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Merged
4 commits merged into from
Oct 27, 2018
Merged

Devel stabmax #10

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2a51bbe
Strict check of maximum stabilization time
May 29, 2018
e8ca92f
dO2 overflow issue fix
Oct 27, 2018
d94622f
Update
Oct 27, 2018
094da21
Undo max check
Oct 27, 2018
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42 changes: 21 additions & 21 deletions O2-PIcurveMeasurement.js
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Original file line number Diff line number Diff line change
Expand Up @@ -8,23 +8,23 @@ var UserDefinedProtocol = {
photosynthesisMeasurementPeriod: 3600,
turbidostatSynchronization: false,
growthStabilitySynchronization: false,
stirrerIntensityValues: [30, 60],
stirrerIntensityValues: [50, 75],
lightStepMultiplierValues: [ 1 ],
lightStepMultiplierColors: ['red'],
photosynthesisCurveLightMultiplierValues: [ 1 ]
}

/* globals
importPackage, java, Packages, theGroup, theAccessory, theExperiment, theLogger, ProtoConfig, ETrendFunction, result:true
importPackage, java, Packages, theGroup, theAccessory, theExperiment, theLogger, ProtoConfig, ETrendFunction, result: true
*/

/**
* PI-Curves Measurement
*
* @script PI-Curves Measurement - Photosynthesis Efficiency Quantification
* @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
* @version 1.2.1
* @modified 21.4.2018 (JaCe)
* @version 1.2.2
* @modified 26.10.2018 (JaCe)
* @notes For proper function of the script following protocols have to be disabled: "Lights", "Bubble intr. valve" and "Stirrer"
*
* @param {number} oxygenMeasurementDuration [s] Duration of O2 evolution measurement
Expand Down Expand Up @@ -127,32 +127,32 @@ if (experimentDuration >= measurementTime) {
}
if ((experimentDuration > (resumeTime - UserDefinedProtocol.respirationMeasurementDuration)) && !photosynthesis) {
theAccessory.context().put('photosynthesis', 1)
if (UserDefinedProtocol.respirationMeasurementDuration > 0) {
light0.suspend(resumeTime)
light1.suspend(resumeTime)
}
regCoefLin = theAccessory.getDataHistory().regression(ETrendFunction.LIN, Math.ceil(UserDefinedProtocol.photosynthesisRateCurveEvalFraction * UserDefinedProtocol.oxygenMeasurementDuration / UserDefinedProtocol.oxygenRapidMeasurementInterval))
debugLogger('O2 evol. parameters: ' + regCoefLin.join(', '))
rateO2Evol = theAccessory.context().get('rateO2Evol', [])
rateO2EvolR2 = theAccessory.context().get('rateO2EvolR2', [])
rateO2Evol[changeCounter] = round(regCoefLin[1] * 600, 2)
rateO2EvolR2[changeCounter] = round(regCoefLin[2], 3)
if (UserDefinedProtocol.respirationMeasurementDuration > 0) {
light0.suspend(resumeTime)
light1.suspend(resumeTime)
// TODO should be function1
}
// TODO should be function1
}
if ((experimentDuration > resumeTime) && !respiration) {
theAccessory.context().put('respiration', 1)
bubbles.setRunningProtoConfig(ProtoConfig.ON)
stirrer.setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.stirrerIntensityValues[0]))
if (UserDefinedProtocol.respirationMeasurementDuration > 0) {
light0.resume(experimentDuration)
light1.resume(experimentDuration)
controlLights(theAccessory.context().getDouble('light0Value', light0.getValue()), theAccessory.context().getDouble('light1Value', light1.getValue()))
regCoefLin = theAccessory.getDataHistory().regression(ETrendFunction.LIN, Math.ceil(UserDefinedProtocol.photosynthesisRateCurveEvalFraction * UserDefinedProtocol.respirationMeasurementDuration / UserDefinedProtocol.oxygenRapidMeasurementInterval))
debugLogger('O2 resp. parameters: ' + regCoefLin.join(', '))
rateO2Resp = theAccessory.context().get('rateO2Resp', [])
rateO2RespR2 = theAccessory.context().get('rateO2RespR2', [])
