Instrument

Bases: NBOBaseClass

Represents the XML element Instrument.

This element describes the Instrument used to capture the Image. It is primarily a container referring to the list of hardware components included in a given Microscope. The list consists of the Microscope Stand, Microscope Table, Light Source, Light Source Coupling, Sample Holder, Focusing, Objective, Filter, Dichroic, Additional Lens (including a commonly used Magnification Changer, also known as Optovar), Additional Mirroring Device, Polarization Optics, Prism, Optical Aperture, Optical Device, Detector and Calibration Tool. The Filter element can be either composed of separate Excitation, Emission filters, and Dichroic mirrors or a single Filter Set. An Instrument might have multiple Light Sources, Detectors, Objectives, and Filters, etc. Each of these has its own ID attribute, which can be referred to from the Image, Plane or more commonly Channel elements associated with a given Image Acquisition session. It is understood that the Light Path configuration can be different for each Channel, but cannot be different for each timepoint or each Plane of an XYZ stack.

getTypeName()

Returns the class type name.

Returns:

Type	Description
string	The class type name

getXMLName()

Returns the XML element name corresponding to this class.

Returns:

Type	Description
string	The XML element name

getNBOType()

Returns the NBO Type corresponding to this class.

Returns:

Type	Description
int	The NBO Type value

getChildren()

Returns a list of all classes derived from this class.

Returns:

Type	Description
List[NBOBaseClass]	The list of derived classes

getSubElements()

Returns a list of all child elements contained in this class.

Returns:

Type	Description
List[NBOBaseClass]	The list of child classes

fromJsonFile(path)

Populates this object from a JSON file.

Parameters:

Name	Type	Description	Default
path	string	The path to the JSON file	required

fromMicroMetaAppJsonFile(path)

Populates this object from a JSON file generated by MicroMeta App.

Parameters:

Name	Type	Description	Default
path	string	The path to the JSON file	required

fromJsonString(json_string)

Populates this object from a JSON string.

Parameters:

Name	Type	Description	Default
json_string	string	The JSON content as a string	required

fromXmlFile(path)

Populates this object from a XML file.

Parameters:

Name	Type	Description	Default
path	string	The path to the XML file	required

fromXmlString(xml_string)

Populates this object from a XML string.

Parameters:

Name	Type	Description	Default
xml_string	string	The XML content as a string	required

toXmlFile(filename)

Serializes this object to an XML file.

Parameters:

Name	Type	Description	Default
filename	string	The path to the output XML file	required

toXmlString()

Serializes this object to an XML string.

Returns:

Type	Description
string	A string containing the XML representation of this object

setID(value)

Sets the value of the ID attribute.

A Unique Identifier for this component.

Parameters:

Name	Type	Description	Default
value	InstrumentID_Type	The value to set	required

getID()

Returns the value of the ID attribute.

A Unique Identifier for this component.

Returns:

Type	Description
InstrumentID_Type	The value of the attribute

resetID()

Resets the ID attribute to an unset state.

A Unique Identifier for this component.

hasID()

Checks whether the optional ID attribute is present.

A Unique Identifier for this component.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setName(value)

Sets the value of the Name attribute.

A User-defined Name for this component.

Parameters:

Name	Type	Description	Default
value	Denomination_Type	The value to set	required

getName()

Returns the value of the Name attribute.

A User-defined Name for this component.

Returns:

Type	Description
Denomination_Type	The value of the attribute

resetName()

Resets the Name attribute to an unset state.

A User-defined Name for this component.

hasName()

Checks whether the optional Name attribute is present.

A User-defined Name for this component.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise

setMicroscopeStandGroup_List(value)

Sets the list of MicroscopeStandGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[MicroscopeStand_Type]	The new list of MicroscopeStandGroup elements	required

getMicroscopeStandGroup_List()

Returns the list of MicroscopeStandGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[MicroscopeStand_Type]	The list of MicroscopeStandGroup elements

addToMicroscopeStandGroup_List(value)

Adds a new MicroscopeStandGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	MicroscopeStand_Type	The element to add	required

clearMicroscopeStandGroup_List()

Clear the list of MicroscopeStandGroup.

