py-neuromodulation 0.0.4__py3-none-any.whl → 0.0.6__py3-none-any.whl

py_neuromodulation/nm_stream_offline.py

@@ -1,359 +0,0 @@
-"""Module for offline data streams."""
-
-import os
-from joblib import Parallel, delayed
-import numpy as np
-import pandas as pd
-from itertools import count
-import logging
-
-logger = logging.getLogger("PynmLogger")
-
-import mne
-
-from py_neuromodulation import (
-    nm_generator,
-    nm_IO,
-    nm_stream_abc,
-    nm_define_nmchannels,
-)
-
-_PathLike = str | os.PathLike
-
-
-class _OfflineStream(nm_stream_abc.PNStream):
-    """Offline stream base class.
-    This class can be inhereted for different types of offline streams, e.g. epoch-based or continuous.
-
-    Parameters
-    ----------
-    nm_stream_abc : nm_stream_abc.PNStream
-    """
-
-    def _add_target(
-        self, feature_series: pd.Series, data: np.ndarray
-    ) -> pd.Series:
-        """Add target channels to feature series.
-
-        Parameters
-        ----------
-        feature_series : pd.Series
-        data : np.ndarray
-            Raw data with shape (n_channels, n_samples). Channels not for feature computation are also included
-
-        Returns
-        -------
-        pd.Series
-            feature series with target channels added
-        """
-
-        if self.nm_channels["target"].sum() > 0:
-            if not self.target_idx_initialized:
-                self.target_indexes = self.nm_channels[
-                    self.nm_channels["target"] == 1
-                ].index
-                self.target_names = self.nm_channels.loc[
-                    self.target_indexes, "name"
-                ].to_list()
-                self.target_idx_initialized = True
-
-            for target_idx, target_name in zip(
-                self.target_indexes, self.target_names
-            ):
-                feature_series[target_name] = data[target_idx, -1]
-        return feature_series
-
-    def _add_timestamp(
-        self, feature_series: pd.Series, cnt_samples: int
-    ) -> pd.Series:
-        """Add time stamp in ms.
-
-        Due to normalization run_analysis needs to keep track of the counted
-        samples. These are accessed here for time conversion.
-        """
-        feature_series["time"] = cnt_samples * 1000 / self.sfreq
-
-        if self.verbose:
-            logging.info(
-                str(np.round(feature_series["time"] / 1000, 2))
-                + " seconds of data processed"
-            )
-
-        return feature_series
-
-    def _handle_data(self, data: np.ndarray | pd.DataFrame) -> np.ndarray:
-        names_expected = self.nm_channels["name"].to_list()
-
-        if isinstance(data, np.ndarray):
-            if not len(names_expected) == data.shape[0]:
-                raise ValueError(
-                    "If data is passed as an array, the first dimension must"
-                    " match the number of channel names in `nm_channels`.\n"
-                    f" Number of data channels (data.shape[0]): {data.shape[0]}\n"
-                    f" Length of nm_channels[\"name\"]: {len(names_expected)}."
-                )
-            return data
-        names_data = data.columns.to_list()
-        if not (
-            len(names_expected) == len(names_data)
-            and sorted(names_expected) == sorted(names_data)
-        ):
-            raise ValueError(
-                "If data is passed as a DataFrame, the"
-                "column names must match the channel names in `nm_channels`.\n"
-                f"Input dataframe column names: {names_data}\n"
-                f"Expected (from nm_channels[\"name\"]): : {names_expected}."
-            )
-        return data.to_numpy().transpose()
-
-    def _check_settings_for_parallel(self):
-        """Check specified settings and raise error if parallel processing is not possible.
-
-        Raises:
-            ValueError: depending on the settings, parallel processing is not possible
-        """
-
-        if "raw_normalization" in self.settings["preprocessing"]:
-            raise ValueError(
-                "Parallel processing is not possible with raw_normalization normalization."
-            )
-        if self.settings["postprocessing"]["feature_normalization"] is True:
-            raise ValueError(
-                "Parallel processing is not possible with feature normalization."
