define_tif_zip.bsh

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
System.out.println("=========================================================");
System.out.println("Directory:");
image_file_directory = System.getProperty( "image_file_directory" );
xml_filename = System.getProperty( "xml_filename" );

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

// Dataset settings
System.out.println("=========================================================");
System.out.println("Dataset:");
image_file_pattern = System.getProperty( "image_file_pattern" );
type_of_dataset = System.getProperty( "type_of_dataset" );
timepoints = System.getProperty( "timepoints" );
angles = System.getProperty( "angles" );

System.out.println( "image_file_pattern = " + image_file_pattern );
System.out.println( "type_of_dataset = " + type_of_dataset );
System.out.println( "timepoints = " + timepoints );
System.out.println( "angles = " + angles );

multiple_timepoints = System.getProperty( "multiple_timepoints" );
multiple_channels = System.getProperty( "multiple_channels" );
multiple_illumination_directions = System.getProperty( "multiple_illumination_directions" );
multiple_angles = System.getProperty( "multiple_angles" );
imglib_container = System.getProperty( "imglib_container" );

System.out.println( "multiple_timepoints = " + multiple_timepoints );
System.out.println( "multiple_channels = " + multiple_channels );
System.out.println( "multiple_illumination_directions = " + multiple_illumination_directions );
System.out.println( "multiple_angles = " + multiple_angles );
System.out.println( "imglib_container = " + imglib_container );

System.out.println("---------------------------------------------------------");
System.out.println("Channel setting:");

// Channel switch: parses channels and determines if Single or Multi Channel
// assembles the appropriate string for the channel setting
channels = System.getProperty( "channels" ); 

String channel_string = null;
		
String delims = "[,]";
String[] channel_token = channels.split(delims);
		
if (channels.equalsIgnoreCase(""))
	{
	System.out.println("Warning: There are no channels set");
	}
			
else if ( channel_token.length == 1  )
	{
	channel_string="";
	System.out.println("Single Channel");
	}
		
	else if ( channel_token.length > 1)
	{
	channel_string = "channels_=" + channels + " ";
	System.out.println("Multi Channel");
	}
		
System.out.println( "Channels = " + channel_string );


System.out.println("---------------------------------------------------------");
System.out.println("Illumination setting:");
// Illuminatin switch: parses illumination and determines if there is a single
// or multiple illumination sides and then assembles the illum_string

illumination = System.getProperty( "illumination" );

String illum_string = null;
		
String delims = "[,]";
String[] illum_token = illumination.split(delims);
		
if (illumination.equalsIgnoreCase(""))
	{
	System.out.println("Warning: There are no illuminations set");
	}
			
	else if ( illum_token.length == 1  )
	{
	illum_string="";
	System.out.println("One illumination side or fused illumination");
	}
		
	else if ( illum_token.length > 1)
	{
	illum_string = "illumination_=" + illumination + " ";
	System.out.println("Dual Illumination sides");
	}
		
System.out.println( "Illuminations = " + illum_string );

// Calibaration
// Calibaration
System.out.println("=========================================================");
System.out.println("Calibration:");
manual_calibration_tif = System.getProperty( "manual_calibration_tif" );
float czi_pixel_distance_x = Float.parseFloat( System.getProperty( "pixel_distance_x" ) );
float czi_pixel_distance_y = Float.parseFloat( System.getProperty( "pixel_distance_y" ) );
float czi_pixel_distance_z = Float.parseFloat( System.getProperty( "pixel_distance_z" ) );
czi_pixel_unit = System.getProperty( "pixel_unit" );

// builds string for calibration override
if (manual_calibration_tif.equalsIgnoreCase( "No" ) )
{
	modify_calibration = "calibration_definition=[Load voxel-size(s) from file(s)] ";
	manual_calibration_string = "";
	System.out.println( modify_calibration );
}

else if (manual_calibration_tif.equalsIgnoreCase( "Yes" ) )
{
	
	modify_calibration = "calibration_definition=[User define voxel-size(s)] ";
	manual_calibration_string = " pixel_distance_x=" + pixel_distance_x + " " +
				    "pixel_distance_y=" + pixel_distance_y + " " +
				    "pixel_distance_z=" + pixel_distance_z + " " +
				    "pixel_unit=" + pixel_unit + " ";
	System.out.println( "Calibration set to manual" );
	System.out.println( modify_calibration );
	System.out.println( "manual_calibration_string:" + manual_calibration_string );
}

else
{
	System.out.println( "Manual calibration setting bad" );
}


System.out.println("=========================================================");
System.out.println("Start plugin:");

System.out.println("Define Multi-View Dataset , type_of_dataset=[" + type_of_dataset + "] " +
	"xml_filename=[" + xml_filename + ".xml] " +
	"multiple_timepoints=[" + multiple_timepoints + "] " +
	"multiple_channels=[" + multiple_channels + "] " +
	"_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " + 
	"multiple_angles=[" + multiple_angles + "] " +
	"image_file_directory=" + image_file_directory + " " +
	"image_file_pattern=" + image_file_pattern + " " + 
	"timepoints_=" + timepoints + " " +
	channel_string +
	illum_string +
	"acquisition_angles_=" + acquisition_angles + " " +  
	"calibration_type=[Same voxel-size for all views] " +
	modify_calibration +
	"imglib2_data_container=[" + imglib_container + "]" + 
	manual_calibration_string +
	"");

// Executes Fiji plugin

try {
IJ.run("Define Multi-View Dataset", 
	"type_of_dataset=[" + type_of_dataset + "] " +
	"xml_filename=[" + xml_filename + ".xml] " +
	"multiple_timepoints=[" + multiple_timepoints + "] " +
	"multiple_channels=[" + multiple_channels + "] " +
	"_____multiple_illumination_directions=[" + multiple_illumination_directions + "] " + 
	"multiple_angles=[" + multiple_angles + "] " +
	"image_file_directory=" + image_file_directory + " " +
	"image_file_pattern=" + image_file_pattern + " " + 
	"timepoints_=" + timepoints + " " +
	channel_string +
	illum_string +
	"acquisition_angles_=" + angles + " " +  
	"calibration_type=[Same voxel-size for all views] " +
	modify_calibration + 
	"imglib2_data_container=[" + imglib_container + "]" + 
	manual_calibration_string +
	"");
}
catch ( e ) { 

    print( "[define_tif_zip] caught exception: "+e );
    //important to fail the process if exception occurs
    runtime.exit(1);
    
}
/* shutdown */
runtime.exit(0);