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"""
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Christopher Lausted, Institute for Systems Biology
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Last modified on 100519 (yymmdd)
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Scripts 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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def test_io_module():
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print "Loading SPR data files..."
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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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print "Writing SPR data files..."
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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 "Done with test_io_module."
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return
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def test_cal_module_vu_module():
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print "Loading an SPR data file..."
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ba1 = readicmtxt("example-icm.txt")
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print "Plotting the raw data file..."
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dotgraph(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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dualgraph(ba1, ba2, "Uncalibrated and 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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ba3 = bgsubt(ba2)
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linegraph(ba3, "Calibrated Referenced SPR Data")
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print "Test of scatterplot using time points 500, 1000, 1500, 2000"
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scatterplot(ba3, 3600, 4200, 3600, 4700, "Scatterplot")
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print "Cutting out an interval..."
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ba3 = copyinterval(ba3, 2800, 6200)
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linegraph(ba3)
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print "Done with test test_cal_module_vu_module."
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return
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def test_mdl_module_fit_module():
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print "Test the model module..."
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## Set some default parameters.
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dpar = {'t1': {'value':30.0, 'min':30.0, 'max':30.0, 'fixed':'fixed'} }
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dpar['rmax'] = {'value':100.0, 'min':1.0, 'max':1000.0, 'fixed':'fixed'}
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dpar['conc'] = {'value':1e-5, 'min':1e-12, 'max':1e1, 'fixed':'fixed'}
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dpar['cofa'] = {'value':1.0, 'min':1e-10, 'max':1e10, 'fixed':'fixed'}
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dpar['kon'] = {'value':2e4, 'min':1e1, 'max':1e8, 'fixed':'fixed'}
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dpar['t2'] = {'value':150.0, 'min':10.0, 'max':1000.0, 'fixed':'fixed'}
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dpar['koff'] = {'value':1.0e-2, 'min':1e-8, 'max':1e-1, 'fixed':'fixed'}
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dpar['t3'] = {'value':270.0, 'min':270.0, 'max':270.0, 'fixed':'fixed'}
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## Create ba with three ROIs and 300 datapoints.
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ba0 = BiosensorArray(3,300)
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for roi in ba0.roi:
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roi.time = arange(300, dtype=float) ## Samples every 1 second.
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roi.value = zeros(300, dtype=float) + 20 ## Baseline signal is 20 units.
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roi.params = deepcopy(dpar)
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roi.model = simple1to1
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## Set the dilution factors
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ba0.roi[0].params['cofa']['value'] = 1.0 / 27
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ba0.roi[1].params['cofa']['value'] = 1.0 / 9
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ba0.roi[2].params['cofa']['value'] = 1.0 / 3
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## Simulate the data and plot it.
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for roi in ba0.roi:
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roi.value = roi.model(roi.time, roi.value, roi.params)
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linegraph(ba0, "Simulation")
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## Constrain rmax belowtrue value to show what happens.
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print "Testing the fitting..."
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ba1 = deepcopy(ba0)
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## Set one kon, koff, rmax to float.
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ba1.roi[0].params['koff']['fixed'] = 'float'
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ba1.roi[0].params['kon']['fixed'] = 'float'
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ba1.roi[0].params['rmax'] = {'value':10.0, 'min':1.0, 'max':80.0, 'fixed':'float'}
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ba1.roi[1].params['koff']['fixed'] = 0
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ba1.roi[1].params['kon']['fixed'] = 0
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ba1.roi[1].params['rmax']['fixed'] = 0
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ba1.roi[2].params['koff']['fixed'] = 0
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ba1.roi[2].params['kon']['fixed'] = 0
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ba1.roi[2].params['rmax']['fixed'] = 0
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## Fit and then plot.
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mclma(ba1.roi)
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for roi in ba1.roi:
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roi.value =roi.model(roi.time, roi.value, roi.params)
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dualgraph(ba0, ba1, "Fitted Data with an incorrect rmax constraint")
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print "Done with test test_mdl_module_fit_module."
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return
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def demo_mtl():
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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': 5e4}
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roi0.params['t2'] = {'value': 150.0}
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roi0.params['koff'] = {'value': 5e-3}
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roi0.params['t3'] = {'value': 270.0}
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roi0.params['kmtl'] = {'value': 2e6}
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roi0.name = "kmtl=2e6"
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roi0.model = simple1to1_mtl
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roi0.value =roi0.model(roi0.time, roi0.value, roi0.params)
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ba1 = deepcopy(ba0)
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roi0 = ba1.roi[0]
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roi0.name = "No MTL"
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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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dualgraph(ba0, ba1, "With and without MTL")
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print "Done with test demo_mtl."
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## Run selected test or tests.
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#test_io_module()
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#test_cal_module_vu_module()
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#demo_mtl()
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test_mdl_module_fit_module()
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