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

py_neuromodulation/ConnectivityDecoding/_get_grid_hull.m

@@ -0,0 +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
+
+
+
+
+

py_neuromodulation/ConnectivityDecoding/_get_grid_whole_brain.py

@@ -0,0 +1,95 @@
+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

@@ -0,0 +1,107 @@
+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