liquidhandling

package
v0.0.0-...-a011eca Latest Latest
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 Go to latest Published: Jun 4, 2022 License: BSD-3-Clause, GPL-2.0 Imports: 11 Imported by: 0

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Index

Constants

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const (
	XCorrection = 14.38
	YCorrection = 11.24
)

These values correct for the Glison Driver offset and will eventually be removed

Variables

This section is empty.

Functions

This section is empty.

Types

type AdaptorGroup 

type AdaptorGroup struct {
	// contains filtered or unexported fields
}

AdaptorGroup simulate a set of adaptors which are physically attached

func NewAdaptorGroup 

func NewAdaptorGroup(assembly *wtype.LHHeadAssembly) *AdaptorGroup

NewAdaptorGroup convert a HeadAssembly into an AdaptorGroup for simulation

func (*AdaptorGroup) GetAdaptor 

func (self *AdaptorGroup) GetAdaptor(i int) (*AdaptorState, error)

GetAdaptor get an adaptor state

func (*AdaptorGroup) GetAdaptors 

func (self *AdaptorGroup) GetAdaptors() []*AdaptorState

func (*AdaptorGroup) GetPosition 

func (self *AdaptorGroup) GetPosition() wtype.Coordinates3D

func (*AdaptorGroup) GetRobot 

func (self *AdaptorGroup) GetRobot() *RobotState

func (*AdaptorGroup) LoadAdaptor 

func (self *AdaptorGroup) LoadAdaptor(pos int, adaptor *AdaptorState)

func (*AdaptorGroup) NumAdaptors 

func (self *AdaptorGroup) NumAdaptors() int

CountAdaptors count the adaptors

func (*AdaptorGroup) SetDriveSpeed 

func (self *AdaptorGroup) SetDriveSpeed(a wunit.Axis, v wunit.Velocity) error

func (*AdaptorGroup) SetPosition 

func (self *AdaptorGroup) SetPosition(p wtype.Coordinates3D) error

func (*AdaptorGroup) SetRobot 

func (self *AdaptorGroup) SetRobot(r *RobotState)

type AdaptorState 

type AdaptorState struct {
	// contains filtered or unexported fields
}

AdaptorState Represent the physical state and layout of the adaptor

func NewAdaptorState 

func NewAdaptorState(name string,
	independent bool,
	channels int,
	channel_offset wtype.Coordinates3D, coneRadius float64,
	params *wtype.LHChannelParameter,
	tipBehaviour wtype.TipLoadingBehaviour) *AdaptorState

func (*AdaptorState) AutoRefillsTipboxes 

func (self *AdaptorState) AutoRefillsTipboxes() bool

func (*AdaptorState) GetChannel 

func (self *AdaptorState) GetChannel(ch int) *ChannelState

GetChannel

func (*AdaptorState) GetChannelCount 

func (self *AdaptorState) GetChannelCount() int

GetChannelCount

func (*AdaptorState) GetGroup 

func (self *AdaptorState) GetGroup() *AdaptorGroup

GetGroup

func (*AdaptorState) GetIndex 

func (self *AdaptorState) GetIndex() int

func (*AdaptorState) GetName 

func (self *AdaptorState) GetName() string

GetName

func (*AdaptorState) GetParamsForChannel 

func (self *AdaptorState) GetParamsForChannel(ch int) *wtype.LHChannelParameter

GetParamsForChannel

func (*AdaptorState) GetPosition 

func (self *AdaptorState) GetPosition() wtype.Coordinates3D

GetPosition

func (*AdaptorState) GetTipCoordsToLoad 

func (self *AdaptorState) GetTipCoordsToLoad(tb *wtype.LHTipbox, num int) ([][]wtype.WellCoords, error)

GetTipsToLoad get which tips would be loaded by the adaptor given the tiploading behaviour returns an error if OverridesLoadTipsCommand is false or there aren't enough tips

func (*AdaptorState) GetTipCount 

func (self *AdaptorState) GetTipCount() int

GetTipCount

func (*AdaptorState) IsIndependent 

func (self *AdaptorState) IsIndependent() bool

IsIndependent

func (*AdaptorState) OverridesLoadTipsCommand 

func (self *AdaptorState) OverridesLoadTipsCommand() bool

func (*AdaptorState) SetGroup 

func (self *AdaptorState) SetGroup(g *AdaptorGroup)

