Note
This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected before the end of 2016.
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.
See also
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.
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.
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 |
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”.
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
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"
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}