Science/track_sample.tl

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mission TrackAndSample {
  arguments {
    # Almost every mission should start with an overall timeout and a NeedCommsTime. Drift Missions will have an acoustic timeout instead of a NeedCommsTime.

    # You probably need to change these.

    NumSamplers = 1 count
      """
      Total number of ESP cartridges (Maximum 60) or CANON samplers. Set to 0
      to disable sampling.
      """

    StartIndex = 1 count
      """
      Start index in ESP settings. If re-running mission, can skip settings of
      already-completed samples. Default is 1 (no skipping).
      """

    CANONSamplerRotateOnly = 0 bool

    MissionTimeout = 20 hour
      """
      Maximum duration of mission
      """

    AcousticTrackingTimeout = 240 hour
      """
      If the vehicle does not receive an acoustic signal for more than this
      length of time, it will surface for communications. Set longer than
      MissionTimeout to effectively disable.
      """

    NeedCommsTimeInTransit = 60 minute
      """
      On yo-yo transects, how often to surface for commumications
      """

    NeedCommsTimePatchTracking = 300 minute
      """
      Maximum time between surfacings for communications during patch
      tracking. This is checked only on every NumRoundsBtnCrossLegSurfacings
      rounds of CrossLeg.
      """

    NeedCommsTimeMarginPatchTracking = 60 minute
      """
      In case vehicle does not surface on periodic rounds of InLeg or
      CrossLeg, vehicle will be forced to surface at
      NeedCommsTimePatchTracking+NeedCommsTimeMarginPatchTracking.
      """

    WaitAfterBouncing = 5 minute
      """
      During tracking, after the vehicle bounces off the boundary (defined by
      minimum distance to shore or polygon sides), wait this long before
      re-checking the distance.
      """

    MaxWaitNoFiring = 2 hour
      """
      If no firing after more than MaxWaitNoFiring, terminate mission.
      """

    MaxWaitNotAchievingDepth = 0.5 hour
      """
      Maximum wait time the vehicle cannot reach the targeted depth.
      """

    LatPatchTrackingStart = NaN degree
      """
      Latitude of patch tracking start location. If nan, transit is skipped.
      """

    # debug
    #     </Description><Units:degree/><Value>36.810</Value></DefineArg>

    LonPatchTrackingStart = NaN degree
      """
      Longitude of patch tracking start location. If nan, transit is skipped.
      """

    # debug
    #     </Description><Units:degree/><Value>-121.855</Value></DefineArg>

    SendSampleStatusAndData = true
      """
      Whether to senddata to acoustic modem.
      """

    # debug
    #     </Description><False/></DefineArg>

    SendDataToMultipleModems = false
      """
      Whether to senddata to more than one modem.
      """

    # debug
    #     </Description><True/></DefineArg>

    modemId1 = 1 enum
      """
      Modem ID1. Initialized to 1.
      """

    modemId2 = 4 enum
      """
      Modem ID2. Initialized to 4.
      """

    SampleAtPeakChl = false
      """
      Whether to sample at peak-chl
      """

    # debug
    #     </Description><True/></DefineArg>

    InitialDiveDuration = 1.0 minute
      """
      On the first dive for looking for the chl max, run at SpeedInitialDive
      for this duration (e.g., 1 m/s spiral to dive fast).
      """

    SpeedTransit = 1.0 meter_per_second
      """
      Vehicle speed when transiting.
      """

    SpeedInitialDive = 1.0 meter_per_second
      """
      Vehicle speed during initial dive (for looking for the chl max). 0.0 for
      drift mode (prop off); 1.0 for spiral mode (prop on). Initialized to 1
      m/s.
      """

    SpeedSampling = 1.0 meter_per_second
      """
      Vehicle speed during sampling: 0.0 for drift mode (prop off); 1.0 for
      donut mode (prop on). Initialized to 1 m/s.
      """

    # debug
    #     </Description><Units:meter_per_second/><Value>0</Value></DefineArg>

    RudderAngleInitialDive = 9 degree
      """
      Rudder angle in initial spiral-down to leave surface. Initialized to 9
      degrees.
      """

    RudderAngleDonutSampling = 13 degree
      """
      Rudder angle during donut sampling.
      """

    MaxDepth = 50 meter
      """
      Maximum depth for the entire mission.
      """

    MinWaterDepth = 10 meter
      """
      Minimum water depth for the entire mission.
      """

    MinAltitude = 7 meter
      """
      Minimum altitude for the entire mission.
      """

    MinOffshore = 2 kilometer
      """
      Minimum offshore distance for the entire mission.
      """

    MarginMinOffshore = 100 meter
      """
      If closer than MinOffshore+MarginMinOffshore, turn back from shore.
      """

    MinDistFromPolygonSides = 200 meter
      """
      If a operational safety polygon is specified and the vehicle is closer
      than this minimum distance to the polygon sides, turn back.
      """

    DeepBoundSampler = 45 meter
      """
      Deep depth bound for sampling operation
      """

    ShallowBoundChl = 4.5 meter
      """
      Shallow depth bound for chl-peak detection.
      """

    DeepBoundChl = 17 meter
      """
      Deep depth bound for chl-peak detection.
      """

    VertMargin = 3 meter
      """
      Deep bound for vertical chl-peak finding maneuver = DeepBoundChl +
      VertMargin.
      """

    BeginThresholdChl = 1.0 microgram_per_liter
      """
      If non-NaN, sets threshold for starting horizontal patch detection
      """

    TriggerThresholdChl = 2.5 microgram_per_liter
      """
      If non-NaN, sets threshold for triggering sampling. Chl value of 2.5
      mug/L corresponds to HS2 fluorescence reading of 0.001 on Dorado.
      """

    WpBearing = 90 degree
      """
      Bearing being followed in the current leg. Set this to initialize start
      direction of patch tracking.
      """

    # debug
    #     </Description><Units:degree/><Value>270</Value></DefineArg>

    OffPeakFraction = 90 percent
      """
      When filtered horizontal value is this fraction of the peak, consider it
      outside the patch.
      """

    # debug
    #     </Description><Units:percent/><Value>75</Value></DefineArg>

    PatchTrackingRounds = 5 count
      """
      Maximum number of rounds (one round = cross; continued cross; in; out)
      """

    # debug
    #     </Description><Units:count/><Value>3</Value></DefineArg>

    NumRoundsBtnCrossLegSurfacings = 5 count
      """
      Every so many rounds, vehicle surfaces on CrossLeg. Set to a big number
      to practially disable surfacing on CrossLeg.
      """

    WpMaxDistance = 1000 meter
      """
      Maximum length of each tracking leg
      """

    WpTimeout = 4000 second
      """
      Maximum duration of each tracking leg
      """

    DetectionTimeout = 30 minute
      """
      Look for signal for this long. If none found within this timeout, switch
      to the next leg.
      """

    PatchTrackingYoYoMinDepth = 4.5 meter
      """
      Minimum depth while performing the YoYo behavior.
      """

    PatchTrackingYoYoMaxDepth = 27 meter
      """
      Maximum depth while performing the YoYo behavior.
      """

    YoYoMinAltitude = 9 meter
      """
      Minimum altitude while performing the YoYo behavior (for
      bottom-terminated YoYos).
      """

    CartridgeTypeCommon = -6 count
      """
      Cartridge type value common to all samples unless set differently. Initialized to -6.
      """

    # Cartridge type for individual cartridges:

    CartridgeType[1..60] = NaN count
      """
      Cartridge {$}.
      """

    # If TempDiffFromPeakChl is NaN, will use Temp, or DepDiffFromPeakChl, or Dep. SampleAtPeakChl must be True to use this setting.

    TempDiffFromPeakChlCommon = NaN kelvin # debug: 0 kelvin
      """
      Value common to all samples unless set differently: target temperature difference from the peak-chl temperature. Initialized to NaN.
      """

    # For individual samples: target temperature difference from the peak-chl temperature.

    TempDiffFromPeakChl[1..60] = {
      1..1 : NaN kelvin,
      2..2 : NaN kelvin,
      3..60 : NaN kelvin
    }
      """
      Sample {$}.
      """

    # If Temp is NaN, will use TempDiffFromPeakChl, or DepDiffFromPeakChl, or Dep. SampleAtPeakChl must be True to use this setting.

    TempCommon = NaN celsius # debug: 0 celsius
      """
      Value common to all samples unless set differently: pre-designated temperature. Initialized to NaN.
      """

    # For individual samples: pre-designated temperature.

    Temp[1..60] = {
      1..1 : NaN celsius,
      2..2 : NaN celsius,
      3..60 : NaN celsius
    }
      """
      Sample {$}.
      """

    # If DepDiffFromPeakChl is NaN, will use TempDiffFromPeakChl, Temp, or Dep. SampleAtPeakChl must be True to use this setting.

