From 539e4c8d1946b6fbba190bfc64c99d0b6b910ea2 Mon Sep 17 00:00:00 2001
From: "Tu, Ethan" <tuethan@msu.edu>
Date: Thu, 27 Feb 2020 16:57:27 -0500
Subject: [PATCH] Replace pk1Comp.py
---
pk_optimizer/pk1Comp.py | 66 ++++++++++++-----------------------------
1 file changed, 19 insertions(+), 47 deletions(-)
diff --git a/pk_optimizer/pk1Comp.py b/pk_optimizer/pk1Comp.py
index f7daa6a..074c8f9 100644
--- a/pk_optimizer/pk1Comp.py
+++ b/pk_optimizer/pk1Comp.py
@@ -1,9 +1,6 @@
#!/usr/bin/env python
# coding: utf-8
-# In[1]:
-
-
# Import commands
from scipy.stats import gamma
import numpy as np
@@ -16,7 +13,7 @@ class pk1Comp:
"""The pk1Comp object is a one compartment PK model that outputs graphs of mass of tracer over time."""
- def __init__ (self, numParam = 4, Flow = 1, Vp = 0.1, Visf = 0.5, PS = 0.15):
+ def __init__ (self, numParam = 4, Flow = 1, Vol = 0.5, PS = 0.15):
"""Initializes the model with default parameter values for flow, Vp, Visf, and PS.
Parameters
@@ -36,24 +33,26 @@ class pk1Comp:
PS : double
PS is the permeability-surface area constant in mL/(g*min). Defaults to 0.15.
"""
-
+ if numParam <= 0 or Flow <= 0 or Vol < 0 or PS<0 or PS>10 or Vol>10:
+ raise ValueError("Input values are incorrect.")
+
# Declare Variables for initial conditions
self.numParam = numParam
self.Flow = Flow
- self.Vp = Vp
- self.Visf = Visf
+ self.Vol = Vol
self.PS = PS
- C0 = 0 # Initial concentration of tracer in plasma
- tmax = 10 #Time in seconds
- dt = 0.1 #Time step
- a = 2. # Alpha for gamma distribution
- rv = gamma(a, loc = 2, scale = 0.65) #input function
+ self.C0 = 0 # Initial concentration of tracer in plasma
+ self.tmax = 10 #Time in seconds
+ self.dt = 1 #Time step
+ self.a = 2. # Alpha for gamma distribution
+ self.rv = gamma(self.a, loc = 2, scale = 0.65) #input function
+ self.sol = []
# Define the time array
- time = np.arange(0, tmax + dt, dt)
+ self.time = np.arange(0, self.tmax + self.dt, self.dt)
# Derivative function
- def derivs(curr_vals, time):
+ def derivs(self, curr_vals, time):
"""Finds derivatives of ODEs.
Parameters
@@ -71,13 +70,13 @@ class pk1Comp:
"""
# Define value of input function Cin
- Cin = rv.pdf(time)
+ Cin = self.rv.pdf(time)
# Unpack the current values of the variables we wish to "update" from the curr_vals list
C = curr_vals
# Right-hand side of odes, which are used to computer the derivative
- dC_dt = flow*(Cin - C)/Vol
+ dC_dt = self.Flow*(Cin - C)/self.Vol
#Cout = C
return dC_dt
@@ -93,8 +92,8 @@ class pk1Comp:
# Plot the results using the values stored in the solution variable, "sol"
# Plot Cp using the "0" element from the solution
plt.figure(1)
- plt.plot(time, rv.pdf(time), color = 'blue', label = 'Input Function')
- plt.plot(time, sol[:,0],color="green", label = 'Cout')
+ plt.plot(self.time, self.rv.pdf(self.time), color = 'blue', label = 'Input Function')
+ plt.plot(self.time, self.sol[:,0],color="green", label = 'Cout')
# Plot Cisf using the "1" element from the solution
#plt.plot(time, sol[:,1],color="purple", label = 'Cisf')
@@ -107,34 +106,7 @@ class pk1Comp:
"""Main function to run and solve ODEs"""
# Store the initial values in a list
- init = [C0]
+ init = [self.C0]
# Solve the odes with odeint
- sol = odeint(derivs, init, time)
-
- #Mass_plasma = Vp * sol[:,0] #mass of tracer in plasma
- #Mass_isf = Visf * sol[:,1] #mass of tracer in isf
- #Tp = Vp/(flow + PS) # mean transit time
- #E = 1 - np.exp(-PS/flow) #extraction fraction
- #Q = Mass_plasma + Mass_isf
-
- #print('The mean transit time is ' + str(Tp))
- #print('The extraction fraction is ' + str(E))
-
- # Plot mass of tracer using the "2" element from the solution
- #plt.figure(2)
- #plt.plot(time, Mass_plasma,color="red", label = 'Plasma')
- # Plot mass of tracer in tissue using the "3" element from the solution
- #plt.plot(time, Mass_isf,color="black", label = 'Interstitial Space')
- #plt.plot(time, Q, color="blue", label = 'Total mass')
- #plt.xlabel('Time [s]')
- #plt.ylabel('Mass [mg]')
- #plt.legend(loc = 'best')
- #plt.grid()
-
-
-# In[ ]:
-
-
-
-
+ self.sol = odeint(self.derivs, init, self.time).round(4)
--
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