pyNIBS 0.2024.8__py3-none-any.whl → 0.2026.1__py3-none-any.whl

pynibs/hdf5_io/xdmf.py

@@ -15,48 +15,54 @@ The module includes functions for:
 
 This module is primarily used for handling and visualizing data related to neuroimaging and brain stimulation studies.
 """
-import warnings
 import os
 import h5py
-import numpy as np
 import pynibs
+import numpy as np
+import warnings
 
 
-def write_xdmf_surf(data_hdf_fn_out, data_names, data_xdmf_fn, geo_hdf_fn, data_dims,
+def write_xdmf_surf(data_hdf, data_names, data_dims, data_xdmf_fn=None, geo_hdf_fn=None,
                     data_in_tris=True, data_prefix='/data/tris/'):
     """
     Write XDMF files for surfaces, such as ROIs.
 
     Parameters
     ----------
-    data_hdf_fn_out : str
-
+    data_hdf : str
+        Filename of the HDF5 file containing the data.
     data_names : list of str
-
+        Names of the data arrays to be included in the XDMF file.
     data_xdmf_fn : str
-
+        Filename of the output XDMF file.
     geo_hdf_fn : str
-
+        Filename of the HDF5 file containing the geometry data.
     data_dims : list of int
         The data dimensions.
     data_in_tris : bool, default: True.
-
+        If True, the data is assumed to be in triangles. If False, it is assumed to be in tetrahedra.
     data_prefix : str, default: '/data/tris/'
-
+        Prefix for the data arrays in the HDF5 file.
 
     Returns
     -------
     <File> : .xdmf file
-        Descriptor file pointing to geo and data .hdf5 files
+        Descriptor file pointing to geo and data .hdf5 files.
     """
     if not data_in_tris:
         raise NotImplementedError
+    if geo_hdf_fn is None:
+        geo_hdf_fn = data_hdf
     # if geo file exists in same folder then data file only use relative path
-    if os.path.split(data_hdf_fn_out)[0] == os.path.split(geo_hdf_fn)[0]:
+    if os.path.split(data_hdf)[0] == os.path.split(geo_hdf_fn)[0]:
         geo_hdf_fn_xdmf = os.path.basename(geo_hdf_fn)
     else:
         geo_hdf_fn_xdmf = geo_hdf_fn
 
+    if data_xdmf_fn is None:
+        data_xdmf_fn = data_hdf.replace('.hdf5', '.xdmf')
+        data_xdmf_fn = data_xdmf_fn.replace('.h5', '.xdmf')
+
     with open(data_xdmf_fn, 'w') as xdmf, h5py.File(geo_hdf_fn, 'r') as h5_geo:
         # write xdmf file linking the data to the surfaces in geo_hdf_fn
         xdmf.write('<?xml version="1.0"?>\n')
@@ -116,13 +122,13 @@ def write_xdmf_surf(data_hdf_fn_out, data_names, data_xdmf_fn, geo_hdf_fn, data_
             for idx, dat in enumerate(data_dims):
                 xdmf.write(f'<Attribute Name="{data_names[idx]}" AttributeType="Scalar" Center="Cell">\n')
                 xdmf.write(f'<DataItem Format="HDF" Dimensions="{str(n_tris)} {str(data_dims[idx])}">\n')
-                xdmf.write(os.path.basename(data_hdf_fn_out) + ':' + data_prefix + data_names[idx] + '\n')
+                xdmf.write(os.path.basename(data_hdf) + ':' + data_prefix + data_names[idx] + '\n')
                 xdmf.write('</DataItem>\n')
                 xdmf.write('</Attribute>\n')
 