SetGroup

func (*AdaptorState) SetOffset 

func (self *AdaptorState) SetOffset(p wtype.Coordinates3D)

func (*AdaptorState) SetOverridesLoadTipsCommand 

func (self *AdaptorState) SetOverridesLoadTipsCommand(v bool)

func (*AdaptorState) SetPosition 

func (self *AdaptorState) SetPosition(p wtype.Coordinates3D) error

func (*AdaptorState) SummarisePositions 

func (self *AdaptorState) SummarisePositions(channelsColliding []int) string

SummarisePositions get a human readable description of the X,Y,Z position of the adaptor, as well as which type of tips are loaded on which channels. channelsColliding provides an optional list of channel indexes which have been detected as being involved in a collision, which will also be displayed in the output.

func (*AdaptorState) SummariseTips 

func (self *AdaptorState) SummariseTips() string

String summarize the state of the adaptor

type ChannelState 

type ChannelState struct {
	// contains filtered or unexported fields
}

ChannelState Represent the physical state of a single channel

func NewChannelState 

func NewChannelState(number int, adaptor *AdaptorState, position wtype.Coordinates3D, radius float64) *ChannelState

func (*ChannelState) Aspirate 

func (self *ChannelState) Aspirate(volume wunit.Volume) error

Aspirate

func (*ChannelState) Dispense 

func (self *ChannelState) Dispense(volume *wunit.Volume) error

Dispense

func (*ChannelState) GetAbsolutePosition 

func (self *ChannelState) GetAbsolutePosition() wtype.Coordinates3D

GetAbsolutePosition get the channel's absolute position

func (*ChannelState) GetBounds 

func (self *ChannelState) GetBounds(channelClearance float64) wtype.BBox

func (*ChannelState) GetCollisions 

func (self *ChannelState) GetCollisions(settings *SimulatorSettings, channelClearance float64) []wtype.LHObject

GetCollisions get collisions with this channel. channelClearance defined a height below the channel/tip to include

func (*ChannelState) GetContents 

func (self *ChannelState) GetContents() *wtype.Liquid

GetContents get the contents of the loaded tip, retuns nil if no contents or no tip

func (*ChannelState) GetRadius 

func (self *ChannelState) GetRadius() float64

func (*ChannelState) GetRelativePosition 

func (self *ChannelState) GetRelativePosition() wtype.Coordinates3D

GetRelativePosition get the channel's position relative to the head

func (*ChannelState) GetTarget 

func (self *ChannelState) GetTarget() wtype.LHObject

GetTarget get the LHObject below the adaptor

func (*ChannelState) GetTip 

func (self *ChannelState) GetTip() *wtype.LHTip

GetTip get the loaded tip, returns nil if none loaded

func (*ChannelState) HasTip 

func (self *ChannelState) HasTip() bool

HasTip is a tip loaded

func (*ChannelState) IsEmpty 

func (self *ChannelState) IsEmpty() bool

IsEmpty returns true only if a tip is loaded and contains liquid

func (*ChannelState) LoadTip 

func (self *ChannelState) LoadTip(tip *wtype.LHTip)

LoadTip

func (*ChannelState) SetRelativePosition 

func (self *ChannelState) SetRelativePosition(v wtype.Coordinates3D)

SetRelativePosition get the channel's position relative to the head

func (*ChannelState) UnloadTip 

func (self *ChannelState) UnloadTip() *wtype.LHTip

UnloadTip

type CollisionError 

type CollisionError struct {
	// contains filtered or unexported fields
}

CollisionError generated when a physical collision occurs

func NewCollisionError 

func NewCollisionError(state *RobotState, channelsColliding map[int][]int, objectsColliding []wtype.LHObject) *CollisionError

