1 |
"""
|
2 |
Christopher Lausted, Institute for Systems Biology
|
3 |
Last modified on 100425 (yymmdd)
|
4 |
Small script 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 |
print "Test the model module..."
|
28 |
ba0 = BiosensorArray(1,300) ## Create ba1 with one ROI and 300 datapoints.
|
29 |
roi0 = ba0.roi[0]
|
30 |
roi0.time = arange(300, dtype=float) ## Samples every 1 second.
|
31 |
roi0.value = zeros(300, dtype=float) + 20 ## Baseline signal is 20 units.
|
32 |
roi0.params = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':True} }
|
33 |
roi0.params['rmax'] = {'value': 100.0}
|
34 |
roi0.params['conc'] = {'value': 1e-6}
|
35 |
roi0.params['kon'] = {'value': 2e4}
|
36 |
roi0.params['t2'] = {'value': 150.0}
|
37 |
roi0.params['koff'] = {'value': 1e-3}
|
38 |
roi0.params['t3'] = {'value': 270.0}
|
39 |
roi0.model = simple1to1
|
40 |
roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
|
41 |
linegraph(ba0, "Simulation")
|
42 |
|
43 |
ba1 = copyinterval(ba0, 20, 240)
|
44 |
linegraph(ba1, "Trimmed")
|
45 |
exit()
|
46 |
|
47 |
print "Testing the fitting..."
|
48 |
ba1 = deepcopy(ba0)
|
49 |
roi0 = ba1.roi[0]
|
50 |
roi0.params['koff'] = {'value':1.0e-2, 'min':1e-8, 'max':1e-1, 'fixed':False}
|
51 |
roi0.params['kon'] = {'value':1.0e2, 'min':1e1, 'max':1e8, 'fixed':False}
|
52 |
roi0.params['rmax'] = {'value':50, 'min':1, 'max':90, 'fixed':False}
|
53 |
clma(roi0)
|
54 |
roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
|
55 |
dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
|
56 |
#exit()
|
57 |
|
58 |
|
59 |
print "Loading an SPR data file..."
|
60 |
#ba1 = readbiosensor("example-biosensor.txt")
|
61 |
ba1 = readicmtxt("example-icm.txt")
|
62 |
#ba1 = readsprit("example-sprit.txt")
|
63 |
#ba1 = applykey(ba1, "example-key.tsv")
|
64 |
#ba1.set_plot_all()
|
65 |
#ba1.set_plot_list(range(6))
|
66 |
#ba1.plot()
|
67 |
|
68 |
#writesprit(ba1,"testwritesprit.txt")
|
69 |
#writeclamp(ba1,"testwriteclamp.txt")
|
70 |
#writebiosensor(ba1, "testwritebiosensor.txt")
|
71 |
|
72 |
print "Plotting the raw data file..."
|
73 |
linegraph(ba1)
|
74 |
#dotgraph(ba1)
|
75 |
#dualgraph(ba1, ba1)
|
76 |
|
77 |
print "Plotting the calibrated data..."
|
78 |
ba2 = calibrate(ba1, ba1, 2850, 3120)
|
79 |
linegraph(ba2, "Calibrated SPR Data")
|
80 |
|
81 |
print "Use ROI #16 as background, subtract, and plot..."
|
82 |
bgset(ba2, 16)
|
83 |
ba2 = bgsubt(ba2)
|
84 |
linegraph(ba2, "Calibrated & Referenced SPR Data")
|
85 |
|
86 |
print "Test of scatterplot using time points 500, 1000, 1500, 2000"
|
87 |
scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
|
88 |
|
89 |
print "Done with test."
|