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root/osprai/osprai/trunk/modelclass1.py
Revision: 1
Committed: Wed Mar 17 05:34:43 2010 UTC (9 years, 7 months ago) by clausted
File size: 3237 byte(s)
Log Message:
Initial import of Osprai project
Line File contents
1 """
2 Provide the model for curvefitting.
3
4 Yuhang Wan, Feb25, 2010
5 __version__ = "1.0"
6
7 This is a basic 1:1 reaction model.
8
9 """
10
11 import numpy as np
12 import pylab as plt
13
14
15 class modelclass(object):
16 def __init__ (self, parainfo=[] ):
17 self.parainfo = parainfo
18 ## self.pfloat = []
19
20 def wizard(self, ):
21 '''This function helps you to create a parameter information list.
22 This is a basic 1:1 reaction model, where there are 7 parameters:
23 Rmax,Kon,Koff,Conc,t_on,t_off,t_out'''
24 print ('')
25 pname = ['rmax','kon','koff','c','ton','toff','tout']
26 parainfo = []
27 for i in range(7):
28 print i
29 tmp={}
30 tmp['name'] = pname[i]
31 vstr = raw_input("input the value of parameter '%s', if a series, seperate with ',': " %pname[i])
32 vtmp = vstr.strip().split(',')
33 tmp['number'] = len(vtmp)
34 if len(vtmp) == 1:
35 vtmp = float(vtmp[0])
36 else:
37 vtmp = map(float, vtmp)
38 tmp['value'] = vtmp
39 tmp['fixed'] = bool(input("Is '%s' fixed? (1/0): " %pname[i]))
40
41 parainfo.append(tmp)
42 ##parainfo.append({'name':'', 'value':0., 'fixed':0, 'number':0})
43 self.parainfo = parainfo
44
45
46 def function(self, t, paralist):
47 '''This function calculates the theoretical curve through the
48 parameter list you give.
49 '''
50 # for the basic 1:1 model
51
52 ## Assign the parameters to calculate the curve
53 for p in paralist:
54 if p['name'] == 'rmax': rmax = p['value']
55 elif p['name'] == 'kon': kon = p['value']
56 elif p['name'] == 'koff': koff = p['value']
57 elif p['name'] == 'c': c = p['value']
58 elif p['name'] == 'ton': ton = p['value']
59 elif p['name'] == 'toff': toff = p['value']
60 elif p['name'] == 'tout': tout = p['value']
61 else: print p['name'], p['value']
62
63
64 t1 = ton ##100 ##234 # Initial injection
65 t2 = toff ##178 ##570 # Wash, begin of the dissociation
66 t3 = tout ##400 ##840 # End wash
67
68 ## Must iterate through data, numerical integration.
69 g = np.zeros(len(t), dtype=float)
70
71 for i in range(1,len(t)):
72 if (t[i] > t3): break #Speed things up.
73 if (t1 < t[i] < t2):
74 ## Association
75 dG = kon*c*(rmax-g[i-1]) - koff*g[i-1]
76 elif (t2 < t[i] < t3):
77 ## Dissociation
78 dG = 0 - koff*g[i-1]
79 else:
80 dG = 0
81 if (abs(g[i]) > 999999999): dG = 0
82
83 g[i] = g[i-1] + dG * (t[i] - t[i-1])
84
85 return g
86
87
88 def updatemodel(self, parainfo):
89 '''This function helps to update the parameter information.
90 Usually used when you want to keep the fitted value as the
91 initial guess for next curve fitting.
92 '''
93 self.parainfo = parainfo
94
95