NewCollisionError make a new collision

func (*CollisionError) CollisionDescription 

func (self *CollisionError) CollisionDescription() string

func (*CollisionError) Error 

func (self *CollisionError) Error() string

func (*CollisionError) GetStateAtError 

func (self *CollisionError) GetStateAtError() string

func (*CollisionError) Instruction 

func (self *CollisionError) Instruction() driver.TerminalRobotInstruction

func (*CollisionError) InstructionDescription 

func (self *CollisionError) InstructionDescription() string

func (*CollisionError) InstructionIndex 

func (self *CollisionError) InstructionIndex() int

func (*CollisionError) SetInstructionDescription 

func (self *CollisionError) SetInstructionDescription(d string)

func (*CollisionError) Severity 

func (self *CollisionError) Severity() simulator.ErrorSeverity

type DetailedLHError 

type DetailedLHError interface {
	GetStateAtError() string
}

type Frequency 

type Frequency int
const (
	WarnNever Frequency = iota
	WarnOnce
	WarnAlways
)

type GenericError 

type GenericError struct {
	// contains filtered or unexported fields
}

func (*GenericError) Error 

func (self *GenericError) Error() string

func (*GenericError) GetStateAtError 

func (self *GenericError) GetStateAtError() string

func (*GenericError) Instruction 

func (self *GenericError) Instruction() driver.TerminalRobotInstruction

func (*GenericError) InstructionIndex 

func (self *GenericError) InstructionIndex() int

func (*GenericError) Severity 

func (self *GenericError) Severity() simulator.ErrorSeverity

type LiquidhandlingError 

type LiquidhandlingError interface {
	simulator.SimulationError
	Instruction() driver.TerminalRobotInstruction
	InstructionIndex() int
}

func NewGenericError 

func NewGenericError(state *RobotState, severity simulator.ErrorSeverity, message string) LiquidhandlingError

func NewGenericErrorf 

func NewGenericErrorf(state *RobotState, severity simulator.ErrorSeverity, format string, a ...interface{}) LiquidhandlingError

func NewTipsNotInWellError 

func NewTipsNotInWellError(vlh *VirtualLiquidHandler, description string, channels []int) LiquidhandlingError

type RobotState 

type RobotState struct {
	// contains filtered or unexported fields
}

RobotState Represent the physical state of a liquidhandling robot

func NewRobotState 

func NewRobotState() *RobotState

func (*RobotState) AddAdaptorGroup 

func (self *RobotState) AddAdaptorGroup(a *AdaptorGroup)

AddAdaptorGroup

func (*RobotState) Finalize 

func (self *RobotState) Finalize()

Finalize

func (*RobotState) GetAdaptor 

func (self *RobotState) GetAdaptor(groupIndex int, adaptorIndex int) (*AdaptorState, error)

func (*RobotState) GetAdaptorGroup 

func (self *RobotState) GetAdaptorGroup(num int) (*AdaptorGroup, error)

GetAdaptorGroup

func (*RobotState) GetAdaptors 

func (self *RobotState) GetAdaptors() []*AdaptorState

func (*RobotState) GetDeck 

func (self *RobotState) GetDeck() *wtype.LHDeck

GetDeck

func (*RobotState) Initialize 

func (self *RobotState) Initialize()

Initialize

func (*RobotState) IsFinalized 

func (self *RobotState) IsFinalized() bool

IsFinalized

func (*RobotState) IsInitialized 

func (self *RobotState) IsInitialized() bool

IsInitialized

func (*RobotState) NumAdaptorGroups 

func (self *RobotState) NumAdaptorGroups() int

GetNumberOfAdaptorGroups

func (*RobotState) NumAdaptors 

func (self *RobotState) NumAdaptors() int

func (*RobotState) SetDeck 

func (self *RobotState) SetDeck(deck *wtype.LHDeck)

