py-neuromodulation 0.0.6__py3-none-any.whl → 0.0.7__py3-none-any.whl

py_neuromodulation/default_settings.yaml

@@ -193,6 +193,7 @@ coherence_settings:
   method:
     coh: true
     icoh: true
+  nperseg: 128
 
 fooof_settings:
   aperiodic:

py_neuromodulation/features/bispectra.py

@@ -96,11 +96,8 @@ class Bispectra(NMFeature):
     def calc_feature(self, data: np.ndarray) -> dict:
         from pybispectra import compute_fft, WaveShape
 
-        # PyBispectra's compute_fft uses PQDM to parallelize the calculation per channel
-        # Is this necessary? Maybe the overhead of parallelization is not worth it
-        # considering that we incur in it once per batch of data
         fft_coeffs, freqs = compute_fft(
-            data=np.expand_dims(data, axis=(0)),
+            data=np.expand_dims(data, axis=0),
             sampling_freq=self.sfreq,
             n_points=data.shape[1],
             verbose=False,
@@ -127,12 +124,11 @@ class Bispectra(NMFeature):
             f1s=tuple(self.settings.f1s),  # type: ignore
             f2s=tuple(self.settings.f2s),  # type: ignore
         )
+        waveshape = waveshape.results.get_results(copy=False)  # can overwrite obj with array
 
         feature_results = {}
         for ch_idx, ch_name in enumerate(self.ch_names):
-            bispectrum = waveshape._bicoherence[
-                ch_idx
-            ]  # Same as waveshape.results._data, skips a copy
+            bispectrum = waveshape[ch_idx]
 
             for component in self.settings.components.get_enabled():
                 spectrum_ch = COMPONENT_DICT[component](bispectrum)

py_neuromodulation/features/coherence.py

@@ -26,7 +26,7 @@ class CoherenceFeatures(BoolSelector):
     mean_fband: bool = True
     max_fband: bool = True
     max_allfbands: bool = True
-
+    
 
 ListOfTwoStr = Annotated[list[str], Field(min_length=2, max_length=2)]
 
@@ -35,6 +35,7 @@ class CoherenceSettings(NMBaseModel):
     features: CoherenceFeatures = CoherenceFeatures()
     method: CoherenceMethods = CoherenceMethods()
     channels: list[ListOfTwoStr] = []
+    nperseg: int = Field(default=128, ge=0)
     frequency_bands: list[str] = Field(default=["high_beta"], min_length=1)
 
     @field_validator("frequency_bands")
@@ -49,6 +50,7 @@ class CoherenceObject:
         window: str,
         fbands: list[FrequencyRange],
         fband_names: list[str],
+        nperseg: int,
         ch_1_name: str,
         ch_2_name: str,
         ch_1_idx: int,
@@ -65,6 +67,7 @@ class CoherenceObject:
         self.ch_2 = ch_2_name
         self.ch_1_idx = ch_1_idx
         self.ch_2_idx = ch_2_idx
+        self.nperseg = nperseg
         self.coh = coh
         self.icoh = icoh
         self.features_coh = features_coh
@@ -79,14 +82,15 @@ class CoherenceObject:
     def get_coh(self, feature_results, x, y):
         from scipy.signal import welch, csd
 
-        self.f, self.Pxx = welch(x, self.sfreq, self.window, nperseg=128)
-        self.Pyy = welch(y, self.sfreq, self.window, nperseg=128)[1]
-        self.Pxy = csd(x, y, self.sfreq, self.window, nperseg=128)[1]
+        self.f, self.Pxx = welch(x, self.sfreq, self.window, nperseg=self.nperseg)
+        self.Pyy = welch(y, self.sfreq, self.window, nperseg=self.nperseg)[1]
+        self.Pxy = csd(x, y, self.sfreq, self.window, nperseg=self.nperseg)[1]
 
         if self.coh:
-            self.coh_val = np.abs(self.Pxy**2) / (self.Pxx * self.Pyy)
+            # XXX: gives different output to abs(Sxy) / sqrt(Sxx * Syy)
+            self.coh_val = np.abs(self.Pxy) ** 2 / (self.Pxx * self.Pyy)
         if self.icoh:
-            self.icoh_val = np.array(self.Pxy / (self.Pxx * self.Pyy)).imag
+            self.icoh_val = self.Pxy.imag / np.sqrt(self.Pxx * self.Pyy)
 
         for coh_idx, coh_type in enumerate([self.coh, self.icoh]):
             if coh_type:
@@ -180,6 +184,7 @@ class Coherence(NMFeature):
                     "hann",
                     fband_specs,
                     fband_names,
+                    self.settings.nperseg,
                     ch_1_name,
                     ch_2_name,
                     ch_1_idx,