No description available in the XSD standard.

setMicroscopeTable_List(value)

Sets the list of MicroscopeTable elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[MicroscopeTable]	The new list of MicroscopeTable elements	required

getMicroscopeTable_List()

Returns the list of MicroscopeTable elements.

No description available in the XSD standard.

Returns:

Type	Description
List[MicroscopeTable]	The list of MicroscopeTable elements

addToMicroscopeTable_List(value)

Adds a new MicroscopeTable element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	MicroscopeTable	The element to add	required

clearMicroscopeTable_List()

Clear the list of MicroscopeTable.

No description available in the XSD standard.

setSoftwareGroup_List(value)

Sets the list of SoftwareGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[Software_Type]	The new list of SoftwareGroup elements	required

getSoftwareGroup_List()

Returns the list of SoftwareGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Software_Type]	The list of SoftwareGroup elements

addToSoftwareGroup_List(value)

Adds a new SoftwareGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Software_Type	The element to add	required

clearSoftwareGroup_List()

Clear the list of SoftwareGroup.

No description available in the XSD standard.

setEnvironmentalControlDevice_List(value)

Sets the list of EnvironmentalControlDevice elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[EnvironmentalControlDevice]	The new list of EnvironmentalControlDevice elements	required

getEnvironmentalControlDevice_List()

Returns the list of EnvironmentalControlDevice elements.

No description available in the XSD standard.

Returns:

Type	Description
List[EnvironmentalControlDevice]	The list of EnvironmentalControlDevice elements

addToEnvironmentalControlDevice_List(value)

Adds a new EnvironmentalControlDevice element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	EnvironmentalControlDevice	The element to add	required

clearEnvironmentalControlDevice_List()

Clear the list of EnvironmentalControlDevice.

No description available in the XSD standard.

setLightSourceGroup_List(value)

Sets the list of LightSourceGroup elements.

This element describes the light source(s) available in this microscope

Parameters:

Name	Type	Description	Default
value	List[LightSource_Type]	The new list of LightSourceGroup elements	required

getLightSourceGroup_List()

Returns the list of LightSourceGroup elements.

This element describes the light source(s) available in this microscope

Returns:

Type	Description
List[LightSource_Type]	The list of LightSourceGroup elements

addToLightSourceGroup_List(value)

Adds a new LightSourceGroup element to this object.

This element describes the light source(s) available in this microscope

Parameters:

Name	Type	Description	Default
value	LightSource_Type	The element to add	required

clearLightSourceGroup_List()

Clear the list of LightSourceGroup.

This element describes the light source(s) available in this microscope

setLightSourceCouplingGroup_List(value)

Sets the list of LightSourceCouplingGroup elements.

This element describes the method(s) used to couple the light source with the light path moving through speciment to the detector

Parameters:

Name	Type	Description	Default
value	List[LightSourceCoupling_Type]	The new list of LightSourceCouplingGroup elements	required

getLightSourceCouplingGroup_List()

Returns the list of LightSourceCouplingGroup elements.

This element describes the method(s) used to couple the light source with the light path moving through speciment to the detector

Returns:

Type	Description
List[LightSourceCoupling_Type]	The list of LightSourceCouplingGroup elements

addToLightSourceCouplingGroup_List(value)

Adds a new LightSourceCouplingGroup element to this object.

This element describes the method(s) used to couple the light source with the light path moving through speciment to the detector

Parameters:

Name	Type	Description	Default
value	LightSourceCoupling_Type	The element to add	required

clearLightSourceCouplingGroup_List()

Clear the list of LightSourceCouplingGroup.

This element describes the method(s) used to couple the light source with the light path moving through speciment to the detector

setObjective_List(value)

Sets the list of Objective elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[Objective]	The new list of Objective elements	required

getObjective_List()

Returns the list of Objective elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Objective]	The list of Objective elements

addToObjective_List(value)

Adds a new Objective element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Objective	The element to add	required

clearObjective_List()

Clear the list of Objective.