-            )
-        if self.settings["features"]["bursts"] is True:
-            raise ValueError(
-                "Parallel processing is not possible with burst estimation."
-            )
-
-    def _process_batch(self, data_batch, cnt_samples):
-        feature_series = self.run_analysis.process(
-            data_batch.astype(np.float64)
-        )
-        feature_series = self._add_timestamp(feature_series, cnt_samples)
-        feature_series = self._add_target(
-            feature_series=feature_series, data=data_batch
-        )
-        return feature_series
-
-    def _run_offline(
-        self,
-        data: np.ndarray,
-        out_path_root: _PathLike | None = None,
-        folder_name: str = "sub",
-        parallel: bool = False,
-        n_jobs: int = -2,
-    ) -> pd.DataFrame:
-        generator = nm_generator.raw_data_generator(
-            data=data,
-            settings=self.settings,
-            sfreq=self.sfreq,
-        )
-
-        sample_add = self.sfreq / self.run_analysis.sfreq_features
-
-        offset_time = self.settings["segment_length_features_ms"]
-        # offset_start = np.ceil(offset_time / 1000 * self.sfreq).astype(int)
-        offset_start = offset_time / 1000 * self.sfreq
-
-        if parallel:
-            l_features = Parallel(n_jobs=n_jobs, verbose=10)(
-                delayed(self._process_batch)(data_batch, cnt_samples)
-                for data_batch, cnt_samples in zip(
-                    generator, count(offset_start, sample_add)
-                )
-            )
-
-        else:
-            l_features = []
-            cnt_samples = offset_start
-            while True:
-                data_batch = next(generator, None)
-                if data_batch is None:
-                    break
-                feature_series = self.run_analysis.process(
-                    data_batch.astype(np.float64)
-                )
-                feature_series = self._add_timestamp(
-                    feature_series, cnt_samples
-                )
-
-                feature_series = self._add_target(
-                    feature_series=feature_series, data=data_batch
-                )
-
-                l_features.append(feature_series)
-
-                cnt_samples += sample_add
-        feature_df = pd.DataFrame(l_features)
-
-        self.save_after_stream(out_path_root, folder_name, feature_df)
-
-        return feature_df
-
-    def plot_raw_signal(
-        self,
-        sfreq: float = None,
-        data: np.array = None,
-        lowpass: float = None,
-        highpass: float = None,
-        picks: list = None,
-        plot_time: bool = True,
-        plot_psd: bool = False,
-    ) -> None:
-        """Use MNE-RawArray Plot to investigate PSD or raw_signal plot.
-
-        Parameters
-        ----------
-        sfreq : float
-            sampling frequency [Hz]
-        data : np.array, optional
-            data (n_channels, n_times), by default None
-        plot_time : bool, optional
-            mne.io.RawArray.plot(), by default True
-        plot_psd : bool, optional
-            mne.io.RawArray.plot(), by default True
-
-        Raises
-        ------
-        ValueError
-            raise Exception when no data is passed
-        """
-        if self.data is None and data is None:
-            raise ValueError("No data passed to plot_raw_signal function.")
-
-        if data is None and self.data is not None:
-            data = self.data
-
-        if sfreq is None:
-            sfreq = self.sfreq
-
-        if self.nm_channels is not None:
-            ch_names = self.nm_channels["name"].to_list()
-            ch_types = self.nm_channels["type"].to_list()
-        else:
-            ch_names = [f"ch_{i}" for i in range(data.shape[0])]
-            ch_types = ["ecog" for i in range(data.shape[0])]
-
-        # create mne.RawArray
-        info = mne.create_info(
-            ch_names=ch_names, sfreq=sfreq, ch_types=ch_types
-        )
-        raw = mne.io.RawArray(data, info)
-
-        if picks is not None:
-            raw = raw.pick(picks)
-        self.raw = raw
-        if plot_time:
-            raw.plot(highpass=highpass, lowpass=lowpass)
-        if plot_psd:
-            raw.compute_psd().plot()
-
-
-class Stream(_OfflineStream):
