ViewVC Help
View File | Revision Log | Show Annotations | View Changeset | Root Listing
root/osprai/osprai/trunk/test.py
Revision: 27
Committed: Wed May 19 01:49:52 2010 UTC (9 years, 6 months ago) by clausted
File size: 4503 byte(s)
Log Message:
New LMA function in fit_module allows us to simultaneously fit parameters to the data in several ROIs that share that parameter.  This is not yet fully tested.  More comments have been added to ba_class.  The __all__ variable has been added to osprai_one to assist the automatic documentation.
Line File contents
1 """
2 Christopher Lausted, Institute for Systems Biology
3 Last modified on 100518 (yymmdd)
4 Scripts 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 def test_io_module():
28 print "Loading SPR data files..."
29 ba1 = readbiosensor("example-biosensor.txt")
30 ba1 = readicmtxt("example-icm.txt")
31 ba1 = readsprit("example-sprit.txt")
32 ba1 = applykey(ba1, "example-key.tsv")
33 print "Writing SPR data files..."
34 writesprit(ba1,"testwritesprit.txt")
35 writeclamp(ba1,"testwriteclamp.txt")
36 writebiosensor(ba1, "testwritebiosensor.txt")
37 print "Done with test_io_module."
38
39
40 def test_cal_module_vu_module():
41 print "Loading an SPR data file..."
42 ba1 = readicmtxt("example-icm.txt")
43
44 print "Plotting the raw data file..."
45 dotgraph(ba1)
46
47 print "Plotting the calibrated data..."
48 ba2 = calibrate(ba1, ba1, 2850, 3120)
49 linegraph(ba2, "Calibrated SPR Data")
50 dualgraph(ba1, ba2, "Uncalibrated and Calibrated SPR Data")
51
52 print "Use ROI #16 as background, subtract, and plot..."
53 bgset(ba2, 16)
54 ba3 = bgsubt(ba2)
55 linegraph(ba3, "Calibrated Referenced SPR Data")
56
57 print "Test of scatterplot using time points 500, 1000, 1500, 2000"
58 scatterplot(ba3, 3600, 4200, 3600, 4700, "Scatterplot")
59
60 print "Cutting out an interval..."
61 ba3 = copyinterval(ba3, 2800, 6200)
62 linegraph(ba3)
63 print "Done with test test_cal_module_vu_module."
64
65
66 def test_mdl_module_fit_module():
67 print "Test the model module..."
68 ba0 = BiosensorArray(1,300) ## Create ba with one ROI and 300 datapoints.
69 roi0 = ba0.roi[0]
70 roi0.time = arange(300, dtype=float) ## Samples every 1 second.
71 roi0.value = zeros(300, dtype=float) + 20 ## Baseline signal is 20 units.
72 roi0.params = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':True} }
73 roi0.params['rmax'] = {'value': 100.0}
74 roi0.params['conc'] = {'value': 1e-6}
75 roi0.params['kon'] = {'value': 2e4}
76 roi0.params['t2'] = {'value': 150.0}
77 roi0.params['koff'] = {'value': 1e-3}
78 roi0.params['t3'] = {'value': 270.0}
79 roi0.model = simple1to1
80 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
81 linegraph(ba0, "Simulation")
82
83 ## Constrain rmax<80 when it really is 100 to show what happens.
84 print "Testing the fitting..."
85 ba1 = deepcopy(ba0)
86 roi0 = ba1.roi[0]
87 roi0.params['koff'] = {'value':1.0e-2, 'min':1e-8, 'max':1e-1, 'fixed':False}
88 roi0.params['kon'] = {'value':1.0e2, 'min':1e1, 'max':1e8, 'fixed':False}
89 roi0.params['rmax'] = {'value':150, 'min':120, 'max':190, 'fixed':False}
90 mclma([roi0])
91 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
92 dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
93 print "Done with test test_mdl_module_fit_module."
94
95
96 def demo_mtl():
97 print "Test the model module..."
98 ba0 = BiosensorArray(1,300) ## Create ba1 with one ROI and 300 datapoints.
99 roi0 = ba0.roi[0]
100 roi0.time = arange(300, dtype=float) ## Samples every 1 second.
101 roi0.value = zeros(300, dtype=float) + 20 ## Baseline signal is 20 units.
102 roi0.params = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':True} }
103 roi0.params['rmax'] = {'value': 100.0}
104 roi0.params['conc'] = {'value': 1e-6}
105 roi0.params['kon'] = {'value': 5e4}
106 roi0.params['t2'] = {'value': 150.0}
107 roi0.params['koff'] = {'value': 5e-3}
108 roi0.params['t3'] = {'value': 270.0}
109 roi0.params['kmtl'] = {'value': 2e6}
110 roi0.name = "kmtl=2e6"
111 roi0.model = simple1to1_mtl
112 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
113
114 ba1 = deepcopy(ba0)
115 roi0 = ba1.roi[0]
116 roi0.name = "No MTL"
117 roi0.model = simple1to1
118 roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
119 dualgraph(ba0, ba1, "With and without MTL")
120 print "Done with test demo_mtl."
121
122
123 ## Run selected test or tests.
124 #test_io_module()
125 #test_cal_module_vu_module()
126 #demo_mtl()
127 test_mdl_module_fit_module()