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

py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m

@@ -1,34 +1,34 @@
-addpath('C:\code\wjn_toolbox');
-addpath(genpath('C:\code\leaddbs'));
-addpath(genpath('C:\code\spm12'));
-
-
-%%
-ctx = wjn_mni_cortex();
-downsample_ctx=ctx.vertices(1:20:end,:); %downsample by 10
-
-save("downsampled_cortex.mat", "downsample_ctx")
-
-figure;
-scatter3(downsample_ctx(:,1), downsample_ctx(:,2), downsample_ctx(:,3), 'filled');
-title('3D Scatter Plot Example');
-xlabel('X-axis');
-ylabel('Y-axis');
-zlabel('Z-axis');
-grid on;
-
-
-
-PATH_OUT = "D:\Connectome_RMAP_OUT\ROIs";
-
-for a =1:size(downsample_ctx,1)
-    disp(a)
-    roiname  = fullfile(PATH_OUT, strcat('ROI-', string(a), '.nii'));
-    mni = [downsample_ctx(a, 1) downsample_ctx(a, 2) downsample_ctx(a, 3)];
-    wjn_spherical_roi(roiname,mni,4);
-end
-
-
-
-
-
+addpath('C:\code\wjn_toolbox');
+addpath(genpath('C:\code\leaddbs'));
+addpath(genpath('C:\code\spm12'));
+
+
+%%
+ctx = wjn_mni_cortex();
+downsample_ctx=ctx.vertices(1:20:end,:); %downsample by 10
+
+save("downsampled_cortex.mat", "downsample_ctx")
+
+figure;
+scatter3(downsample_ctx(:,1), downsample_ctx(:,2), downsample_ctx(:,3), 'filled');
+title('3D Scatter Plot Example');
+xlabel('X-axis');
+ylabel('Y-axis');
+zlabel('Z-axis');
+grid on;
+
+
+
+PATH_OUT = "D:\Connectome_RMAP_OUT\ROIs";
+
+for a =1:size(downsample_ctx,1)
+    disp(a)
+    roiname  = fullfile(PATH_OUT, strcat('ROI-', string(a), '.nii'));
+    mni = [downsample_ctx(a, 1) downsample_ctx(a, 2) downsample_ctx(a, 3)];
+    wjn_spherical_roi(roiname,mni,4);
+end
+
+
+
+
+

py_neuromodulation/ConnectivityDecoding/_get_grid_whole_brain.py

@@ -1,106 +1,95 @@
-import nibabel as nib
-import numpy as np
-import scipy.io as sio
-import os
-from matplotlib import pyplot as plt
-
-
-class NiiToMNI:
-
-    def __init__(
-        self,
-        PATH_nii_file: str = r"C:\code\RMap_ROI_Estimation\Automated Anatomical Labeling 3 (Rolls 2020).nii",
-    ) -> None:
-
-        self.img = nib.load(PATH_nii_file)
-        self.data = self.img.get_fdata()
-
-    def downsample_nii(
-        self,
-        resampling_factor: int = 150,
-    ):
-
-        # PATH_MNI_TO_ATLAS = r"C:\code\mni_to_atlas\src\mni_to_atlas\atlases\AAL.nii"
-        # img_mni_to_atlas = nib.load(PATH_MNI_TO_ATLAS)
-
-        x_dim, y_dim, z_dim = self.data.shape
-
-        # Create arrays of voxel coordinates
-        x_coords, y_coords, z_coords = np.meshgrid(
-            range(x_dim), range(y_dim), range(z_dim), indexing="ij"
-        )
-
-        # Downsample here the voxels --> check lateron if the voxels have non-zero values
-        x_c_flatten = x_coords.flatten()[::resampling_factor]
-        y_c_flatten = y_coords.flatten()[::resampling_factor]
-        z_c_flatten = z_coords.flatten()[::resampling_factor]
-
-        # Combine coordinates into a single array
-        voxel_coordinates = np.column_stack(
-            (
-                x_c_flatten,
-                y_c_flatten,
-                z_c_flatten,
-                np.ones(x_c_flatten.shape[0]),
-            )
-        )
-
-        aff_m = self.img.affine
-        aff_m[0, 0] = 2
-        aff_m[0, 3] = -90
-
-        mni_coordinates = np.dot(aff_m, voxel_coordinates.T).T[:, :3]
-
-        return mni_coordinates
-
-    def select_non_zero_voxels(
-        self,
-        mni_coordinates: np.array,
-    ):
-
-        coords = np.hstack(
-            (mni_coordinates, np.ones((mni_coordinates.shape[0], 1)))
-        )
-
-        # and transform back to get the voxel values
-        voxels_downsampled = np.array(
-            np.linalg.solve(self.img.affine, coords.T).T
