py-neuromodulation 0.1.4__py3-none-any.whl → 0.1.7__py3-none-any.whl

py_neuromodulation/default_settings.yaml

@@ -54,10 +54,10 @@ raw_normalization_settings:
   clip: 3
 
 preprocessing_filter:
-  bandstop_filter: true
-  lowpass_filter: true
-  highpass_filter: true
-  bandpass_filter: true
+  bandstop_filter: false
+  lowpass_filter: false
+  highpass_filter: false
+  bandpass_filter: false
   bandstop_filter_settings: [100, 160] # [low_hz, high_hz]
   bandpass_filter_settings: [3, 200] # [hz, _hz]
   lowpass_filter_cutoff_hz: 200
@@ -245,3 +245,4 @@ bispectrum_settings:
     mean: true
     sum: true
     var: true
+

py_neuromodulation/features/fooof.py

@@ -87,17 +87,21 @@ class FooofAnalyzer(NMFeature):
 
         spectra = np.abs(rfft(data[:, -self.num_samples :]))  # type: ignore
 
-        self.fm.fit(self.f_vec, spectra, self.settings.freq_range_hz)
+        try:
+            self.fm.fit(self.f_vec, spectra, self.settings.freq_range_hz)
+        except:
+            failed_fits = list(range(len(self.ch_names)))
 
         if not self.fm.has_model or self.fm.null_inds_ is None:
-            raise RuntimeError("FOOOF failed to fit model to data.")
-
-        failed_fits: list[int] = self.fm.null_inds_
+            failed_fits = list(range(len(self.ch_names)))
+        else:
+            failed_fits: list[int] = self.fm.null_inds_
 
         feature_results = {}
         for ch_idx, ch_name in enumerate(self.ch_names):
             FIT_PASSED = ch_idx not in failed_fits
-            exp = self.fm.get_params("aperiodic_params", "exponent")[ch_idx]
+            if FIT_PASSED:
+                exp = self.fm.get_params("aperiodic_params", "exponent")[ch_idx]
 
             for feat in self.settings.aperiodic.get_enabled():
                 f_name = f"{ch_name}_fooof_a_{self.feat_name_map[feat]}"

py_neuromodulation/features/sharpwaves.py

@@ -85,16 +85,16 @@ class SharpwaveSettings(NMBaseModel):
             self.estimator[est] = []
 
     @model_validator(mode="after")
-    def test_settings(cls, settings):
+    def test_settings(self):
         # check if all features are also enabled via an estimator
-        estimator_list = [est for list_ in settings.estimator.values() for est in list_]
+        estimator_list = [est for list_ in self.estimator.values() for est in list_]
 
-        for used_feature in settings.sharpwave_features.get_enabled():
+        for used_feature in self.sharpwave_features.get_enabled():
             assert (
                 used_feature in estimator_list
             ), f"Add estimator key for {used_feature}"
 
-        return settings
+        return self
 
 
 class SharpwaveAnalyzer(NMFeature):
@@ -151,7 +151,9 @@ class SharpwaveAnalyzer(NMFeature):
             self.filters = np.vstack([f for _, f in self.list_filter])
             self.filters = np.tile(self.filters[None, :, :], (len(self.ch_names), 1, 1))
         else:
-            self.filters = [np.tile(f, (len(self.ch_names), 1)) for _, f in self.list_filter]
+            self.filters = [
+                np.tile(f, (len(self.ch_names), 1)) for _, f in self.list_filter
+            ]
 
         self.used_features = self.sw_settings.sharpwave_features.get_enabled()
 