SetDeck

func (*RobotState) SummariseAdaptors 

func (self *RobotState) SummariseAdaptors(channelsColliding map[int][]int) string

func (*RobotState) SummariseDeck 

func (self *RobotState) SummariseDeck() string

func (*RobotState) SummariseState 

func (self *RobotState) SummariseState(channelsColliding map[int][]int) string

type SimulatorSettings 

type SimulatorSettings struct {
	// contains filtered or unexported fields
}

func DefaultSimulatorSettings 

func DefaultSimulatorSettings() *SimulatorSettings

func (*SimulatorSettings) EnableAutoChannelWarning 

func (self *SimulatorSettings) EnableAutoChannelWarning(f Frequency)

func (*SimulatorSettings) EnableLiquidTypeWarning 

func (self *SimulatorSettings) EnableLiquidTypeWarning(f Frequency)

func (*SimulatorSettings) EnablePipetteSpeedWarning 

func (self *SimulatorSettings) EnablePipetteSpeedWarning(f Frequency)

func (*SimulatorSettings) EnableTipLoadingOverride 

func (self *SimulatorSettings) EnableTipLoadingOverride(b bool)

func (*SimulatorSettings) EnableTipboxCheck 

func (self *SimulatorSettings) EnableTipboxCheck(b bool)

func (*SimulatorSettings) EnableTipboxCollision 

func (self *SimulatorSettings) EnableTipboxCollision(b bool)

func (*SimulatorSettings) IsAutoChannelWarningEnabled 

func (self *SimulatorSettings) IsAutoChannelWarningEnabled() bool

func (*SimulatorSettings) IsLiquidTypeWarningEnabled 

func (self *SimulatorSettings) IsLiquidTypeWarningEnabled() bool

func (*SimulatorSettings) IsPipetteSpeedWarningEnabled 

func (self *SimulatorSettings) IsPipetteSpeedWarningEnabled() bool

func (*SimulatorSettings) IsTipLoadingOverrideEnabled 

func (self *SimulatorSettings) IsTipLoadingOverrideEnabled() bool

func (*SimulatorSettings) IsTipboxCheckEnabled 

func (self *SimulatorSettings) IsTipboxCheckEnabled() bool

func (*SimulatorSettings) IsTipboxCollisionEnabled 

func (self *SimulatorSettings) IsTipboxCollisionEnabled() bool

func (*SimulatorSettings) MaxDispenseHeight 

func (self *SimulatorSettings) MaxDispenseHeight() float64

func (*SimulatorSettings) SetMaxDispenseHeight 

func (self *SimulatorSettings) SetMaxDispenseHeight(f float64)

type TipsNotInWellError 

type TipsNotInWellError struct {
	*GenericError
	// contains filtered or unexported fields
}

TipsNotInWellError generated when aspirate is called and there are no tips in a well

func (*TipsNotInWellError) GetStateAtError 

func (self *TipsNotInWellError) GetStateAtError() string

type VirtualLiquidHandler 

type VirtualLiquidHandler struct {
	// contains filtered or unexported fields
}

Simulate a liquid handler Driver

func NewVirtualLiquidHandler 

func NewVirtualLiquidHandler(props *liquidhandling.LHProperties, settings *SimulatorSettings) (*VirtualLiquidHandler, error)

Create a new VirtualLiquidHandler which mimics an LHDriver

func (*VirtualLiquidHandler) AddError 

func (self *VirtualLiquidHandler) AddError(message string)

func (*VirtualLiquidHandler) AddErrorf 

func (self *VirtualLiquidHandler) AddErrorf(format string, a ...interface{})

func (*VirtualLiquidHandler) AddInfo 

func (self *VirtualLiquidHandler) AddInfo(message string)

func (*VirtualLiquidHandler) AddInfof 

func (self *VirtualLiquidHandler) AddInfof(format string, a ...interface{})

func (*VirtualLiquidHandler) AddPlateTo 

func (self *VirtualLiquidHandler) AddPlateTo(position string, plate interface{}, name string) driver.CommandStatus

AddPlateTo - used

func (*VirtualLiquidHandler) AddWarning 

func (self *VirtualLiquidHandler) AddWarning(message string)

func (*VirtualLiquidHandler) AddWarningf 

func (self *VirtualLiquidHandler) AddWarningf(format string, a ...interface{})

func (*VirtualLiquidHandler) Aspirate 

func (self *VirtualLiquidHandler) Aspirate(volume []float64, overstroke []bool, head int, multi int,
	platetype []string, what []string, llf []bool) driver.CommandStatus

