Merge pull request #11 from GCRI-DoAB/devel

Devel

Author: Jan Červený

LL-Luminostat.js

@@ -0,0 +1,71 @@
+// static parameters
+var odLinMin = 0.5
+var odLinMax = 1.23
+var lightMin = 400
+var expRegMult = 281.9177
+var expRegExpo = 1.016269
+
+/**
+* Luminostat regulator
+*
+* @script Lights - Luminostat
+* @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
+* @version 0.1.1
+* @modified 11.7.2018 (JaCe)
+*
+* @notes For proper function of the script a pump has to be set to ID 4
+*
+* @param {number} odLinMin Min OD for linear regulated range
+* @param {number} odLinMax Max OD for linear regulated range
+* @param {number} lightMin Min light for linear regulated range
+* @param {number} expRegMult Exponential regression multiplier
+* @param {number} expRegExpo Exponential regression exponent
+*
+* @return Light intensity
+*
+*/
+
+// dynamic parameters
+var lightMax = lightMin * (1 + (odLinMax - odLinMin) / odLinMin)
+
+importPackage(java.util)
+importPackage(java.lang)
+importPackage(Packages.psi.bioreactor.core.protocol)
+
+function round(number, decimals) {
+    // Rounding specific decimal point number
+    return +(Math.round(number + 'e+' + decimals) + 'e-' + decimals)
+}
+
+function controlLight(odValue) {
+    // Check for OD noise/overshots and do primitive OD averaging
+    if (theAccessory.context().getInt('odNoise', 1)) {
+        theAccessory.context().put('odNoise', 0)
+        theAccessory.context().put('odLast', odValue)
+        return null
+    }
+    if (Math.abs(1 - odValue / odLast) < 0.04) {
+        odValue = (odValue + odLast) / 2
+        theAccessory.context().put('odLast', odValue)
+        if (odValue > odLinMax) {
+            result = Math.min(expRegMult * Math.exp(expRegExpo * odValue), theAccessory.getMax());
+        } else if (odValue > odLinMin) {
+            result = Math.min(lightMin + (lightMax - lightMin) * (odValue - odLinMin) / (odLinMax - odLinMin), theAccessory.getMax());
+        } else {
+            result = theAccessory.getValue();
+        }
+    } else {
+        theAccessory.context().put('odNoise', 1)
+        theAccessory.context().put('odLast', odValue)
+        return null
+    }
+}
+
+// dynamic parameters
+var odSensor = theGroup.getAccessory("od-sensors.od-680") // query OD accessory by key
+var odValue = odSensor.getValue()
+var odLast = theAccessory.context().getDouble('odLast', 0.0)
+
+if (!isNaN(odValue) && (round(odValue, 3) !== round(odLast, 3))) {
+    controlLight(odValue)
+}

O2-PIcurveMeasurement.js

@@ -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
@@ -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
       }
     }
@@ -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)