py-neuromodulation 0.0.4__py3-none-any.whl → 0.0.5__py3-none-any.whl

py_neuromodulation/nm_projection.py

@@ -1,394 +1,370 @@
-from typing import Optional, Union
-
-import numpy as np
-import pandas as pd
-
-from py_neuromodulation import nm_plots
-
-
-class Projection:
-    def __init__(
-        self,
-        settings: dict,
-        grid_cortex: pd.DataFrame,
-        grid_subcortex: pd.DataFrame,
-        coords: dict,
-        nm_channels: pd.DataFrame,
-        plot_projection: bool = False,
-    ) -> None:
-
-        self.test_settings(settings)
-
-        self.grid_cortex = grid_cortex
-        self.grid_subcortex = grid_subcortex
-        self.coords = coords
-        self.nm_channels = nm_channels
-        self.project_cortex = settings["postprocessing"]["project_cortex"]
-        self.project_subcortex = settings["postprocessing"][
-            "project_subcortex"
-        ]
-        self.max_dist_cortex = settings["project_cortex_settings"][
-            "max_dist_mm"
-        ]
-        self.max_dist_subcortex = settings["project_subcortex_settings"][
-            "max_dist_mm"
-        ]
-        self.ecog_channels: Optional[list] = None
-        self.lfp_channels: Optional[list] = None
-
-        self.idx_chs_ecog: list = (
-            []
-        )  # feature series indexes for ecog channels
-        self.names_chs_ecog: list = []  # feature series name of ecog features
-        self.idx_chs_lfp: list = []  # feature series indexes for lfp channels
-        self.names_chs_lfp: list = []  # feature series name of lfp features
-        self.feature_names: Optional[list] = None
-        self.initialized: bool = False
-
-        self.remove_not_used_ch_from_coords()  # remove beforehand non used channels from coords
-
-        if len(self.coords["cortex_left"]["positions"]) == 0:
-            self.sess_right = True
-            self.ecog_strip = self.coords["cortex_right"]["positions"]
-            self.ecog_strip_names = self.coords["cortex_right"]["ch_names"]
-        elif len(self.coords["cortex_right"]["positions"]) == 0:
-            self.sess_right = False
-            self.ecog_strip = self.coords["cortex_left"]["positions"]
-            self.ecog_strip_names = self.coords["cortex_left"]["ch_names"]
-
-        if (
-            self.sess_right is True
-            and len(self.coords["subcortex_right"]["positions"]) > 0
-        ):
-            self.lfp_elec = self.coords["subcortex_right"]["positions"]
-            self.lfp_elec_names = self.coords["subcortex_right"]["ch_names"]
-        elif (
-            self.sess_right is False
-            and len(self.coords["subcortex_left"]["positions"]) > 0
-        ):
-            self.lfp_elec = self.coords["subcortex_left"]["positions"]
-            self.lfp_elec_names = self.coords["subcortex_left"]["ch_names"]
-
-        self._initialize_channels()
-
-        (
-            self.proj_matrix_cortex,
-            self.proj_matrix_subcortex,
-        ) = self.calc_projection_matrix()
-
-        if self.project_cortex:
-            self.active_cortex_gridpoints = np.nonzero(
-                self.proj_matrix_cortex.sum(axis=1)
-            )[0]
-        if self.project_subcortex:
-            self.active_subcortex_gridpoints = np.nonzero(
-                self.proj_matrix_subcortex.sum(axis=1)
-            )[0]
-
-        if plot_projection is True:
-            nmplotter = nm_plots.NM_Plot(
-                ecog_strip=self.ecog_strip,
-                grid_cortex=self.grid_cortex.to_numpy(),
-                grid_subcortex=self.grid_subcortex.to_numpy(),
-                sess_right=self.sess_right,
-                proj_matrix_cortex=self.proj_matrix_cortex,
-            )
-            nmplotter.plot_cortex()
-
-    @staticmethod
-    def test_settings(s: dict):
-        if s["postprocessing"]["project_cortex"] is True:
-            assert isinstance(
-                s["project_cortex_settings"]["max_dist_mm"], (float, int)
-            )
-        if s["postprocessing"]["project_subcortex"] is True:
-            assert isinstance(
-                s["project_subcortex_settings"]["max_dist_mm"], (float, int)
-            )
-
-    def remove_not_used_ch_from_coords(self):
-        ch_not_used = self.nm_channels.query(
-            '(used==0) or (status=="bad")'
-        ).name
-        if len(ch_not_used) > 0:
-            for ch in ch_not_used:
-                for key_ in self.coords:
-                    for idx, ch_coords in enumerate(
-                        self.coords[key_]["ch_names"]
-                    ):
-                        if ch.startswith(ch_coords):
-                            # delete index
-                            self.coords[key_]["positions"] = np.delete(
-                                self.coords[key_]["positions"], idx, axis=0
-                            )
-                            self.coords[key_]["ch_names"].remove(ch)
-
-    def calc_proj_matrix(
-        self,
-        max_dist: Union[int, float],
-        grid: np.ndarray,
-        coord_array: np.ndarray,
-    ) -> np.ndarray:
-        """Calculate projection matrix."""