    DepDiffFromPeakChlCommon = NaN meter # debug: 0 meter
      """
      Value common to all samples unless set differently: depth difference (positive: deeper; negative: shallower) from the peak-chl depth for taking comparison samples. Initialized to NaN.
      """

    # For individual samples: depth difference (positive: deeper; negative: shallower) from the peak-chl depth for taking comparison samples.

    DepDiffFromPeakChl[1..60] = {
      1..1 : NaN meter,
      2..2 : NaN meter,
      3..60 : NaN meter
    }
      """
      Sample {$}.
      """

    # If Dep is NaN, will use TempDiffFromPeakChl, or Temp, or Dep.

    DepCommon = NaN meter
      """
      Value common to all samples unless set differently: Pre-designated depth. Initialized to NaN.
      """

    # For individual samples: pre-designated depth.
    Dep[1..60] = {
      1..1 : NaN meter,
      2..2 : NaN meter,
      3..60 : NaN meter
    }
      """
      Sample {$}.
      """

    # Wait duration for the depth undulation to damp down. Sample 1's is longer than that of the other samples.

    WaitDepUndulation[1..60] = {
      1..1 : 10.0 minute,
      2..60 : 5.0 minute
    }
      """
      Sample {$}.
      """

    # Use caution when changing these.

    UpRate = -0.04 meter_per_second
      """
      Go-up depth rate (Negative depth rate means going up).
      """

    DownRate = 0.2 meter_per_second
      """
      Go-down depth rate (Positive depth rate means going down).
      """

    # You probably do not need to change these.

    IntervalRestartLogs = 24 hour

    UseCANONSampler = Science:CANONSampler.loadAtStartup
      """
      Whether to use CANON Sampler to sample.
      """

    UseESP = Science:ESPComponent.loadAtStartup
      """
      Whether to use ESP to sample.
      """

    CANONSamplerTriggerTimeout = 1 minute
      """
      How long to wait for a CANON Sampler sample to start.
      """

    CANONSamplerTimeout = Science:CANONSampler.sampleTimeout
      """
      How long to wait for a CANON Sampler sample to complete.
      """

    RiseFromTurningDepth = 2.5 meter
      """
      Peak chl on a profile is registered at the beginning of the next yoyo
      profile. In this mission, the peak chl on the descending profile is
      saved when the vehicle has turned onto the next yoyo profile (ascending
      profile) and is at least "RiseFromDeepTurningPoint" away from the
      turning depth.
      """

    DepChangeThreshAttitudeFlip = 2.0 meter
      """
      Depth change threshold for determining vehicle attitude flip.
      """

    YoYoUpPitch = 20 degree
      """
      Vehicle up pitch while performing the YoYo behavior.
      """

    YoYoDownPitch = -20 degree
      """
      Vehicle down pitch while performing the YoYo behavior.
      """

    Turn = 90 degree
      """
      Amount to turn at each leg
      """

    NumOfProfilesSlidingwindow = 100 count
      """
      Length of horizontal sliding window. Picks the highest yoyo-wise chl
      peak (after low-pass filtering by a filter of length
      FilterWidthHorizontal) within this window. Ignore older highs because
      ocean is changing.
      """

    LPWindowLength = 20 count
      """
      Low-pass window length (based on depth sensor sampling interval 0.4
      second) for low-pass filtering.
      """

    MedianFilterLength = 5 count
      """
      Median filter length (only for chlorophyll fluorescence which tends to
      have spikes). The median-filtered signal enters the succeeding low-pass
      filter. If set to 1, then no median filtering, i.e., the raw
      fluorescence signal directly enters the low-pass filter.
      """

    # debug
    #     </Description><Units:count/><Value>1</Value></DefineArg>

    FilterWidthHorizontal = 4 count
      """
      Width of boxcar filter used in horizontal patch detection
      """

    GainProportional = 1 none
      """
      Proportional gain for temperature holding control loop.
      """

    # debug
    #     </Description><Units:none/><Value>2</Value></DefineArg>

    GainIntegral = 0 none
      """
      Integral gain for temperature holding control loop.
      """

    # debug
    #     </Description><Units:none/><Value>0.75</Value></DefineArg>

    GainDerivative = 0 none
      """
      Derivative gain for temperature holding control loop.
      """

    VariationPerMeter = 0.2 reciprocal_meter
      """
      Expected temperature change per meter.
      """

    # debug
    #     </Description><Units:reciprocal_meter/><Value>0.25</Value></DefineArg>
    #     </Description><Units:reciprocal_meter/><Value>0.01</Value></DefineArg>

    BuoyDiveAccel = 0.0025 meter_per_second_squared
      """
      In buoyancy-only mode, maxBuoyDiveAccel needs to be set at least an
      order of magnitude higher than that in Control.cfg.
      """

    BuoyancyNeutral = Control:VerticalControl.buoyancyNeutral
      """
      Buoyancy bladder position while performing the YoYo behavior. Defaults
      to buoyancyNeutral setting in the Config/Control.cfg file. Set to NaN cc
      for active buoyancy
      """

    MassDefault = Control:VerticalControl.massDefault
      """
      Static setting for mass during the mission. Set to NaN mm for active
      mass position
      """
  }

  output {
    # Internal variables that you should not change

    Reverse = 180 degree
      """
      Change in bearing which reverses vehicle direction
      """

    TwoPi = 360 degree
      """
      Applied to stop run-up of angles
      """

    CntRounds = 1 count
      """
      Count of sweep rounds (initilized to 1).
      """

    TrackingCompleted = false
      """
      Initialized to False.
      """

    PatchDetectOn = false
      """
      Mission sets this to true when the patch has been crossed. Initialized
      to False.
      """

    WpDone = true
      """
      Mission sets this to true when the cross-patch waypoint has been
      reached. Initialized to True.
      """

    FlagTurnBack = false
      """
      Flag of turning back from shore. Initialized to False.
      """

    CrossLegToPatchCenterCompleted = false
      """
      Initialized to False.
      """

    CrossLegSearchForPeakStarted = false
      """
      Initialized to False.
      """

    ElapsedSinceStartOrLastSample = 0 hour
      """
      The mission sets this variable to reset the sample timer.
      """

    ElapsedTime = 0 hour
      """
      Only for syslog.
      """

    CartType = -6 count
      """
      Cartridge type. Initialized to -6.
      """

    CartridgeTypeIndividual = -6 count
      """
      Initialized to -6.
      """

    TempSet = NaN kelvin
      """
      Temperature for sampling. Initialized to NaN.
      """

    TempDesignated = NaN kelvin
      """
      Temperature if pre-designated. Initialized to NaN.
      """

    TempIndividual = NaN kelvin
      """
      Initialized to NaN.
      """

    TempDiffPeakChl = NaN kelvin
      """
      Temp difference if setting relative to peak-chl temperature. Initialized
      to NaN.
      """

    TempDiffFromPeakChlIndividual = NaN kelvin
      """
      Initialized to NaN.
      """

    DepthSet = 10.0 meter
      """
      Depth for sampling. Initialized to 10 m.
      """

    DepthDesignated = NaN meter
      """
      Depth if pre-designated. Initialized to NaN.
      """

    DepIndividual = NaN meter
      """
      Initialized to NaN.
      """

    DepDiffPeakChl = NaN meter
      """
      Depth difference (positive: deeper; negative: shallower) from the
      peak-chl depth for taking comparison samples. Initialized to NaN.
      """

    DepDiffFromPeakChlIndividual = NaN meter
      """
      Depth difference (positive: deeper; negative: shallower) from the
      peak-chl depth for taking comparison samples. Initialized to NaN.
      """

    WaitDepthUndulation = 10.0 minute
      """
      Wait duration for the depth undulation to damp down. Initialized to 10
      minutes.
      """

    WaitDepUndulationIndividual = 10.0 minute
      """
      Wait duration for the depth undulation to damp down. Initialized to 10
      minutes.
      """

    SampleCountIncreased = true
      """
      Sample count is increased.
      """

    SampleOptionsSet = false
      """
      Sample option settings already set. Initialized to false.
      """

    SampleCompleted = false
      """
      Sampling completed. Initialized to false.
      """

    StoppedForBeingOutsideOfPolygon = false
      """
      Mission stopped because the vehicle is outside of the polygon.
      Initialized to False.
      """

    StoppedForNaNPatchPeak = false
      """
      Mission stopped because of no firing for too long. Initialized to false.
      """

