ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/osprai/osprai/trunk/test.py
Revision: 24
Committed: Wed Apr 28 01:00:17 2010 UTC (9 years, 3 months ago) by clausted
File size: 2656 byte(s)
Log Message:
Added copyinterval() to cal_module.  This cuts out a slice of SPR data between two timepoints and puts it in a new ba object.  
Line User Rev File contents
1 clausted 7 """
2     Christopher Lausted, Institute for Systems Biology
3 clausted 20 Last modified on 100425 (yymmdd)
4 clausted 23 Small script to test various OSPRAI components.
5 clausted 7 """
6    
7 clausted 23 ## 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 clausted 19 ## Reload Osprai libraries in case code has changed.
15 clausted 23 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 clausted 7
24 clausted 23
25 clausted 19 print "Test the model module..."
26 clausted 23 ba0 = BiosensorArray(1,300) ## Create ba1 with one ROI and 300 datapoints.
27 clausted 19 roi0 = ba0.roi[0]
28 clausted 23 roi0.time = arange(300, dtype=float) ## Samples every 1 second.
29     roi0.value = zeros(300, dtype=float) + 20 ## Baseline signal is 20 units.
30 clausted 20 roi0.params = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':True} }
31 clausted 19 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 clausted 23 roi0.model = simple1to1
38 clausted 19 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
39 clausted 23 linegraph(ba0, "Simulation")
40 clausted 19
41 clausted 24 ba1 = copyinterval(ba0, 20, 240)
42     linegraph(ba1, "Trimmed")
43     exit()
44    
45 clausted 19 print "Testing the fitting..."
46     ba1 = deepcopy(ba0)
47     roi0 = ba1.roi[0]
48 clausted 20 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 clausted 23 clma(roi0)
52 clausted 19 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
53 clausted 23 dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
54     #exit()
55 clausted 19
56    
57 clausted 14 print "Loading an SPR data file..."
58 clausted 23 #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 clausted 11 #ba1.set_plot_all()
63     #ba1.set_plot_list(range(6))
64     #ba1.plot()
65 clausted 7
66 clausted 23 #writesprit(ba1,"testwritesprit.txt")
67     #writeclamp(ba1,"testwriteclamp.txt")
68     #writebiosensor(ba1, "testwritebiosensor.txt")
69 clausted 7
70 clausted 14 print "Plotting the raw data file..."
71 clausted 23 linegraph(ba1)
72     #dotgraph(ba1)
73     #dualgraph(ba1, ba1)
74 clausted 11
75 clausted 14 print "Plotting the calibrated data..."
76 clausted 23 ba2 = calibrate(ba1, ba1, 2850, 3120)
77     linegraph(ba2, "Calibrated SPR Data")
78 clausted 12
79 clausted 14 print "Use ROI #16 as background, subtract, and plot..."
80 clausted 23 bgset(ba2, 16)
81     ba2 = bgsubt(ba2)
82     linegraph(ba2, "Calibrated & Referenced SPR Data")
83 clausted 14
84     print "Test of scatterplot using time points 500, 1000, 1500, 2000"
85 clausted 23 scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
86 clausted 14
87     print "Done with test."