Removes all 32 bits file from an Operetta dataset - crops values above 65535 #BIOP #Fiji #Operetta

SanitizeOperetta32bitsTiffs.groovy

#@File(label = "Select the 'Images' folder of your Operetta dataset", style = "directory") folder
#@TaskService taskService


def task = taskService.createTask("Operetta Sanitizer ")

try {
	task.setStatusMessage("Listing files...")
	task.setProgressMaximum(0)
	def fileList = folder.list() as List
	
	task.setStatusMessage("number of files: "+fileList.size()+" dataset:"+FilenameUtils.getName(folder.getParent()))
	task.setProgressMaximum(fileList.size())
	
	def lock = new Object()
	fileList.parallelStream().forEach{filename -> {
		def file = new File(folder, filename)
		//IJ.log(file.getName())
		String extension = FilenameUtils.getExtension(filename)
		if (("tiff".equals(extension))||("tif".equals(extension))) {
			def reader = new MinimalTiffReader()
			try {
				def omeMeta = MetadataTools.createOMEXMLMetadata()
    			reader.setMetadataStore(omeMeta)
	        	reader.setId(file.getAbsolutePath())
        		reader.setSeries(0)
	        	def pixelType = omeMeta.getPixelsType(0)
				reader.close()
	        	if (pixelType == PixelType.FLOAT) {
            		println(file.getName()+" is 32 bits! Converting to 16 bits")
            		def image = (new Opener()).openImage(file.getAbsolutePath())
            		image.getProcessor().setMinAndMax(0, 65535);
            		image.setProcessor(image.getProcessor().convertToShortProcessor(true))
            		String path = file.getAbsolutePath()
            		file.delete()
            		new FileSaver(image).saveAsTiff(path)        		
        		}
			} catch (def e) {
				IJ.log(e.getMessage())
			}
		}
		synchronized(lock) {
			task.setProgressValue(task.getProgressValue()+1)
		}
	}}
} finally {
	task.run(() -> {})
}

import org.apache.commons.io.FilenameUtils
import ij.IJ
import loci.formats.in.MinimalTiffReader
import loci.formats.meta.IMetadata
import ome.xml.model.enums.PixelType
import loci.formats.MetadataTools
import ij.io.Opener
import ij.io.FileSaver