ezmsg-sigproc 1.7.0__py3-none-any.whl → 2.10.0__py3-none-any.whl

ezmsg/sigproc/__version__.py

@@ -1,16 +1,34 @@
-# file generated by setuptools_scm
+# file generated by setuptools-scm
 # don't change, don't track in version control
+
+__all__ = [
+    "__version__",
+    "__version_tuple__",
+    "version",
+    "version_tuple",
+    "__commit_id__",
+    "commit_id",
+]
+
 TYPE_CHECKING = False
 if TYPE_CHECKING:
-    from typing import Tuple, Union
+    from typing import Tuple
+    from typing import Union
+
     VERSION_TUPLE = Tuple[Union[int, str], ...]
+    COMMIT_ID = Union[str, None]
 else:
     VERSION_TUPLE = object
+    COMMIT_ID = object
 
 version: str
 __version__: str
 __version_tuple__: VERSION_TUPLE
 version_tuple: VERSION_TUPLE
+commit_id: COMMIT_ID
+__commit_id__: COMMIT_ID
+
+__version__ = version = '2.10.0'
+__version_tuple__ = version_tuple = (2, 10, 0)
 
-__version__ = version = '1.7.0'
-__version_tuple__ = version_tuple = (1, 7, 0)
+__commit_id__ = commit_id = None

ezmsg/sigproc/activation.py

@@ -1,14 +1,10 @@
-import typing
-
-import numpy as np
-import scipy.special
 import ezmsg.core as ez
+import scipy.special
+from ezmsg.baseproc import BaseTransformer, BaseTransformerUnit
 from ezmsg.util.messages.axisarray import AxisArray
 from ezmsg.util.messages.util import replace
-from ezmsg.util.generator import consumer
 
 from .spectral import OptionsEnum
-from .base import GenAxisArray
 
 
 class ActivationFunction(OptionsEnum):
@@ -39,10 +35,35 @@ ACTIVATIONS = {
 }
 
 
-@consumer
+class ActivationSettings(ez.Settings):
+    function: str | ActivationFunction = ActivationFunction.NONE
+    """An enum value from ActivationFunction or a string representing the activation function.
+         Possible values are: SIGMOID, EXPIT, LOGIT, LOGEXPIT, "sigmoid", "expit", "logit", "log_expit".
+         SIGMOID and EXPIT are equivalent. See :obj:`scipy.special.expit` for more details."""
+
+
+class ActivationTransformer(BaseTransformer[ActivationSettings, AxisArray, AxisArray]):
+    def _process(self, message: AxisArray) -> AxisArray:
+        if type(self.settings.function) is ActivationFunction:
+            func = ACTIVATIONS[self.settings.function]
+        else:
+            # str type handling
+            function = self.settings.function.lower()
+            if function not in ActivationFunction.options():
+                raise ValueError(f"Unrecognized activation function {function}. Must be one of {ACTIVATIONS.keys()}")
+            function = list(ACTIVATIONS.keys())[ActivationFunction.options().index(function)]
+            func = ACTIVATIONS[function]
+
+        return replace(message, data=func(message.data))
+
+
+class Activation(BaseTransformerUnit[ActivationSettings, AxisArray, AxisArray, ActivationTransformer]):
+    SETTINGS = ActivationSettings
+
+
 def activation(
     function: str | ActivationFunction,
-) -> typing.Generator[AxisArray, AxisArray, None]:
+) -> ActivationTransformer:
     """
     Transform the data with a simple activation function.
 
@@ -51,37 +72,7 @@ def activation(
          Possible values are: SIGMOID, EXPIT, LOGIT, LOGEXPIT, "sigmoid", "expit", "logit", "log_expit".
          SIGMOID and EXPIT are equivalent. See :obj:`scipy.special.expit` for more details.
 
-    Returns: A primed generator that, when passed an input message via `.send(msg)`, yields an AxisArray
-     with the data payload containing a transformed version of the input data.
+    Returns: :obj:`ActivationTransformer`
 
     """
-    if type(function) is ActivationFunction:
-        func = ACTIVATIONS[function]
-    else:
-        # str type. There's probably an easier way to support either enum or str argument. Oh well this works.
-        function: str = function.lower()
-        if function not in ActivationFunction.options():
-            raise ValueError(
-                f"Unrecognized activation function {function}. Must be one of {ACTIVATIONS.keys()}"
-            )
-        function = list(ACTIVATIONS.keys())[
-            ActivationFunction.options().index(function)
-        ]
-        func = ACTIVATIONS[function]
-
-    msg_out = AxisArray(np.array([]), dims=[""])
-
-    while True:
-        msg_in: AxisArray = yield msg_out
-        msg_out = replace(msg_in, data=func(msg_in.data))
-
-
-class ActivationSettings(ez.Settings):
-    function: str = ActivationFunction.NONE
-
-
-class Activation(GenAxisArray):
-    SETTINGS = ActivationSettings
-
-    def construct_generator(self):
-        self.STATE.gen = activation(function=self.SETTINGS.function)
+    return ActivationTransformer(ActivationSettings(function=function))