             # tissue_type
-            xdmf.write('<Attribute Name="tissue_type" AttributeType="Scalar" Center="Node">\n')
-            xdmf.write('<DataItem Format="HDF" Dimensions="' + str(n_nodes) + ' 1">\n')
+            xdmf.write('<Attribute Name="tissue_type" AttributeType="Scalar" Center="Cell">\n')
+            xdmf.write('<DataItem Format="HDF" Dimensions="' + str(n_tris) + ' 1">\n')
             xdmf.write(geo_hdf_fn_xdmf + ':' + '/mesh/elm/' + lookup_str_tri + surf + '\n')
             xdmf.write('</DataItem>\n')
             xdmf.write('</Attribute>\n')
@@ -143,13 +149,13 @@ def write_xdmf(hdf5_fn, hdf5_geo_fn=None, overwrite_xdmf=False, overwrite_array=
     Parameters
     ----------
     hdf5_fn : str
-        Filename of hdf5 file containing the data
+        Filename of hdf5 file containing the data.
     hdf5_geo_fn : str, optional
-        Filename of hdf5 file containing the geometry
+        Filename of hdf5 file containing the geometry.
     overwrite_xdmf : bool, default: False
         Overwrite existing xdmf file if present.
     overwrite_array : bool, default: False
-        Overwrite existing arrays if present
+        Overwrite existing arrays if present.
     verbose : bool
         Print output.
     mode : str, default: "r+"
@@ -159,15 +165,14 @@ def write_xdmf(hdf5_fn, hdf5_geo_fn=None, overwrite_xdmf=False, overwrite_array=
     Returns
     -------
     fn_xml : str
-        Filename of the created .xml file
+        Filename of the created .xml file.
     <File> : .xdmf file
-        hdf5_fn[-4].xdmf (only data if hdf5Geo_fn provided)
+        hdf5_fn[-4].xdmf (only data if hdf5Geo_fn provided).
     <File> : .hdf5 file
-        hdf5_fn changed if neccessary
+        hdf5_fn changed if neccessary.
     <File> : .hdf5 file
-        hdf5geo_fn containing spatial data
+        hdf5geo_fn containing spatial data.
     """
-
     if os.path.splitext(hdf5_fn)[1] not in ['.hdf5', '.h5', '.hdf']:
         print("Provide .hdf5 filename for existing file.")
         return
@@ -1126,7 +1131,7 @@ def create_position_path_xdmf(sorted_fn, coil_pos_fn, output_xdmf, stim_intens=N
     Other Parameters
     ----------------
     coil_sorted : str
-        Path to coil positions in sorted_fn
+        Path to coil positions in sorted_fn.
     """
     # get datasets for nodes used in path, goal value, intensity
     sorted_data = h5py.File(sorted_fn, 'r')[coil_sorted][:]
@@ -1262,15 +1267,15 @@ def create_fibre_xdmf(fn_fibre_geo_hdf5, fn_fibre_data_hdf5=None, overwrite=True
     Parameters
     ----------
     fn_fibre_geo_hdf5 : str
-        Path to fibre_geo.hdf5 file containing the geometry (in /plot subfolder created with create_fibre_geo_hdf5())
+        Path to fibre_geo.hdf5 file containing the geometry (in /plot subfolder created with create_fibre_geo_hdf5()).
     fn_fibre_data_hdf5 : str (optional) default: None
-        Path to fibre_data.hdf5 file containing the data to plot (in parent folder)
+        Path to fibre_data.hdf5 file containing the data to plot (in parent folder).
     fibre_points_path : str (optional) default: fibre_points
-        Path to fibre point array in .hdf5 file
+        Path to fibre point array in .hdf5 file.
     fibre_con_path : str (optional) default: fibre_con
-        Path to fibre connectivity array in .hdf5 file
+        Path to fibre connectivity array in .hdf5 file.
     fibre_data_path : str (optional) default: ""
-        Path to parent data folder in data.hdf5 file (Default: no parent folder)
+        Path to parent data folder in data.hdf5 file (Default: no parent folder).
 
