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root/osprai/osprai/trunk/test.py
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# Line 1 | Line 1
1   """
2   Christopher Lausted, Institute for Systems Biology
3 < Last modified on 100408 (yymmdd)
3 > Last modified on 100425 (yymmdd)
4   Small script to test ba_class, io_module, etc.
5   """
6  
7   ## Import modules.
8 + import numpy as np
9 + import ba_class as ba
10   import vu_module as vu
11   import io_module as io
12 < ## Reload in case code has changed.
12 > import cal_module as cal
13 > import mdl_module as mdl
14 > import fit_module as fit
15 > from sys import exit
16 > from copy import deepcopy
17 > ## Reload Osprai libraries in case code has changed.
18 > reload(ba)
19   reload (vu)
20   reload(io)
21 + reload(cal)
22 + reload(mdl)
23 + reload(fit)
24  
25 + print "Test the model module..."
26 + ba0 = ba.BiosensorArray(1,300)  ## Create ba1 with one ROI and 300 datapoints.
27 + roi0 = ba0.roi[0]
28 + roi0.time = np.arange(300, dtype=float)  ## Samples every 1 second.
29 + roi0.value = np.zeros(300, dtype=float) + 20  ## Baseline signal is 20 units.
30 + roi0.params = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':True} }
31 + roi0.params['rmax'] =  {'value': 100.0}
32 + roi0.params['conc'] =  {'value': 1e-6}
33 + roi0.params['kon'] =   {'value': 2e4}
34 + roi0.params['t2'] =    {'value': 150.0}
35 + roi0.params['koff'] =  {'value': 1e-3}
36 + roi0.params['t3'] =    {'value': 270.0}
37 + roi0.model = mdl.simple1to1
38 + roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
39 + vu.linegraph(ba0, "Simulation")
40 +
41 + print "Testing the fitting..."
42 + ba1 = deepcopy(ba0)
43 + roi0 = ba1.roi[0]
44 + roi0.params['koff'] = {'value':1.0e-2, 'min':1e-8, 'max':1e-1, 'fixed':False}
45 + roi0.params['kon'] =  {'value':1.0e2, 'min':1e1, 'max':1e8, 'fixed':False}
46 + roi0.params['rmax'] =  {'value':50, 'min':1, 'max':90, 'fixed':False}
47 + fit.clma(roi0)
48 + roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
49 + vu.dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
50 + exit()
51 +
52 +
53 + print "Loading an SPR data file..."
54   #ba1 = io.readbiosensor("example-biosensor.txt")
55   ba1 = io.readicmtxt("example-icm.txt")
56   #ba1 = io.readsprit("example-sprit.txt")
# Line 23 | Line 63
63   #io.writeclamp(ba1,"testwriteclamp.txt")
64   #io.writebiosensor(ba1, "testwritebiosensor.txt")
65  
66 + print "Plotting the raw data file..."
67   vu.linegraph(ba1)
68 < vu.dotgraph(ba1)
69 < vu.dualgraph(ba1, ba1)
68 > #vu.dotgraph(ba1)
69 > #vu.dualgraph(ba1, ba1)
70 >
71 > print "Plotting the calibrated data..."
72 > ba2 = cal.calibrate(ba1, ba1, 2850, 3120)
73 > vu.linegraph(ba2, "Calibrated SPR Data")
74 >
75 > print "Use ROI #16 as background, subtract, and plot..."
76 > cal.bgset(ba2, 16)
77 > ba2 = cal.bgsubt(ba2)
78 > vu.linegraph(ba2, "Calibrated & Referenced SPR Data")
79 >
80 > print "Test of scatterplot using time points 500, 1000, 1500, 2000"
81 > vu.scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
82  
83 < input("Done with test. Press any key")
83 > print "Done with test."
84 > #input("Done with test. Press any key")

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