-
-        channels = coord_array.shape[0]
-        distance_matrix = np.zeros([grid.shape[1], channels])
-
-        for project_point in range(grid.shape[1]):
-            for channel in range(coord_array.shape[0]):
-                distance_matrix[project_point, channel] = np.linalg.norm(
-                    grid[:, project_point] - coord_array[channel, :]
-                )
-
-        proj_matrix = np.zeros(distance_matrix.shape)
-        for grid_point in range(distance_matrix.shape[0]):
-            used_channels = np.where(
-                distance_matrix[grid_point, :] < max_dist
-            )[0]
-
-            rec_distances = distance_matrix[grid_point, used_channels]
-            sum_distances = np.sum(1 / rec_distances)
-
-            for _, used_channel in enumerate(used_channels):
-                proj_matrix[grid_point, used_channel] = (
-                    1 / distance_matrix[grid_point, used_channel]
-                ) / sum_distances
-        return proj_matrix
-
-    def calc_projection_matrix(self):
-        """Calculates a projection matrix based on the used coordinate arrays
-
-        Returns
-        -------
-        proj_matrix_cortex (np.array)
-            cortical projection_matrix in shape [grid contacts, channel contact] defaults to None
-        proj_matrix_subcortex (np.array)
-            subcortical projection_matrix in shape [grid contacts, channel contact] defaults to None
-        """        
-
-        proj_matrix_run = np.empty(2, dtype=object)
-
-        if self.sess_right is True:
-
-            if self.project_cortex:
-                cortex_grid_right = np.copy(self.grid_cortex)
-                cortex_grid_right[:, 0] = cortex_grid_right[:, 0] * -1
-                self.cortex_grid_right = np.array(cortex_grid_right.T)
-            else:
-                self.cortex_grid_right = None
-
-            if self.project_subcortex:
-                subcortex_grid_right = np.copy(self.grid_subcortex)
-                subcortex_grid_right[:, 0] = subcortex_grid_right[:, 0] * -1
-                self.subcortex_grid_right = np.array(subcortex_grid_right).T
-            else:
-                self.subcortex_grid_right = None
-
-            grid_session = [self.cortex_grid_right, self.subcortex_grid_right]
-
-        else:
-            if self.project_cortex:
-                self.cortex_grid_left = np.array(self.grid_cortex.T)
-            else:
-                self.cortex_grid_left = None
-            if self.project_subcortex:
-                self.subcortex_grid_left = np.array(self.grid_subcortex.T)
-            else:
-                self.subcortex_grid_left = None
-
-            grid_session = [self.cortex_grid_left, self.subcortex_grid_left]
-
-        coord_array = [
-            self.ecog_strip if grid_session[0] is not None else None,
-            self.lfp_elec if grid_session[1] is not None else None,
-        ]
-
-        for loc_, grid in enumerate(grid_session):
-            if loc_ == 0:  # cortex
-                max_dist = self.max_dist_cortex
-            elif loc_ == 1:  # subcortex
-                max_dist = self.max_dist_subcortex
-
-            if grid_session[loc_] is not None:
-                proj_matrix_run[loc_] = self.calc_proj_matrix(
-                    max_dist, grid, coord_array[loc_]
-                )
-
-        return proj_matrix_run[0], proj_matrix_run[1]  # cortex, subcortex
-
-    def _initialize_channels(self) -> None:
-        """Initialize channel names via nm_channel new_name column"""
-
-        if self.project_cortex:
-            self.ecog_channels = self.nm_channels.query(
-                '(type=="ecog") and (used == 1) and (status=="good")'
-            ).name.to_list()
-
-            chs_ecog = self.ecog_channels.copy()
-            for ecog_channel in chs_ecog:
-                if ecog_channel not in self.ecog_strip_names:
-                    self.ecog_channels.remove(ecog_channel)
-            # write ecog_channels to be new_name
-            self.ecog_channels = list(
-                self.nm_channels.query("name == @self.ecog_channels").new_name
-            )
-
-        if self.project_subcortex:
-            self.lfp_channels = self.nm_channels.query(
