compare individually

Author: HengyeZhu

NeuroML2/compare_MC/RE/compare_individual.py

@@ -0,0 +1,119 @@
+import numpy as np
+import matplotlib.pyplot as plt
+import json
+import os
+
+def plot_individual_comparisons():
+    dat_file = "RE_reduced_cell_step_test.RE_reduced_cell_pop.v.dat"
+    json_file = "RE_reduced_hh2_data.json"
+    ina_hh2_dat_file = "hh2_na_iDensity.dat"
+    ik_hh2_dat_file = "hh2_k_iDensity.dat"
+    m_hh2_na_dat_file = "m_hh2_na_state.dat"
+    h_hh2_na_dat_file = "h_hh2_na_state.dat"
+    n_hh2_k_dat_file = "n_hh2_k_state.dat"
+    
+    dat_data = np.loadtxt(dat_file)
+    time_dat = dat_data[:, 0] 
+    voltage_dat = dat_data[:, 1] * 1000
+
+    ina_hh2_dat_data = np.loadtxt(ina_hh2_dat_file)
+    time_ina_hh2_dat = ina_hh2_dat_data[:, 0]
+    ina_hh2_dat = ina_hh2_dat_data[:, 1] * -0.1
+
+    ik_hh2_dat_data = np.loadtxt(ik_hh2_dat_file)
+    time_ik_hh2_dat = ik_hh2_dat_data[:, 0]
+    ik_hh2_dat = ik_hh2_dat_data[:, 1] * -0.1
+
+    m_hh2_na_dat_data = np.loadtxt(m_hh2_na_dat_file)
+    time_m_hh2_na_dat = m_hh2_na_dat_data[:, 0]
+    m_hh2_na_dat = m_hh2_na_dat_data[:, 1]
+
+    h_hh2_na_dat_data = np.loadtxt(h_hh2_na_dat_file)
+    time_h_hh2_na_dat = h_hh2_na_dat_data[:, 0]
+    h_hh2_na_dat = h_hh2_na_dat_data[:, 1]
+
+    n_hh2_k_dat_data = np.loadtxt(n_hh2_k_dat_file)
+    time_n_hh2_k_dat = n_hh2_k_dat_data[:, 0]
+    n_hh2_k_dat = n_hh2_k_dat_data[:, 1]
+    
+    with open(json_file, 'r') as f:
+        json_data = json.load(f)
+    
+    voltage_json = json_data['simData']['V_soma']['cell_0']
+    ina_hh2_json = json_data['simData']['ina']['cell_0']
+    ik_hh2_json = json_data['simData']['ik']['cell_0']
+    m_hh2_na_json = json_data['simData']['m_hh2_na']['cell_0']
+    h_hh2_na_json = json_data['simData']['h_hh2_na']['cell_0']
+    n_hh2_k_json = json_data['simData']['n_hh2_k']['cell_0']
+    
+    dt = 1e-6
+    time_json = np.arange(len(voltage_json)) * dt
+
+    plt.figure(figsize=(10, 6))
+    plt.plot(time_dat, voltage_dat, 'b-', label='nml Voltage', linewidth=2)
+    plt.plot(time_json, voltage_json, 'r--', label='netpyne Voltage', linewidth=1.5)
+    plt.xlabel('Time (s)')
+    plt.ylabel('Voltage (mV)')
+    plt.title('Voltage Comparison')
+    plt.legend()
+    plt.grid(True, linestyle='--', alpha=0.7)
+    plt.savefig("voltage_comparison.png", dpi=300, bbox_inches='tight')
+    plt.close()
+
+    plt.figure(figsize=(10, 6))
+    plt.plot(time_ina_hh2_dat, ina_hh2_dat, 'b-', label='nml ina_hh2', linewidth=2)
+    plt.plot(time_json, ina_hh2_json, 'r--', label='netpyne ina_hh2', linewidth=1.5)
+    plt.xlabel('Time (s)')
+    plt.ylabel('ina_hh2')
+    plt.title('ina_hh2 Comparison')
+    plt.legend()
+    plt.grid(True, linestyle='--', alpha=0.7)
+    plt.savefig("ina_comparison.png", dpi=300, bbox_inches='tight')
+    plt.close()
+
+    plt.figure(figsize=(10, 6))
+    plt.plot(time_ik_hh2_dat, ik_hh2_dat, 'b-', label='nml ik_hh2', linewidth=2)
+    plt.plot(time_json, ik_hh2_json, 'r--', label='netpyne ik_hh2', linewidth=1.5)
+    plt.xlabel('Time (s)')
+    plt.ylabel('ik_hh2')
+    plt.title('ik_hh2 Comparison')
+    plt.legend()
+    plt.grid(True, linestyle='--', alpha=0.7)
+    plt.savefig("ik_comparison.png", dpi=300, bbox_inches='tight')
+    plt.close()
+
+    plt.figure(figsize=(10, 6))
+    plt.plot(time_m_hh2_na_dat, m_hh2_na_dat, 'b-', label='nml m_hh2_na', linewidth=2)
+    plt.plot(time_json, m_hh2_na_json, 'r--', label='netpyne m_hh2_na', linewidth=1.5)
+    plt.xlabel('Time (s)')
+    plt.ylabel('m_hh2_na')
+    plt.title('m_hh2_na Comparison')
+    plt.legend()
+    plt.grid(True, linestyle='--', alpha=0.7)
+    plt.savefig("m_hh2_na_comparison.png", dpi=300, bbox_inches='tight')
+    plt.close()
+
+    plt.figure(figsize=(10, 6))
+    plt.plot(time_h_hh2_na_dat, h_hh2_na_dat, 'b-', label='nml h_hh2_na', linewidth=2)
+    plt.plot(time_json, h_hh2_na_json, 'r--', label='netpyne h_hh2_na', linewidth=1.5)
+    plt.xlabel('Time (s)')
+    plt.ylabel('h_hh2_na')
+    plt.title('h_hh2_na Comparison')
+    plt.legend()
+    plt.grid(True, linestyle='--', alpha=0.7)
+    plt.savefig("h_hh2_na_comparison.png", dpi=300, bbox_inches='tight')
+    plt.close()
+
+    plt.figure(figsize=(10, 6))
+    plt.plot(time_n_hh2_k_dat, n_hh2_k_dat, 'b-', label='nml n_hh2_k', linewidth=2)
+    plt.plot(time_json, n_hh2_k_json, 'r--', label='netpyne n_hh2_k', linewidth=1.5)
+    plt.xlabel('Time (s)')
+    plt.ylabel('n_hh2_k')
+    plt.title('n_hh2_k Comparison')
+    plt.legend()
+    plt.grid(True, linestyle='--', alpha=0.7)
+    plt.savefig("n_hh2_k_comparison.png", dpi=300, bbox_inches='tight')
+    plt.close()
+
+if __name__ == "__main__":
+    plot_individual_comparisons()