Skip to content

Commit 5376d46

Browse files
HengyeZhuHengyeZhu
committed
compare nml and netpy
1 parent a807204 commit 5376d46

File tree

3 files changed

+52
-39
lines changed

3 files changed

+52
-39
lines changed

‎NeuroML2/compare_MC/RE/cadad.channel.nml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -4,7 +4,7 @@
44
xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2 https://raw.github.com/NeuroML/NeuroML2/development/Schemas/NeuroML2/NeuroML_v2beta3.xsd"
55
id="cadad">
66

7-
<concentrationModel id="cadad_RE_soma" type="cadad" ion="ca" cainf="2.4e-4 mM" taur="5 ms" depth="1 um"/>
7+
<cadad id="cadad_RE_soma" ion="ca" cainf="2.4e-4 mM" taur="5 ms" depth="1 um"/>
88

99
<ComponentType name="cadad" extends="concentrationModel">
1010

‎NeuroML2/compare_MC/RE/compare_all.png‎

224 KB
Loading

‎NeuroML2/compare_all.py‎

Lines changed: 51 additions & 38 deletions
Original file line numberDiff line numberDiff line change
@@ -2,69 +2,82 @@
22
import matplotlib.pyplot as plt
33
import json
44
import os
5-
65
def compare_all():
76
dat_file = "/home/gluciferd/Macaque_auditory_thalamocortical_model_data/NeuroML2/compare_MC/RE/RE_reduced_cell_step_test.RE_reduced_cell_pop.v.dat"
87
json_file = "/home/gluciferd/Macaque_auditory_thalamocortical_model_data/NeuroML2/compare_MC/RE/RE_reduced_itre_data.json"
98
m_itre_dat_file = "/home/gluciferd/Macaque_auditory_thalamocortical_model_data/NeuroML2/compare_MC/RE/m_itre_state.dat"
109
h_itre_dat_file = "/home/gluciferd/Macaque_auditory_thalamocortical_model_data/NeuroML2/compare_MC/RE/h_itre_state.dat"
11-
10+
ica_itre_dat_file = "/home/gluciferd/Macaque_auditory_thalamocortical_model_data/NeuroML2/compare_MC/RE/itre_iDensity.dat"
11+
caConc_dat_file = "/home/gluciferd/Macaque_auditory_thalamocortical_model_data/NeuroML2/compare_MC/RE/caConc.dat"
12+
1213
dat_data = np.loadtxt(dat_file)
1314
time_dat = dat_data[:, 0]
1415
voltage_dat = dat_data[:, 1] * 1000
15-
1616
m_itre_dat_data = np.loadtxt(m_itre_dat_file)
1717
time_m_itre_dat = m_itre_dat_data[:, 0]
1818
m_itre_dat = m_itre_dat_data[:, 1]
19-
2019
h_itre_dat_data = np.loadtxt(h_itre_dat_file)
2120
time_h_itre_dat = h_itre_dat_data[:, 0]
2221
h_itre_dat = h_itre_dat_data[:, 1]
23-
22+
ica_itre_dat_data = np.loadtxt(ica_itre_dat_file)
23+
time_ica_itre_dat = ica_itre_dat_data[:, 0]
24+
ica_itre_dat = ica_itre_dat_data[:, 1]
25+
caConc_dat_data = np.loadtxt(caConc_dat_file)
26+
time_caConc_dat = caConc_dat_data[:, 0]
27+
caConc_dat = caConc_dat_data[:, 1]
28+
2429
with open(json_file, 'r') as f:
2530
json_data = json.load(f)
26-
2731
voltage_json = json_data['simData']['V_soma']['cell_0']
2832
h_itre_json = json_data['simData']['h_itre']['cell_0']
2933
m_itre_json = json_data['simData']['m_itre']['cell_0']
30-
34+
ica_itre_json = json_data['simData']['ica_itre']['cell_0']
35+
caConc_json = json_data['simData']['caConc_itre']['cell_0']
36+
3137
dt = 1e-5
3238
time_json = np.arange(len(voltage_json)) * dt
33-
34-
plt.figure(figsize=(15, 5))
35-
36-
plt.subplot(1, 3, 1)
37-
plt.plot(time_dat, voltage_dat, 'b-', label='nml Voltage', linewidth=2)
38-
plt.plot(time_json, voltage_json, 'r--', label='netpyne Voltage', linewidth=1.5)
39-
plt.xlabel('Time (s)', fontsize=10)
40-
plt.ylabel('Voltage (mV)', fontsize=10)
41-
plt.title('Voltage Comparison', fontsize=12)
42-
plt.legend(fontsize=8)