ezmsg/sigproc/adaptive_lattice_notch.py

@@ -0,0 +1,212 @@
+import ezmsg.core as ez
+import numpy as np
+import numpy.typing as npt
+import scipy.signal
+from ezmsg.baseproc import BaseStatefulTransformer, processor_state
+from ezmsg.util.messages.axisarray import AxisArray, CoordinateAxis
+from ezmsg.util.messages.util import replace
+
+
+class AdaptiveLatticeNotchFilterSettings(ez.Settings):
+    """Settings for the Adaptive Lattice Notch Filter."""
+
+    gamma: float = 0.995
+    """Pole-zero contraction factor"""
+    mu: float = 0.99
+    """Smoothing factor"""
+    eta: float = 0.99
+    """Forgetting factor"""
+    axis: str = "time"
+    """Axis to apply filter to"""
+    init_notch_freq: float | None = None
+    """Initial notch frequency. Should be < nyquist."""
+    chunkwise: bool = False
+    """Speed up processing by updating the target freq once per chunk only."""
+
+
+@processor_state
+class AdaptiveLatticeNotchFilterState:
+    """State for the Adaptive Lattice Notch Filter."""
+
+    s_history: npt.NDArray | None = None
+    """Historical `s` values for the adaptive filter."""
+
+    p: npt.NDArray | None = None
+    """Accumulated product for reflection coefficient update"""
+
+    q: npt.NDArray | None = None
+    """Accumulated product for reflection coefficient update"""
+
+    k1: npt.NDArray | None = None
+    """Reflection coefficient"""
+
+    freq_template: CoordinateAxis | None = None
+    """Template for the frequency axis on the output"""
+
+    zi: npt.NDArray | None = None
+    """Initial conditions for the filter, updated after every chunk"""
+
+
+class AdaptiveLatticeNotchFilterTransformer(
+    BaseStatefulTransformer[
+        AdaptiveLatticeNotchFilterSettings,
+        AxisArray,
+        AxisArray,
+        AdaptiveLatticeNotchFilterState,
+    ]
+):
+    """
+    Adaptive Lattice Notch Filter implementation as a stateful transformer.
+
+    https://biomedical-engineering-online.biomedcentral.com/articles/10.1186/1475-925X-13-170
+
+    The filter automatically tracks and removes frequency components from the input signal.
+    It outputs the estimated frequency (in Hz) and the filtered sample.
+    """
+
+    def _hash_message(self, message: AxisArray) -> int:
+        ax_idx = message.get_axis_idx(self.settings.axis)
+        sample_shape = message.data.shape[:ax_idx] + message.data.shape[ax_idx + 1 :]
+        return hash((message.key, message.axes[self.settings.axis].gain, sample_shape))
+
+    def _reset_state(self, message: AxisArray) -> None:
+        ax_idx = message.get_axis_idx(self.settings.axis)
+        sample_shape = message.data.shape[:ax_idx] + message.data.shape[ax_idx + 1 :]
+
+        fs = 1 / message.axes[self.settings.axis].gain
+        init_f = (
+            self.settings.init_notch_freq if self.settings.init_notch_freq is not None else 0.07178314656435313 * fs
+        )
+        init_omega = init_f * (2 * np.pi) / fs
+        init_k1 = -np.cos(init_omega)
+
+        """Reset filter state to initial values."""
+        self._state = AdaptiveLatticeNotchFilterState()
+        self._state.s_history = np.zeros((2,) + sample_shape, dtype=float)
+        self._state.p = np.zeros(sample_shape, dtype=float)
+        self._state.q = np.zeros(sample_shape, dtype=float)
+        self._state.k1 = init_k1 + np.zeros(sample_shape, dtype=float)
+        self._state.freq_template = CoordinateAxis(
+            data=np.zeros((0,) + sample_shape, dtype=float),
+            dims=[self.settings.axis] + message.dims[:ax_idx] + message.dims[ax_idx + 1 :],
+            unit="Hz",
+        )
+
+        # Initialize the initial conditions for the filter
+        self._state.zi = np.zeros((2, np.prod(sample_shape)), dtype=float)
+        # Note: we could calculate it properly, but as long as we are initializing s_history with zeros,
+        #  it will always be zero.
+        # a = [1, init_k1 * (1 + self.settings.gamma), self.settings.gamma]
+        # b = [1]
+        # s = np.reshape(self._state.s_history, (2, -1))
+        # for feat_ix in range(np.prod(sample_shape)):
+        #     self._state.zi[:, feat_ix] = scipy.signal.lfiltic(b, a, s[::-1, feat_ix], x=None)
+
+    def _process(self, message: AxisArray) -> AxisArray:
+        x_data = message.data
+        ax_idx = message.get_axis_idx(self.settings.axis)
+
+        # TODO: Time should be moved to -1th axis, not the 0th axis
+        if message.dims[0] != self.settings.axis:
+            x_data = np.moveaxis(x_data, ax_idx, 0)
+
+        # Access settings once