-                '(type=="lfp" or type=="seeg" or type=="dbs") \
-              and (used == 1) and (status=="good")'
-            ).name.to_list()
-            # project only channels that are in the coords
-            # this also deletes channels of the other hemisphere
-            chs_lfp = self.lfp_channels.copy()
-            for lfp_channel in chs_lfp:
-                if lfp_channel not in self.lfp_elec_names:
-                    self.lfp_channels.remove(lfp_channel)
-            # write lfp_channels to be new_name
-            self.lfp_channels = list(
-                self.nm_channels.query("name == @self.lfp_channels").new_name
-            )
-
-    def init_projection_run(self, feature_series: pd.Series) -> None:
-        """Initialize indexes for respective channels in feature series computed by nm_features.py"""
-        #  here it is assumed that only one hemisphere is recorded at a time!
-        if self.project_cortex:
-            for ecog_channel in self.ecog_channels:
-                self.idx_chs_ecog.append(
-                    [
-                        ch_idx
-                        for ch_idx, ch in enumerate(feature_series.keys())
-                        if ch.startswith(ecog_channel)
-                    ]
-                )
-                self.names_chs_ecog.append(
-                    [
-                        ch
-                        for _, ch in enumerate(feature_series.keys())
-                        if ch.startswith(ecog_channel)
-                    ]
-                )
-            if self.names_chs_ecog:
-                # get feature_names; given by ECoG sequency of features
-                self.feature_names = [
-                    feature_name[len(self.ecog_channels[0]) + 1 :]
-                    for feature_name in self.names_chs_ecog[0]
-                ]
-
-        if self.project_subcortex:
-            # for lfp_channels select here only the ones from the correct hemisphere!
-            for lfp_channel in self.lfp_channels:
-                self.idx_chs_lfp.append(
-                    [
-                        ch_idx
-                        for ch_idx, ch in enumerate(feature_series.keys())
-                        if ch.startswith(lfp_channel)
-                    ]
-                )
-                self.names_chs_lfp.append(
-                    [
-                        ch
-                        for _, ch in enumerate(feature_series.keys())
-                        if ch.startswith(lfp_channel)
-                    ]
-                )
-            if not self.feature_names and self.names_chs_lfp:
-                # get feature_names; given by LFP sequency of features
-                self.feature_names = [
-                    feature_name[len(self.lfp_channels[0]) + 1 :]
-                    for feature_name in self.names_chs_lfp[0]
-                ]
-
-        self.initialized = True
-
-    def project_features(self, feature_series: pd.Series) -> pd.Series:
-        """Project data, given idx_chs_ecog/stn"""
-
-        if not self.initialized:
-            self.init_projection_run(feature_series=feature_series)
-
-        dat_cortex = (
-            np.vstack(
-                [
-                    feature_series.iloc[idx_ch].values
-                    for idx_ch in self.idx_chs_ecog
-                ]
-            )
-            if self.project_cortex
-            else None
-        )
-
-        dat_subcortex = (
-            np.vstack(
-                [
-                    feature_series.iloc[idx_ch].values
-                    for idx_ch in self.idx_chs_lfp
-                ]
-            )
-            if self.project_subcortex
-            else None
-        )
-
-        # project data
-        (
-            proj_cortex_array,
-            proj_subcortex_array,
-        ) = self.get_projected_cortex_subcortex_data(dat_cortex, dat_subcortex)
-
-        features_new = {}
-        # proj_cortex_array has shape grid_points x feature_number
-        if self.project_cortex:
-
-            features_new = features_new | {
-                "gridcortex_"
-                + str(act_grid_point)
-                + "_"
