Pixels

Bases: NBOBaseClass

Represents the XML element Pixels.

The Pixels element is going to be removed in the future, but it is still required. This is just notice that the contents of Pixels will be moved up to Image in a future release. This is because there has only been 1 Pixels object in each Image for some time. The concept of multiple Pixels sets for one Image failed to take off. It is therefore redundant. The Image will be unreadable if any of the required Pixel attributes are missing. The Pixels themselves can be stored within the OME-XML compressed by Plane, and encoded in Base64. Or the Pixels may be stored in TIFF format. The Pixels element should contain a list of BinData or TiffData, each containing a single Plane of pixels. These Pixels elements, when read in document order, must produce a 5-D Pixel array of the size specified in this element, and in the dimension order specified by 'DimensionOrder'. All of the values in the Pixels object when present should match the same value stored in any associated TIFF format (e.g. SizeX should be the same). Where there is a mismatch our readers will take the value from the TIFF structure as overriding the value in the OME-XML. This is simply a pragmatic decision as it increases the likelihood of reading data from a slightly incorrect file.

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 component.

Parameters:

Name	Type	Description	Default
value	PixelsID_Type	The value to set	required

getID()

Returns the value of the ID attribute.

A Unique Identifier for this component.

Returns:

Type	Description
PixelsID_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

setDimensionOrder(value)

Sets the value of the DimensionOrder attribute.

This field records the order in which the individual Planes of data are interleaved in the Image.

Parameters:

Name	Type	Description	Default
value	PixelsDimensionOrder_Type	The value to set	required

getDimensionOrder()

Returns the value of the DimensionOrder attribute.

This field records the order in which the individual Planes of data are interleaved in the Image.

Returns:

Type	Description
PixelsDimensionOrder_Type	The value of the attribute

resetDimensionOrder()

Resets the DimensionOrder attribute to an unset state.

This field records the order in which the individual Planes of data are interleaved in the Image.

hasDimensionOrder()

Checks whether the optional DimensionOrder attribute is present.

This field records the order in which the individual Planes of data are interleaved in the Image.

Returns:

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

setSizeX(value)

Sets the value of the SizeX attribute.

This field records the X size of the Pixel data array.

Parameters:

Name	Type	Description	Default
value	PositiveInt_Type	The value to set	required

getSizeX()

Returns the value of the SizeX attribute.

This field records the X size of the Pixel data array.

Returns:

Type	Description
PositiveInt_Type	The value of the attribute

resetSizeX()

Resets the SizeX attribute to an unset state.

This field records the X size of the Pixel data array.

hasSizeX()

Checks whether the optional SizeX attribute is present.

This field records the X size of the Pixel data array.

Returns:

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

setSizeY(value)

Sets the value of the SizeY attribute.

This field records the Y size of the Pixel data array.

Parameters:

Name	Type	Description	Default
value	PositiveInt_Type	The value to set	required

getSizeY()

Returns the value of the SizeY attribute.

This field records the Y size of the Pixel data array.

Returns:

Type	Description
PositiveInt_Type	The value of the attribute

resetSizeY()

Resets the SizeY attribute to an unset state.

This field records the Y size of the Pixel data array.

hasSizeY()

Checks whether the optional SizeY attribute is present.

This field records the Y size of the Pixel data array.

Returns:

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

setSizeZ(value)

Sets the value of the SizeZ attribute.

This field records the number of Z-Planes acquired for this Image.

Parameters:

Name	Type	Description	Default
value	PositiveInt_Type	The value to set	required

getSizeZ()

Returns the value of the SizeZ attribute.

This field records the number of Z-Planes acquired for this Image.

Returns:

Type	Description
PositiveInt_Type	The value of the attribute

resetSizeZ()

Resets the SizeZ attribute to an unset state.

This field records the number of Z-Planes acquired for this Image.

hasSizeZ()

Checks whether the optional SizeZ attribute is present.

This field records the number of Z-Planes acquired for this Image.

