A groovy script usable in FIJI to export images of a lif file (should work with other bioformats supported format). User can specify the series to export using comma (1,2,3) or a range using dash (1-5) , or nothing to export all series #BIOP #FIJI #groovy #export #bioformats

ijs-export_lif_zprojAvailable.groovy

#@ File image_path 
#@ String seriesNbr
#@ String (choices={"max","avg","sum","none"}) zProj


import org.apache.commons.io.FilenameUtils

import ij.*
import ij.plugin.ZProjector
import ij.io.FileSaver	

import loci.formats.ImageReader
import loci.plugins.BF
import loci.plugins.in.ImporterOptions


/*
 *  Get image info : dir, name and create the output_dir
 */ 

dir = image_path.getParent()
image_name = image_path.getName() 
image_basename = FilenameUtils.getBaseName( image_name )
	
println dir + image_name

	
// From the user choice, we create a serie , or range of serie
def seriesIdxes 
if (seriesNbr.isInteger()) { 
	seriesIdxes = ( seriesNbr.toInteger() )
} else { 

	if (  seriesNbr =~ /.*,.*/){ 
		seriesIdxes = ( seriesNbr.split(",") )
	} else if (  seriesNbr =~ /.*-.*/){
		range = seriesNbr.split("-")
		seriesIdxes = ( (range[0] as int) .. (range[1] as int) )

	} else if (seriesNbr.equals("")) {
		img_rd = new ImageReader()
		img_rd.setId( image_path.toString() )
		seriesCount = img_rd.getSeriesCount()
		seriesIdxes = ( 0 .. seriesCount-1 )
	} else {
		println "Please enter a valid Serie index(es) :\n- single number \n- a list on number comma separated (1,3,9) \n- a range eg (2-8)"
		return
	}
	
}

// create an output dir and prepare output file path
def output_dir = new File( dir , "output" )
output_dir.mkdirs()


imp_option = new ImporterOptions()
imp_option.setId(image_path.toString())

seriesIdxes.each{ serieIdx ->	

	
	imp_option.setSeriesOn(serieIdx, true)
	// returns a ImagePlus[]
	bfimp = BF.openImagePlus(imp_option) 
	
	// do a projection
	def final_imp = bfimp.first()
	image_lif_name = final_imp.getTitle()
	image_lif_name = image_lif_name.replaceAll("/","_") // to handle sub folder within lif ile
	
	if ( ! zProj.equals("none") ) final_imp = ZProjector.run(bfimp[0], zProj); 
	
	
	def output_path = new File ( output_dir , image_lif_name+"_"+zProj+"zProj_i" + serieIdx +".tif" )
	
	// save file
	def fs = new FileSaver(final_imp)
	fs.saveAsTiff(output_path.toString() )

 	println "From : "+ image_basename + " : " + serieIdx +" serie done!"
	imp_option.setSeriesOn(serieIdx, false)
}

return