ModelLoad_Analyse.java

/*
 * To the extent possible under law, the ImageJ developers have waived
 * all copyright and related or neighboring rights to this tutorial code.
 *
 * See the CC0 1.0 Universal license for details:
 *     http://creativecommons.org/publicdomain/zero/1.0/
 */

package org.vcell.imagej.plugin;

import java.awt.Dimension;
import java.awt.Image;
import java.util.ArrayList;
import java.util.Hashtable;

import javax.swing.ImageIcon;
import javax.swing.JDialog;
import javax.swing.JFrame;
import javax.swing.JProgressBar;
import javax.swing.SwingUtilities;

/*import org.eclipse.swt.widgets.Text; */
import org.scijava.command.ContextCommand;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.ui.DialogPrompt.MessageType;
import org.scijava.ui.UIService;
import org.vcell.imagej.helper.VCellHelper;
import org.vcell.imagej.helper.VCellHelper.BasicStackDimensions;
import org.vcell.imagej.helper.VCellHelper.IJDataList;
import org.vcell.imagej.helper.VCellHelper.VCellModelSearchResults;

import net.imagej.ImageJ;
import net.imglib2.img.array.ArrayImg;
import net.imglib2.img.array.ArrayImgs;
import net.imglib2.img.basictypeaccess.array.DoubleArray;
import net.imglib2.type.numeric.real.DoubleType;

/**
 * This example illustrates how to create an ImageJ {@link ContextCommand} plugin that uses VCellHelper.
 * <p>
 * You should replace the parameter fields with your own inputs and outputs,
 * and replace the {@link run} method implementation with your own logic.
 * </p>
 * <p>
 * To add VCellHelper to this project,
 * rt-click on topmost tree element
 * "imagej-plugin2"->Properties->Libraries tab->Add External Jars...->
 * File Dialog->{EclipseVCellWorkspaceRootDir}/vcell/vcell-imagej-helper/target/vcell-imagej-helper-0.0.1-SNAPSHOT.jar.
 * </p>
 * <p>
 * Once vcell-imagej-helper-0.0.1-SNAPSHOT.jar has been added to the Libraries tab open
 * the small arrow to the left and select "Source Attachment"->Add/Edit->External Location->
 * External File Dialog->{EclipseVCellWorkspaceRootDir}/vcell/vcell-imagej-helper/target/vcell-imagej-helper-0.0.1-SNAPSHOT-sources.jar.
 * </p>
  */

@Plugin(type = ContextCommand.class, menuPath = "Plugins>ModelLoad_Analyse")
public class ModelLoad_Analyse extends ContextCommand {
	
	// ModelLoad_Analyse(Toolkit.getDefaultToolkit().getImage(JFrame_Icon.class.getResource("/images/ccam")));
    //
    // Feel free to add more parameters here...
    //
	
	//"colreeze\",\"Monkeyflower_pigmentation_v2\",\"Pattern_formation\",\"WT\",null,null\n"+e.getMessage(), "Search failed", MessageType.ERROR_MESSAGE);
	//displayProgressBar(false, null, null);

//These are the Parameters for our GUI which will be the model information for the generation of the output image
	//The dimensions of our GUI is generated automatically according to the number of information 

	@Parameter
	private UIService uiService;

  	@Parameter
	private VCellHelper vcellHelper;
  	
  	
	@Parameter
	private String vCellUser = "colreeze";
	
	@Parameter
	private String  vCellModel = "Monkeyflower_pigmentation_v2";
	
	@Parameter
	private String application = "Pattern_formation";
	
	@Parameter
	private String simulation = "WT";
	
	@Parameter
	private String variable = "A";
	
	@Parameter
	private int  timePoint = 500;
	
	/* @Parameter
	private String  imageName; */
	
	/* @Parameter */
	/*private String size; */

    /**
     * This main function serves for development purposes.
     * It allows you to run the plugin immediately out of
     * your integrated development environment (IDE).
     *
     * @param args whatever, it's ignored
     * @throws Exception
     */
    public static void main(final String... args) throws Exception {
        // create the ImageJ application context with all available services
    	
 
        final ImageJ ij = new ImageJ();
        ij.ui().showUI();
    }

    //These are for showing the progress in loading the result images after clicking OK on the GUI with the required information

    private JDialog progressDialog = null;
	private final Dimension dim = new Dimension(200,25); //these dimensions are for showing the loading of Image after clicking over OK on the information on the GUI
	//@SuppressWarnings("serial")	//omitted a serialVersionUID (not mandatory)
	private final JProgressBar jProgressBar = new JProgressBar(0,100)  //for showing the percentage of loading
	{
		/**
		 * 
		 */
		private static final long serialVersionUID = 1L;
		@Override
		public Dimension getPreferredSize() {
			// TODO Auto-generated method stub
			return dim;
		}
		@Override
		public Dimension getSize(Dimension rv) {
			// TODO Auto-generated method stub
			return dim;
		}
	};


    private void displayProgressBar(boolean bShow,String message,String title) {
    	if(progressDialog == null) {
			JFrame applicationFrame = (JFrame)uiService.getDefaultUI().getApplicationFrame();


			progressDialog = new JDialog(applicationFrame,"Checking for VCell Client",false);
			progressDialog.getContentPane().add(jProgressBar);
			jProgressBar.setStringPainted(true);
			progressDialog.pack();
    	}
		SwingUtilities.invokeLater(new Runnable() {
			@Override
			public void run() {
				if(!bShow) {
					progressDialog.setVisible(false);
					return;
				}
				jProgressBar.setValue(0);
				progressDialog.setTitle(title);
				jProgressBar.setString(message);
				progressDialog.setVisible(true);
			}
		});
    }