-                + feature_name: proj_cortex_array[act_grid_point, feature_idx]
-                for feature_idx, feature_name in enumerate(self.feature_names)
-                for act_grid_point in self.active_cortex_gridpoints
-            }
-        if self.project_subcortex:
-            features_new = features_new | {
-                "gridsubcortex_"
-                + str(act_grid_point)
-                + "_"
-                + feature_name: proj_subcortex_array[
-                    act_grid_point, feature_idx
-                ]
-                for feature_idx, feature_name in enumerate(self.feature_names)
-                for act_grid_point in self.active_subcortex_gridpoints
-            }
-        feature_series = pd.concat([feature_series, pd.Series(features_new)])
-
-        return feature_series
-
-    def get_projected_cortex_subcortex_data(
-        self,
-        dat_cortex: Optional[np.ndarray] = None,
-        dat_subcortex: Optional[np.ndarray] = None,
-    ) -> tuple[Optional[np.ndarray], Optional[np.ndarray]]:
-        """Project cortical and subcortical data to predefined projection matrices
-
-        Parameters
-        ----------
-        dat_cortex : np.ndarray, optional
-            cortical features, by default None
-        dat_subcortex : np.ndarray, optional
-            subcortical features, by default None
-
-        Returns
-        -------
-        proj_cortex : np.ndarray
-            projected cortical features, by detault None
-        proj_subcortex : np.ndarray
-            projected subcortical features, by detault None
-        """
-        proj_cortex = None
-        proj_subcortex = None
-
-        if dat_cortex is not None:
-            proj_cortex = self.proj_matrix_cortex @ dat_cortex
-        if dat_subcortex is not None:
-            proj_subcortex = self.proj_matrix_subcortex @ dat_subcortex
-
-        return proj_cortex, proj_subcortex
+import numpy as np
+import pandas as pd
+from pydantic import Field
+from py_neuromodulation.nm_types import NMBaseModel
+from typing import TYPE_CHECKING
+
+if TYPE_CHECKING:
+    from py_neuromodulation.nm_settings import NMSettings
+
+
+class ProjectionSettings(NMBaseModel):
+    max_dist_mm: float = Field(default=20.0, gt=0.0)
+
+
+class Projection:
+    def __init__(
+        self,
+        settings: "NMSettings",
+        grid_cortex: pd.DataFrame,
+        grid_subcortex: pd.DataFrame,
+        coords: dict,
+        nm_channels: pd.DataFrame,
+        plot_projection: bool = False,
+    ) -> None:
+        self.grid_cortex = grid_cortex
+        self.grid_subcortex = grid_subcortex
+        self.coords = coords
+        self.nm_channels = nm_channels
+        self.project_cortex = settings.postprocessing.project_cortex
+        self.project_subcortex = settings.postprocessing.project_subcortex
+        self.max_dist_cortex = settings.project_cortex_settings.max_dist_mm
+        self.max_dist_subcortex = settings.project_subcortex_settings.max_dist_mm
+        self.ecog_channels: list  # None case never handled, no need for default value
+        self.lfp_channels: list  # None case never handled, no need for default value
+
+        self.idx_chs_ecog: list = []  # feature series indexes for ecog channels
+        self.names_chs_ecog: list = []  # feature series name of ecog features
+        self.idx_chs_lfp: list = []  # feature series indexes for lfp channels
+        self.names_chs_lfp: list = []  # feature series name of lfp features
+        self.feature_names: list | None = None
+        self.initialized: bool = False
+
+        self.remove_not_used_ch_from_coords()  # remove beforehand non used channels from coords
+
+        if len(self.coords["cortex_left"]["positions"]) == 0:
+            self.sess_right = True
+            self.ecog_strip = self.coords["cortex_right"]["positions"]
+            self.ecog_strip_names = self.coords["cortex_right"]["ch_names"]
+        elif len(self.coords["cortex_right"]["positions"]) == 0:
+            self.sess_right = False
+            self.ecog_strip = self.coords["cortex_left"]["positions"]
+            self.ecog_strip_names = self.coords["cortex_left"]["ch_names"]
+
+        if self.sess_right and len(self.coords["subcortex_right"]["positions"]) > 0:
