py-neuromodulation 0.0.5__py3-none-any.whl → 0.0.7__py3-none-any.whl

py_neuromodulation/nm_generator.py

@@ -1,45 +0,0 @@
-from collections.abc import Iterator
-from typing import TYPE_CHECKING
-import numpy as np
-
-if TYPE_CHECKING:
-    from py_neuromodulation.nm_settings import NMSettings
-
-
-def raw_data_generator(
-    data: np.ndarray,
-    settings: "NMSettings",
-    sfreq: float,
-) -> Iterator[tuple[np.ndarray, np.ndarray]]:
-    """
-    This generator function mimics online data acquisition.
-    The data are iteratively sampled with settings.sampling_rate_features_hz
-
-    Arguments
-    ---------
-        data (np array): shape (channels, time)
-        settings (nm_settings.NMSettings): settings object
-        sfreq (float): sampling frequency of the data
-
-    Returns
-    -------
-        np.array: 1D array of time stamps
-        np.array: new batch for run function of full segment length shape
-    """
-    sfreq_new = settings.sampling_rate_features_hz
-    offset_time = settings.segment_length_features_ms
-    offset_start = offset_time / 1000 * sfreq
-
-    ratio_samples_features = sfreq / sfreq_new
-
-    ratio_counter = 0
-    for cnt in range(
-        data.shape[1] + 1
-    ):  # shape + 1 guarantees that the last sample is also included
-        if (cnt - offset_start) >= ratio_samples_features * ratio_counter:
-            ratio_counter += 1
-
-            yield (
-                np.arange(cnt - offset_start, cnt) / sfreq,
-                data[:, np.floor(cnt - offset_start).astype(int) : cnt],
-            )