	//This is for exception handling and pausing the execution of the thread for 50 miliseconds
    private Hashtable<String,Thread> threadHash = new Hashtable<String,Thread>();
    private void startJProgressThread0(String lastName,String newName) {
    	if(lastName != null && threadHash.get(lastName) != null) {
	    	threadHash.get(lastName).interrupt();
	    	while(threadHash.get(lastName) != null) {
	    		try {
					Thread.sleep(50);	//pauses or stops the execution of current thread for 50 miliseconds
				} catch (InterruptedException e) {
					// TODO Auto-generated catch block
					e.printStackTrace();
					break;
				}
	    	}
    	}
    	if(newName == null) {
    		return;
    	}
    	 
    	final Thread progressThread = new Thread(new Runnable(){
			@Override
			public void run() {
				final int[] progress = new int[] {1};
				while(progressDialog.isVisible()) {
					if(Thread.currentThread().isInterrupted()) {
						break;
					}
//this is an instance of an anonymous implementation of the Runnable interface and passing it to 'invokeLater', which will put it on a queue.
					SwingUtilities.invokeLater(new Runnable() {
						@Override
						public void run() {
							jProgressBar.setValue(progress[0]);
						}});
					progress[0]++;
					//and now a try catch exection to pause the thread for certain miliseconds
					try {
						Thread.sleep(500);
					} catch (InterruptedException e) {
						break;
					}
				}
				threadHash.remove(Thread.currentThread().getName());
			}});
  //  	setDaemon() method of thread class is used to mark the thread either daemon thread or a user thread. Its life depends on the user threads i.e. when all user threads die, JVM terminates this thread automatically. It must be invoked before the thread is started.    	
    	threadHash.put(newName, progressThread);
		progressThread.setName(newName);
		progressThread.setDaemon(true);//So not block JVM exit
		progressThread.start();
    }
    
	@Override
	public void run() {
//This segment is for checking the activation of VCell		
		displayProgressBar(true, "Checking listening ports...", "Checking for VCell Client");
		startJProgressThread0(null,"Check");
//this does the checking for the status of the VCell Port	
		//If the VCell Port is active
      try {
    	  //Find the port that a separately running VCell client is listening on
    	  //
			System.out.println("vcell service port="+vcellHelper.findVCellApiServerPort());
			//uiService.getDisplayViewer(textDisplay).dispose();
			displayProgressBar(false, null, null);
		} 
    //If the VCell Port is inactive, Exception occurs
      catch (Exception e) {
			//e.printStackTrace();
			displayProgressBar(false, null, null);
			//uiService.getDisplayViewer(textDisplay).dispose();
			uiService.showDialog("Activate VCell client ImageJ service\nTools->'Start Fiji (ImageJ) service'\n"+e.getMessage(), "Couldn't contact VCell client", MessageType.ERROR_MESSAGE);
			return;
		}
      
      
		displayProgressBar(true, "Searching...", "Searching VCell Models");
		startJProgressThread0("Check","Search");
		
//This segments takes the appropriate values and produces the desired results according to the model and the information realted to it
		String theCacheKey = null;
	      VCellHelper.VCellModelSearch vcms = new VCellHelper.VCellModelSearch(VCellHelper.ModelType.bm,vCellUser,vCellModel,application,simulation,null,null);
	      try {
			ArrayList<VCellModelSearchResults> vcmsr = vcellHelper.getSearchedModelSimCacheKey(false,vcms,null);
			if(vcmsr.size() == 0) {
				throw new Exception("No Results for search found");
			}
			theCacheKey = vcmsr.get(0).getCacheKey();
			System.out.println("theCacheKey="+theCacheKey);
			displayProgressBar(false, null, null);
		} catch (Exception e) {
			// TODO Auto-generated catch block
			//e.printStackTrace();
			uiService.showDialog("VCellHelper.ModelType.bm,vCellUser,vCellModel,application,simulation,null,null\n"+e.getMessage(), "Search failed", MessageType.ERROR_MESSAGE);
			displayProgressBar(false, null, null);
		}		 
      
      displayProgressBar(true, "Loading Data...", "Loading Data");
      startJProgressThread0("Search","getTimePointData");

		//This segment is for displaying the results
      try {
    	  String var = variable;
    	  int[] time = new int[] {timePoint};
    	  IJDataList tpd = vcellHelper.getTimePointData(theCacheKey,var,VCellHelper.VARTYPE_POSTPROC.NotPostProcess,time,0);
    	  double[] data = tpd.ijData[0].getDoubleData();
    	  BasicStackDimensions bsd = tpd.ijData[0].stackInfo;
    	  System.out.println(bsd.xsize+" "+bsd.ysize);
    	  ArrayImg<DoubleType, DoubleArray> testimg = ArrayImgs.doubles( data, bsd.xsize,bsd.ysize);
    	  uiService.show(testimg);
    	  
    	  displayProgressBar(false, null, null);
	} catch (Exception e) {
		// TODO Auto-generated catch block
//		e.printStackTrace();
		uiService.showDialog("theCacheKey,var,VCellHelper.VARTYPE_POSTPROC.NotPostProcess,time,0\n"+e.getMessage(), "getTimePoint(...) failed", MessageType.ERROR_MESSAGE);
		displayProgressBar(false, null, null);

	}
      startJProgressThread0("getTimePointData",null);
	}
}