Units

A number of properties in the OME model are physical measurements which inherently have a unit associated with them. Earlier versions of OME defined a default unit for the measurement. Now users, clients, and acquisition systems can specify the unit themselves rather than converting their internal unit to the OME default.

Supported units

Each of the supported units contain a number of values from the International System of Units (SI) in the most common prefixes from yotta (10^24) to yocto (10^-24). The Length unit also contains values from the Imperial system as well as internal values which are internal to OME: reference frame and pixel.

Unit fields

The following fields in the OMERO model have a unit type:

Class	Field	Type	Default value
Channel	EmissionWavelength	Length	nm
Channel	ExcitationWavelength	Length	nm
Channel	PinholeSize	Length	µm
Detector	Voltage	ElectricPotential	V
DetectorSettings	ReadOutRate	Frequency	MHz
DetectorSettings	Voltage	ElectricPotential	V
ImagingEnvironment	AirPressure	Pressure	mbar
ImagingEnvironment	Temperature	Temperature	°C
Laser	RepetitionRate	Frequency	Hz
Laser	Wavelength	Length	nm
LightSource	Power	Power	mW
LightSourceSettings	Wavelength	Length	nm
Objective	WorkingDistance	Length	µm
Pixels	PhysicalSizeX	Length	µm
Pixels	PhysicalSizeY	Length	µm
Pixels	PhysicalSizeZ	Length	µm
Pixels	TimeIncrement	Time	s
Plane	DeltaT	Time	s
Plane	ExposureTime	Time	s
Plane	PositionX	Length	reference frame
Plane	PositionY	Length	reference frame
Plane	PositionZ	Length	reference frame
Plate	WellOriginX	Length	reference frame
Plate	WellOriginY	Length	reference frame
Shape	FontSize	Length	pt
Shape	StrokeWidth	Length	pixel
StageLabel	X	Length	reference frame
StageLabel	Y	Length	reference frame
StageLabel	Z	Length	reference frame
TransmittanceRange	CutIn	Length	nm
TransmittanceRange	CutInTolerance	Length	nm
TransmittanceRange	CutOut	Length	nm
TransmittanceRange	CutOutTolerance	Length	nm
WellSample	PositionX	Length	reference frame
WellSample	PositionY	Length	reference frame

Units of type reference frame cannot be assumed comparable to units from other properties including those with type reference frame.

Unit objects

Each unit quantity consists of a double-precision scalar and an enumeration which chooses one of the pre-defined values from the model. In code, uppercase spellings of the enumerations are used, while in the schema, in OME-XML files, and in the database, the Unicode symbol for the unit is used.

Language	Representation
Ice	enum UnitsLength { MICROM, … };
Java and Python	omero.model.enums.UnitsLength.MICROM
C++	omero::model::enums::MICROM
PostgreSQL	‘µm’::unitslength

Defining a unit

Pixels p = ...; // Defined elsewhere
Length l = new LengthI(2.1, UnitsLength.MICROM); // µm
p.setPhysicalSizeX(l);
p.setPhysicalSizeY(l);
iUpdatePrx.saveObject(p);

The above stores a Pixels object in the database with X and Y physical lengths of “µm”.

Converting a unit

Often a measurement will not be in the most convenient unit for display, e.g. 0.00001 mm. could better be expressed in microns. In order to convert between units, pass the measurement that you have available to a constructor of the same type, passing in the target unit that you would like to see:

Pixels p = ...; // As saved above
Length l1 = p.getPhysicalSizeX(); // 2.1 microns
Length l2 = new LengthI(x1, UnitsLength.NM); // As nanometers

Getting a symbol

The enumerations used in the “units” field of each measurement is of type omero.model.enums.UnitsNAME where NAME is Length, Temperature, etc. These members of that enumeration are all uppercased, code-safe versions of the unit name. To get the symbol as defined in the SI specification, for example, use the getSymbol method:

Length l1 = ...; // As above
l1.getSymbol(); // Returns "µm"

Querying units

In HQL queries, the scalar and the enumeration value can be separately retrieved.

select planeInfo.exposureTime.value from PlaneInfo planeInfo ...

will retrieve just the double scalar value while

select planeInfo.exposureTime.unit from PlaneInfo planeInfo ...

will retrieve a string representation of the enum which can be used in each language to create an enum object, e.g.:

UnitsTime.valueOf(unit); // Java
getattr(UnitsTime, unit) # Python

To load the symbolic representation of the enum which is used internally in the database and is more concise, use an HQL cast:

select cast(planeInfo.exposureTime.unit as text) from PlaneInfo planeInfo ...

Returning the entire unit quantity will result in a hash map with the various representations:

select planeInfo.exposureTime from PlaneInfo planeInfo ...
{'symbol': 's', 'unit': 'SECOND', 'value': 1.2000000476837158}