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

pynibs/util/rotations.py

@@ -38,7 +38,6 @@ def quat_rotation_angle(q):
     alpha : float
         Rotation angle of quaternion in rad.
     """
-
     if len(q) == 3:
         return 2 * np.arcsin(np.linalg.norm(q))
     elif len(q) == 4:
@@ -87,7 +86,6 @@ def rot_to_quat(rot):
     q : np.ndarray of float
         Quaternion, full (length=4).
     """
-
     rot = rot.flatten()
     t = 1. + rot[0] + rot[4] + rot[8]
     if t > np.finfo(rot.dtype).eps:
@@ -121,10 +119,15 @@ def quaternion_conjugate(q):
     """
     https://stackoverflow.com/questions/15425313/inverse-quaternion
 
-    :param q:
-    :type q:
-    :return:
-    :rtype:
+    Parameters
+    ----------
+    q : np.ndarray
+        Input quaternion.
+
+    Returns
+    -------
+    np.ndarray
+        Conjugate of the input quaternion.
     """
     return np.array((-q[0], -q[1], -q[2]))
 
@@ -185,7 +188,6 @@ def euler_angles_to_rotation_matrix(theta):
     r : np.ndarray
         (3) Rotation matrix (z, y', x'').
     """
-
     # theta in rad
     r_x = np.array([[1., 0., 0.],
                     [0., math.cos(theta[0]), -math.sin(theta[0])],
@@ -277,7 +279,6 @@ def rotate_matsimnibs_euler(axis, angle, matsimnibs, metric='rad'):
     rotated_matsimnibs : np.ndarray
         (4, 4) Rotated system.
     """
-
     if metric.lower().startswith('deg'):
         angle = np.deg2rad(angle)
     elif not metric.lower().startswith('rad'):
@@ -317,7 +318,7 @@ def rotate_matsimnibs_euler(axis, angle, matsimnibs, metric='rad'):
 
 def rotmat_from_vecs(vec1, vec2):
     """
-    Find the rotation matrix that aligns vec1 to vec2
+    Find the rotation matrix that aligns vec1 to vec2.
 
