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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 + 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 <
22 < ba1 = io.readsprit("example-sprit.txt")
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")
57 > #ba1 = io.applykey(ba1, "example-key.tsv")
58   #ba1.set_plot_all()
59 + #ba1.set_plot_list(range(6))
60   #ba1.plot()
61  
62   #io.writesprit(ba1,"testwritesprit.txt")
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)
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 < ba2 = io.applykey(ba1, "example-key.tsv")
81 < #ba2.set_plot_all()
19 < #ba2.plot()
20 <
21 < ba3 = io.readicmtxt("example-icm.txt")
22 < ba3.set_plot_all()
23 < ba3.plot()
80 > print "Test of scatterplot using time points 500, 1000, 1500, 2000"
81 > vu.scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
82  
83   print "Done with test."
84 + #input("Done with test. Press any key")

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