Added 'courtemanche-ramirez-1998-RushLarsen'/Changed PMJ delay calcul…

…us to use the minLAT of the coupled ventricular cells

ToDo

@@ -32,4 +32,7 @@ When the minimum number of PMJs is not reached the solver will be in an infinite
 <t> <sv_1> <sv_2> <sv_3> ... <sv_n>
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 .   .       .       .           .
-.   .       .       .           .
+.   .       .       .           .
+
+
+Fix the "save_multiple_cell_state_variables". It cannot find the proper cell center.

example_configs/activation_time_and_apd_example.ini

@@ -0,0 +1,64 @@
+[main]
+num_threads=4
+dt_pde=0.01
+simulation_time=5000.0
+abort_on_no_activity=false
+use_adaptivity=false
+
+[update_monodomain]
+main_function=update_monodomain_default
+
+[save_result]
+print_rate=10
+mesh_print_rate=100
+mesh_format=ensight
+output_dir=./outputs/cable_save_activation_time_and_apd_example
+init_function=init_save_with_activation_times
+end_function=end_save_with_activation_times
+main_function=save_with_activation_times
+time_threshold=0.0
+activation_threshold=-50.0
+apd_threshold=-70.0
+save_visible_mask=false
+remove_older_simulation=true
+
+[assembly_matrix]
+init_function=set_initial_conditions_fvm
+sigma_x=0.0000176
+sigma_y=0.0000176
+sigma_z=0.0000176
+library_file=shared_libs/libdefault_matrix_assembly.so
+main_function=homogeneous_sigma_assembly_matrix
+
+[linear_system_solver]
+tolerance=1e-16
+use_preconditioner=no
+max_iterations=500
+library_file=shared_libs/libdefault_linear_system_solver.so
+use_gpu=no
+main_function=conjugate_gradient
+init_function=init_conjugate_gradient
+end_function=end_conjugate_gradient
+
+[domain]
+name=Cable Mesh with no fibrosis
+start_dx=100.0
+start_dy=100.0
+start_dz=100.0
+cable_length=10000.0
+main_function=initialize_grid_with_cable_mesh
+
+[ode_solver]
+adaptive=false
+dt=0.01
+use_gpu=false
+gpu_id=0
+library_file= shared_libs/libToRORd_dynCl_mixed_endo_mid_epi.so
+
+[stim_plain]
+start = 0.0
+duration = 2.0
+current = -53.0
+x_limit = 500.0
+period=1000.0
+main_function=stim_if_x_less_than

scripts/reader_acm.py

@@ -0,0 +1,69 @@
+import sys
+
+def read_acm_file (filename, target_center_x, target_center_y, target_center_z):
+    file = open(filename)
+    counter_lines = 0
+    for line in file:
+        if (counter_lines > 1):
+            line = line.strip()
+            new_line = line.replace(",", " ")
+
+            # Cell geometry section
+            first_open_bracket_id = new_line.find('[')          # find() -> lowest index
+            first_close_bracket_id = new_line.find(']')         
+            second_open_bracket_id = new_line.rfind('[')        # rfind() -> hightest index
+            second_close_bracket_id = new_line.rfind(']')
+            cell_geometry_data = new_line[0:first_open_bracket_id]
+            tokens = cell_geometry_data.split()
+            center_x, center_y, center_z, dx, dy, dz = float(tokens[0]), float(tokens[1]), float(tokens[2]), float(tokens[3]), float(tokens[4]), float(tokens[5])
+            #print("%g %g %g %g %g %g" % (center_x, center_y, center_y, dx, dy, dz))
+
+            # Activation time section
+            activation_time_values = []
+            activation_time_data = new_line[first_open_bracket_id+1:first_close_bracket_id].split()
+            for value in activation_time_data:
+                activation_time_values.append(float(value))
+            #print(activation_time_values)
+
+            # APD section
+            apd_values = []
+            apd_data = new_line[second_open_bracket_id+1:second_close_bracket_id].split()
+            for value in apd_data:
+                apd_values.append(float(value))
+            #print(apd_values)
+
+            # SUCESS: Found the target cell!
+            if (center_x == target_center_x and center_y == target_center_y and center_z == target_center_z):
+                return activation_time_values, apd_values
+
+        counter_lines = counter_lines + 1
+    file.close()
+    return activation_time_values, apd_values
+
+def main():
+
+    if len(sys.argv) != 5:
+        print("-------------------------------------------------------------------------")
+        print("Usage:> python %s <input_file> <center_x> <center_y> <center_z>" % sys.argv[0])
+        print("-------------------------------------------------------------------------")
+        print("<input_file> = Input \".acm\" file with the activation time and APD data")
+        print("<center_x> = Cell center x position")
+        print("<center_y> = Cell center y position")
+        print("<center_z> = Cell center z position")
+        print("-------------------------------------------------------------------------")
+        return 1
+
+    input_file = sys.argv[1]
+    target_center_x = float(sys.argv[2])
+    target_center_y = float(sys.argv[3])
+    target_center_z = float(sys.argv[4])
+
+    activation_time_values, apd_values = read_acm_file(input_file, target_center_x, target_center_y, target_center_z)
+    print("Activation times:")
+    print(activation_time_values)
+    print()
+    print("APDs:")
+    print(apd_values)
+
+if __name__ == "__main__":
+	main()