py_neuromodulation/nm_stream_abc.py

@@ -1,166 +0,0 @@
-"""Module that contains NMStream ABC."""
-
-from abc import ABC, abstractmethod
-
-import pandas as pd
-
-from py_neuromodulation.nm_run_analysis import DataProcessor
-from py_neuromodulation.nm_settings import NMSettings
-from py_neuromodulation.nm_types import _PathLike, FeatureName
-from py_neuromodulation import nm_IO, PYNM_DIR
-
-
-class NMStream(ABC):
-    def __init__(
-        self,
-        sfreq: float,
-        nm_channels: pd.DataFrame | _PathLike,
-        settings: "NMSettings | _PathLike | None" = None,
-        line_noise: float | None = 50,
-        sampling_rate_features_hz: float | None = None,
-        path_grids: _PathLike | None = None,
-        coord_names: list | None = None,
-        stream_name: str
-        | None = "example_stream",  # Timon: do we need those in the nmstream_abc?
-        stream_lsl: bool = False,
-        coord_list: list | None = None,
-        verbose: bool = True,
-    ) -> None:
-        """Stream initialization
-
-        Parameters
-        ----------
-        sfreq : float
-            sampling frequency of data in Hertz
-        nm_channels : pd.DataFrame | _PathLike
-            parametrization of channels (see nm_define_channels.py for initialization)
-        settings : NMSettings | _PathLike | None, optional
-            Initialized nm_settings.NMSettings object, by default the py_neuromodulation/nm_settings.yaml are read
-            and passed into a settings object
-        line_noise : float | None, optional
-            line noise, by default 50
-        sampling_rate_features_hz : float | None, optional
-            feature sampling rate, by default None
-        path_grids : _PathLike | None, optional
-            path to grid_cortex.tsv and/or gird_subcortex.tsv, by default Non
-        coord_names : list | None, optional
-            coordinate name in the form [coord_1_name, coord_2_name, etc], by default None
-        coord_list : list | None, optional
-            coordinates in the form [[coord_1_x, coord_1_y, coord_1_z], [coord_2_x, coord_2_y, coord_2_z],], by default None
-        verbose : bool, optional
-            print out stream computation time information, by default True
-        """
-        self.settings: NMSettings = NMSettings.load(settings)
-
-        # If features that use frequency ranges are on, test them against nyquist frequency
-        use_freq_ranges: list[FeatureName] = [
-            "bandpass_filter",
-            "stft",
-            "fft",
-            "welch",
-            "bursts",
-            "coherence",
-            "nolds",
-            "bispectrum",
-        ]
-
-        need_nyquist_check = any(
-            (f in use_freq_ranges for f in self.settings.features.get_enabled())
-        )
-
-        if need_nyquist_check:
-            assert all(
-                fb.frequency_high_hz < sfreq / 2
-                for fb in self.settings.frequency_ranges_hz.values()
-            ), (
-                "If a feature that uses frequency ranges is selected, "
-                "the frequency band ranges need to be smaller than the nyquist frequency.\n"
-                f"Got sfreq = {sfreq} and fband ranges:\n {self.settings.frequency_ranges_hz}"
-            )
-
-        if sampling_rate_features_hz is not None:
-            self.settings.sampling_rate_features_hz = sampling_rate_features_hz
-
-        self.nm_channels = self._load_nm_channels(nm_channels)
-        if path_grids is None:
-            path_grids = PYNM_DIR
-        self.path_grids = path_grids
-        self.verbose = verbose
-        self.sfreq = sfreq
-        self.line_noise = line_noise
-        self.coord_names = coord_names
-        self.coord_list = coord_list
-        self.sess_right = None
-        self.projection = None
-        self.model = None
-
-        self.data_processor = DataProcessor(
-            sfreq=self.sfreq,
-            settings=self.settings,
-            nm_channels=self.nm_channels,
-            path_grids=self.path_grids,
-            coord_names=coord_names,
-            coord_list=coord_list,
-            line_noise=line_noise,
-            verbose=self.verbose,
-        )
-
-    @abstractmethod
-    def run(self) -> pd.DataFrame:
-        """Reinitialize the stream
-        This might be handy in case the nm_channels or nm_settings changed
-        """
-
-        self.data_processor = DataProcessor(
-            sfreq=self.sfreq,
-            settings=self.settings,
-            nm_channels=self.nm_channels,
-            path_grids=self.path_grids,
-            coord_names=self.coord_names,
-            coord_list=self.coord_list,
-            line_noise=self.line_noise,
-            verbose=self.verbose,
-        )
-
-    @staticmethod
-    def _load_nm_channels(
-        nm_channels: pd.DataFrame | _PathLike,
-    ) -> pd.DataFrame:
-        if not isinstance(nm_channels, pd.DataFrame):
-            nm_channels = nm_IO.load_nm_channels(nm_channels)
-
-        if nm_channels.query("used == 1 and target == 0").shape[0] == 0:
-            raise ValueError(
-                "No channels selected for analysis that have column 'used' = 1 and 'target' = 0. Please check your nm_channels"
-            )
-
-        return nm_channels
-
-    def save_after_stream(
-        self,
-        out_dir: _PathLike = "",
-        prefix: str = "",
-        feature_arr: pd.DataFrame | None = None,
-    ) -> None:
-        """Save features, settings, nm_channels and sidecar after run"""
-
-        self.save_sidecar(out_dir, prefix)
-
-        if feature_arr is not None:
-            nm_IO.save_features(feature_arr, out_dir, prefix)
-
-        self.save_settings(out_dir, prefix)
-
-        self.save_nm_channels(out_dir, prefix)
-
-    def save_nm_channels(self, out_dir: _PathLike, prefix: str = "") -> None:
-        self.data_processor.save_nm_channels(out_dir, prefix)
-
-    def save_settings(self, out_dir: _PathLike, prefix: str = "") -> None:
-        self.data_processor.save_settings(out_dir, prefix)
-
-    def save_sidecar(self, out_dir: _PathLike, prefix: str = "") -> None:
-        """Save sidecar incduing fs, coords, sess_right to
-        out_path_root and subfolder 'folder_name'"""
-        additional_args = {"sess_right": self.sess_right}
-        self.data_processor.save_sidecar(out_dir, prefix, additional_args)

py_neuromodulation-0.0.5.dist-info/RECORD

@@ -1,83 +0,0 @@
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