    StoppedForNoFiringForTooLong = false
      """
      Mission stopped because of no firing for too long. Initialized to false.
      """

    StoppedForNoFiringChlBelowTriggerThresh = false
      """
      Mission stopped because of no firing because the peak chl is lower than
      TriggerThresholdChl. Initialized to false.
      """

    ElapsedSinceStartOrLastDistCheck = 0 hour
      """
      The mission sets this variable to reset the timer for checking distance
      to shore and polygon sides.
      """

    PatchPeakChl = NaN microgram_per_liter

    PatchPeakDepth = NaN meter

    PatchPeakLatitude = NaN degree

    PatchPeakLongitude = NaN degree

    PatchPeakDistance = 0 meter

    DepthLogged = 0.0 meter

    TempLogged = 0.0 celsius

    ChlLogged = 0.0 microgram_per_liter

    SamplingPartStartCommsCompleted = false
      """
      Initialized to false.
      """

    StartVerticalManeuver = false
      """
      Start vertical maneuver and sampling (initialized to false).
      """

    FlagTempSet = false
      """
      Flag of target temperature having been set. Initialized to false.
      """

    FlagTargetDepthSet = false
      """
      Flag of target depth having been set. Initialized to false.
      """

    FlagGoUp = false
      """
      Go-up flag (set to true when going up. Initialized to false).
      """

    FlagGoDown = false
      """
      Go-down flag (set to true when going down. Initialized to false).
      """

    FlagInitialDiveCompleted = false
      """
      Flag of initial dive completed. Initialized to false.
      """

    FlagPeakChlDepthSet = false
      """
      Flag of peak-chl depth having been set (set to true when the chl-peak
      depth has been set. Initialized to false).
      """

    FlagPeakChlTempSet = false
      """
      Flag of peak-chl temperature having been set (set to true when the
      chl-peak temperature has been set. Initialized to false).
      """

    EnableSettingPeakDepth = true
      """
      Enables setting peak-chl depth. Initialized to true.
      """

    FlagFirstDive = true
      """
      Flag of first dive to find the peak-chl (true only for the first dive;
      false afterwards).
      """

    FlagSamplingOngoing = false
      """
      Flag of water sampling in process (initialized to false).
      """

    PeakChlDepthSet = 10.0 meter
      """
      Peak-chl depth detected on a dive. Initialized to 10 meters.
      """

    PeakChlTemperatureSet = NaN kelvin
      """
      Peak-chl temperature detected on a dive, and set for chl-peak holding.
      Initialized to NaN.
      """

    PeakChlSet = 0.0 microgram_per_liter
      """
      Peak-chl value detected on a dive.
      """

    SyslogGoUp = false
      """
      Flag of logging "GoUp" in syslog (initialized to false).
      """

    SyslogGoDown = false
      """
      Flag of logging "GoDown" in syslog (initialized to false).
      """

    CntSamples = 1 count
      """
      Count of water samples (initilized to 1).
      """

    SendDataAllCompleted = false
      """
      Initialized to false.
      """

    CallSendData = true
      """
      Initialized to true.
      """

    TouchedDeepBoundSampler = false
      """
      Initialized to false.
      """

    TouchedDeepBoundSamplerFlagSet = false
      """
      Initialized to false.
      """

    ModemID = 1 enum
      """
      Modem ID. Set to modemId1 or modemId2. Initialized to 1.
      """
  }

  # Missions should almost always start with a timeout and a NeedComms aggregate. Drift missions will not use NeedComms.

  timeout duration=MissionTimeout

  # Missions should almost always start with standard safety envelopes

  behavior Sample:AbortSample {
    run in parallel
  }

  insert Insert/StandardEnvelopes.tl

  assign in sequence StandardEnvelopes:MinAltitude = MinAltitude

  assign in sequence StandardEnvelopes:MaxDepth = MaxDepth

  assign in sequence StandardEnvelopes:MinOffshore = MinOffshore

  insert Insert/AbortDrift.tl {
    redefineArg AcousticTimeout = AcousticTrackingTimeout
  }

  insert Insert/SampleAtDepth.tl {
    redefineArg MaxWaitNotReachingDepth = MaxWaitNotAchievingDepth
  }

  insert Insert/Science.tl {
    redefineArg PeakDetectChlActive = true
    redefineArg LowPassWindowLength = LPWindowLength
    redefineArg MedianFilterLen = MedianFilterLength
    redefineArg PeakShallowBound = ShallowBoundChl
    redefineArg PeakDeepBound = DeepBoundChl
    redefineArg DepChangeThreshForAttitudeFlip = DepChangeThreshAttitudeFlip
  }

  behavior Guidance:WaterDepthEnvelope {
    run in parallel

    set minWaterDepth = MinWaterDepth
  }

  insert id="NeedComms" Insert/NeedComms.tl

  assign in parallel Control:VerticalControl.maxBuoyDiveAccel = BuoyDiveAccel

  # Many missions will keep mass position fixed at the default. This mission allows the buoyancy volume to change to track the chlorophyll peak while drifting.

  behavior Guidance:Pitch {
    run in parallel

    set massPosition = MassDefault
  }

  behavior Guidance:AltitudeEnvelope {
    """
    Another altitude envelope for the YoYo behavior. This envelope
    should fall within the limits of the standard safety envelopes in
    Insert/StandardEnvelopes.tl in order to avoid commanding high pitch
    angles for bottom-terminated YoYos.
    """

    run in parallel

    set minAltitude = YoYoMinAltitude
  }

  # Automatically restart logs

  aggregate CycleLogs {
    run in parallel

    aggregate {
      run in sequence

      behavior Guidance:Wait {
        run in sequence

        set duration = IntervalRestartLogs
      }

      syslog important "Restarting logs."

      behavior Guidance:Execute {
        run in sequence

        set command = "restart logs"
      }
    }
  }

  aggregate TrackPatch {
    run in sequence

    behavior Guidance:Buoyancy {
      run in parallel

      set position = BuoyancyNeutral
    }

    behavior Guidance:SetSpeed {
      run in parallel

      set speed = SpeedTransit
    }

    aggregate SyslogWpMaxDistanceReached {
      run when ( called )

      aggregate SyslogWpMaxDistanceReachedPatchPeakIsNaN {
        run in sequence

        break if (
          PatchPeakChl >= 0.0 microgram_per_liter
          or StoppedForNaNPatchPeak
        )

        syslog important "WpMaxDistance reached. Patch peak value is NaN. Stopping mission."

        behavior Guidance:Execute {
          run in sequence

          set command = "stop"
        }

        assign in sequence StoppedForNaNPatchPeak = true
      }

      aggregate SyslogWpMaxDistanceReachedChl {
        run in sequence

        break if (
          not ( PatchPeakChl >= 0.0 microgram_per_liter )
        )

        syslog important "WpMaxDistance reached. Patch value is " + PatchPeakChl~microgram_per_liter
             + "at " + PatchPeakLatitude~degree + "," + PatchPeakLongitude~degree + ", distance = "
             + PatchPeakDistance~meter
      }
    }

    aggregate SyslogTurnBack {
      run when ( called )

      aggregate SyslogTurnBackFromShoreChl {
        run in sequence

        break if (
          not ( Universal:distance_from_shore <= ( MinOffshore + MarginMinOffshore ) )
        )

        syslog important "Latitude = " + Universal:latitude~degree + ", longitude = "
             + Universal:longitude~degree + ". Turn back from shore because distance_from_shore ("
             + Universal:distance_from_shore~meter + ") is less than OffshoreDistanceTurnBack ("
             + MinOffshore~meter + "+" + MarginMinOffshore~meter + "). Patch value is "
             + PatchPeakChl~microgram_per_liter + "at " + PatchPeakLatitude~degree + ","
             + PatchPeakLongitude~degree + ", distance = " + PatchPeakDistance~meter
      }

      aggregate SyslogTurnBackFromWallChl {
        run in sequence

        break if (
          not (
            Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
            and ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides <= MinDistFromPolygonSides )
          )
        )

        syslog important "Latitude = " + Universal:latitude~degree + ", longitude = "
             + Universal:longitude~degree
             + ". Turn back from wall because shortest_distance_from_polygon_sides ("
             + Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides~meter
             + ") to side "
             + Derivation:ShortestDistanceToPolygonSidesCalculator.side_shortest_distance~count
             + " is less than MinDistFromPolygonSides (" + MinDistFromPolygonSides~meter
             + "). Patch value is " + PatchPeakChl~microgram_per_liter + "at " + PatchPeakLatitude~degree
             + "," + PatchPeakLongitude~degree + ", distance = " + PatchPeakDistance~meter
      }
    }