-        ).astype(int)[:, :3]
-
-        ival = []
-        coord_ = []
-        for i in range(voxels_downsampled.shape[0]):
-            ival.append(self.data[tuple(voxels_downsampled[i, :])])
-            coord_.append(mni_coordinates[i, :])
-
-        # get only voxel values non-zero
-        ival = np.array(ival)
-        coord_ = np.array(coord_)
-        ival_non_zero = ival[ival != 0]
-        coord_non_zero = coord_[ival != 0]
-        print(coord_non_zero.shape)
-
-        return coord_non_zero, ival_non_zero
-
-    def plot_3d_coordinates(self, coord_non_zero: np.array):
-        fig = plt.figure()
-        ax = fig.add_subplot(111, projection="3d")
-        ax.scatter(
-            coord_non_zero[:, 0],
-            coord_non_zero[:, 1],
-            coord_non_zero[:, 2],
-            s=50,
-            alpha=0.2,
-        )
-        plt.show()
-
-
-if __name__ == "__main__":
-
-    nii_to_mni = NiiToMNI(
-        PATH_nii_file=r"C:\code\py_neuromodulation\ConnectivityDecoding\Automated Anatomical Labeling 3 (Rolls 2020).nii"
-    )
-    mni_coordinates = nii_to_mni.downsample_nii(resampling_factor=150)
-    coord_non_zero, ival_non_zero = nii_to_mni.select_non_zero_voxels(
-        mni_coordinates
-    )
+import nibabel as nib
+import numpy as np
+from matplotlib import pyplot as plt
+
+
+class NiiToMNI:
+    def __init__(
+        self,
+        PATH_nii_file: str = r"C:\code\RMap_ROI_Estimation\Automated Anatomical Labeling 3 (Rolls 2020).nii",
+    ) -> None:
+        self.img = nib.Nifti1Image.from_filename(PATH_nii_file)
+        self.data = self.img.get_fdata()
+
+    def downsample_nii(
+        self,
+        resampling_factor: int = 150,
+    ):
+        # PATH_MNI_TO_ATLAS = r"C:\code\mni_to_atlas\src\mni_to_atlas\atlases\AAL.nii"
+        # img_mni_to_atlas = nib.load(PATH_MNI_TO_ATLAS)
+
+        x_dim, y_dim, z_dim = self.data.shape
+
+        # Create arrays of voxel coordinates
+        x_coords, y_coords, z_coords = np.meshgrid(
+            range(x_dim), range(y_dim), range(z_dim), indexing="ij"
+        )
+
+        # Downsample here the voxels --> check lateron if the voxels have non-zero values
+        x_c_flatten = x_coords.flatten()[::resampling_factor]
+        y_c_flatten = y_coords.flatten()[::resampling_factor]
+        z_c_flatten = z_coords.flatten()[::resampling_factor]
+
+        # Combine coordinates into a single array
+        voxel_coordinates = np.column_stack(
+            (
+                x_c_flatten,
+                y_c_flatten,
+                z_c_flatten,
+                np.ones(x_c_flatten.shape[0]),
+            )
+        )
+
+        aff_m = self.img.affine
+        aff_m[0, 0] = 2
+        aff_m[0, 3] = -90
+
+        mni_coordinates = np.dot(aff_m, voxel_coordinates.T).T[:, :3]
+
+        return mni_coordinates
+
+    def select_non_zero_voxels(
+        self,
+        mni_coordinates: np.ndarray,
+    ):
+        coords = np.hstack((mni_coordinates, np.ones((mni_coordinates.shape[0], 1))))
+
+        # and transform back to get the voxel values
+        voxels_downsampled = np.array(
+            np.linalg.solve(self.img.affine, coords.T).T
+        ).astype(int)[:, :3]
+
+        ival = []
+        coord_ = []
+        for i in range(voxels_downsampled.shape[0]):
+            ival.append(self.data[tuple(voxels_downsampled[i, :])])
+            coord_.append(mni_coordinates[i, :])
+
+        # get only voxel values non-zero
+        ival_arr = np.array(ival)
+        coord_arr = np.array(coord_)
+        ival_non_zero = ival_arr[ival != 0]
+        coord_non_zero = coord_arr[ival != 0]
+        print(coord_non_zero.shape)
+
