New Semantic Types
Defining New Semantic Types in OME-XMLSemantic types (STs) are defined in XML according to the Semantic Type definition schema.
The following excerpt from OME Core Types
Instrument.ome
defines the ST <SemanticType Name= "LightSource" AppliesTo = "G"> <Element Name= "Manufacturer" DBLocation = "LIGHT_SOURCES.MANUFACTURER" DataType = "string"/> <Element Name= "Model" DBLocation = "LIGHT_SOURCES.MODEL" DataType = "string"/> <Element Name= "SerialNumber" DBLocation = "LIGHT_SOURCES.SERIAL_NUMBER" DataType = "string"/> <Element Name= "Instrument" DBLocation = "LIGHT_SOURCES.INSTRUMENT" DataType = "reference" RefersTo = "Instrument"/> </SemanticType> When a ST definition XML file is imported into OME, it is interpreted to produce the appropriate database tables and columns. The ST's attributes are stored as rows of the ST's table: ome=# select * from light_sources; attribute_id | model | instrument | serial_number | module_execution_id | manufacturer --------------+-------------------+------------+---------------+---------------------+-------------- 93 | WMD Laser | 92 | 123skdjhf1234 | 14 | Olympus 95 | Realy Bright Lite | 92 | 123skdjhf1456 | 14 | Olympus (2 rows) Pixels and Derived Semantic Types
Attributes of ST
A lot of logic in the OME backend deals with
We have developed a special, ad-hock, sort of inheritance based on the <SemanticType Name="FrequencySpace" AppliesTo="I"> <Description> The frequency space (i.e. the Fourier Transform of Real space) is, in general, complex. We represent it by its magnitude and phase rather than its real and imaginary parts. Magnitude(F) = sqrt (real(F)^2 + imag(F)^2). Also Phase(F) = atan(imag(F)/real(F)). The magnitude is encoded as channel 0 and the phase is channel 1 of the output pixels set. </Description> <Element Name="Parent" DBLocation="FOURIER.MAG_AND_PHASE" DataType = "reference" RefersTo = "PixelsSlice"/> </SemanticType> Document Actions |