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

pynibs/optimization/workhorses.py

@@ -1,7 +1,5 @@
 import scipy
 import numpy as np
-from sklearn.neighbors import KernelDensity
-
 import pynibs
 
 
@@ -34,9 +32,9 @@ def mc(idx_list, array, ele_idx_1, mode="cols", **kwargs):
 
     for ind in idx_list:
         if mode == "cols":
-            res.append(pynibs.mutual_coherence(array[ind, :]))
+            res.append(pynibs.util.utils.mutual_coherence(array[ind, :]))
         elif mode == "rows":
-            res.append(pynibs.mutual_coherence(array[ind, :].transpose()))
+            res.append(pynibs.util.utils.mutual_coherence(array[ind, :].transpose()))
         else:
             raise NotImplementedError("Specified mode not implemented. Choose 'rows' or 'cols'.")
 
@@ -392,9 +390,9 @@ def dist_mc(idx_list, array, ele_idx_1, ele_idx_2, mode="cols", **kwargs):
 
         # mc
         if mode == "cols":
-            res_mc[j] = pynibs.mutual_coherence(array_mc[ind, :])
+            res_mc[j] = pynibs.util.utils.mutual_coherence(array_mc[ind, :])
         elif mode == "rows":
-            res_mc[j] = pynibs.mutual_coherence(array_mc[ind, :].transpose())
+            res_mc[j] = pynibs.util.utils.mutual_coherence(array_mc[ind, :].transpose())
         else:
             raise NotImplementedError("Specified mode not implemented. Choose 'rows' or 'cols'.")
 
@@ -444,6 +442,7 @@ def coverage_prepare(idx_list, array, zap_idx, **kwargs):
     x = np.zeros((n_x, len(idx_list)))
     y = np.zeros((n_x, len(idx_list)))
 
+    from sklearn.neighbors import KernelDensity
     kde = KernelDensity(bandwidth=0.03, kernel='gaussian')
 
     for j, ind in enumerate(idx_list):
@@ -658,9 +657,9 @@ def fim_mc(idx_list, array, ele_idx_1, ele_idx_2, e_opt, c=None, mode="rows", **
 
         # mc
         if mode == "cols":
-            res_mc[j] = pynibs.mutual_coherence(array_mc[ind, :])
+            res_mc[j] = pynibs.util.utils.mutual_coherence(array_mc[ind, :])
         elif mode == "rows":
-            res_mc[j] = pynibs.mutual_coherence(array_mc[ind, :].transpose())
+            res_mc[j] = pynibs.util.utils.mutual_coherence(array_mc[ind, :].transpose())
         else:
             raise NotImplementedError("Specified mode not implemented. Choose 'rows' or 'cols'.")
 

pynibs/regression/__init__.py

@@ -1,11 +1,13 @@
 """
-This holds methods for the TMS-based cortical localization approach as published in [1]_
+This holds methods for the TMS-based cortical localization approach as published in [1]_ and [2]_.
 
 References
 ----------
 .. [1] 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.
+.. [2] 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>`_
 """
 from .regression import *
-from .score_types import *
 from .dual_node_detection import *