     Parameters
     ----------
@@ -338,3 +339,109 @@ def rotmat_from_vecs(vec1, vec2):
     kmat = np.array([[0, -v[2], v[1]], [v[2], 0, -v[0]], [-v[1], v[0], 0]])
     rotation_matrix = np.eye(3) + kmat + kmat.dot(kmat) * ((1 - c) / (s ** 2))
     return Rotation.from_matrix(rotation_matrix)
+
+
+def matsim2paraview(matsim):
+    """
+    Convert a matsimnibs matrix to a format that can be used in ParaView.
+
+    Parameters
+    ----------
+    matsim
+        (4, 4) matsimnibs matrix.
+    """
+    print(f"rotations: {Rotation.from_matrix(matsim[:3, :3]).as_euler('xyz', degrees=True)}")
+    print(f"position: {matsim[:3, 3]}")
+
+
+def points_to_triangles(points, triangles):
+    """
+    Compute the closest points on a triangle mesh to a set of points.
+
+    Taken from https://stackoverflow.com/questions/32342620/closest-point-projection-of-a-3d-point-to-3d-triangles-with-numpy-scipy
+
+    Parameters
+    ----------
+    points : np.ndarray
+        (n, 3) Points to project.
+    triangles : np.ndarray
+        (m, 3, 3) Triangle points.
+
+    Returns
+    -------
+    np.ndarray
+        (n, 3) Closest points on the triangle mesh.
+    """
+    with np.errstate(all='ignore'):
+        # Unpack triangle points
+        p0, p1, p2 = np.asarray(triangles).swapaxes(0, 1)
+
+        # Calculate triangle edges
+        e0 = p1 - p0
+        e1 = p2 - p0
+        a = np.einsum('...i,...i', e0, e0)
+        b = np.einsum('...i,...i', e0, e1)
+        c = np.einsum('...i,...i', e1, e1)
+
+        # Calculate determinant and denominator
+        det = a * c - b * b
+        invDet = 1. / det
+        denom = a - 2 * b + c
+
+        # Project to the edges
+        p = p0 - points[:, np.newaxis]
+        d = np.einsum('...i,...i', e0, p)
+        e = np.einsum('...i,...i', e1, p)
+        u = b * e - c * d
+        v = b * d - a * e
+
+        # Calculate numerators
+        bd = b + d
+        ce = c + e
+        numer0 = (ce - bd) / denom
+        numer1 = (c + e - b - d) / denom
+        da = -d / a
+        ec = -e / c
+
+        # Vectorize test conditions
+        m0 = u + v < det
+        m1 = u < 0
+        m2 = v < 0
+        m3 = d < 0
+        m4 = (a + d > b + e)
+        m5 = ce > bd
+
+        t0 = m0 & m1 & m2 & m3
+        t1 = m0 & m1 & m2 & ~m3
+        t2 = m0 & m1 & ~m2
+        t3 = m0 & ~m1 & m2
+        t4 = m0 & ~m1 & ~m2
+        t5 = ~m0 & m1 & m5
+        t6 = ~m0 & m1 & ~m5
+        t7 = ~m0 & m2 & m4
+        t8 = ~m0 & m2 & ~m4
+        t9 = ~m0 & ~m1 & ~m2
+
+        u = np.where(t0, np.clip(da, 0, 1), u)
+        v = np.where(t0, 0, v)
+        u = np.where(t1, 0, u)
+        v = np.where(t1, 0, v)
+        u = np.where(t2, 0, u)
+        v = np.where(t2, np.clip(ec, 0, 1), v)
+        u = np.where(t3, np.clip(da, 0, 1), u)
+        v = np.where(t3, 0, v)
+        u *= np.where(t4, invDet, 1)
+        v *= np.where(t4, invDet, 1)
+        u = np.where(t5, np.clip(numer0, 0, 1), u)
+        v = np.where(t5, 1 - u, v)
+        u = np.where(t6, 0, u)
+        v = np.where(t6, 1, v)
+        u = np.where(t7, np.clip(numer1, 0, 1), u)
+        v = np.where(t7, 1 - u, v)
+        u = np.where(t8, 1, u)
+        v = np.where(t8, 0, v)
+        u = np.where(t9, np.clip(numer1, 0, 1), u)
+        v = np.where(t9, 1 - u, v)
+
+        # Return closest points
+        return (p0.T + u[:, np.newaxis] * e0.T + v[:, np.newaxis] * e1.T).swapaxes(2, 1)

pynibs/util/{simnibs.py → simnibs_io.py}

@@ -2,19 +2,17 @@ import gc
 import os
 import re
 import copy
-
 import h5py
 import tqdm
-import trimesh
-
-try:
-    import simnibs
-except (ModuleNotFoundError, ImportError):
-    print("SimNIBS not found. Some functions might not work.")
 import warnings
 import collections
 import numpy as np
-
+try:
+    from simnibs import ElementData
+except ImportError:
+    from simnibs.mesh_tools.mesh_io import ElementData
+except (ModuleNotFoundError, ImportError) as e:
+    print("SimNIBS not found. Some functions might not work.")
 import pynibs
 
 
@@ -78,7 +76,7 @@ def e_field_gradient_between_wm_gm(
     e_field_gradient_per_mm = e_field_gradient / gray_matter_thickness
     relative_e_field_gradient_per_mm = e_field_gradient_per_mm / e_field_center * 100
 
-    return simnibs.ElementData(relative_e_field_gradient_per_mm, name='rel_gradient_per_mm', mesh=roi_surf)
+    return ElementData(relative_e_field_gradient_per_mm, name='rel_gradient_per_mm', mesh=roi_surf)
 
 
 def e_field_angle_theta(surface, mesh):
@@ -107,7 +105,7 @@ def e_field_angle_theta(surface, mesh):
     angle = np.array([np.arccos(np.dot(a, b)) / np.pi * 180 for a, b in
                       zip(tri_normal, e_at_roi_cell_centers_normalized)])
 