Returns:

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

setSizeC(value)

Sets the value of the SizeC attribute.

This field records the number of Channels used in this Image

Parameters:

Name	Type	Description	Default
value	PositiveInt_Type	The value to set	required

getSizeC()

Returns the value of the SizeC attribute.

This field records the number of Channels used in this Image

Returns:

Type	Description
PositiveInt_Type	The value of the attribute

resetSizeC()

Resets the SizeC attribute to an unset state.

This field records the number of Channels used in this Image

hasSizeC()

Checks whether the optional SizeC attribute is present.

This field records the number of Channels used in this Image

Returns:

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

setSizeT(value)

Sets the value of the SizeT attribute.

This field records the number of Timepoints (often referred to as Frames) used in this Image.

Parameters:

Name	Type	Description	Default
value	PositiveInt_Type	The value to set	required

getSizeT()

Returns the value of the SizeT attribute.

This field records the number of Timepoints (often referred to as Frames) used in this Image.

Returns:

Type	Description
PositiveInt_Type	The value of the attribute

resetSizeT()

Resets the SizeT attribute to an unset state.

This field records the number of Timepoints (often referred to as Frames) used in this Image.

hasSizeT()

Checks whether the optional SizeT attribute is present.

This field records the number of Timepoints (often referred to as Frames) used in this Image.

Returns:

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

setPhysicalSizeX(value)

Sets the value of the PhysicalSizeX attribute.

This field records the real world Physical Width represented by a Pixel in this Image. This measure is often referred to as X Pixel Size.

Parameters:

Name	Type	Description	Default
value	PositiveFloat_Type	The value to set	required

getPhysicalSizeX()

Returns the value of the PhysicalSizeX attribute.

This field records the real world Physical Width represented by a Pixel in this Image. This measure is often referred to as X Pixel Size.

Returns:

Type	Description
PositiveFloat_Type	The value of the attribute

resetPhysicalSizeX()

Resets the PhysicalSizeX attribute to an unset state.

This field records the real world Physical Width represented by a Pixel in this Image. This measure is often referred to as X Pixel Size.

hasPhysicalSizeX()

Checks whether the optional PhysicalSizeX attribute is present.

This field records the real world Physical Width represented by a Pixel in this Image. This measure is often referred to as X Pixel Size.

Returns:

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

setPhysicalSizeXUnit(value)

Sets the value of the PhysicalSizeXUnit attribute.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	UnitsLength_Type	The value to set	required

getPhysicalSizeXUnit()

Returns the value of the PhysicalSizeXUnit attribute.

No description available in the XSD standard.

Returns:

Type	Description
UnitsLength_Type	The value of the attribute

resetPhysicalSizeXUnit()

Resets the PhysicalSizeXUnit attribute to an unset state.

No description available in the XSD standard.

hasPhysicalSizeXUnit()

Checks whether the optional PhysicalSizeXUnit attribute is present.

No description available in the XSD standard.

Returns:

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

setPhysicalSizeY(value)

Sets the value of the PhysicalSizeY attribute.

This field records the real world Physical Height represented by a Pixel in this Image. This measure is often referred to as Y Pixel Size.

Parameters:

Name	Type	Description	Default
value	PositiveFloat_Type	The value to set	required

getPhysicalSizeY()

Returns the value of the PhysicalSizeY attribute.

This field records the real world Physical Height represented by a Pixel in this Image. This measure is often referred to as Y Pixel Size.

Returns:

Type	Description
PositiveFloat_Type	The value of the attribute

resetPhysicalSizeY()

Resets the PhysicalSizeY attribute to an unset state.

This field records the real world Physical Height represented by a Pixel in this Image. This measure is often referred to as Y Pixel Size.

hasPhysicalSizeY()

Checks whether the optional PhysicalSizeY attribute is present.

This field records the real world Physical Height represented by a Pixel in this Image. This measure is often referred to as Y Pixel Size.

