Merge pull request #1 from apdavison/hk/add-examples

NeuralEnsemble · Jul 24, 2024 · 45f5fa2 · 45f5fa2
2 parents 1b358db + 221d8ac
commit 45f5fa2
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diff --git a/examples/one_neuron_example.py b/examples/one_neuron_example.py
@@ -1,6 +1,8 @@
 # encoding: utf-8
 """
-A simple native NEST example of simulating One Neuron with the help of PyNN.
+A conversion to PyNN of the "One neuron example" from the NEST examples gallery.
+
+See: https://nest-simulator.readthedocs.io/en/stable/auto_examples/one_neuron.html
 
 
 Usage: one_neuron_example.py [-h] [--plot-figure] [--debug DEBUG] simulator
@@ -27,23 +29,23 @@
 # === Define parameters ========================================================
 
 cell_params = {
-    "v_rest": -70.0, # (mV)
-    "v_reset": -70.0, # (mV)
-    "cm": 0.250, # (nF)
-    "tau_m": 10, # (ms)
-    "tau_refrac": 2, # (ms)
-    "tau_syn_E": 2, # (ms)
-    "tau_syn_I": 2, # (ms)
-    "v_thresh": -55.0, # (mV)
-    "i_offset": 0.376, # (nA)
+    "v_rest": -70.0,  # (mV)
+    "v_reset": -70.0,  # (mV)
+    "cm": 0.250,  # (nF)
+    "tau_m": 10,  # (ms)
+    "tau_refrac": 2,  # (ms)
+    "tau_syn_E": 2,  # (ms)
+    "tau_syn_I": 2,  # (ms)
+    "v_thresh": -55.0,  # (mV)
+    "i_offset": 0.376,  # (nA)
 }
 
 # === Build the network ========================================================
 
-sim.setup(timestep=0.1) # (ms)
+sim.setup(timestep=0.1)  # (ms)
 
 cell_type = sim.IF_curr_alpha(**cell_params)
-neuron = sim.Population(1, cell_type, label="Neuron 1")
+neuron = sim.Population(1, cell_type, initial_values={"v": -70.0}, label="Simulation result")
 neuron.record("v")
 
 
@@ -54,23 +56,32 @@
 data_v = neuron.get_data().segments[0].filter(name="v")[0]
 
 if options.plot_figure:
-    figure_filename = normalized_filename("Results", "one_neuron_example", "png",
-                                          options.simulator, sim.num_processes())
+    from neo import AsciiSignalIO
+    from quantities import kHz
+
+    reference_data = AsciiSignalIO(
+        "one_neuron_example_reference_data.txt", sampling_rate=1 * kHz
+    ).read_block()
+
+    figure_filename = normalized_filename(
+        "Results", "one_neuron_example", "png", options.simulator, sim.num_processes()
+    )
     Figure(
         Panel(
-            data_v[:,0],
+            reference_data.segments[0].analogsignals[0],
+            data_v[:, 0],
             xticks=True,
             yticks=True,
             xlabel="Time (in ms)",
-            ylabel="Membrane Potential (mV)"
+            ylabel="Membrane Potential (mV)",
+            line_properties=[{"lw": 3}, {"lw": 1}],
+            data_labels=["Reference data", "Simulation result"]
         ),
         title="One Neuron",
-        annotations="One Neuron Example using PyNN"
+        annotations=f"One Neuron Example using PyNN (simulator: {options.simulator})",
     ).save(figure_filename)
     print(figure_filename)
 
 # === Clean up and quit ========================================================
 
 sim.end()
-
-