    aggregate TransitToPatchTrackingStartLocation {
      run in sequence

      break if (
        isNaN ( LatPatchTrackingStart )
        or ( isNaN ( LonPatchTrackingStart ) )
      )

      assign in sequence NeedComms:DiveInterval = NeedCommsTimeInTransit

      behavior Guidance:DepthEnvelope {
        run in parallel

        set minDepth = PatchTrackingYoYoMinDepth
        set maxDepth = PatchTrackingYoYoMaxDepth
        set downPitch = YoYoDownPitch
        set upPitch = YoYoUpPitch
      }

      behavior Guidance:AltitudeEnvelope {
        """
        Another altitude envelope for the YoYo behavior. This
        envelope should fall within the limits of the standard
        safety envelopes in Insert/StandardEnvelopes.tl in order to
        avoid commanding high pitch angles for bottom-terminated
        YoYos.
        """

        run in parallel

        set minAltitude = YoYoMinAltitude
      }

      behavior Guidance:YoYo {
        run in parallel

        set downPitch = YoYoDownPitch
        set upPitch = YoYoUpPitch
      }

      behavior Guidance:Waypoint {
        run in sequence

        set latitude = LatPatchTrackingStart
        set longitude = LonPatchTrackingStart
      }
    }

    aggregate TrackingStart {
      run in sequence

      call id="TrackingStartComms" refId="NeedComms"

      assign in sequence ElapsedSinceStartOrLastDistCheck = 0 hour
    }

    aggregate PatchTracking {
      run in sequence repeat=PatchTrackingRounds

      break if ( TrackingCompleted )

      assign in sequence NeedComms:DiveInterval = NeedCommsTimePatchTracking + NeedCommsTimeMarginPatchTracking

      assign in sequence CrossLegToPatchCenterCompleted = false

      assign in sequence CrossLegSearchForPeakStarted = false

      behavior Guidance:DepthEnvelope {
        run in parallel

        set minDepth = PatchTrackingYoYoMinDepth
        set maxDepth = PatchTrackingYoYoMaxDepth
        set downPitch = YoYoDownPitch
        set upPitch = YoYoUpPitch
      }

      behavior Guidance:AltitudeEnvelope {
        """
        Another altitude envelope for the YoYo behavior. This
        envelope should fall within the limits of the standard
        safety envelopes in Insert/StandardEnvelopes.tl in order to
        avoid commanding high pitch angles for bottom-terminated
        YoYos.
        """

        run in parallel

        set minAltitude = YoYoMinAltitude
      }

      behavior Guidance:YoYo {
        run in parallel

        set downPitch = YoYoDownPitch
        set upPitch = YoYoUpPitch
      }

      aggregate OutsideOfPolygon {
        run in parallel

        break if (
          not ( Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup )
          or (
            Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
            and Derivation:ShortestDistanceToPolygonSidesCalculator.inside_polygon
          )
          or StoppedForBeingOutsideOfPolygon
        )

        syslog important "Latitude = " + Universal:latitude~degree + ", longitude = "
             + Universal:longitude~degree + ". The vehicle is outside of the polygon. Stopping mission."

        behavior Guidance:Execute {
          run in sequence

          set command = "stop"
        }

        assign in sequence StoppedForBeingOutsideOfPolygon = true
      }

      aggregate ChlPatchDetection {
        run when ( PatchDetectOn )

        behavior Trigger:PeakDetectHorizontal id="PatchTrackTrigger" {
          run in sequence

          break if ( WpDone )

          set patchTracking = true
          set detectFrom = Science:PeakChl
          set detectTrough = false
          set depthFrom = Science:PeakChlDepth
          set latitudeFrom = Science:PeakChlLatitude
          set longitudeFrom = Science:PeakChlLongitude
          set beginThreshold = BeginThresholdChl
          set offPeakFraction = OffPeakFraction
          set filterWidth = FilterWidthHorizontal
          set numProfilesSlidingwindow = NumOfProfilesSlidingwindow
          set detectTimeout = DetectionTimeout
          outputArg PatchPeakChl = peakDetect
          outputArg PatchPeakDepth = peakDepth
          outputArg PatchPeakLatitude = peakLatitude
          outputArg PatchPeakLongitude = peakLongitude
          outputArg PatchPeakDistance = peakDistance
        }

        syslog important "Peak found before WpMaxDistance is reached. Patch value is "
             + PatchPeakChl~microgram_per_liter + "at " + PatchPeakLatitude~degree + ","
             + PatchPeakLongitude~degree + ", distance = " + PatchPeakDistance~meter

        sendData service=express (
          PatchPeakChl,
          PatchPeakDepth,
          PatchPeakLatitude,
          PatchPeakLongitude
        )

        assign in sequence PatchDetectOn = false

        assign in sequence WpDone = true
      }

      aggregate CrossLegToPatchCenter {
        """
        This is a short run back to patch center.
        """

        run in sequence

        assign in sequence WpBearing = ( WpBearing + Reverse ) % TwoPi

        syslog important "Bearing for CrossLeg: " + WpBearing~degree

        behavior Guidance:Waypoint id="CrossWp" {
          run in sequence

          timeout duration=WpTimeout

          set distanceDelta = PatchPeakDistance
          set distanceDeltaBearing = WpBearing
          set waterFrame = true
        }

        assign in sequence PatchDetectOn = true

        assign in sequence WpDone = false

        assign id="PresetValueBeforeCrossLegSearchForPeak" in sequence PatchPeakDistance = 0 meter

        assign in sequence CrossLegToPatchCenterCompleted = true
      }

      aggregate SurfaceAfterCrossLegToPatchCenter {
        run when (
          CntRounds % NumRoundsBtnCrossLegSurfacings == 0 count
          and CrossLegToPatchCenterCompleted
          and ( not ( CrossLegSearchForPeakStarted ) )
          or (
            elapsed ( Universal:time_fix ) > NeedCommsTimePatchTracking
            and CrossLegToPatchCenterCompleted
            and ( not ( CrossLegSearchForPeakStarted ) )
          )
        )

        break if (
          CntRounds % PatchTrackingRounds == 0 count
        )

        call id="CrossLegComms" refId="NeedComms"
      }

      aggregate SwitchToSamplingAfterCrossLegToPatchCenter {
        run in sequence

        break if (
          not (
            CntRounds % PatchTrackingRounds == 0 count
            and CrossLegToPatchCenterCompleted
          )
        )

        syslog important "Desired rounds of crosslegs completed and back to patch center. Switch to sampling."

        assign in sequence TrackingCompleted = true
      }

      aggregate CrossLegSearchForPeak {
        """
        This is a long run to the edge of the patch to search for
        the peak.
        """

        run in sequence

        break if (
          WpDone
          or ( PatchDetectOn == false )
        )

        assign in sequence CrossLegSearchForPeakStarted = true

        assign in sequence FlagTurnBack = false

        syslog important "Bearing for continued CrossLeg: " + WpBearing~degree

        aggregate CrossLegSearchForPeakNormal {
          run in sequence

          break if (
            Universal:distance_from_shore <= ( MinOffshore + MarginMinOffshore )
            and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
            or (
              Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
              and ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides <= MinDistFromPolygonSides )
              and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
            )
          )

          behavior Guidance:Waypoint id="CrossPeakWp" {
            run in sequence

            timeout duration=WpTimeout

            set distanceDelta = WpMaxDistance
            set distanceDeltaBearing = WpBearing
            set waterFrame = true
          }

          call id="SyslogWpMaxDistanceReachedOnCrossLeg" refId="SyslogWpMaxDistanceReached"

          assign in sequence PatchDetectOn = false

          assign in sequence WpDone = true
        }

        aggregate CrossLegSearchForPeakTurnBack {
          run in sequence

          break if (
            FlagTurnBack
            or (
              not (
                Universal:distance_from_shore <= ( MinOffshore + MarginMinOffshore )
                and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
                or (
                  Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
                  and ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides <= MinDistFromPolygonSides )
                  and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
                )
              )
            )
          )

          call id="SyslogTurnBackOnCrossLeg" refId="SyslogTurnBack"

          assign in sequence ElapsedSinceStartOrLastDistCheck = 0 hour

          assign in sequence PatchDetectOn = false

          assign in sequence WpDone = true

          assign in sequence FlagTurnBack = true
        }
      }

      aggregate InLeg {
        run in sequence

        assign in sequence WpBearing = ( WpBearing + Reverse ) % TwoPi

        syslog important "Bearing for InLeg: " + WpBearing~degree

        behavior Guidance:Waypoint id="InLegWp" {
          """
          Simply drive back towards the patch center
          """

