From 924c396300b2ff95215aa59b9a970ac0e7b454d1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sun, 16 Aug 2020 19:52:20 +0200
Subject: [PATCH 01/47] Initial version of PSO

---
 PP-GrowthOptimizer.js | 66 ++++++++++++++++++++++++++++++++++++++++---
 1 file changed, 62 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 4f50be4..4c7cc15 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -7,6 +7,7 @@ var UserDefinedProtocol = {
   // -optimizer parameters
   controlledParameter: 'none',
   controlledParameterSteps: [[ 1100, 25 ], [ 440, 25 ], [ 55, 25 ]],
+  particleSwarmOptimizer: true,
   // -optimizer stability check
   growthStatistics: true,
   regressionODType: 680,
@@ -28,7 +29,7 @@ var UserDefinedProtocol = {
 }
 
 /* global
-  importPackage, java, Packages, theGroup, theAccessory, theExperiment, theLogger, ProtoConfig, ETrendFunction, result: true
+  importPackage, java, Packages, theServer, theGroup, theAccessory, theExperiment, theLogger, ProtoConfig, ETrendFunction, result: true
 */
 
 /**
@@ -39,7 +40,7 @@ var UserDefinedProtocol = {
  * @copyright Jan Červený 2020(c)
  * @license MIT
  * @version 3.3.0
- * @modified 14.8.2020 (JaCe)
+ * @modified 16.8.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -220,6 +221,9 @@ function round (number, decimals) {
   // Rounding specific decimal point number
   return +(Math.round(number + 'e+' + decimals) + 'e-' + decimals)
 }
+function getRandomOnInterval(min, max) {
+  return Math.random() * (max - min) + min;
+}
 function debugLogger (message, status) {
   if ((status === undefined) || (status === 1) || (status === 'on')) {
     theLogger.info('[' + theGroup.getName() + '] ' + message)
@@ -375,7 +379,7 @@ function controlPump () {
     if ((stepDuration[stepCounter] > 0) && UserDefinedProtocol.growthStatistics) {
       var DHCapacity = (Math.floor(stepDuration[stepCounter] / UserDefinedProtocol.ODReadoutInterval) - 3) > 0 ? (Math.floor(stepDuration[stepCounter] / UserDefinedProtocol.ODReadoutInterval) - 3) : 60
       var regCoefExp = odSensorRegression.getDataHistory().regression(ETrendFunction.EXP, Math.ceil(DHCapacity - (UserDefinedProtocol.growthRateEvalFrac ? DHCapacity * (UserDefinedProtocol.growthRateEvalFrac / 100) : UserDefinedProtocol.growthRateEvalDelay / UserDefinedProtocol.ODReadoutInterval)))
-      debugLogger('Growth parameters: ' + regCoefExp.join(', '))
+      debugLogger('Growth parameters: A=' + regCoefExp[0] +', B=' + regCoefExp[1] + ', R2=' + regCoefExp[2])
       if (Number(regCoefExp[2]) >= UserDefinedProtocol.regressionCoDMin / 100) {
         stepDoublingTime[stepCounter] = (1 / (Number(regCoefExp[1]) * 3600 * 10)) * Math.LN2
         theAccessory.context().put('stepCounter', ++stepCounter)
@@ -419,7 +423,9 @@ function controlPump () {
           theAccessory.context().put('modeStabilized', 1)
           // changeCounter = theAccessory.context().getInt('changeCounter', 0)
           theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
-          if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
+          if (UserDefinedProtocol.particleSwarmOptimizer) {
+            controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTimeAvg))
+          } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
             if (changeCounter < (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
               controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[++changeCounter])
               theAccessory.context().put('changeCounter', changeCounter)
@@ -453,3 +459,55 @@ function controlPump () {
     return null // pump not influenced
   }  
 }
+// PSO implementation
+function PSO (particleFitness) {
+  /**
+   * Particle Swarm Optimization.
+   * 
+   * Changes parameter(s) in optimal way as evaluated by PSO algorithm. It requires actual fitness of the particle that is expected to be minimized, e.g. doubling time.
+   * 
+   * @param {number}    particleFitness   Fitness of the particle.
+   * 
+   * @return {array}         New parameters / conditions.          
+   */
+  theAccessory.context().put('particleFitness', particleFitness)
+  var parameterSearchRange = [15, 35]
+  var particlePosition = theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParameterSteps[0])
+  var particleBestPosition = theAccessory.context().get('particleBestPosition', particlePosition)
+  var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
+  var particleStep = theAccessory.context().get('particleStep', 0.2 * parameterSearchRange[1] - parameterSearchRange[0]) // TODO change to multiparameter
+  var swarmLeader = theServer.getGroupByName('DoAB-PBR01-group') // TODO add identifier from UserDefinedProtocol instead
+  var swarmBestPosition = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition)
+  var swarmBestFitness = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestFitness', particleFitness)
+  var neighborsList = ['DoAB-PBR02-group','DoAB-PBR03-group','DoAB-PBR04-group','DoAB-PBR05-group'] // TODO  add  identifier from UserDefinedProtocol. !!! needs to be adjusted for each particle
+  var neighborsPosition = neighborsList.slice()
+  neighborsPosition.forEach(function(value, index, arr) { arr[index] = theServer.getGroupByName(value).context().get('particlePosition', undefined) * 2 })
+  var neighborsFitness = neighborsList.slice()
+  neighborsFitness.forEach(function(value, index, arr) { arr[index] = theServer.getGroupByName(value).context().get('particleFitness', undefined) })
+  var neighborsBestFitness = Math.min.apply(null, neighborsFitness)
+  var neighborsBestPosition = neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness)]
+  var newPosition = []
+  // try {
+  //   swarmBestPosition = swarmBestPosition.split(',')
+  // } catch (error) {
+  //   debugLogger('BioArInEO-PSO ERROR. ' + error.name + ' : ' + error.message)
+  // }
+  // for i in range(len(Swarm.multiparametric_space)):
+  var particleCognitionLearning = 2.1
+  var particleSocialLearning = 2.1
+  var particleGlobalLearning = 1.1
+  var particleInertiaWeighting = 2 * 0.9 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
+  var newStep = particleInertiaWeighting * particleStep + particleCognitionLearning * Math.random() * (particleBestPosition - particlePosition) + particleSocialLearning * Math.random() * (neighborsBestPosition - particlePosition) + particleGlobalLearning * Math.random() * (swarmBestPosition - particlePosition)
+  theAccessory.context().put('particleStep', newStep)
+  if (!(particleFitness > swarmBestFitness)) {
+    theAccessory.context().put('particleBestFitness', particleFitness)
+    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestFitness', particleFitness)
+    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestParticle', theGroup)
+  } else if (!(particleFitness > particleBestFitness)) {
+    theAccessory.context().put('particleBestFitness', particleFitness)
+  }
+  newPosition.push(particlePosition + newStep)
+  theAccessory.context().put('particlePosition', newPosition)
+  debugLogger('BioArInEO-PSO new step is ' + newStep + ' and position is ' + newPosition)
+  return newPosition
+}

From 7f8f0a9f74fe133f72cf0d43ce3585761c2e0bb2 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Mon, 17 Aug 2020 08:57:53 +0200
Subject: [PATCH 02/47] Parameter space limit handling added

---
 PP-GrowthOptimizer.js | 20 ++++++++++++---
 jsDoc.js              | 57 +++++++++++++++++++++++++++++++++++++++++++
 2 files changed, 73 insertions(+), 4 deletions(-)
 create mode 100644 jsDoc.js

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 4c7cc15..2c2a950 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -39,8 +39,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.3.0
- * @modified 16.8.2020 (JaCe)
+ * @version 3.3.1
+ * @modified 17.8.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -466,6 +466,8 @@ function PSO (particleFitness) {
    * 
    * Changes parameter(s) in optimal way as evaluated by PSO algorithm. It requires actual fitness of the particle that is expected to be minimized, e.g. doubling time.
    * 
+   * @since 3.3.0
+   * 
    * @param {number}    particleFitness   Fitness of the particle.
    * 
    * @return {array}         New parameters / conditions.          
@@ -475,7 +477,8 @@ function PSO (particleFitness) {
   var particlePosition = theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParameterSteps[0])
   var particleBestPosition = theAccessory.context().get('particleBestPosition', particlePosition)
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
-  var particleStep = theAccessory.context().get('particleStep', 0.2 * parameterSearchRange[1] - parameterSearchRange[0]) // TODO change to multiparameter
+  var particleStep = theAccessory.context().get('particleStep', 0.2 * parameterSearchRange[1] - parameterSearchRange[0]) // TODO change to multiparameter version
+  var maxStep = 5 // TODO adjust to multiparameter version, i.e. for each parameter reccommended limit (5 is for temperature)
   var swarmLeader = theServer.getGroupByName('DoAB-PBR01-group') // TODO add identifier from UserDefinedProtocol instead
   var swarmBestPosition = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition)
   var swarmBestFitness = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestFitness', particleFitness)
@@ -498,6 +501,9 @@ function PSO (particleFitness) {
   var particleGlobalLearning = 1.1
   var particleInertiaWeighting = 2 * 0.9 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
   var newStep = particleInertiaWeighting * particleStep + particleCognitionLearning * Math.random() * (particleBestPosition - particlePosition) + particleSocialLearning * Math.random() * (neighborsBestPosition - particlePosition) + particleGlobalLearning * Math.random() * (swarmBestPosition - particlePosition)
+  if (newStep > maxStep) {
+    newStep = maxStep
+  } 
   theAccessory.context().put('particleStep', newStep)
   if (!(particleFitness > swarmBestFitness)) {
     theAccessory.context().put('particleBestFitness', particleFitness)
@@ -506,7 +512,13 @@ function PSO (particleFitness) {
   } else if (!(particleFitness > particleBestFitness)) {
     theAccessory.context().put('particleBestFitness', particleFitness)
   }
-  newPosition.push(particlePosition + newStep)
+  if ((particlePosition + newStep) > parameterSearchRange[1]) {
+    newPosition.push(parameterSearchRange[1])
+  } else if ((particlePosition + newStep) < parameterSearchRange[0]) {
+    newPosition.push(parameterSearchRange[0])
+  } else {
+    newPosition.push(particlePosition + newStep)
+  }
   theAccessory.context().put('particlePosition', newPosition)
   debugLogger('BioArInEO-PSO new step is ' + newStep + ' and position is ' + newPosition)
   return newPosition
diff --git a/jsDoc.js b/jsDoc.js
new file mode 100644
index 0000000..2bbed38
--- /dev/null
+++ b/jsDoc.js
@@ -0,0 +1,57 @@
+Functions should be formatted as follows:
+
+Summary: A brief, one line explanation of the purpose of the function. Use a period at the end.
+Description: A supplement to the summary, providing a more detailed description. Use a period at the end.
+@deprecated x.x.x: Only use for deprecated functions, and provide the version the function was deprecated which should always be 3-digit (e.g. @since 3.6.0), and the function to use instead.
+@since x.x.x: Should be 3-digit for initial introduction (e.g. @since 3.6.0). If significant changes are made, additional @since tags, versions, and descriptions should be added to serve as a changelog.
+@access: Only use for functions if private. If the function is private, it is intended for internal use only, and there will be no documentation for it in the code reference.
+@class: Use for class constructors.
+@augments: For class constuctors, list direct parents.
+@mixes: List mixins that are mixed into the object.
+@alias: If this function is first assigned to a temporary variable this allows you to change the name it’s documented under.
+@memberof: Namespace that this function is contained within if JSDoc is unable to resolve this automatically.
+@static: For classes, used to mark that a function is a static method on the class constructor.
+@see: A function or class relied on.
+@link: URL that provides more information.
+@fires: Event fired by the function. Events tied to a specific class should list the class name.
+@listens: Events this function listens for. An event must be prefixed with the event namespace. Events tied to a specific class should list the class name.
+@global: Marks this function as a global function to be included in the global namespace.
+@param: Give a brief description of the variable; denote particulars (e.g. if the variable is optional, its default) with JSDoc @param syntax. Use a period at the end.
+@yield: For generator functions, a description of the values expected to be yielded from this function. As with other descriptions, include a period at the end.
+@return: Note the period after the description.
+
+/**
+ * Summary. (use period)
+ *
+ * Description. (use period)
+ *
+ * @since      x.x.x
+ * @deprecated x.x.x Use new_function_name() instead.
+ * @access     private
+ *
+ * @class
+ * @augments parent
+ * @mixes    mixin
+ *
+ * @alias    realName
+ * @memberof namespace
+ *
+ * @see  Function/class relied on
+ * @link URL
+ * @global
+ *
+ * @fires   eventName
+ * @fires   className#eventName
+ * @listens event:eventName
+ * @listens className~event:eventName
+ *
+ * @param {type}   var           Description.
+ * @param {type}   [var]         Description of optional variable.
+ * @param {type}   [var=default] Description of optional variable with default variable.
+ * @param {Object} objectVar     Description.
+ * @param {type}   objectVar.key Description of a key in the objectVar parameter.
+ *
+ * @yield {type} Yielded value description.
+ *
+ * @return {type} Return value description.
+ */

From 80caf625bd210ca3008822ef69d69f9b56f6014c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Wed, 19 Aug 2020 10:56:35 +0200
Subject: [PATCH 03/47] Bufixes, code optimization and sendMail implementation

---
 PP-GrowthOptimizer.js | 70 +++++++++++++++++++++++++++----------------
 1 file changed, 44 insertions(+), 26 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 2c2a950..4bc7e3a 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -5,8 +5,8 @@ var UserDefinedProtocol = {
   turbidostatODType: 720,
   ODReadoutInterval: 60,
   // -optimizer parameters
-  controlledParameter: 'none',
-  controlledParameterSteps: [[ 1100, 25 ], [ 440, 25 ], [ 55, 25 ]],
+  controlledParameter: 'temperature',
+  controlledParameterSteps: [ 25 ],
   particleSwarmOptimizer: true,
   // -optimizer stability check
   growthStatistics: true,
@@ -39,8 +39,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.3.1
- * @modified 17.8.2020 (JaCe)
+ * @version 3.3.2
+ * @modified 19.8.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -183,7 +183,7 @@ try {
     result = controlPump()
   }
 } catch (error) {
-  debugLogger('O2 evol./resp. activity check ERROR. ' + error.name + ' : ' + error.message)
+  debugLogger('The pump activity ERROR. ' + error.name + ' : ' + error.message)
 }
 /**
   function setODSensorString (ODType) {
@@ -244,13 +244,13 @@ function controlParameter (parameter, values) {
       unit = ' uE'
       light0.setRunningProtoConfig(new ProtoConfig(Number(values[0]))) // Red
       light1.setRunningProtoConfig(new ProtoConfig(Number(values[1]))) // Blue || White
-      debugLogger('Lights changed.')
+      debugLogger('Lights changed. Channel 0 set to ' + round(values[0], 0) + unit + ' and channel 1 set to ' + round(values[1], 0) + unit)
       break
     case 'temperature':
       var thermoreg = theGroup.getAccessory('thermo.thermo-reg')
-      unit = String.fromCharCode(176) + 'C'
+      unit = ' ' + String.fromCharCode(176) + 'C'
       thermoreg.setRunningProtoConfig(new ProtoConfig(Number(values)))
-      debugLogger('Temperature changed.')
+      debugLogger('Temperature changed. Thermoregulator set to ' + round(values, 2) + unit)
       break
     case 'GMS':
       var valve0 = UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg') // CO2
@@ -260,19 +260,19 @@ function controlParameter (parameter, values) {
       valve1.setRunningProtoConfig(new ProtoConfig(Number(values[1])))
       var flowAir = valve0.getProtoConfigValue()
       var flowCO2 = valve1.getProtoConfigValue()
-      debugLogger('GMS settings changed. Gas Mixing set to Air flow ' + round(flowAir, 2) + ' ml/min and CO2 flow ' + round(flowCO2, 2) + ' ml/min (' + round((flowCO2 / (flowCO2 + flowAir) + 400 / 1e6) * 100, 1) + '%)')
+      debugLogger('GMS settings changed. Gas Mixing set to Air flow ' + round(flowAir, 0) + unit + ' and CO2 flow ' + round(flowCO2, 1) + unit + ' (' + round((flowCO2 / (flowCO2 + flowAir) + 395 / 1e6) * 100, 1) + '%)')
       break
     case 'stirrer':
       var stirrer = theGroup.getAccessory('pwm.stirrer')
       unit = '%'
       stirrer.setRunningProtoConfig(new ProtoConfig(Number(values)))
-      debugLogger('Stirrer changed.')
+      debugLogger('Stirrer changed. Stirrer set to ' + round(values, 0) + unit)
       break
     case 'ODRange':
       theAccessory.context().put('odMinModifier', Number(values[0]) / UserDefinedProtocol.turbidostatODMin)
       theAccessory.context().put('odMaxModifier', Number(values[1]) / UserDefinedProtocol.turbidostatODMax)
       unit = ' AU'
-      debugLogger('Turbidostat OD range changed.')
+      debugLogger('Turbidostat settings changed. OD range set to ' + round(values[0], 3) + ' - ' + round(values[1], 3) + unit)
       break
     default:
       return null
@@ -337,7 +337,14 @@ function controlPump () {
   }
   if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= Number(theExperiment.getDurationSec()) && (stepCounter !== 0)) {
     theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
-    if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
+    if (UserDefinedProtocol.particleSwarmOptimizer) {
+      var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
+      controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTime[stepDoublingTime.length - 1])) //TODO change to average of last n steps 
+      theAccessory.context().remove('stepCounter')
+      theAccessory.context().remove('expDuration')
+      theAccessory.context().remove('stepDoublingTime')
+      theAccessory.context().remove('stabilizedTime')
+    } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
       if (changeCounter < (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
         controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[++changeCounter])
         theAccessory.context().put('changeCounter', changeCounter)
@@ -352,7 +359,7 @@ function controlPump () {
       theAccessory.context().remove('expDuration')
       theAccessory.context().remove('stepDoublingTime')
       theAccessory.context().remove('stabilizedTime')
-    }
+    }  
   }
   // Start step growth rate evaluation
   if (((odValue > (UserDefinedProtocol.turbidostatODMax * odMaxModifier)) && !pumpState)) {
@@ -361,7 +368,7 @@ function controlPump () {
     // var stepCounter = theAccessory.context().getInt('stepCounter', 0)
     var expDuration = theAccessory.context().get('expDuration', 0.0)
     var stepDuration = theAccessory.context().get('stepDuration', 0.0)
-    var stepDoublingTime = theAccessory.context().get('stepDoublingTime', 0.0)
+    var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
     var stabilizedTime = theAccessory.context().getInt('stabilizedTime', 0)
     // var stabilizedTimeMax = theAccessory.context().getInt('stabilizedTimeMax', 0)
     if (!Array.isArray(expDuration)) {
@@ -422,7 +429,7 @@ function controlPump () {
         if (((stepDoublingTimeIC95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.intervalOfConfidenceMax / 100) && (Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) && (stabilizedTime <= Number(theExperiment.getDurationSec())))) {
           theAccessory.context().put('modeStabilized', 1)
           // changeCounter = theAccessory.context().getInt('changeCounter', 0)
-          theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
+          theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
           if (UserDefinedProtocol.particleSwarmOptimizer) {
             controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTimeAvg))
           } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
@@ -472,23 +479,30 @@ function PSO (particleFitness) {
    * 
    * @return {array}         New parameters / conditions.          
    */
+  debugLogger('BioArInEO-PSO executed') 
   theAccessory.context().put('particleFitness', particleFitness)
   var parameterSearchRange = [15, 35]
-  var particlePosition = theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParameterSteps[0])
-  var particleBestPosition = theAccessory.context().get('particleBestPosition', particlePosition)
+  var particlePosition = Number(theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParameterSteps[0])) //TODO multidimensional support
+  theAccessory.context().put('particlePosition', particlePosition)
+  var particleBestPosition = Number(theAccessory.context().get('particleBestPosition', particlePosition))
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
   var particleStep = theAccessory.context().get('particleStep', 0.2 * parameterSearchRange[1] - parameterSearchRange[0]) // TODO change to multiparameter version
   var maxStep = 5 // TODO adjust to multiparameter version, i.e. for each parameter reccommended limit (5 is for temperature)
   var swarmLeader = theServer.getGroupByName('DoAB-PBR01-group') // TODO add identifier from UserDefinedProtocol instead
-  var swarmBestPosition = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition)
+  var swarmBestPosition = Number(swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition))
   var swarmBestFitness = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestFitness', particleFitness)
-  var neighborsList = ['DoAB-PBR02-group','DoAB-PBR03-group','DoAB-PBR04-group','DoAB-PBR05-group'] // TODO  add  identifier from UserDefinedProtocol. !!! needs to be adjusted for each particle
-  var neighborsPosition = neighborsList.slice()
-  neighborsPosition.forEach(function(value, index, arr) { arr[index] = theServer.getGroupByName(value).context().get('particlePosition', undefined) * 2 })
-  var neighborsFitness = neighborsList.slice()
-  neighborsFitness.forEach(function(value, index, arr) { arr[index] = theServer.getGroupByName(value).context().get('particleFitness', undefined) })
+  debugLogger('BioArInEO-PSO best swarm position is ' + swarmBestPosition + ' with fitness ' + swarmBestFitness)
+  var neighborsList = ['DoAB-PBR02-group'] // TODO  add  identifier from UserDefinedProtocol. !!! needs to be adjusted for each particle
+  var neighborsPosition = []
+  var neighborsFitness = []
+  var index, len
+  for ( index = 0, len = neighborsList.length; index < len; ++index) {
+    neighborsPosition.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particlePosition', particlePosition));
+    neighborsFitness.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particleFitness', particleFitness))
+  }
   var neighborsBestFitness = Math.min.apply(null, neighborsFitness)
-  var neighborsBestPosition = neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness)]
+  var neighborsBestPosition = Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness)])
+  debugLogger('BioArInEO-PSO best neighbors position is ' + neighborsBestPosition + ' with fitness ' + neighborsBestFitness)
   var newPosition = []
   // try {
   //   swarmBestPosition = swarmBestPosition.split(',')
@@ -499,17 +513,21 @@ function PSO (particleFitness) {
   var particleCognitionLearning = 2.1
   var particleSocialLearning = 2.1
   var particleGlobalLearning = 1.1
-  var particleInertiaWeighting = 2 * 0.9 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
+  var particleInertiaWeighting = 2 * 0.8 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
+  debugLogger('BioArInEO-PSO evaluating new step') 
   var newStep = particleInertiaWeighting * particleStep + particleCognitionLearning * Math.random() * (particleBestPosition - particlePosition) + particleSocialLearning * Math.random() * (neighborsBestPosition - particlePosition) + particleGlobalLearning * Math.random() * (swarmBestPosition - particlePosition)
   if (newStep > maxStep) {
     newStep = maxStep
   } 
   theAccessory.context().put('particleStep', newStep)
   if (!(particleFitness > swarmBestFitness)) {
+    theAccessory.context().put('particleBestPosition', particlePosition)
     theAccessory.context().put('particleBestFitness', particleFitness)
+    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestPosition', particlePosition)
     swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestFitness', particleFitness)
     swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestParticle', theGroup)
   } else if (!(particleFitness > particleBestFitness)) {
+    theAccessory.context().put('particleBestPosition', particlePosition)
     theAccessory.context().put('particleBestFitness', particleFitness)
   }
   if ((particlePosition + newStep) > parameterSearchRange[1]) {
@@ -519,7 +537,7 @@ function PSO (particleFitness) {
   } else {
     newPosition.push(particlePosition + newStep)
   }
-  theAccessory.context().put('particlePosition', newPosition)
   debugLogger('BioArInEO-PSO new step is ' + newStep + ' and position is ' + newPosition)
+  theServer.sendMail('PSO on ' + theGroup.getName() , 'INFO', ': new step is ' + newStep + ' and position is ' + newPosition) // Email notifications
   return newPosition
 }