-    return simnibs.ElementData(angle, name="theta", mesh=surface)
+    return ElementData(angle, name="theta", mesh=surface)
 
 
 def precompute_geo_info_for_layer_field_interpolation(simnibs_mesh, roi):
@@ -300,6 +298,11 @@ def calc_e_in_midlayer_roi(
     (roi.n_tris, 4) : np.vstack((e_mag, e_norm, e_tan, e_angle)).transpose() for the midlayer
         (len(roi.layers)x(roi.layers[idx].surface.n_tris,4)) : np.vstack((e_mag, e_norm, e_tan, e_angle)).transpose()
     """
+    try:
+        from simnibs import ElementData
+    except ImportError:
+        from simnibs.mesh_tools.mesh_io import ElementData
+    import simnibs
     # set default return quantities
     if qoi is None:
         qoi = ['E', 'mag', 'norm', 'tan', 'angle']
@@ -340,15 +343,15 @@ def calc_e_in_midlayer_roi(
     # We used to use (v, dadt) but nowadays E is enough
     if isinstance(e, tuple):
         e = e[0]
-    # simnibs calls this with empty data so find out about the results dimensions
+    # simnibs calls this with empty data to find out about the results dimensions
     if (e == 0).all():
         return np.zeros((max_num_elmts, ret_arr_num_components))
 
     # calc QOIs (all calculations are performed in the element centers)
-    data = simnibs.ElementData(e, name='E', mesh=mesh)
+    data = ElementData(e, name='E', mesh=mesh)
 
     interp_res_per_surface = dict()
-    mesh.elmdata.append(simnibs.ElementData(e, name='E', mesh=mesh))
+    mesh.elmdata.append(ElementData(e, name='E', mesh=mesh))
 
     for surface_id, surface in interpolation_surfaces.items():
         print(f"Computing {surface_id}")
@@ -473,6 +476,9 @@ def read_coil_geo(fn_coil_geo):
                 mag_or_vec = [float(f) for f in mag_or_vec.split(', ')]
                 if len(mag_or_vec) > 1:
                     mag_or_vec = np.linalg.norm(mag_or_vec)
+                elif isinstance(mag_or_vec, list):
+                    mag_or_vec = mag_or_vec[0]
+                    # elif
                 # else:
                 #     mag_or_vec = mag_or_vec[0]
                 dipole_pos.append(pos)
@@ -512,24 +518,25 @@ def check_mesh(mesh, verbose=False):
     neg_tets : np.ndarray
         Element indicies for negative volume tets (0-indexed)
     """
+    import simnibs
     if isinstance(mesh, str):
         mesh = simnibs.read_msh(mesh)
     tris = mesh.elm.node_number_list[mesh.elm.triangles - 1][:, :3]
     points_tri = mesh.nodes[tris]
-    tri_area = pynibs.calc_tri_surface(points_tri)
+    tri_area = pynibs.mesh.calc_tri_surface(points_tri)
     zero_tris = np.argwhere(np.isclose(tri_area, 0, atol=1e-13))
     if verbose:
         print(f"{len(zero_tris)} zero surface triangles found.")
 
     tets = mesh.elm.node_number_list[mesh.elm.tetrahedra - 1]
     points_tets = mesh.nodes[tets]
-    tets_volume = pynibs.calc_tet_volume(points_tets)
+    tets_volume = pynibs.mesh.calc_tet_volume(points_tets)
     zero_tets = np.argwhere(np.isclose(tets_volume, 0, atol=1e-13))
     if verbose:
         print(f"{len(zero_tets)} zero volume tetrahedra found.")
 
     tet_idx = mesh.elm.node_number_list[mesh.elm.tetrahedra - 1]
-    vol = pynibs.calc_tet_volume(mesh.nodes.node_coord[tet_idx - 1], abs=False)
+    vol = pynibs.mesh.calc_tet_volume(mesh.nodes.node_coord[tet_idx - 1], abs=False)
     neg_idx = np.argwhere(vol > 0)
     if verbose:
         print(f"{len(neg_idx)} negative tets found.")
@@ -556,6 +563,7 @@ def fix_mesh(mesh, verbose=False):
     -------
     fixed_mesh : simnibs.Mesh
     """
+    import simnibs
     if isinstance(mesh, str):
         mesh = simnibs.read_msh(mesh)
 
@@ -611,6 +619,8 @@ def smooth_mesh(mesh, output_fn, smooth=.8, approach='taubin', skin_only_output=
 
        Left: original, spiky mesh. Right: smoothed mesh.
     """
+    import trimesh
+    import simnibs
     if isinstance(mesh, str):
         mesh = simnibs.mesh_io.read_msh(mesh)
 
@@ -689,7 +699,7 @@ def get_opt_mat(folder, roi=0):
     """
     Load optimal coil position/orientation matsimnibs from SimNIBS online FEM.
 