Returns:

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

setPhysicalSizeYUnit(value)

Sets the value of the PhysicalSizeYUnit attribute.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	UnitsLength_Type	The value to set	required

getPhysicalSizeYUnit()

Returns the value of the PhysicalSizeYUnit attribute.

No description available in the XSD standard.

Returns:

Type	Description
UnitsLength_Type	The value of the attribute

resetPhysicalSizeYUnit()

Resets the PhysicalSizeYUnit attribute to an unset state.

No description available in the XSD standard.

hasPhysicalSizeYUnit()

Checks whether the optional PhysicalSizeYUnit attribute is present.

No description available in the XSD standard.

Returns:

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

setPhysicalSizeZ(value)

Sets the value of the PhysicalSizeZ attribute.

This field records the real world Physical distance between the individual Z-Planes recorded for this Image. This measure is sometimes referred to as Z Pixel or Voxel Size.

Parameters:

Name	Type	Description	Default
value	PositiveFloat_Type	The value to set	required

getPhysicalSizeZ()

Returns the value of the PhysicalSizeZ attribute.

This field records the real world Physical distance between the individual Z-Planes recorded for this Image. This measure is sometimes referred to as Z Pixel or Voxel Size.

Returns:

Type	Description
PositiveFloat_Type	The value of the attribute

resetPhysicalSizeZ()

Resets the PhysicalSizeZ attribute to an unset state.

This field records the real world Physical distance between the individual Z-Planes recorded for this Image. This measure is sometimes referred to as Z Pixel or Voxel Size.

hasPhysicalSizeZ()

Checks whether the optional PhysicalSizeZ attribute is present.

This field records the real world Physical distance between the individual Z-Planes recorded for this Image. This measure is sometimes referred to as Z Pixel or Voxel Size.

Returns:

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

setPhysicalSizeZUnit(value)

Sets the value of the PhysicalSizeZUnit attribute.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	UnitsLength_Type	The value to set	required

getPhysicalSizeZUnit()

Returns the value of the PhysicalSizeZUnit attribute.

No description available in the XSD standard.

Returns:

Type	Description
UnitsLength_Type	The value of the attribute

resetPhysicalSizeZUnit()

Resets the PhysicalSizeZUnit attribute to an unset state.

No description available in the XSD standard.

hasPhysicalSizeZUnit()

Checks whether the optional PhysicalSizeZUnit attribute is present.

No description available in the XSD standard.

Returns:

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

setTimeIncrement(value)

Sets the value of the TimeIncrement attribute.

In cases in which a time series is acquired with a global timing specification setting, this field describes the time between each sequential plane (or frame) in the series (i.e., from the start of time point 1 to the start of time point 2). Examples include, a video stream or a multi-dimensional Acquisition routine. Note that, this field is not intended to substitute the Timestamp attribute recorded in Plane. Also note that in case this field is not relevant e.g. a time lapse Acquisition with irregular increments, the value -1 should be used to indicate that only the Timestamps (in the Plane element) are valid.

Parameters:

Name	Type	Description	Default
value	PositiveFloat_Type	The value to set	required

getTimeIncrement()

Returns the value of the TimeIncrement attribute.

In cases in which a time series is acquired with a global timing specification setting, this field describes the time between each sequential plane (or frame) in the series (i.e., from the start of time point 1 to the start of time point 2). Examples include, a video stream or a multi-dimensional Acquisition routine. Note that, this field is not intended to substitute the Timestamp attribute recorded in Plane. Also note that in case this field is not relevant e.g. a time lapse Acquisition with irregular increments, the value -1 should be used to indicate that only the Timestamps (in the Plane element) are valid.

Returns:

Type	Description
PositiveFloat_Type	The value of the attribute

resetTimeIncrement()

Resets the TimeIncrement attribute to an unset state.

