fixing various bugs fmod + adding nerve_results.fasc_pties, units MV kV

nrv/fmod/FEM/fenics_utils/_FEMSimulation.py

@@ -334,7 +334,7 @@ def __init_domain(self):
         if not self.domain_status:
             # RECOVERING THE GEOMETRY
             self.domain, self.subdomains, self.boundaries = read_gmsh(
-                self.mesh, comm=self.comm, rank=self.rank, gdim=3
+                self.mesh, comm=self.comm, rank=self.rank, gdim=self.D
             )
             # SPACE FOR INTEGRATION
             if self.inbound:

nrv/fmod/FEM/mesh_creator/_NerveMshCreator.py

@@ -179,7 +179,7 @@ def save(
         blacklist += [
             "model",
         ]
-        if self.is_generated and save:
+        if self.is_generated and (save or mshfname is not None):
             if mshfname is None:
                 mshfname = rmv_ext(fname) + ".msh"
             super().save(fname=mshfname, generate=False)

nrv/fmod/_recording.py

@@ -245,9 +245,10 @@ def compute_PSA_anisotropic_footprint(
             surface = surface = np.pi * (d / cm) * (np.gradient(x_axon) / cm)
             d_internode = np.gradient(x_axon)
 
-        sx = sigma_yy * sigma_zz
-        sy = sigma_xx * sigma_zz
-        sz = sigma_xx * sigma_yy
+        #!! Modified tc 12/12/24 added **0.5 
+        sx = (sigma_yy * sigma_zz)**.5
+        sy = (sigma_xx * sigma_zz)**.5
+        sz = (sigma_xx * sigma_yy)**.5
 
         electrical_distance = (
             4
@@ -670,6 +671,7 @@ def compute_footprints(self, x_axon, y_axon, z_axon, d, ID, myelinated=False):
                                 self.sigma_xx,
                                 self.sigma_yy,
                                 self.sigma_zz,
+                                True,
                             )
                     if point.method == "LSA":
                         if self.isotropic:

nrv/nmod/results/_nerve_results.py

@@ -63,6 +63,28 @@ def axons_type(self) -> np.ndarray:
         """
         return self.axons_pop_properties[:,[0,2]]
 
+    @property
+    def fasc_properties(self) -> np.ndarray:
+        """
+        Porperties of axons population of each fascicles
+
+        Returns
+        -------
+        np.ndarray (self.n_ax, 6)
+            ndarray gathering, for all fascicles in the nerve, fascicle IDs, diameter and y and z positions.
+        """
+        fasc_keys = self.fascicle_keys
+        _fasc = np.zeros((self.n_fasc, 4))
+        for i_fasc, key in enumerate(fasc_keys):
+            fasc_ = self[key]
+            _fasc[i_fasc, :] = np.array([
+                fasc_.ID,
+                fasc_.D,
+                fasc_.y_grav_center,
+                fasc_.z_grav_center,
+            ])
+        return _fasc
+
     @property
     def axons_pop_properties(self) -> np.ndarray:
         """

nrv/ui/_axon_postprocessing.py

@@ -1187,7 +1187,7 @@ def is_blocked(results:axon_results, AP_start:float|None=None, freq:float|None=N
 
 
 
-def sample_keys(results:axon_results, keys_to_sample:str|set[str]={}, t_start_rec:float=0, t_stop_rec:float=-1, sample_dt:None|float=None, x_bounds:None|float|tuple[float]=None, keys_to_remove:str|set[str]={}, keys_to_keep:set[str]={})->axon_results:
+def sample_keys(results:axon_results, keys_to_sample:str|set[str]={}, t_start_rec:float=0, t_stop_rec:float=-1, sample_dt:None|float=None, i_sampled_t:None|np.ndarray=None, x_bounds:None|float|tuple[float]=None, keys_to_remove:str|set[str]={}, keys_to_keep:set[str]={})->axon_results:
     """
     Undersample the membrane coductivity (``results["g_mem"]``) key and remove most of the `axon_results` keys to alliviate RAM usage.
 
@@ -1232,38 +1232,43 @@ def sample_keys(results:axon_results, keys_to_sample:str|set[str]={}, t_start_re
     if len(set(keys_to_sample) - set(results.keys())):
         rise_error(set(keys_to_sample) - set(results.keys()), "keys are missing to apply postprocessing. Please check simulation parameters")
     else:
-        if t_stop_rec < 0:
-            t_stop_rec=results.t_sim
-
-        if sample_dt is None:
-            sample_dt=results.dt
-
+        # x - sampling array
         if x_bounds is None:
-            x_bounds=(0,results.L)
-
-        if np.iterable(x_bounds):
+            I_x = np.arange(len(results["x_rec"]))
+            x_bounds = (0, results["x_rec"][-1])
+        elif np.iterable(x_bounds):
             I_x = np.argwhere((results["x_rec"]>x_bounds[0])&(results["x_rec"]<x_bounds[1]))[:,0]
         else:
             x_bounds = [x_bounds]
             I_x = np.array([np.argmin(abs(results["x_rec"]-x_bounds[0]))])
-
         N_x = len(I_x)
-        i_t_min = np.argwhere(results["t"]>t_start_rec)[0][0]
-        i_t_max = np.argwhere(results["t"]<t_stop_rec)[-1][0]
 
-        t_APs = [k for k in range(i_t_min,i_t_max)]
-        t_APs = t_APs[::int(sample_dt/results.dt)]
+        # t - sampling array
+        if i_sampled_t is not None:
+            t_APs = i_sampled_t
+        else:
+            if t_stop_rec < 0:
+                i_t_max = len(results["t"])
+            else:
+                i_t_max = np.argwhere(results["t"]<=t_stop_rec)[-1][0]
+            if sample_dt is None:
+                sample_dt=results.dt
+            i_t_min = np.argwhere(results["t"]>=t_start_rec)[0][0]
+
+            t_APs = [k for k in range(i_t_min,i_t_max)]
+            t_APs = t_APs[::int(sample_dt/results.dt)]
 
         # Under sampling to reduce memory consumption
         results["x_rec"] = results["x_rec"][I_x] - x_bounds[0]
-        results["t"] = results["t"][t_APs]
+        if "t" in results:
+            results["t"] = results["t"][t_APs]
         for key in keys_to_sample:
             results[key] = results[key][np.ix_(I_x, t_APs)]
-
         ###############################
         ## remove non nevessary data ##
         ###############################
         list_keys =  {
+        "ID",
         "x_rec",
         "rec",
         "Nseg_per_sec",

nrv/utils/_units.py

@@ -12,7 +12,7 @@
             - Existing
         *   - Voltage
             - mV
-            - uV, V
+            - uV, V, kV, MV
         *   - Time
             - ms
             - us, s, minute, hour, day
@@ -54,6 +54,8 @@
 ######################
 uV = 1e-3 * mV
 V = 1e3 * mV
+kV = 1e3 * V
+MV = 1e3 * kV
 
 #############################
 ## time prefixes and units ##