dataset

type AbsorbanceData interface {
	Absorbance(wellname string, wavelength int, options ...interface{}) (average wtype.Absorbance, err error)
	AllAbsorbanceData() (map[string][]wtype.Absorbance, error)
}

type AbsorbanceTimeCourseData interface {
	AbsorbanceData
	TimeCourseData
}

type FluorescenceData interface {
	Fluorescence(wellname string, excitationWavelength, emissionWavelength int, options ...interface{}) (average float64, err error)
}

type FluorescenceTimeCourseData interface {
	FluorescenceData
	TimeCourseData
}

type MarsData struct {
	User            string
	Path            string
	TestID          int
	Testname        string
	Date            time.Time
	Time            time.Time
	ID1             string
	ID2             string
	ID3             string
	Description     string
	Dataforeachwell map[string]WellData
}

type MoreSettings struct {
	Calibrate     string `xml:"Calibrate"`
	CarriageSpeed string `xml:"CarriageSpeed"`
	ReadOrder     string `xml:"ReadOrder"`
}

type PRMeasurement struct {
	EWavelength int           //	excitation wavelength
	RWavelength int           //	emission wavelength
	Reading     float64       //int           // 	value read
	Xoff        int           //	position - x, relative to well centre
	Yoff        int           //	position - y, relative to well centre
	Zoff        int           // 	position - z, relative to well centre
	Timestamp   time.Duration // instant measurement was taken
	Temp        float64       //int       //   temperature
	O2          int           // o2 conc when measurement was taken
	CO2         int           // co2 conc when measurement was taken
	EBand       int
	RBand       int
	Script      int
	Gain        int
	// ReadingType is the annotation found in the column header in the exported mars excel file
	// e.g. Raw Data (Abs Scan)
	ReadingType string
}

type PRMeasurementSet []PRMeasurement

type PROutput struct {
	Readings []PRMeasurementSet
}

type PlateReaderData interface {
	ReadingsAsAverage(wellname string, emexortime platereader.FilterOption, fieldvalue interface{}) (average float64, err error)
}

type Reading struct {
	Wavelength Wavelength `xml:"Wavelength"`
	Wells      []Well     `xml:"Wells"`
}

type SpectraMaxData struct {
	Name       xml.Name           `xml:"Experiment"`
	Experiment []XMLPlateSections `xml:"PlateSections"`
}

type TimeCourseData interface {
	TimeCourse(wellname string, exWavelength int, emWavelength int, scriptnumber int) (xaxis []time.Duration, yaxis []float64, err error)
}

type Wavelength struct {
	Index int     `xml:"WavelengthIndex,attr"`
	Wells []Wells `xml:"Wells"`
}

type WavelengthSettings struct {
	NumberOfWavelengths int      `xml:"NumberOfWavelengths,attr"`
	Wavelength          []string `xml:"Wavelength"`
}

type Well struct {
	ID       string `xml:"ID,attr"`     // Single reading
	WellID   string `xml:"WellID,attr"` // Scan data
	Name     string `xml:"Name,attr"`
	Row      int    `xml:"Row,attr"`
	Column   int    `xml:"Col,attr"`
	RawData  string `xml:"RawData"`
	WaveData string `xml:"WaveData"` // Scan data
}

type WellData struct {
	Well            string // in a1 format
	Name            string
	Data            PROutput
	Injected        bool
	InjectionVolume float64
}

type Wells struct {
	Wells []Well `xml:"Well"`
}

type XMLInstrumentSettings struct {
	ReadMode           platereader.ReadMode `xml:"ReadMode,attr"`
	ReadType           platereader.ReadType `xml:"ReadType,attr"`
	PlateType          string               `xml:"PlateType,attr"` // may need to change to a string for now since it's unlikely the plate names in the platereader software will correspond to those in antha
	AutoMix            bool                 `xml:"AutoMix"`
	MoreSettings       MoreSettings         `xml:"MoreSettings"`
	WavelengthSettings WavelengthSettings   `xml:"WavelengthSettings"`
}

type XMLPlateSection struct {
	Name               string                `xml:"Name,attr"`
	InstrumentInfo     string                `xml:"InstrumentInfo,attr"`
	ReadTime           customTime            `xml:"ReadTime,attr"`
	Barcode            string                `xml:"Barcode"`
	InstrumentSettings XMLInstrumentSettings `xml:"InstrumentSettings"`
	Wavelengths        []Reading             `xml:"Wavelengths"`
	TemperatureData    wunit.Temperature     `xml:"TemperatureData"`
}

type XMLPlateSections struct {
	PlateSections []XMLPlateSection `xml:"PlateSection"`
}