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""" |
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Christopher Lausted, Institute for Systems Biology |
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Last modified on 100422 (yymmdd) |
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Small script to test ba_class, io_module, etc. |
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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 modules. |
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import numpy as np |
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import ba_class as ba |
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import vu_module as vu |
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import io_module as io |
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import cal_module as cal |
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import mdl_module as mdl |
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import fit_module as fit |
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from sys import exit |
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from copy import deepcopy |
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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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## Reload Osprai libraries in case code has changed. |
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reload(ba) |
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reload (vu) |
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reload(io) |
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reload(cal) |
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reload(mdl) |
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reload(fit) |
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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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## 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 = ba.BiosensorArray(1,300) ## Create ba1 with one ROI and 300 datapoints. |
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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 = np.arange(300, dtype=float) ## Samples every 1 second. |
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roi0.value = np.zeros(300, dtype=float) + 20 ## Baseline signal is 20 units. |
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roi0.params = {'t1': {'value':30.0, 'min':60.0, 'max':60.0, 'fixed':True} } |
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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 = mdl.simple1to1 |
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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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vu.linegraph(ba0, "Simulation") |
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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':0.1, 'min':1e-10, 'max':1e10, 'fixed':False} |
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roi0.params['kon'] = {'value':0.1, 'min':1e-10, 'max':1e10, 'fixed':False} |
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roi0.params['rmax'] = {'value':150, 'min':150, 'max':150, 'fixed':True} |
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fit.lma(roi0) |
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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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vu.dualgraph(ba0, ba1, "Fitted Data with an incorrect Rmax parameter") |
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exit() |
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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 = io.readbiosensor("example-biosensor.txt") |
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ba1 = io.readicmtxt("example-icm.txt") |
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#ba1 = io.readsprit("example-sprit.txt") |
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#ba1 = io.applykey(ba1, "example-key.tsv") |
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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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#io.writesprit(ba1,"testwritesprit.txt") |
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#io.writeclamp(ba1,"testwriteclamp.txt") |
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#io.writebiosensor(ba1, "testwritebiosensor.txt") |
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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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vu.linegraph(ba1) |
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#vu.dotgraph(ba1) |
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#vu.dualgraph(ba1, ba1) |
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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 = cal.calibrate(ba1, ba1, 2850, 3120) |
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vu.linegraph(ba2, "Calibrated SPR 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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cal.bgset(ba2, 16) |
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ba2 = cal.bgsubt(ba2) |
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vu.linegraph(ba2, "Calibrated & Referenced SPR Data") |
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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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vu.scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot") |
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scatterplot(ba2, 3600, 4200, 3600, 4700, "Scatterplot") |
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print "Done with test." |
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#input("Done with test. Press any key") |