@@ -282,7 +284,9 @@ class SharpwaveAnalyzer(NMFeature):
                 if feature_name == "num_peaks":
                     key_name = f"{ch_name}_Sharpwave_{feature_name}_{filter_name}"
                     if len(waveform_results[feature_name]) == 1:
-                        dict_ch_features[key_name][key_name_pt] = waveform_results[feature_name][0]
+                        dict_ch_features[key_name][key_name_pt] = waveform_results[
+                            feature_name
+                        ][0]
                         continue
                     else:
                         raise ValueError("num_peaks should be a list with length 1")
@@ -317,8 +321,12 @@ class SharpwaveAnalyzer(NMFeature):
                 for ch_name in self.ch_names:
                     for filter_name in self.filter_names:
                         key_name = f"{ch_name}_Sharpwave_num_peaks_{filter_name}"
-                        feature_results[key_name] = np_mean([dict_ch_features[key_name]["Peak"],
-                                                            dict_ch_features[key_name]["Trough"]])
+                        feature_results[key_name] = np_mean(
+                            [
+                                dict_ch_features[key_name]["Peak"],
+                                dict_ch_features[key_name]["Trough"],
+                            ]
+                        )
         else:
             # otherwise, save all write all "flattened" key value pairs in feature_results
             for key, subdict in dict_ch_features.items():

py_neuromodulation/processing/rereference.py

@@ -55,7 +55,7 @@ class ReReferencer(NMPreprocessor):
             # if ind not in channels_used:
             #    continue
             ref = refs[ind]
-            if ref.lower() == "none" or pd.isnull(ref):
+            if ref.lower() == "none" or pd.isnull(ref) or channels["status"][ind] != "good":
                 ref_idx = None
                 continue
             if ref.lower() == "average":
@@ -78,7 +78,12 @@ class ReReferencer(NMPreprocessor):
                         )
                     ref_idx.append(ch_names.index(ref_chan))
             ref_matrix[ind, ref_idx] = -1 / len(ref_idx)
+        
         self.ref_matrix = ref_matrix
+        
+        # only index good channels
+        good_idxs = np.where(channels["status"] == "good")[0]
+        self.ref_matrix = self.ref_matrix[good_idxs, :][:, good_idxs]
 
     def process(self, data: np.ndarray) -> np.ndarray:
         """Rereference data according to the initialized ReReferencer class.

py_neuromodulation/stream/data_processor.py

@@ -143,12 +143,17 @@ class DataProcessor:
     ) -> tuple[list[str], list[str], list[int], np.ndarray]:
         """Get used feature and label info from channels"""
         channels = self.channels
-        ch_names_used = channels[channels["used"] == 1]["new_name"].tolist()
-        ch_types_used = channels[channels["used"] == 1]["type"].tolist()
+        ch_names_used = channels.query("used == 1 and status == 'good'")["new_name"].tolist()
+        ch_types_used = channels.query("used == 1 and status == 'good'")["type"].tolist()
 
         # used channels for feature estimation
         feature_idx = np.where(channels["used"] & ~channels["target"])[0].tolist()
 
+        # remove the idxs of status == "bad"
+        feature_idx = [
+            idx for idx in feature_idx if channels.loc[idx, "status"] == "good"
+        ]
+
         # If multiple targets exist, select only the first
         label_idx = np.where(channels["target"] == 1)[0]
 

py_neuromodulation/utils/channels.py

@@ -46,6 +46,7 @@ def set_channels(
             For this, the channel names must contain the substring "_L_" and/or
             "_R_" (lower or upper case). CAVE: Adjacent channels will be
             determined using the sort() function.
+            Re-reference can be also "average" for common-average-referencing
         bads :  str | list of str, default: None
             channels that should be marked as bad and not be used for
             average re-referencing etc.
@@ -127,9 +128,12 @@ def set_channels(
     if isinstance(reference, str):
         if reference.lower() == "default":
             df = _get_default_references(df=df, ch_names=ch_names, ch_types=ch_types)
+        elif reference.lower() == "average":
+            df["rereference"] = ["average" if df["used"][ch_idx] == 1 else "None"
+                                 for ch_idx in range(len(ch_names))]
         else:
             raise ValueError(
-                "`reference` must be either `default`, `None` or "
+                "`reference` must be either `default`, `None`, `average` or "
                 "an iterable of new reference channel names. "
                 f"Got: {reference}."
             )

py_neuromodulation/utils/pydantic_extensions.py

@@ -5,10 +5,11 @@ from typing import (
     get_args,
     get_type_hints,
     Literal,
+    Unpack,
+    TypedDict,
     cast,
     Sequence,
 )
-from typing_extensions import Unpack, TypedDict
 from pydantic import BaseModel, GetCoreSchemaHandler, ConfigDict
 
 from pydantic_core import (
@@ -118,23 +119,13 @@ class _NMExtraFieldInputs(TypedDict, total=False):
     custom_metadata: dict[str, Any]
 