-    Parameter:
+    Parameters
     ----------
     folder : str
         Folder with optimization results.
@@ -737,7 +747,7 @@ def get_skin_cortex_distance(mesh, coords, radius=5):
     mesh : str or simnibs.Mesh
         Mesh object or .msh filename.
     coords : np.ndarray
-        [3,] x,y,z coordinates to compute skin-cortex-distacnce for.
+        [3,] x,y,z coordinates to compute skin-cortex-distance for.
     radius : float, default: 5
         Spherical radius around ``coords`` to include points in for SCD computation.
 
@@ -746,7 +756,7 @@ def get_skin_cortex_distance(mesh, coords, radius=5):
     SCD : np.ndarray of float
         Skin-cortex distance.
     elm_in_roi : np.ndarray of int
-        Elelement numbers from mesh.elm.elm_number that where used to calculate PCD for.
+        Element numbers from mesh.elm.elm_number that where used to calculate PCD for.
     """
     from simnibs import read_msh
     if isinstance(mesh, str):

pynibs/util/{util.py → utils.py}

@@ -7,8 +7,6 @@ import warnings
 import itertools
 import subprocess
 import numpy as np
-from scipy.special import binom
-from sklearn.neighbors import KernelDensity
 import pynibs
 
 
@@ -23,7 +21,7 @@ def tal2mni(coords, direction='tal2mni', style='nonlinear'):
     ----------
     coords : np.ndarray or list
         x,y,z coordinates.
-    direction : str, default: 'tal2mni
+    direction : str, default: 'tal2mni'
         Transformation direction. One of ('tal2mni', 'mni2tal').
     style : str, default: 'nonlinear'
         Transformation style. One of ('linear', 'nonlinear').
@@ -31,7 +29,7 @@ def tal2mni(coords, direction='tal2mni', style='nonlinear'):
     Returns
     -------
     coords_trans : np.ndarray
-
+        Transformed coordinates.
     """
     assert direction in ['tal2mni',
                          'mni2tal'], f"direction parameter '{direction}' invalid. Choose 'tal2mni' or 'mni2tal'."
@@ -84,7 +82,6 @@ def rd(array, array_ref):
     rd : ndarray of float
         (array.shape[1]) Relative difference between the columns of array and array_ref.
     """
-
     return np.linalg.norm(array - array_ref) / np.linalg.norm(array_ref)
 
 
@@ -115,7 +112,7 @@ def generalized_extreme_value_distribution(x, mu, sigma, k):
 
 def differential_evolution(fobj, bounds, mut=0.8, crossp=0.7, popsize=20, its=1000, **kwargs):
     """
-    Differential evolution optimization algorithm
+    Differential evolution optimization algorithm.
 
     Parameters
     ----------
@@ -139,7 +136,7 @@ def differential_evolution(fobj, bounds, mut=0.8, crossp=0.7, popsize=20, its=10
     best : dict
         Dictionary containing the best values.
     fitness : float
-        Fitness value of best solution.
+        Fitness value of the best solution.
     """
     if kwargs is None:
         kwargs = dict()
@@ -299,6 +296,7 @@ def likelihood_posterior(x, y, fun, bounds=None, verbose=True, normalized_params
     x_bins_loc = np.linspace(np.min(x_pre) + dx_bins / 2, np.max(x_pre) - dx_bins / 2, n_bins)
 
     # determine probabilities of observations
+    from sklearn.neighbors import KernelDensity
     kde = KernelDensity(bandwidth=0.01, kernel='gaussian')
 
     likelihood = []
@@ -314,7 +312,7 @@ def likelihood_posterior(x, y, fun, bounds=None, verbose=True, normalized_params
         try:
             kde_bins = kde.fit(y_post[mask][:, np.newaxis])
         except ValueError:
-            warnings.warn("kde.fit(y_post[mask][:, np.newaxis]) yield NaN ... skipping bin")
+            warnings.warn("kde.fit(y_post[mask][:, np.newaxis]) yield nan ... skipping bin")
             continue
 
         # get probability densities at data
@@ -345,7 +343,7 @@ def mutual_coherence(array):
     Calculate the mutual coherence of a matrix A. It can also be referred as the cosine of the smallest angle
     between two columns.
 