          run in sequence

          timeout duration=WpTimeout

          set distanceDelta = PatchPeakDistance
          set distanceDeltaBearing = WpBearing
          set waterFrame = true
        }

        assign in sequence WpBearing = ( WpBearing - Turn ) % TwoPi

        assign id="FlipSignOfTurnAngle" in sequence Turn = ( Turn + Reverse ) % TwoPi

        syslog important "Bearing for OutLeg: " + WpBearing~degree

        assign in sequence PatchDetectOn = true

        assign in sequence WpDone = false

        assign id="PresetValueBeforeOutLeg" in sequence PatchPeakDistance = 0 meter
      }

      aggregate OutLeg {
        """
        Drive outward until edge of patch is detected.
        """

        run in sequence

        break if (
          WpDone
          or ( PatchDetectOn == false )
        )

        assign in sequence FlagTurnBack = false

        assign in sequence CntRounds = CntRounds + 1 count

        aggregate OutLegNormal {
          run in sequence

          break if (
            Universal:distance_from_shore <= ( MinOffshore + MarginMinOffshore )
            and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
            or (
              Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
              and ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides <= MinDistFromPolygonSides )
              and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
            )
          )

          behavior Guidance:Waypoint id="OutLegWp" {
            run in sequence

            timeout duration=WpTimeout

            set distanceDelta = WpMaxDistance
            set distanceDeltaBearing = WpBearing
            set waterFrame = true
          }

          call id="SyslogWpMaxDistanceReachedOnOutLeg" refId="SyslogWpMaxDistanceReached"

          assign id="AssignPatchDetectOffInOutLeg" in sequence PatchDetectOn = false

          assign id="AssignWpDoneInOutLeg" in sequence WpDone = true
        }

        aggregate OutLegTurnBack {
          run in sequence

          break if (
            FlagTurnBack
            or (
              not (
                Universal:distance_from_shore <= ( MinOffshore + MarginMinOffshore )
                and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
                or (
                  Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
                  and ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides <= MinDistFromPolygonSides )
                  and ( elapsed ( ElapsedSinceStartOrLastDistCheck ) > WaitAfterBouncing )
                )
              )
            )
          )

          call id="SyslogTurnBackOnOutLeg" refId="SyslogTurnBack"

          assign in sequence ElapsedSinceStartOrLastDistCheck = 0 hour

          assign in sequence PatchDetectOn = false

          assign in sequence WpDone = true

          assign in sequence FlagTurnBack = true
        }
      }
    }
  }

  aggregate TriggerSampling {
    run when ( called )

    aggregate TriggerESP {
      run in sequence

      break if ( not ( UseESP ) )

      assign in sequence DepthLogged = Universal:depth

      assign in sequence TempLogged = Universal:sea_water_temperature

      assign in sequence ChlLogged = Universal:mass_concentration_of_chlorophyll_in_sea_water

      syslog important "Trigger sampling. DepthLogged, TempLogged, ChlLogged = " + DepthLogged~meter
           + ", " + TempLogged~celsius + ", " + ChlLogged~microgram_per_liter + "."

      behavior Science:ESPCartridgeSelect {
        run in sequence

        timeout duration=P1M

        set cartridgeType = CartType
      }

      readDatum {
        Science:ESPComponent.sampling
      }

      syslog important "Wait for ESP sampling to complete."

      readDatum {
        Science:ESPComponent.sample_number
      }
    }

    aggregate TriggerCANON {
      run in sequence

      break if ( not ( UseCANONSampler ) )

      assign in sequence DepthLogged = Universal:depth

      assign in sequence TempLogged = Universal:sea_water_temperature

      assign in sequence ChlLogged = Universal:mass_concentration_of_chlorophyll_in_sea_water

      syslog important "Trigger sampling. DepthLogged, TempLogged, ChlLogged = " + DepthLogged~meter
           + ", " + TempLogged~celsius + ", " + ChlLogged~microgram_per_liter + "."

      assign in parallel Science:CANONSampler.sampleTimeout = CANONSamplerTimeout

      assign in parallel Science:CANONSampler.rotateOnly = CANONSamplerRotateOnly

      readDatum id="TriggerCANONSampler" {
        timeout duration=CANONSamplerTriggerTimeout {
          syslog important "Timed out triggering CANONSampler. Stopping mission."

          behavior Guidance:Execute {
            run in sequence

            set command = "stop"
          }
        }

        Science:CANONSampler.sampling
      }

      readDatum {
        timeout duration=CANONSamplerTimeout {
          syslog important "Timed out sampling with CANONSampler. Stopping mission."

          behavior Guidance:Execute {
            run in sequence

            set command = "stop"
          }
        }

        Science:CANONSampler.sample_number
      }
    }
  }

  aggregate DampDown {
    run when ( called )

    syslog important "Wait " + WaitDepthUndulation~minute
         + " for the depth undulation to damp down."

    behavior Guidance:Wait {
      run in sequence

      set duration = WaitDepthUndulation
    }
  }

  aggregate DoSendDirect {
    run when ( called )

    syslog important "ModemID = " + ModemID~enum

    behavior Sensor:SendDirect {
      run in sequence

      set destType = "modem"
      set destId = ModemID
      set destName = "_.LRAUVcntSamples"
      set value = CntSamples

      set unit = "count"
    }

    syslog important "TrackAndSample.CntSamples = " + CntSamples~count

    aggregate SendDirectESP {
      run in sequence

      break if ( not ( UseESP ) )

      behavior Sensor:SendDirect {
        run in sequence

        set destType = "modem"
        set destId = ModemID
        set destName = "_.ESPsampleNumber"
        set value = Science:ESPComponent.sample_number
        set unit = "count"
      }

      behavior Sensor:SendDirect {
        run in sequence

        set destType = "modem"
        set destId = ModemID
        set destName = "_.ESPcartridgeType"
        set value = Science:ESPComponent.cartridge
        set unit = "count"
      }

      behavior Sensor:SendDirect {
        run in sequence

        set destType = "modem"
        set destId = ModemID
        set destName = "_.ESPsampleVolume"
        set value = Science:ESPComponent.sampleVolume
        set unit = "milliliter"
      }

      syslog important "Science:ESPComponent.sample_number = "
           + Science:ESPComponent.sample_number~count

      syslog important "Science:ESPComponent.cartridge = " + Science:ESPComponent.cartridge~count

      syslog important "Science:ESPComponent.sampleVolume = "
           + Science:ESPComponent.sampleVolume~milliliter
    }

    aggregate SendDirectCANON {
      run in sequence

      break if ( not ( UseCANONSampler ) )

      behavior Sensor:SendDirect {
        run in sequence

        set destType = "modem"
        set destId = ModemID
        set destName = "_.CANONsampleNumber"
        set value = Science:CANONSampler.sample_number
        set unit = "count"
      }

      syslog important "Science:CANONSampler.sample_number = "
           + Science:CANONSampler.sample_number~count
    }

    behavior Sensor:SendDirect {
      run in sequence

      set destType = "modem"
      set destId = ModemID
      set destName = "_.sampleDepth"
      set value = Universal:depth
      set unit = "meter"
    }

    behavior Sensor:SendDirect {
      run in sequence

      set destType = "modem"
      set destId = ModemID
      set destName = "_.sampleTemperature"
      set value = Universal:sea_water_temperature
      set unit = "celsius"
    }

    behavior Sensor:SendDirect {
      run in sequence

      set destType = "modem"
      set destId = ModemID
      set destName = "_.sampleChlorophyll"
      set value = Universal:mass_concentration_of_chlorophyll_in_sea_water
      set unit = "microgram_per_liter"
    }

    syslog important "Universal:depth = " + Universal:depth~meter

    syslog important "Universal:sea_water_temperature = " + Universal:sea_water_temperature~celsius

    syslog important "Universal:mass_concentration_of_chlorophyll_in_sea_water = "
         + Universal:mass_concentration_of_chlorophyll_in_sea_water~microgram_per_liter
  }

  aggregate SendData {
    run when ( called )

    aggregate SendTo1Modem {
      run in sequence

      break if ( SendDataToMultipleModems )

      assign in sequence ModemID = modemId1

      syslog important "Set ModemID to " + ModemID~enum + "."

      call refId="DoSendDirect"
    }

    aggregate SendTo2Modems {
      run in sequence

      break if ( not ( SendDataToMultipleModems ) )

      assign in sequence ModemID = modemId1

      syslog important "Set ModemID to " + ModemID~enum + "."

      call refId="DoSendDirect"

      assign in sequence ModemID = modemId2

      syslog important "Set ModemID to " + ModemID~enum + "."