     Returns
     -------
@@ -1361,7 +1366,7 @@ def data_superimpose(fn_in_hdf5_data, fn_in_geo_hdf5, fn_out_hdf5_data, data_hdf
         Filename of .hdf5 data output file containing the superimposed data.
     data_hdf5_path: str
         Path in .hdf5 data file where data is stored (e.g. ``'/data/tris/'``).
-    data_substitute: float or np.NaN, default: -1
+    data_substitute: float or np.nan, default: -1
         Data substitute with this number for all points in the inflated brain, which do not belong to
         the given data set.
     normalize: bool or str, default: False
@@ -1376,7 +1381,6 @@ def data_superimpose(fn_in_hdf5_data, fn_in_geo_hdf5, fn_out_hdf5_data, data_hdf
     <File>: .hdf5 file
         Overlayed data.
     """
-
     n_subjects = len(fn_in_hdf5_data)
     data_dic = [dict() for _ in range(n_subjects)]
     labels = [''] * n_subjects

pynibs/mesh/__init__.py

@@ -1,3 +1,3 @@
 from .mesh_struct import *
 from .transformations import *
-from .utils import *
+from .utils import *

pynibs/mesh/mesh_struct.py

@@ -5,14 +5,12 @@ regions of interest (ROIs).
 The module includes the following classes:
 
 - `TetrahedraLinear`: This class represents a mesh consisting of linear tetrahedra. It provides methods for
-calculating various quantities of interest (QOIs) in the mesh, interpolating data between nodes and elements,
-calculating the electric field and current density, and more.
-
+  calculating various quantities of interest (QOIs) in the mesh, interpolating data between nodes and elements,
+  calculating the electric field and current density, and more.
 - `Mesh`: This class is a general mesh class to initialize default attributes and provides methods to fill default
-values based on the approach, write the mesh data to an HDF5 file, and print the mesh information.
-
+  values based on the approach, write the mesh data to an HDF5 file, and print the mesh information.
 - `ROI`: This class represents a region of interest (ROI) in the mesh. It provides methods to write the ROI data to
-an HDF5 file and print the ROI information.
+  an HDF5 file and print the ROI information.
 
 Each class and method in this module is documented with docstrings providing more detailed information about its
 purpose, parameters, and return values.
@@ -41,38 +39,37 @@ class TetrahedraLinear:
     Parameters
     ----------
     points : array of float [N_points x 3]
-        Vertices of FE mesh
+        Vertices of FE mesh.
     triangles : np.ndarray of int [N_tri x 3]
-        Connectivity of points forming triangles
+        Connectivity of points forming triangles.
     triangles_regions : np.ndarray of int [N_tri x 1]
-        Region identifiers of triangles
+        Region identifiers of triangles.
     tetrahedra : np.ndarray of int [N_tet x 4]
-        Connectivity of points forming tetrahedra
+        Connectivity of points forming tetrahedra.
     tetrahedra_regions : np.ndarray of int [N_tet x 1]
-        Region identifiers of tetrahedra
+        Region identifiers of tetrahedra.
 
     Attributes
     ----------
     N_points : int
-        Number of vertices
+        Number of vertices.
     N_tet : int
-        Number of tetrahedra
+        Number of tetrahedra.
     N_tri : int
-        Number of triangles
+        Number of triangles.
     N_region : int
-        Number of regions
+        Number of regions.
     region : np.ndarray of int
-        Region labels
+        Region labels.
     tetrahedra_volume : np.ndarray of float [N_tet x 1]
-        Volumes of tetrahedra
+        Volumes of tetrahedra.
     tetrahedra_center : np.ndarray of float [N_tet x 1]
-        Center of tetrahedra
+        Center of tetrahedra.
     triangles_center : np.ndarray of float [N_tri x 1]
-        Center of triangles
+        Center of triangles.
     triangles_normal : np.ndarray of float [N_tri x 3]
-        Normal components of triangles pointing outwards
+        Normal components of triangles pointing outwards.
     """
-
     def __init__(self, points, triangles, triangles_regions, tetrahedra, tetrahedra_regions):
         """ Initialize TetrahedraLinear class """
         self.points = points
@@ -93,7 +90,7 @@ class TetrahedraLinear:
             p2_tet = self.points[self.tetrahedra[:, 1], :]
             p3_tet = self.points[self.tetrahedra[:, 2], :]
             p4_tet = self.points[self.tetrahedra[:, 3], :]
-            self.tetrahedra_volume = pynibs.calc_tetrahedra_volume_cross(p1_tet, p2_tet, p3_tet, p4_tet)
+            self.tetrahedra_volume = pynibs.mesh.calc_tetrahedra_volume_cross(p1_tet, p2_tet, p3_tet, p4_tet)
             self.tetrahedra_center = 1.0 / 4 * (p1_tet + p2_tet + p3_tet + p4_tet)
 