-    mutual_coherence = mutual_coherence(array)
+    ``mutual_coherence = mutual_coherence(array)``
 
     Parameters
     ----------
@@ -357,7 +355,6 @@ def mutual_coherence(array):
     mutual_coherence : float
         Mutual coherence.
     """
-
     array = array / np.linalg.norm(array, axis=0)[np.newaxis, :]
     t = np.matmul(array.conj().T, array)
     np.fill_diagonal(t, 0.0)
@@ -374,7 +371,7 @@ def get_cartesian_product(array_list):
     """
     Generate a cartesian product of input arrays (all combinations).
 
-    cartesian_product = get_cartesian_product(array_list)
+    ``cartesian_product = get_cartesian_product(array_list)``
 
     Parameters
     ----------
@@ -388,10 +385,13 @@ def get_cartesian_product(array_list):
 
     Examples
     --------
-     .. code-block:: python
+
+    .. code-block:: python
+
         import pygpc
         out = pygpc.get_cartesian_product(([1, 2, 3], [4, 5], [6, 7]))
         out
+
     """
     cartesian_product = [element for element in itertools.product(*array_list)]
     return np.array(cartesian_product)
@@ -419,7 +419,7 @@ def norm_percentile(data, percentile):
 def compute_chunks(seq, num):
     """
     Splits up a sequence _seq_ into _num_ chunks of similar size.
-    If len(seq) < num, (num-len(seq)) empty chunks are returned so that len(out) == num.
+    If ``len(seq) < num``, (num-len(seq)) empty chunks are returned so that ``len(out) == num``.
 
     Parameters
     ----------
@@ -485,9 +485,6 @@ def bash(command):
     """
     print(("Running " + command))
     return os.popen(command).read()
-    # process = subprocess.Popen(command.split(), stdout=subprocess.PIPE, shell=True)
-    # output, error = process.communicate()
-    # return output, error
 
 
 def bash_call(command):
@@ -516,7 +513,7 @@ def invert(trans):
     rot_inv : np.ndarray of float
         (3, 3) Inverse rotation matrix.
     """
-    rot = pynibs.normalize_rot(trans[:3, :3].flatten())
+    rot = pynibs.utils.rotation.normalize_rot(trans[:3, :3].flatten())
     result = np.zeros((4, 4))
     result[3, 3] = 1.0
     t = -rot.T.dot(trans[:3, 3])
@@ -599,7 +596,7 @@ def unique_rows(a):
 
     Returns
     -------
-    a_unique : np.array
+    a_unique : np.ndarray
         (k, n) array a with only unique rows.
     """
     b = np.ascontiguousarray(a).view(np.dtype((np.void, a.dtype.itemsize * a.shape[1])))
@@ -627,6 +624,7 @@ def calc_n_network_combs(n_e, n_c, n_i):
     n_comb : int
         Number of combinations.
     """
+    from scipy.special import binom
     return binom(n_e, n_i) * np.sum([((n_i - 1) ** k) * binom(n_c, k) for k in range(1, n_c)])
 
 
@@ -634,13 +632,13 @@ def load_muaps(fn_muaps, fs=1e6, fs_downsample=1e5):
     # load MUAPs and downsample
     with h5py.File(fn_muaps, "r") as f:
         muaps_orig = f["MUAPShapes"][:]
-    N_MU = muaps_orig.shape[1]
+    n_mu = muaps_orig.shape[1]
 
     t_muap_orig = np.linspace(0, 1 / fs * (muaps_orig.shape[0] - 1), muaps_orig.shape[0])
     t_muap = np.linspace(0, t_muap_orig[-1], int(t_muap_orig[-1] * fs_downsample + 1))
-    muaps = np.zeros((len(t_muap), N_MU))
+    muaps = np.zeros((len(t_muap), n_mu))
 