43-
plt.grid(True, linestyle='--', alpha=0.7)
44-
45-
plt.subplot(1, 3, 2)
46-
plt.plot(time_h_itre_dat, h_itre_dat, 'b-', label='nml h_itre', linewidth=2)
47-
plt.plot(time_json, h_itre_json, 'r--', label='netpyne h_itre', linewidth=1.5)
48-
plt.xlabel('Time (s)', fontsize=10)
49-
plt.ylabel('h_itre', fontsize=10)
50-
plt.title('h_itre Comparison', fontsize=12)
51-
plt.legend(fontsize=8)
52-
plt.grid(True, linestyle='--', alpha=0.7)
53-
54-
plt.subplot(1, 3, 3)
55-
plt.plot(time_m_itre_dat, m_itre_dat, 'b-', label='nml m_itre', linewidth=2)
56-
plt.plot(time_json, m_itre_json, 'r--', label='netpyne m_itre', linewidth=1.5)
57-
plt.xlabel('Time (s)', fontsize=10)
58-
plt.ylabel('m_itre', fontsize=10)
59-
plt.title('m_itre Comparison', fontsize=12)
60-
plt.legend(fontsize=8)
61-
plt.grid(True, linestyle='--', alpha=0.7)
62-
39+
40+
fig, axes = plt.subplots(3, 2, figsize=(15, 15))
41+
axes[0, 0].plot(time_dat, voltage_dat, 'b-', label='nml Voltage', linewidth=2)
42+
axes[0, 0].plot(time_json, voltage_json, 'r--', label='netpyne Voltage', linewidth=1.5)
43+
axes[0, 0].set_xlabel('Time (s)', fontsize=10)
44+
axes[0, 0].set_ylabel('Voltage (mV)', fontsize=10)
45+
axes[0, 0].set_title('Voltage Comparison', fontsize=12)
46+
axes[0, 0].legend(fontsize=8)
47+
axes[0, 0].grid(True, linestyle='--', alpha=0.7)
48+
axes[0, 1].plot(time_h_itre_dat, h_itre_dat, 'b-', label='nml h_itre', linewidth=2)
49+
axes[0, 1].plot(time_json, h_itre_json, 'r--', label='netpyne h_itre', linewidth=1.5)
50+
axes[0, 1].set_xlabel('Time (s)', fontsize=10)
51+
axes[0, 1].set_ylabel('h_itre', fontsize=10)
52+
axes[0, 1].set_title('h_itre Comparison', fontsize=12)
53+
axes[0, 1].legend(fontsize=8)
54+
axes[0, 1].grid(True, linestyle='--', alpha=0.7)
55+
axes[1, 0].plot(time_m_itre_dat, m_itre_dat, 'b-', label='nml m_itre', linewidth=2)
56+
axes[1, 0].plot(time_json, m_itre_json, 'r--', label='netpyne m_itre', linewidth=1.5)
57+
axes[1, 0].set_xlabel('Time (s)', fontsize=10)
58+
axes[1, 0].set_ylabel('m_itre', fontsize=10)
59+
axes[1, 0].set_title('m_itre Comparison', fontsize=12)
60+
axes[1, 0].legend(fontsize=8)
61+
axes[1, 0].grid(True, linestyle='--', alpha=0.7)
62+
axes[1, 1].plot(time_ica_itre_dat, ica_itre_dat, 'b-', label='nml ica_itre', linewidth=2)
63+
axes[1, 1].plot(time_json, ica_itre_json, 'r--', label='netpyne ica_itre', linewidth=1.5)
64+
axes[1, 1].set_xlabel('Time (s)', fontsize=10)
65+
axes[1, 1].set_ylabel('ica_itre', fontsize=10)
66+
axes[1, 1].set_title('ica_itre Comparison', fontsize=12)
67+
axes[1, 1].legend(fontsize=8)
68+
axes[1, 1].grid(True, linestyle='--', alpha=0.7)
69+
axes[2, 0].plot(time_caConc_dat, caConc_dat, 'b-', label='nml caConc', linewidth=2)
70+
axes[2, 0].plot(time_json, caConc_json, 'r--', label='netpyne caConc', linewidth=1.5)
71+
axes[2, 0].set_xlabel('Time (s)', fontsize=10)
72+
axes[2, 0].set_ylabel('caConc', fontsize=10)
73+
axes[2, 0].set_title('caConc Comparison', fontsize=12)
74+
axes[2, 0].legend(fontsize=8)
75+
axes[2, 0].grid(True, linestyle='--', alpha=0.7)
76+
axes[2, 1].axis('off')
6377
plt.tight_layout()
6478
current_dir = os.getcwd()
6579
save_path = os.path.join(current_dir, "compare_all.png")
6680
plt.savefig(save_path, dpi=300, bbox_inches='tight')
6781
plt.show()
68-
6982
if __name__ == "__main__":
7083
compare_all()

0 commit comments

Comments
 (0)