export_output.bsh

// Load Fiji dependencies
import ij.IJ; 		// calls imagej
import ij.Prefs; 	// calls imagej settings
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");

Prefs.setThreads(1); 	// defines the number of threads allowed 
print("Threads: "+Prefs.getThreads()); // prints thread setting in output

System.out.println("Start loading parameters");

// Directory, and first .czi
System.out.println("=========================================================");
System.out.println("Directory:");
image_file_directory = System.getProperty( "image_file_directory" );
first_xml_filename = System.getProperty( "first_xml_filename" );
hdf5_xml_filename = System.getProperty( "hdf5_xml_filename" );

System.out.println( "dir=" + image_file_directory );
System.out.println( "xml_filename=" + first_xml_filename );
System.out.println( "hdf5_xml_filename=" + hdf5_xml_filename );

// Dataset settings
System.out.println("=========================================================");
System.out.println("Dataset:");
resave_angle = System.getProperty( "resave_angle" );
resave_channel = System.getProperty( "resave_channel" );
resave_illumination = System.getProperty( "resave_illumination" );
resave_timepoint = System.getProperty( "resave_timepoint" );

System.out.println( "resave_angle=" + resave_angle );
System.out.println( "resave_channel=" + resave_channel );
System.out.println( "resave_illumination=" + resave_illumination );
System.out.println( "resave_timepoint=" + resave_timepoint);

// Hdf5 settings
System.out.println("=========================================================");
System.out.println("Hdf5 settings:");
subsampling_factors = System.getProperty( "subsampling_factors" );
hdf5_chunk_sizes = System.getProperty( "hdf5_chunk_sizes" );
timepoints_per_partition = System.getProperty( "timepoints_per_partition" );
setups_per_partition = System.getProperty( "setups_per_partition" );
run_only_job_number = System.getProperty( "run_only_job_number" );

System.out.println( "subsampling_factors=" + subsampling_factors);
System.out.println( "hdf5_chunk_sizes=" + hdf5_chunk_sizes );
System.out.println( "timepoints_per_partition=" + timepoints_per_partition );
System.out.println( "setups_per_partition=" + setups_per_partition );
System.out.println( "run_only_job_number=" + run_only_job_number );

// Add a switch for choosing between 16 or 32 bit
output_data_type = System.getProperty( "output_data_type" );
System.out.println( "Output Datatype = " + output_data_type );

convert_32bit = System.getProperty( "convert_32bit" );

if ( output_data_type.equalsIgnoreCase( "32Bit" ) )
	{
		data_string = "convert_32bit=" + convert_32bit;
	}
else if ( output_data_type.equalsIgnoreCase( "16Bit" ) )
	{
		data_string = "";
	}

System.out.println( "Data string = " + data_string );

// Activate cluster processing
System.out.println("=========================================================");
System.out.println("Cluster setting:");
try{
IJ.run("Toggle Cluster Processing", "display_cluster");
}
catch ( e ) { 
	print( "[export_output::cluster setting] caught exception: "+e );
	//important to fail the process if exception occurs
	runtime.exit(1);
}
	
// Executes Fiji plugin
System.out.println("=========================================================");
System.out.println("Start plugin:");
try{
IJ.run("As HDF5",
	"select_xml=" + image_file_directory + first_xml_filename + ".xml " +
	"resave_angle=[" + resave_angle + "] " +
	"resave_channel=[" + resave_channel + "] " +
	"resave_illumination=[" + resave_illumination + "] " +
	"resave_timepoint=[" + resave_timepoint + "] " +
	"manual_mipmap_setup " +
	"subsampling_factors=[" + subsampling_factors + "] " +
	"hdf5_chunk_sizes=[" + hdf5_chunk_sizes + "] " +
	"split_hdf5 " +
	"timepoints_per_partition=" + timepoints_per_partition + " " +
	"setups_per_partition=" + setups_per_partition + " " +
	"run_only_job_number=" + run_only_job_number + " " +
	"use_deflate_compression " +
	"export_path=" + image_file_directory + hdf5_xml_filename + " " +
	data_string + "");
}
catch ( e ) { 
	print( "[export_output::resaving] caught exception: "+e );
	//important to fail the process if exception occurs
	runtime.exit(1);
}
	
/* shutdown */
System.exit(0);