Aspirate - used

func (*VirtualLiquidHandler) Close 

func (self *VirtualLiquidHandler) Close() driver.CommandStatus

Close - notimplement in CRI

func (*VirtualLiquidHandler) CountErrors 

func (self *VirtualLiquidHandler) CountErrors() int

CountErrors

func (*VirtualLiquidHandler) Dispense 

func (self *VirtualLiquidHandler) Dispense(volume []float64, blowout []bool, head int, multi int,
	platetype []string, what []string, llf []bool) driver.CommandStatus

Dispense - used

func (*VirtualLiquidHandler) DriverType 

func (self *VirtualLiquidHandler) DriverType() ([]string, error)

func (*VirtualLiquidHandler) Finalize 

func (self *VirtualLiquidHandler) Finalize() driver.CommandStatus

Finalize - used

func (*VirtualLiquidHandler) GetAdaptorState 

func (self *VirtualLiquidHandler) GetAdaptorState(adaptor int) (*AdaptorState, error)

GetAdaptorState Currently we only support one adaptor group

func (*VirtualLiquidHandler) GetCapabilities 

func (self *VirtualLiquidHandler) GetCapabilities() (liquidhandling.LHProperties, driver.CommandStatus)

GetCapabilites - used

func (*VirtualLiquidHandler) GetCurrentPosition 

func (self *VirtualLiquidHandler) GetCurrentPosition(head int) (string, driver.CommandStatus)

GetCurrentPosition - unused

func (*VirtualLiquidHandler) GetErrors 

func (self *VirtualLiquidHandler) GetErrors() []simulator.SimulationError

GetErrors

func (*VirtualLiquidHandler) GetFirstError 

func (self *VirtualLiquidHandler) GetFirstError(minimumSeverity simulator.ErrorSeverity) simulator.SimulationError

GetFirstError get the first error that's at least as bad as minimum severity

func (*VirtualLiquidHandler) GetHeadState 

func (self *VirtualLiquidHandler) GetHeadState(head int) (string, driver.CommandStatus)

GetHeadState - unused

func (*VirtualLiquidHandler) GetLastMove 

func (self *VirtualLiquidHandler) GetLastMove() string

func (*VirtualLiquidHandler) GetLastTarget 

func (self *VirtualLiquidHandler) GetLastTarget() wtype.LHObject

func (*VirtualLiquidHandler) GetObjectAt 

func (self *VirtualLiquidHandler) GetObjectAt(slot string) wtype.LHObject

func (*VirtualLiquidHandler) GetOutputFile 

func (self *VirtualLiquidHandler) GetOutputFile() ([]byte, driver.CommandStatus)

GetOutputFile - used, but not in instruction stream

func (*VirtualLiquidHandler) GetPositionState 

func (self *VirtualLiquidHandler) GetPositionState(position string) (string, driver.CommandStatus)

GetPositionState - unused

func (*VirtualLiquidHandler) GetProperties 

func (self *VirtualLiquidHandler) GetProperties() *liquidhandling.LHProperties

func (*VirtualLiquidHandler) GetStatus 

func (self *VirtualLiquidHandler) GetStatus() (driver.Status, driver.CommandStatus)

GetStatus - unused

func (*VirtualLiquidHandler) GetWellAt 

func (self *VirtualLiquidHandler) GetWellAt(pl wtype.PlateLocation) *wtype.LHWell

GetWellAt return the internal model of the well at the given location, or nil if not found

func (*VirtualLiquidHandler) Go 

func (self *VirtualLiquidHandler) Go() driver.CommandStatus

Go - unused

func (*VirtualLiquidHandler) Initialize 

func (self *VirtualLiquidHandler) Initialize() driver.CommandStatus

Initialize - used

func (*VirtualLiquidHandler) LightsOff 

func (self *VirtualLiquidHandler) LightsOff() driver.CommandStatus

Lights Off - notimplemented in compositerobotinstruction

func (*VirtualLiquidHandler) LightsOn 

func (self *VirtualLiquidHandler) LightsOn() driver.CommandStatus

Lights On - not implemented in compositerobotinstruction

func (*VirtualLiquidHandler) LoadAdaptor 

func (self *VirtualLiquidHandler) LoadAdaptor(param int) driver.CommandStatus

LoadAdaptor - notimplemented in CRI

func (*VirtualLiquidHandler) LoadHead 

func (self *VirtualLiquidHandler) LoadHead(param int) driver.CommandStatus

LoadHead - unused

func (*VirtualLiquidHandler) LoadTips 

func (self *VirtualLiquidHandler) LoadTips(channels []int, head, multi int,
	platetypeS, positionS, well []string) driver.CommandStatus

