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

py_neuromodulation/nm_rereference.py

@@ -1,95 +1,97 @@
-"""Re-referencing Module."""
-import numpy as np
-import pandas as pd
-
-
-class ReReferencer:
-    ref_matrix: np.ndarray
-
-    def __init__(
-        self,
-        sfreq: int | float,
-        nm_channels: pd.DataFrame,
-    ) -> None:
-        """Initialize real-time rereference information.
-
-        Parameters
-        ----------
-        sfreq : int | float
-            Sampling frequency. Is not used, only kept for compatibility.
-        nm_channels : Pandas DataFrame
-            Dataframe containing information about rereferencing, as
-            specified in nm_channels.csv.
-
-
-        Raises:
-            ValueError: rereferencing using undefined channel
-            ValueError: rereferencing to same channel
-        """
-        nm_channels = nm_channels[nm_channels["used"] == 1].reset_index(
-            drop=True
-        )
-        # (channels_used,) = np.where((nm_channels.used == 1))
-
-        ch_names = nm_channels["name"].tolist()
-
-        # no re-referencing is being performed when there is a single channel present only
-        if nm_channels.shape[0] in (0, 1):
-            self.ref_matrix = None
-            return
-
-        ch_types = nm_channels["type"]
-        refs = nm_channels["rereference"]
-
-        type_map = {}
-        for ch_type in ch_types.unique():
-            type_map[ch_type] = np.where(
-                (ch_types == ch_type) & (nm_channels["status"] == "good")
-            )[0]
-
-        ref_matrix = np.zeros((len(nm_channels), len(nm_channels)))
-        for ind in range(len(nm_channels)):
-            ref_matrix[ind, ind] = 1
-            # if ind not in channels_used:
-            #    continue
-            ref = refs[ind]
-            if ref.lower() == "none" or pd.isnull(ref):
-                ref_idx = None
-                continue
-            if ref.lower() == "average":
-                ch_type = ch_types[ind]
-                ref_idx = type_map[ch_type][type_map[ch_type] != ind]
-            else:
-                ref_idx = []
-                ref_channels = ref.split("&")
-                for ref_chan in ref_channels:
-                    if ref_chan not in ch_names:
-                        raise ValueError(
-                            "One or more of the reference channels are not"
-                            " part of the recording channels. First missing"
-                            f" channel: {ref_chan}."
-                        )
-                    if ref_chan == ch_names[ind]:
-                        raise ValueError(
-                            "You cannot rereference to the same channel."
-                            f" Channel: {ref_chan}."
-                        )
-                    ref_idx.append(ch_names.index(ref_chan))
-            ref_matrix[ind, ref_idx] = -1 / len(ref_idx)
-        self.ref_matrix = ref_matrix
-
-    def process(self, data: np.ndarray) -> np.ndarray:
-        """Rereference data according to the initialized ReReferencer class.
-
-        Args:
-            data (numpy ndarray) :
-                shape(n_channels, n_samples) - data to be rereferenced.
-
-        Returns:
-            reref_data (numpy ndarray):
-            shape(n_channels, n_samples) - rereferenced data
-        """
-        if self.ref_matrix is not None:
-            return self.ref_matrix @ data
-        else:
-            return data
+"""Re-referencing Module."""
+
+import numpy as np
+import pandas as pd
+
+from py_neuromodulation.nm_preprocessing import NMPreprocessor
+
+
+class ReReferencer(NMPreprocessor):
+    def __init__(
+        self,
+        sfreq: float,
+        nm_channels: pd.DataFrame,
+    ) -> None:
+        """Initialize real-time rereference information.
+
+        Parameters
+        ----------
+        sfreq : float
+            Sampling frequency. Is not used, only kept for compatibility.
+        nm_channels : Pandas DataFrame
+            Dataframe containing information about rereferencing, as
+            specified in nm_channels.csv.
+
+
+        Raises:
+            ValueError: rereferencing using undefined channel
+            ValueError: rereferencing to same channel
+        """
+
+        self.ref_matrix: np.ndarray | None
+
+        nm_channels = nm_channels[nm_channels["used"] == 1].reset_index(drop=True)
+        # (channels_used,) = np.where((nm_channels.used == 1))
+
+        ch_names = nm_channels["name"].tolist()
+
+        # no re-referencing is being performed when there is a single channel present only
+        if nm_channels.shape[0] in (0, 1):
+            self.ref_matrix = None
+            return
+
+        ch_types = nm_channels["type"]
+        refs = nm_channels["rereference"]
+
+        type_map = {}
+        for ch_type in ch_types.unique():
+            type_map[ch_type] = np.where(
+                (ch_types == ch_type) & (nm_channels["status"] == "good")
+            )[0]
+
+        ref_matrix = np.zeros((len(nm_channels), len(nm_channels)))
+        for ind in range(len(nm_channels)):
+            ref_matrix[ind, ind] = 1
+            # if ind not in channels_used:
+            #    continue
+            ref = refs[ind]
+            if ref.lower() == "none" or pd.isnull(ref):
+                ref_idx = None
+                continue
+            if ref.lower() == "average":
+                ch_type = ch_types[ind]
+                ref_idx = type_map[ch_type][type_map[ch_type] != ind]
+            else:
+                ref_idx = []
+                ref_channels = ref.split("&")
+                for ref_chan in ref_channels:
+                    if ref_chan not in ch_names:
+                        raise ValueError(
+                            "One or more of the reference channels are not"
+                            " part of the recording channels. First missing"
+                            f" channel: {ref_chan}."
+                        )
+                    if ref_chan == ch_names[ind]:
+                        raise ValueError(
+                            "You cannot rereference to the same channel."
+                            f" Channel: {ref_chan}."
+                        )
+                    ref_idx.append(ch_names.index(ref_chan))
+            ref_matrix[ind, ref_idx] = -1 / len(ref_idx)
+        self.ref_matrix = ref_matrix
+
+    def process(self, data: np.ndarray) -> np.ndarray:
+        """Rereference data according to the initialized ReReferencer class.
+
+        Args:
+            data (numpy ndarray) :
+                shape(n_channels, n_samples) - data to be rereferenced.
+
+        Returns:
+            reref_data (numpy ndarray):
+                shape(n_channels, n_samples) - rereferenced data
+        """
+        if self.ref_matrix is not None:
+            return self.ref_matrix @ data
+        else:
+            return data

