xml_merge.bsh

import ij.IJ;
import ij.ImagePlus;
import java.lang.Runtime;
import java.io.File;
import java.io.FilenameFilter;
 
runtime = Runtime.getRuntime();
System.out.println(runtime.availableProcessors() + " cores available for multi-threading");


System.out.println( "Load Parameters:");

	// Getting parameters from job file
image_file_directory = System.getProperty( "image_file_directory" );

merged_xml = System.getProperty( "merged_xml" );
if ( ! merged_xml.endsWith(".xml") )
    merged_xml = merged.xml + ".xml";
     
// Printing parameters into output file
System.out.println( "directory=" + image_file_directory );
System.out.println( "merged_xml=" + merged_xml );

System.out.println( "=======================================================" );
System.out.println( "Start to merge .xml files" );

// Executing Fiji plugin
try {
IJ.run("Merge Cluster Jobs", 
	"directory=" + image_file_directory + " " + 	
	"filename_contains=job_ " + 
	"filename_also_contains=.xml " +
	"display " +
	"merged_xml=" + merged_xml);
}
catch ( e ) { 

    print( "[xml_merge] caught exception: "+e );
    //important to fail the process if exception occurs
    runtime.exit(1);
    
}

/* shutdown */
runtime.exit(0);