From 61999d9e0768dd4e88a2b101caaf1cd1bf657349 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Wed, 19 Aug 2020 11:05:35 +0200
Subject: [PATCH 04/47] PSO particle initial step direction randomized

---
 PP-GrowthOptimizer.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 4bc7e3a..82c24c5 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -486,7 +486,7 @@ function PSO (particleFitness) {
   theAccessory.context().put('particlePosition', particlePosition)
   var particleBestPosition = Number(theAccessory.context().get('particleBestPosition', particlePosition))
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
-  var particleStep = theAccessory.context().get('particleStep', 0.2 * parameterSearchRange[1] - parameterSearchRange[0]) // TODO change to multiparameter version
+  var particleStep = theAccessory.context().get('particleStep', 0.2 * (parameterSearchRange[1] - parameterSearchRange[0]) * Math.sign(getRandomOnInterval(-1, 1))) // TODO change to multiparameter version
   var maxStep = 5 // TODO adjust to multiparameter version, i.e. for each parameter reccommended limit (5 is for temperature)
   var swarmLeader = theServer.getGroupByName('DoAB-PBR01-group') // TODO add identifier from UserDefinedProtocol instead
   var swarmBestPosition = Number(swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition))

From 0fe05837e6293064ae5cc7428e117e8aca2aa2c1 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Wed, 19 Aug 2020 18:38:54 +0200
Subject: [PATCH 05/47] No support for Math.sign() fixed

---
 PP-GrowthOptimizer.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 82c24c5..a3d87f5 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -486,7 +486,7 @@ function PSO (particleFitness) {
   theAccessory.context().put('particlePosition', particlePosition)
   var particleBestPosition = Number(theAccessory.context().get('particleBestPosition', particlePosition))
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
-  var particleStep = theAccessory.context().get('particleStep', 0.2 * (parameterSearchRange[1] - parameterSearchRange[0]) * Math.sign(getRandomOnInterval(-1, 1))) // TODO change to multiparameter version
+  var particleStep = theAccessory.context().get('particleStep', 0.2 * (parameterSearchRange[1] - parameterSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
   var maxStep = 5 // TODO adjust to multiparameter version, i.e. for each parameter reccommended limit (5 is for temperature)
   var swarmLeader = theServer.getGroupByName('DoAB-PBR01-group') // TODO add identifier from UserDefinedProtocol instead
   var swarmBestPosition = Number(swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition))

From 07e796717c5e3caab82c9b496a81d35ba9c2fccb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Thu, 20 Aug 2020 14:24:59 +0200
Subject: [PATCH 06/47] PSO fitness averaging when stabilizationTimeMax

---
 PP-GrowthOptimizer.js | 23 ++++++++++++++---------
 1 file changed, 14 insertions(+), 9 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index a3d87f5..83a51ba 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -39,8 +39,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.3.2
- * @modified 19.8.2020 (JaCe)
+ * @version 3.3.3
+ * @modified 20.8.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -231,6 +231,9 @@ function debugLogger (message, status) {
     return null
   }
 }
+function getSumArrReduce(total, num) {
+  return total + num;
+}
 function controlParameter (parameter, values) {
   // Control accessory functions
   if ((parameter === undefined) || (parameter === 'none') || (values === undefined)) {
@@ -339,7 +342,8 @@ function controlPump () {
     theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
     if (UserDefinedProtocol.particleSwarmOptimizer) {
       var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
-      controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTime[stepDoublingTime.length - 1])) //TODO change to average of last n steps 
+      stepDoublingTime = stepDoublingTime.length > 2 ? stepDoublingTime.reduce(getSumArrReduce, 0) / stepDoublingTime.length : stepDoublingTime[stepDoublingTime.length - 1]
+      controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTime))
       theAccessory.context().remove('stepCounter')
       theAccessory.context().remove('expDuration')
       theAccessory.context().remove('stepDoublingTime')
@@ -480,10 +484,10 @@ function PSO (particleFitness) {
    * @return {array}         New parameters / conditions.          
    */
   debugLogger('BioArInEO-PSO executed') 
-  theAccessory.context().put('particleFitness', particleFitness)
+  theAccessory.context().put('particleLastFitness', particleFitness)
   var parameterSearchRange = [15, 35]
   var particlePosition = Number(theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParameterSteps[0])) //TODO multidimensional support
-  theAccessory.context().put('particlePosition', particlePosition)
+  theAccessory.context().put('particleLastPosition', particlePosition)
   var particleBestPosition = Number(theAccessory.context().get('particleBestPosition', particlePosition))
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
   var particleStep = theAccessory.context().get('particleStep', 0.2 * (parameterSearchRange[1] - parameterSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
@@ -497,8 +501,8 @@ function PSO (particleFitness) {
   var neighborsFitness = []
   var index, len
   for ( index = 0, len = neighborsList.length; index < len; ++index) {
-    neighborsPosition.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particlePosition', particlePosition));
-    neighborsFitness.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particleFitness', particleFitness))
+    neighborsPosition.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particleLastPosition', particlePosition));
+    neighborsFitness.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particleLastFitness', particleFitness))
   }
   var neighborsBestFitness = Math.min.apply(null, neighborsFitness)
   var neighborsBestPosition = Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness)])
@@ -511,8 +515,8 @@ function PSO (particleFitness) {
   // }
   // for i in range(len(Swarm.multiparametric_space)):
   var particleCognitionLearning = 2.1
-  var particleSocialLearning = 2.1
-  var particleGlobalLearning = 1.1
+  var particleSocialLearning = 1.1
+  var particleGlobalLearning = 1.6
   var particleInertiaWeighting = 2 * 0.8 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
   debugLogger('BioArInEO-PSO evaluating new step') 
   var newStep = particleInertiaWeighting * particleStep + particleCognitionLearning * Math.random() * (particleBestPosition - particlePosition) + particleSocialLearning * Math.random() * (neighborsBestPosition - particlePosition) + particleGlobalLearning * Math.random() * (swarmBestPosition - particlePosition)
@@ -537,6 +541,7 @@ function PSO (particleFitness) {
   } else {
     newPosition.push(particlePosition + newStep)
   }
+  theAccessory.context().put('particlePosition', newPosition)
   debugLogger('BioArInEO-PSO new step is ' + newStep + ' and position is ' + newPosition)
   theServer.sendMail('PSO on ' + theGroup.getName() , 'INFO', ': new step is ' + newStep + ' and position is ' + newPosition) // Email notifications
   return newPosition

From 3a80951ce5a9b4e9abb29f1f5e446c9919bb2c42 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Thu, 20 Aug 2020 15:09:22 +0200
Subject: [PATCH 07/47] PSO parameters optimized + Dt averaging interval
 reduced

---
 PP-GrowthOptimizer.js | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 83a51ba..42520db 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -342,7 +342,8 @@ function controlPump () {
     theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
     if (UserDefinedProtocol.particleSwarmOptimizer) {
       var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
-      stepDoublingTime = stepDoublingTime.length > 2 ? stepDoublingTime.reduce(getSumArrReduce, 0) / stepDoublingTime.length : stepDoublingTime[stepDoublingTime.length - 1]
+      var len = stepDoublingTime.length
+      stepDoublingTime = len > 2 ? stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
       controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTime))
       theAccessory.context().remove('stepCounter')
       theAccessory.context().remove('expDuration')

From 4622bafe18910eb8f405b7353e5e9e0583dcd74d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sun, 23 Aug 2020 22:27:31 +0200
Subject: [PATCH 08/47] Bugfixes

---
 PP-GrowthOptimizer.js | 53 +++++++++++++++++++++++--------------------
 1 file changed, 28 insertions(+), 25 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 42520db..98e8a21 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -1,23 +1,23 @@
 var UserDefinedProtocol = {
   // -turbidostat settings
-  turbidostatODMin: 0.4,
-  turbidostatODMax: 0.425,
+  turbidostatODMin: 0.18,
+  turbidostatODMax: 0.195,
   turbidostatODType: 720,
   ODReadoutInterval: 60,
   // -optimizer parameters
   controlledParameter: 'temperature',
-  controlledParameterSteps: [ 25 ],
+  controlledParameterSteps: [ 28 ],
   particleSwarmOptimizer: true,
   // -optimizer stability check
   growthStatistics: true,
   regressionODType: 680,
-  regressionCoDMin: 75,
-  stabilizationTimeMin: 12,
-  stabilizationTimeMax: 36,
-  growthRateEvalFrac: 2 / 3,
+  regressionCoDMin: 60,
+  stabilizationTimeMin: 3,
+  stabilizationTimeMax: 7,
+  growthRateEvalFrac: 3 / 4,
   analyzedSteps: 6,
-  growthTrendMax: 1.5,
-  intervalOfConfidenceMax: 3.5,
+  growthTrendMax: 15,
+  intervalOfConfidenceMax: 35,
   // -peristaltic pump settings
   peristalticPumpID: 5,
   peristalticPumpSpeed: 100,
@@ -39,8 +39,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.3.3
- * @modified 20.8.2020 (JaCe)
+ * @version 3.3.4
+ * @modified 23.8.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -339,7 +339,7 @@ function controlPump () {
     debugLogger('OD range reversed.', 0)
   }
   if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= Number(theExperiment.getDurationSec()) && (stepCounter !== 0)) {
-    theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
+    theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600) // TODO allocate var for getDurationSec
     if (UserDefinedProtocol.particleSwarmOptimizer) {
       var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
       var len = stepDoublingTime.length
@@ -448,12 +448,12 @@ function controlPump () {
               controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[1])
               theAccessory.context().put('changeCounter', 1)
             }
-            theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
-            theAccessory.context().remove('stepCounter')
-            theAccessory.context().remove('expDuration')
-            theAccessory.context().remove('stepDoublingTime')
-            theAccessory.context().remove('stabilizedTime')
           }
+          theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
+          theAccessory.context().remove('stepCounter')
+          theAccessory.context().remove('expDuration')
+          theAccessory.context().remove('stepDoublingTime')
+          theAccessory.context().remove('stabilizedTime')
         }
       }
     }
@@ -484,15 +484,18 @@ function PSO (particleFitness) {
    * 
    * @return {array}         New parameters / conditions.          
    */
+  if (particleFitness === undefined) {
+    particleFitness = [ 999.9 ]
+  }
   debugLogger('BioArInEO-PSO executed') 
   theAccessory.context().put('particleLastFitness', particleFitness)
-  var parameterSearchRange = [15, 35]
+  var parameterSearchRange = [ 18, 38 ]
   var particlePosition = Number(theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParameterSteps[0])) //TODO multidimensional support
-  theAccessory.context().put('particleLastPosition', particlePosition)
-  var particleBestPosition = Number(theAccessory.context().get('particleBestPosition', particlePosition))
+  theAccessory.context().put('particleLastPosition', particlePosition
+  var particleBestPosition = Number(theAccessory.context().get('particleBestPosition', particlePosition)
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
   var particleStep = theAccessory.context().get('particleStep', 0.2 * (parameterSearchRange[1] - parameterSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
-  var maxStep = 5 // TODO adjust to multiparameter version, i.e. for each parameter reccommended limit (5 is for temperature)
+  var maxStep = 150 // TODO adjust to multiparameter version, i.e. for each parameter reccommended limit (5 is for temperature)
   var swarmLeader = theServer.getGroupByName('DoAB-PBR01-group') // TODO add identifier from UserDefinedProtocol instead
   var swarmBestPosition = Number(swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition))
   var swarmBestFitness = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestFitness', particleFitness)
@@ -521,9 +524,9 @@ function PSO (particleFitness) {
   var particleInertiaWeighting = 2 * 0.8 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
   debugLogger('BioArInEO-PSO evaluating new step') 
   var newStep = particleInertiaWeighting * particleStep + particleCognitionLearning * Math.random() * (particleBestPosition - particlePosition) + particleSocialLearning * Math.random() * (neighborsBestPosition - particlePosition) + particleGlobalLearning * Math.random() * (swarmBestPosition - particlePosition)
-  if (newStep > maxStep) {
-    newStep = maxStep
-  } 
+  if (Math.abs(newStep) > maxStep) {
+    newStep = maxStep * (newStep > 0 ? 1 : -1)
+  }
   theAccessory.context().put('particleStep', newStep)
   if (!(particleFitness > swarmBestFitness)) {
     theAccessory.context().put('particleBestPosition', particlePosition)
@@ -544,6 +547,6 @@ function PSO (particleFitness) {
   }
   theAccessory.context().put('particlePosition', newPosition)
   debugLogger('BioArInEO-PSO new step is ' + newStep + ' and position is ' + newPosition)
-  theServer.sendMail('PSO on ' + theGroup.getName() , 'INFO', ': new step is ' + newStep + ' and position is ' + newPosition) // Email notifications
+  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': new step is ' + newStep + ' and position is ' + newPosition) // Email notifications
   return newPosition
 }

From cab280f44a961c1bbaedeef2a504184731e40533 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Mon, 24 Aug 2020 23:32:56 +0200
Subject: [PATCH 09/47] Multiparametric PSO implemented

---
 PP-GrowthOptimizer.js | 132 +++++++++++++++++++++++++++---------------
 1 file changed, 86 insertions(+), 46 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 98e8a21..9d93dd1 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -8,6 +8,12 @@ var UserDefinedProtocol = {
   controlledParameter: 'temperature',
   controlledParameterSteps: [ 28 ],
   particleSwarmOptimizer: true,
+  controlledParameters: [ 'temperature' ],
+  controlledParametersIC: [ 28 ],
+  parametersSearchRange: [ 18, 38 ],
+  parametersMaxStep: [ 5 ],
+  swarmLeaderGroup: 'DoAB-PBR01-group',
+  particleNeighborsGroupList: [ 'DoAB-PBR02-group' ],
   // -optimizer stability check
   growthStatistics: true,
   regressionODType: 680,
@@ -21,7 +27,7 @@ var UserDefinedProtocol = {
   // -peristaltic pump settings
   peristalticPumpID: 5,
   peristalticPumpSpeed: 100,
-  peristalticPumpSlowDownRange: 25,
+  peristalticPumpSlowDownRange: 20,
   peristalticPumpSlowDownFactor: 75,
   // -advanced options
   growthRateEvalDelay: 420,
@@ -39,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.3.4
- * @modified 23.8.2020 (JaCe)
+ * @version 3.4.1
+ * @modified 24.8.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -249,6 +255,19 @@ function controlParameter (parameter, values) {
       light1.setRunningProtoConfig(new ProtoConfig(Number(values[1]))) // Blue || White
       debugLogger('Lights changed. Channel 0 set to ' + round(values[0], 0) + unit + ' and channel 1 set to ' + round(values[1], 0) + unit)
       break
+    case 'light-red':
+      var light0 = theGroup.getAccessory('actinic-lights.light-Red')
+      unit = ' uE'
+      light0.setRunningProtoConfig(new ProtoConfig(Number(values))) // Red
+      debugLogger('Red Light changed. Light set to ' + round(values, 0) + unit)
+      break
+    case 'light-white':
+    case 'light-blue':
+      var light1 = theGroup.getAccessory(theAccessory.context().get('light1String', 'actinic-lights.light-Blue'))
+      unit = ' uE'
+      light1.setRunningProtoConfig(new ProtoConfig(Number(values))) // Blue || White
+      debugLogger('White/blue light changed. Light set to ' + round(values, 0) + unit)
+      break
     case 'temperature':
       var thermoreg = theGroup.getAccessory('thermo.thermo-reg')
       unit = ' ' + String.fromCharCode(176) + 'C'
@@ -344,7 +363,7 @@ function controlPump () {
       var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
       var len = stepDoublingTime.length
       stepDoublingTime = len > 2 ? stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
-      controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTime))
+      PSO(stepDoublingTime)
       theAccessory.context().remove('stepCounter')
       theAccessory.context().remove('expDuration')
       theAccessory.context().remove('stepDoublingTime')
@@ -436,7 +455,7 @@ function controlPump () {
           // changeCounter = theAccessory.context().getInt('changeCounter', 0)
           theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
           if (UserDefinedProtocol.particleSwarmOptimizer) {
-            controlParameter(UserDefinedProtocol.controlledParameter, PSO(stepDoublingTimeAvg))
+            PSO(stepDoublingTimeAvg)
           } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
             if (changeCounter < (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
               controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[++changeCounter])
@@ -487,47 +506,73 @@ function PSO (particleFitness) {
   if (particleFitness === undefined) {
     particleFitness = [ 999.9 ]
   }
-  debugLogger('BioArInEO-PSO executed') 
   theAccessory.context().put('particleLastFitness', particleFitness)
-  var parameterSearchRange = [ 18, 38 ]
-  var particlePosition = Number(theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParameterSteps[0])) //TODO multidimensional support
-  theAccessory.context().put('particleLastPosition', particlePosition
-  var particleBestPosition = Number(theAccessory.context().get('particleBestPosition', particlePosition)
+  var particlePosition = theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParametersIC)
+  debugLogger('BioArInEO-PSO executed with fitness ' + particleFitness + ' and position ' + particlePosition) 
+  theAccessory.context().put('particleLastPosition', particlePosition)
+  var particleBestPosition = theAccessory.context().get('particleBestPosition', particlePosition)
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
-  var particleStep = theAccessory.context().get('particleStep', 0.2 * (parameterSearchRange[1] - parameterSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
-  var maxStep = 150 // TODO adjust to multiparameter version, i.e. for each parameter reccommended limit (5 is for temperature)
-  var swarmLeader = theServer.getGroupByName('DoAB-PBR01-group') // TODO add identifier from UserDefinedProtocol instead
-  var swarmBestPosition = Number(swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition))
+  var swarmLeader = theServer.getGroupByName(UserDefinedProtocol.swarmLeaderGroup)
+  var swarmBestPosition = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition)
   var swarmBestFitness = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestFitness', particleFitness)
-  debugLogger('BioArInEO-PSO best swarm position is ' + swarmBestPosition + ' with fitness ' + swarmBestFitness)
-  var neighborsList = ['DoAB-PBR02-group'] // TODO  add  identifier from UserDefinedProtocol. !!! needs to be adjusted for each particle
-  var neighborsPosition = []
-  var neighborsFitness = []
-  var index, len
-  for ( index = 0, len = neighborsList.length; index < len; ++index) {
-    neighborsPosition.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particleLastPosition', particlePosition));
-    neighborsFitness.push(theServer.getGroupByName(neighborsList[index]).getAccessory('pumps.pump-5').context().get('particleLastFitness', particleFitness))
+  var neighborsList = UserDefinedProtocol.particleNeighborsGroupList
+  var parametersSearchRange = UserDefinedProtocol.parametersSearchRange
+  var particleStep =  theAccessory.context().get('particleStep', undefined)
+  var temporaryTest = false
+  if (particleStep === undefined) {
+    temporaryTest = true
+    particleStep = []
   }
-  var neighborsBestFitness = Math.min.apply(null, neighborsFitness)
-  var neighborsBestPosition = Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness)])
-  debugLogger('BioArInEO-PSO best neighbors position is ' + neighborsBestPosition + ' with fitness ' + neighborsBestFitness)
+  var maxStep = []
+  var neighborsBestPosition = []
+  var neighborsBestFitness = []
   var newPosition = []
-  // try {
-  //   swarmBestPosition = swarmBestPosition.split(',')
-  // } catch (error) {
-  //   debugLogger('BioArInEO-PSO ERROR. ' + error.name + ' : ' + error.message)
-  // }
-  // for i in range(len(Swarm.multiparametric_space)):
+  var newStep = []
   var particleCognitionLearning = 2.1
   var particleSocialLearning = 1.1
   var particleGlobalLearning = 1.6
   var particleInertiaWeighting = 2 * 0.8 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
-  debugLogger('BioArInEO-PSO evaluating new step') 
-  var newStep = particleInertiaWeighting * particleStep + particleCognitionLearning * Math.random() * (particleBestPosition - particlePosition) + particleSocialLearning * Math.random() * (neighborsBestPosition - particlePosition) + particleGlobalLearning * Math.random() * (swarmBestPosition - particlePosition)
-  if (Math.abs(newStep) > maxStep) {
-    newStep = maxStep * (newStep > 0 ? 1 : -1)
+  var temporaryNeighborPosition
+  var neighborsPosition = []
+  var neighborsFitness = []
+  for (var index = 0, len = UserDefinedProtocol.controlledParameters.length; index < len; index++) {
+    debugLogger('BioArInEO-PSO evaluating new step for ' + UserDefinedProtocol.controlledParameters[index]) 
+    if (len > 1) {
+      parametersSearchRange = UserDefinedProtocol.parametersSearchRange[index]
+    }
+    if (temporaryTest) {
+      particleStep.push(0.2 * (parametersSearchRange[1] - parametersSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
+    }
+    debugLogger('BioArInEO-PSO particle step is ' + particleStep[index]) 
+    maxStep.push(Number(UserDefinedProtocol.parametersMaxStep[index]))
+    debugLogger('BioArInEO-PSO particle max step is ' + maxStep[index])
+    for (var indexN = 0, lenN = neighborsList.length; indexN < lenN; ++indexN) {
+      temporaryNeighborPosition = theServer.getGroupByName(neighborsList[indexN]).getAccessory('pumps.pump-5').context().get('particleLastPosition', undefined)
+      neighborsPosition = []
+      neighborsFitness = []
+      if (temporaryNeighborPosition === undefined) {
+        neighborsPosition.push(particlePosition[index])
+      } else {
+        neighborsPosition.push(temporaryNeighborPosition[index])
+      }
+      neighborsFitness.push(theServer.getGroupByName(neighborsList[indexN]).getAccessory('pumps.pump-5').context().get('particleLastFitness', particleFitness))
+    }
+    neighborsBestFitness.push(Math.min.apply(null, neighborsFitness))
+    neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
+    debugLogger('BioArInEO-PSO neighbors best position is [ ' + neighborsBestPosition[index] + '] with fitness ' + neighborsBestFitness[index])
+    newStep.push(particleInertiaWeighting * particleStep[index] + particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) + particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) + particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]))
+    if (Math.abs(newStep[index]) > maxStep[index]) {
+      newStep[index] = maxStep[index] * (newStep[index] > 0 ? 1 : -1)
+    }
+    if ((particlePosition[index] + newStep[index]) > UserDefinedProtocol.parametersSearchRange[1]) {
+      newPosition.push(UserDefinedProtocol.parametersSearchRange[1])
+    } else if ((particlePosition[index] + newStep[index]) < UserDefinedProtocol.parametersSearchRange[0]) {
+      newPosition.push(UserDefinedProtocol.parametersSearchRange[0])
+    } else {
+      newPosition.push(particlePosition[index] + newStep[index])
+    }
+    controlParameter(UserDefinedProtocol.controlledParameters[index], newPosition[index])
   }
-  theAccessory.context().put('particleStep', newStep)
   if (!(particleFitness > swarmBestFitness)) {
     theAccessory.context().put('particleBestPosition', particlePosition)
     theAccessory.context().put('particleBestFitness', particleFitness)
@@ -538,15 +583,10 @@ function PSO (particleFitness) {
     theAccessory.context().put('particleBestPosition', particlePosition)
     theAccessory.context().put('particleBestFitness', particleFitness)
   }
-  if ((particlePosition + newStep) > parameterSearchRange[1]) {
-    newPosition.push(parameterSearchRange[1])
-  } else if ((particlePosition + newStep) < parameterSearchRange[0]) {
-    newPosition.push(parameterSearchRange[0])
-  } else {
-    newPosition.push(particlePosition + newStep)
-  }
+  theAccessory.context().put('particleStep', newStep)
   theAccessory.context().put('particlePosition', newPosition)
-  debugLogger('BioArInEO-PSO new step is ' + newStep + ' and position is ' + newPosition)
-  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': new step is ' + newStep + ' and position is ' + newPosition) // Email notifications
-  return newPosition
+  debugLogger('BioArInEO-PSO best swarm position is [ ' + swarmBestPosition + ' ] with fitness ' + swarmBestFitness)
+  debugLogger('BioArInEO-PSO best neighbors position is [ ' + neighborsBestPosition + ' ] with fitness ' + neighborsBestFitness[0])
+  debugLogger('BioArInEO-PSO new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]')
+  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]') // Email notifications
 }