         else:
@@ -265,8 +262,8 @@ class TetrahedraLinear:
             # transform point data to element data
             if verbose:
                 print("Transforming point data to element data")
-            e_normal = pynibs.data_nodes2elements(data=e_normal, con=con_gm)
-            e_tan = pynibs.data_nodes2elements(data=e_tan, con=con_gm)
+            e_normal = pynibs.mesh.data_nodes2elements(data=e_normal, con=con_gm)
+            e_tan = pynibs.mesh.data_nodes2elements(data=e_tan, con=con_gm)
 
             # crop results data to ROI
             # if not roi_mask_bool.all():
@@ -431,8 +428,8 @@ class TetrahedraLinear:
             # transform point data to element data
             if verbose:
                 print("Transforming point data to element data")
-            e_normal = pynibs.data_nodes2elements(data=e_normal, con=con_gm)
-            e_tan = pynibs.data_nodes2elements(data=e_tan, con=con_gm)
+            e_normal = pynibs.mesh.data_nodes2elements(data=e_normal, con=con_gm)
+            e_tan = pynibs.mesh.data_nodes2elements(data=e_tan, con=con_gm)
 
             # crop results data to ROI
             # if not roi_mask_bool.all():
@@ -468,6 +465,7 @@ class TetrahedraLinear:
             - "components" : return x, y, and z component of tangential and normal components
             - "magnitude" : return magnitude of tangential and normal component (normal with sign for direction)
 
+
         Returns
         -------
         E_normal : np.ndarray of float
@@ -508,7 +506,7 @@ class TetrahedraLinear:
         n = n / np.tile(normal_norm, (1, 3))
 
         # interpolate magnetic vector potential to central surface points (primary electric field)
-        # E_pri = griddata(self.points, dAdt, surf_mid, method='linear', fill_value=np.NaN, rescale=False)
+        # E_pri = griddata(self.points, dAdt, surf_mid, method='linear', fill_value=np.nan, rescale=False)
         if verbose:
             print("Interpolating magnetic vector potential to central surface points (primary electric field)")
         e_pri = self.calc_QOI_in_points_tet_idx(qoi=dAdt,
@@ -533,7 +531,7 @@ class TetrahedraLinear:
 
         if verbose:
             print("Determine gradient of scalar electric potential on midlayer surface (E_sec_tangential)")
-        e_sec_tan = pynibs.calc_gradient_surface(phi=phi_surf_mid_nodes,
+        e_sec_tan = pynibs.mesh.calc_gradient_surface(phi=phi_surf_mid_nodes,
                                                  points=roi.node_coord_mid,
                                                  triangles=roi.node_number_list)
 
@@ -567,18 +565,17 @@ class TetrahedraLinear:
         Parameters
         ----------
         E : np.ndarray of float [N_tri x 3]
-            Induced electric field given in the tetrahedra centre of the mesh instance
+            Induced electric field given in the tetrahedra centre of the mesh instance.
         roi : pynibs.roi.RegionOfInterestSurface
-            RegionOfInterestSurface object class instance
+            RegionOfInterestSurface object class instance.
 
