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root/osprai/osprai/trunk/test.py
Revision: 26
Committed: Fri May 14 22:36:12 2010 UTC (9 years, 7 months ago) by clausted
File size: 2695 byte(s)
Log Message:
Added mass-transport limitation model simple1to1_mtl.

Line File contents
1 """
2 Christopher Lausted, Institute for Systems Biology
3 Last modified on 100425 (yymmdd)
4 Small script to test various OSPRAI components.
5 """
6
7 ## Import libaries
8 import ba_class
9 import vu_module
10 import io_module
11 import cal_module
12 import mdl_module
13 import fit_module
14 import osprai_one
15 ## Reload Osprai libraries in case code has changed.
16 reload(ba_class)
17 reload (vu_module)
18 reload(io_module)
19 reload(cal_module)
20 reload(mdl_module)
21 reload(fit_module)
22 reload(osprai_one)
23 ## Or just import this next one...
24 from osprai_one import *
25
26
27 print "Test the model module..."
28 ba0 = BiosensorArray(1,300) ## Create ba1 with one ROI and 300 datapoints.
29 roi0 = ba0.roi[0]
30 roi0.time = arange(300, dtype=float) ## Samples every 1 second.
31 roi0.value = zeros(300, dtype=float) + 20 ## Baseline signal is 20 units.
32 roi0.params = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':True} }
33 roi0.params['rmax'] = {'value': 100.0}
34 roi0.params['conc'] = {'value': 1e-6}
35 roi0.params['kon'] = {'value': 2e4}
36 roi0.params['t2'] = {'value': 150.0}
37 roi0.params['koff'] = {'value': 1e-3}
38 roi0.params['t3'] = {'value': 270.0}
39 roi0.model = simple1to1
40 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
41 linegraph(ba0, "Simulation")
42
43 ba1 = copyinterval(ba0, 20, 240)
44 linegraph(ba1, "Trimmed")
45 exit()
46
47 print "Testing the fitting..."
48 ba1 = deepcopy(ba0)
49 roi0 = ba1.roi[0]
50 roi0.params['koff'] = {'value':1.0e-2, 'min':1e-8, 'max':1e-1, 'fixed':False}
51 roi0.params['kon'] = {'value':1.0e2, 'min':1e1, 'max':1e8, 'fixed':False}
52 roi0.params['rmax'] = {'value':50, 'min':1, 'max':90, 'fixed':False}
53 clma(roi0)
54 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
55 dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
56 #exit()
57
58
59 print "Loading an SPR data file..."
60 #ba1 = readbiosensor("example-biosensor.txt")
61 ba1 = readicmtxt("example-icm.txt")
62 #ba1 = readsprit("example-sprit.txt")
63 #ba1 = applykey(ba1, "example-key.tsv")
64 #ba1.set_plot_all()
65 #ba1.set_plot_list(range(6))
66 #ba1.plot()
67
68 #writesprit(ba1,"testwritesprit.txt")
69 #writeclamp(ba1,"testwriteclamp.txt")
70 #writebiosensor(ba1, "testwritebiosensor.txt")
71
72 print "Plotting the raw data file..."
73 linegraph(ba1)
74 #dotgraph(ba1)
75 #dualgraph(ba1, ba1)
76
77 print "Plotting the calibrated data..."
78 ba2 = calibrate(ba1, ba1, 2850, 3120)
79 linegraph(ba2, "Calibrated SPR Data")
80
81 print "Use ROI #16 as background, subtract, and plot..."
82 bgset(ba2, 16)
83 ba2 = bgsubt(ba2)
84 linegraph(ba2, "Calibrated & Referenced SPR Data")
85
86 print "Test of scatterplot using time points 500, 1000, 1500, 2000"
87 scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
88
89 print "Done with test."