From c45610d42f0d991c5cbb7ba89b0dff71565a7c17 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Fri, 28 Aug 2020 07:37:52 +0200
Subject: [PATCH 10/47] Modifications in to allow single channel GMS (CO2)
 change

---
 PP-GrowthOptimizer.js | 18 ++++++++++++++----
 1 file changed, 14 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 9d93dd1..ea93055 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -251,6 +251,7 @@ function controlParameter (parameter, values) {
       var light0 = theGroup.getAccessory('actinic-lights.light-Red')
       var light1 = theGroup.getAccessory(theAccessory.context().get('light1String', 'actinic-lights.light-Blue'))
       unit = ' uE'
+      values = Array(values, values)
       light0.setRunningProtoConfig(new ProtoConfig(Number(values[0]))) // Red
       light1.setRunningProtoConfig(new ProtoConfig(Number(values[1]))) // Blue || White
       debugLogger('Lights changed. Channel 0 set to ' + round(values[0], 0) + unit + ' and channel 1 set to ' + round(values[1], 0) + unit)
@@ -280,10 +281,19 @@ function controlParameter (parameter, values) {
       unit = ' ml/min'
       valve0.setRunningProtoConfig(new ProtoConfig(Number(values[0])))
       valve1.setRunningProtoConfig(new ProtoConfig(Number(values[1])))
-      var flowAir = valve0.getProtoConfigValue()
-      var flowCO2 = valve1.getProtoConfigValue()
+      var flowCO2 = valve0.getProtoConfigValue()
+      var flowAir = valve1.getProtoConfigValue()
       debugLogger('GMS settings changed. Gas Mixing set to Air flow ' + round(flowAir, 0) + unit + ' and CO2 flow ' + round(flowCO2, 1) + unit + ' (' + round((flowCO2 / (flowCO2 + flowAir) + 395 / 1e6) * 100, 1) + '%)')
       break
+      case 'GMS-CO2':
+        var valve0 = UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg') // CO2
+        var valve1 = UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-1-reg') // Air
+        unit = ' ml/min'
+        valve0.setRunningProtoConfig(new ProtoConfig(Number(values)))
+        var flowCO2 = valve0.getProtoConfigValue()
+        var flowAir = valve1.getProtoConfigValue()
+        debugLogger('GMS settings changed. Gas Mixing set to Air flow ' + round(flowAir, 0) + unit + ' and CO2 flow ' + round(flowCO2, 1) + unit + ' (' + round((flowCO2 / (flowCO2 + flowAir) + 395 / 1e6) * 100, 1) + '%)')
+        break
     case 'stirrer':
       var stirrer = theGroup.getAccessory('pwm.stirrer')
       unit = '%'
@@ -571,7 +581,7 @@ function PSO (particleFitness) {
     } else {
       newPosition.push(particlePosition[index] + newStep[index])
     }
-    controlParameter(UserDefinedProtocol.controlledParameters[index], newPosition[index])
+    controlParameter(UserDefinedProtocol.controlledParameters[index], round(newPosition[index], 2))
   }
   if (!(particleFitness > swarmBestFitness)) {
     theAccessory.context().put('particleBestPosition', particlePosition)
@@ -588,5 +598,5 @@ function PSO (particleFitness) {
   debugLogger('BioArInEO-PSO best swarm position is [ ' + swarmBestPosition + ' ] with fitness ' + swarmBestFitness)
   debugLogger('BioArInEO-PSO best neighbors position is [ ' + neighborsBestPosition + ' ] with fitness ' + neighborsBestFitness[0])
   debugLogger('BioArInEO-PSO new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]')
-  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]') // Email notifications
+  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': for fitness ' + particleFitness + ' new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]') // Email notifications
 }

From 5d1171184a9ffabbdef986d7b66f9a098b2f34c0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Tue, 1 Sep 2020 08:35:35 +0200
Subject: [PATCH 11/47] Adjusted fitness averaging when stabilizedTimeMax
 reached

---
 PP-GrowthOptimizer.js | 25 +++++++++++++------------
 1 file changed, 13 insertions(+), 12 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index ea93055..9869e07 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -165,6 +165,10 @@ if (!theAccessory.context().getInt('initiated', 0)) {
       }
       theAccessory.context().put('OD7XYString', OD7XYString)
     }
+    if (UserDefinedProtocol.turbidostatODMin > UserDefinedProtocol.turbidostatODMax) {
+      debugLogger('OD range reversed.')
+      theExperiment.addEvent('OD range set in reversed order - will be automatically corrected.')
+    }
     controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[0])
     theAccessory.context().put('initiated', 1)
     debugLogger('Peristaltic Pump - Growth Optimizer initialization successful.')
@@ -365,15 +369,14 @@ function controlPump () {
   // Check for reversed OD range
   if (UserDefinedProtocol.turbidostatODMin > UserDefinedProtocol.turbidostatODMax) {
     UserDefinedProtocol.turbidostatODMin = (UserDefinedProtocol.turbidostatODMax - UserDefinedProtocol.turbidostatODMin) + (UserDefinedProtocol.turbidostatODMax = UserDefinedProtocol.turbidostatODMin)
-    debugLogger('OD range reversed.', 0)
   }
   if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= Number(theExperiment.getDurationSec()) && (stepCounter !== 0)) {
     theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600) // TODO allocate var for getDurationSec
     if (UserDefinedProtocol.particleSwarmOptimizer) {
       var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
       var len = stepDoublingTime.length
-      stepDoublingTime = len > 2 ? stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
-      PSO(stepDoublingTime)
+      var stepDoublingTimeAvg = len > 2 ? len > UserDefinedProtocol.analyzedSteps ? stepDoublingTime.slice(len - UserDefinedProtocol.analyzedSteps, len).reduce(getSumArrReduce, 0) / (UserDefinedProtocol.analyzedSteps) : stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
+      PSO(stepDoublingTimeAvg)
       theAccessory.context().remove('stepCounter')
       theAccessory.context().remove('expDuration')
       theAccessory.context().remove('stepDoublingTime')
@@ -533,7 +536,6 @@ function PSO (particleFitness) {
     temporaryTest = true
     particleStep = []
   }
-  var maxStep = []
   var neighborsBestPosition = []
   var neighborsBestFitness = []
   var newPosition = []
@@ -554,8 +556,7 @@ function PSO (particleFitness) {
       particleStep.push(0.2 * (parametersSearchRange[1] - parametersSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
     }
     debugLogger('BioArInEO-PSO particle step is ' + particleStep[index]) 
-    maxStep.push(Number(UserDefinedProtocol.parametersMaxStep[index]))
-    debugLogger('BioArInEO-PSO particle max step is ' + maxStep[index])
+    debugLogger('BioArInEO-PSO particle max step is ' + UserDefinedProtocol.parametersMaxStep[index])
     for (var indexN = 0, lenN = neighborsList.length; indexN < lenN; ++indexN) {
       temporaryNeighborPosition = theServer.getGroupByName(neighborsList[indexN]).getAccessory('pumps.pump-5').context().get('particleLastPosition', undefined)
       neighborsPosition = []
@@ -571,13 +572,13 @@ function PSO (particleFitness) {
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
     debugLogger('BioArInEO-PSO neighbors best position is [ ' + neighborsBestPosition[index] + '] with fitness ' + neighborsBestFitness[index])
     newStep.push(particleInertiaWeighting * particleStep[index] + particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) + particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) + particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]))
-    if (Math.abs(newStep[index]) > maxStep[index]) {
-      newStep[index] = maxStep[index] * (newStep[index] > 0 ? 1 : -1)
+    if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {
+      newStep[index] = Number(UserDefinedProtocol.parametersMaxStep[index]) * (newStep[index] > 0 ? 1 : -1)
     }
-    if ((particlePosition[index] + newStep[index]) > UserDefinedProtocol.parametersSearchRange[1]) {
-      newPosition.push(UserDefinedProtocol.parametersSearchRange[1])
-    } else if ((particlePosition[index] + newStep[index]) < UserDefinedProtocol.parametersSearchRange[0]) {
-      newPosition.push(UserDefinedProtocol.parametersSearchRange[0])
+    if ((particlePosition[index] + newStep[index]) > parametersSearchRange[1]) {
+      newPosition.push(parametersSearchRange[1])
+    } else if ((particlePosition[index] + newStep[index]) < parametersSearchRange[0]) {
+      newPosition.push(parametersSearchRange[0])
     } else {
       newPosition.push(particlePosition[index] + newStep[index])
     }

From 1603ec7f1758d1e758c4ca51313e0de252b05bcf Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Tue, 8 Sep 2020 06:45:37 +0200
Subject: [PATCH 12/47] Improved behavior for trigger of stabilizationTimeMax

---
 PP-GrowthOptimizer.js | 19 +++++++------------
 1 file changed, 7 insertions(+), 12 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 9869e07..1fe8970 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -255,7 +255,6 @@ function controlParameter (parameter, values) {
       var light0 = theGroup.getAccessory('actinic-lights.light-Red')
       var light1 = theGroup.getAccessory(theAccessory.context().get('light1String', 'actinic-lights.light-Blue'))
       unit = ' uE'
-      values = Array(values, values)
       light0.setRunningProtoConfig(new ProtoConfig(Number(values[0]))) // Red
       light1.setRunningProtoConfig(new ProtoConfig(Number(values[1]))) // Blue || White
       debugLogger('Lights changed. Channel 0 set to ' + round(values[0], 0) + unit + ' and channel 1 set to ' + round(values[1], 0) + unit)
@@ -370,17 +369,13 @@ function controlPump () {
   if (UserDefinedProtocol.turbidostatODMin > UserDefinedProtocol.turbidostatODMax) {
     UserDefinedProtocol.turbidostatODMin = (UserDefinedProtocol.turbidostatODMax - UserDefinedProtocol.turbidostatODMin) + (UserDefinedProtocol.turbidostatODMax = UserDefinedProtocol.turbidostatODMin)
   }
-  if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= Number(theExperiment.getDurationSec()) && (stepCounter !== 0)) {
+  if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= Number(theExperiment.getDurationSec()) && !pumpState) {
     theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600) // TODO allocate var for getDurationSec
+    var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
     if (UserDefinedProtocol.particleSwarmOptimizer) {
-      var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
       var len = stepDoublingTime.length
       var stepDoublingTimeAvg = len > 2 ? len > UserDefinedProtocol.analyzedSteps ? stepDoublingTime.slice(len - UserDefinedProtocol.analyzedSteps, len).reduce(getSumArrReduce, 0) / (UserDefinedProtocol.analyzedSteps) : stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
       PSO(stepDoublingTimeAvg)
-      theAccessory.context().remove('stepCounter')
-      theAccessory.context().remove('expDuration')
-      theAccessory.context().remove('stepDoublingTime')
-      theAccessory.context().remove('stabilizedTime')
     } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
       if (changeCounter < (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
         controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[++changeCounter])
@@ -392,11 +387,11 @@ function controlPump () {
         controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[1])
         theAccessory.context().put('changeCounter', 1)
       }
-      theAccessory.context().remove('stepCounter')
-      theAccessory.context().remove('expDuration')
-      theAccessory.context().remove('stepDoublingTime')
-      theAccessory.context().remove('stabilizedTime')
-    }  
+    } 
+    theAccessory.context().remove('stepCounter')
+    theAccessory.context().remove('expDuration')
+    theAccessory.context().remove('stepDoublingTime')
+    theAccessory.context().remove('stabilizedTime')
   }
   // Start step growth rate evaluation
   if (((odValue > (UserDefinedProtocol.turbidostatODMax * odMaxModifier)) && !pumpState)) {

From 18384aca75bb9cd6972c8e51058ca4ae6d92b90a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Tue, 15 Sep 2020 10:12:15 +0200
Subject: [PATCH 13/47] Mail announcement for standard optimizer added

---
 PP-GrowthOptimizer.js | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 1fe8970..384db51 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -5,9 +5,9 @@ var UserDefinedProtocol = {
   turbidostatODType: 720,
   ODReadoutInterval: 60,
   // -optimizer parameters
-  controlledParameter: 'temperature',
+  controlledParameter: 'none',
   controlledParameterSteps: [ 28 ],
-  particleSwarmOptimizer: true,
+  particleSwarmOptimizer: false,
   controlledParameters: [ 'temperature' ],
   controlledParametersIC: [ 28 ],
   parametersSearchRange: [ 18, 38 ],
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.1
- * @modified 24.8.2020 (JaCe)
+ * @version 3.4.2
+ * @modified 10.9.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -99,6 +99,7 @@ importPackage(Packages.psi.bioreactor.core.regression)
 if (!theAccessory.context().getInt('initiated', 0)) {
   try {
     theAccessory.context().clear()
+    theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
     theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
     var light1String
     if (theGroup.getAccessory('actinic-lights.light-Blue') === null) {
@@ -475,6 +476,7 @@ function controlPump () {
               controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[1])
               theAccessory.context().put('changeCounter', 1)
             }
+            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position') // Email notifications
           }
           theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
           theAccessory.context().remove('stepCounter')

From 6c27998bd96566bd931d3496c798d25108827d97 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Thu, 1 Oct 2020 09:36:53 +0200
Subject: [PATCH 14/47] Added PSO swarm best particle logging

---
 PP-GrowthOptimizer.js | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 384db51..ac5b6d3 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -525,6 +525,7 @@ function PSO (particleFitness) {
   var swarmLeader = theServer.getGroupByName(UserDefinedProtocol.swarmLeaderGroup)
   var swarmBestPosition = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestPosition', particlePosition)
   var swarmBestFitness = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestFitness', particleFitness)
+  var swarmBestParticle = swarmLeader.getAccessory('pumps.pump-5').context().get('swarmBestParticle', undefined)
   var neighborsList = UserDefinedProtocol.particleNeighborsGroupList
   var parametersSearchRange = UserDefinedProtocol.parametersSearchRange
   var particleStep =  theAccessory.context().get('particleStep', undefined)
@@ -567,7 +568,7 @@ function PSO (particleFitness) {
     }
     neighborsBestFitness.push(Math.min.apply(null, neighborsFitness))
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
-    debugLogger('BioArInEO-PSO neighbors best position is [ ' + neighborsBestPosition[index] + '] with fitness ' + neighborsBestFitness[index])
+    debugLogger('BioArInEO-PSO neighbors best position is [ ' + neighborsBestPosition[index] + ' ] with fitness ' + neighborsBestFitness[index])
     newStep.push(particleInertiaWeighting * particleStep[index] + particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) + particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) + particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]))
     if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {
       newStep[index] = Number(UserDefinedProtocol.parametersMaxStep[index]) * (newStep[index] > 0 ? 1 : -1)
@@ -586,7 +587,8 @@ function PSO (particleFitness) {
     theAccessory.context().put('particleBestFitness', particleFitness)
     swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestPosition', particlePosition)
     swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestFitness', particleFitness)
-    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestParticle', theGroup)
+    swarmBestParticle = theGroup
+    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestParticle', swarmBestParticle)
   } else if (!(particleFitness > particleBestFitness)) {
     theAccessory.context().put('particleBestPosition', particlePosition)
     theAccessory.context().put('particleBestFitness', particleFitness)
@@ -594,6 +596,7 @@ function PSO (particleFitness) {
   theAccessory.context().put('particleStep', newStep)
   theAccessory.context().put('particlePosition', newPosition)
   debugLogger('BioArInEO-PSO best swarm position is [ ' + swarmBestPosition + ' ] with fitness ' + swarmBestFitness)
+  debugLogger('BioArInEO-PSO best swarm particle is ' + swarmBestParticle)
   debugLogger('BioArInEO-PSO best neighbors position is [ ' + neighborsBestPosition + ' ] with fitness ' + neighborsBestFitness[0])
   debugLogger('BioArInEO-PSO new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]')
   theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': for fitness ' + particleFitness + ' new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]') // Email notifications

From f1a7271a80fa999561b9ecd51665fefeca3a5fe9 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sat, 3 Oct 2020 23:29:00 +0200
Subject: [PATCH 15/47] Correction of IC95 evalution to respect population
 sample limit

