Added ploting nml outout

.gitignore

@@ -1 +1,6 @@
 /__pycache__
+/models/IClamp_GenericMuscleCell.net.nml
+/models/IClamp_GenericNeuronCell.net.nml
+/models/LEMS_Sim_IClamp_GenericMuscleCell.xml
+/report.Sim_IClamp_GenericMuscleCell.txt
+/report.Sim_IClamp_GenericNeuronCell.txt

app.py

@@ -127,22 +127,33 @@ with tab_model:
     with st.form("form_model"):
 
         from model import run_model
+        from model import MODELS
 
         text = st.text_area("Current injection level:", "4.1 pA")
+        model_to_sim = st.selectbox('Model to simulate', list(MODELS.keys()))
 
         submitted = st.form_submit_button("Submit")
 
         if submitted:
+            response, traces, events = run_model(text, model_to_sim)
+            st.info(response)
             try:
-                response = run_model(text)
-                st.info(response)
 
                 import numpy as np
                 import matplotlib.pyplot as plt
 
-                arr = np.random.normal(1, 1, size=100)
                 fig, ax = plt.subplots()
-                ax.hist(arr, bins=20)
+
+                for key in sorted(traces.keys()):
+                    if key != "t":
+                        ts = traces['t']
+                        vs = traces[key]
+                        ax.plot(ts,vs, label=key)
+                        ax.legend()
+                                                
+                        plt.xlabel("Time (ms)")
+                        plt.ylabel("(SI units)")
+                
 
                 st.pyplot(fig)
             except Exception as e:

model.py

@@ -9,14 +9,19 @@ from neuromllite.utils import load_simulation_json
 from neuromllite.utils import load_network_json
 from neuromllite.NetworkGenerator import generate_and_run
 
-def run_model(text, verbose = False):
+MODELS = {'Muscle model': ["models/Sim_IClamp_GenericMuscleCell.json","models/IClamp_GenericMuscleCell.json"],
+          'Neuron model': ["models/Sim_IClamp_GenericNeuronCell.json","models/IClamp_GenericNeuronCell.json"]}
 
-    info = '''Running models with: [%s]...
+def run_model(text, model, verbose = False):
 
-'''%text
+    info = '''Running [%s] with parameter: [%s]...
 
-    sim_file = "models/Sim_IClamp_GenericMuscleCell.json"
-    net_file = "models/IClamp_GenericMuscleCell.json"
+'''%(model,text)
+
+    print(info)
+
+    sim_file = MODELS[model][0]
+    net_file = MODELS[model][1]
 
     sim = load_simulation_json(sim_file)
     net = load_network_json(net_file)
@@ -37,14 +42,16 @@ def run_model(text, verbose = False):
                                       network=net, 
                                       simulator="jNeuroML",
                                       base_dir='./models',
+                                      target_dir='./models',
                                       return_results=True)
 
-    info+="""Results returned: %s"""%(list(traces.keys()))
+    #info+="""Results returned: %s"""%(list(traces.keys()))
+    info+="""Finished simulation!"""
 
     
 
     print(info)
 
-    return info
+    return info, traces, events
 
 

requirements.txt

@@ -6,4 +6,5 @@ asyncio
 langchain_experimental
 wormneuroatlas
 neuromllite
-matplotlib
+matplotlib
+pylems