+            self.lfp_elec = self.coords["subcortex_right"]["positions"]
+            self.lfp_elec_names = self.coords["subcortex_right"]["ch_names"]
+        elif (
+            self.sess_right is False
+            and len(self.coords["subcortex_left"]["positions"]) > 0
+        ):
+            self.lfp_elec = self.coords["subcortex_left"]["positions"]
+            self.lfp_elec_names = self.coords["subcortex_left"]["ch_names"]
+
+        self._initialize_channels()
+
+        (
+            self.proj_matrix_cortex,
+            self.proj_matrix_subcortex,
+        ) = self.calc_projection_matrix()
+
+        if self.project_cortex:
+            self.active_cortex_gridpoints = np.nonzero(
+                self.proj_matrix_cortex.sum(axis=1)
+            )[0]
+        if self.project_subcortex:
+            self.active_subcortex_gridpoints = np.nonzero(
+                self.proj_matrix_subcortex.sum(axis=1)
+            )[0]
+
+        if plot_projection:
+            from py_neuromodulation.nm_plots import NM_Plot
+
+            nmplotter = NM_Plot(
+                ecog_strip=self.ecog_strip,
+                grid_cortex=self.grid_cortex.to_numpy(),
+                grid_subcortex=self.grid_subcortex.to_numpy(),
+                sess_right=self.sess_right,
+                proj_matrix_cortex=self.proj_matrix_cortex,
+            )
+            nmplotter.plot_cortex()
+
+    def remove_not_used_ch_from_coords(self):
+        ch_not_used = self.nm_channels.query('(used==0) or (status=="bad")').name
+        if len(ch_not_used) > 0:
+            for ch in ch_not_used:
+                for key_ in self.coords:
+                    for idx, ch_coords in enumerate(self.coords[key_]["ch_names"]):
+                        if ch.startswith(ch_coords):
+                            # delete index
+                            self.coords[key_]["positions"] = np.delete(
+                                self.coords[key_]["positions"], idx, axis=0
+                            )
+                            self.coords[key_]["ch_names"].remove(ch)
+
+    def calc_proj_matrix(
+        self,
+        max_dist: float,
+        grid: np.ndarray,
+        coord_array: np.ndarray,
+    ) -> np.ndarray:
+        """Calculate projection matrix."""
+
+        channels = coord_array.shape[0]
+        distance_matrix = np.zeros([grid.shape[1], channels])
+
+        for project_point in range(grid.shape[1]):
+            for channel in range(coord_array.shape[0]):
+                distance_matrix[project_point, channel] = np.linalg.norm(
+                    grid[:, project_point] - coord_array[channel, :]
+                )
+
+        proj_matrix = np.zeros(distance_matrix.shape)
+        for grid_point in range(distance_matrix.shape[0]):
+            used_channels = np.where(distance_matrix[grid_point, :] < max_dist)[0]
+
+            rec_distances = distance_matrix[grid_point, used_channels]
+            sum_distances: float = np.sum(1 / rec_distances)
+
+            for _, used_channel in enumerate(used_channels):
+                proj_matrix[grid_point, used_channel] = (
+                    1 / distance_matrix[grid_point, used_channel]
+                ) / sum_distances
+        return proj_matrix
+
+    def calc_projection_matrix(self):
+        """Calculates a projection matrix based on the used coordinate arrays
+
+        Returns
+        -------
+        proj_matrix_cortex (np.array)
+            cortical projection_matrix in shape [grid contacts, channel contact] defaults to None
+        proj_matrix_subcortex (np.array)
+            subcortical projection_matrix in shape [grid contacts, channel contact] defaults to None
+        """
+
+        proj_matrix_run = np.empty(2, dtype=object)
+
+        if self.sess_right:
+            if self.project_cortex:
+                cortex_grid_right = np.copy(self.grid_cortex)
+                cortex_grid_right[:, 0] = cortex_grid_right[:, 0] * -1
+                self.cortex_grid_right = np.array(cortex_grid_right.T)
+            else:
+                self.cortex_grid_right = None
+
+            if self.project_subcortex:
+                subcortex_grid_right = np.copy(self.grid_subcortex)
