Restructure repository

[norepinephrine_wm.git] / norepinephrine_wm / newmodel.py

diff --git a/norepinephrine_wm/newmodel.py b/norepinephrine_wm/newmodel.py
deleted file mode 100644 (file)
index 4a4b54b..0000000
--- a/norepinephrine_wm/newmodel.py
+++ /dev/null
@@ -1,112 +0,0 @@
-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()