      call refId="DoSendDirect"
    }

    assign in sequence SendDataAllCompleted = true
  }

  aggregate SetSampleOptions {
    run when ( called )

    aggregate SettingCartridgeTypeIndividual {
      run in sequence

      break if (
        isNaN ( CartridgeTypeIndividual )
        or ( not ( UseESP ) )
      )

      assign in sequence CartType = CartridgeTypeIndividual
    }

    aggregate SettingCartridgeTypeCommon {
      run in sequence

      break if (
        not ( isNaN ( CartridgeTypeIndividual ) )
        or ( not ( UseESP ) )
      )

      assign in sequence CartType = CartridgeTypeCommon
    }

    aggregate SettingTempDiffFromPeakChlIndividual {
      run in sequence

      break if ( isNaN ( TempDiffFromPeakChlIndividual ) )

      assign in sequence TempDiffPeakChl = TempDiffFromPeakChlIndividual
    }

    aggregate SettingTempDiffFromPeakChlCommon {
      run in sequence

      break if (
        not ( isNaN ( TempDiffFromPeakChlIndividual ) )
      )

      assign in sequence TempDiffPeakChl = TempDiffFromPeakChlCommon
    }

    aggregate SettingDepDiffFromPeakChlIndividual {
      run in sequence

      break if ( isNaN ( DepDiffFromPeakChlIndividual ) )

      assign in sequence DepDiffPeakChl = DepDiffFromPeakChlIndividual
    }

    aggregate SettingDepDiffFromPeakChlCommon {
      run in sequence

      break if (
        not ( isNaN ( DepDiffFromPeakChlIndividual ) )
      )

      assign in sequence DepDiffPeakChl = DepDiffFromPeakChlCommon
    }

    aggregate SettingDepIndividual {
      run in sequence

      break if ( isNaN ( DepIndividual ) )

      assign in sequence DepthDesignated = DepIndividual
    }

    aggregate SettingDepCommon {
      run in sequence

      break if ( not ( isNaN ( DepIndividual ) ) )

      assign in sequence DepthDesignated = DepCommon
    }

    aggregate SettingTempIndividual {
      run in sequence

      break if ( isNaN ( TempIndividual ) )

      assign in sequence TempDesignated = TempIndividual
    }

    aggregate SettingTempCommon {
      run in sequence

      break if ( not ( isNaN ( TempIndividual ) ) )

      assign in sequence TempDesignated = TempCommon
    }

    assign in sequence WaitDepthUndulation = WaitDepUndulationIndividual

    syslog important "Set CartType (if ESP), TempDiffPeakChl, DepDiffPeakChl, TempDesignated, DepthDesignated, WaitDepthUndulation to "
         + CartType~count + ", " + TempDiffPeakChl~kelvin + ", " + DepDiffPeakChl~meter + ", "
         + TempDesignated~celsius + ", " + DepthDesignated~meter + ", " + WaitDepthUndulation~minute
         + "."
  }

  aggregate SamplingPartStart {
    run in sequence

    break if ( not ( TrackingCompleted ) )

    call id="SamplingPartStartComms" refId="NeedComms"

    aggregate SamplingPartStartSetFlagGoDown {
      run in sequence

      break if (
        not ( SampleAtPeakChl )
        or (
          isNaN ( TempDiffFromPeakChl[1] )
          and ( isNaN ( TempDiffFromPeakChlCommon ) )
          and ( isNaN ( DepDiffFromPeakChl[1] ) )
          and ( isNaN ( DepDiffFromPeakChlCommon ) )
        )
      )

      assign in sequence FlagGoDown = true
    }

    assign in sequence SamplingPartStartCommsCompleted = true

    assign in sequence ElapsedSinceStartOrLastSample = 0 hour

    assign in sequence StartVerticalManeuver = true
  }

  aggregate SetSpeedRudderAngleInitialDive {
    run when (
      StartVerticalManeuver
      and ( not ( FlagInitialDiveCompleted ) )
      and ( CntSamples == 1 count )
    )

    break if ( not ( SampleAtPeakChl ) )

    behavior Guidance:SetSpeed {
      run in parallel

      set speed = SpeedInitialDive
    }

    behavior Guidance:Point {
      run in parallel

      set rudderAngle = RudderAngleInitialDive
    }

    behavior Guidance:Wait {
      run in sequence

      set duration = InitialDiveDuration
    }

    assign in sequence FlagInitialDiveCompleted = true
  }

  aggregate FindPeakChlVertical {
    run in sequence

    break if (
      not ( StartVerticalManeuver )
      or ( CntSamples > NumSamplers )
    )

    aggregate FindPeak {
      run while ( SampleAtPeakChl )

      aggregate FindPeakSpiralMode {
        run while ( SpeedSampling > 0.0 meter_per_second )

        behavior Guidance:SetSpeed {
          run in parallel

          set speed = SpeedSampling
        }

        behavior Guidance:Point {
          run in parallel

          set rudderAngle = RudderAngleDonutSampling
        }

        behavior Guidance:Buoyancy {
          run in parallel

          set position = BuoyancyNeutral
        }
      }

      aggregate FindPeakDriftMode {
        run while (
          not ( SpeedSampling > 0.0 meter_per_second )
        )

        behavior Guidance:SetSpeed {
          run in parallel

          set speed = 0.0 meter_per_second
        }

        behavior Guidance:Point {
          run in parallel

          set rudderAngle = 0.0 degree
        }
      }

      aggregate SetDepthRateGoDown {
        run while (
          FlagGoDown
          and StartVerticalManeuver
        )

        behavior Guidance:Pitch {
          run in parallel

          set depthRate = DownRate
        }
      }

      aggregate SetDepthRateGoUp {
        run while (
          FlagGoUp
          and StartVerticalManeuver
        )

        behavior Guidance:Pitch {
          run in parallel

          set depthRate = UpRate
        }
      }

      aggregate LogGoDown {
        run when (
          FlagGoDown
          and ( not ( SyslogGoDown ) )
          and StartVerticalManeuver
        )

        assign in sequence DepthLogged = Universal:depth

        syslog important "Go down from " + DepthLogged~meter

        assign in sequence SyslogGoDown = true
      }

      aggregate SetFlagGoUp {
        run when (
          isNaN ( TempDesignated )
          and ( isNaN ( DepthDesignated ) )
          and SampleAtPeakChl
          and FlagFirstDive
          and ( Universal:depth > ( DeepBoundChl + VertMargin ) )
          and ( not ( FlagGoUp ) )
          and StartVerticalManeuver
        )

        assign in sequence FlagGoUp = true

        assign in sequence FlagGoDown = false

        assign in sequence SyslogGoDown = false
      }

      aggregate LogGoUp {
        run when (
          FlagGoUp
          and ( not ( SyslogGoUp ) )
          and StartVerticalManeuver
        )

        assign in sequence DepthLogged = Universal:depth

        syslog important "Go up from " + DepthLogged~meter

        assign in sequence SyslogGoUp = true
      }

      aggregate SetChlPeakTempDepth {
        run when (
          FlagFirstDive
          and SampleAtPeakChl
          and EnableSettingPeakDepth
          and ( not ( FlagPeakChlDepthSet ) )
          and FlagGoUp
          and ( Universal:depth < ( DeepBoundChl + VertMargin - RiseFromTurningDepth ) )
          and ( Science:PeakChlDepth > ShallowBoundChl )
          and StartVerticalManeuver
        )

        assign in sequence PeakChlDepthSet = Science:PeakChlDepth

        assign in sequence PeakChlTemperatureSet = Science:PeakChlTemperature

        assign in sequence PeakChlSet = Science:PeakChl

        assign in sequence FlagFirstDive = false

        assign in sequence FlagPeakChlDepthSet = true

        assign in sequence DepthLogged = Universal:depth

        assign in sequence ChlLogged = Universal:mass_concentration_of_chlorophyll_in_sea_water

        assign in sequence FlagGoUp = false

        assign in sequence FlagGoDown = false

        assign in sequence SyslogGoUp = false

        assign in sequence SyslogGoDown = false

        syslog important "Set peak-chl depth and temp. DepthLogged, ChlLogged, PeakChlDepthSet, PeakChlTemperatureSet, PeakChlSet = "
             + DepthLogged~meter + ", " + ChlLogged~microgram_per_liter + ", " + PeakChlDepthSet~meter + ", "
             + PeakChlTemperatureSet~celsius + ", " + PeakChlSet~microgram_per_liter

        assign in sequence FlagPeakChlTempSet = true
      }
    }
  }

  aggregate IsothermOrDepthHolding {
    run in parallel

    break if ( CntSamples > NumSamplers )