+                subcortex_grid_right[:, 0] = subcortex_grid_right[:, 0] * -1
+                self.subcortex_grid_right = np.array(subcortex_grid_right).T
+            else:
+                self.subcortex_grid_right = None
+
+            grid_session = [self.cortex_grid_right, self.subcortex_grid_right]
+
+        else:
+            if self.project_cortex:
+                self.cortex_grid_left = np.array(self.grid_cortex.T)
+            else:
+                self.cortex_grid_left = None
+            if self.project_subcortex:
+                self.subcortex_grid_left = np.array(self.grid_subcortex.T)
+            else:
+                self.subcortex_grid_left = None
+
+            grid_session = [self.cortex_grid_left, self.subcortex_grid_left]
+
+        coord_array = [
+            self.ecog_strip if grid_session[0] is not None else None,
+            self.lfp_elec if grid_session[1] is not None else None,
+        ]
+
+        for loc_, grid in enumerate(grid_session):
+            if loc_ == 0:  # cortex
+                max_dist = self.max_dist_cortex
+            elif loc_ == 1:  # subcortex
+                max_dist = self.max_dist_subcortex
+
+            if grid_session[loc_] is not None:
+                proj_matrix_run[loc_] = self.calc_proj_matrix(
+                    max_dist, grid, coord_array[loc_]
+                )
+
+        return proj_matrix_run[0], proj_matrix_run[1]  # cortex, subcortex
+
+    def _initialize_channels(self) -> None:
+        """Initialize channel names via nm_channel new_name column"""
+
+        if self.project_cortex:
+            self.ecog_channels = self.nm_channels.query(
+                '(type=="ecog") and (used == 1) and (status=="good")'
+            ).name.to_list()
+
+            chs_ecog = self.ecog_channels.copy()
+            for ecog_channel in chs_ecog:
+                if ecog_channel not in self.ecog_strip_names:
+                    self.ecog_channels.remove(ecog_channel)
+            # write ecog_channels to be new_name
+            self.ecog_channels = list(
+                self.nm_channels.query("name == @self.ecog_channels").new_name
+            )
+
+        if self.project_subcortex:
+            self.lfp_channels = self.nm_channels.query(
+                '(type=="lfp" or type=="seeg" or type=="dbs") \
+              and (used == 1) and (status=="good")'
+            ).name.to_list()
+            # project only channels that are in the coords
+            # this also deletes channels of the other hemisphere
+            chs_lfp = self.lfp_channels.copy()
+            for lfp_channel in chs_lfp:
+                if lfp_channel not in self.lfp_elec_names:
+                    self.lfp_channels.remove(lfp_channel)
+            # write lfp_channels to be new_name
+            self.lfp_channels = list(
+                self.nm_channels.query("name == @self.lfp_channels").new_name
+            )
+
+    def init_projection_run(self, feature_dict: dict) -> None:
+        """Initialize indexes for respective channels in feature series computed by nm_features.py"""
+        #  here it is assumed that only one hemisphere is recorded at a time!
+        if self.project_cortex:
+            for ecog_channel in self.ecog_channels:
+                self.idx_chs_ecog.append(
+                    [
+                        ch_idx
+                        for ch_idx, ch in enumerate(feature_dict.keys())
+                        if ch.startswith(ecog_channel)
+                    ]
+                )
+                self.names_chs_ecog.append(
+                    [
+                        ch
+                        for _, ch in enumerate(feature_dict.keys())
+                        if ch.startswith(ecog_channel)
+                    ]
+                )
+            if self.names_chs_ecog:
+                # get feature_names; given by ECoG sequency of features
+                self.feature_names = [
+                    feature_name[len(self.ecog_channels[0]) + 1 :]
+                    for feature_name in self.names_chs_ecog[0]
+                ]
+
+        if self.project_subcortex:
+            # for lfp_channels select here only the ones from the correct hemisphere!
