/

figures/MAM2EBRAINS/.ipynb_checkpoints/M2E_LOAD_DATA-checkpoint.py

@@ -26,10 +26,10 @@ def load_and_create_data(M):
         simulated areas.
     """
     # Instantiate an analysis class and load spike data
-    A = Analysis(network=M, 
-                 simulation=M.simulation, 
-                 data_list=['spikes'],
-                 load_areas=None)
+    # A = Analysis(network=M, 
+    #              simulation=M.simulation, 
+    #              data_list=['spikes'],
+    #              load_areas=None)
     
 
     """
@@ -57,39 +57,12 @@ def load_and_create_data(M):
         If set to 'complete', all populations the respective areas
         are included. Defaults to 'complete'.
     """
-    A.create_pop_rates()
+    # A.create_pop_rates()
+    subprocess.run(['python3', './figures/Schmidt2018_dyn/compute_pop_rates.py'])
+    # subprocess.run(['Rscript', '--vanilla', 'compute_bold_signal.R', fn, out_fn])
     print("Computing population rates done")
 
     
-    """
-    Calculate synchrony as the coefficient of variation of the population rate
-    and store in member synchrony. Uses helper function synchrony.
-    If the synchrony has previously been stored with the
-    same parameters, they are loaded from file.
-
-
-    Parameters
-    ----------
-    t_min : float, optional
-        Minimal time in ms of the simulation to take into account
-        for the calculation. Defaults to 500 ms.
-    t_max : float, optional
-        Maximal time in ms of the simulation to take into account
-        for the calculation. Defaults to the simulation time.
-    areas : list, optional
-        Which areas to include in the calculcation.
-        Defaults to all loaded areas.
-    pops : list or {'complete'}, optional
-        Which populations to include in the calculation.
-        If set to 'complete', all populations the respective areas
-        are included. Defaults to 'complete'.
-    resolution : float, optional
-        Resolution of the population rate. Defaults to 1 ms.
-    """
-    A.create_synchrony()
-    print("Computing synchrony done")
-
-    
     """
     Calculate poulation-averaged LvR (see Shinomoto et al. 2009) and
     store as member pop_LvR. Uses helper function LvR.
@@ -110,7 +83,7 @@ def load_and_create_data(M):
         If set to 'complete', all populations the respective areas
         are included. Defaults to 'complete'.
     """
-    A.create_pop_LvR()
+    # A.create_pop_LvR()
     print("Computing population LvR done")
     
     
@@ -146,7 +119,7 @@ def load_and_create_data(M):
         - 'alpha_time_window' : time constant of the alpha function
         - 'rect_time_window' : width of the moving rectangular function
     """
-    A.create_rate_time_series()
+    # A.create_rate_time_series()
     print("Computing rate time series done")
     
     
@@ -184,7 +157,7 @@ def load_and_create_data(M):
 #     A.create_synaptic_input()
 #     print("Computing synaptic input done")
     
-    A.save()
+    # A.save()
     
     # """
     # Compute BOLD signal for a given area from the time series of
@@ -197,4 +170,4 @@ def load_and_create_data(M):
     # except FileNotFoundError:
     #     raise FileNotFoundError("Executing R failed. Did you install R?")
     
-    return A
\ No newline at end of file
+    # return A
\ No newline at end of file

figures/MAM2EBRAINS/M2E_LOAD_DATA.py

@@ -26,10 +26,10 @@ def load_and_create_data(M):
         simulated areas.
     """
     # Instantiate an analysis class and load spike data
-    A = Analysis(network=M, 
-                 simulation=M.simulation, 
-                 data_list=['spikes'],
-                 load_areas=None)
+    # A = Analysis(network=M, 
+    #              simulation=M.simulation, 
+    #              data_list=['spikes'],
+    #              load_areas=None)
     
 
     """
@@ -57,39 +57,12 @@ def load_and_create_data(M):
         If set to 'complete', all populations the respective areas
         are included. Defaults to 'complete'.
     """
-    A.create_pop_rates()
+    # A.create_pop_rates()
+    subprocess.run(['python3', './figures/Schmidt2018_dyn/compute_pop_rates.py'])
+    # subprocess.run(['Rscript', '--vanilla', 'compute_bold_signal.R', fn, out_fn])
     print("Computing population rates done")
 
     
-    """
-    Calculate synchrony as the coefficient of variation of the population rate
-    and store in member synchrony. Uses helper function synchrony.
-    If the synchrony has previously been stored with the
-    same parameters, they are loaded from file.
-
-
-    Parameters
-    ----------
-    t_min : float, optional
-        Minimal time in ms of the simulation to take into account
-        for the calculation. Defaults to 500 ms.
-    t_max : float, optional
-        Maximal time in ms of the simulation to take into account
-        for the calculation. Defaults to the simulation time.
-    areas : list, optional
-        Which areas to include in the calculcation.
-        Defaults to all loaded areas.
-    pops : list or {'complete'}, optional
-        Which populations to include in the calculation.
-        If set to 'complete', all populations the respective areas
-        are included. Defaults to 'complete'.
-    resolution : float, optional
-        Resolution of the population rate. Defaults to 1 ms.
-    """
-    A.create_synchrony()
-    print("Computing synchrony done")
-
-    
     """
     Calculate poulation-averaged LvR (see Shinomoto et al. 2009) and
     store as member pop_LvR. Uses helper function LvR.
@@ -110,7 +83,7 @@ def load_and_create_data(M):
         If set to 'complete', all populations the respective areas
         are included. Defaults to 'complete'.
     """
-    A.create_pop_LvR()
+    # A.create_pop_LvR()
     print("Computing population LvR done")
     
     
@@ -146,7 +119,7 @@ def load_and_create_data(M):
         - 'alpha_time_window' : time constant of the alpha function
         - 'rect_time_window' : width of the moving rectangular function
     """
-    A.create_rate_time_series()
+    # A.create_rate_time_series()
     print("Computing rate time series done")
     
     
@@ -184,7 +157,7 @@ def load_and_create_data(M):
 #     A.create_synaptic_input()
 #     print("Computing synaptic input done")
     
-    A.save()
+    # A.save()
     
     # """
     # Compute BOLD signal for a given area from the time series of
@@ -197,4 +170,4 @@ def load_and_create_data(M):
     # except FileNotFoundError:
     #     raise FileNotFoundError("Executing R failed. Did you install R?")
     
-    return A
\ No newline at end of file
+    # return A
\ No newline at end of file

figures/MAM2EBRAINS/M2E_visualize_resting_state.py

@@ -35,7 +35,7 @@ def set_boxplot_props(d):
     pl.setp(d['means'], marker='x', color='k',
             markerfacecolor='k', markeredgecolor='k', markersize=3.)
 
-def plot_resting_state(M, A, label_spikes, data_path):
+def plot_resting_state(M, A, data_path):
     t_sim = M.simulation.params["t_sim"]
     
     """