+        gamma = self.settings.gamma
+        eta = self.settings.eta
+        mu = self.settings.mu
+        fs = 1 / message.axes[self.settings.axis].gain
+
+        # Pre-compute constants
+        one_minus_eta = 1 - eta
+        one_minus_mu = 1 - mu
+        gamma_plus_1 = 1 + gamma
+        omega_scale = fs / (2 * np.pi)
+
+        # For the lattice filter with constant k1:
+        # s_n = x_n - k1*(1+gamma)*s_n_1 - gamma*s_n_2
+        # This is equivalent to an IIR filter with b=1, a=[1, k1*(1+gamma), gamma]
+
+        # For the output filter:
+        # y_n = s_n + 2*k1*s_n_1 + s_n_2
+        # We can treat this as a direct-form FIR filter applied to s_out
+
+        if self.settings.chunkwise:
+            # Process each chunk using current filter parameters
+            # Reshape input and prepare output arrays
+            _s = self._state.s_history.reshape((2, -1))
+            _x = x_data.reshape((x_data.shape[0], -1))
+            s_n = np.zeros_like(_x)
+            y_out = np.zeros_like(_x)
+
+            # Apply static filter for each feature dimension
+            for ix, k in enumerate(self._state.k1.flatten()):
+                # Filter to get s_n (notch filter state)
+                a_s = [1, k * gamma_plus_1, gamma]
+                s_n[:, ix], self._state.zi[:, ix] = scipy.signal.lfilter([1], a_s, _x[:, ix], zi=self._state.zi[:, ix])
+
+                # Apply output filter to get y_out
+                b_y = [1, 2 * k, 1]
+                y_out[:, ix] = scipy.signal.lfilter(b_y, [1], s_n[:, ix])
+
+            # Update filter parameters using final values from the chunk
+            s_n_reshaped = s_n.reshape((s_n.shape[0],) + x_data.shape[1:])
+            s_final = s_n_reshaped[-1]  # Current s_n
+            s_final_1 = s_n_reshaped[-2]  # s_n_1
+            s_final_2 = s_n_reshaped[-3] if len(s_n_reshaped) > 2 else self._state.s_history[0]  # s_n_2
+
+            # Update p and q using final values
+            self._state.p = eta * self._state.p + one_minus_eta * (s_final_1 * (s_final + s_final_2))
+            self._state.q = eta * self._state.q + one_minus_eta * (2 * (s_final_1 * s_final_1))
+
+            # Update reflection coefficient
+            new_k1 = -self._state.p / (self._state.q + 1e-8)  # Avoid division by zero
+            new_k1 = np.clip(new_k1, -1, 1)  # Clip to prevent instability
+            self._state.k1 = mu * self._state.k1 + one_minus_mu * new_k1  # Smoothed
+
+            # Calculate frequency from updated k1 value
+            omega_n = np.arccos(-self._state.k1)
+            freq = omega_n * omega_scale
+            freq_out = np.full_like(x_data.reshape(x_data.shape), freq)
+
+            # Update s_history for next chunk
+            self._state.s_history = s_n_reshaped[-2:].reshape((2,) + x_data.shape[1:])
+
+            # Reshape y_out back to original dimensions
+            y_out = y_out.reshape(x_data.shape)
+
+        else:
+            # Perform filtering, sample-by-sample
+            y_out = np.zeros_like(x_data)
+            freq_out = np.zeros_like(x_data)
+            for sample_ix, x_n in enumerate(x_data):
+                s_n_1 = self._state.s_history[-1]
+                s_n_2 = self._state.s_history[-2]
+
+                s_n = x_n - self._state.k1 * gamma_plus_1 * s_n_1 - gamma * s_n_2
+                y_out[sample_ix] = s_n + 2 * self._state.k1 * s_n_1 + s_n_2
+
+                # Update filter parameters
+                self._state.p = eta * self._state.p + one_minus_eta * (s_n_1 * (s_n + s_n_2))
+                self._state.q = eta * self._state.q + one_minus_eta * (2 * (s_n_1 * s_n_1))
+
+                # Update reflection coefficient
+                new_k1 = -self._state.p / (self._state.q + 1e-8)  # Avoid division by zero
+                new_k1 = np.clip(new_k1, -1, 1)  # Clip to prevent instability
+                self._state.k1 = mu * self._state.k1 + one_minus_mu * new_k1  # Smoothed
+
+                # Compute normalized angular frequency using equation 13 from the paper
+                omega_n = np.arccos(-self._state.k1)
+                freq_out[sample_ix] = omega_n * omega_scale  # As Hz
+
+                # Update for next iteration
+                self._state.s_history[-2] = s_n_1
+                self._state.s_history[-1] = s_n
+
+        return replace(
+            message,
+            data=y_out,
+            axes={
+                **message.axes,
+                "freq": replace(self._state.freq_template, data=freq_out),
+            },
+        )