+        return coord_non_zero, ival_non_zero
+
+    def plot_3d_coordinates(self, coord_non_zero: np.ndarray):
+        fig = plt.figure()
+        ax = fig.add_subplot(111, projection="3d")
+        ax.scatter(
+            coord_non_zero[:, 0],
+            coord_non_zero[:, 1],
+            coord_non_zero[:, 2],
+            s=50,
+            alpha=0.2,
+        )
+        plt.show()
+
+
+if __name__ == "__main__":
+    nii_to_mni = NiiToMNI(
+        PATH_nii_file=r"C:\code\py_neuromodulation\ConnectivityDecoding\Automated Anatomical Labeling 3 (Rolls 2020).nii"
+    )
+    mni_coordinates = nii_to_mni.downsample_nii(resampling_factor=150)
+    coord_non_zero, ival_non_zero = nii_to_mni.select_non_zero_voxels(mni_coordinates)

py_neuromodulation/ConnectivityDecoding/_helper_write_connectome.py

@@ -1,119 +1,107 @@
-import nibabel as nib
-import numpy as np
-import scipy.io as sio
-import os
-from matplotlib import pyplot as plt
-
-
-def write_connectome_mat(
-    PATH_Fingerprints: str = r"D:\Connectome_RMAP_OUT\ROIs\HCP1000 6K",
-    PATH_CONNECTOME: str = os.path.join(
-        "py_neuromodulation",
-        "ConnectivityDecoding",
-        "connectome_struct.mat",
-    ),
-    func_: bool = False,
-):
-
-    # connectome = sio.loadmat(PATH_CONNECTOME)  # check if read was successful
-
-    # load all fingerprints and put them in .npy
-    dict_connectome = {}
-    if func_ is False:
-        files_fps = [f for f in os.listdir(PATH_Fingerprints) if ".nii" in f]
-    else:
-        files_fps = [
-            f
-            for f in os.listdir(PATH_Fingerprints)
-            if "func_seed_AvgR_Fz.nii" in f
-        ]
-
-    # I except 1025 files, check which ones are missing
-    missing_files = []
-
-    for i in range(1, 1026):
-
-        MISSING = False
-
-        if func_ is False:
-            if f"ROI-{i}_struc_seed.nii" not in files_fps:
-                missing_files.append(f"ROI-{i}_struc_seed.nii")
-                MISSING = True
-        else:
-            if f"ROI-{i}_func_seed_AvgR_Fz.nii" not in files_fps:
-                missing_files.append(f"ROI-{i}_func_seed_AvgR_Fz.nii")
-                MISSING = True
-
-        if MISSING:
-            ROI_file = os.path.join(
-                r"D:\Connectome_RMAP_OUT\whole_brain\ROIs", f"ROI-{i}.nii"
-            )
-            # copy the ROI file to the following folder:
-            PATH_ROI_OUT = (
-                r"D:\Connectome_RMAP_OUT\whole_brain\ROI_missing_struc"
-            )
-            import shutil
-
-            shutil.copy(ROI_file, os.path.join(PATH_ROI_OUT, f"ROI-{i}.nii"))
-
-    for idx, f in enumerate(files_fps):
-        # load the .nii file and put it all in in a dictionary with the name of the file
-        fp = (
-            nib.load(os.path.join(PATH_Fingerprints, f))
-            .get_fdata()
-            .astype(np.float16)
-        )
-        if "struc" in f:
-            dict_connectome[f[f.find("ROI-") + 4 : f.find("_struc")]] = fp
-        else:
-            dict_connectome[
-                f[f.find("ROI-") + 4 : f.find("_func_seed_AvgR_Fz.nii")]
-            ] = fp
-
-        print(idx)
-    # save the dictionary
-    sio.savemat(
-        PATH_CONNECTOME,
-        dict_connectome,
-    )
-
-
-if __name__ == "__main__":
-
-    write_connectome_mat(
-        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\whole_brain\struc\HCP1000 6K",
-        PATH_CONNECTOME=os.path.join(
-            "py_neuromodulation",
-            "ConnectivityDecoding",
-            "connectome_whole_brain_struc.mat",
-        ),
-    )  # 58 files are missing
-
-    write_connectome_mat(
-        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\whole_brain\func",
