feat: add script to create summary readme for channels

Author: sanjayankur31

NeuroML2/compare_MC/IT2/compare/create_summary_readme.py

@@ -10,6 +10,10 @@
 
 
 from pathlib import Path
+from contextlib import chdir
+import json
+import numpy as np
+from pyneuroml.plot import generate_plot
 
 
 cwd = Path('.')
@@ -20,15 +24,40 @@
 md_text += "|---------|------------|----------------|---------------|--------------|--------------|\n"
 
 for d in directories:
-    print(f"Looking in {d.name}")
+    print(f"--> Processing {d.name}")
     channel = d.name
     mod_source = f"[{channel}.mod](../mod/{channel}.mod)"
     nml_source = f"[{channel}.channel.nml](../{channel}.channel.nml)"
-    np_plot = list(d.glob("netpyne*png"))[0]
-    nml_plot = list(d.glob("nml*png"))[0]
+    np_data = list(d.glob("netpyne*json"))[0]
+    np_plot = np_data.name.replace(".json", ".png")
+    nml_data = list(d.glob("nml*dat"))[0]
+    nml_plot = f"nml_{channel}.png"
     combined_plot = f"{d.name}/Figure_1.png"
 
     md_text += f"| {channel} | {mod_source} | {nml_source} | ![{channel} NetPyNE]({np_plot}) | ![{channel} NML]({nml_plot}) | ![{channel} combined]({combined_plot})\n"
 
+    combined_figure = Path(d) / Path("Figure_1.png")
+
+    if not combined_figure.exists():
+        print("--> All required figures not found, re-generating")
+        with chdir(d):
+            dat_data = np.loadtxt(nml_data.name)
+            time_dat = dat_data[:, 0]
+            voltage_dat = dat_data[:, 1] * 1000
+
+            voltage_json = None
+            time_json = None
+
+            with open(np_data.name, 'r') as f:
+                json_data = json.load(f)
+
+                voltage_json = json_data['simData']['V_soma']['cell_0']
+
+                dt = 1e-5
+                time_json = np.arange(len(voltage_json)) * dt
+
+            generate_plot([time_dat, time_json], [voltage_dat, voltage_json], title="Comparison of Voltage from nml and netpyne", labels=["NML", "NetPyNE"], colors=["b", "r"], linestyles=["-", "--"], xaxis="Time (s)", yaxis="Voltage (mV)", show_plot_already=False, title_above_plot=True, save_figure_to="Figure_1.png", close_plot=True, xlim=[min(time_dat[0], time_json[0]), max(time_dat[-1], time_json[-1])], font_size=12)
+
+print("--> Writing README.md")
 with open("README.md", 'w') as f:
     print(md_text, file=f)