define_czi.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" );
first_czi = System.getProperty( "first_czi" );

System.out.println( "xml_file_path = " + image_file_directory + first_xml_filename + ".xml" );
System.out.println( "first_czi_path = " + image_file_directory + first_czi );

// Dataset settings
System.out.println("---------------------------------------------------------");
System.out.println("Angle Settings:");

// Angle settings
// Parses angles and determines the number of angles
// uses tokens of string angles to assemble the string for angle_string
// via StringBuilder
angles = System.getProperty( "angles" );
System.out.println( "Angles = " + angles );

// Parses string angles
String delims = "[,]";
String[] angle_token = angles.split(delims);

// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder angle_string = new StringBuilder();
String angle_part;

	for ( int angle = 0; angle < angle_token.length; angle++) {
		int num_angles = angle + 1;
		angle_part = "angle_" + num_angles + "=" + angle_token[angle];
		angle_string.append(angle_part);
		angle_string.append(" ");
		}

System.out.println( angle_string );

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

// Channel settings
// This parses channels and determines the number of channels
// then uses the tokens of channels to assemble the necessary string
// for channel_string via StringBuilder
channels = System.getProperty( "channels" );
System.out.println( "Channel Names = " + channels );

// Parses string channel_names
String delims = "[,]";
String[] channel_token = channels.split(delims);

// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder channel_string = new StringBuilder();
String channel_part;

	for ( int channel = 0; channel < channel_token.length; channel++) {
		int num_channel = channel + 1;
		channel_part = "channel_" + num_channel + "=" + channel_token[channel];
		channel_string.append(channel_part);
		channel_string.append(" ");
		}
System.out.println( "Channel String = " + channel_string );

System.out.println("---------------------------------------------------------");
System.out.println("Illumination Settings:");

// Illuminatin settings
// This parses illumination and determines the number of illuminations
// then uses the tokens of illuminations to assemble the string for 
// illum_string via StringBuilder
illumination = System.getProperty( "illumination" );
System.out.println( "Illumination = " + illumination );

// Parses string illumination
String delims = "[,]";
String[] illum_token = illumination.split(delims);

// Builds string using the number of tokens and inserts the tokens in the string
StringBuilder illum_string = new StringBuilder();
String illum_part;

	for ( int illum= 0; illum< illum_token.length; illum++) {
		int num_illum = illum + 1;
		illum_part = "_______illumination_" + num_illum + "=" + illum_token[illum];
		illum_string.append(illum_part);
		illum_string.append(" ");
		}

System.out.println( illum_string );

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

rotation_around = System.getProperty( "rotation_around" );
System.out.println( "rotation_around = " + rotation_around );

// Calibaration
System.out.println("=========================================================");
System.out.println("Calibration:");
manual_calibration_czi = System.getProperty( "manual_calibration_czi" );
float czi_pixel_distance_x = Float.parseFloat( System.getProperty( "czi_pixel_distance_x" ) );
float czi_pixel_distance_y = Float.parseFloat( System.getProperty( "czi_pixel_distance_y" ) );
float czi_pixel_distance_z = Float.parseFloat( System.getProperty( "czi_pixel_distance_z" ) );
czi_pixel_unit = System.getProperty( "czi_pixel_unit" );

// builds string for calibration override
if (manual_calibration_czi.equalsIgnoreCase( "No" ) )
{
	modify_calibration = "";
	manual_calibration_string = "";
	System.out.println( "Calibration set to automatic" );
}

else if (manual_calibration_czi.equalsIgnoreCase( "Yes" ) )
{
	
	modify_calibration = "modify_calibration ";
	manual_calibration_string = "pixel_distance_x=" + czi_pixel_distance_x + " " +
				    "pixel_distance_y=" + czi_pixel_distance_y + " " +
				    "pixel_distance_z=" + czi_pixel_distance_z + " " +
				    "pixel_unit=" + czi_pixel_unit + " ";
	System.out.println( "Calibration set to manual" );
	System.out.println( "modify_calibration:" + modify_calibration );
	System.out.println( "manual_calibration_string:" + manual_calibration_string );
}

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

// Executes Fiji plugin
System.out.println("=========================================================");
System.out.println("Start plugin:");
System.out.println("Define Multi-View Dataset type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
	"xml_filename=" + first_xml_filename + ".xml " +
	"browse=" + image_file_directory + first_czi + " " + 
	"first_czi=" + image_file_directory + first_czi + " " + 
	angle_string +
	channel_string + 
 	illum_string +
	modify_calibration +
	"modify_rotation_axis " +
	manual_calibration_string +
	"rotation_around=" + rotation_around + 
	"");

try {
IJ.run("Define Multi-View Dataset", 
	"type_of_dataset=[Zeiss Lightsheet Z.1 Dataset (LOCI Bioformats)] " +
	"xml_filename=" + first_xml_filename + ".xml " +
	"browse=" + image_file_directory + first_czi + " " + 
	"first_czi=" + image_file_directory + first_czi + " " + 
	angle_string +
	channel_string + 
	illum_string +
	modify_calibration + 
	"modify_rotation_axis " +
	manual_calibration_string + 
	"rotation_around=" + rotation_around + "");
}
catch ( e ) { 

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