         Returns
         -------
         E_normal : np.ndarray of float [N_points x 3]
-            Normal vector of electric field on GM-WM surface
+            Normal vector of electric field on GM-WM surface.
         E_tangential : np.ndarray of float [N_points x 3]
-            Tangential vector of electric field on GM-WM surface
+            Tangential vector of electric field on GM-WM surface.
         """
-
         e_gm_wm_surface = E[roi.tet_idx_nodes_mid, :]
 
         # determine surface normal vector (normalized)
@@ -604,17 +601,15 @@ class TetrahedraLinear:
         Parameters
         ----------
         qoi : np.ndarray of float
-            Quantity of interest in nodes of tetrahedra mesh instance
+            Quantity of interest in nodes of tetrahedra mesh instance.
         points_out : np.ndarray of float
-            Point coordinates (x, y, z) where the qoi is going to be interpolated by linear basis functions
+            Point coordinates (x, y, z) where the qoi is going to be interpolated by linear basis functions.
 
         Returns
         -------
         qoi_out : np.ndarray of float
-            Quantity of interest in points_out
-
+            Quantity of interest in points_out.
         """
-
         n_phi_points_out = points_out.shape[0]
         qoi_out = np.zeros(
             [n_phi_points_out, qoi.shape[1] if qoi.ndim > 1 else 1])
@@ -634,14 +629,14 @@ class TetrahedraLinear:
         # 4 points in tetrahedra
         for i in range(n_phi_points_out):
             start = time.time()
-            vtest1 = pynibs.calc_tetrahedra_volume_cross(np.tile(points_out[i, :], (p1_all.shape[0], 1)),
+            vtest1 = pynibs.mesh.calc_tetrahedra_volume_cross(np.tile(points_out[i, :], (p1_all.shape[0], 1)),
                                                          p2_all,
                                                          p3_all,
                                                          p4_all)
             tet_idx_bool_1 = (vtest1 >= 0)
             tet_idx_1 = np.nonzero(tet_idx_bool_1)[0]
 
-            vtest2 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx_1, :],
+            vtest2 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx_1, :],
                                                          np.tile(
                                                              points_out[i, :], (tet_idx_1.shape[0], 1)),
                                                          p3_all[tet_idx_1, :],
@@ -649,7 +644,7 @@ class TetrahedraLinear:
             tet_idx_bool_2 = (vtest2 >= 0)
             tet_idx_2 = tet_idx_1[np.nonzero(tet_idx_bool_2)[0]]
 
-            vtest3 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx_2, :],
+            vtest3 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx_2, :],
                                                          p2_all[tet_idx_2, :],
                                                          np.tile(
                                                              points_out[i, :], (tet_idx_2.shape[0], 1)),
@@ -657,7 +652,7 @@ class TetrahedraLinear:
             tet_idx_bool_3 = (vtest3 >= 0)
             tet_idx_3 = tet_idx_2[np.nonzero(tet_idx_bool_3)[0]]
 
-            vtest4 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx_3, :],
+            vtest4 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx_3, :],
                                                          p2_all[tet_idx_3, :],
                                                          p3_all[tet_idx_3, :],
                                                          np.tile(points_out[i, :], (tet_idx_3.shape[0], 1)))
@@ -665,19 +660,19 @@ class TetrahedraLinear:
             tet_idx = tet_idx_3[np.nonzero(tet_idx_bool_4)[0]]
 
             # calculate subvolumes of final tetrahedron and its total volume
-            vsub1 = pynibs.calc_tetrahedra_volume_cross(points_out[i, :][np.newaxis],
+            vsub1 = pynibs.mesh.calc_tetrahedra_volume_cross(points_out[i, :][np.newaxis],
                                                         p2_all[tet_idx, :],
                                                         p3_all[tet_idx, :],
                                                         p4_all[tet_idx, :])
-            vsub2 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
+            vsub2 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
                                                         points_out[i, :][np.newaxis],
                                                         p3_all[tet_idx, :],
                                                         p4_all[tet_idx, :])
-            vsub3 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
+            vsub3 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
                                                         p2_all[tet_idx, :],
                                                         points_out[i, :][np.newaxis],
                                                         p4_all[tet_idx, :])
-            vsub4 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
+            vsub4 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
                                                         p2_all[tet_idx, :],
                                                         p3_all[tet_idx, :],
                                                         points_out[i, :][np.newaxis], )
@@ -700,19 +695,17 @@ class TetrahedraLinear:
         Parameters
         ----------
         qoi : np.ndarray of float
-            Quantity of interest in nodes of tetrahedra mesh instance
+            Quantity of interest in nodes of tetrahedra mesh instance.
         points_out : np.ndarray of float
-            Point coordinates (x, y, z) where the qoi is going to be interpolated by linear basis functions
+            Point coordinates (x, y, z) where the qoi is going to be interpolated by linear basis functions.
         tet_idx : np.ndarray of int
-            Element indices where the points_out are sitting
+            Element indices where the points_out are sitting.
 