-    for i in range(N_MU):
+    for i in range(n_mu):
         muaps[:, i] = np.interp(t_muap, t_muap_orig, muaps_orig[:, i])
 
     return muaps, t_muap
@@ -653,7 +651,7 @@ def cross_product(A, B):
     Parameters
     ----------
     A : np.ndarray of float
-        (2, (N, 3))
+        (2, (N, 3)) Input vectors, the cross product is evaluated between.
     B : np.ndarray of float
         (2, (N, 3)) Input vectors, the cross product is evaluated between.
 

pynibs/visualization/para.py

@@ -856,7 +856,7 @@ def surface_vector_plot(ps):
     t2LUTColorBar.AddRangeAnnotations = 0
     t2LUTColorBar.AutomaticAnnotations = 0
     t2LUTColorBar.DrawNanAnnotation = 0
-    t2LUTColorBar.NanAnnotation = 'NaN'
+    t2LUTColorBar.NanAnnotation = 'nan'
     t2LUTColorBar.TextPosition = 'Ticks right/top, annotations left/bottom'
     # t2LUTColorBar.AspectRatio = ps['colorbar_aspectratio']  # paraview.NotSupportedException: 'AspectRatio' is obsolete as of ParaView 5.4. Use the 'ScalarBarThickness' property to set the width instead.
 
@@ -1746,7 +1746,7 @@ def surface_vector_plot_vtu(ps):
     eLUTColorBar.AddRangeAnnotations = 0
     eLUTColorBar.AutomaticAnnotations = 0
     eLUTColorBar.DrawNanAnnotation = 0
-    eLUTColorBar.NanAnnotation = 'NaN'
+    eLUTColorBar.NanAnnotation = 'nan'
     eLUTColorBar.TextPosition = 'Ticks right/top, annotations left/bottom'
     # eLUTColorBar.AspectRatio = ps['colorbar_aspectratio']  # paraview.NotSupportedException: 'AspectRatio' is obsolete as of ParaView 5.4. Use the 'ScalarBarThickness' property to set the width instead.
 
@@ -2854,7 +2854,7 @@ def volume_plot(ps):
     eLUTColorBar.AddRangeAnnotations = 0
     eLUTColorBar.AutomaticAnnotations = 0
     eLUTColorBar.DrawNanAnnotation = 0
-    eLUTColorBar.NanAnnotation = 'NaN'
+    eLUTColorBar.NanAnnotation = 'nan'
     eLUTColorBar.TextPosition = 'Ticks right/top, annotations left/bottom'
     # eLUTColorBar.AspectRatio = ps['colorbar_aspectratio']  # paraview.NotSupportedException: 'AspectRatio' is obsolete as of ParaView 5.4. Use the 'ScalarBarThickness' property to set the width instead.
     eLUTColorBar.Title = ps['colorbar_label']
@@ -3868,7 +3868,7 @@ def volume_plot_vtu(ps):
     eLUTColorBar.AddRangeAnnotations = 0
     eLUTColorBar.AutomaticAnnotations = 0
     eLUTColorBar.DrawNanAnnotation = 0
-    eLUTColorBar.NanAnnotation = 'NaN'
+    eLUTColorBar.NanAnnotation = 'nan'
     eLUTColorBar.TextPosition = 'Ticks right/top, annotations left/bottom'
     # eLUTColorBar.AspectRatio = ps['colorbar_aspectratio']  # paraview.NotSupportedException: 'AspectRatio' is obsolete as of ParaView 5.4. Use the 'ScalarBarThickness' property to set the width instead.
     eLUTColorBar.Title = ps['colorbar_label']

pynibs/visualization/render_3D.py

@@ -22,8 +22,8 @@ def render_coil_positions(
     optionally also display a second set of coil positions,
     optionally also display a surface (e.g. gray matter or skin)
 
-    Parameters:
-    -----------
+    Parameters
+    ----------
     coil_conf_set_1_positions : np.ndarray
         The "center" coordinates of the primary coil configurations
     coil_conf_set_1_orientations : np.ndarray
@@ -38,8 +38,8 @@ def render_coil_positions(
         Name of the surface to display. Currently supported: "skin", "skull", "csf", "gm", "wm"
         Only valid if 'fn_mesh' has been provided.
 