---
 PP-GrowthOptimizer.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index ac5b6d3..ad65e1a 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -445,7 +445,7 @@ function controlPump () {
         for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps); i--) {
           stepDoublingTimeSD += Math.pow(stepDoublingTime[i] - stepDoublingTimeAvg, 2)
         }
-        stepDoublingTimeSD = Math.sqrt(stepDoublingTimeSD / UserDefinedProtocol.analyzedSteps)
+        stepDoublingTimeSD = Math.sqrt(stepDoublingTimeSD / (UserDefinedProtocol.analyzedSteps - 1))
         stepDoublingTimeIC95 = stepDoublingTimeSD / Math.sqrt(UserDefinedProtocol.analyzedSteps) * 1.96
         // Trend of steps doubling time
         for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps); i--) {

From c496f48e898aa1d3d9b0f2df72fc38ca527e1a62 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Wed, 7 Oct 2020 08:21:00 +0200
Subject: [PATCH 16/47] Fixed GMS default help parameters set

---
 PP-GrowthOptimizer.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index ad65e1a..24673a8 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -61,8 +61,8 @@ var UserDefinedProtocol = {
  * @param {string} controlledParameter ['none'/'temperature'/'lights'/'GMS'/'stirrer'/'ODRange'] - Supported parameters to control by the script
  * @param {array} controlledParameterSteps - List of values for the controlled parameter. Examples:
  *                temperature = [ 28, 32, 34, 30, 26, 22 ]; // [oC]
- *                lights = [[ 55, 25 ],[ 110, 25 ],[ 220, 25 ],[ 440, 25 ],[ 880,25 ]]; // [uE]
- *                GMS = [[ 195.88, 5.873 ],[ 195.88, 12.478 ],[ 185.30, 18.257 ],[ 185.30,25.274 ]]; // [ml/min]
+ *                lights = [[ 55, 25 ], [ 110, 25 ], [ 220, 25 ], [ 440, 25 ], [ 880,25 ]]; // [uE]
+ *                GMS = [[ 9.6, 990 ], [ 19.6, 1880 ], [ 39.6, 1940 ]]; // [ml/min]
  *                stirrer = [ 30, 50, 65, 80, 95 ]; // [%] !!! works only with SW version 0.7.14 and later
  *                ODRange = [[0.4, 0.425], [0.2, 0.215], [0.1, 0.113]]; // [AU]
  * -optimizer stability check

From 3bd7453a9ad084d58dc2e809b8022373d746bf4a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Fri, 23 Oct 2020 16:06:43 +0200
Subject: [PATCH 17/47] Updated list for handling of control parameters
 warnings

---
 PP-GrowthOptimizer.js | 26 +++++++++++++++++++++++---
 1 file changed, 23 insertions(+), 3 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 24673a8..2f754cb 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.2
- * @modified 10.9.2020 (JaCe)
+ * @version 3.4.3
+ * @modified 7.10.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -121,6 +121,21 @@ if (!theAccessory.context().getInt('initiated', 0)) {
           theExperiment.addEvent('!!! Disable WHITE LIGHT protocol')
         }
         break
+      case 'light-red':
+        if (theGroup.getAccessory('actinic-lights.light-Red').getProtoConfigValue()) {
+          theExperiment.addEvent('!!! Disable RED LIGHT protocol')
+        }
+        break
+      case 'light-blue':
+        if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
+          theExperiment.addEvent('!!! Disable RED LIGHT protocol')
+        }
+        break
+      case 'light-white':
+        if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
+          theExperiment.addEvent('!!! Disable RED LIGHT protocol')
+        }
+        break
       case 'temperature':
         if (theGroup.getAccessory('thermo.thermo-reg').getProtoConfigValue()) {
           theExperiment.addEvent('!!! Disable THERMOREGULATOR protocol')
@@ -134,6 +149,11 @@ if (!theAccessory.context().getInt('initiated', 0)) {
           theExperiment.addEvent('!!! Disable GMS Air/N2 protocol')
         }
         break
+      case 'GMS-CO2':
+        if (UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg').getProtoConfigValue()) {
+          theExperiment.addEvent('!!! Disable GMS CO2 protocol')
+        } 
+        break     
       case 'stirrer':
         if (theGroup.getAccessory('pwm.stirrer').getProtoConfigValue()) {
           theExperiment.addEvent('!!! Disable STIRRER protocol')
@@ -289,7 +309,7 @@ function controlParameter (parameter, values) {
       var flowAir = valve1.getProtoConfigValue()
       debugLogger('GMS settings changed. Gas Mixing set to Air flow ' + round(flowAir, 0) + unit + ' and CO2 flow ' + round(flowCO2, 1) + unit + ' (' + round((flowCO2 / (flowCO2 + flowAir) + 395 / 1e6) * 100, 1) + '%)')
       break
-      case 'GMS-CO2':
+    case 'GMS-CO2':
         var valve0 = UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg') // CO2
         var valve1 = UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-1-reg') // Air
         unit = ' ml/min'

From 735f195738eb4adff253957e83e2fe76b5c83748 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sat, 24 Oct 2020 22:37:08 +0200
Subject: [PATCH 18/47] Added logging for uncorrected new step

---
 PP-GrowthOptimizer.js | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 2f754cb..338814e 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.3
- * @modified 7.10.2020 (JaCe)
+ * @version 3.4.4
+ * @modified 23.10.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -588,8 +588,9 @@ function PSO (particleFitness) {
     }
     neighborsBestFitness.push(Math.min.apply(null, neighborsFitness))
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
-    debugLogger('BioArInEO-PSO neighbors best position is [ ' + neighborsBestPosition[index] + ' ] with fitness ' + neighborsBestFitness[index])
+    debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is [ ' + neighborsBestPosition[index] + ' ] with fitness ' + neighborsBestFitness[index])
     newStep.push(particleInertiaWeighting * particleStep[index] + particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) + particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) + particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]))
+    debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is [ ' + newStep[index] + ' ]')
     if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {
       newStep[index] = Number(UserDefinedProtocol.parametersMaxStep[index]) * (newStep[index] > 0 ? 1 : -1)
     }

From a349c34449266519c33e914f15f1180872ba984b Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Tue, 27 Oct 2020 15:53:45 +0100
Subject: [PATCH 19/47] PSO logging improvements

---
 PP-GrowthOptimizer.js | 15 +++++++--------
 1 file changed, 7 insertions(+), 8 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 338814e..8a0b25c 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.4
- * @modified 23.10.2020 (JaCe)
+ * @version 3.4.5
+ * @modified 26.10.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -456,6 +456,7 @@ function controlPump () {
         var sumY = 0
         var sumX2 = 0
         // var sumY2 = 0
+        // TODO if trend then accumulate steps as [analyzedSteps inf]
         // Average of steps doubling time
         for (var i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps); i--) {
           stepDoublingTimeAvg += Number(stepDoublingTime[i])
@@ -538,7 +539,7 @@ function PSO (particleFitness) {
   }
   theAccessory.context().put('particleLastFitness', particleFitness)
   var particlePosition = theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParametersIC)
-  debugLogger('BioArInEO-PSO executed with fitness ' + particleFitness + ' and position ' + particlePosition) 
+  debugLogger('BioArInEO-PSO executed with fitness ' + particleFitness + ' and position [ ' + particlePosition + ' ]') 
   theAccessory.context().put('particleLastPosition', particlePosition)
   var particleBestPosition = theAccessory.context().get('particleBestPosition', particlePosition)
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
@@ -566,15 +567,13 @@ function PSO (particleFitness) {
   var neighborsPosition = []
   var neighborsFitness = []
   for (var index = 0, len = UserDefinedProtocol.controlledParameters.length; index < len; index++) {
-    debugLogger('BioArInEO-PSO evaluating new step for ' + UserDefinedProtocol.controlledParameters[index]) 
     if (len > 1) {
       parametersSearchRange = UserDefinedProtocol.parametersSearchRange[index]
     }
     if (temporaryTest) {
       particleStep.push(0.2 * (parametersSearchRange[1] - parametersSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
     }
-    debugLogger('BioArInEO-PSO particle step is ' + particleStep[index]) 
-    debugLogger('BioArInEO-PSO particle max step is ' + UserDefinedProtocol.parametersMaxStep[index])
+    debugLogger('BioArInEO-PSO particle step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + particleStep[index] + ' (max ' + UserDefinedProtocol.parametersMaxStep[index] + ' )') 
     for (var indexN = 0, lenN = neighborsList.length; indexN < lenN; ++indexN) {
       temporaryNeighborPosition = theServer.getGroupByName(neighborsList[indexN]).getAccessory('pumps.pump-5').context().get('particleLastPosition', undefined)
       neighborsPosition = []
@@ -588,9 +587,9 @@ function PSO (particleFitness) {
     }
     neighborsBestFitness.push(Math.min.apply(null, neighborsFitness))
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
-    debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is [ ' + neighborsBestPosition[index] + ' ] with fitness ' + neighborsBestFitness[index])
+    debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + neighborsBestPosition[index] + ' with fitness ' + neighborsBestFitness[index])
     newStep.push(particleInertiaWeighting * particleStep[index] + particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) + particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) + particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]))
-    debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is [ ' + newStep[index] + ' ]')
+    debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index])
     if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {
       newStep[index] = Number(UserDefinedProtocol.parametersMaxStep[index]) * (newStep[index] > 0 ? 1 : -1)
     }

From 16e5f61252905de3a905b3c095623d864019385c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Tue, 27 Oct 2020 23:06:50 +0100
Subject: [PATCH 20/47] Improved logging of PSO numbers (rounding toFixed(2))

---
 PP-GrowthOptimizer.js | 16 ++++++++--------
 1 file changed, 8 insertions(+), 8 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 8a0b25c..c7ee134 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -539,7 +539,7 @@ function PSO (particleFitness) {
   }
   theAccessory.context().put('particleLastFitness', particleFitness)
   var particlePosition = theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParametersIC)
-  debugLogger('BioArInEO-PSO executed with fitness ' + particleFitness + ' and position [ ' + particlePosition + ' ]') 
+  debugLogger('BioArInEO-PSO executed with fitness ' + particleFitness.toFixed(2) + ' and position [ ' + particlePosition.map(function(ae){return ae.toFixed(2)}) + ' ]') 
   theAccessory.context().put('particleLastPosition', particlePosition)
   var particleBestPosition = theAccessory.context().get('particleBestPosition', particlePosition)
   var particleBestFitness = theAccessory.context().get('particleBestFitness', particleFitness)
@@ -573,7 +573,7 @@ function PSO (particleFitness) {
     if (temporaryTest) {
       particleStep.push(0.2 * (parametersSearchRange[1] - parametersSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
     }
-    debugLogger('BioArInEO-PSO particle step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + particleStep[index] + ' (max ' + UserDefinedProtocol.parametersMaxStep[index] + ' )') 
+    debugLogger('BioArInEO-PSO particle step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + particleStep[index].toFixed(2) + ' (max ' + UserDefinedProtocol.parametersMaxStep[index].toFixed(2) + ' )') 
     for (var indexN = 0, lenN = neighborsList.length; indexN < lenN; ++indexN) {
       temporaryNeighborPosition = theServer.getGroupByName(neighborsList[indexN]).getAccessory('pumps.pump-5').context().get('particleLastPosition', undefined)
       neighborsPosition = []
@@ -587,9 +587,9 @@ function PSO (particleFitness) {
     }
     neighborsBestFitness.push(Math.min.apply(null, neighborsFitness))
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
-    debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + neighborsBestPosition[index] + ' with fitness ' + neighborsBestFitness[index])
+    debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + neighborsBestPosition[index].toFixed(2) + ' with fitness ' + neighborsBestFitness[index].toFixed(2))
     newStep.push(particleInertiaWeighting * particleStep[index] + particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) + particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) + particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]))
-    debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index])
+    debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index].toFixed(2))
     if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {
       newStep[index] = Number(UserDefinedProtocol.parametersMaxStep[index]) * (newStep[index] > 0 ? 1 : -1)
     }
@@ -615,9 +615,9 @@ function PSO (particleFitness) {
   }
   theAccessory.context().put('particleStep', newStep)
   theAccessory.context().put('particlePosition', newPosition)
-  debugLogger('BioArInEO-PSO best swarm position is [ ' + swarmBestPosition + ' ] with fitness ' + swarmBestFitness)
+  debugLogger('BioArInEO-PSO best swarm position is [ ' + swarmBestPosition.map(function(ae){return ae.toFixed(2)}) + ' ] with fitness ' + swarmBestFitness.toFixed(2))
   debugLogger('BioArInEO-PSO best swarm particle is ' + swarmBestParticle)
-  debugLogger('BioArInEO-PSO best neighbors position is [ ' + neighborsBestPosition + ' ] with fitness ' + neighborsBestFitness[0])
-  debugLogger('BioArInEO-PSO new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]')
-  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': for fitness ' + particleFitness + ' new step is [ ' + newStep + ' ] and position is [ ' + newPosition + ' ]') // Email notifications
+  debugLogger('BioArInEO-PSO best neighbors position is [ ' + neighborsBestPosition.map(function(ae){return ae.toFixed(2)}) + ' ] with fitness ' + neighborsBestFitness[0].toFixed(2))
+  debugLogger('BioArInEO-PSO new step is [ ' + newStep.map(function(ae){return ae.toFixed(2)}) + ' ] and position is [ ' + newPosition.map(function(ae){return ae.toFixed(2)}) + ' ]')
+  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': for fitness ' + particleFitness.toFixed(2) + ' new step is [ ' + newStep.toFixed(2) + ' ] and position is [ ' + newPosition.map(function(ae){return ae.toFixed(2)}) + ' ]') // Email notifications
 }

From d5fa51771df9bc69d48365c4ed3c464a1aaaf5b3 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Wed, 28 Oct 2020 18:37:05 +0100
Subject: [PATCH 21/47] Fixed array toFixed() for PSO email notification

---
 PP-GrowthOptimizer.js | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index c7ee134..d08c9d2 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -619,5 +619,5 @@ function PSO (particleFitness) {
   debugLogger('BioArInEO-PSO best swarm particle is ' + swarmBestParticle)
   debugLogger('BioArInEO-PSO best neighbors position is [ ' + neighborsBestPosition.map(function(ae){return ae.toFixed(2)}) + ' ] with fitness ' + neighborsBestFitness[0].toFixed(2))
   debugLogger('BioArInEO-PSO new step is [ ' + newStep.map(function(ae){return ae.toFixed(2)}) + ' ] and position is [ ' + newPosition.map(function(ae){return ae.toFixed(2)}) + ' ]')
-  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': for fitness ' + particleFitness.toFixed(2) + ' new step is [ ' + newStep.toFixed(2) + ' ] and position is [ ' + newPosition.map(function(ae){return ae.toFixed(2)}) + ' ]') // Email notifications
+  theServer.sendMail('PSO on ' + theGroup.getName() , 'NONE', ': for fitness ' + particleFitness.toFixed(2) + ' new step is [ ' + newStep.map(function(ae){return ae.toFixed(2)}) + ' ] and position is [ ' + newPosition.map(function(ae){return ae.toFixed(2)}) + ' ]') // Email notifications
 }

From 3c7e01f8fbf8053de1624cac32cb29e8fe74cbb5 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Thu, 19 Nov 2020 20:03:55 +0100
Subject: [PATCH 22/47] Implementation of try-catch error mechanism

---
 O2-PIcurveMeasurement.js | 221 ++++++++++++++++++++-------------------
 1 file changed, 114 insertions(+), 107 deletions(-)

diff --git a/O2-PIcurveMeasurement.js b/O2-PIcurveMeasurement.js
index 4a8bf52..43d7fe2 100644
--- a/O2-PIcurveMeasurement.js
+++ b/O2-PIcurveMeasurement.js
@@ -23,10 +23,10 @@ var UserDefinedProtocol = {
  *
  * @script PI-Curves Measurement - Photosynthesis Efficiency Quantification
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
- * @copyright Jan Červený 2019(c)
+ * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 1.2.3
- * @modified 16.3.2019 (JaCe)
+ * @version 1.2.4
+ * @modified 14.11.2020 (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
@@ -70,120 +70,127 @@ function controlLights (intensityRed, intensityBlue) {
   light0.setRunningProtoConfig(new ProtoConfig(intensityRed))
   light1.setRunningProtoConfig(new ProtoConfig(intensityBlue))
 }
-if (!theAccessory.context().getBool('initialization', false)) {
-  theAccessory.context().clear()
-  if (theGroup.getAccessory('pwm.stirrer').getProtoConfigValue()) {
-    theExperiment.addEvent('!!! Disable stirrer protocol.')
-  }
-  if (theGroup.getAccessory('switches.valve-0').getProtoConfigValue()) {
-    theExperiment.addEvent('!!! Disable bubble intr. valve protocol.')
-  }
-  theAccessory.getDataHistory().setCapacity(Math.max(UserDefinedProtocol.oxygenMeasurementDuration, UserDefinedProtocol.respirationMeasurementDuration))
-  theAccessory.context().put('rateO2Evol', [])
-  theAccessory.context().put('rateO2EvolR2', [])
-  theAccessory.context().put('rateO2Resp', [])
-  theAccessory.context().put('rateO2RespR2', [])
-  theAccessory.context().put('initialization', true)
-  theGroup.getAccessory('pwm.stirrer').setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.stirrerIntensityValues[0]))
-  theGroup.getAccessory('switches.valve-0').setRunningProtoConfig(ProtoConfig.ON)
-  measurementTime = experimentDuration + 600
-  theAccessory.context().put('measurementTime', measurementTime)
-  var light1String
-  if (theGroup.getAccessory('actinic-lights.light-Blue') === null) {
-    light1String = 'actinic-lights.light-White'
-  } else {
-    light1String = 'actinic-lights.light-Blue'
+if (!theAccessory.context().getBool('initiated', false)) {
+  try {
+    theAccessory.context().clear()
+    if (theGroup.getAccessory('pwm.stirrer').getProtoConfigValue()) {
+      theExperiment.addEvent('!!! Disable stirrer protocol.')
+    }
+    if (theGroup.getAccessory('switches.valve-0').getProtoConfigValue()) {
+      theExperiment.addEvent('!!! Disable bubble intr. valve protocol.')
+    }
+    theAccessory.getDataHistory().setCapacity(Math.max(UserDefinedProtocol.oxygenMeasurementDuration, UserDefinedProtocol.respirationMeasurementDuration))
+    theAccessory.context().put('rateO2Evol', [])
+    theAccessory.context().put('rateO2EvolR2', [])
+    theAccessory.context().put('rateO2Resp', [])
+    theAccessory.context().put('rateO2RespR2', [])
+    theAccessory.context().put('initiated', true)
+    theGroup.getAccessory('pwm.stirrer').setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.stirrerIntensityValues[0]))
+    theGroup.getAccessory('switches.valve-0').setRunningProtoConfig(ProtoConfig.ON)
+    measurementTime = experimentDuration + 600
+    theAccessory.context().put('measurementTime', measurementTime)
+    var light1String
+    if (theGroup.getAccessory('actinic-lights.light-Blue') === null) {
+      light1String = 'actinic-lights.light-White'
+    } else {
+      light1String = 'actinic-lights.light-Blue'
+    }
+    theAccessory.context().put('light1String', light1String)
+    debugLogger('Photosynthesis Efficiency Quantification initialization successful.')
+  } catch (error) {
+    debugLogger('Initialization ERROR. ' + error.name + ' : ' + error.message)
   }
-  theAccessory.context().put('light1String', light1String)
-  debugLogger('PI-Curves Measurement - Photosynthesis Efficiency Quantification initialization successful.')
 }
 if (experimentDuration >= measurementTime) {
-  var stirrer, bubbles
-  var turbidostat = theGroup.getAccessory('pumps.pump-5')
-  var dilution = UserDefinedProtocol.turbidostatSynchronization ? turbidostat.context().getInt('modeDilution', 0) : 1
-  var stabilized = UserDefinedProtocol.growthStabilitySynchronization ? turbidostat.context().getInt('modeStabilized', 0) : 1
-  if (dilution && stabilized) {
-    var regCoefLin, rateO2Evol, rateO2Resp, rateO2EvolR2, rateO2RespR2
-    var changeCounter = theAccessory.context().getInt('changeCounter', 0)
-    var multiplierStep = theAccessory.context().getInt('multiplierStep', 0)
-    var resumeTime = theAccessory.context().getInt('resumeTime', 0)
-    // PI-curve phase parameters
-    var bubblingSuspended = theAccessory.context().getInt('bubblingSuspended', 0)
-    var photosynthesis = theAccessory.context().getInt('photosynthesis', 0)
-    var respiration = theAccessory.context().getInt('respiration', 0)
-    // Accessories inicialization
-    stirrer = theGroup.getAccessory('pwm.stirrer')
-    bubbles = theGroup.getAccessory('switches.valve-0')
-    var light0 = theGroup.getAccessory('actinic-lights.light-Red')
-    var light1 = theGroup.getAccessory(theAccessory.context().get('light1String', 'actinic-lights.light-Blue'))
-    if (!bubblingSuspended) {
-      theAccessory.context().put('bubblingSuspended', 1)
-      theAccessory.context().put('modeO2EvolResp', 1)
-      resumeTime = experimentDuration + UserDefinedProtocol.oxygenMeasurementDuration + UserDefinedProtocol.respirationMeasurementDuration
-      theAccessory.context().put('resumeTime', resumeTime)
-      theAccessory.context().put('light0Value', light0.getValue())
-      theAccessory.context().put('light1Value', light1.getValue())
-      bubbles.setRunningProtoConfig(ProtoConfig.OFF)
-      stirrer.setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.stirrerIntensityValues[1]))
-      controlLights(light0.getValue() * UserDefinedProtocol.lightStepMultiplierValues[changeCounter] * UserDefinedProtocol.photosynthesisCurveLightMultiplierValues[multiplierStep], light1.getValue() * UserDefinedProtocol.lightStepMultiplierValues[changeCounter] * UserDefinedProtocol.photosynthesisCurveLightMultiplierValues[multiplierStep])
-    }
-    if ((experimentDuration > (resumeTime - UserDefinedProtocol.respirationMeasurementDuration)) && !photosynthesis) {
-      theAccessory.context().put('photosynthesis', 1)
-      if (UserDefinedProtocol.respirationMeasurementDuration > 0) {
-        light0.suspend(resumeTime)
-        light1.suspend(resumeTime)
+  try {
+    var stirrer, bubbles
+    var turbidostat = theGroup.getAccessory('pumps.pump-5')
+    var dilution = UserDefinedProtocol.turbidostatSynchronization ? turbidostat.context().getInt('modeDilution', 0) : 1
+    var stabilized = UserDefinedProtocol.growthStabilitySynchronization ? turbidostat.context().getInt('modeStabilized', 0) : 1
+    if (dilution && stabilized) {
+      var regCoefLin, rateO2Evol, rateO2Resp, rateO2EvolR2, rateO2RespR2
+      var changeCounter = theAccessory.context().getInt('changeCounter', 0)
+      var multiplierStep = theAccessory.context().getInt('multiplierStep', 0)
+      var resumeTime = theAccessory.context().getInt('resumeTime', 0)
+      // PI-curve phase parameters
+      var bubblingSuspended = theAccessory.context().getInt('bubblingSuspended', 0)
+      var photosynthesis = theAccessory.context().getInt('photosynthesis', 0)
+      var respiration = theAccessory.context().getInt('respiration', 0)
+      // Accessories inicialization
+      stirrer = theGroup.getAccessory('pwm.stirrer')
+      bubbles = theGroup.getAccessory('switches.valve-0')
+      var light0 = theGroup.getAccessory('actinic-lights.light-Red')
+      var light1 = theGroup.getAccessory(theAccessory.context().get('light1String', 'actinic-lights.light-Blue'))
+      if (!bubblingSuspended) {
+        theAccessory.context().put('bubblingSuspended', 1)
+        theAccessory.context().put('modeO2EvolResp', 1)
+        resumeTime = experimentDuration + UserDefinedProtocol.oxygenMeasurementDuration + UserDefinedProtocol.respirationMeasurementDuration
+        theAccessory.context().put('resumeTime', resumeTime)
+        theAccessory.context().put('light0Value', light0.getValue())
+        theAccessory.context().put('light1Value', light1.getValue())
+        bubbles.setRunningProtoConfig(ProtoConfig.OFF)
+        stirrer.setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.stirrerIntensityValues[1]))
+        controlLights(light0.getValue() * UserDefinedProtocol.lightStepMultiplierValues[changeCounter] * UserDefinedProtocol.photosynthesisCurveLightMultiplierValues[multiplierStep], light1.getValue() * UserDefinedProtocol.lightStepMultiplierValues[changeCounter] * UserDefinedProtocol.photosynthesisCurveLightMultiplierValues[multiplierStep])
       }
-      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)
-      // 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)
+      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)
         // TODO should be function1
       }
-    }
-    if (experimentDuration > (resumeTime + UserDefinedProtocol.relaxationPhaseDuration)) {
-      theAccessory.context().put('bubblingSuspended', 0)
-      theAccessory.context().put('photosynthesis', 0)
-      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))
+      if ((experimentDuration > resumeTime) && !respiration) {
+        theAccessory.context().put('respiration', 1)
         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('rateO2Evol', [])
-        theAccessory.context().put('rateO2EvolR2', [])
-        theAccessory.context().put('rateO2Resp', [])
-        theAccessory.context().put('rateO2RespR2', [])
-        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.')
+        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)
+          // TODO should be function1
+        }
+      }
+      if (experimentDuration > (resumeTime + UserDefinedProtocol.relaxationPhaseDuration)) {
+        theAccessory.context().put('bubblingSuspended', 0)
+        theAccessory.context().put('photosynthesis', 0)
+        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('rateO2Evol', [])
+          theAccessory.context().put('rateO2EvolR2', [])
+          theAccessory.context().put('rateO2Resp', [])
+          theAccessory.context().put('rateO2RespR2', [])
+          theExperiment.addEvent('PI-CURVE done. O2 rates are ' + rateO2Evol.join(', ') + ' and ' + rateO2Resp.join(', ') + ' units/min (R2 ' + rateO2EvolR2.join(', ') + ' and ' + rateO2RespR2.join(', ') + ')')
+        }
       }
+      result = UserDefinedProtocol.oxygenRapidMeasurementInterval
     }
-    result = UserDefinedProtocol.oxygenRapidMeasurementInterval
+  } catch (error) {
+    debugLogger('O2/resp measurement ERROR. ' + error.name + ' : ' + error.message)
   }
 } else if (experimentDuration > theAccessory.context().getInt('checkupTime', 0)) {
   // 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

