
-
-        self.ll = ll
+        super().__init__(EPOCH_LABELS, "epoch", *args, **kwargs)
 
     def add_flag_cat(self, kind, bad_epoch_inds, epochs):
         """Add information on time periods flagged by pyLossless.
@@ -194,17 +226,27 @@ def add_flag_cat(self, kind, bad_epoch_inds, epochs):
         self[kind] = bad_epoch_inds
         self.ll.add_pylossless_annotations(bad_epoch_inds, kind, epochs)
 
-    def load_from_raw(self, raw):
+    def load_from_raw(self, raw, events, config):
         """Load pylossless annotations from raw object."""
         sfreq = raw.info["sfreq"]
+        tmax = config["epoching"]["epochs_args"]["tmax"]
+        tmin = config["epoching"]["epochs_args"]["tmin"]
+        starts = events[:, 0] / sfreq - tmin
+        stops = events[:, 0] / sfreq + tmax
         for annot in raw.annotations:
-            if annot["description"].upper().startswith("BAD_LL"):
-                ind_onset = int(np.round(annot["onset"] * sfreq))
-                ind_dur = int(np.round(annot["duration"] * sfreq))
-                inds = np.arange(ind_onset, ind_onset + ind_dur)
-                if annot["description"] not in self:
-                    self[annot["description"]] = list()
-                self[annot["description"]].append(inds)
+            if annot["description"].upper().startswith("BAD_LL_"):
+                onset = annot["onset"]
+                offset = annot["onset"] + annot["duration"]
+                mask = (
+                    (starts >= onset) & (starts < offset)
+                    | (stops > onset) & (stops <= offset)
+                    | (onset <= starts) & (offset >= stops)
+                )
+                inds = np.where(mask)[0]
+                desc = annot["description"].lower().replace("bad_ll_", "")
+                if desc not in self:
+                    self[desc] = np.array([])
+                self[desc] = np.concatenate((self[desc], inds))
 
 
 class FlaggedICs(pd.DataFrame):

pylossless/pipeline.py

@@ -719,6 +719,9 @@ def find_breaks(self):
         """
         if "find_breaks" not in self.config or not self.config["find_breaks"]:
             return
+        if not self.raw.annotations:
+            logger.debug("No annotations found in raw object. Skipping find_breaks.")
+            return
         breaks = annotate_break(self.raw, **self.config["find_breaks"])
         self.raw.set_annotations(breaks + self.raw.annotations)
 
@@ -1229,9 +1232,20 @@ def run_dataset(self, paths):
         for path in paths:
             self.run(path)
 
-    # TODO: Finish docstring
     def load_ll_derivative(self, derivatives_path):
-        """Load a completed pylossless derivative state."""
+        """Load a completed pylossless derivative state.
+
+        Parameters
+        ----------
+        derivatives_path : str | mne_bids.BIDSPath
+            Path to a saved pylossless derivatives.
+
+        Returns
+        -------
+        :class:`~pylossless.pipeline.LosslessPipeline`
+            Returns an instance of :class:`~pylossless.pipeline.LosslessPipeline`
+            for the loaded pylossless derivative state.
+        """
         if not isinstance(derivatives_path, BIDSPath):
             derivatives_path = get_bids_path_from_fname(derivatives_path)
         self.raw = mne_bids.read_raw_bids(derivatives_path)
@@ -1260,7 +1274,7 @@ def load_ll_derivative(self, derivatives_path):
         self.flags["ch"].load_tsv(flagged_chs_fpath.fpath)
 
         # Load Flagged Epochs
-        self.flags["epoch"].load_from_raw(self.raw)
+        self.flags["epoch"].load_from_raw(self.raw, self.get_events(), self.config)
 
         return self
 

pylossless/tests/test_pipeline.py

@@ -1,5 +1,6 @@
 from pathlib import Path
 import mne
+import mne_bids
 import pytest
 import shutil
 
@@ -61,6 +62,9 @@ def test_find_breaks(logging):
         pipeline.find_breaks(message="Looking for break periods between tasks")
     else:
         pipeline.find_breaks()
+        # Now explicitly remove annotations and make sure we avoid MNE's error.
+        pipeline.raw.set_annotations(None)
+        pipeline.find_breaks()
     Path(config_fname).unlink()  # delete config file
 
 
@@ -72,3 +76,36 @@ def test_deprecation():
     # with pytest.raises(DeprecationWarning, match=f"config_fname is deprecated"):
     # DeprecationWarning are currently ignored by pytest given our toml file
     pipeline.config_fname = pipeline.config_fname
+
+
+@pytest.mark.filterwarnings("ignore:Converting data files to EDF format")
+def test_load_flags(pipeline_fixture, tmp_path):
+    """Test running the pipeline."""
+    bids_root = tmp_path / "derivatives" / "pylossless"
+    print(bids_root)
+
+    subject = "pd6"
+    datatype = "eeg"
+    session = "off"
+    task = "rest"
+    suffix = "eeg"
+    bids_path = mne_bids.BIDSPath(
+        subject=subject,
+        session=session,
+        task=task,
+        suffix=suffix,
+        datatype=datatype,
+        root=bids_root
+    )
+
+    pipeline_fixture.save(bids_path,
+                          overwrite=False, format="EDF", event_id=None)
+    pipeline = ll.LosslessPipeline().load_ll_derivative(bids_path)
+
+    assert pipeline_fixture.flags['ch'] == pipeline.flags['ch']
+    pipeline.flags['ch']["bridge"] = ["xx"]
+    assert pipeline_fixture.flags['ch'] != pipeline.flags['ch']
+
+    assert pipeline_fixture.flags['epoch'] == pipeline.flags['epoch']
+    pipeline.flags['epoch']["bridge"] = ["noisy"]
+    assert pipeline_fixture.flags['epoch'] == pipeline.flags['epoch']

requirements_rtd.txt

@@ -0,0 +1 @@
+-e .