py_neuromodulation/nm_resample.py

@@ -1,50 +1,59 @@
-"""Module for resampling."""
-import mne
-import numpy as np
-
-
-class Resampler:
-    """Resample data.
-
-    Parameters
-    ----------
-    sfreq : int | float
-        Original sampling frequency.
-
-    Attributes
-    ----------
-    up: float
-        Factor to upsample by.
-    """
-
-    def __init__(
-        self,
-        sfreq: int | float,
-        resample_freq_hz: int | float,
-    ) -> None:
-
-        assert isinstance(resample_freq_hz, (float, int))
-
-        self.sfreq_new: int | float = resample_freq_hz
-        ratio = float(self.sfreq_new / sfreq)
-        if ratio == 1.0:
-            self.up = 0.0
-        else:
-            self.up = ratio
-
-    def process(self, data: np.ndarray) -> np.ndarray:
-        """Resample raw data using mne.filter.resample.
-
-        Parameters
-        ----------
-        data : np.ndarray
-            Data to resample
-
-        Returns
-        -------
-        np.ndarray
-            Resampled data
-        """
-        if not self.up:
-            return data
-        return mne.filter.resample(data.astype(np.float64), up=self.up, down=1.0)
+"""Module for resampling."""
+
+import numpy as np
+from py_neuromodulation.nm_types import NMBaseModel, Field
+
+
+from py_neuromodulation.nm_preprocessing import NMPreprocessor
+
+
+class ResamplerSettings(NMBaseModel):
+    resample_freq_hz: float = Field(default=1000, gt=0)
+
+
+class Resampler(NMPreprocessor):
+    """Resample data.
+
+    Parameters
+    ----------
+    sfreq : float
+        Original sampling frequency.
+
+    Attributes
+    ----------
+    up: float
+        Factor to upsample by.
+    """
+
+    def __init__(
+        self,
+        sfreq: float,
+        resample_freq_hz: float,
+    ) -> None:
+        self.settings = ResamplerSettings(resample_freq_hz=resample_freq_hz)
+
+        ratio = float(resample_freq_hz / sfreq)
+        if ratio == 1.0:
+            self.up = 0.0
+        else:
+            self.up = ratio
+
+    def process(self, data: np.ndarray) -> np.ndarray:
+        """Resample raw data using mne.filter.resample.
+
+        Parameters
+        ----------
+        data : np.ndarray
+            Data to resample
+
+        Returns
+        -------
+        np.ndarray
+            Resampled data
+        """
+        if not self.up:
+            return data
+
+        from mne.filter import resample
+
+        return resample(data.astype(np.float64), up=self.up, down=1.0)