 
-class _NMFieldInfoInputs(_FieldInfoInputs, _NMExtraFieldInputs, total=False):
-    """Combine pydantic FieldInfo inputs with PyNM additional inputs"""
-
-    pass
-
-
-class _NMFromFieldInfoInputs(_FromFieldInfoInputs, _NMExtraFieldInputs, total=False):
-    """Combine pydantic FieldInfo.from_field inputs with PyNM additional inputs"""
-
-    pass
-
-
 class NMFieldInfo(FieldInfo):
     # Add default values for any other custom fields here
     _default_values = {}
 
-    def __init__(self, **kwargs: Unpack[_NMFieldInfoInputs]) -> None:
+    def __init__(
+        self, **kwargs: Unpack[_FieldInfoInputs | _NMExtraFieldInputs]
+    ) -> None:
         self.sequence: bool = kwargs.pop("sequence", False)  # type: ignore
         self.custom_metadata: dict[str, Any] = kwargs.pop("custom_metadata", {})
         super().__init__(**kwargs)
@@ -162,7 +153,7 @@ class NMFieldInfo(FieldInfo):
     @staticmethod
     def from_field(
         default: Any = PydanticUndefined,
-        **kwargs: Unpack[_NMFromFieldInfoInputs],
+        **kwargs: Unpack[_FromFieldInfoInputs | _NMExtraFieldInputs],
     ) -> "NMFieldInfo":
         if "annotation" in kwargs:
             raise TypeError('"annotation" is not permitted as a Field keyword argument')
@@ -178,7 +169,7 @@ class NMFieldInfo(FieldInfo):
 
 def NMField(
     default: Any = PydanticUndefined,
-    **kwargs: Unpack[_NMFromFieldInfoInputs],
+    **kwargs: Unpack[_FromFieldInfoInputs | _NMExtraFieldInputs],
 ) -> Any:
     return NMFieldInfo.from_field(default=default, **kwargs)
 
@@ -197,7 +188,7 @@ class NMBaseModel(BaseModel):
             super().__init__(*args, **kwargs)
             return
 
-        field_names = list(self.model_fields.keys())
+        field_names = list(self.__class__.model_fields.keys())
         # If we have more positional args than fields, that's an error
         if len(args) > len(field_names):
             raise ValueError(
@@ -238,7 +229,7 @@ class NMBaseModel(BaseModel):
 
     @property
     def fields(self) -> dict[str, FieldInfo | NMFieldInfo]:
-        return self.model_fields  # type: ignore
+        return self.__class__.model_fields  # type: ignore
 
     def serialize_with_metadata(self):
         result: dict[str, Any] = {"__field_type__": self.__class__.__name__}

py_neuromodulation/utils/types.py

@@ -135,17 +135,17 @@ class BoolSelector(NMBaseModel):
     def get_enabled(self):
         return [
             f
-            for f in self.model_fields.keys()
+            for f in self.__class__.model_fields.keys()
             if (isinstance(self[f], bool) and self[f])
         ]
 
     def enable_all(self):
-        for f in self.model_fields.keys():
+        for f in self.__class__.model_fields.keys():
             if isinstance(self[f], bool):
                 self[f] = True
 
     def disable_all(self):
-        for f in self.model_fields.keys():
+        for f in self.__class__.model_fields.keys():
             if isinstance(self[f], bool):
                 self[f] = False
 