         Returns
         -------
         qoi_out : np.ndarray of float
             Quantity of interest in points_out
-
         """
-
         n_phi_points_out = points_out.shape[0]
         qoi_out = np.zeros([n_phi_points_out, qoi.shape[1] if qoi.ndim > 1 else 1])
 
@@ -722,19 +715,19 @@ class TetrahedraLinear:
         p4_all = self.points[self.tetrahedra[:, 3], :]
 
         # determine sub-volumes
-        vsub1 = pynibs.calc_tetrahedra_volume_cross(points_out,
+        vsub1 = pynibs.mesh.calc_tetrahedra_volume_cross(points_out,
                                                     p2_all[tet_idx, :],
                                                     p3_all[tet_idx, :],
                                                     p4_all[tet_idx, :])
-        vsub2 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
+        vsub2 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
                                                     points_out,
                                                     p3_all[tet_idx, :],
                                                     p4_all[tet_idx, :])
-        vsub3 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
+        vsub3 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
                                                     p2_all[tet_idx, :],
                                                     points_out,
                                                     p4_all[tet_idx, :])
-        vsub4 = pynibs.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
+        vsub4 = pynibs.mesh.calc_tetrahedra_volume_cross(p1_all[tet_idx, :],
                                                     p2_all[tet_idx, :],
                                                     p3_all[tet_idx, :],
                                                     points_out)
@@ -747,19 +740,19 @@ class TetrahedraLinear:
 
         # for i in range(N_phi_points_out):
         #     # calculate subvolumes of final tetrahedron and its total volume
-        #     Vsub1 = pynibs.calc_tetrahedra_volume_cross(points_out[i, :][np.newaxis],
+        #     Vsub1 = pynibs.mesh.calc_tetrahedra_volume_cross(points_out[i, :][np.newaxis],
         #                                               p2_all[tet_idx[i], :][np.newaxis],
         #                                               p3_all[tet_idx[i], :][np.newaxis],
         #                                               P4_all[tet_idx[i], :][np.newaxis])
-        #     vsub2 = pynibs.calc_tetrahedra_volume_cross(P1_all[tet_idx[i], :][np.newaxis],
+        #     vsub2 = pynibs.mesh.calc_tetrahedra_volume_cross(P1_all[tet_idx[i], :][np.newaxis],
         #                                               points_out[i, :][np.newaxis],
         #                                               p3_all[tet_idx[i], :][np.newaxis],
         #                                               P4_all[tet_idx[i], :][np.newaxis])
-        #     Vsub3 = pynibs.calc_tetrahedra_volume_cross(P1_all[tet_idx[i], :][np.newaxis],
+        #     Vsub3 = pynibs.mesh.calc_tetrahedra_volume_cross(P1_all[tet_idx[i], :][np.newaxis],
         #                                               p2_all[tet_idx[i], :][np.newaxis],
         #                                               points_out[i, :][np.newaxis],
         #                                               P4_all[tet_idx[i], :][np.newaxis])
-        #     Vsub4 = pynibs.calc_tetrahedra_volume_cross(P1_all[tet_idx[i], :][np.newaxis],
+        #     Vsub4 = pynibs.mesh.calc_tetrahedra_volume_cross(P1_all[tet_idx[i], :][np.newaxis],
         #                                               p2_all[tet_idx[i], :][np.newaxis],
         #                                               p3_all[tet_idx[i], :][np.newaxis],
         #                                               points_out[i, :][np.newaxis])
@@ -778,12 +771,12 @@ class TetrahedraLinear:
         Parameters
         ----------
         data : np.ndarray [N_nodes x N_data]
-            Data in nodes
+            Data in nodes.
 