In cases in which a time series is acquired with a global timing specification setting, this field describes the time between each sequential plane (or frame) in the series (i.e., from the start of time point 1 to the start of time point 2). Examples include, a video stream or a multi-dimensional Acquisition routine. Note that, this field is not intended to substitute the Timestamp attribute recorded in Plane. Also note that in case this field is not relevant e.g. a time lapse Acquisition with irregular increments, the value -1 should be used to indicate that only the Timestamps (in the Plane element) are valid.

hasTimeIncrement()

Checks whether the optional TimeIncrement attribute is present.

In cases in which a time series is acquired with a global timing specification setting, this field describes the time between each sequential plane (or frame) in the series (i.e., from the start of time point 1 to the start of time point 2). Examples include, a video stream or a multi-dimensional Acquisition routine. Note that, this field is not intended to substitute the Timestamp attribute recorded in Plane. Also note that in case this field is not relevant e.g. a time lapse Acquisition with irregular increments, the value -1 should be used to indicate that only the Timestamps (in the Plane element) are valid.

Returns:

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

setTimeIncrementUnit(value)

Sets the value of the TimeIncrementUnit attribute.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	UnitsTime_Type	The value to set	required

getTimeIncrementUnit()

Returns the value of the TimeIncrementUnit attribute.

No description available in the XSD standard.

Returns:

Type	Description
UnitsTime_Type	The value of the attribute

resetTimeIncrementUnit()

Resets the TimeIncrementUnit attribute to an unset state.

No description available in the XSD standard.

hasTimeIncrementUnit()

Checks whether the optional TimeIncrementUnit attribute is present.

No description available in the XSD standard.

Returns:

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

setPixelType(value)

Sets the value of the PixelType attribute.

This field records the data type used to represent the Pixel Intensity in the Image.

Parameters:

Name	Type	Description	Default
value	PixelType_Type	The value to set	required

getPixelType()

Returns the value of the PixelType attribute.

This field records the data type used to represent the Pixel Intensity in the Image.

Returns:

Type	Description
PixelType_Type	The value of the attribute

resetPixelType()

Resets the PixelType attribute to an unset state.

This field records the data type used to represent the Pixel Intensity in the Image.

hasPixelType()

Checks whether the optional PixelType attribute is present.

This field records the data type used to represent the Pixel Intensity in the Image.

Returns:

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

setInterleaved(value)

Sets the value of the Interleaved attribute.

This field records the order in which the Channels are arranged within the data block: True if Channels are stored RGBRGBRGB...; False if Channels are stored RRR...GGG...BBB…

Parameters:

Name	Type	Description	Default
value	boolean	The value to set	required

getInterleaved()

Returns the value of the Interleaved attribute.

This field records the order in which the Channels are arranged within the data block: True if Channels are stored RGBRGBRGB...; False if Channels are stored RRR...GGG...BBB…

Returns:

Type	Description
boolean	The value of the attribute

resetInterleaved()

Resets the Interleaved attribute to an unset state.

This field records the order in which the Channels are arranged within the data block: True if Channels are stored RGBRGBRGB...; False if Channels are stored RRR...GGG...BBB…

hasInterleaved()

Checks whether the optional Interleaved attribute is present.

This field records the order in which the Channels are arranged within the data block: True if Channels are stored RGBRGBRGB...; False if Channels are stored RRR...GGG...BBB…

Returns:

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

setSignificantBits(value)

Sets the value of the SignificantBits attribute.

This field records the number of bits within the type storing each Pixel value that are significant. e.g.,. you can store 12-bit data within a 16-bit type. This does not reduce the storage requirements but can be a useful indicator when processing or viewing the Image data.

Parameters:

Name	Type	Description	Default
value	PositiveInt_Type	The value to set	required

getSignificantBits()

Returns the value of the SignificantBits attribute.

This field records the number of bits within the type storing each Pixel value that are significant. e.g.,. you can store 12-bit data within a 16-bit type. This does not reduce the storage requirements but can be a useful indicator when processing or viewing the Image data.

Returns:

Type	Description
PositiveInt_Type	The value of the attribute

resetSignificantBits()

Resets the SignificantBits attribute to an unset state.