{py_neuromodulation-0.0.6.dist-info → py_neuromodulation-0.0.7.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: py_neuromodulation
-Version: 0.0.6
+Version: 0.0.7
 Summary: Real-time analysis of intracranial neurophysiology recordings.
 Project-URL: bugtracker, https://github.com/neuromodulation/py_neuromodulation/issues
 Project-URL: repository, https://github.com/neuromodulation/py_neuromodulation
@@ -36,20 +36,21 @@ Classifier: Topic :: Software Development :: Libraries :: Python Modules
 Requires-Python: >=3.11
 Requires-Dist: fooof
 Requires-Dist: joblib>=1.3.2
+Requires-Dist: llvmlite>=0.43.0
 Requires-Dist: matplotlib>=3.9.0
 Requires-Dist: mne
 Requires-Dist: mne-bids>=0.8
 Requires-Dist: mne-connectivity
 Requires-Dist: mne-lsl>=1.2.0
 Requires-Dist: mrmr-selection
-Requires-Dist: nolds
+Requires-Dist: nolds>=0.6.1
+Requires-Dist: numba>=0.60.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pandas>=2.0.0
 Requires-Dist: pyarrow>=14.0.2
 Requires-Dist: pybispectra>=1.2.0
 Requires-Dist: pydantic>=2.7.3
 Requires-Dist: pyparrm
-Requires-Dist: pyqt5
 Requires-Dist: scikit-learn>=0.24.2
 Requires-Dist: scikit-optimize
 Requires-Dist: scipy>=1.7.1
@@ -108,7 +109,7 @@ The original intention for writing this toolbox was movement decoding from invas
 The application however could be any neural decoding problem.
 *py_neuromodulation* offers wrappers around common practice machine learning methods for efficient analysis.
 
-Find the documentation here http://py-neuromodulation.readthedocs.io for example usage and parametrization.
+Find the documentation here neuromodulation.github.io/py_neuromodulation/ for example usage and parametrization.
 
 Installation
 ============
@@ -119,25 +120,15 @@ py_neuromodulation requires at least python 3.10. For installation you can use p
 
     pip install py-neuromodulation
 
-Alternatively you can also install the package in a conda environment:
+Alternatively you can also clone the pacakge and install it using `uv <https://docs.astral.sh/uv/>`_:
 
 .. code-block::
 
-    conda create -n pynm-test python=3.11
-    conda activate pynm-test
+    uv python install 3.10
+    uv venv
+    . .venv/bin/activate
+    uv sync
 
-Then install the packages listed in the `pyproject.toml`:
-
-.. code-block::
-
-    pip install .
-
-
-Optionally the ipython kernel can be specified for the installed pynm-test conda environment:
-
-.. code-block::
-
-    ipython kernel install --user --name=pynm-test
 
 Then *py_neuromodulation* can be imported via:
 