{py_neuromodulation-0.1.4.dist-info → py_neuromodulation-0.1.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: py_neuromodulation
-Version: 0.1.4
+Version: 0.1.7
 Summary: Real-time analysis of intracranial neurophysiology recordings.
 Project-URL: Homepage, https://neuromodulation.github.io/py_neuromodulation/
 Project-URL: Documentation, https://neuromodulation.github.io/py_neuromodulation/
@@ -92,9 +92,18 @@ Requires-Dist: pytest-xdist; extra == 'test'
 Requires-Dist: pytest>=8.0.2; extra == 'test'
 Description-Content-Type: text/x-rst
 
+
+
 py_neuromodulation
 ==================
 
+Journal of Open Source Science publication:
+
+.. image:: https://joss.theoj.org/papers/10.21105/joss.08258/status.svg
+   :target: https://doi.org/10.21105/joss.08258
+
+
+
 Documentation: https://neuromodulation.github.io/py_neuromodulation/
 
 Analyzing neural data can be a troublesome, trial and error prone,

{py_neuromodulation-0.1.4.dist-info → py_neuromodulation-0.1.7.dist-info}/RECORD

@@ -1,5 +1,5 @@
 py_neuromodulation/__init__.py,sha256=gu0XWs6bzSMJ7JTu8xxFMCPj6TY0nQ6Q0tuBkK7onRI,2996
-py_neuromodulation/default_settings.yaml,sha256=tEKmC16yQwy1MFMRI8cdshT8tTdZ35DB5SqqlNWES04,6387
+py_neuromodulation/default_settings.yaml,sha256=7e2UYayioKx85HeW43OyVS7CvWEt37yeITp0lJCPFGU,6393
 py_neuromodulation/grid_cortex.tsv,sha256=k2QOkHY1ej3lJ33LD6DOPVlTynzB3s4BYaoQaoUCyYc,643
 py_neuromodulation/grid_subcortex.tsv,sha256=oCQDYLDdYSa1DAI9ybwECfuzWulFzXqKHyf7oZ1oDBM,25842
 py_neuromodulation/lsl_api.cfg,sha256=oKJ5S_9mJjLUCuI4i1jZVOOquNebzdCDIMQWv1gwT3U,39
@@ -36,13 +36,13 @@ py_neuromodulation/features/bispectra.py,sha256=BzI0UsMnBWal6qtqmTmLOR20IA_Wly7E
 py_neuromodulation/features/bursts.py,sha256=HPLZ7EHbDjDthN96bRgUjb9JDvSoZkf-aYGroI9GLdM,11574
 py_neuromodulation/features/coherence.py,sha256=RmY-KPROZbsnmjewOrZjFO4KEq7D_D5P4sgZ3W_CCaw,9238
 py_neuromodulation/features/feature_processor.py,sha256=S1hFg7Ke5CaD64sti0ZaTBL-KnOrIjliq3ytpO01Wls,3976
-py_neuromodulation/features/fooof.py,sha256=9HJjjmkFcchDy8ZsSn3DKPla-Ns-Hx5xaln6C0OkTEE,5191
+py_neuromodulation/features/fooof.py,sha256=YF3i_RgzJ4SMTRkOBPXB4hQNppcSKhS0S-KS0bTbpt8,5319
 py_neuromodulation/features/hjorth_raw.py,sha256=mRPioPHJdN73AGErRbJ5S1Vz__qEQ89jAKaeN5k8eXo,1845
 py_neuromodulation/features/linelength.py,sha256=8BTctvr9Zj8TEK2HLJqi73j_y2Xgt8lKK-mJhv8eAsM,641