    aggregate HoldTempInDonutMode {
      run while (
        FlagTempSet
        and StartVerticalManeuver
        and ( not ( TouchedDeepBoundSampler ) )
        and ( not ( FlagGoUp ) )
        and ( not ( FlagGoDown ) )
        and ( SpeedSampling > 0.0 meter_per_second )
        and (
          not ( Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup )
          or (
            Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
            and (
              not ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides >= 0.0 meter )
              or ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides > MinDistFromPolygonSides )
            )
          )
        )
        and ( Universal:distance_from_shore > ( MinOffshore + MarginMinOffshore ) )
      )

      break if ( FlagTargetDepthSet )

      behavior Guidance:DepthServo {
        run in parallel

        set input = Universal:sea_water_temperature
        set holdValue = TempSet
        set proportionalGain = GainProportional
        set integralGain = GainIntegral
        set derivativeGain = GainDerivative
        set changePerMeter = VariationPerMeter
      }

      behavior Guidance:SetSpeed {
        run in parallel

        set speed = SpeedSampling
      }

      behavior Guidance:Point {
        run in parallel

        set rudderAngle = RudderAngleDonutSampling
      }

      behavior Guidance:Buoyancy {
        run in parallel

        set position = BuoyancyNeutral
      }
    }

    aggregate HoldTempInDriftMode {
      run while (
        FlagTempSet
        and StartVerticalManeuver
        and ( not ( TouchedDeepBoundSampler ) )
        and ( not ( FlagGoUp ) )
        and ( not ( FlagGoDown ) )
        and ( not ( SpeedSampling > 0.0 meter_per_second ) )
        and (
          not ( Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup )
          or (
            Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
            and (
              not ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides >= 0.0 meter )
              or ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides > MinDistFromPolygonSides )
            )
          )
        )
        and ( Universal:distance_from_shore > ( MinOffshore + MarginMinOffshore ) )
      )

      break if ( FlagTargetDepthSet )

      behavior Guidance:DepthServo {
        run in parallel

        set input = Universal:sea_water_temperature
        set holdValue = TempSet
        set proportionalGain = GainProportional
        set integralGain = GainIntegral
        set derivativeGain = GainDerivative
        set changePerMeter = VariationPerMeter
      }

      behavior Guidance:SetSpeed {
        run in parallel

        set speed = 0.0 meter_per_second
      }

      behavior Guidance:Point {
        run in parallel

        set rudderAngle = 0.0 degree
      }
    }

    aggregate HoldDepthInDonutMode {
      run while (
        FlagTargetDepthSet
        and StartVerticalManeuver
        and ( not ( TouchedDeepBoundSampler ) )
        and ( not ( FlagGoUp ) )
        and ( not ( FlagGoDown ) )
        and ( SpeedSampling > 0.0 meter_per_second )
        and (
          not ( Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup )
          or (
            Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
            and (
              not ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides >= 0.0 meter )
              or ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides > MinDistFromPolygonSides )
            )
          )
        )
        and ( Universal:distance_from_shore > ( MinOffshore + MarginMinOffshore ) )
      )

      break if ( FlagTempSet )

      behavior Guidance:SetSpeed {
        run in parallel

        set speed = SpeedSampling
      }

      behavior Guidance:Point {
        run in parallel

        set rudderAngle = RudderAngleDonutSampling
      }

      behavior Guidance:Buoyancy {
        run in parallel

        set position = BuoyancyNeutral
      }
    }

    aggregate HoldDepthInDriftMode {
      run while (
        FlagTargetDepthSet
        and StartVerticalManeuver
        and ( not ( TouchedDeepBoundSampler ) )
        and ( not ( FlagGoUp ) )
        and ( not ( FlagGoDown ) )
        and ( not ( SpeedSampling > 0.0 meter_per_second ) )
        and (
          not ( Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup )
          or (
            Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
            and (
              not ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides >= 0.0 meter )
              or ( Derivation:ShortestDistanceToPolygonSidesCalculator.shortest_distance_to_polygon_sides > MinDistFromPolygonSides )
            )
          )
        )
        and ( Universal:distance_from_shore > ( MinOffshore + MarginMinOffshore ) )
      )

      break if ( FlagTempSet )

      behavior Guidance:SetSpeed {
        run in parallel

        set speed = 0.0 meter_per_second
      }

      behavior Guidance:Point {
        run in parallel

        set rudderAngle = 0.0 degree
      }
    }
  }

  aggregate ClampDepthDuringIsothermHolding {
    run in parallel

    break if ( CntSamples > NumSamplers )

    aggregate ClampToDeepBoundSampler {
      run while (
        FlagTempSet
        and StartVerticalManeuver
        and TouchedDeepBoundSampler
      )

      behavior Guidance:Pitch {
        run in parallel

        set depth = DeepBoundSampler
      }
    }
  }

  aggregate SetFlagClampDepthDuringIsothermHolding {
    run in parallel

    break if ( CntSamples > NumSamplers )

    aggregate SetFlagDeepBoundSampler {
      run when (
        FlagTempSet
        and ( Universal:depth > DeepBoundSampler )
        and ( not ( TouchedDeepBoundSamplerFlagSet ) )
      )

      syslog important "Clamp depth to DeepBoundSampler = " + DeepBoundSampler~meter
           + ", because attempted temp is deeper."

      assign in sequence TouchedDeepBoundSampler = true

      assign in sequence TouchedDeepBoundSamplerFlagSet = true
    }
  }

  aggregate TakeSamples {
    run in parallel

    break if (
      CntSamples > NumSamplers
      or ( not ( StartVerticalManeuver ) )
      or (
        SampleAtPeakChl
        and ( not ( FlagInitialDiveCompleted ) )
      )
    )

    aggregate OutsideOfPolygon {
      run in parallel

      break if (
        not ( Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup )
        or (
          Derivation:ShortestDistanceToPolygonSidesCalculator.loadAtStartup
          and Derivation:ShortestDistanceToPolygonSidesCalculator.inside_polygon
        )
        or StoppedForBeingOutsideOfPolygon
      )

      syslog important "Latitude = " + Universal:latitude~degree + ", longitude = "
           + Universal:longitude~degree + ". Outside of the polygon. Stopping mission."

      behavior Guidance:Execute {
        run in sequence

        set command = "stop"
      }

      assign in sequence StoppedForBeingOutsideOfPolygon = true
    }

    aggregate NoFiringForTooLong {
      run when (
        elapsed ( ElapsedSinceStartOrLastSample ) > MaxWaitNoFiring
        and ( not ( FlagSamplingOngoing ) )
        and ( not ( StoppedForNoFiringForTooLong ) )
      )

      assign in sequence ElapsedTime = elapsed ( ElapsedSinceStartOrLastSample )

      syslog important "No firing for too long. Stopping mission. ElapsedTime, MaxWaitNoFiring = "
           + ElapsedTime~minute + ", " + MaxWaitNoFiring~minute

      behavior Guidance:Execute {
        run in sequence

        set command = "stop"
      }

      assign in sequence StoppedForNoFiringForTooLong = true
    }

    macro $k = 1..60 {
      aggregate SetOptionsOfSample$k {
        run when (
          CntSamples + StartIndex - 1 count == $k count
          and ( not ( SampleOptionsSet ) )
          and SampleCountIncreased
        )

        assign in sequence CartridgeTypeIndividual = CartridgeType[$k]

        assign in sequence TempDiffFromPeakChlIndividual = TempDiffFromPeakChl[$k]

        assign in sequence DepDiffFromPeakChlIndividual = DepDiffFromPeakChl[$k]

        assign in sequence DepIndividual = Dep[$k]

        assign in sequence TempIndividual = Temp[$k]

        assign in sequence WaitDepUndulationIndividual = WaitDepUndulation[$k]

        call id="SetOptionsForSample$k" refId="SetSampleOptions"

        assign in sequence SampleOptionsSet = true
      }
    }

    aggregate SetFiringTempRelativeToChlPeak {
      run when (
        StartVerticalManeuver
        and SampleOptionsSet
        and ( not ( isNaN ( TempDiffPeakChl ) ) )
        and FlagPeakChlTempSet
        and ( not ( FlagTempSet ) )
      )

      assign in sequence TempSet = PeakChlTemperatureSet + TempDiffPeakChl

      assign in sequence FlagTempSet = true
    }

    aggregate SetFiringTempAbsolute {
      run when (
        StartVerticalManeuver
        and SampleOptionsSet
        and ( not ( isNaN ( TempDesignated ) ) )
        and ( not ( FlagTempSet ) )
      )