This field records the number of bits within the type storing each Pixel value that are significant. e.g.,. you can store 12-bit data within a 16-bit type. This does not reduce the storage requirements but can be a useful indicator when processing or viewing the Image data.

hasSignificantBits()

Checks whether the optional SignificantBits attribute is present.

This field records the number of bits within the type storing each Pixel value that are significant. e.g.,. you can store 12-bit data within a 16-bit type. This does not reduce the storage requirements but can be a useful indicator when processing or viewing the Image data.

Returns:

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

setBigEndian(value)

Sets the value of the BigEndian attribute.

This field is True if the pixels data was written in BigEndian order. If this value is present, it should match the value used in BinData or TiffData. If it is not, a reader should be used that honors the value used in the BinData or TiffData. This value is useful for MetadataOnly files and is to allow for future storage solutions.

Parameters:

Name	Type	Description	Default
value	boolean	The value to set	required

getBigEndian()

Returns the value of the BigEndian attribute.

This field is True if the pixels data was written in BigEndian order. If this value is present, it should match the value used in BinData or TiffData. If it is not, a reader should be used that honors the value used in the BinData or TiffData. This value is useful for MetadataOnly files and is to allow for future storage solutions.

Returns:

Type	Description
boolean	The value of the attribute

resetBigEndian()

Resets the BigEndian attribute to an unset state.

This field is True if the pixels data was written in BigEndian order. If this value is present, it should match the value used in BinData or TiffData. If it is not, a reader should be used that honors the value used in the BinData or TiffData. This value is useful for MetadataOnly files and is to allow for future storage solutions.

hasBigEndian()

Checks whether the optional BigEndian attribute is present.

This field is True if the pixels data was written in BigEndian order. If this value is present, it should match the value used in BinData or TiffData. If it is not, a reader should be used that honors the value used in the BinData or TiffData. This value is useful for MetadataOnly files and is to allow for future storage solutions.

Returns:

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

setPlane_List(value)

Sets the list of Plane elements.

No description available in the XSD standard.

Parameters:

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

getPlane_List()

Returns the list of Plane elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Plane]	The list of Plane elements

addToPlane_List(value)

Adds a new Plane element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Plane	The element to add	required

clearPlane_List()

Clear the list of Plane.

No description available in the XSD standard.

setChannel_List(value)

Sets the list of Channel elements.

No description available in the XSD standard.

Parameters:

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

getChannel_List()

Returns the list of Channel elements.

No description available in the XSD standard.

Returns:

Type	Description
List[Channel]	The list of Channel elements

addToChannel_List(value)

Adds a new Channel element to this object.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Channel	The element to add	required

clearChannel_List()

Clear the list of Channel.

No description available in the XSD standard.

setAdditionalDimensionMap(value)

Sets the value of the AdditionalDimensionMap element.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	AdditionalDimensionMap	The value to set	required

getAdditionalDimensionMap()

Returns the value of the AdditionalDimensionMap element.

No description available in the XSD standard.

Returns:

Type	Description
AdditionalDimensionMap	The value of the element

resetAdditionalDimensionMap()

Resets the AdditionalDimensionMap element to an unset state.

No description available in the XSD standard.

hasAdditionalDimensionMap()

Checks whether the optional AdditionalDimensionMap element is present.

No description available in the XSD standard.

Returns:

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

setpixels_choice(value)

Sets the value of the pixels_choice element.

No description available in the XSD standard.

Parameters:

Name	Type	Description	Default
value	Pixels_Choice	The value to set	required

getpixels_choice()

Returns the value of the pixels_choice element.

No description available in the XSD standard.

Returns:

Type	Description
Pixels_Choice	The value of the element

resetpixels_choice()

Resets the pixels_choice element to an unset state.

No description available in the XSD standard.

haspixels_choice()

Checks whether the optional pixels_choice element is present.

No description available in the XSD standard.

Returns:

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