No description available in the XSD standard.

setOpticalAssemblyGroup_List(value)

Sets the list of OpticalAssemblyGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[OpticalAssembly_Type]	The new list of OpticalAssemblyGroup elements	required

getOpticalAssemblyGroup_List()

Returns the list of OpticalAssemblyGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[OpticalAssembly_Type]	The list of OpticalAssemblyGroup elements

addToOpticalAssemblyGroup_List(value)

Adds a new OpticalAssemblyGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	OpticalAssembly_Type	The element to add	required

clearOpticalAssemblyGroup_List()

Clear the list of OpticalAssemblyGroup.

No description available in the XSD standard.

setOpticalApertureGroup_List(value)

Sets the list of OpticalApertureGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[OpticalAperture_Type]	The new list of OpticalApertureGroup elements	required

getOpticalApertureGroup_List()

Returns the list of OpticalApertureGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[OpticalAperture_Type]	The list of OpticalApertureGroup elements

addToOpticalApertureGroup_List(value)

Adds a new OpticalApertureGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	OpticalAperture_Type	The element to add	required

clearOpticalApertureGroup_List()

Clear the list of OpticalApertureGroup.

No description available in the XSD standard.

setStageInsert_List(value)

Sets the list of StageInsert elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[StageInse]	The new list of StageInsert elements	required

getStageInsert_List()

Returns the list of StageInsert elements.

No description available in the XSD standard.

Returns:

Type	Description
List[StageInse]	The list of StageInsert elements

addToStageInsert_List(value)

Adds a new StageInsert element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	StageInsert	The element to add	required

clearStageInsert_List()

Clear the list of StageInsert.

No description available in the XSD standard.

setSamplePositioningGroup_List(value)

Sets the list of SamplePositioningGroup elements.

This element describes the objective lens and stage positioning device(s) available in this microscope. An Instrument may have more than one of these devices. The type of Focusing Device is specified by one of the child-element which are 'MechanicalStage', 'PiezoElectricSate', or 'PiezoElectricObjective'

Parameters:

Name	Type	Description	Default
value	List[SamplePositioning_Type]	The new list of SamplePositioningGroup elements	required

getSamplePositioningGroup_List()

Returns the list of SamplePositioningGroup elements.

This element describes the objective lens and stage positioning device(s) available in this microscope. An Instrument may have more than one of these devices. The type of Focusing Device is specified by one of the child-element which are 'MechanicalStage', 'PiezoElectricSate', or 'PiezoElectricObjective'

Returns:

Type	Description
List[SamplePositioning_Type]	The list of SamplePositioningGroup elements

addToSamplePositioningGroup_List(value)

Adds a new SamplePositioningGroup element to this object.

This element describes the objective lens and stage positioning device(s) available in this microscope. An Instrument may have more than one of these devices. The type of Focusing Device is specified by one of the child-element which are 'MechanicalStage', 'PiezoElectricSate', or 'PiezoElectricObjective'

Parameters:

Name	Type	Description	Default
value	SamplePositioning_Type	The element to add	required

clearSamplePositioningGroup_List()

Clear the list of SamplePositioningGroup.

This element describes the objective lens and stage positioning device(s) available in this microscope. An Instrument may have more than one of these devices. The type of Focusing Device is specified by one of the child-element which are 'MechanicalStage', 'PiezoElectricSate', or 'PiezoElectricObjective'

setFocusStabilizationDevice_List(value)

Sets the list of FocusStabilizationDevice elements.

This element describes the focus stabilization device(s) available for this microscope

Parameters:

Name	Type	Description	Default
value	List[FocusStabilizationDevice]	The new list of FocusStabilizationDevice elements	required

getFocusStabilizationDevice_List()

Returns the list of FocusStabilizationDevice elements.

This element describes the focus stabilization device(s) available for this microscope

Returns:

Type	Description
List[FocusStabilizationDevice]	The list of FocusStabilizationDevice elements

addToFocusStabilizationDevice_List(value)

Adds a new FocusStabilizationDevice element to this object.

This element describes the focus stabilization device(s) available for this microscope

Parameters:

Name	Type	Description	Default
value	FocusStabilizationDevice	The element to add	required

clearFocusStabilizationDevice_List()

Clear the list of FocusStabilizationDevice.