LoadTips - used

func (*VirtualLiquidHandler) Message 

func (self *VirtualLiquidHandler) Message(level int, title, text string, showcancel bool) driver.CommandStatus

Message - unused

func (*VirtualLiquidHandler) Mix 

func (self *VirtualLiquidHandler) Mix(head int, volume []float64, platetype []string, cycles []int,
	multi int, what []string, blowout []bool) driver.CommandStatus

Mix - used

func (*VirtualLiquidHandler) Move 

func (self *VirtualLiquidHandler) Move(deckpositionS []string, wellcoords []string, reference []int,
	offsetX, offsetY, offsetZ []float64, platetypeS []string,
	head int) driver.CommandStatus

Move command - used

func (*VirtualLiquidHandler) MoveRaw 

func (self *VirtualLiquidHandler) MoveRaw(head int, x, y, z float64) driver.CommandStatus

Move raw - not yet implemented in compositerobotinstruction

func (*VirtualLiquidHandler) Open 

func (self *VirtualLiquidHandler) Open() driver.CommandStatus

Open - notimplemented in CRI

func (*VirtualLiquidHandler) RemoveAllPlates 

func (self *VirtualLiquidHandler) RemoveAllPlates() driver.CommandStatus

RemoveAllPlates - used

func (*VirtualLiquidHandler) RemovePlateAt 

func (self *VirtualLiquidHandler) RemovePlateAt(position string) driver.CommandStatus

RemovePlateAt - unused

func (*VirtualLiquidHandler) ResetPistons 

func (self *VirtualLiquidHandler) ResetPistons(head, channel int) driver.CommandStatus

ResetPistons - used

func (*VirtualLiquidHandler) SetDriveSpeed 

func (self *VirtualLiquidHandler) SetDriveSpeed(drive string, rate float64) driver.CommandStatus

SetDriveSpeed sets the speed at which the head will move. Drive should be one of "X", "Y", "Z", rate is expressed in mm/s. XXX Bug: it is currently not possible to select which head assembly should be affected currently assume we're talking about group zero

func (*VirtualLiquidHandler) SetPipetteSpeed 

func (self *VirtualLiquidHandler) SetPipetteSpeed(head, channel int, rate float64) driver.CommandStatus

SetPipetteSpeed - used

func (*VirtualLiquidHandler) SetPositionState 

func (self *VirtualLiquidHandler) SetPositionState(position string, state driver.PositionState) driver.CommandStatus

SetPositionState - unused

func (*VirtualLiquidHandler) Simulate 

func (self *VirtualLiquidHandler) Simulate(instructions []liquidhandling.TerminalRobotInstruction) error

Simulate simulate the list of instructions

func (*VirtualLiquidHandler) Stop 

func (self *VirtualLiquidHandler) Stop() driver.CommandStatus

Stop - unused

func (*VirtualLiquidHandler) UnloadAdaptor 

func (self *VirtualLiquidHandler) UnloadAdaptor(param int) driver.CommandStatus

UnloadAdaptor - notimplemented in CRI

func (*VirtualLiquidHandler) UnloadHead 

func (self *VirtualLiquidHandler) UnloadHead(param int) driver.CommandStatus

UnloadHead - unused

func (*VirtualLiquidHandler) UnloadTips 

func (self *VirtualLiquidHandler) UnloadTips(channels []int, head, multi int,
	platetype, position, well []string) driver.CommandStatus

UnloadTips - used

func (*VirtualLiquidHandler) UpdateMetaData 

func (self *VirtualLiquidHandler) UpdateMetaData(props *liquidhandling.LHProperties) driver.CommandStatus

UpdateMetaData - used

func (*VirtualLiquidHandler) Wait 

func (self *VirtualLiquidHandler) Wait(time float64) driver.CommandStatus

Wait - used

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