+            for lfp_channel in self.lfp_channels:
+                self.idx_chs_lfp.append(
+                    [
+                        ch_idx
+                        for ch_idx, ch in enumerate(feature_dict.keys())
+                        if ch.startswith(lfp_channel)
+                    ]
+                )
+                self.names_chs_lfp.append(
+                    [
+                        ch
+                        for _, ch in enumerate(feature_dict.keys())
+                        if ch.startswith(lfp_channel)
+                    ]
+                )
+            if not self.feature_names and self.names_chs_lfp:
+                # get feature_names; given by LFP sequency of features
+                self.feature_names = [
+                    feature_name[len(self.lfp_channels[0]) + 1 :]
+                    for feature_name in self.names_chs_lfp[0]
+                ]
+
+        self.initialized = True
+
+    def project_features(self, feature_dict: dict) -> None:
+        """Project data, given idx_chs_ecog/stn"""
+
+        if not self.initialized:
+            self.init_projection_run(feature_dict)
+
+        dat_cortex = (
+            np.array(
+                [
+                    np.array([feature_dict[ch] for ch in ch_names])
+                    for ch_names in self.names_chs_ecog
+                ]
+            )
+            if self.project_cortex
+            else None
+        )
+
+        dat_subcortex = (
+            np.array(
+                [
+                    np.array([feature_dict[ch] for ch in ch_names])
+                    for ch_names in self.names_chs_lfp
+                ]
+            )
+            if self.project_subcortex
+            else None
+        )
+
+        # project data
+        # get_projected_cortex_subcortex_data can return None
+        # but None is not handled and will throw error in the code below
+
+        proj_cortex_array: np.ndarray
+        proj_subcortex_array: np.ndarray
+        (proj_cortex_array, proj_subcortex_array) = (
+            self.get_projected_cortex_subcortex_data(dat_cortex, dat_subcortex)
+        )  # type: ignore # Ignore None return
+
+        features_new: dict = {}
+        # proj_cortex_array has shape grid_points x feature_number
+        if self.project_cortex:
+            features_new = features_new | {
+                "gridcortex_"
+                + str(act_grid_point)
+                + "_"
+                + feature_name: proj_cortex_array[act_grid_point, feature_idx]
+                for feature_idx, feature_name in enumerate(self.feature_names)  # type: ignore # Empty list handled above
+                for act_grid_point in self.active_cortex_gridpoints
+            }
+        if self.project_subcortex:
+            features_new = features_new | {
+                "gridsubcortex_"
+                + str(act_grid_point)
+                + "_"
+                + feature_name: proj_subcortex_array[act_grid_point, feature_idx]
+                for feature_idx, feature_name in enumerate(self.feature_names)  # type: ignore # Empty list handled above
+                for act_grid_point in self.active_subcortex_gridpoints
+            }
+
+        feature_dict.update(features_new)
+
+    def get_projected_cortex_subcortex_data(
+        self,
+        dat_cortex: np.ndarray | None = None,
+        dat_subcortex: np.ndarray | None = None,
+    ) -> tuple[np.ndarray | None, np.ndarray | None]:
+        """Project cortical and subcortical data to predefined projection matrices
+
+        Parameters
+        ----------
+        dat_cortex : np.ndarray, optional
+            cortical features, by default None
+        dat_subcortex : np.ndarray, optional
+            subcortical features, by default None
+
+        Returns
+        -------
+        proj_cortex : np.ndarray
+            projected cortical features, by detault None
+        proj_subcortex : np.ndarray
+            projected subcortical features, by detault None
+        """
+        proj_cortex = None
+        proj_subcortex = None
+
+        if dat_cortex is not None:
+            proj_cortex = self.proj_matrix_cortex @ dat_cortex
+        if dat_subcortex is not None:
+            proj_subcortex = self.proj_matrix_subcortex @ dat_subcortex
+
+        return proj_cortex, proj_subcortex