         Returns
         -------
         data_elements : np.ndarray [N_elements x N_data]
-            Data in elements
+            Data in elements.
         """
         data_elements = np.sum(data[self.tetrahedra[:, i]] for i in range(4)) / 4.0
 
@@ -791,19 +784,19 @@ class TetrahedraLinear:
 
     def data_elements2nodes(self, data):
         """
-        Transforms an data in tetrahedra into the nodes after Zienkiewicz et al. (1992) [1]_.
+        Transforms data in tetrahedra into the nodes after Zienkiewicz et al. (1992) [1]_.
         Can only transform volume data, i.e. needs the data in the surrounding tetrahedra to average it to the nodes.
         Will not work well for discontinuous fields (like E, if several tissues are used).
 
         Parameters
         ----------
         data : np.ndarray [N_elements x N_data]
-            Data in tetrahedra
+            Data in tetrahedra.
 
         Returns
         -------
         data_nodes : np.ndarray [N_nodes x N_data]
-            Data in nodes
+            Data in nodes.
 
         Notes
         -----
@@ -811,7 +804,6 @@ class TetrahedraLinear:
            posteriori error estimates. Part 1: The recovery technique." International Journal for
            Numerical Methods in Engineering 33.7 (1992): 1331-1364.
         """
-
         # check dimension of input data
         if data.ndim == 1:
             data = data[:, np.newaxis]
@@ -897,14 +889,13 @@ class TetrahedraLinear:
         Parameters
         ----------
         tetrahedra_indices : np.ndarray
-            Indices of the tetrehedra where the outer volume is to be determined (default: all tetrahedra)
+            Indices of the tetrahedra where the outer volume is to be determined (default: all tetrahedra).
 
         Returns
         -------
         faces : np.ndarray
-            List of nodes in faces in arbitrary order
+            List of nodes in faces in arbitrary order.
         """
-
         if tetrahedra_indices is None:
             tetrahedra_indices = self.tetrahedra_index
 
@@ -930,14 +921,13 @@ class TetrahedraLinear:
         Parameters
         ----------
         phi : np.ndarray of float [N_nodes]
-            Scalar DOF the gradient is calculated for
+            Scalar DOF the gradient is calculated for.
 
         Returns
         -------
         grad_phi : np.ndarray of float [N_tet x 3]
-            Gradient of Scalar DOF in tetrahedra center
+            Gradient of Scalar DOF in tetrahedra center.
         """
-
         a1 = np.vstack((self.points[self.tetrahedra[:, 3], :] - self.points[self.tetrahedra[:, 1], :],
                         self.points[self.tetrahedra[:, 2], :] -
                         self.points[self.tetrahedra[:, 0], :],
@@ -1033,7 +1023,7 @@ class TetrahedraLinear:
         Returns
         -------
         <File> : .txt file
-            Element indices of the tetrahedra touching the surfaces (outer-most elements)
+            Element indices of the tetrahedra touching the surfaces (outer-most elements).
         """
         # determine indices of the 2 adjacent tetrahedra with common face on
         # surface
@@ -1121,25 +1111,24 @@ class TetrahedraLinear:
         Parameters
         ----------
         E : np.ndarray of float [N_tri x 3]
-            Electric field data on surfaces
+            Electric field data on surfaces.
         fname : str
             Filename of the .txt file containing the tetrahedra indices, which are adjacent to the surface triangles
-            generated by the method "calc_surface_adjacent_tetrahedra_idx_list(self, fname)"
+            generated by the method "calc_surface_adjacent_tetrahedra_idx_list(self, fname)".
 