rateO2Resp[changeCounter] = round(regCoefLin[1] * 600, 2)
rateO2RespR2[changeCounter] = round(regCoefLin[2], 3)
controlLights(theAccessory.context().getDouble('light0Value', light0.getValue()), theAccessory.context().getDouble('light1Value', light1.getValue()))
light0.resume(experimentDuration)
light1.resume(experimentDuration)
// TODO should be function1
}
}
Expand All @@ -162,29 +162,29 @@ if (experimentDuration >= measurementTime) {
theAccessory.context().put('respiration', 0)
theAccessory.context().put('changeCounter', ++changeCounter)
if (changeCounter >= UserDefinedProtocol.lightStepMultiplierValues.length) {
theAccessory.context().put('changeCounter', 0)
theAccessory.context().put('measurementTime', experimentDuration + UserDefinedProtocol.photosynthesisMeasurementPeriod - UserDefinedProtocol.lightStepMultiplierValues.length * (UserDefinedProtocol.oxygenMeasurementDuration + UserDefinedProtocol.respirationMeasurementDuration + UserDefinedProtocol.relaxationPhaseDuration))
bubbles.setRunningProtoConfig(ProtoConfig.ON)
stirrer.setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.stirrerIntensityValues[0]))
theAccessory.context().put('modeO2EvolResp', 0)
multiplierStep = multiplierStep < (UserDefinedProtocol.photosynthesisCurveLightMultiplierValues.length - 1) ? ++multiplierStep : 0
theAccessory.context().put('multiplierStep', multiplierStep)
rateO2Evol = theAccessory.context().get('rateO2Evol', [])
rateO2EvolR2 = theAccessory.context().get('rateO2EvolR2', [])
rateO2Resp = theAccessory.context().get('rateO2Resp', [])
rateO2RespR2 = theAccessory.context().get('rateO2RespR2', [])
theAccessory.context().put('changeCounter', 0)
theAccessory.context().put('measurementTime', experimentDuration + UserDefinedProtocol.photosynthesisMeasurementPeriod - UserDefinedProtocol.lightStepMultiplierValues.length * (UserDefinedProtocol.oxygenMeasurementDuration + UserDefinedProtocol.respirationMeasurementDuration + UserDefinedProtocol.relaxationPhaseDuration))
theExperiment.addEvent('PI-curve DONE. O2 rates are ' + rateO2Evol.join(', ') + ' and ' + rateO2Resp.join(', ') + ' units/min (R2 ' + rateO2EvolR2.join(', ') + ' and ' + rateO2RespR2.join(', ') + ')')
theAccessory.context().put('rateO2Evol', [])
theAccessory.context().put('rateO2EvolR2', [])
theAccessory.context().put('rateO2Resp', [])
theAccessory.context().put('rateO2RespR2', [])
bubbles.setRunningProtoConfig(ProtoConfig.ON)
stirrer.setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.stirrerIntensityValues[0]))
theAccessory.context().put('modeO2EvolResp', 0)
multiplierStep = multiplierStep < (UserDefinedProtocol.photosynthesisCurveLightMultiplierValues.length - 1) ? ++multiplierStep : 0
theAccessory.context().put('multiplierStep', multiplierStep)
theExperiment.addEvent('PI-curve DONE. O2 rates are ' + rateO2Evol.join(', ') + ' and ' + rateO2Resp.join(', ') + ' units/min (R2 ' + rateO2EvolR2.join(', ') + ' and ' + rateO2RespR2.join(', ') + ')')
debugLogger('PI-curve finished.')
}
}
result = UserDefinedProtocol.oxygenRapidMeasurementInterval
}
} else if (experimentDuration > theAccessory.context().getInt('checkupTime', 0)) {
// Here comes a hack that solves an issue with strange periodic behaviour of both bubble interrupting valve and stirrer, when they turn off in uncontrolled manner - most likely bug in the software
// Here comes a hack that solves an issue with strange periodic behaviour of both the bubble interrupting valve and the stirrer, when they turn off in uncontrolled manner - most likely bug in the software
stirrer = theGroup.getAccessory('pwm.stirrer')
bubbles = theGroup.getAccessory('switches.valve-0')
theAccessory.context().put('checkupTime', experimentDuration + 10)
Expand Down