From de1ccc5c3a888bdfec7b6224ef0c10acfbec9d21 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Thu, 19 Nov 2020 20:07:29 +0100
Subject: [PATCH 23/47] Fixed neighbours "scanning" and cognitionPart
 "self-awareness"

---
 PP-GrowthOptimizer.js | 18 +++++++++++-------
 1 file changed, 11 insertions(+), 7 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index d08c9d2..4f75cb7 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -564,9 +564,11 @@ function PSO (particleFitness) {
   var particleGlobalLearning = 1.6
   var particleInertiaWeighting = 2 * 0.8 / (particleCognitionLearning + particleSocialLearning + particleGlobalLearning - 2)
   var temporaryNeighborPosition
-  var neighborsPosition = []
-  var neighborsFitness = []
+  var neighborsPosition
+  var neighborsFitness
   for (var index = 0, len = UserDefinedProtocol.controlledParameters.length; index < len; index++) {
+    neighborsPosition = []
+    neighborsFitness = []
     if (len > 1) {
       parametersSearchRange = UserDefinedProtocol.parametersSearchRange[index]
     }
@@ -576,8 +578,6 @@ function PSO (particleFitness) {
     debugLogger('BioArInEO-PSO particle step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + particleStep[index].toFixed(2) + ' (max ' + UserDefinedProtocol.parametersMaxStep[index].toFixed(2) + ' )') 
     for (var indexN = 0, lenN = neighborsList.length; indexN < lenN; ++indexN) {
       temporaryNeighborPosition = theServer.getGroupByName(neighborsList[indexN]).getAccessory('pumps.pump-5').context().get('particleLastPosition', undefined)
-      neighborsPosition = []
-      neighborsFitness = []
       if (temporaryNeighborPosition === undefined) {
         neighborsPosition.push(particlePosition[index])
       } else {
@@ -587,9 +587,13 @@ function PSO (particleFitness) {
     }
     neighborsBestFitness.push(Math.min.apply(null, neighborsFitness))
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
-    debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + neighborsBestPosition[index].toFixed(2) + ' with fitness ' + neighborsBestFitness[index].toFixed(2))
-    newStep.push(particleInertiaWeighting * particleStep[index] + particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) + particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) + particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]))
-    debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index].toFixed(2))
+    //debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + neighborsBestPosition[index].toFixed(2) + ' with fitness ' + neighborsBestFitness[index].toFixed(2))
+    // PSO steps for debugging
+    var cognitionPart = particleFitness > particleBestFitness ? particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) : 0
+    var socialPart = particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index])
+    var globalPart = particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index])
+    newStep.push(particleInertiaWeighting * particleStep[index] + cognitionPart + socialPart + globalPart)
+    //debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index].toFixed(2) + 'with [ ' + Array(cognitionPart,socialPart,globalPart).toString() + ' ]')
     if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {
       newStep[index] = Number(UserDefinedProtocol.parametersMaxStep[index]) * (newStep[index] > 0 ? 1 : -1)
     }

From 7d7df9c03db98aa5c15a9715228c208d88867f66 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Fri, 20 Nov 2020 09:17:55 +0100
Subject: [PATCH 24/47] Corrected swarm best properties logging

---
 PP-GrowthOptimizer.js | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 4f75cb7..fe3b118 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -575,7 +575,7 @@ function PSO (particleFitness) {
     if (temporaryTest) {
       particleStep.push(0.2 * (parametersSearchRange[1] - parametersSearchRange[0]) * (getRandomOnInterval(-1, 1) > 0 ? 1 : -1)) // ! PSI PBR JS doesn't support Math.sign()
     }
-    debugLogger('BioArInEO-PSO particle step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + particleStep[index].toFixed(2) + ' (max ' + UserDefinedProtocol.parametersMaxStep[index].toFixed(2) + ' )') 
+    debugLogger('BioArInEO-PSO particle step for ' + UserDefinedProtocol.controlledParameters[index] + ' was ' + particleStep[index].toFixed(2) + ' (|max| ' + UserDefinedProtocol.parametersMaxStep[index].toFixed(2) + ' )') 
     for (var indexN = 0, lenN = neighborsList.length; indexN < lenN; ++indexN) {
       temporaryNeighborPosition = theServer.getGroupByName(neighborsList[indexN]).getAccessory('pumps.pump-5').context().get('particleLastPosition', undefined)
       if (temporaryNeighborPosition === undefined) {
@@ -607,11 +607,12 @@ function PSO (particleFitness) {
     controlParameter(UserDefinedProtocol.controlledParameters[index], round(newPosition[index], 2))
   }
   if (!(particleFitness > swarmBestFitness)) {
+    swarmBestPosition = particlePosition
+    swarmBestFitness = particleFitness
     theAccessory.context().put('particleBestPosition', particlePosition)
     theAccessory.context().put('particleBestFitness', particleFitness)
-    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestPosition', particlePosition)
-    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestFitness', particleFitness)
-    swarmBestParticle = theGroup
+    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestPosition', swarmBestPosition)
+    swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestFitness', swarmBestFitness)
     swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestParticle', swarmBestParticle)
   } else if (!(particleFitness > particleBestFitness)) {
     theAccessory.context().put('particleBestPosition', particlePosition)

From 6efc4a0f55facec79b2e168821fd27d85bde0594 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sat, 28 Nov 2020 13:26:03 +0100
Subject: [PATCH 25/47] Improved logging and email notifications

---
 PP-GrowthOptimizer.js | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index fe3b118..4475658 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.5
- * @modified 26.10.2020 (JaCe)
+ * @version 3.4.6
+ * @modified 20.11.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -497,7 +497,8 @@ function controlPump () {
               controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[1])
               theAccessory.context().put('changeCounter', 1)
             }
-            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position') // Email notifications
+            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' and position [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') 
+            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') // Email notification
           }
           theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
           theAccessory.context().remove('stepCounter')
@@ -593,7 +594,7 @@ function PSO (particleFitness) {
     var socialPart = particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index])
     var globalPart = particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index])
     newStep.push(particleInertiaWeighting * particleStep[index] + cognitionPart + socialPart + globalPart)
-    //debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index].toFixed(2) + 'with [ ' + Array(cognitionPart,socialPart,globalPart).toString() + ' ]')
+    debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index].toFixed(2) + ' with [ ' + Array(cognitionPart.toFixed(2),socialPart.toFixed(2),globalPart.toFixed(2)).toString() + ' ]')
     if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {
       newStep[index] = Number(UserDefinedProtocol.parametersMaxStep[index]) * (newStep[index] > 0 ? 1 : -1)
     }
@@ -609,6 +610,7 @@ function PSO (particleFitness) {
   if (!(particleFitness > swarmBestFitness)) {
     swarmBestPosition = particlePosition
     swarmBestFitness = particleFitness
+    swarmBestParticle = theGroup
     theAccessory.context().put('particleBestPosition', particlePosition)
     theAccessory.context().put('particleBestFitness', particleFitness)
     swarmLeader.getAccessory('pumps.pump-5').context().put('swarmBestPosition', swarmBestPosition)

From 4a1f001071f77bef7affc1e07748ba9487dbd96c Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Wed, 2 Dec 2020 13:57:19 +0100
Subject: [PATCH 26/47] Improved logging and email notifications

---
 PP-GrowthOptimizer.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 4475658..0470d95 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.6
- * @modified 20.11.2020 (JaCe)
+ * @version 3.4.8
+ * @modified 2.12.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -497,7 +497,7 @@ function controlPump () {
               controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[1])
               theAccessory.context().put('changeCounter', 1)
             }
-            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' and position [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') 
+            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' and new position is [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') 
             theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') // Email notification
           }
           theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
@@ -590,7 +590,7 @@ function PSO (particleFitness) {
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
     //debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + neighborsBestPosition[index].toFixed(2) + ' with fitness ' + neighborsBestFitness[index].toFixed(2))
     // PSO steps for debugging
-    var cognitionPart = particleFitness > particleBestFitness ? particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) : 0
+    var cognitionPart = !(particleFitness < particleBestFitness) ? particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) : 0
     var socialPart = particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index])
     var globalPart = particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index])
     newStep.push(particleInertiaWeighting * particleStep[index] + cognitionPart + socialPart + globalPart)

From 8e0bfce31db01dd448f10891c1f3d809959c4d13 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Thu, 3 Dec 2020 07:36:49 +0100
Subject: [PATCH 27/47] PSO new position setting improvement (when best of the
 best)

---
 PP-GrowthOptimizer.js | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 0470d95..b64d640 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.8
- * @modified 2.12.2020 (JaCe)
+ * @version 3.4.9
+ * @modified 3.12.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -590,9 +590,9 @@ function PSO (particleFitness) {
     neighborsBestPosition.push(Number(neighborsPosition[neighborsFitness.indexOf(neighborsBestFitness[index])]))
     //debugLogger('BioArInEO-PSO neighbors best position for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + neighborsBestPosition[index].toFixed(2) + ' with fitness ' + neighborsBestFitness[index].toFixed(2))
     // PSO steps for debugging
-    var cognitionPart = !(particleFitness < particleBestFitness) ? particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) : 0
-    var socialPart = particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index])
-    var globalPart = particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index])
+    var cognitionPart = particleFitness > particleBestFitness ? particleCognitionLearning * Math.random() * (particleBestPosition[index] - particlePosition[index]) : 0
+    var socialPart = particleFitness > neighborsBestFitness[index] ? particleSocialLearning * Math.random() * (neighborsBestPosition[index] - particlePosition[index]) : 0
+    var globalPart = particleFitness > swarmBestFitness ? particleGlobalLearning * Math.random() * (swarmBestPosition[index] - particlePosition[index]) : 0
     newStep.push(particleInertiaWeighting * particleStep[index] + cognitionPart + socialPart + globalPart)
     debugLogger('BioArInEO-PSO new uncorrected step for ' + UserDefinedProtocol.controlledParameters[index] + ' is ' + newStep[index].toFixed(2) + ' with [ ' + Array(cognitionPart.toFixed(2),socialPart.toFixed(2),globalPart.toFixed(2)).toString() + ' ]')
     if (Math.abs(newStep[index]) > Number(UserDefinedProtocol.parametersMaxStep[index])) {

From 32a225d67935ea5d9f563c28e51b9f283896a5d6 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Fri, 4 Dec 2020 10:42:28 +0100
Subject: [PATCH 28/47] Changed behavior of stabilizedMin/Max check

---
 PP-GrowthOptimizer.js | 9 +++++----
 1 file changed, 5 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index b64d640..406d98a 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.4.9
- * @modified 3.12.2020 (JaCe)
+ * @version 3.5.0
+ * @modified 4.12.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -430,8 +430,8 @@ function controlPump () {
       theAccessory.context().put('expDuration', expDuration)
       theAccessory.context().put('stepDuration', stepDuration)
       theAccessory.context().put('stepDoublingTime', stepDoublingTime)
-      theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
-      theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
+      // theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
+      // theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
       odSensorRegression.getDataHistory().setCapacity(600)
     }
     expDuration[stepCounter] = theExperiment.getDurationSec()
@@ -500,6 +500,7 @@ function controlPump () {
             debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' and new position is [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') 
             theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') // Email notification
           }
+          theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
           theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
           theAccessory.context().remove('stepCounter')
           theAccessory.context().remove('expDuration')

From 075767123ebf80437ca7cd2ae8d8f1aaea2080b7 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sun, 20 Dec 2020 09:28:18 +0100
Subject: [PATCH 29/47] Improved changing of multistep parameter (fun)

---
 PP-GrowthOptimizer.js | 67 +++++++++++++++++++++++++------------------
 1 file changed, 39 insertions(+), 28 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 406d98a..537abbe 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.5.0
- * @modified 4.12.2020 (JaCe)
+ * @version 3.5.1
+ * @modified 19.12.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -336,6 +336,38 @@ function controlParameter (parameter, values) {
   theAccessory.context().put('controlledParameterText', parameter + ' ' + (Array.isArray(values) ? values.join(' and ') : values) + unit)
   theExperiment.addEvent(parameter[0].toUpperCase() + parameter.slice(1) + ' changed to ' + (Array.isArray(values) ? values.join(' and ') : values) + unit)
 }
+function changeParameter(parameter,direction) {
+  if ((parameter === undefined) || (parameter === 'none')) {
+    return null
+  }
+  if(direction === undefined) {
+    direction = theAccessory.context().get('controlledParameterDirection', 'next')
+  }
+  var controlledParameterPosition = theAccessory.context().getInt('controlledParameterPosition', 1)
+  var positions = []
+  positions.push(UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
+  var len = UserDefinedProtocol.controlledParameterSteps.length
+  if(direction === 'reverse') {
+    direction = (theAccessory.context().get('controlledParameterDirection', 'next') === 'previous') ? 'next' : 'previous'
+  }
+  switch(direction) {
+    case 'next':
+      if(++controlledParameterPosition > len) {
+        theAccessory.context().put('controlledParameterDirection', 'previous')
+        controlledParameterPosition = controlledParameterPosition - 2
+      }
+      break;
+    case 'previous':
+      if(--controlledParameterPosition < 1) {
+        theAccessory.context().put('controlledParameterDirection', 'next')
+        controlledParameterPosition = controlledParameterPosition + 2
+      }
+      break;
+    default:
+  }
+  controlParameter(parameter, UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
+  return positions.push(UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
+}
 // Control activity of the peristaltic pump 
 function controlPump () {
   // Following code ready for functional implementation
@@ -398,16 +430,7 @@ function controlPump () {
       var stepDoublingTimeAvg = len > 2 ? len > UserDefinedProtocol.analyzedSteps ? stepDoublingTime.slice(len - UserDefinedProtocol.analyzedSteps, len).reduce(getSumArrReduce, 0) / (UserDefinedProtocol.analyzedSteps) : stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
       PSO(stepDoublingTimeAvg)
     } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
-      if (changeCounter < (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
-        controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[++changeCounter])
-        theAccessory.context().put('changeCounter', changeCounter)
-      } else if (changeCounter < 2 * (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
-        controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[2 * (UserDefinedProtocol.controlledParameterSteps.length - 1) - (++changeCounter)])
-        theAccessory.context().put('changeCounter', changeCounter)
-      } else {
-        controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[1])
-        theAccessory.context().put('changeCounter', 1)
-      }
+      var position = changeParameter(UserDefinedProtocol.controlledParameter)
     } 
     theAccessory.context().remove('stepCounter')
     theAccessory.context().remove('expDuration')
@@ -418,12 +441,10 @@ function controlPump () {
   if (((odValue > (UserDefinedProtocol.turbidostatODMax * odMaxModifier)) && !pumpState)) {
     theAccessory.context().put('modeDilution', 1)
     theAccessory.context().put('modeStabilized', 0)
-    // var stepCounter = theAccessory.context().getInt('stepCounter', 0)
     var expDuration = theAccessory.context().get('expDuration', 0.0)
     var stepDuration = theAccessory.context().get('stepDuration', 0.0)
     var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
     var stabilizedTime = theAccessory.context().getInt('stabilizedTime', 0)
-    // var stabilizedTimeMax = theAccessory.context().getInt('stabilizedTimeMax', 0)
     if (!Array.isArray(expDuration)) {
       stepCounter = 0
       expDuration = []; stepDuration = []; stepDoublingTime = []
@@ -482,23 +503,13 @@ function controlPump () {
         // Growth stability test and parameters control
         if (((stepDoublingTimeIC95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.intervalOfConfidenceMax / 100) && (Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) && (stabilizedTime <= Number(theExperiment.getDurationSec())))) {
           theAccessory.context().put('modeStabilized', 1)
-          // changeCounter = theAccessory.context().getInt('changeCounter', 0)
           theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
           if (UserDefinedProtocol.particleSwarmOptimizer) {
             PSO(stepDoublingTimeAvg)
           } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
-            if (changeCounter < (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
-              controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[++changeCounter])
-              theAccessory.context().put('changeCounter', changeCounter)
-            } else if (changeCounter < 2 * (UserDefinedProtocol.controlledParameterSteps.length - 1)) {
-              controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[2 * (UserDefinedProtocol.controlledParameterSteps.length - 1) - (++changeCounter)])
-              theAccessory.context().put('changeCounter', changeCounter)
-            } else {
-              controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[1])
-              theAccessory.context().put('changeCounter', 1)
-            }
-            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' and new position is [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') 
-            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position [ ' + UserDefinedProtocol.controlledParameterSteps[changeCounter].toFixed(2) + ' ]') // Email notification
+            var positions = changeParameter(UserDefinedProtocol.controlledParameter)
+            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for ' + positions[0].toFixed(2) + ' and new position is [ ' + positions[1].toFixed(2) + ' ]') 
+            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position [ ' + UserDefinedProtocol.controlledParameterSteps[position - 1].toFixed(2) + ' ]') // Email notification
           }
           theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
           theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
@@ -537,7 +548,7 @@ function PSO (particleFitness) {
    * @return {array}         New parameters / conditions.          
    */
   if (particleFitness === undefined) {
-    particleFitness = [ 999.9 ]
+    particleFitness = 999.9
   }
   theAccessory.context().put('particleLastFitness', particleFitness)
   var particlePosition = theAccessory.context().get('particlePosition', UserDefinedProtocol.controlledParametersIC)

