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"""
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cal: Calibration module for SPRI data in a ba class.
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Christopher Lausted, Institute for Systems Biology,
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OSPRAI developers
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Last modified on 100426 (yymmdd)
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Example:
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#import cal_module as cal
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#io_module as io
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#baC = io.readsprit("calibrationdata.txt")
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#ba1 = io.readsprit("spritdata.txt")
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#ba2 = cal.calibrate(ba1, baCal, t1, t2, n1, n2)
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#cal.bgset(ba2, bgroi)
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#ba3 = cal.bgsubt(ba2)
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"""
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__version__ = "100426"
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## Import libraries
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import ba_class as ba
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import numpy as np
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from copy import deepcopy
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def calibrate(ba0, baCal, t1, t2, n1=1335700, n2=1336600):
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"""
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Use data in baCal to calibrate ba0.
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A simple two-point linear calibration using timepoints t1 and t2 and
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corresponding refractive indices n1 and n2. If n1 and n2 are not given,
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assume 1x PBS (n1=1335700uRIU) and 2xPBS (n2=1336600uRIU).
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Average 30 seconds of data (t-15 to 5+15 seconds).
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The ba object returned will remember the slopes and intercepts used.
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"""
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## Error checking
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if (len(ba0.roi) != len(baCal.roi)):
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print "Error: The ba objects are of different size."
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return ba0
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## Continue.
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ba2 = deepcopy(ba0)
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for i, iroi in enumerate(baCal.roi):
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## Average values of camera units around t1 and t2.
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cu1 = np.average(iroi.time2val(t1-15, t1+15))
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cu2 = np.average(iroi.time2val(t2-15, t2+15))
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## Calculate and record slope and intercept parameters.
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slope = (n2 - n1) / (cu2 - cu1)
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intercept = n2 - (slope * cu2)
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## Apply the calibration to the new ba object.
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ba2.roi[i].calibM = slope
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ba2.roi[i].calibB = intercept
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ba2.roi[i].value = ba0.roi[i].value * slope + intercept ## type np.array.
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return ba2
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## End of calibrate().
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def bgsubt(ba0):
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"""Apply the background subtraction and return a new ba object."""
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ba1 = deepcopy(ba0)
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for i in range(len(ba0.roi)):
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bg = ba0.roi[i].bgroi[0] ## TODO: Only uses first bgroi for now.
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bg -= 1 ## Decide if index or id base 0 or 1.
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ba1.roi[i].value = ba0.roi[i].value - ba0.roi[bg].value ## type np.array.
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return ba1
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## End of bgsubt().
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def bgset(ba0, i):
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"""Set i as the background ROI for all of the ROIs."""
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for iroi in ba0.roi: iroi.bgroi = [i]
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return
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## End of bgset().
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def copyinterval(ba0, t1, t2):
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"""Copy data from the interval between t1 and t2 and return a new ba object."""
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ba1 = deepcopy(ba0)
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for i in range(len(ba0.roi)):
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dp1 = ba0.roi[i].time2dp(t1)
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dp2 = ba0.roi[i].time2dp(t2)
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ba1.roi[i].time = ba1.roi[i].time[dp1:dp2]
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ba1.roi[i].value = ba1.roi[i].value[dp1:dp2]
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return ba1
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## End of copyinterval().
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################################# End of module ################################# |
