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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 100425 (yymmdd)
4 < Small script to test ba_class, io_module, etc.
4 > Small script to test various OSPRAI components.
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
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   ## Reload Osprai libraries in case code has changed.
15 < reload(ba)
16 < reload (vu)
17 < reload(io)
18 < reload(cal)
19 < reload(mdl)
20 < reload(fit)
15 > reload(ba_class)
16 > reload (vu_module)
17 > reload(io_module)
18 > reload(cal_module)
19 > reload(mdl_module)
20 > reload(fit_module)
21 > ## Or just import this next one...
22 > from osprai_one import *
23 >
24  
25   print "Test the model module..."
26 < ba0 = ba.BiosensorArray(1,300)  ## Create ba1 with one ROI and 300 datapoints.
26 > ba0 = 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.
28 > roi0.time = arange(300, dtype=float)  ## Samples every 1 second.
29 > roi0.value = 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}
# Line 34 | Line 34
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
37 > roi0.model = simple1to1
38   roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
39 < vu.linegraph(ba0, "Simulation")
39 > linegraph(ba0, "Simulation")
40 >
41 > ba1 = copyinterval(ba0, 20, 240)
42 > linegraph(ba1, "Trimmed")
43 > exit()
44  
45   print "Testing the fitting..."
46   ba1 = deepcopy(ba0)
# Line 44 | Line 48
48   roi0.params['koff'] = {'value':1.0e-2, 'min':1e-8, 'max':1e-1, 'fixed':False}
49   roi0.params['kon'] =  {'value':1.0e2, 'min':1e1, 'max':1e8, 'fixed':False}
50   roi0.params['rmax'] =  {'value':50, 'min':1, 'max':90, 'fixed':False}
51 < fit.clma(roi0)
51 > clma(roi0)
52   roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
53 < vu.dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
54 < exit()
53 > dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
54 > #exit()
55  
56  
57   print "Loading an SPR data file..."
58 < #ba1 = io.readbiosensor("example-biosensor.txt")
59 < ba1 = io.readicmtxt("example-icm.txt")
60 < #ba1 = io.readsprit("example-sprit.txt")
61 < #ba1 = io.applykey(ba1, "example-key.tsv")
58 > #ba1 = readbiosensor("example-biosensor.txt")
59 > ba1 = readicmtxt("example-icm.txt")
60 > #ba1 = readsprit("example-sprit.txt")
61 > #ba1 = applykey(ba1, "example-key.tsv")
62   #ba1.set_plot_all()
63   #ba1.set_plot_list(range(6))
64   #ba1.plot()
65  
66 < #io.writesprit(ba1,"testwritesprit.txt")
67 < #io.writeclamp(ba1,"testwriteclamp.txt")
68 < #io.writebiosensor(ba1, "testwritebiosensor.txt")
66 > #writesprit(ba1,"testwritesprit.txt")
67 > #writeclamp(ba1,"testwriteclamp.txt")
68 > #writebiosensor(ba1, "testwritebiosensor.txt")
69  
70   print "Plotting the raw data file..."
71 < vu.linegraph(ba1)
72 < #vu.dotgraph(ba1)
73 < #vu.dualgraph(ba1, ba1)
71 > linegraph(ba1)
72 > #dotgraph(ba1)
73 > #dualgraph(ba1, ba1)
74  
75   print "Plotting the calibrated data..."
76 < ba2 = cal.calibrate(ba1, ba1, 2850, 3120)
77 < vu.linegraph(ba2, "Calibrated SPR Data")
76 > ba2 = calibrate(ba1, ba1, 2850, 3120)
77 > linegraph(ba2, "Calibrated SPR Data")
78  
79   print "Use ROI #16 as background, subtract, and plot..."
80 < cal.bgset(ba2, 16)
81 < ba2 = cal.bgsubt(ba2)
82 < vu.linegraph(ba2, "Calibrated & Referenced SPR Data")
80 > bgset(ba2, 16)
81 > ba2 = bgsubt(ba2)
82 > linegraph(ba2, "Calibrated & Referenced SPR Data")
83  
84   print "Test of scatterplot using time points 500, 1000, 1500, 2000"
85 < vu.scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
85 > scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
86  
87   print "Done with test."
84 #input("Done with test. Press any key")

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