From e101430fff443e616faf4229e855da0ed94d5beb Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sun, 20 Dec 2020 09:32:40 +0100
Subject: [PATCH 30/47] Improved changing of multistep parameter (fun)

---
 PP-GrowthOptimizer.js | 7 ++++---
 1 file changed, 4 insertions(+), 3 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 537abbe..b07f04f 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -366,7 +366,8 @@ function changeParameter(parameter,direction) {
     default:
   }
   controlParameter(parameter, UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
-  return positions.push(UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
+  positions.push(UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
+  return positions
 }
 // Control activity of the peristaltic pump 
 function controlPump () {
@@ -508,8 +509,8 @@ function controlPump () {
             PSO(stepDoublingTimeAvg)
           } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
             var positions = changeParameter(UserDefinedProtocol.controlledParameter)
-            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for ' + positions[0].toFixed(2) + ' and new position is [ ' + positions[1].toFixed(2) + ' ]') 
-            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' set new position [ ' + UserDefinedProtocol.controlledParameterSteps[position - 1].toFixed(2) + ' ]') // Email notification
+            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
+            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' at [ ' + positions[0].toFixed(2) + ' ] set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
           }
           theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
           theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)

From d1328cf814205b2e2c1d0818f056cc2aefc8c03d Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sun, 20 Dec 2020 19:28:11 +0100
Subject: [PATCH 31/47] parameterChange() bug fixes

---
 PP-GrowthOptimizer.js | 21 +++++++++------------
 1 file changed, 9 insertions(+), 12 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index b07f04f..3bdd8b7 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -336,7 +336,7 @@ function controlParameter (parameter, values) {
   theAccessory.context().put('controlledParameterText', parameter + ' ' + (Array.isArray(values) ? values.join(' and ') : values) + unit)
   theExperiment.addEvent(parameter[0].toUpperCase() + parameter.slice(1) + ' changed to ' + (Array.isArray(values) ? values.join(' and ') : values) + unit)
 }
-function changeParameter(parameter,direction) {
+function changeParameter(parameter, direction) {
   if ((parameter === undefined) || (parameter === 'none')) {
     return null
   }
@@ -365,6 +365,7 @@ function changeParameter(parameter,direction) {
       break;
     default:
   }
+  theAccessory.context().put('controlledParameterPosition', controlledParameterPosition)
   controlParameter(parameter, UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
   positions.push(UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
   return positions
@@ -399,7 +400,6 @@ function controlPump () {
   var odNoise = theAccessory.context().getInt('odNoise', 1)
   var odMinModifier = theAccessory.context().getDouble('odMinModifier', 1.0)
   var odMaxModifier = theAccessory.context().getDouble('odMaxModifier', 1.0)
-  var changeCounter = theAccessory.context().getInt('changeCounter', 0)
   var stepCounter = theAccessory.context().getInt('stepCounter', 0)
   // Check for OD noise/overshots and primitive OD averaging
   if (!isNaN(odValue) && (round(odValue, 3) !== round(odLast, 3))) {
@@ -424,19 +424,22 @@ function controlPump () {
     UserDefinedProtocol.turbidostatODMin = (UserDefinedProtocol.turbidostatODMax - UserDefinedProtocol.turbidostatODMin) + (UserDefinedProtocol.turbidostatODMax = UserDefinedProtocol.turbidostatODMin)
   }
   if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= Number(theExperiment.getDurationSec()) && !pumpState) {
-    theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600) // TODO allocate var for getDurationSec
+    // TODO allocate var for getDurationSec
     var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
     if (UserDefinedProtocol.particleSwarmOptimizer) {
       var len = stepDoublingTime.length
       var stepDoublingTimeAvg = len > 2 ? len > UserDefinedProtocol.analyzedSteps ? stepDoublingTime.slice(len - UserDefinedProtocol.analyzedSteps, len).reduce(getSumArrReduce, 0) / (UserDefinedProtocol.analyzedSteps) : stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
       PSO(stepDoublingTimeAvg)
     } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
-      var position = changeParameter(UserDefinedProtocol.controlledParameter)
+      var positions = changeParameter(UserDefinedProtocol.controlledParameter)
+      debugLogger('OPTIMIZER executed on max. time with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
+      theServer.sendMail('OPTIMIZER (max. time) on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
     } 
+    theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
+    theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
     theAccessory.context().remove('stepCounter')
     theAccessory.context().remove('expDuration')
     theAccessory.context().remove('stepDoublingTime')
-    theAccessory.context().remove('stabilizedTime')
   }
   // Start step growth rate evaluation
   if (((odValue > (UserDefinedProtocol.turbidostatODMax * odMaxModifier)) && !pumpState)) {
@@ -445,15 +448,12 @@ function controlPump () {
     var expDuration = theAccessory.context().get('expDuration', 0.0)
     var stepDuration = theAccessory.context().get('stepDuration', 0.0)
     var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
-    var stabilizedTime = theAccessory.context().getInt('stabilizedTime', 0)
     if (!Array.isArray(expDuration)) {
       stepCounter = 0
       expDuration = []; stepDuration = []; stepDoublingTime = []
       theAccessory.context().put('expDuration', expDuration)
       theAccessory.context().put('stepDuration', stepDuration)
       theAccessory.context().put('stepDoublingTime', stepDoublingTime)
-      // theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
-      // theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
       odSensorRegression.getDataHistory().setCapacity(600)
     }
     expDuration[stepCounter] = theExperiment.getDurationSec()
@@ -472,7 +472,6 @@ function controlPump () {
         var stepDoublingTimeSD = 0
         var stepDoublingTimeIC95 = 0
         var stepTrend = 0
-        // var stepCoD = 0
         var sumXY = 0
         var sumX = 0
         var sumY = 0
@@ -499,7 +498,6 @@ function controlPump () {
           sumXY += Number(expDuration[i]) * Number(stepDoublingTime[i])
         }
         stepTrend = (UserDefinedProtocol.analyzedSteps * sumXY - sumX * sumY) / (UserDefinedProtocol.analyzedSteps * sumX2 - Math.pow(sumX, 2)) * 3600
-        // stepCoD = (UserDefinedProtocol.analyzedSteps * sumXY - sumX * sumY) / (Math.sqrt((UserDefinedProtocol.analyzedSteps * sumX2 - Math.pow(sumX, 2)) * (UserDefinedProtocol.analyzedSteps * sumY2 - Math.pow(sumY, 2))))
         theExperiment.addEvent('Steps doubling time Avg: ' + round(stepDoublingTimeAvg, 2) + ' h, IC95 ' + round(stepDoublingTimeIC95, 2) + ' h (' + round(stepDoublingTimeIC95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
         // Growth stability test and parameters control
         if (((stepDoublingTimeIC95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.intervalOfConfidenceMax / 100) && (Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) && (stabilizedTime <= Number(theExperiment.getDurationSec())))) {
@@ -510,14 +508,13 @@ function controlPump () {
           } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
             var positions = changeParameter(UserDefinedProtocol.controlledParameter)
             debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
-            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': for fitness ' + stepDoublingTimeAvg + ' at [ ' + positions[0].toFixed(2) + ' ] set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
+            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
           }
           theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
           theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
           theAccessory.context().remove('stepCounter')
           theAccessory.context().remove('expDuration')
           theAccessory.context().remove('stepDoublingTime')
-          theAccessory.context().remove('stabilizedTime')
         }
       }
     }

From 68e3a2ebf48903e6e5619c479fa88e43a9b891ed Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Sun, 20 Dec 2020 19:38:37 +0100
Subject: [PATCH 32/47] Improved experiment duration var handling

---
 PP-GrowthOptimizer.js | 22 +++++++++++-----------
 1 file changed, 11 insertions(+), 11 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 3bdd8b7..1a8132f 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -99,8 +99,8 @@ importPackage(Packages.psi.bioreactor.core.regression)
 if (!theAccessory.context().getInt('initiated', 0)) {
   try {
     theAccessory.context().clear()
-    theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
-    theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
+    theAccessory.context().put('stabilizedTime', Number(theExperiment.getDurationSec()) + UserDefinedProtocol.stabilizationTimeMin * 3600)
+    theAccessory.context().put('stabilizedTimeMax', Number(theExperiment.getDurationSec()) + UserDefinedProtocol.stabilizationTimeMax * 3600)
     var light1String
     if (theGroup.getAccessory('actinic-lights.light-Blue') === null) {
       light1String = 'actinic-lights.light-White'
@@ -376,6 +376,7 @@ function controlPump () {
   // setODSensorString("turbidostat");
   // setODSensorString("regression");
   var odSensorString, odSensorRegressionString
+  var experimentDuration = Number(theExperiment.getDurationSec())
   switch (UserDefinedProtocol.turbidostatODType) {
     case 680:
       odSensorString = 'od-sensors.od-680'
@@ -423,8 +424,7 @@ function controlPump () {
   if (UserDefinedProtocol.turbidostatODMin > UserDefinedProtocol.turbidostatODMax) {
     UserDefinedProtocol.turbidostatODMin = (UserDefinedProtocol.turbidostatODMax - UserDefinedProtocol.turbidostatODMin) + (UserDefinedProtocol.turbidostatODMax = UserDefinedProtocol.turbidostatODMin)
   }
-  if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= Number(theExperiment.getDurationSec()) && !pumpState) {
-    // TODO allocate var for getDurationSec
+  if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= experimentDuration && !pumpState) {
     var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
     if (UserDefinedProtocol.particleSwarmOptimizer) {
       var len = stepDoublingTime.length
@@ -435,8 +435,8 @@ function controlPump () {
       debugLogger('OPTIMIZER executed on max. time with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
       theServer.sendMail('OPTIMIZER (max. time) on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
     } 
-    theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
-    theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
+    theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
+    theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
     theAccessory.context().remove('stepCounter')
     theAccessory.context().remove('expDuration')
     theAccessory.context().remove('stepDoublingTime')
@@ -456,7 +456,7 @@ function controlPump () {
       theAccessory.context().put('stepDoublingTime', stepDoublingTime)
       odSensorRegression.getDataHistory().setCapacity(600)
     }
-    expDuration[stepCounter] = theExperiment.getDurationSec()
+    expDuration[stepCounter] = experimentDuration
     stepDuration[stepCounter] = expDuration[stepCounter] - theAccessory.context().getInt('lastPumpStop', expDuration[stepCounter])
     if ((stepDuration[stepCounter] > 0) && UserDefinedProtocol.growthStatistics) {
       var DHCapacity = (Math.floor(stepDuration[stepCounter] / UserDefinedProtocol.ODReadoutInterval) - 3) > 0 ? (Math.floor(stepDuration[stepCounter] / UserDefinedProtocol.ODReadoutInterval) - 3) : 60
@@ -500,7 +500,7 @@ function controlPump () {
         stepTrend = (UserDefinedProtocol.analyzedSteps * sumXY - sumX * sumY) / (UserDefinedProtocol.analyzedSteps * sumX2 - Math.pow(sumX, 2)) * 3600
         theExperiment.addEvent('Steps doubling time Avg: ' + round(stepDoublingTimeAvg, 2) + ' h, IC95 ' + round(stepDoublingTimeIC95, 2) + ' h (' + round(stepDoublingTimeIC95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
         // Growth stability test and parameters control
-        if (((stepDoublingTimeIC95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.intervalOfConfidenceMax / 100) && (Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) && (stabilizedTime <= Number(theExperiment.getDurationSec())))) {
+        if (((stepDoublingTimeIC95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.intervalOfConfidenceMax / 100) && (Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) && (stabilizedTime <= experimentDuration))) {
           theAccessory.context().put('modeStabilized', 1)
           theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
           if (UserDefinedProtocol.particleSwarmOptimizer) {
@@ -510,8 +510,8 @@ function controlPump () {
             debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
             theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
           }
-          theAccessory.context().put('stabilizedTime', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMin * 3600)
-          theAccessory.context().put('stabilizedTimeMax', theExperiment.getDurationSec() + UserDefinedProtocol.stabilizationTimeMax * 3600)
+          theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
+          theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
           theAccessory.context().remove('stepCounter')
           theAccessory.context().remove('expDuration')
           theAccessory.context().remove('stepDoublingTime')
@@ -522,7 +522,7 @@ function controlPump () {
     return theAccessory.getMax() * UserDefinedProtocol.peristalticPumpSpeed / 100 // fast
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier)) && pumpState) {
     theAccessory.context().put('modeDilution', 0)
-    theAccessory.context().put('lastPumpStop', theExperiment.getDurationSec())
+    theAccessory.context().put('lastPumpStop', experimentDuration)
     debugLogger('Pump stopped.')
     return ProtoConfig.OFF // pump off
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier + ((UserDefinedProtocol.turbidostatODMax * odMaxModifier) - (UserDefinedProtocol.turbidostatODMin * odMinModifier)) * UserDefinedProtocol.peristalticPumpSlowDownRange / 100)) && pumpState) {

From 43e9a0cbc572885c5782d30b5b72c5278cd494f0 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Mon, 21 Dec 2020 08:32:44 +0100
Subject: [PATCH 33/47] Multiple code improvements

---
 PP-GrowthOptimizer.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 1a8132f..fc8e024 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.5.1
- * @modified 19.12.2020 (JaCe)
+ * @version 3.5.2
+ * @modified 20.12.2020 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).

From ec357f554bf6627e2c452c2318b0c09be4e93e26 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Jan=20=C4=8Cerven=C3=BD?= <cerveny.j@gmail.com>
Date: Mon, 21 Dec 2020 20:24:48 +0100
Subject: [PATCH 34/47] Fixed stabilizedTime previous accident removal

---
 PP-GrowthOptimizer.js | 26 ++++++++++++++------------
 1 file changed, 14 insertions(+), 12 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index fc8e024..9b644c1 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -368,6 +368,7 @@ function changeParameter(parameter, direction) {
   theAccessory.context().put('controlledParameterPosition', controlledParameterPosition)
   controlParameter(parameter, UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
   positions.push(UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
+  debugLogger('parameterChange() positions are ' + positions.toString())
   return positions
 }
 // Control activity of the peristaltic pump 
@@ -426,20 +427,20 @@ function controlPump () {
   }
   if (theAccessory.context().getInt('stabilizedTimeMax', 0) <= experimentDuration && !pumpState) {
     var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
+    var len = stepDoublingTime.length
+    var stepDoublingTimeAvg = len > 2 ? len > UserDefinedProtocol.analyzedSteps ? stepDoublingTime.slice(len - UserDefinedProtocol.analyzedSteps, len).reduce(getSumArrReduce, 0) / (UserDefinedProtocol.analyzedSteps) : stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
+    theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
+    theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
+    theAccessory.context().remove('stepCounter')
+    theAccessory.context().remove('expDuration')
+    theAccessory.context().remove('stepDoublingTime')
     if (UserDefinedProtocol.particleSwarmOptimizer) {
-      var len = stepDoublingTime.length
-      var stepDoublingTimeAvg = len > 2 ? len > UserDefinedProtocol.analyzedSteps ? stepDoublingTime.slice(len - UserDefinedProtocol.analyzedSteps, len).reduce(getSumArrReduce, 0) / (UserDefinedProtocol.analyzedSteps) : stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
       PSO(stepDoublingTimeAvg)
     } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
       var positions = changeParameter(UserDefinedProtocol.controlledParameter)
       debugLogger('OPTIMIZER executed on max. time with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
       theServer.sendMail('OPTIMIZER (max. time) on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
     } 
-    theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
-    theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
-    theAccessory.context().remove('stepCounter')
-    theAccessory.context().remove('expDuration')
-    theAccessory.context().remove('stepDoublingTime')
   }
   // Start step growth rate evaluation
   if (((odValue > (UserDefinedProtocol.turbidostatODMax * odMaxModifier)) && !pumpState)) {
@@ -448,6 +449,7 @@ function controlPump () {
     var expDuration = theAccessory.context().get('expDuration', 0.0)
     var stepDuration = theAccessory.context().get('stepDuration', 0.0)
     var stepDoublingTime = theAccessory.context().get('stepDoublingTime', [ 999.9 ])
+    var stabilizedTime = theAccessory.context().getInt('stabilizedTime', 0)
     if (!Array.isArray(expDuration)) {
       stepCounter = 0
       expDuration = []; stepDuration = []; stepDoublingTime = []
@@ -502,6 +504,11 @@ function controlPump () {
         // Growth stability test and parameters control
         if (((stepDoublingTimeIC95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.intervalOfConfidenceMax / 100) && (Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) && (stabilizedTime <= experimentDuration))) {
           theAccessory.context().put('modeStabilized', 1)
+          theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
+          theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
+          theAccessory.context().remove('stepCounter')
+          theAccessory.context().remove('expDuration')
+          theAccessory.context().remove('stepDoublingTime')
           theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
           if (UserDefinedProtocol.particleSwarmOptimizer) {
             PSO(stepDoublingTimeAvg)
@@ -510,11 +517,6 @@ function controlPump () {
             debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
             theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
           }
-          theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
-          theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
-          theAccessory.context().remove('stepCounter')
-          theAccessory.context().remove('expDuration')
-          theAccessory.context().remove('stepDoublingTime')
         }
       }
     }

From e651e9556a71fcb8fd0c80a7e9e7659a2ea6b985 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Tue, 26 Jan 2021 11:42:59 +0100
Subject: [PATCH 35/47] Added (PSO) initial check for protocol state of
 controlled parameters

---
 PP-GrowthOptimizer.js | 119 ++++++++++++++++++++++--------------------
 1 file changed, 63 insertions(+), 56 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 9b644c1..5f76069 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -45,8 +45,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.5.2
- * @modified 20.12.2020 (JaCe)
+ * @version 3.5.3
+ * @modified 26.1.2021 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -108,63 +108,70 @@ if (!theAccessory.context().getInt('initiated', 0)) {
       light1String = 'actinic-lights.light-Blue'
     }
     theAccessory.context().put('light1String', light1String)
-    switch (UserDefinedProtocol.controlledParameter) {
-      case 'lights':
-        if (theGroup.getAccessory('actinic-lights.light-Red').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable RED LIGHT protocol')
-        }
-        if (light1String === 'actinic-lights.light-Blue') {
+    if (UserDefinedProtocol.particleSwarmOptimizer) {
+     var parameters = UserDefinedProtocol.controlledParameters
+    } else {
+      var parameters = UserDefinedProtocol.controlledParameter
+    }
+    for (x of parameters) {
+      switch (UserDefinedProtocol.controlledParameter) {
+        case 'lights':
+          if (theGroup.getAccessory('actinic-lights.light-Red').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable RED LIGHT protocol')
+          }
+          if (light1String === 'actinic-lights.light-Blue') {
+            if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
+              theExperiment.addEvent('!!! Disable BLUE LIGHT protocol')
+            }
+          } else if (theGroup.getAccessory('actinic-lights.light-White').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable WHITE LIGHT protocol')
+          }
+          break
+        case 'light-red':
+          if (theGroup.getAccessory('actinic-lights.light-Red').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable RED LIGHT protocol')
+          }
+          break
+        case 'light-blue':
           if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
             theExperiment.addEvent('!!! Disable BLUE LIGHT protocol')
           }
-        } else if (theGroup.getAccessory('actinic-lights.light-White').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable WHITE LIGHT protocol')
-        }
-        break
-      case 'light-red':
-        if (theGroup.getAccessory('actinic-lights.light-Red').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable RED LIGHT protocol')
-        }
-        break
-      case 'light-blue':
-        if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable RED LIGHT protocol')
-        }
-        break
-      case 'light-white':
-        if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable RED LIGHT protocol')
-        }
-        break
-      case 'temperature':
-        if (theGroup.getAccessory('thermo.thermo-reg').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable THERMOREGULATOR protocol')
-        }
-        break
-      case 'GMS':
-        if (UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable GMS CO2 protocol')
-        }
-        if (UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-1-reg').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable GMS Air/N2 protocol')
-        }
-        break
-      case 'GMS-CO2':
-        if (UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable GMS CO2 protocol')
-        } 
-        break     
-      case 'stirrer':
-        if (theGroup.getAccessory('pwm.stirrer').getProtoConfigValue()) {
-          theExperiment.addEvent('!!! Disable STIRRER protocol')
-        }
-        break
-      case 'ODRange':
-        break
-      case 'none':
-        break
-      default:
-        theExperiment.addEvent('!!! Unknown parameter set for control - check controlledParameter setting')
+          break
+        case 'light-white':
+          if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable WHITE LIGHT protocol')
+          }
+          break
+        case 'temperature':
+          if (theGroup.getAccessory('thermo.thermo-reg').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable THERMOREGULATOR protocol')
+          }
+          break
+        case 'GMS':
+          if (UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable GMS CO2 protocol')
+          }
+          if (UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-1-reg').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable GMS Air/N2 protocol')
+          }
+          break
+        case 'GMS-CO2':
+          if (UserDefinedProtocol.groupGMS.getAccessory('gas-mixer.valve-0-reg').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable GMS CO2 protocol')
+          } 
+          break     
+        case 'stirrer':
+          if (theGroup.getAccessory('pwm.stirrer').getProtoConfigValue()) {
+            theExperiment.addEvent('!!! Disable STIRRER protocol')
+          }
+          break
+        case 'ODRange':
+          break
+        case 'none':
+          break
+        default:
+          theExperiment.addEvent('!!! Unknown parameter set for control - check controlledParameter setting')
+      }
     }
     if (UserDefinedProtocol.turbidostatODType === 680 || UserDefinedProtocol.regressionODType === 680) {
       if (Number(theGroup.getAccessory('od-sensors.od-680').getProtoConfigValue()) !== UserDefinedProtocol.ODReadoutInterval) {