-        PATH_CONNECTOME=os.path.join(
-            "py_neuromodulation",
-            "ConnectivityDecoding",
-            "connectome_whole_brain_func.mat",
-        ),
-        func_=True,
-    )
-
-    write_connectome_mat(
-        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\hull\func\GSP 1000 (Yeo 2011)_Full Set (Yeo 2011)",
-        PATH_CONNECTOME=os.path.join(
-            "py_neuromodulation",
-            "ConnectivityDecoding",
-            "connectome_hull_func.mat",
-        ),
-        func_=True,
-    )  # all there
-
-    write_connectome_mat(
-        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\hull\struc\HCP1000 6K",
-        PATH_CONNECTOME=os.path.join(
-            "py_neuromodulation",
-            "ConnectivityDecoding",
-            "connectome_hull_struc.mat",
-        ),
-    )  # 5 missing
+import nibabel as nib
+import numpy as np
+import scipy.io as sio
+import os
+
+
+def write_connectome_mat(
+    PATH_Fingerprints: str = r"D:\Connectome_RMAP_OUT\ROIs\HCP1000 6K",
+    PATH_CONNECTOME: str = os.path.join(
+        "py_neuromodulation",
+        "ConnectivityDecoding",
+        "connectome_struct.mat",
+    ),
+    func_: bool = False,
+):
+    # connectome = sio.loadmat(PATH_CONNECTOME)  # check if read was successful
+
+    # load all fingerprints and put them in .npy
+    dict_connectome = {}
+    if func_ is False:
+        files_fps = [f for f in os.listdir(PATH_Fingerprints) if ".nii" in f]
+    else:
+        files_fps = [
+            f for f in os.listdir(PATH_Fingerprints) if "func_seed_AvgR_Fz.nii" in f
+        ]
+
+    # I except 1025 files, check which ones are missing
+    missing_files = []
+
+    for i in range(1, 1026):
+        MISSING = False
+
+        if func_ is False:
+            if f"ROI-{i}_struc_seed.nii" not in files_fps:
+                missing_files.append(f"ROI-{i}_struc_seed.nii")
+                MISSING = True
+        else:
+            if f"ROI-{i}_func_seed_AvgR_Fz.nii" not in files_fps:
+                missing_files.append(f"ROI-{i}_func_seed_AvgR_Fz.nii")
+                MISSING = True
+
+        if MISSING:
+            ROI_file = os.path.join(
+                r"D:\Connectome_RMAP_OUT\whole_brain\ROIs", f"ROI-{i}.nii"
+            )
+            # copy the ROI file to the following folder:
+            PATH_ROI_OUT = r"D:\Connectome_RMAP_OUT\whole_brain\ROI_missing_struc"
+            import shutil
+
+            shutil.copy(ROI_file, os.path.join(PATH_ROI_OUT, f"ROI-{i}.nii"))
+
+    for idx, f in enumerate(files_fps):
+        # load the .nii file and put it all in in a dictionary with the name of the file
+        fp = nib.load(os.path.join(PATH_Fingerprints, f)).get_fdata().astype(np.float16)
+        if "struc" in f:
+            dict_connectome[f[f.find("ROI-") + 4 : f.find("_struc")]] = fp
+        else:
+            dict_connectome[
+                f[f.find("ROI-") + 4 : f.find("_func_seed_AvgR_Fz.nii")]
+            ] = fp
+
+        print(idx)
+    # save the dictionary
+    sio.savemat(
+        PATH_CONNECTOME,
+        dict_connectome,
+    )
+
+
+if __name__ == "__main__":
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\whole_brain\struc\HCP1000 6K",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_whole_brain_struc.mat",
+        ),
+    )  # 58 files are missing
+
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\whole_brain\func",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_whole_brain_func.mat",
+        ),
+        func_=True,
+    )
+
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\hull\func\GSP 1000 (Yeo 2011)_Full Set (Yeo 2011)",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_hull_func.mat",