This element describes the focus stabilization device(s) available for this microscope

setOpticsHolderGroup_List(value)

Sets the list of OpticsHolderGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[OpticsHolder_Type]	The new list of OpticsHolderGroup elements	required

getOpticsHolderGroup_List()

Returns the list of OpticsHolderGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[OpticsHolder_Type]	The list of OpticsHolderGroup elements

addToOpticsHolderGroup_List(value)

Adds a new OpticsHolderGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	OpticsHolder_Type	The element to add	required

clearOpticsHolderGroup_List()

Clear the list of OpticsHolderGroup.

No description available in the XSD standard.

setFilterGroup_List(value)

Sets the list of FilterGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[Filter_Type]	The new list of FilterGroup elements	required

getFilterGroup_List()

Returns the list of FilterGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Filter_Type]	The list of FilterGroup elements

addToFilterGroup_List(value)

Adds a new FilterGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Filter_Type	The element to add	required

clearFilterGroup_List()

Clear the list of FilterGroup.

No description available in the XSD standard.

setMirroringDeviceGroup_List(value)

Sets the list of MirroringDeviceGroup elements.

This element describes mirror component(s) available in this microscope

Parameters:

Name	Type	Description	Default
value	List[MirroringDevice_Type]	The new list of MirroringDeviceGroup elements	required

getMirroringDeviceGroup_List()

Returns the list of MirroringDeviceGroup elements.

This element describes mirror component(s) available in this microscope

Returns:

Type	Description
List[MirroringDevice_Type]	The list of MirroringDeviceGroup elements

addToMirroringDeviceGroup_List(value)

Adds a new MirroringDeviceGroup element to this object.

This element describes mirror component(s) available in this microscope

Parameters:

Name	Type	Description	Default
value	MirroringDevice_Type	The element to add	required

clearMirroringDeviceGroup_List()

Clear the list of MirroringDeviceGroup.

This element describes mirror component(s) available in this microscope

setLensGroup_List(value)

Sets the list of LensGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[Lens_Type]	The new list of LensGroup elements	required

getLensGroup_List()

Returns the list of LensGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Lens_Type]	The list of LensGroup elements

addToLensGroup_List(value)

Adds a new LensGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Lens_Type	The element to add	required

clearLensGroup_List()

Clear the list of LensGroup.

No description available in the XSD standard.

setPrism_List(value)

Sets the list of Prism elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[Prism]	The new list of Prism elements	required

getPrism_List()

Returns the list of Prism elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Prism]	The list of Prism elements

addToPrism_List(value)

Adds a new Prism element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Prism	The element to add	required

clearPrism_List()

Clear the list of Prism.

No description available in the XSD standard.

setPolarizationOptics_List(value)

Sets the list of PolarizationOptics elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[PolarizationOptics]	The new list of PolarizationOptics elements	required

getPolarizationOptics_List()

Returns the list of PolarizationOptics elements.

No description available in the XSD standard.

Returns:

Type	Description
List[PolarizationOptics]	The list of PolarizationOptics elements

addToPolarizationOptics_List(value)

Adds a new PolarizationOptics element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	PolarizationOptics	The element to add	required

clearPolarizationOptics_List()

Clear the list of PolarizationOptics.

No description available in the XSD standard.

setDetectorGroup_List(value)

Sets the list of DetectorGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[Detector_Type]	The new list of DetectorGroup elements	required

getDetectorGroup_List()

Returns the list of DetectorGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Detector_Type]	The list of DetectorGroup elements

addToDetectorGroup_List(value)

Adds a new DetectorGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Detector_Type	The element to add	required

clearDetectorGroup_List()

Clear the list of DetectorGroup.

No description available in the XSD standard.

setTIRFHardwareModule_List(value)

Sets the list of TIRFHardwareModule elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[TIRFHardwareModule]	The new list of TIRFHardwareModule elements	required

getTIRFHardwareModule_List()

Returns the list of TIRFHardwareModule elements.

No description available in the XSD standard.

Returns:

Type	Description
List[TIRFHardwareModule]	The list of TIRFHardwareModule elements

addToTIRFHardwareModule_List(value)

Adds a new TIRFHardwareModule element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	TIRFHardwareModule	The element to add	required

clearTIRFHardwareModule_List()

Clear the list of TIRFHardwareModule.