 py_neuromodulation/features/mne_connectivity.py,sha256=lQHLIXmoyDOWf5agmGMLeq1cQLiG6ud-vYf75CpYTVI,4109
 py_neuromodulation/features/nolds.py,sha256=jNCKQlIfmcAhmzjTAJMbFPhRuPtYZF5BDzR4qHlLp1k,3374
 py_neuromodulation/features/oscillatory.py,sha256=KzQQ3EA75G-hJVmL_YBybWTnuNJFZXAM0aBHudr-dvM,7806
-py_neuromodulation/features/sharpwaves.py,sha256=UpNsaD77Kf5wY22cEhQ9WMNxiBVxjxzDfcsVqubYgm0,18562
+py_neuromodulation/features/sharpwaves.py,sha256=lnX6y4JsNQ7B0iU0W9GDkqvldVHO9FyoaUF1cMHuCbs,18714
 py_neuromodulation/filter/__init__.py,sha256=ut1q8daCZoN7lhTKURGpk1X5oKiS3eSNqR7SkZyGDJw,128
 py_neuromodulation/filter/kalman_filter.py,sha256=-aSAq7KcJ8LUjUThsQtTaIcvz-Qtavik6ltk59j7O-Q,2194
 py_neuromodulation/filter/kalman_filter_external.py,sha256=_7FFq-1GQY9mNA0EvmaM4wQ46DVkHC9bYFIgiw9b6nY,61367
@@ -82,28 +82,28 @@ py_neuromodulation/processing/data_preprocessor.py,sha256=4_yTKl9efCRFDicStgArQl
 py_neuromodulation/processing/filter_preprocessing.py,sha256=uIp2ewKQe3ojvGLHK26e9fLubEHOg9UF3uypTLkktFg,3611
 py_neuromodulation/processing/normalization.py,sha256=ixzl4zBotppQjJwCYdU2tGR_sJEf2mtYTfCRlRRd8E4,6150
 py_neuromodulation/processing/projection.py,sha256=JYYRG9_PcPL7a2ge3FjrCWiEIaCXGIKKegTjW1ecQ_Y,14772
-py_neuromodulation/processing/rereference.py,sha256=n9zLNDkuqeP7zwrP5bhsiXF9eYVPwqI4hZvvQzZ5cks,3304
+py_neuromodulation/processing/rereference.py,sha256=X8YdOGt6mVxIE6gfkP7b1OsQVY7SXE-PMHZBgu_gP4k,3526
 py_neuromodulation/processing/resample.py,sha256=J87gjTSqWM7dDB1ZkoMo9EP3iAL4bI03K9RAMzCCowQ,1354
 py_neuromodulation/stream/__init__.py,sha256=4kagKtWOLKKZ7l6Dag1EpOFBOf8vv1eu2ll7EYbFD2Y,266
 py_neuromodulation/stream/backend_interface.py,sha256=Qn2iUH4l3VNfTXXWNJykseNzZQQAZF0M-5e_nd4qjMM,1789
-py_neuromodulation/stream/data_processor.py,sha256=-uSeszbqN51xBxFwa46YCpMjX5HHgN_aXDJ--aDdUhQ,12204
+py_neuromodulation/stream/data_processor.py,sha256=pBXyma25KNl1npWLEHBYXcJ35fFoByzPd8WaaT5OdUQ,12398
 py_neuromodulation/stream/generator.py,sha256=UKLuM8gz2YLBuVQnQNkkOOKhwsyW27ZgvRJ_5BK7Glo,1588
 py_neuromodulation/stream/mnelsl_player.py,sha256=KksAWzr78JPqPlECweWZ7JThoxmTVWGo1_-m-fEL0N4,6351
 py_neuromodulation/stream/mnelsl_stream.py,sha256=-uHMCNLZwIcjiT9AMGWkJit5GsZjEJYkpki_DoaLzWY,4352
 py_neuromodulation/stream/settings.py,sha256=--K4NOlR3QNmg4ISgtvC1z_Ucf7MvGChvocck3w6LoI,11832
 py_neuromodulation/stream/stream.py,sha256=tcIH0tW99qxrMS3GeRF45xe9K3PO6FB8JlYESH5uNDk,16593
