Channel

Bases: NBOBaseClass

Represents the XML element Channel.

Each Image has to have at least one Plane and one Channel. The Channel element stores information about how the each Image Channel was acquired. The total number of Channel elements for a given Image must equal to SizeC.

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

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 Channel.

Parameters:

Name	Type	Description	Default
value	ChannelID_Type	The value to set	required

getID()

Returns the value of the ID attribute.

A unique identifier for this Channel.

Returns:

Type	Description
ChannelID_Type	The value of the attribute

resetID()

Resets the ID attribute to an unset state.

A unique identifier for this Channel.

hasID()

Checks whether the optional ID attribute is present.

A unique identifier for this Channel.

Returns:

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

setName(value)

Sets the value of the Name attribute.

A Name for this Channel that is suitable for presentation to the user.

Parameters:

Name	Type	Description	Default
value	Denomination_Type	The value to set	required

getName()

Returns the value of the Name attribute.

A Name for this Channel that is suitable for presentation to the user.

Returns:

Type	Description
Denomination_Type	The value of the attribute

resetName()

Resets the Name attribute to an unset state.

A Name for this Channel that is suitable for presentation to the user.

hasName()

Checks whether the optional Name attribute is present.

A Name for this Channel that is suitable for presentation to the user.

Returns:

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

setIlluminationType(value)

Sets the value of the IlluminationType attribute.

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

Parameters:

Name	Type	Description	Default
value	ImagingMethodList_Type	The value to set	required

getIlluminationType()

Returns the value of the IlluminationType attribute.

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

Returns:

Type	Description
ImagingMethodList_Type	The value of the attribute

resetIlluminationType()

Resets the IlluminationType attribute to an unset state.

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

hasIlluminationType()

Checks whether the optional IlluminationType attribute is present.

This field describes the Light Microscopy Illumination method performed in this case. Allowable terms were obtained from the Biological Imaging Methods Ontology (Fbbi; https://www.ebi.ac.uk/ols/ontologies/fbbi) Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345).

Returns:

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

setIlluminationTypeTermAcession(value)

Sets the value of the IlluminationTypeTermAcession attribute.

This field records the Accession ID for the term used to describe the Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

Parameters:

Name	Type	Description	Default
value	string	The value to set	required

getIlluminationTypeTermAcession()

Returns the value of the IlluminationTypeTermAcession attribute.

This field records the Accession ID for the term used to describe the Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

Returns:

Type	Description
string	The value of the attribute

resetIlluminationTypeTermAcession()

Resets the IlluminationTypeTermAcession attribute to an unset state.

This field records the Accession ID for the term used to describe the Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

hasIlluminationTypeTermAcession()

Checks whether the optional IlluminationTypeTermAcession attribute is present.

This field records the Accession ID for the term used to describe the Illumination Type. A sub-classes of Light Microscopy term (http://purl.obolibrary.org/obo/FBbi_00000345) is recommended.

Returns:

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

setContrastMethod(value)

Sets the value of the ContrastMethod attribute.

This field describes the technique used to achieve contrast for this Channel.

Parameters:

Name	Type	Description	Default
value	ChannelContrastMethod_Type	The value to set	required

getContrastMethod()

Returns the value of the ContrastMethod attribute.

This field describes the technique used to achieve contrast for this Channel.

Returns:

Type	Description
ChannelContrastMethod_Type	The value of the attribute

resetContrastMethod()

Resets the ContrastMethod attribute to an unset state.

This field describes the technique used to achieve contrast for this Channel.

hasContrastMethod()

Checks whether the optional ContrastMethod attribute is present.

This field describes the technique used to achieve contrast for this Channel.

Returns:

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

setColor(value)

Sets the value of the Color attribute.

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

Parameters:

Name	Type	Description	Default
value	Color_Type	The value to set	required

getColor()

Returns the value of the Color attribute.

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

Returns:

Type	Description
Color_Type	The value of the attribute

resetColor()

Resets the Color attribute to an unset state.

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

hasColor()

Checks whether the optional Color attribute is present.

This field records the Color used to render this Channel - encoded as RGBA. The default value is -1 corresponding #FFFFFFFF, so solid white (it is a signed 32 bit value).

Returns:

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

setSamplesPerPixel(value)

Sets the value of the SamplesPerPixel attribute.

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

Parameters:

Name	Type	Description	Default
value	PositiveInt_Type	The value to set	required

getSamplesPerPixel()

Returns the value of the SamplesPerPixel attribute.

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

Returns:

Type	Description
PositiveInt_Type	The value of the attribute

resetSamplesPerPixel()

Resets the SamplesPerPixel attribute to an unset state.

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

hasSamplesPerPixel()

Checks whether the optional SamplesPerPixel attribute is present.

This field is prevalently used for RGB Images and records the number of samples the detector takes to form each pixel value. [units:none]

Returns:

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

setFluorophore_List(value)

Sets the list of Fluorophore elements.

No description available in the XSD standard.

Parameters:

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

getFluorophore_List()

Returns the list of Fluorophore elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Fluorophore]	The list of Fluorophore elements

addToFluorophore_List(value)

Adds a new Fluorophore element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Fluorophore	The element to add	required

clearFluorophore_List()

Clear the list of Fluorophore.

No description available in the XSD standard.

setLightPath(value)

Sets the value of the LightPath element.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	LightPath	The value to set	required

getLightPath()

Returns the value of the LightPath element.

No description available in the XSD standard.

Returns:

Type	Description
LightPath	The value of the element

resetLightPath()

Resets the LightPath element to an unset state.

No description available in the XSD standard.

hasLightPath()

Checks whether the optional LightPath element is present.

No description available in the XSD standard.

Returns:

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

setExcitationCalibration_List(value)

Sets the list of ExcitationCalibration elements.

No description available in the XSD standard.

Parameters:

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

getExcitationCalibration_List()

Returns the list of ExcitationCalibration elements.

No description available in the XSD standard.

Returns:

Type	Description
List[ExcitationCalibration]	The list of ExcitationCalibration elements

addToExcitationCalibration_List(value)

Adds a new ExcitationCalibration element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	ExcitationCalibration	The element to add	required

clearExcitationCalibration_List()

Clear the list of ExcitationCalibration.

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