No description available in the XSD standard.

setConfocalScannerGroup_List(value)

Sets the list of ConfocalScannerGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[ConfocalScanner_Type]	The new list of ConfocalScannerGroup elements	required

getConfocalScannerGroup_List()

Returns the list of ConfocalScannerGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[ConfocalScanner_Type]	The list of ConfocalScannerGroup elements

addToConfocalScannerGroup_List(value)

Adds a new ConfocalScannerGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	ConfocalScanner_Type	The element to add	required

clearConfocalScannerGroup_List()

Clear the list of ConfocalScannerGroup.

No description available in the XSD standard.

setAcoustoOpticalDeviceGroup_List(value)

Sets the list of AcoustoOpticalDeviceGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[AcoustoOpticalDevice_Type]	The new list of AcoustoOpticalDeviceGroup elements	required

getAcoustoOpticalDeviceGroup_List()

Returns the list of AcoustoOpticalDeviceGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[AcoustoOpticalDevice_Type]	The list of AcoustoOpticalDeviceGroup elements

addToAcoustoOpticalDeviceGroup_List(value)

Adds a new AcoustoOpticalDeviceGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	AcoustoOpticalDevice_Type	The element to add	required

clearAcoustoOpticalDeviceGroup_List()

Clear the list of AcoustoOpticalDeviceGroup.

No description available in the XSD standard.

setElectroOpticalDeviceGroup_List(value)

Sets the list of ElectroOpticalDeviceGroup elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[ElectroOpticalDevice_Type]	The new list of ElectroOpticalDeviceGroup elements	required

getElectroOpticalDeviceGroup_List()

Returns the list of ElectroOpticalDeviceGroup elements.

No description available in the XSD standard.

Returns:

Type	Description
List[ElectroOpticalDevice_Type]	The list of ElectroOpticalDeviceGroup elements

addToElectroOpticalDeviceGroup_List(value)

Adds a new ElectroOpticalDeviceGroup element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	ElectroOpticalDevice_Type	The element to add	required

clearElectroOpticalDeviceGroup_List()

Clear the list of ElectroOpticalDeviceGroup.

No description available in the XSD standard.

setMicrolensArray_List(value)

Sets the list of MicrolensArray elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[MicrolensArray]	The new list of MicrolensArray elements	required

getMicrolensArray_List()

Returns the list of MicrolensArray elements.

No description available in the XSD standard.

Returns:

Type	Description
List[MicrolensArray]	The list of MicrolensArray elements

addToMicrolensArray_List(value)

Adds a new MicrolensArray element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	MicrolensArray	The element to add	required

clearMicrolensArray_List()

Clear the list of MicrolensArray.

No description available in the XSD standard.

setIntensityCalibrationTool_List(value)

Sets the list of IntensityCalibrationTool elements.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	List[IntensityCalibrationTool]	The new list of IntensityCalibrationTool elements	required

getIntensityCalibrationTool_List()

Returns the list of IntensityCalibrationTool elements.

No description available in the XSD standard.

Returns:

Type	Description
List[IntensityCalibrationTool]	The list of IntensityCalibrationTool elements

addToIntensityCalibrationTool_List(value)

Adds a new IntensityCalibrationTool element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	IntensityCalibrationTool	The element to add	required

clearIntensityCalibrationTool_List()

Clear the list of IntensityCalibrationTool.

No description available in the XSD standard.

setAnnotationRef(value)

Sets the value of the AnnotationRef element.

This is a simple multi-line comment or annotation describing this component.

Parameters:

Name	Type	Description	Default
value	AnnotationRef	The value to set	required

getAnnotationRef()

Returns the value of the AnnotationRef element.

This is a simple multi-line comment or annotation describing this component.

Returns:

Type	Description
AnnotationRef	The value of the element

resetAnnotationRef()

Resets the AnnotationRef element to an unset state.

This is a simple multi-line comment or annotation describing this component.

hasAnnotationRef()

Checks whether the optional AnnotationRef element is present.

This is a simple multi-line comment or annotation describing this component.

Returns:

Type	Description
boolean	true if the optional attribute has been set, false otherwise