diff --git a/pk_optimizer/pk1Comp.ipynb b/pk_optimizer/pk1Comp.ipynb
deleted file mode 100644
index b6512f2782f88e57f65f38f39e03040a47d40c1c..0000000000000000000000000000000000000000
--- a/pk_optimizer/pk1Comp.ipynb
+++ /dev/null
@@ -1,168 +0,0 @@
-{
- "cells": [
- {
- "cell_type": "code",
- "execution_count": 1,
- "metadata": {},
- "outputs": [],
- "source": [
- "# Import commands\n",
- "from scipy.stats import gamma\n",
- "import numpy as np\n",
- "import matplotlib.pyplot as plt\n",
- "#%matplotlib inline\n",
- "from scipy.integrate import odeint \n",
- "import math as math\n",
- "\n",
- "class pk1Comp:\n",
- " \n",
- " \"\"\"The pk1Comp object is a one compartment PK model that outputs graphs of mass of tracer over time.\"\"\"\n",
- "\n",
- " def __init__ (self, numParam = 4, Flow = 1, Vp = 0.1, Visf = 0.5, PS = 0.15):\n",
- " \n",
- " \"\"\"Initializes the model with default parameter values for flow, Vp, Visf, and PS.\n",
- " Parameters\n",
- " ---------- \n",
- " numParam: int\n",
- " numParam is the number of parameters you want to optimize for the model. Defaults to 4.\n",
- " \n",
- " Flow : double\n",
- " Flow is the flow of plasma through the blood vessel in mL/(mL*min). Defaults to 1.\n",
- " \n",
- " Vp : double\n",
- " Vp is the volume of plasma in mL. Defaults to 0.1.\n",
- " \n",
- " Visf : double\n",
- " Visf is the volume of interstitial fluid in mL. Defaults to 0.5.\n",
- " \n",
- " PS : double\n",
- " PS is the permeability-surface area constant in mL/(g*min). Defaults to 0.15. \n",
- " \"\"\"\n",
- " \n",
- " # Declare Variables for initial conditions\n",
- " self.numParam = numParam\n",
- " self.Flow = Flow\n",
- " self.Vp = Vp\n",
- " self.Visf = Visf\n",
- " self.PS = PS\n",
- " C0 = 0 # Initial concentration of tracer in plasma\n",
- " tmax = 10 #Time in seconds\n",
- " dt = 0.1 #Time step\n",
- " a = 2. # Alpha for gamma distribution\n",
- " rv = gamma(a, loc = 2, scale = 0.65) #input function\n",
- "\n",
- " # Define the time array\n",
- " time = np.arange(0, tmax + dt, dt)\n",
- " \n",
- " # Derivative function\n",
- " def derivs(curr_vals, time):\n",
- " \"\"\"Finds derivatives of ODEs.\n",
- " \n",
- " Parameters\n",
- " ---------- \n",
- " curr_vals : double[]\n",
- " curr_vals it he current values of the variables we wish to \"update\" from the curr_vals list.\n",
- " \n",
- " time : double[]\n",
- " time is our time array from 0 to tmax with timestep dt.\n",
- " \n",
- " Returns\n",
- " -------\n",
- " dc_dt : double[]\n",
- " contains the derivative of concentrations with respect to time.\n",
- " \"\"\"\n",
- "\n",
- " # Define value of input function Cin\n",
- " Cin = rv.pdf(time) \n",
- "\n",
- " # Unpack the current values of the variables we wish to \"update\" from the curr_vals list\n",
- " C = curr_vals\n",
- "\n",
- " # Right-hand side of odes, which are used to computer the derivative\n",
- " dC_dt = flow*(Cin - C)/Vol\n",
- " #Cout = C\n",
- " return dC_dt\n",
- " \n",
- " def getPlot(self):\n",
- " \"\"\"Plots the solution of the solved ODEs.\n",
- " \n",
- " Parameters\n",
- " ---------- \n",
- " self : self\n",
- " Passes variables needed from self. \n",
- " \"\"\"\n",
- " \n",
- " # Plot the results using the values stored in the solution variable, \"sol\"\n",
- " # Plot Cp using the \"0\" element from the solution\n",
- " plt.figure(1)\n",
- " plt.plot(time, rv.pdf(time), color = 'blue', label = 'Input Function')\n",
- " plt.plot(time, sol[:,0],color=\"green\", label = 'Cout')\n",
- "\n",
- " # Plot Cisf using the \"1\" element from the solution\n",
- " #plt.plot(time, sol[:,1],color=\"purple\", label = 'Cisf')\n",
- " plt.xlabel('Time [s]')\n",
- " plt.ylabel('Concentration [mM]')\n",
- " plt.legend(loc = 'best')\n",
- " plt.grid()\n",
- " \n",
- " def main(self):\n",
- " \"\"\"Main function to run and solve ODEs\"\"\"\n",
- " \n",
- " # Store the initial values in a list\n",
- " init = [C0]\n",
- "\n",
- " # Solve the odes with odeint\n",
- " sol = odeint(derivs, init, time)\n",
- "\n",
- " #Mass_plasma = Vp * sol[:,0] #mass of tracer in plasma\n",
- " #Mass_isf = Visf * sol[:,1] #mass of tracer in isf\n",
- " #Tp = Vp/(flow + PS) # mean transit time\n",
- " #E = 1 - np.exp(-PS/flow) #extraction fraction\n",
- " #Q = Mass_plasma + Mass_isf\n",
- "\n",
- " #print('The mean transit time is ' + str(Tp))\n",
- " #print('The extraction fraction is ' + str(E))\n",
- "\n",
- " # Plot mass of tracer using the \"2\" element from the solution\n",
- " #plt.figure(2)\n",
- " #plt.plot(time, Mass_plasma,color=\"red\", label = 'Plasma')\n",
- " # Plot mass of tracer in tissue using the \"3\" element from the solution\n",
- " #plt.plot(time, Mass_isf,color=\"black\", label = 'Interstitial Space')\n",
- " #plt.plot(time, Q, color=\"blue\", label = 'Total mass')\n",
- " #plt.xlabel('Time [s]')\n",
- " #plt.ylabel('Mass [mg]')\n",
- " #plt.legend(loc = 'best')\n",
- " #plt.grid()\n",
- "\n"
- ]
- },
- {
- "cell_type": "code",
- "execution_count": null,
- "metadata": {},
- "outputs": [],
- "source": []
- }
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- "language": "python",
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