NaN bug fixed

analytical_correct.py

@@ -4,6 +4,7 @@
 import parameters as params
 
 import argparse
+import warnings
 
 
 def V(n):
@@ -103,8 +104,10 @@ def adjust_phi_angle(p):
     rxy = ele_pos - proj_rxyz_rz
     x = np.cross(p, dp_loc)
     cos_phi = np.dot(rxy, x.T) / np.dot(np.linalg.norm(rxy, axis=1).reshape(len(rxy),1), np.linalg.norm(x, axis=1).reshape(1, len(x)))
+    if abs(cos_phi).max() - 1 > 1e-10:
+        warnings.warn("cos_phi out of [-1 - 1e-10, 1 + 1e-10]", RuntimeWarning)
     cos_phi = np.nan_to_num(cos_phi)
-    phi_temp = np.arccos(cos_phi)
+    phi_temp = np.arccos(np.maximum(-1, np.minimum(1, cos_phi)))
     phi = phi_temp
     range_test = np.dot(rxy, p.T)
     for i in range(len(r_ele)):
@@ -187,6 +190,12 @@ def compute_phi(s12, s23, s34, I):
 I = 1.
 n = np.arange(1, 100)
 
+# test for NaN bug
+src_pos = [-3.850000e+00, 6.668396e+00, 0.05]
+snk_pos = [-3.850000e+00, 6.668396e+00, -0.05]
+s12, s23, s34 = conductivity(params.sigma_skull20)
+assert not np.isnan(compute_phi(s12, s23, s34, I)).any()
+
 for dipole in params.dipole_list:
     print('Now computing for dipole: ', dipole['name'])
     src_pos = dipole['src_pos']

figure3.py

@@ -17,7 +17,7 @@
                     const='Sri98_no_bn1',
                     default='Sri98',
                     dest='sri98',
-                    help='a path to the result directory')
+                    help='use Analytical_Sri98_no_bn1*.npz files')
 
 args = parser.parse_args()
 

figure4.py

@@ -22,7 +22,7 @@
                     const='Sri98_no_bn1',
                     default='Sri98',
                     dest='sri98',
-                    help='a path to the result directory')
+                    help='use Analytical_Sri98_no_bn1*.npz files')
 
 args = parser.parse_args()