 py_neuromodulation/utils/__init__.py,sha256=Ok3STMpsflCTclJC9C1iQgdT-3HNGMM7U45w5Oespr4,46
-py_neuromodulation/utils/channels.py,sha256=bDUZZ8MB3T-Kcs6zI52MUmvC8qx9KAH-F9U0GyND79U,10649
+py_neuromodulation/utils/channels.py,sha256=QYgDqB5lgTlPLSgpHMA_6U_AgIwWAoHxYF_1haeuggw,10934
 py_neuromodulation/utils/database.py,sha256=VEFsmbYDQWwaoZKmJCG8oyWoDTbfSiT_p0n7da9_Pn4,4755
 py_neuromodulation/utils/file_writer.py,sha256=eJLx3hK1-1VHKFXWHl4bPZH-dJ8zplUBLVQPDOa_VgQ,3427
 py_neuromodulation/utils/io.py,sha256=uE4k3ScspRy_RuWrrV7cdosH4eKxJKAkvnr5KC8SG6A,11515
 py_neuromodulation/utils/keyboard.py,sha256=swoxYhf4Q3pj50EKALUFt6hREfXnoXq2Z2q01IahPe8,1505
 py_neuromodulation/utils/logging.py,sha256=eIBFBRaAMb3KJnoxNFiCkMrTGzWwgfeDs8m5iq6FxN8,2178
 py_neuromodulation/utils/perf.py,sha256=10LYM13iTuWA-il-EMMOyZke3-1gcFEa6WLlHsJLO50,5471
-py_neuromodulation/utils/pydantic_extensions.py,sha256=nkgq8QHeKSJgmf1cBThBLQ9prdeZZ3_Pyeogs-WnHTA,11030
-py_neuromodulation/utils/types.py,sha256=hT4U9uj4PhHfu8cO7xE1oXj_KT1uHtP-rNY_cDbofr0,4643
-py_neuromodulation-0.1.4.dist-info/METADATA,sha256=VHAB6P_4FPz5JZtaJHtI15rXEMRuBbThJX8fKOv8-wE,7733
-py_neuromodulation-0.1.4.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-py_neuromodulation-0.1.4.dist-info/entry_points.txt,sha256=hImSrCn9vJcwocoeehqNyJ-qj5Hgfrg2o6MPAnIaAa0,60
-py_neuromodulation-0.1.4.dist-info/licenses/LICENSE,sha256=EMBwuBRPBo-WkHSjqxZ55E6j95gKNBZ8x30pt-VGfrM,1118
-py_neuromodulation-0.1.4.dist-info/RECORD,,
+py_neuromodulation/utils/pydantic_extensions.py,sha256=Z7dpGw6cKuXM1CM5AKYzlbdItGfsDT1Yx8MHSNA0VP0,10751
+py_neuromodulation/utils/types.py,sha256=3AukBYuOqZJ5Mw6ZimRIYxGRSDdmMU9lsnaZkPUNWRA,4673
+py_neuromodulation-0.1.7.dist-info/METADATA,sha256=u__cUSnRv36x-Ac1o_Imm8l3WTXjTAUKt9KtBcdkjMM,7903
+py_neuromodulation-0.1.7.dist-info/WHEEL,sha256=WLgqFyCfm_KASv4WHyYy0P3pM_m7J5L9k2skdKLirC8,87
+py_neuromodulation-0.1.7.dist-info/entry_points.txt,sha256=hImSrCn9vJcwocoeehqNyJ-qj5Hgfrg2o6MPAnIaAa0,60
+py_neuromodulation-0.1.7.dist-info/licenses/LICENSE,sha256=EMBwuBRPBo-WkHSjqxZ55E6j95gKNBZ8x30pt-VGfrM,1118
+py_neuromodulation-0.1.7.dist-info/RECORD,,

{py_neuromodulation-0.1.4.dist-info → py_neuromodulation-0.1.7.dist-info}/WHEEL

@@ -1,4 +1,4 @@
 Wheel-Version: 1.0
-Generator: hatchling 1.27.0
+Generator: hatchling 1.28.0
 Root-Is-Purelib: true
 Tag: py3-none-any