From 7d238d5d79a206f93a99b1b12f5c80dc103101e9 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Tue, 26 Jan 2021 12:01:41 +0100
Subject: [PATCH 36/47] Added (PSO) initial check for protocol state of
 controlled parameters

---
 PP-GrowthOptimizer.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 5f76069..98b8c4a 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -109,12 +109,12 @@ if (!theAccessory.context().getInt('initiated', 0)) {
     }
     theAccessory.context().put('light1String', light1String)
     if (UserDefinedProtocol.particleSwarmOptimizer) {
-     var parameters = UserDefinedProtocol.controlledParameters
+      var parameters = UserDefinedProtocol.controlledParameters
     } else {
-      var parameters = UserDefinedProtocol.controlledParameter
+      var parameters = [ UserDefinedProtocol.controlledParameter ]
     }
-    for (x of parameters) {
-      switch (UserDefinedProtocol.controlledParameter) {
+    for (var i = 0; i < parameters.length; i++) {
+      switch (parameters[i]) {
         case 'lights':
           if (theGroup.getAccessory('actinic-lights.light-Red').getProtoConfigValue()) {
             theExperiment.addEvent('!!! Disable RED LIGHT protocol')

From 775f6d6a402febebfef5ad2ea10f8440774c4949 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Tue, 26 Jan 2021 12:26:47 +0100
Subject: [PATCH 37/47] Added (PSO) initial check for protocol state of
 controlled parameters and IC set

---
 PP-GrowthOptimizer.js | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 98b8c4a..d0b3c2b 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -110,8 +110,10 @@ if (!theAccessory.context().getInt('initiated', 0)) {
     theAccessory.context().put('light1String', light1String)
     if (UserDefinedProtocol.particleSwarmOptimizer) {
       var parameters = UserDefinedProtocol.controlledParameters
+      var values = UserDefinedProtocol.controlledParametersIC
     } else {
       var parameters = [ UserDefinedProtocol.controlledParameter ]
+      var values = UserDefinedProtocol.controlledParameterSteps
     }
     for (var i = 0; i < parameters.length; i++) {
       switch (parameters[i]) {
@@ -171,7 +173,9 @@ if (!theAccessory.context().getInt('initiated', 0)) {
           break
         default:
           theExperiment.addEvent('!!! Unknown parameter set for control - check controlledParameter setting')
+          continue
       }
+      controlParameter(parameters[i], values[i])
     }
     if (UserDefinedProtocol.turbidostatODType === 680 || UserDefinedProtocol.regressionODType === 680) {
       if (Number(theGroup.getAccessory('od-sensors.od-680').getProtoConfigValue()) !== UserDefinedProtocol.ODReadoutInterval) {
@@ -197,7 +201,6 @@ if (!theAccessory.context().getInt('initiated', 0)) {
       debugLogger('OD range reversed.')
       theExperiment.addEvent('OD range set in reversed order - will be automatically corrected.')
     }
-    controlParameter(UserDefinedProtocol.controlledParameter, UserDefinedProtocol.controlledParameterSteps[0])
     theAccessory.context().put('initiated', 1)
     debugLogger('Peristaltic Pump - Growth Optimizer initialization successful.')
   } catch (error) {

From e0bf4a6e09e653d23196d66278db9eddb0b9f69a Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Fri, 19 Mar 2021 18:24:58 +0100
Subject: [PATCH 38/47] Initial carbonization mod

---
 PP-GrowthOptimizer.js | 60 +++++++++++++++++++++++++++++++++++++++----
 1 file changed, 55 insertions(+), 5 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index d0b3c2b..5325081 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -31,7 +31,11 @@ var UserDefinedProtocol = {
   peristalticPumpSlowDownFactor: 75,
   // -advanced options
   growthRateEvalDelay: 420,
-  groupGMS: theGroup
+  groupGMS: theGroup,
+  mediaCarbonization: false,
+  carbonizationOff: 4.2,
+  carbonizationNormal: 8.4,
+  carbonizationBoost: 37.0
 }
 
 /* global
@@ -45,8 +49,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.5.3
- * @modified 26.1.2021 (JaCe)
+ * @version 3.6.0
+ * @modified 19.3.2021 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -66,7 +70,7 @@ var UserDefinedProtocol = {
  *                stirrer = [ 30, 50, 65, 80, 95 ]; // [%] !!! works only with SW version 0.7.14 and later
  *                ODRange = [[0.4, 0.425], [0.2, 0.215], [0.1, 0.113]]; // [AU]
  * -optimizer stability check
- * @param {number} growthStatistics [true/false] - Enable or disable calculation of growth statistics. Note that the doubling time (Dt) calculation also includes information about the fit coefficient of determination (CoD in %), known as R-squared
+ * @param {boolean} growthStatistics [true/false] - Enable or disable calculation of growth statistics. Note that the doubling time (Dt) calculation also includes information about the fit coefficient of determination (CoD in %), known as R-squared
  * @param {number} regressionODType [680/720/735] - OD sensor used for doubling time determination
  * @param {number} regressionCoDMin [%] - Minimum accpeted coefficient of determination for staility check evaluation (values below are ignored)
  * @param {number} stabilizationTimeMin [h] - Minimum duration of each characterization step
@@ -84,6 +88,10 @@ var UserDefinedProtocol = {
  * @param {number} growthRateEvalDelay [s] - Time after dilution where data for doubling time determination are ignored. By default growthRateEvalFrac, i.e. only limited fraction of the data points is used for calculations.
  *                 This is to prevent influence of post dilution effect on doubling time evaluation. If 0 or false, growthRateEvalDelay is used instead. Note that to completely disable data limitation you need to set both growthRateEvalFrac and growthRateEvalDelay to 0.
  * @param {string} groupGMS - Identifies the group that contains Gas Mixing System. System value - do not change unless sure what you are doing!
+ * @param {boolean} mediaCarbonization [true/false] - Enable or disable media carbonization during turbidostat pump action.
+ * @param {double} carbonizationOff [ml/min] - GMS CO2 channel flow when no carbonization of media is activated.
+ * @param {double} carbonizationNormal [ml/min] - GMS CO2 channel flow when weak carbonization of media is activated.
+ * @param {double} carbonizationBoost [ml/min] - GMS CO2 channel flow when intensive carbonization of media is activated.
  *
  * @return Flow of external/additional pump
  *
@@ -208,6 +216,27 @@ if (!theAccessory.context().getInt('initiated', 0)) {
   }
 }
 
+// Trigger media carbonization
+if (UserDefinedProtocol.groupGMS === theGroup) {
+  try {
+    switch(theAccessory.context().getInt('carbonization', 0)) {
+      case -1:
+        theGroup.getAccessory('gas-mixer.valve-0-reg').setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.carbonizationOff))
+        theAccessory.context().put('carbonization', 0)
+        break
+      case 1: 
+        theGroup.getAccessory('gas-mixer.valve-0-reg').setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.carbonizationNormal))
+        break
+      case 2: 
+        theGroup.getAccessory('gas-mixer.valve-0-reg').setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.carbonizationBoost))
+        break
+      default:
+    }
+  } catch (error) {
+    debugLogger('Carbonization ERROR. ' + error.name + ' : ' + error.message)
+  }
+}
+
 // Set the pump
 try {
   var pumpState = !isNaN(theAccessory.getValue())
@@ -531,14 +560,35 @@ function controlPump () {
       }
     }
     debugLogger('Pump max speed.')
+    if (UserDefinedProtocol.mediaCarbonization && ((theAccessory.context().getDouble('pHpostDilution',7.0) - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0)) {
+      debugLogger('Carbonization initiated')
+      theAccessory.context().put('carbonization', 1)
+      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', 1)
+    }
+    theAccessory.context().put('pHpreDilution', theGroup.getAccessory('probes.ph').getValue())
     return theAccessory.getMax() * UserDefinedProtocol.peristalticPumpSpeed / 100 // fast
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier)) && pumpState) {
     theAccessory.context().put('modeDilution', 0)
     theAccessory.context().put('lastPumpStop', experimentDuration)
     debugLogger('Pump stopped.')
+    if (theAccessory.context().get('carbonization', 0)) {
+      debugLogger('Carbonization terminated')
+      theAccessory.context().put('carbonization', 0)
+      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', -1)
+    }
+    theAccessory.context().put('pHpostDilution', theGroup.getAccessory('probes.ph').getValue())
     return ProtoConfig.OFF // pump off
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier + ((UserDefinedProtocol.turbidostatODMax * odMaxModifier) - (UserDefinedProtocol.turbidostatODMin * odMinModifier)) * UserDefinedProtocol.peristalticPumpSlowDownRange / 100)) && pumpState) {
-    debugLogger('Pump low speed.', 0)
+    debugLogger('Pump low speed', 0)
+    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && !theAccessory.context().get('carbonization', 0)) {
+      debugLogger('Carbonization boost')
+      theAccessory.context().put('carbonization', 1)
+      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', 2)
+    } else {
+      debugLogger('Carbonization terminated')
+      theAccessory.context().put('carbonization', 0)
+      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', -1)
+    }
     return theAccessory.getMax() * UserDefinedProtocol.peristalticPumpSpeed / 100 * UserDefinedProtocol.peristalticPumpSlowDownFactor / 100 // slow down the pump
   } else {
     return null // pump not influenced

From 0e73e2d79f81d99eec6586dcbda3ae3f54974784 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Sun, 21 Mar 2021 08:25:57 +0100
Subject: [PATCH 39/47] Carbonization boost better handling

---
 PP-GrowthOptimizer.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 5325081..90e4658 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -580,9 +580,9 @@ function controlPump () {
     return ProtoConfig.OFF // pump off
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier + ((UserDefinedProtocol.turbidostatODMax * odMaxModifier) - (UserDefinedProtocol.turbidostatODMin * odMinModifier)) * UserDefinedProtocol.peristalticPumpSlowDownRange / 100)) && pumpState) {
     debugLogger('Pump low speed', 0)
-    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && !theAccessory.context().get('carbonization', 0)) {
+    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && (theAccessory.context().get('carbonization', 0) < 2)) {
       debugLogger('Carbonization boost')
-      theAccessory.context().put('carbonization', 1)
+      theAccessory.context().put('carbonization', 2)
       theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', 2)
     } else {
       debugLogger('Carbonization terminated')

From b7765e7ae8e934b1092f84bcb9b2162de2288162 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Sun, 21 Mar 2021 09:41:03 +0100
Subject: [PATCH 40/47] Revert "Carbonization boost better handling"

This reverts commit 0e73e2d79f81d99eec6586dcbda3ae3f54974784.
---
 PP-GrowthOptimizer.js | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 90e4658..5325081 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -580,9 +580,9 @@ function controlPump () {
     return ProtoConfig.OFF // pump off
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier + ((UserDefinedProtocol.turbidostatODMax * odMaxModifier) - (UserDefinedProtocol.turbidostatODMin * odMinModifier)) * UserDefinedProtocol.peristalticPumpSlowDownRange / 100)) && pumpState) {
     debugLogger('Pump low speed', 0)
-    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && (theAccessory.context().get('carbonization', 0) < 2)) {
+    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && !theAccessory.context().get('carbonization', 0)) {
       debugLogger('Carbonization boost')
-      theAccessory.context().put('carbonization', 2)
+      theAccessory.context().put('carbonization', 1)
       theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', 2)
     } else {
       debugLogger('Carbonization terminated')

From b365768d55f4f20271256eadf8ae775246fcbedf Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Sun, 21 Mar 2021 09:43:56 +0100
Subject: [PATCH 41/47] Better boosted carbonization handling

---
 PP-GrowthOptimizer.js | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 5325081..65b07d1 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -580,11 +580,11 @@ function controlPump () {
     return ProtoConfig.OFF // pump off
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier + ((UserDefinedProtocol.turbidostatODMax * odMaxModifier) - (UserDefinedProtocol.turbidostatODMin * odMinModifier)) * UserDefinedProtocol.peristalticPumpSlowDownRange / 100)) && pumpState) {
     debugLogger('Pump low speed', 0)
-    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && !theAccessory.context().get('carbonization', 0)) {
+    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && (theAccessory.context().get('carbonization', 0) < 2)) {
       debugLogger('Carbonization boost')
-      theAccessory.context().put('carbonization', 1)
+      theAccessory.context().put('carbonization', 2)
       theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', 2)
-    } else {
+    } else if (UserDefinedProtocol.mediaCarbonization && (theAccessory.context().get('carbonization', 0) == 1)) {
       debugLogger('Carbonization terminated')
       theAccessory.context().put('carbonization', 0)
       theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', -1)

From a03ceec74e036fc6ac51410cbc33a40cd7bf1e8c Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Mon, 22 Mar 2021 21:38:45 +0100
Subject: [PATCH 42/47] Improved groupGMS addresing

---
 PP-GrowthOptimizer.js | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 65b07d1..a8e515d 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -87,7 +87,7 @@ var UserDefinedProtocol = {
  * -advanced options
  * @param {number} growthRateEvalDelay [s] - Time after dilution where data for doubling time determination are ignored. By default growthRateEvalFrac, i.e. only limited fraction of the data points is used for calculations.
  *                 This is to prevent influence of post dilution effect on doubling time evaluation. If 0 or false, growthRateEvalDelay is used instead. Note that to completely disable data limitation you need to set both growthRateEvalFrac and growthRateEvalDelay to 0.
- * @param {string} groupGMS - Identifies the group that contains Gas Mixing System. System value - do not change unless sure what you are doing!
+ * @param {object} groupGMS - Identifies the group that contains Gas Mixing System. System value - do not change unless sure what you are doing! Example: theServer.getGroupByName('GROUP-NAME')
  * @param {boolean} mediaCarbonization [true/false] - Enable or disable media carbonization during turbidostat pump action.
  * @param {double} carbonizationOff [ml/min] - GMS CO2 channel flow when no carbonization of media is activated.
  * @param {double} carbonizationNormal [ml/min] - GMS CO2 channel flow when weak carbonization of media is activated.
@@ -563,7 +563,7 @@ function controlPump () {
     if (UserDefinedProtocol.mediaCarbonization && ((theAccessory.context().getDouble('pHpostDilution',7.0) - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0)) {
       debugLogger('Carbonization initiated')
       theAccessory.context().put('carbonization', 1)
-      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', 1)
+      UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', 1)
     }
     theAccessory.context().put('pHpreDilution', theGroup.getAccessory('probes.ph').getValue())
     return theAccessory.getMax() * UserDefinedProtocol.peristalticPumpSpeed / 100 // fast
@@ -574,7 +574,7 @@ function controlPump () {
     if (theAccessory.context().get('carbonization', 0)) {
       debugLogger('Carbonization terminated')
       theAccessory.context().put('carbonization', 0)
-      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', -1)
+      UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', -1)
     }
     theAccessory.context().put('pHpostDilution', theGroup.getAccessory('probes.ph').getValue())
     return ProtoConfig.OFF // pump off
@@ -583,11 +583,11 @@ function controlPump () {
     if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && (theAccessory.context().get('carbonization', 0) < 2)) {
       debugLogger('Carbonization boost')
       theAccessory.context().put('carbonization', 2)
-      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', 2)
+      UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', 2)
     } else if (UserDefinedProtocol.mediaCarbonization && (theAccessory.context().get('carbonization', 0) == 1)) {
       debugLogger('Carbonization terminated')
       theAccessory.context().put('carbonization', 0)
-      theServer.getGroupByName(UserDefinedProtocol.groupGMS).getAccessory('pumps.pump-5').context().put('carbonization', -1)
+      UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', -1)
     }
     return theAccessory.getMax() * UserDefinedProtocol.peristalticPumpSpeed / 100 * UserDefinedProtocol.peristalticPumpSlowDownFactor / 100 // slow down the pump
   } else {

From 1501261003034029e69f0fdf8c15be66e8e18046 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Thu, 22 Apr 2021 16:51:09 +0200
Subject: [PATCH 43/47] White light addressing corrected

---
 PP-GrowthOptimizer.js | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index a8e515d..c08d367 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -1,7 +1,7 @@
 var UserDefinedProtocol = {
   // -turbidostat settings
-  turbidostatODMin: 0.18,
-  turbidostatODMax: 0.195,
+  turbidostatODMin: 0.3325,
+  turbidostatODMax: 0.3367,
   turbidostatODType: 720,
   ODReadoutInterval: 60,
   // -optimizer parameters
@@ -49,8 +49,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.6.0
- * @modified 19.3.2021 (JaCe)
+ * @version 3.6.1
+ * @modified 21.4.2021 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -148,7 +148,7 @@ if (!theAccessory.context().getInt('initiated', 0)) {
           }
           break
         case 'light-white':
-          if (theGroup.getAccessory('actinic-lights.light-Blue').getProtoConfigValue()) {
+          if (theGroup.getAccessory('actinic-lights.light-White').getProtoConfigValue()) {
             theExperiment.addEvent('!!! Disable WHITE LIGHT protocol')
           }
           break

From f442aa9fed3555cf206925abc38e20c8f3830650 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Mon, 26 Apr 2021 12:49:13 +0200
Subject: [PATCH 44/47] IC95 to CI95 global renaming

---
 PP-GrowthOptimizer.js | 83 +++++++++++++++++++++++--------------------
 1 file changed, 44 insertions(+), 39 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index c08d367..f64bacf 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -17,13 +17,13 @@ var UserDefinedProtocol = {
   // -optimizer stability check
   growthStatistics: true,
   regressionODType: 680,
-  regressionCoDMin: 60,
-  stabilizationTimeMin: 3,
-  stabilizationTimeMax: 7,
+  regressionCoDMin: 75,
+  stabilizationTimeMin: 8,
+  stabilizationTimeMax: 24,
   growthRateEvalFrac: 3 / 4,
   analyzedSteps: 6,
-  growthTrendMax: 15,
-  intervalOfConfidenceMax: 35,
+  growthTrendMax: 1.5,
+  CI95AmplitudeMax: 2.5,
   // -peristaltic pump settings
   peristalticPumpID: 5,
   peristalticPumpSpeed: 100,
@@ -49,8 +49,8 @@ var UserDefinedProtocol = {
  * @author CzechGlobe - Department of Adaptive Biotechnologies (JaCe)
  * @copyright Jan Červený 2020(c)
  * @license MIT
- * @version 3.6.1
- * @modified 21.4.2021 (JaCe)
+ * @version 3.6.2
+ * @modified 26.4.2021 (JaCe)
  *
  * @notes For proper functionality of the script "OD Regulator" protocol has to be disabled as well as chosen
  *        controlled accessory protocols (i.e. Lights, Thermoregulation, GMS, Stirrer).
@@ -78,7 +78,7 @@ var UserDefinedProtocol = {
  * @param {number} growthRateEvalFrac [0-1] - Defines whether to use particular fraction of the data points for doubling time determination.
  * @param {number} analyzedSteps [-] - Number of steps to be analyzed for stability check
  * @param {number} growthTrendMax [%] - Maximum growth speed trend in time
- * @param {number} intervalOfConfidenceMax [%] - Maximum allowed percents of 95% Confidence Interval
+ * @param {number} intervalOfConfidenceAmplitudeMax [%] - Maximum allowed amblitude of 95% Confidence Interval in percents from mean
  * -peristaltic pump settings
  * @param {number} peristalticPumpID [3-7] - Defines peristaltic pump ID set to the pump that is used for fresh media supply (quasi-continuous mode)
  * @param {number} peristalticPumpSpeed [%] - Nominal pump speed used for dilution of the suspension
@@ -104,7 +104,7 @@ importPackage(Packages.psi.bioreactor.core.protocol)
 importPackage(Packages.psi.bioreactor.core.regression)
 