{py_neuromodulation-0.0.6.dist-info → py_neuromodulation-0.0.7.dist-info}/RECORD

@@ -1,5 +1,5 @@
 py_neuromodulation/__init__.py,sha256=MaOF7mCNRjR9MgcCnk9b7dYJICVJthiWlZVf365lXOo,2831
-py_neuromodulation/default_settings.yaml,sha256=g7UcCxmcQtg7YySj3WAhQ-hdqJlOYrvZYZtMcJuWzpQ,5552
+py_neuromodulation/default_settings.yaml,sha256=06KzRz8eLAa5--gmrYsr_bn9UOzSMIpuktrPKNaSc4A,5568
 py_neuromodulation/grid_cortex.tsv,sha256=k2QOkHY1ej3lJ33LD6DOPVlTynzB3s4BYaoQaoUCyYc,643
 py_neuromodulation/grid_subcortex.tsv,sha256=oCQDYLDdYSa1DAI9ybwECfuzWulFzXqKHyf7oZ1oDBM,25842
 py_neuromodulation/ConnectivityDecoding/Automated Anatomical Labeling 3 (Rolls 2020).nii,sha256=Sp-cjF_AuT0Tlilb5s8lB14hVgkXJiR2uKMS9nOQOeg,902981
@@ -30,9 +30,9 @@ py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMe
 py_neuromodulation/data/sub-testsub/ses-EphysMedOff/ieeg/sub-testsub_ses-EphysMedOff_task-gripforce_run-0_ieeg.vmrk,sha256=BD-VmcKe7dR0vGzzkv4c09QnSwc3zYeAWDGJIzWEOI0,540
 py_neuromodulation/features/__init__.py,sha256=zpulQ3IaKh6yNSnCBIRa5IC3SZ7FlKNQxHLF50yTdQU,1567
 py_neuromodulation/features/bandpower.py,sha256=rpkY2dNayXYng1BmZxyKTxgrJFnrslPaKVUpoNXE6EA,6152
-py_neuromodulation/features/bispectra.py,sha256=FvXzvkhoKaOZNjYckJgMSscAA4ShN-g8ufwe6-2zNGw,5509
+py_neuromodulation/features/bispectra.py,sha256=BzI0UsMnBWal6qtqmTmLOR20IA_Wly7EIy0wCK0QgVQ,5272
 py_neuromodulation/features/bursts.py,sha256=7-I81RYSZEm5pbIKc6wXmfxmJ4Q6V41CfJXebqkGGDw,11467
-py_neuromodulation/features/coherence.py,sha256=I6w7bUwIh9rte9mYXEB1XX7HYwFJw0OG0IeMpJtR2LU,8798
+py_neuromodulation/features/coherence.py,sha256=j1J7GHTElVuAl7x2NsGVpoQLQ9npxyznJ6HM7Nzb49k,9040
 py_neuromodulation/features/feature_processor.py,sha256=CT05jNks681LOcyr2yHe1KaUryJXm52_53hNmEhuWnM,3972
 py_neuromodulation/features/fooof.py,sha256=RouqFikiKf_JSiEel569lfjzfYRE7CEvBlgvuj53Xj4,5016
 py_neuromodulation/features/hjorth_raw.py,sha256=mRPioPHJdN73AGErRbJ5S1Vz__qEQ89jAKaeN5k8eXo,1845
@@ -83,7 +83,7 @@ py_neuromodulation/utils/io.py,sha256=-qAwtFSsumfzY6dkYSKGySE8_RH1c2M1NDxC_ZQrUV
 py_neuromodulation/utils/keyboard.py,sha256=swoxYhf4Q3pj50EKALUFt6hREfXnoXq2Z2q01IahPe8,1505
 py_neuromodulation/utils/logging.py,sha256=eIBFBRaAMb3KJnoxNFiCkMrTGzWwgfeDs8m5iq6FxN8,2178
 py_neuromodulation/utils/types.py,sha256=QVq3wAgMcw5zKPa_Kj2QQ2Gt2CYavO_PAka3RAZdfwo,7310
-py_neuromodulation-0.0.6.dist-info/METADATA,sha256=UcYGczR0VlQ_98AKZe6J-x8Ml-wiie9d7Th7paCeziY,7216
-py_neuromodulation-0.0.6.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
-py_neuromodulation-0.0.6.dist-info/licenses/LICENSE,sha256=EMBwuBRPBo-WkHSjqxZ55E6j95gKNBZ8x30pt-VGfrM,1118
-py_neuromodulation-0.0.6.dist-info/RECORD,,
+py_neuromodulation-0.0.7.dist-info/METADATA,sha256=GnkK958mbJYayCTmPLr9c1lYj3s0cXg4LCqL0SHSQdw,7045
+py_neuromodulation-0.0.7.dist-info/WHEEL,sha256=1yFddiXMmvYK7QYTqtRNtX66WJ0Mz8PYEiEUoOUUxRY,87
+py_neuromodulation-0.0.7.dist-info/licenses/LICENSE,sha256=EMBwuBRPBo-WkHSjqxZ55E6j95gKNBZ8x30pt-VGfrM,1118
+py_neuromodulation-0.0.7.dist-info/RECORD,,