Restructure repository

[norepinephrine_wm.git] / model.py

diff --git a/model.py b/model.py
new file mode 100644 (file)
index 0000000..4a4b54b
--- /dev/null
+++ b/model.py
@@ -0,0 +1,112 @@
+import numpy as np
+import matplotlib.pyplot as plt
+from os import mkdir
+
+# Refer to parameters.txt for documentation
+dt = 0.001
+t_cue = 1.0
+cue_scale = 1.0
+perceived = 0 # ???
+time_scale = 0.4
+steps = 100
+
+class Alpha(object):
+    def __init__(self):
+        self.x = np.logspace(0, 3, steps)
+        self.y = 1 / (1 + (999 * np.exp(-0.1233 * (self.x / self.offset))))
+        
+        self.gain = []
+        self.bias = []
+        
+    def calcgb(self, gaind, biasd):
+        for i in range(steps):
+            y = self.y[i]
+            self.gain.append(1 + gaind * y)
+            self.bias.append(1 + biasd * y)
+
+    def plot(self):
+        try:
+            mkdir("./out")
+        except FileExistsError:
+            pass
+
+        out = f"./out/{self.__class__.__name__}"
+        plt.plot(self.x, self.y)
+
+        plt.xlabel("Norepinephrine concentration (nM)")
+        plt.ylabel("Activity (%)")
+        plt.title("Norepinepherine Concentration vs Neuron Activity in " +
+            self.pretty)
+
+        plt.vlines(self.ki, 0, 1, linestyles="dashed")
+        plt.text(1.1 * self.ki, 0.1, "Affinity")
+
+        plt.hlines(0.5, 0, 1000, linestyles="dashed")
+        plt.text(1, 0.51, "50%")
+
+        plt.xscale("log")
+        gc = plt.gca()
+        gc.set_yticklabels(['{:.0f}%'.format(x * 100) for x in gc.get_yticks()])
+
+        plt.draw()
+        plt.savefig(f"{out}-norep-activity.png", dpi=1000)
+        
+        #######################################################################
+        
+        plt.plot(self.x, self.gain)
+        
+        plt.xlabel("Norepinephrine concentration (nM)")
+        plt.ylabel("Gain")
+        plt.title(f"Concentration vs Gain in {self.pretty}")
+
+        plt.draw()
+        plt.savefig(f"{out}-concentration-gain.png", dpi=1000)
+        
+        #######################################################################
+        
+        plt.plot(self.x, self.bias)
+        
+        plt.xlabel("Norepinephrine concentration (nM)")
+        plt.ylabel("Bias")
+        plt.title("Concentration vs Bias in " + self.pretty)
+        
+        plt.draw()
+        plt.savefig(f"{out}-concentration-bias.png", dpi=1000)
+
+class Alpha1(Alpha):
+    def __init__(self):
+        self.ki = 330
+        self.offset = 5.895
+        self.pretty = "α1 Receptor"
+        self.gaind = 0.1
+        self.biasd = 0.1
+        super().__init__()
+        
+    def calcgb(self):
+        super().calcgb(self.gaind, self.biasd)
+
+class Alpha2(Alpha):
+    def __init__(self):
+        self.ki = 56
+        self.offset = 1
+        self.pretty = "α2 Receptor"
+        self.gaind = -0.04
+        self.biasd = -0.02
+        super().__init__()
+        
+    def calcgb(self):
+        super().calcgb(self.gaind, self.biasd)
+
+def main():
+    plt.style.use("ggplot")
+    
+    a1 = Alpha1()
+    a1.calcgb()
+    a1.plot()
+
+    a2 = Alpha2()
+    a2.calcgb()
+    a2.plot()
+
+if __name__ == "__main__":
+    main()