         Returns
         -------
         En_pos : np.ndarray of float [N_tri x 3]
-            Normal component of electric field of top side (outside) of surface
+            Normal component of electric field of top side (outside) of surface.
         En_neg : np.ndarray of float [N_tri x 3]
-            Normal component of electric field of bottom side (inside) of surface
+            Normal component of electric field of bottom side (inside) of surface.
         n : np.ndarray of float [N_tri x 3]
             Normal vector
         Et : np.ndarray of float [N_tri x 3]
-            Tangential component of electric field lying in surface
+            Tangential component of electric field lying in surface.
         t : np.ndarray of float [N_tri x 3]
-            Tangential vector
+            Tangential vector.
         """
-
         n = self.triangles_normal
         en_pos = np.zeros((self.N_tri, 1))
         en_neg = np.zeros((self.N_tri, 1))
@@ -1166,25 +1155,24 @@ class TetrahedraLinear:
 
     def get_faces(self, tetrahedra_indexes=None):
         """
-        Creates a list of nodes in each face and a list of faces in each tetrahedra.
+        Creates a list of nodes in each face and a list of faces in each tetrahedron.
 
         Parameters
         ----------
         tetrahedra_indexes : np.ndarray
-            Indices of the tetrehedra where the faces are to be determined (default: all tetrahedra)
+            Indices of the tetrehedra where the faces are to be determined (default: all tetrahedra).
 
         Returns
         -------
         faces : np.ndarray
             List of nodes in faces, in arbitrary order
-        th_faces : np.ndarray
-            List of faces in each tetrahedra, starts at 0, order=((0, 2, 1), (0, 1, 3), (0, 3, 2), (1, 2, 3))
+        th_faces : np.ndarray.
+            List of faces in each tetrahedron, starts at 0, order=((0, 2, 1), (0, 1, 3), (0, 3, 2), (1, 2, 3)).
         face_adjacency_list : np.ndarray
             List of tetrahedron adjacent to each face, filled with -1 if a face is in a
             single tetrahedron. Not in the normal element ordering, but only in the order
-            the tetrahedra are presented
+            the tetrahedra are presented.
         """
-
         if tetrahedra_indexes is None:
             tetrahedra_indexes = np.arange(self.tetrahedra.shape[0])
         # th = self[tetrahedra_indexes]
@@ -1225,10 +1213,9 @@ class TetrahedraLinear:
 
 
 class Mesh:
-    """"
+    """
     Mesh class to initialize default attributes.
     """
-
     def __init__(self, mesh_name, subject_id, subject_folder):
         self.subject_id = subject_id
         self.subject_folder = subject_folder
@@ -1277,6 +1264,7 @@ class Mesh:
             'headreco'
             'mri2mesh'
             'charm'
+
         """
         self.approach = approach
         if approach == 'headreco':
@@ -1317,9 +1305,8 @@ class Mesh:
         check_file_exist : bool
             Check if provided filenames exist, warn if not.
         verbose : bool
-            Print self information
+            Print self information.
         """
-
         pynibs.write_dict_to_hdf5(fn_hdf5=fn_hdf5, data=self.__dict__, folder=f"mesh/{self.name}",
                                   check_file_exist=check_file_exist)
         if verbose:
@@ -1340,7 +1327,6 @@ class ROI:
     """
     Region of interest class to initialize default attributes.
     """
-
     def __init__(self, subject_id, roi_name, mesh_name):
         self.subject_id = subject_id
         self.name = roi_name
@@ -1375,9 +1361,8 @@ class ROI:
         check_file_exist : bool
             Check if provided filenames exist, warn if not.
         verbose : bool
-            Print self information
+            Print self information.
         """
-
         pynibs.write_dict_to_hdf5(fn_hdf5=fn_hdf5, data=self.__dict__, folder=f"roi/{self.mesh_name}/{self.name}",
                                   check_file_exist=check_file_exist)
         if verbose: