py-neuromodulation 0.0.3__py3-none-any.whl → 0.0.5__py3-none-any.whl

py_neuromodulation/nm_bursts.py

@@ -1,198 +1,292 @@
-import enum
-import numpy as np
-from typing import Iterable
-from scipy import signal
-
-from py_neuromodulation import nm_features_abc, nm_filter
-
-
-class Burst(nm_features_abc.Feature):
-    def __init__(
-        self, settings: dict, ch_names: Iterable[str], sfreq: float
-    ) -> None:
-        self.s = settings
-        self.sfreq = sfreq
-        self.ch_names = ch_names
-        self.threshold = self.s["burst_settings"]["threshold"]
-        self.time_duration_s = self.s["burst_settings"]["time_duration_s"]
-        self.samples_overlap = int(
-            self.sfreq
-            * (self.s["segment_length_features_ms"] / 1000)
-            / self.s["sampling_rate_features_hz"]
-        )
-
-        self.fband_names = self.s["burst_settings"]["frequency_bands"]
-        self.f_ranges = [
-            self.s["frequency_ranges_hz"][fband_name]
-            for fband_name in self.fband_names
-        ]
-        self.seglengths = np.floor(
-            self.sfreq
-            / 1000
-            * np.array(
-                [
-                    self.s["bandpass_filter_settings"]["segment_lengths_ms"][
-                        fband
-                    ]
-                    for fband in self.fband_names
-                ]
-            )
-        ).astype(int)
-
-        self.num_max_samples_ring_buffer = int(
-            self.sfreq * self.time_duration_s
-        )
-
-        self.bandpass_filter = nm_filter.MNEFilter(
-            f_ranges=self.f_ranges,
-            sfreq=self.sfreq,
-            filter_length=self.sfreq - 1,
-            verbose=False,
-        )
-
-        # create dict with fband, channel specific data store
-        # for previous time_duration_s
-        def init_ch_fband_dict() -> dict:
-            d = {}
-            for ch in self.ch_names:
-                if ch not in d:
-                    d[ch] = {}
-                for fb in self.fband_names:
-                    if fb not in d[ch]:
-                        d[ch][fb] = None
-            return d
-
-        self.data_buffer = init_ch_fband_dict()
-
-    def test_settings(
-        settings: dict,
-        ch_names: Iterable[str],
-        sfreq: int | float,
-    ):
-        assert isinstance(
-            settings["burst_settings"]["threshold"], (float, int)
-        ), f"burst settings threshold needs to be type int or float, got: {settings['burst_settings']['threshold']}"
-        assert (
-            0 < settings["burst_settings"]["threshold"] < 100
-        ), f"burst setting threshold needs to be between 0 and 100, got: {settings['burst_settings']['threshold']}"
-        assert isinstance(
-            settings["burst_settings"]["time_duration_s"], (float, int)
-        ), f"burst settings time_duration_s needs to be type int or float, got: {settings['burst_settings']['time_duration_s']}"
-        assert (
-            settings["burst_settings"]["time_duration_s"] > 0
-        ), f"burst setting time_duration_s needs to be greater than 0, got: {settings['burst_settings']['time_duration_s']}"
-
-        for fband_burst in settings["burst_settings"]["frequency_bands"]:
-            assert fband_burst in list(
-                settings["frequency_ranges_hz"].keys()
-            ), f"bursting {fband_burst} needs to be defined in settings['frequency_ranges_hz']"
-
-        for burst_feature in settings["burst_settings"][
-            "burst_features"
-        ].keys():
-            assert isinstance(
-                settings["burst_settings"]["burst_features"][burst_feature],
-                bool,
-            ), (
-                f"bursting feature {burst_feature} needs to be type bool, "
-                f"got: {settings['burst_settings']['burst_features'][burst_feature]}"
-            )
-
-    def calc_feature(self, data: np.array, features_compute: dict) -> dict:
-        # filter_data returns (n_channels, n_fbands, n_samples)
-        filtered_data = np.abs(
-            signal.hilbert(self.bandpass_filter.filter_data(data), axis=2)
-        )
-        for ch_idx, ch_name in enumerate(self.ch_names):
-            for fband_idx, fband_name in enumerate(self.fband_names):
-                new_dat = filtered_data[ch_idx, fband_idx, :]
-                if self.data_buffer[ch_name][fband_name] is None:
-                    self.data_buffer[ch_name][fband_name] = new_dat
-                else:
-                    self.data_buffer[ch_name][fband_name] = np.concatenate(
-                        (
-                            self.data_buffer[ch_name][fband_name],
-                            new_dat[-self.samples_overlap :],
-                        ),
-                        axis=0,
-                    )[-self.num_max_samples_ring_buffer :]
-
-                # calc features
-                burst_thr = np.percentile(
-                    self.data_buffer[ch_name][fband_name], q=self.threshold
-                )
-
-                burst_amplitude, burst_length = self.get_burst_amplitude_length(
-                    new_dat, burst_thr, self.sfreq
-                )
-
-                features_compute[
-                    f"{ch_name}_bursts_{fband_name}_duration_mean"
-                ] = (np.mean(burst_length) if len(burst_length) != 0 else 0)
-                features_compute[
-                    f"{ch_name}_bursts_{fband_name}_amplitude_mean"
-                ] = (
-                    np.mean([np.mean(a) for a in burst_amplitude])
-                    if len(burst_length) != 0
-                    else 0
-                )
-
-                features_compute[
-                    f"{ch_name}_bursts_{fband_name}_duration_max"
-                ] = (np.max(burst_length) if len(burst_length) != 0 else 0)
-                features_compute[
-                    f"{ch_name}_bursts_{fband_name}_amplitude_max"
-                ] = (
-                    np.max([np.max(a) for a in burst_amplitude])
-                    if len(burst_amplitude) != 0
-                    else 0
-                )
-
-                features_compute[
-                    f"{ch_name}_bursts_{fband_name}_burst_rate_per_s"
-                ] = (
-                    np.mean(burst_length)
-                    / (self.s["segment_length_features_ms"] / 1000)
-                    if len(burst_length) != 0
-                    else 0
-                )
-
-                in_burst = False
-                if self.data_buffer[ch_name][fband_name][-1] > burst_thr:
-                    in_burst = True
-
-                features_compute[f"{ch_name}_bursts_{fband_name}_in_burst"] = (
-                    in_burst
-                )
-        return features_compute
-
-    @staticmethod
-    def get_burst_amplitude_length(
-        beta_averp_norm, burst_thr: float, sfreq: float
-    ):
-        """
-        Analysing the duration of beta burst
-        """
-        bursts = np.zeros((beta_averp_norm.shape[0] + 1), dtype=bool)
-        bursts[1:] = beta_averp_norm >= burst_thr
-        deriv = np.diff(bursts)
-        burst_length = []
-        burst_amplitude = []
-
-        burst_time_points = np.where(deriv == True)[0]
-
-        for i in range(burst_time_points.size // 2):
-            burst_length.append(
-                burst_time_points[2 * i + 1] - burst_time_points[2 * i]
-            )
-            burst_amplitude.append(
-                beta_averp_norm[
-                    burst_time_points[2 * i] : burst_time_points[2 * i + 1]
-                ]
-            )
-
-        # the last burst length (in case isburst == True) is omitted,
-        # since the true burst length cannot be estimated
-        burst_length = np.array(burst_length) / sfreq
-
-        return burst_amplitude, burst_length
+import numpy as np
+
+if np.__version__ >= "2.0.0":
+    from numpy.lib._function_base_impl import _quantile as np_quantile  # type:ignore
+else:
+    from numpy.lib.function_base import _quantile as np_quantile  # type:ignore
+from collections.abc import Sequence
+from itertools import product
+
+from pydantic import Field, field_validator
+from py_neuromodulation.nm_types import BoolSelector, NMBaseModel
+from py_neuromodulation.nm_features import NMFeature
+
+from typing import TYPE_CHECKING, Callable
+
+if TYPE_CHECKING:
+    from py_neuromodulation.nm_settings import NMSettings
+
+
+LARGE_NUM = 2**24
+
+
+def get_label_pos(burst_labels, valid_labels):
+    max_label = np.max(burst_labels, axis=2).flatten()
+    min_label = np.min(
+        burst_labels, axis=2, initial=LARGE_NUM, where=burst_labels != 0
+    ).flatten()
+    label_positions = np.zeros_like(valid_labels)
+    N = len(valid_labels)
+    pos = 0
+    i = 0
+    while i < N:
+        if valid_labels[i] >= min_label[pos] and valid_labels[i] <= max_label[pos]:
+            label_positions[i] = pos
+            i += 1
+        else:
+            pos += 1
+    return label_positions
+
+
+class BurstFeatures(BoolSelector):
+    duration: bool = True
+    amplitude: bool = True
+    burst_rate_per_s: bool = True
+    in_burst: bool = True
+
+
+class BurstSettings(NMBaseModel):
+    threshold: float = Field(default=75, ge=0, le=100)
+    time_duration_s: float = Field(default=30, ge=0)
+    frequency_bands: list[str] = ["low_beta", "high_beta", "low_gamma"]
+    burst_features: BurstFeatures = BurstFeatures()
+
+    @field_validator("frequency_bands")
+    def fbands_spaces_to_underscores(cls, frequency_bands):
+        return [f.replace(" ", "_") for f in frequency_bands]
+
+
+class Burst(NMFeature):
+    def __init__(
+        self, settings: "NMSettings", ch_names: Sequence[str], sfreq: float
+    ) -> None:
+        # Test settings
+        for fband_burst in settings.burst_settings.frequency_bands:
+            assert (
+                fband_burst in list(settings.frequency_ranges_hz.keys())
+            ), f"bursting {fband_burst} needs to be defined in settings['frequency_ranges_hz']"
+
+        from py_neuromodulation.nm_filter import MNEFilter
+
+        self.settings = settings.burst_settings
+        self.sfreq = sfreq
+        self.ch_names = ch_names
+        self.segment_length_features_s = settings.segment_length_features_ms / 1000
+        self.samples_overlap = int(
+            self.sfreq
+            * self.segment_length_features_s
+            / settings.sampling_rate_features_hz
+        )
+
+        self.fband_names = settings.burst_settings.frequency_bands
+
+        f_ranges: list[tuple[float, float]] = [
+            (
+                settings.frequency_ranges_hz[fband_name][0],
+                settings.frequency_ranges_hz[fband_name][1],
+            )
+            for fband_name in self.fband_names
+        ]
+
+        self.bandpass_filter = MNEFilter(
+            f_ranges=f_ranges,
+            sfreq=self.sfreq,
+            filter_length=self.sfreq - 1,
+            verbose=False,
+        )
+        self.filter_data = self.bandpass_filter.filter_data
+
+        self.num_max_samples_ring_buffer = int(
+            self.sfreq * self.settings.time_duration_s
+        )
+
+        self.n_channels = len(self.ch_names)
+        self.n_fbands = len(self.fband_names)
+
+        # Create circular buffer array for previous time_duration_s
+        self.data_buffer = np.empty(
+            (self.n_channels, self.n_fbands, 0), dtype=np.float64
+        )
+
+        self.used_features = self.settings.burst_features.get_enabled()
+
+        self.feature_combinations = list(
+            product(
+                enumerate(self.ch_names),
+                enumerate(self.fband_names),
+                self.settings.burst_features.get_enabled(),
+            )
+        )
+
+        # Variables to store results
+        self.burst_duration_mean: np.ndarray
+        self.burst_duration_max: np.ndarray
+        self.burst_amplitude_max: np.ndarray
+        self.burst_amplitude_mean: np.ndarray
+        self.burst_rate_per_s: np.ndarray
+        self.end_in_burst: np.ndarray
+
+        self.STORE_FEAT_DICT: dict[str, Callable] = {
+            "duration": self.store_duration,
+            "amplitude": self.store_amplitude,
+            "burst_rate_per_s": self.store_burst_rate,
+            "in_burst": self.store_in_burst,
+        }
+
+        self.batch = 0
+
+        # Structure matrix for np.ndimage.label
+        # pixels are connected only to adjacent neighbors along the last axis
+        self.label_structure_matrix = np.zeros((3, 3, 3))
+        self.label_structure_matrix[1, 1, :] = 1
+
+    def calc_feature(self, data: np.ndarray) -> dict:
+        from scipy.signal import hilbert
+        from scipy.ndimage import label, sum_labels as label_sum, mean as label_mean
+
+        filtered_data = np.abs(np.array(hilbert(self.filter_data(data))))
+
+        # Update buffer array
+        batch_size = (
+            filtered_data.shape[-1] if self.batch == 0 else self.samples_overlap
+        )
+
+        self.batch += 1
+        self.data_buffer = np.concatenate(
+            (
+                self.data_buffer,
+                filtered_data[:, :, -batch_size:],
+            ),
+            axis=2,
+        )[:, :, -self.num_max_samples_ring_buffer :]
+
+        # Burst threshold is calculated with the percentile defined in the settings
+        # Call low-level numpy function directly, extra checks not needed
+        burst_thr = np_quantile(self.data_buffer, self.settings.threshold / 100)[
+            :, :, None
+        ]  # Add back the extra dimension
+
+        # Get burst locations as a boolean array, True where data is above threshold (i.e. a burst)
+        bursts = filtered_data >= burst_thr
+
+        # Use np.diff to find the places where bursts start and end
+        # Prepend False at the beginning ensures that data never starts on a burst
+        # Floor division to ignore last burst if series ends in a burst (true burst length unknown)
+        num_bursts = (
+            np.sum(np.diff(bursts, axis=2, prepend=False), axis=2) // 2
+        ).astype(np.float64)  # np.astype added to avoid casting error in np.divide
+
+        # Label each burst with a unique id, limiting connectivity to last axis (see scipy.ndimage.label docs for details)
+        burst_labels = label(bursts, self.label_structure_matrix)[0]  # type: ignore # wrong return type in scipy
+
+        # Remove labels of bursts that are at the end of the dataset, and 0
+        labels_at_end = np.concatenate((np.unique(burst_labels[:, :, -1]), (0,)))
+        valid_labels = np.unique(burst_labels)
+        valid_labels = valid_labels[
+            ~np.isin(valid_labels, labels_at_end, assume_unique=True)
+        ]
+
+        # Find (channel, band) coordinates for each valid label and get an array that maps each valid label to its channel/band
+        # Channel band coordinate is flattened to a 1D array of length (n_channels x n_fbands)
+        label_positions = get_label_pos(burst_labels, valid_labels)
+
+        # Now we're ready to calculate features
+
+        if "duration" in self.used_features or "burst_rate_per_s" in self.used_features:
+            # Handle division by zero using np.divide. Where num_bursts is 0, the result is 0
+            self.burst_duration_mean = (
+                np.divide(
+                    np.sum(bursts, axis=2),
+                    num_bursts,
+                    out=np.zeros_like(num_bursts),
+                    where=num_bursts != 0,
+                )
+                / self.sfreq
+            )
+
+        if "duration" in self.used_features:
+            # First get burst length for each valid burst
+            burst_lengths = (
+                label_sum(bursts, burst_labels, index=valid_labels) / self.sfreq
+            )
+
+            # Now the max needs to be calculated per channel/band
+            # For that, loop over channels/bands, get the corresponding burst lengths, and get the max
+            # Give parameter initial=0 so that when there are no bursts, the max is 0
+            # TODO: it might be interesting to write a C function for this
+            duration_max_flat = np.zeros(self.n_channels * self.n_fbands)
+            for idx in range(self.n_channels * self.n_fbands):
+                duration_max_flat[idx] = np.max(
+                    burst_lengths[label_positions == idx], initial=0
+                )
+
+            self.burst_duration_max = duration_max_flat.reshape(
+                (self.n_channels, self.n_fbands)
+            )
+
+        if "amplitude" in self.used_features:
+            # Max amplitude is just the max of the filtered data where there is a burst
+            self.burst_amplitude_max = (filtered_data * bursts).max(axis=2)
+
+            # The mean is actually a mean of means, so we need the mean for each individual burst
+            label_means = label_mean(filtered_data, burst_labels, index=valid_labels)
+            # Now, loop over channels/bands, get the corresponding burst means, and calculate the mean of means
+            # TODO: it might be interesting to write a C function for this
+            amplitude_mean_flat = np.zeros(self.n_channels * self.n_fbands)
+            for idx in range(self.n_channels * self.n_fbands):
+                mask = label_positions == idx
+                amplitude_mean_flat[idx] = (
+                    np.mean(label_means[mask]) if np.any(mask) else 0
+                )
+
+            self.burst_amplitude_mean = amplitude_mean_flat.reshape(
+                (self.n_channels, self.n_fbands)
+            )
+
+        if "burst_rate_per_s" in self.used_features:
+            self.burst_rate_per_s = (
+                self.burst_duration_mean / self.segment_length_features_s
+            )
+
+        if "in_burst" in self.used_features:
+            self.end_in_burst = bursts[:, :, -1]  # End in burst
+
+        # Create dictionary of features which is the correct return format
+        feature_results = {}
+        for (ch_i, ch), (fb_i, fb), feat in self.feature_combinations:
+            self.STORE_FEAT_DICT[feat](feature_results, ch_i, ch, fb_i, fb)
+
+        return feature_results
+
+    def store_duration(
+        self, feature_results: dict, ch_i: int, ch: str, fb_i: int, fb: str
+    ):
+        feature_results[f"{ch}_bursts_{fb}_duration_mean"] = self.burst_duration_mean[
+            ch_i, fb_i
+        ]
+
+        feature_results[f"{ch}_bursts_{fb}_duration_max"] = self.burst_duration_max[
+            ch_i, fb_i
+        ]
+
+    def store_amplitude(
+        self, feature_results: dict, ch_i: int, ch: str, fb_i: int, fb: str
+    ):
+        feature_results[f"{ch}_bursts_{fb}_amplitude_mean"] = self.burst_amplitude_mean[
+            ch_i, fb_i
+        ]
+        feature_results[f"{ch}_bursts_{fb}_amplitude_max"] = self.burst_amplitude_max[
+            ch_i, fb_i
+        ]
+
+    def store_burst_rate(
+        self, feature_results: dict, ch_i: int, ch: str, fb_i: int, fb: str
+    ):
+        feature_results[f"{ch}_bursts_{fb}_burst_rate_per_s"] = self.burst_rate_per_s[
+            ch_i, fb_i
+        ]
+
+    def store_in_burst(
+        self, feature_results: dict, ch_i: int, ch: str, fb_i: int, fb: str
+    ):
+        feature_results[f"{ch}_bursts_{fb}_in_burst"] = self.end_in_burst[ch_i, fb_i]