-    Returns:
-    --------
+    Returns
+    -------
     True if successful, False in case of a fatal error.
     """
     try:

pynibs-0.2026.1.dist-info/METADATA

@@ -0,0 +1,105 @@
+Metadata-Version: 2.4
+Name: pyNIBS
+Version: 0.2026.1
+Summary: A python toolbox to conduct non-invasive brain stimulation (NIBS) experiments.
+Author: Konstantin Weise, Ole Numssen, Benjamin Kalloch
+Maintainer-email: Konstantin Weise <weise@cbs.mpg.de>, Ole Numssen <numssen@cbs.mpg.de>
+License: GPL3
+Project-URL: Home, https://gitlab.gwdg.de/tms-localization/pynibs
+Project-URL: Docs, https://pynibs.readthedocs.io/
+Project-URL: Twitter, https://www.twitter.com/num_ole
+Project-URL: Bluesky, https://bsky.app/profile/numole.bsky.social
+Project-URL: Download, https://pypi.org/project/pynibs/
+Keywords: NIBS,non-invasive brain stimulation,TMS,FEM
+Classifier: Development Status :: 3 - Alpha
+Classifier: Intended Audience :: Science/Research
+Classifier: Topic :: Scientific/Engineering
+Classifier: Topic :: Software Development :: Build Tools
+Classifier: Programming Language :: Python :: 3.11
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: cython>=0.29.20
+Requires-Dist: h5py>=2.10.0
+Requires-Dist: lmfit
+Requires-Dist: matplotlib>=3.2.1
+Requires-Dist: meshio
+Requires-Dist: nibabel>=3.0.2
+Requires-Dist: nilearn>=0.6.2
+Requires-Dist: numpy<2
+Requires-Dist: ortools
+Requires-Dist: pandas>=1.0.3
+Requires-Dist: pyyaml>=5.3.1
+Requires-Dist: scikit-learn>=0.22.1
+Requires-Dist: scipy>=1.4.1
+Requires-Dist: scikit-image
+Requires-Dist: setuptools>=49.1.0
+Requires-Dist: tqdm>=4.45.0
+Requires-Dist: trimesh>=3.8.11
+Requires-Dist: transformations
+Requires-Dist: fslpy
+Requires-Dist: pygpc>=0.4.1
+Requires-Dist: uncertainties
+Requires-Dist: asteval
+Requires-Dist: jsonschema
+Requires-Dist: tables
+Requires-Dist: vtk
+Requires-Dist: rtree
+Requires-Dist: tvb-gdist
+Dynamic: license-file
+
+# pyNIBS
+Preprocessing, postprocessing, and analyses routines for non-invasive brain stimulation experiments.
+
+[![Latest Release](https://gitlab.gwdg.de/tms-localization/pynibs/-/badges/release.svg)](https://gitlab.gwdg.de/tms-localization/pynibs)
+[![Documentation](https://readthedocs.org/projects/pynibs/badge/)](https://pynibs.readthedocs.io/)
+[![pipeline status](https://gitlab.gwdg.de/tms-localization/pynibs/badges/master/pipeline.svg)](https://gitlab.gwdg.de/tms-localization/pynibs/commits/master)
+[![coverage report](https://gitlab.gwdg.de/tms-localization/pynibs/badges/master/coverage.svg)](https://tms-localization.pages.gwdg.de/pynibs)
+
+![](https://gitlab.gwdg.de/uploads/-/system/project/avatar/9753/Fig_4.png?width=128)
+
+`pyNIBS` provides the functions to allow **cortical mappings** with transcranial magnetic stimulation (TMS) via **functional analysis**. `pyNIBS` is developed to work with [SimNIBS](http://www.simnibs.org), i.e. SimNIBS' meshes and FEM results can directly be used.
+ Currently, [SimNIBS >=4.0](https://github.com/simnibs/simnibs/releases/latest) is supported.
+
+See the [documentation](https://pynibs.readthedocs.io/) for package details and our [protocol](https://doi.org/10.1038/s41596-022-00776-6) publication for a extensive usage examples. Free view only version of the paper: https://t.co/uv7CmVw6tp.
+
+## Installation
+Via PiP:
+
+``` bash
+pip install pynibs
+```
+
