ctrueden/scifio-metadata.groovy

## scifio-metadata.groovy
#@ ImageJ ij
#@ File file

import io.scif.config.SCIFIOConfig;
import io.scif.config.SCIFIOConfig.ImgMode;
import io.scif.ome.OMEMetadata

// Open and display a file as a cell image.
config = new SCIFIOConfig().imgOpenerSetImgModes(ImgMode.CELL)
dataset = ij.scifio().datasetIO().open(file.getAbsolutePath(), config)
ij.ui().show(dataset)

// Extract metadata from a file opened in this manner.
globalMeta = dataset.getProperties().get("scifio.metadata.global")
imageMeta = dataset.getProperties().get("scifio.metadata.image")

// --OR-- We can read _only_ the metadata from a file without opening pixels.
//globalMeta = ij.scifio().initializer().parseMetadata(file.getAbsolutePath())

// Convert globalMeta above to omeMeta
omeMeta = new OMEMetadata(ij.context())
ij.scifio().translator().translate(globalMeta, omeMeta, true)

// Access some metadata from the OME trove. The below
// is just a small example of what the OME API provides.
omexml = omeMeta.getRoot()
iCount = omexml.getInstrumentCount()
for (iIndex = 0; iIndex < iCount; iIndex++) {
	println("Instrument #" + iIndex + ":")
	println("\tID = " + omexml.getInstrumentID(iIndex))
	oCount = omexml.getObjectiveCount(iIndex)
	for (oIndex = 0; oIndex < oCount; oIndex++) {
		println("\tObjective #" + oIndex + ":")
		println("\t\tID = " + omexml.getObjectiveID(iIndex, oIndex))
		println("\t\tLensNA = " + omexml.getObjectiveLensNA(iIndex, oIndex))
		println("\t\tModel = " + omexml.getObjectiveModel(iIndex, oIndex))
		println("\t\tManufacturer = " + omexml.getObjectiveManufacturer(iIndex, oIndex))
	}
}
	#@ ImageJ ij
	#@ File file

	import io.scif.config.SCIFIOConfig;
	import io.scif.config.SCIFIOConfig.ImgMode;
	import io.scif.ome.OMEMetadata

	// Open and display a file as a cell image.
	config = new SCIFIOConfig().imgOpenerSetImgModes(ImgMode.CELL)
	dataset = ij.scifio().datasetIO().open(file.getAbsolutePath(), config)
	ij.ui().show(dataset)

	// Extract metadata from a file opened in this manner.
	globalMeta = dataset.getProperties().get("scifio.metadata.global")
	imageMeta = dataset.getProperties().get("scifio.metadata.image")

	// --OR-- We can read _only_ the metadata from a file without opening pixels.
	//globalMeta = ij.scifio().initializer().parseMetadata(file.getAbsolutePath())

	// Convert globalMeta above to omeMeta
	omeMeta = new OMEMetadata(ij.context())
	ij.scifio().translator().translate(globalMeta, omeMeta, true)

	// Access some metadata from the OME trove. The below
	// is just a small example of what the OME API provides.
	omexml = omeMeta.getRoot()
	iCount = omexml.getInstrumentCount()
	for (iIndex = 0; iIndex < iCount; iIndex++) {
	println("Instrument #" + iIndex + ":")
	println("\tID = " + omexml.getInstrumentID(iIndex))
	oCount = omexml.getObjectiveCount(iIndex)
	for (oIndex = 0; oIndex < oCount; oIndex++) {
	println("\tObjective #" + oIndex + ":")
	println("\t\tID = " + omexml.getObjectiveID(iIndex, oIndex))
	println("\t\tLensNA = " + omexml.getObjectiveLensNA(iIndex, oIndex))
	println("\t\tModel = " + omexml.getObjectiveModel(iIndex, oIndex))
	println("\t\tManufacturer = " + omexml.getObjectiveManufacturer(iIndex, oIndex))
	}
	}