 // Inicialization of the control script
-if (!theAccessory.context().getInt('initiated', 0)) {
+if (!theAccessory.context().get('initiated', false)) {
   try {
     theAccessory.context().clear()
     theAccessory.context().put('stabilizedTime', Number(theExperiment.getDurationSec()) + UserDefinedProtocol.stabilizationTimeMin * 3600)
@@ -209,7 +209,7 @@ if (!theAccessory.context().getInt('initiated', 0)) {
       debugLogger('OD range reversed.')
       theExperiment.addEvent('OD range set in reversed order - will be automatically corrected.')
     }
-    theAccessory.context().put('initiated', 1)
+    theAccessory.context().put('initiated', true)
     debugLogger('Peristaltic Pump - Growth Optimizer initialization successful.')
   } catch (error) {
     debugLogger('Initialization ERROR. ' + error.name + ' : ' + error.message)
@@ -407,7 +407,6 @@ function changeParameter(parameter, direction) {
   theAccessory.context().put('controlledParameterPosition', controlledParameterPosition)
   controlParameter(parameter, UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
   positions.push(UserDefinedProtocol.controlledParameterSteps[controlledParameterPosition-1])
-  debugLogger('parameterChange() positions are ' + positions.toString())
   return positions
 }
 // Control activity of the peristaltic pump 
@@ -470,6 +469,7 @@ function controlPump () {
     var stepDoublingTimeAvg = len > 2 ? len > UserDefinedProtocol.analyzedSteps ? stepDoublingTime.slice(len - UserDefinedProtocol.analyzedSteps, len).reduce(getSumArrReduce, 0) / (UserDefinedProtocol.analyzedSteps) : stepDoublingTime.slice(1, len).reduce(getSumArrReduce, 0) / (len - 1) : stepDoublingTime[len - 1]
     theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
     theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
+    theAccessory.context().remove('stepAccumulated')
     theAccessory.context().remove('stepCounter')
     theAccessory.context().remove('expDuration')
     theAccessory.context().remove('stepDoublingTime')
@@ -511,50 +511,55 @@ function controlPump () {
       if (stepCounter >= UserDefinedProtocol.analyzedSteps) {
         var stepDoublingTimeAvg = 0
         var stepDoublingTimeSD = 0
-        var stepDoublingTimeIC95 = 0
+        var stepDoublingTimeCI95 = 0
         var stepTrend = 0
+        var stepAccumulated = theAccessory.context().getInt('stepAccumulated', 0)
         var sumXY = 0
         var sumX = 0
         var sumY = 0
         var sumX2 = 0
         // var sumY2 = 0
-        // TODO if trend then accumulate steps as [analyzedSteps inf]
         // Average of steps doubling time
-        for (var i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps); i--) {
+        for (var i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
           stepDoublingTimeAvg += Number(stepDoublingTime[i])
         }
-        stepDoublingTimeAvg /= UserDefinedProtocol.analyzedSteps
-        // IC95 of steps doubling time
-        for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps); i--) {
+        stepDoublingTimeAvg /= (UserDefinedProtocol.analyzedSteps + stepAccumulated)
+        // CI95 of steps doubling time
+        for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
           stepDoublingTimeSD += Math.pow(stepDoublingTime[i] - stepDoublingTimeAvg, 2)
         }
-        stepDoublingTimeSD = Math.sqrt(stepDoublingTimeSD / (UserDefinedProtocol.analyzedSteps - 1))
-        stepDoublingTimeIC95 = stepDoublingTimeSD / Math.sqrt(UserDefinedProtocol.analyzedSteps) * 1.96
+        stepDoublingTimeSD = Math.sqrt(stepDoublingTimeSD / (UserDefinedProtocol.analyzedSteps + stepAccumulated - 1))
+        stepDoublingTimeCI95 = stepDoublingTimeSD / Math.sqrt(UserDefinedProtocol.analyzedSteps + stepAccumulated) * 1.96
         // Trend of steps doubling time
-        for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps); i--) {
+        for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
           sumX += Number(expDuration[i])
           sumX2 += Math.pow(expDuration[i], 2)
           sumY += Number(stepDoublingTime[i])
           // sumY2 += Math.pow(stepDoublingTime[i], 2)
           sumXY += Number(expDuration[i]) * Number(stepDoublingTime[i])
         }
-        stepTrend = (UserDefinedProtocol.analyzedSteps * sumXY - sumX * sumY) / (UserDefinedProtocol.analyzedSteps * sumX2 - Math.pow(sumX, 2)) * 3600
-        theExperiment.addEvent('Steps doubling time Avg: ' + round(stepDoublingTimeAvg, 2) + ' h, IC95 ' + round(stepDoublingTimeIC95, 2) + ' h (' + round(stepDoublingTimeIC95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
+        stepTrend = ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumXY - sumX * sumY) / ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumX2 - Math.pow(sumX, 2)) * 3600
+        theExperiment.addEvent('Step doubling time Avg: ' + round(stepDoublingTimeAvg, 2) + ' h, CI95 ' + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (' + round(stepDoublingTimeCI95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
         // Growth stability test and parameters control
-        if (((stepDoublingTimeIC95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.intervalOfConfidenceMax / 100) && (Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) && (stabilizedTime <= experimentDuration))) {
-          theAccessory.context().put('modeStabilized', 1)
-          theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
-          theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
-          theAccessory.context().remove('stepCounter')
-          theAccessory.context().remove('expDuration')
-          theAccessory.context().remove('stepDoublingTime')
-          theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeIC95, 2) + ' h (IC95)')
-          if (UserDefinedProtocol.particleSwarmOptimizer) {
-            PSO(stepDoublingTimeAvg)
-          } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
-            var positions = changeParameter(UserDefinedProtocol.controlledParameter)
-            debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
-            theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
+        if ((Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) || stepAccumulated) {
+            // TODO this solution removes stepTrend criteria check if at least once reached (expecting convergence!!!). May need to be upgraded later.
+            theAccessory.context().put('stepAccumulated', stepAccumulated + 1)
+          if ((stabilizedTime <= experimentDuration) && ((stepDoublingTimeCI95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.CI95AmplitudeMax / 100))) {
+            theAccessory.context().put('modeStabilized', 1)
+            theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
+            theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
+            theAccessory.context().remove('stepAccumulated')
+            theAccessory.context().remove('stepCounter')
+            theAccessory.context().remove('expDuration')
+            theAccessory.context().remove('stepDoublingTime')
+            theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (CI95)')
+            if (UserDefinedProtocol.particleSwarmOptimizer) {
+              PSO(stepDoublingTimeAvg)
+            } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
+              var positions = changeParameter(UserDefinedProtocol.controlledParameter)
+              debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
+              theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
+            }
           }
         }
       }
@@ -571,7 +576,7 @@ function controlPump () {
     theAccessory.context().put('modeDilution', 0)
     theAccessory.context().put('lastPumpStop', experimentDuration)
     debugLogger('Pump stopped.')
-    if (theAccessory.context().get('carbonization', 0)) {
+    if (theAccessory.context().getInt('carbonization', 0)) {
       debugLogger('Carbonization terminated')
       theAccessory.context().put('carbonization', 0)
       UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', -1)
@@ -580,11 +585,11 @@ function controlPump () {
     return ProtoConfig.OFF // pump off
   } else if ((odValue <= (UserDefinedProtocol.turbidostatODMin * odMinModifier + ((UserDefinedProtocol.turbidostatODMax * odMaxModifier) - (UserDefinedProtocol.turbidostatODMin * odMinModifier)) * UserDefinedProtocol.peristalticPumpSlowDownRange / 100)) && pumpState) {
     debugLogger('Pump low speed', 0)
-    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && (theAccessory.context().get('carbonization', 0) < 2)) {
+    if (UserDefinedProtocol.mediaCarbonization && ((theGroup.getAccessory('probes.ph').getValue() - theAccessory.context().getDouble('pHpreDilution',7.0)) > 0) && (theAccessory.context().getInt('carbonization', 0) < 2)) {
       debugLogger('Carbonization boost')
       theAccessory.context().put('carbonization', 2)
       UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', 2)
-    } else if (UserDefinedProtocol.mediaCarbonization && (theAccessory.context().get('carbonization', 0) == 1)) {
+    } else if (UserDefinedProtocol.mediaCarbonization && (theAccessory.context().getInt('carbonization', 0) == 1)) {
       debugLogger('Carbonization terminated')
       theAccessory.context().put('carbonization', 0)
       UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', -1)

From 07dc70c7b5d3036c92e055f71e3bb03e236f006e Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Sat, 1 May 2021 18:14:04 +0200
Subject: [PATCH 45/47] Logging text update

---
 PP-GrowthOptimizer.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index f64bacf..f6f145d 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -1,7 +1,7 @@
 var UserDefinedProtocol = {
   // -turbidostat settings
   turbidostatODMin: 0.3325,
-  turbidostatODMax: 0.3367,
+  turbidostatODMax: 0.3675,
   turbidostatODType: 720,
   ODReadoutInterval: 60,
   // -optimizer parameters
@@ -227,7 +227,7 @@ if (UserDefinedProtocol.groupGMS === theGroup) {
       case 1: 
         theGroup.getAccessory('gas-mixer.valve-0-reg').setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.carbonizationNormal))
         break
-      case 2: 
+      case 2:
         theGroup.getAccessory('gas-mixer.valve-0-reg').setRunningProtoConfig(new ProtoConfig(UserDefinedProtocol.carbonizationBoost))
         break
       default:
@@ -539,7 +539,7 @@ function controlPump () {
           sumXY += Number(expDuration[i]) * Number(stepDoublingTime[i])
         }
         stepTrend = ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumXY - sumX * sumY) / ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumX2 - Math.pow(sumX, 2)) * 3600
-        theExperiment.addEvent('Step doubling time Avg: ' + round(stepDoublingTimeAvg, 2) + ' h, CI95 ' + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (' + round(stepDoublingTimeCI95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
+        theExperiment.addEvent('Average step doubling time is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (CI95, ' + round(stepDoublingTimeCI95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
         // Growth stability test and parameters control
         if ((Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) || stepAccumulated) {
             // TODO this solution removes stepTrend criteria check if at least once reached (expecting convergence!!!). May need to be upgraded later.
@@ -576,7 +576,7 @@ function controlPump () {
     theAccessory.context().put('modeDilution', 0)
     theAccessory.context().put('lastPumpStop', experimentDuration)
     debugLogger('Pump stopped.')
-    if (theAccessory.context().getInt('carbonization', 0)) {
+    if (UserDefinedProtocol.mediaCarbonization && theAccessory.context().getInt('carbonization', 0)) {
       debugLogger('Carbonization terminated')
       theAccessory.context().put('carbonization', 0)
       UserDefinedProtocol.groupGMS.getAccessory('pumps.pump-5').context().put('carbonization', -1)

From 5076415cbf0371335236fc1ce8d613ddae138562 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Tue, 11 May 2021 09:06:33 +0200
Subject: [PATCH 46/47] Fixed stepCounter for failed CoD check

---
 PP-GrowthOptimizer.js | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index f6f145d..009c35d 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -503,12 +503,11 @@ function controlPump () {
       var DHCapacity = (Math.floor(stepDuration[stepCounter] / UserDefinedProtocol.ODReadoutInterval) - 3) > 0 ? (Math.floor(stepDuration[stepCounter] / UserDefinedProtocol.ODReadoutInterval) - 3) : 60
       var regCoefExp = odSensorRegression.getDataHistory().regression(ETrendFunction.EXP, Math.ceil(DHCapacity - (UserDefinedProtocol.growthRateEvalFrac ? DHCapacity * (UserDefinedProtocol.growthRateEvalFrac / 100) : UserDefinedProtocol.growthRateEvalDelay / UserDefinedProtocol.ODReadoutInterval)))
       debugLogger('Growth parameters: A=' + regCoefExp[0] +', B=' + regCoefExp[1] + ', R2=' + regCoefExp[2])
+      theExperiment.addEvent('Doubling time of the step was ' + round((1 / (Number(regCoefExp[1]) * 3600 * 10)) * Math.LN2, 2) + ' h (CoD ' + round(Number(regCoefExp[2]) * 100, 1) + '%)')
       if (Number(regCoefExp[2]) >= UserDefinedProtocol.regressionCoDMin / 100) {
         stepDoublingTime[stepCounter] = (1 / (Number(regCoefExp[1]) * 3600 * 10)) * Math.LN2
-        theAccessory.context().put('stepCounter', ++stepCounter)
-      }
-      theExperiment.addEvent('Doubling time of the step was ' + round((1 / (Number(regCoefExp[1]) * 3600 * 10)) * Math.LN2, 2) + ' h (CoD ' + round(Number(regCoefExp[2]) * 100, 1) + '%)')
-      if (stepCounter >= UserDefinedProtocol.analyzedSteps) {
+        theAccessory.context().put('stepCounter', stepCounter + 1)
+        if (stepCounter >= UserDefinedProtocol.analyzedSteps) {
         var stepDoublingTimeAvg = 0
         var stepDoublingTimeSD = 0
         var stepDoublingTimeCI95 = 0
@@ -562,6 +561,7 @@ function controlPump () {
             }
           }
         }
+        }
       }
     }
     debugLogger('Pump max speed.')

From 9eb7209d1d9d46a89544713c3b78240df5dc8d08 Mon Sep 17 00:00:00 2001
From: JanCervenyy <cerveny.j@gmail.com>
Date: Sat, 22 May 2021 09:10:18 +0200
Subject: [PATCH 47/47] stepCounter increment fix

---
 PP-GrowthOptimizer.js | 100 +++++++++++++++++++++---------------------
 1 file changed, 50 insertions(+), 50 deletions(-)

diff --git a/PP-GrowthOptimizer.js b/PP-GrowthOptimizer.js
index 009c35d..b05c46f 100644
--- a/PP-GrowthOptimizer.js
+++ b/PP-GrowthOptimizer.js
@@ -506,62 +506,62 @@ function controlPump () {
       theExperiment.addEvent('Doubling time of the step was ' + round((1 / (Number(regCoefExp[1]) * 3600 * 10)) * Math.LN2, 2) + ' h (CoD ' + round(Number(regCoefExp[2]) * 100, 1) + '%)')
       if (Number(regCoefExp[2]) >= UserDefinedProtocol.regressionCoDMin / 100) {
         stepDoublingTime[stepCounter] = (1 / (Number(regCoefExp[1]) * 3600 * 10)) * Math.LN2
-        theAccessory.context().put('stepCounter', stepCounter + 1)
+        theAccessory.context().put('stepCounter', ++stepCounter)
         if (stepCounter >= UserDefinedProtocol.analyzedSteps) {
-        var stepDoublingTimeAvg = 0
-        var stepDoublingTimeSD = 0
-        var stepDoublingTimeCI95 = 0
-        var stepTrend = 0
-        var stepAccumulated = theAccessory.context().getInt('stepAccumulated', 0)
-        var sumXY = 0
-        var sumX = 0
-        var sumY = 0
-        var sumX2 = 0
-        // var sumY2 = 0
-        // Average of steps doubling time
-        for (var i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
-          stepDoublingTimeAvg += Number(stepDoublingTime[i])
-        }
-        stepDoublingTimeAvg /= (UserDefinedProtocol.analyzedSteps + stepAccumulated)
-        // CI95 of steps doubling time
-        for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
-          stepDoublingTimeSD += Math.pow(stepDoublingTime[i] - stepDoublingTimeAvg, 2)
-        }
-        stepDoublingTimeSD = Math.sqrt(stepDoublingTimeSD / (UserDefinedProtocol.analyzedSteps + stepAccumulated - 1))
-        stepDoublingTimeCI95 = stepDoublingTimeSD / Math.sqrt(UserDefinedProtocol.analyzedSteps + stepAccumulated) * 1.96
-        // Trend of steps doubling time
-        for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
-          sumX += Number(expDuration[i])
-          sumX2 += Math.pow(expDuration[i], 2)
-          sumY += Number(stepDoublingTime[i])
-          // sumY2 += Math.pow(stepDoublingTime[i], 2)
-          sumXY += Number(expDuration[i]) * Number(stepDoublingTime[i])
-        }
-        stepTrend = ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumXY - sumX * sumY) / ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumX2 - Math.pow(sumX, 2)) * 3600
-        theExperiment.addEvent('Average step doubling time is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (CI95, ' + round(stepDoublingTimeCI95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
-        // Growth stability test and parameters control
-        if ((Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) || stepAccumulated) {
+          var stepDoublingTimeAvg = 0
+          var stepDoublingTimeSD = 0
+          var stepDoublingTimeCI95 = 0
+          var stepTrend = 0
+          var stepAccumulated = theAccessory.context().getInt('stepAccumulated', 0)
+          var sumXY = 0
+          var sumX = 0
+          var sumY = 0
+          var sumX2 = 0
+          // var sumY2 = 0
+          // Average of steps doubling time
+          for (var i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
+            stepDoublingTimeAvg += Number(stepDoublingTime[i])
+          }
+          stepDoublingTimeAvg /= (UserDefinedProtocol.analyzedSteps + stepAccumulated)
+          // CI95 of steps doubling time
+          for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
+            stepDoublingTimeSD += Math.pow(stepDoublingTime[i] - stepDoublingTimeAvg, 2)
+          }
+          stepDoublingTimeSD = Math.sqrt(stepDoublingTimeSD / (UserDefinedProtocol.analyzedSteps + stepAccumulated - 1))
+          stepDoublingTimeCI95 = stepDoublingTimeSD / Math.sqrt(UserDefinedProtocol.analyzedSteps + stepAccumulated) * 1.96
+          // Trend of steps doubling time
+          for (i = (stepCounter - 1); i >= (stepCounter - UserDefinedProtocol.analyzedSteps - stepAccumulated); i--) {
+            sumX += Number(expDuration[i])
+            sumX2 += Math.pow(expDuration[i], 2)
+            sumY += Number(stepDoublingTime[i])
+            // sumY2 += Math.pow(stepDoublingTime[i], 2)
+            sumXY += Number(expDuration[i]) * Number(stepDoublingTime[i])
+          }
+          stepTrend = ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumXY - sumX * sumY) / ((UserDefinedProtocol.analyzedSteps + stepAccumulated) * sumX2 - Math.pow(sumX, 2)) * 3600
+          theExperiment.addEvent('Average step doubling time is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (CI95, ' + round(stepDoublingTimeCI95 / stepDoublingTimeAvg * 100, 1) + '%) with ' + round(stepTrend, 2) + ' h/h trend (' + round(stepTrend / stepDoublingTimeAvg * 100, 1) + '%)')
+          // Growth stability test and parameters control
+          if ((Math.abs(stepTrend / stepDoublingTimeAvg) <= (UserDefinedProtocol.growthTrendMax / 100)) || stepAccumulated) {
             // TODO this solution removes stepTrend criteria check if at least once reached (expecting convergence!!!). May need to be upgraded later.
             theAccessory.context().put('stepAccumulated', stepAccumulated + 1)
-          if ((stabilizedTime <= experimentDuration) && ((stepDoublingTimeCI95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.CI95AmplitudeMax / 100))) {
-            theAccessory.context().put('modeStabilized', 1)
-            theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
-            theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
-            theAccessory.context().remove('stepAccumulated')
-            theAccessory.context().remove('stepCounter')
-            theAccessory.context().remove('expDuration')
-            theAccessory.context().remove('stepDoublingTime')
-            theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (CI95)')
-            if (UserDefinedProtocol.particleSwarmOptimizer) {
-              PSO(stepDoublingTimeAvg)
-            } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
-              var positions = changeParameter(UserDefinedProtocol.controlledParameter)
-              debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]') 
-              theServer.sendMail('OPTIMIZER on ' + theGroup.getName() , 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
+            if ((stabilizedTime <= experimentDuration) && ((stepDoublingTimeCI95 / stepDoublingTimeAvg) <= (UserDefinedProtocol.CI95AmplitudeMax / 100))) {
+              theAccessory.context().put('modeStabilized', 1)
+              theAccessory.context().put('stabilizedTime', experimentDuration + UserDefinedProtocol.stabilizationTimeMin * 3600)
+              theAccessory.context().put('stabilizedTimeMax', experimentDuration + UserDefinedProtocol.stabilizationTimeMax * 3600)
+              theAccessory.context().remove('stepAccumulated')
+              theAccessory.context().remove('stepCounter')
+              theAccessory.context().remove('expDuration')
+              theAccessory.context().remove('stepDoublingTime')
+              theExperiment.addEvent('*** Stabilized doubling time Dt (' + theGroup.getAccessory('thermo.thermo-reg').getValue() + '  ' + String.fromCharCode(176) + 'C, ' + theAccessory.context().getString('controlledParameterText', 'no parameter') + ') is ' + round(stepDoublingTimeAvg, 2) + String.fromCharCode(177) + round(stepDoublingTimeCI95, 2) + ' h (CI95)')
+              if (UserDefinedProtocol.particleSwarmOptimizer) {
+                PSO(stepDoublingTimeAvg)
+              } else if (UserDefinedProtocol.controlledParameterSteps.length > 1) {
+                var positions = changeParameter(UserDefinedProtocol.controlledParameter)
+                debugLogger('OPTIMIZER executed with fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and new position is [ ' + positions[1].toFixed(2) + ' ]')
+                theServer.sendMail('OPTIMIZER on ' + theGroup.getName(), 'NONE', ': fitness ' + stepDoublingTimeAvg.toFixed(2) + ' for [ ' + positions[0].toFixed(2) + ' ] and set new position [ ' + positions[1].toFixed(2) + ' ]') // Email notification
+              }
             }
           }
         }
-        }
       }
     }
     debugLogger('Pump max speed.')