+Or clone the source repository and install the development branch for the most recent version:
+
+``` bash
+git clone https://gitlab.gwdg.de/tms-localization/pynibs
+cd pynibs
+git checkout dev
+pip install -e .
+```
+
+See [here](https://gitlab.gwdg.de/tms-localization/papers/tmsloc_proto/-/blob/2aec4763edf17e7a2ac604403287bc7fb10285ff/README.md) for more detailed installation instructions.
+
+To import CED Signal EMG data use the `export to .mat` feature of Signal. 
+To read `.cfs` files exported with CED Signal you might need to [manually](HOW_TO_INSTALL_BIOSIG.txt) compile the libbiosig package.
+
+
+## Bugs
+For sure. Please open an [issue](https://gitlab.gwdg.de/tms-localization/pynibs/-/issues) or feel free to file a PR.
+
+
+## Citation
+Please cite _Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. NeuroImage, 245, 118654. doi:[10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)_ when using this toolbox in your research.
+
+
+## References
+  - Weise*, K., Numssen*, O., Thielscher, A., Hartwigsen, G., & Knösche, T. R. (2020). A novel approach to localize cortical TMS effects. *NeuroImage*, 209, 116486. doi: [10.1016/j.neuroimage.2019.116486](https://doi.org/10.1016/j.neuroimage.2019.116486)
+  - Numssen, O., Zier, A. L., Thielscher, A., Hartwigsen, G., Knösche, T. R., & Weise, K. (2021). Efficient high-resolution TMS mapping of the human motor cortex by nonlinear regression. *NeuroImage*, 245, 118654. doi: [10.1016/j.neuroimage.2021.118654](https://doi.org/10.1016/j.neuroimage.2021.118654)
+  - Weise*, K., Numssen*, O., Kalloch, B., Zier, A. L., Thielscher, A., Hartwigsen°, G., Knösche°, T. R. (2023). Precise transcranial magnetic stimulation motor-mapping. *Nature Protocols*. doi: [10.1038/s41596-022-00776-6](https://doi.org/10.1038/s41596-022-00776-6) 
+  - Jing, Y., Numssen, O., Weise, K., Kalloch, B., Buchberger, L., Haueisen, J., Hartwigsen, G., Knösche, T. (2023). Modeling the Effects of Transcranial Magnetic Stimulation on Spatial Attention. *Physics in Medicine & Biology*. doi: [10.1088/1361-6560/acff34](https://doi.org/10.1088/1361-6560/acff34)
+  - Numssen*, O., Kuhnke*, P., Weise, K., & Hartwigsen, G. (2024). Electric field based dosing for TMS. *Imaging Neuroscience*. doi: [10.1162/imag_a_00106](https://doi.org/10.1162/imag_a_00106) 
+  - Numssen, O., Martin, S., Williams, K., Knösche, T. R., & Hartwigsen, G. (2024). Quantification of subject motion during TMS via pulsewise coil displacement. *Brain Stimulation, 17*(5), 1045–1047. doi: [10.1016/j.brs.2024.08.009](https://doi.org/10.1016/j.brs.2024.08.009) 
+  - Weise, K., Makaroff, S. N., Numssen, O., Bikson, M., & Knösche, T. R. (2025). Statistical method accounts for microscopic electric field distortions around neurons when simulating activation thresholds. *Brain Stimulation, 18*(2), 280–286. doi: [10.1016/j.brs.2025.02.007](https://doi.org/10.1016/j.brs.2025.02.007)
+  - Jing, Y., Numssen, O., Hartwigsen, G., Knösche, T. R., & Weise, K. (2024). Effects of Electric Field Direction on TMS-based Motor Cortex Mapping. *bioRxiv*. doi: [10.1101/2024.12.10.627753](https://doi.org/10.1101/2024.12.10.627753) 
+  - Numssen*, O., Martin*, C. W., Worbs, T., Thielscher, A., Weise, K., & Knösche, T. R. (2025). Optimizing and assessing multichannel TMS focality. *bioRxiv*. doi: [10.1101/2025.09.19.677136](https://doi.org/10.1101/2025.09.19.677136)