-    def __init__(
-        self,
-        sfreq: int | float,
-        data: np.ndarray | pd.DataFrame = None,
-        nm_channels: pd.DataFrame | _PathLike = None,
-        settings: dict | _PathLike | None = None,
-        sampling_rate_features_hz: float = None,
-        line_noise: int | float | None = 50,
-        path_grids: _PathLike | None = None,
-        coord_names: list | None = None,
-        coord_list: list | None = None,
-        verbose: bool = True,
-    ) -> None:
-        """Stream initialization
-
-        Parameters
-        ----------
-        sfreq : int | float
-            sampling frequency of data in Hertz
-        data : np.ndarray | pd.DataFrame | None, optional
-            data to be streamed with shape (n_channels, n_time), by default None
-        nm_channels : pd.DataFrame | _PathLike
-            parametrization of channels (see nm_define_channels.py for initialization)
-        settings : dict | _PathLike | None, optional
-            features settings can be a dictionary or path to the nm_settings.json, by default the py_neuromodulation/nm_settings.json are read
-        line_noise : int | float | None, optional
-            line noise, by default 50
-        sampling_rate_features_hz : int | 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
-            log stream computation time information, by default True
-        """
-
-        if nm_channels is None and data is not None:
-            nm_channels = nm_define_nmchannels.get_default_channels_from_data(
-                data
-            )
-
-        if nm_channels is None and data is None:
-            raise ValueError(
-                "Either `nm_channels` or `data` must be passed to `Stream`."
-            )
-
-        super().__init__(
-            sfreq,
-            nm_channels,
-            settings,
-            line_noise,
-            sampling_rate_features_hz,
-            path_grids,
-            coord_names,
-            coord_list,
-            verbose,
-        )
-
-        self.data = data
-
-        self.target_idx_initialized = False
-
-    def run(
-        self,
-        data: np.ndarray | pd.DataFrame = None,
-        out_path_root: _PathLike | None = None,
-        folder_name: str = "sub",
-        parallel: bool = False,
-        n_jobs: int = -2,
-    ) -> pd.DataFrame:
-        """Call run function for offline stream.
-
-        Parameters
-        ----------
-        data : np.ndarray | pd.DataFrame
-            shape (n_channels, n_time)
-        out_path_root : _PathLike | None, optional
-            Full path to store estimated features, by default None
-            If None, data is simply returned and not saved
-        folder_name : str, optional
-             folder output name, commonly subject or run name, by default "sub"
-
-        Returns
-        -------
-        pd.DataFrame
-            feature DataFrame
-        """
-
-        super().run()  # reinitialize the stream
-
-        if data is not None:
-            data = self._handle_data(data)
-        elif self.data is not None:
-            data = self._handle_data(self.data)
-        elif self.data is None and data is None:
-            raise ValueError("No data passed to run function.")
-
-        if parallel is True:
-            self._check_settings_for_parallel()
-
-        return self._run_offline(
-            data, out_path_root, folder_name, parallel=parallel, n_jobs=n_jobs
-        )

py_neuromodulation/utils/_logging.py

@@ -1,24 +0,0 @@
-import logging
-
-# include the filename in the log output
-# Configure the logger
-logger = logging.getLogger("PynmLogger")
-logger.setLevel(logging.INFO)
-
-# Create a file handler and set its level to DEBUG
-file_handler = logging.FileHandler("logfile_pynm.log")
-file_handler.setLevel(logging.INFO)
-
-# console_handler = logging.StreamHandler()
-# console_handler.setLevel(logging.DEBUG)
-
-# Create a formatter and add it to the handler
-formatter = logging.Formatter(
-    "%(asctime)s:%(levelname)s:%(name)s:%(filename)s:%(message)s"
-)
-file_handler.setFormatter(formatter)
-# console_handler.setFormatter(formatter)
-
-# Add the file handler to the logger
-logger.addHandler(file_handler)
-# logger.addHandler(console_handler)

py_neuromodulation-0.0.4.dist-info/RECORD

@@ -1,72 +0,0 @@
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