      assign in sequence TempSet = TempDesignated

      assign in sequence FlagTempSet = true

      assign in sequence FlagGoDown = false
    }

    aggregate SetFiringDepthRelativeToChlPeakNormal {
      run when (
        SampleOptionsSet
        and FlagPeakChlDepthSet
        and ( not ( isNaN ( DepDiffPeakChl ) ) )
        and ( not ( FlagTargetDepthSet ) )
        and ( PeakChlDepthSet + DepDiffPeakChl >= ShallowBoundChl )
        and ( PeakChlDepthSet + DepDiffPeakChl <= DeepBoundChl )
      )

      assign in sequence DepthSet = PeakChlDepthSet + DepDiffPeakChl

      assign in sequence FlagTargetDepthSet = true
    }

    aggregate SetFiringDepthRelativeToChlPeakClampedToShallowest {
      run when (
        SampleOptionsSet
        and FlagPeakChlDepthSet
        and ( not ( isNaN ( DepDiffPeakChl ) ) )
        and ( not ( FlagTargetDepthSet ) )
        and ( PeakChlDepthSet + DepDiffPeakChl < ShallowBoundChl )
      )

      assign in sequence DepthSet = ShallowBoundChl

      assign in sequence FlagTargetDepthSet = true
    }

    aggregate SetFiringDepthRelativeToChlPeakClampedToDeepest {
      run when (
        SampleOptionsSet
        and FlagPeakChlDepthSet
        and ( not ( isNaN ( DepDiffPeakChl ) ) )
        and ( not ( FlagTargetDepthSet ) )
        and ( PeakChlDepthSet + DepDiffPeakChl > DeepBoundChl )
      )

      assign in sequence DepthSet = DeepBoundChl

      assign in sequence FlagTargetDepthSet = true
    }

    aggregate SetFiringDepthAbsolute {
      run when (
        SampleOptionsSet
        and ( not ( isNaN ( DepthDesignated ) ) )
        and ( not ( FlagTargetDepthSet ) )
      )

      assign in sequence DepthSet = DepthDesignated

      assign in sequence FlagTargetDepthSet = true

      assign in sequence FlagGoDown = false
    }

    aggregate FiringOnTemp {
      run when (
        SamplingPartStartCommsCompleted
        and StartVerticalManeuver
        and FlagTempSet
        and ( not ( FlagSamplingOngoing ) )
        and ( CntSamples <= NumSamplers )
        and SampleOptionsSet
        and ( not ( SampleCompleted ) )
      )

      aggregate NoFiringChlBelowTriggerThresh {
        run when (
          SampleAtPeakChl
          and ( PeakChlSet < TriggerThresholdChl )
          and ( not ( StoppedForNoFiringChlBelowTriggerThresh ) )
        )

        syslog important "No firing because the peak chl level " + PeakChlSet~microgram_per_liter
             + " is lower than TriggerThresholdChl " + TriggerThresholdChl~microgram_per_liter

        behavior Guidance:Execute {
          run in sequence

          set command = "stop"
        }

        assign in sequence StoppedForNoFiringChlBelowTriggerThresh = true
      }

      assign in sequence FlagSamplingOngoing = true

      assign in sequence SampleCountIncreased = false

      syslog important "Taking sample No." + CntSamples~count + ". Target temp = " + TempSet~celsius
           + "."

      syslog important "If ESP, requesting ESP cartridge type:" + CartType~count

      assign in sequence ElapsedSinceStartOrLastSample = 0 hour

      aggregate TriggerOnTemp {
        run in sequence

        break if (
          UseESP
          and ( isNaN ( CartType ) )
        )

        call id="WaitForDepthDampingDown" refId="DampDown"

        call id="Sampling" refId="TriggerSampling"

        syslog important "Sample No." + CntSamples~count + " completed."

        assign in sequence ElapsedSinceStartOrLastSample = 0 hour

        assign in sequence FlagSamplingOngoing = false

        assign in sequence SampleCompleted = true

        # Don't move the following line

        assign in sequence SampleOptionsSet = false

        assign in sequence FlagTempSet = false
      }

      aggregate SkipOnTemp {
        run in sequence

        break if (
          not ( isNaN ( CartType ) )
          or UseCANONSampler
        )

        assign in sequence FlagSamplingOngoing = false

        assign in sequence SampleCompleted = true

        # Don't move the following line

        assign in sequence SampleOptionsSet = false

        assign in sequence FlagTempSet = false

        assign in sequence SendDataAllCompleted = true

        syslog important "ESP sample skipped (because cartridge type is NaN)."
      }

      aggregate FireOnTempSendData {
        run when (
          not ( isNaN ( CartType ) )
          and SampleCompleted
          and SendSampleStatusAndData
          and CallSendData
        )

        call id="SendDataFireOnTemp" refId="SendData"

        assign in sequence CallSendData = false
      }
    }

    aggregate FiringOnDepth {
      run when (
        SamplingPartStartCommsCompleted
        and StartVerticalManeuver
        and FlagTargetDepthSet
        and ( not ( FlagGoUp ) )
        and ( not ( FlagGoDown ) )
        and ( not ( FlagSamplingOngoing ) )
        and ( CntSamples <= NumSamplers )
        and SampleOptionsSet
        and ( not ( SampleCompleted ) )
      )

      aggregate NoFiringChlBelowTriggerThresh {
        run when (
          SampleAtPeakChl
          and ( PeakChlSet < TriggerThresholdChl )
          and ( not ( StoppedForNoFiringChlBelowTriggerThresh ) )
        )

        syslog important "No firing because the peak chl level " + PeakChlSet~microgram_per_liter
             + " is lower than TriggerThresholdChl " + TriggerThresholdChl~microgram_per_liter

        behavior Guidance:Execute {
          run in sequence

          set command = "stop"
        }

        assign in sequence StoppedForNoFiringChlBelowTriggerThresh = true
      }

      assign in sequence SampleAtDepth:TargetDepth = DepthSet

      assign in sequence SampleAtDepth:SettleTime = WaitDepthUndulation

      assign in sequence FlagSamplingOngoing = true

      assign in sequence SampleCountIncreased = false

      syslog important "Taking sample No." + CntSamples~count + ". Target depth = " + DepthSet~meter
           + "."

      syslog important "If ESP, requesting ESP cartridge type:" + CartType~count

      assign in sequence ElapsedSinceStartOrLastSample = 0 hour

      aggregate TriggerOnDepth {
        run in sequence

        break if (
          UseESP
          and ( isNaN ( CartType ) )
        )

        assign in sequence SampleAtDepth:ESPCartridgeType = CartType

        call id="Sampling" refId="SampleAtDepth"

        syslog important "Sample No." + CntSamples~count + " completed."

        assign in sequence ElapsedSinceStartOrLastSample = 0 hour

        assign in sequence FlagSamplingOngoing = false

        assign in sequence SampleCompleted = true

        # Don't move the following line

        assign in sequence SampleOptionsSet = false

        assign in sequence FlagTargetDepthSet = false
      }

      aggregate SkipOnDepth {
        run in sequence

        break if (
          not ( isNaN ( CartType ) )
          or UseCANONSampler
        )

        assign in sequence FlagSamplingOngoing = false

        assign in sequence SampleCompleted = true

        # Don't move the following line

        assign in sequence SampleOptionsSet = false

        assign in sequence FlagTargetDepthSet = false

        assign in sequence SendDataAllCompleted = true

        syslog important "ESP sample skipped (because cartridge type is NaN)."
      }

      aggregate FireOnDepSendData {
        run when (
          not ( isNaN ( CartType ) )
          and SampleCompleted
          and SendSampleStatusAndData
          and CallSendData
        )

        call id="SendDataFireOnDep" refId="SendData"

        assign in sequence CallSendData = false
      }
    }

    aggregate IncreaseSampleCount {
      run when (
        SampleCompleted
        and ( not ( SendSampleStatusAndData ) )
        or (
          SampleCompleted
          and SendSampleStatusAndData
          and SendDataAllCompleted
        )
        or (
          SampleOptionsSet
          and ( isNaN ( TempDiffPeakChl ) )
          and ( isNaN ( DepDiffPeakChl ) )
          and ( isNaN ( TempDesignated ) )
          and ( isNaN ( DepthDesignated ) )
        )
      )

      assign in sequence CntSamples = CntSamples + 1 count

      assign in sequence SendDataAllCompleted = false

      assign in sequence CallSendData = true

      assign in sequence TouchedDeepBoundSampler = false

      assign in sequence TouchedDeepBoundSamplerFlagSet = false

      assign in sequence SampleCompleted = false

      assign in sequence SampleOptionsSet = false

      assign in sequence SampleCountIncreased = true
    }
  }
}