+        ),
+        func_=True,
+    )  # all there
+
+    write_connectome_mat(
+        PATH_Fingerprints=r"D:\Connectome_RMAP_OUT\hull\struc\HCP1000 6K",
+        PATH_CONNECTOME=os.path.join(
+            "py_neuromodulation",
+            "ConnectivityDecoding",
+            "connectome_hull_struc.mat",
+        ),
+    )  # 5 missing

py_neuromodulation/__init__.py

@@ -1,13 +1,80 @@
-from . import (
-    nm_analysis,
-    nm_stream_abc,
-    nm_cohortwrapper,
-    nm_across_patient_decoding,
-    nm_stream_offline,
-    nm_settings,
-    nm_define_nmchannels,
-)
-from .nm_stream_offline import Stream
-from .nm_run_analysis import DataProcessor
-
-__version__ = "0.1.0.dev1"
+import os
+import platform
+from pathlib import PurePath
+from importlib.metadata import version
+from py_neuromodulation.utils.logging import NMLogger
+
+#####################################
+# Globals and environment variables #
+#####################################
+
+__version__ = version("py_neuromodulation")  # get version from pyproject.toml
+
+# Check if the module is running headless (no display) for tests and doc builds
+PYNM_HEADLESS: bool = not os.environ.get("DISPLAY")
+PYNM_DIR = PurePath(__file__).parent  # Define constant for py_nm directory
+
+os.environ["MPLBACKEND"] = "agg" if PYNM_HEADLESS else "qtagg"  # Set matplotlib backend
+
+# Set  environment variable MNE_LSL_LIB (required to import Stream below)
+LSL_DICT = {
+    "windows_32bit": "windows/x86/liblsl.1.16.2.dll",
+    "windows_64bit": "windows/amd64/liblsl.1.16.2.dll",
+    "darwin_i386": "macos/amd64/liblsl.1.16.2.dylib",
+    "darwin_arm": "macos/arm64/liblsl.1.16.0.dylib",
+    "linux_jammy_32bit": "linux/jammy_x86/liblsl.1.16.2.so",
+    "linux_jammy_64bit": "linux/jammy_amd64/liblsl.1.16.2.so",
+    "linux_focal_64bit": "linux/focal_amd64/liblsl.1.16.2.so",
+    "linux_bionic_64bit": "linux/bionic_amd64/liblsl.1.16.2.so",
+    "linux_bookworm_64bit": "linux/bookworm_amd64/liblsl.1.16.2.so",
+    "linux_noble_64bit": "linux/noble_amd64/liblsl.1.16.2.so",
+    "linux_32bit": "linux/jammy_x86/liblsl.1.16.2.so",
+    "linux_64bit": "linux/jammy_amd64/liblsl.1.16.2.so",
+}
+
+PLATFORM = platform.system().lower().strip()
+ARCH = platform.architecture()[0]
+match PLATFORM:
+    case "windows":
+        KEY = PLATFORM + "_" + ARCH
+    case "darwin":
+        KEY = PLATFORM + "_" + platform.processor()
+    case "linux":
+        DIST = platform.freedesktop_os_release()["VERSION_CODENAME"]
+        KEY = PLATFORM + "_" + DIST + "_" + ARCH
+        if KEY not in LSL_DICT:
+            KEY = PLATFORM + "_" + ARCH
+    case _:
+        KEY = ""
+
+if KEY in LSL_DICT:
+    os.environ["MNE_LSL_LIB"] = str(PYNM_DIR / "liblsl" / LSL_DICT[KEY])
+
+
+# Create global dictionary to store user-defined features
+user_features = {}
+
+
+######################################
+# Logger initialization and settings #
+######################################
+
+logger = NMLogger(__name__)  # logger initialization first to prevent circular import
+
+####################################
+# API: Exposed classes and methods #
+####################################
+from .stream.stream import Stream
+from .stream.data_processor import DataProcessor
+from .stream.settings import NMSettings
+
+from .analysis.feature_reader import FeatureReader
+from .features.feature_processor import add_custom_feature, remove_custom_feature
+
+from .utils import types
+from .utils import io
+
+from . import stream
+from . import analysis
+
+from .stream.settings import get_default_settings, get_fast_compute, reset_settings