Fiji script for extracting image data from HDF5 files

H5_To_Tiff_Converter.groovy

#@File(style="directory", label="Input directory containing H5 files") inDir
#@File(style="directory", label="Output directory for saving converted TIFFs") outDir

import static groovy.io.FileType.FILES
import sc.fiji.hdf5.HDF5ImageJ
import ij.IJ

inDir.eachFileRecurse(FILES) { file ->
	if (file.name.endsWith(".h5")) {
		println("Converting "+ file)
		imp = HDF5ImageJ.hdf5read(file.getAbsolutePath(), "/Data")
		if (imp == null) {
			print(" Error! something failed")
		} else {
			outFile = new File(outDir, file.name.replace(".h5", ".tif"))
			IJ.save(imp, outFile.getAbsolutePath())
		}
		if (imp.isVisible()) imp.close()
	}
}