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"""
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Christopher Lausted, Institute for Systems Biology
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Last modified on 100425 (yymmdd)
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Small script to test various OSPRAI components.
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"""
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## Import libaries
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import ba_class
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import vu_module
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import io_module
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import cal_module
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import mdl_module
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import fit_module
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import osprai_one
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## Reload Osprai libraries in case code has changed.
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reload(ba_class)
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reload (vu_module)
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reload(io_module)
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reload(cal_module)
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reload(mdl_module)
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reload(fit_module)
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reload(osprai_one)
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## Or just import this next one...
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from osprai_one import *
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print "Test the model module..."
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ba0 = BiosensorArray(1,300) ## Create ba1 with one ROI and 300 datapoints.
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roi0 = ba0.roi[0]
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roi0.time = arange(300, dtype=float) ## Samples every 1 second.
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roi0.value = zeros(300, dtype=float) + 20 ## Baseline signal is 20 units.
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roi0.params = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':True} }
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roi0.params['rmax'] = {'value': 100.0}
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roi0.params['conc'] = {'value': 1e-6}
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roi0.params['kon'] = {'value': 2e4}
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roi0.params['t2'] = {'value': 150.0}
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roi0.params['koff'] = {'value': 1e-3}
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roi0.params['t3'] = {'value': 270.0}
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roi0.model = simple1to1
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roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
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linegraph(ba0, "Simulation")
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ba1 = copyinterval(ba0, 20, 240)
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linegraph(ba1, "Trimmed")
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exit()
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print "Testing the fitting..."
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ba1 = deepcopy(ba0)
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roi0 = ba1.roi[0]
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roi0.params['koff'] = {'value':1.0e-2, 'min':1e-8, 'max':1e-1, 'fixed':False}
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roi0.params['kon'] = {'value':1.0e2, 'min':1e1, 'max':1e8, 'fixed':False}
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roi0.params['rmax'] = {'value':50, 'min':1, 'max':90, 'fixed':False}
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clma(roi0)
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roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
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dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter")
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#exit()
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print "Loading an SPR data file..."
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#ba1 = readbiosensor("example-biosensor.txt")
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ba1 = readicmtxt("example-icm.txt")
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#ba1 = readsprit("example-sprit.txt")
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#ba1 = applykey(ba1, "example-key.tsv")
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#ba1.set_plot_all()
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#ba1.set_plot_list(range(6))
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#ba1.plot()
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#writesprit(ba1,"testwritesprit.txt")
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#writeclamp(ba1,"testwriteclamp.txt")
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#writebiosensor(ba1, "testwritebiosensor.txt")
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print "Plotting the raw data file..."
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linegraph(ba1)
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#dotgraph(ba1)
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#dualgraph(ba1, ba1)
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print "Plotting the calibrated data..."
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ba2 = calibrate(ba1, ba1, 2850, 3120)
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linegraph(ba2, "Calibrated SPR Data")
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print "Use ROI #16 as background, subtract, and plot..."
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bgset(ba2, 16)
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ba2 = bgsubt(ba2)
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linegraph(ba2, "Calibrated & Referenced SPR Data")
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print "Test of scatterplot using time points 500, 1000, 1500, 2000"
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scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot")
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print "Done with test."
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