VCellPluginDisplay.txt

/*
 * 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 org.jfree.chart.ChartFactory;	
import org.jfree.chart.JFreeChart;	
import org.jfree.chart.ChartPanel;	
import org.jfree.data.category.CategoryDataset;	
import org.jfree.data.xy.XYDataset;	
import org.jfree.data.xy.DefaultXYDataset;
import javax.swing.JFrame;	
import org.vcell.imagej.helper.VCellHelper.IJTimeSeriesJobResults;	
import org.vcell.imagej.helper.VCellHelper.VCellModelSearch	;
import org.vcell.imagej.helper.VCellHelper.ModelType;
import org.vcell.imagej.helper.VCellHelper.VARTYPE_POSTPROC;
import org.vcell.imagej.helper.VCellHelper.VCellModelSearchResults;

import java.awt.Dimension;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.Hashtable;

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

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.Dataset;
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;



//(See https://github.com/virtualcell/vcell/tree/master/vcell-imagej-helper/src/main/java/org/vcell/imagej/helper/VCellHelper.java)	

//Demo chart in ImageJ of line-scan values from VCell simulation results	
// BioModel "Tutorial_FRAPbinding" owned by user "tutorial" in application "Spatial" for simulation "FRAP binding"	
// values for variable="r" at timePoint=22.0	
// line-scan along x-axis at y=0.0	
// start and end indexes found by moving mouse over x,y data points (-9.24,0.0) and (9.24,0,0) and	
// see index in "info' box at the bottom of the sim results viewer in VCell	
//Create list of datapoint indexes to extract from data

@Plugin(type = ContextCommand.class, menuPath = "Plugins>VCellPluginDisplay")
	
public class VCellPluginDisplay extends ContextCommand {
    //
    // Feel free to add more parameters here...
    //
	
	
	@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 = "C_cyt";
	
	@Parameter
	private int  timePoint = 50;
	
	@Parameter
	private String  imageName = "test";
	
	@Parameter
	int[] timeIndex = {50};
		

    /**
     * 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();
    }

	
	private JDialog progressDialog = null;
	private final Dimension dim = new Dimension(200,25);
	private final JProgressBar jProgressBar = new JProgressBar(0,100) {
		@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);
			}
		});
    }

	    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);
				} 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;
					}
					SwingUtilities.invokeLater(new Runnable() {
						@Override
						public void run() {
							jProgressBar.setValue(progress[0]);
						}});
					progress[0]++;
					try {
						Thread.sleep(500);
					} catch (InterruptedException e) {
						break;
					}
				}
				threadHash.remove(Thread.currentThread().getName());
			}});
    	threadHash.put(newName, progressThread);
		progressThread.setName(newName);
		progressThread.setDaemon(true);//So not block JVM exit
		progressThread.start();
    }
	    
	@Override
	public void run() {
		
		displayProgressBar(true, "Checking listening ports...", "Checking for VCell Client");
		startJProgressThread0(null,"Check");
		
      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);
		} 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");

		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,\"tutorial\",\"Tutorial_MultiApp\",\"3D pde\",\"Simulation4\",null,null\n"+e.getMessage(), "Search failed", MessageType.ERROR_MESSAGE);
			displayProgressBar(false, null, null);
		}
	      
	      displayProgressBar(true, "Loading Data...", "Loading Data");
	      startJProgressThread0("Search","getTimePointData");
/*
	      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+ imageName +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);

	}	
*/		      
	      try {
	    	  String variableName = variable;
	    	  int[] timePointIndexes = new int[] {timePoint};
	    	  String simulationDataCacheKey = String.valueOf(theCacheKey);

	    	  SimpleDateFormat easyDate = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
	    	  Date searchFrom = easyDate.parse("2018-01-01 00:00:00");
	    	  Date  searchTo = easyDate.parse("2100-01-01 00:00:00");
	    	  //int[] dataIndexes = new int[searchTo, searchFrom];
	    	  int simulationJobIndex;
	    	// int[] dataIndexes = (endIndex-startIndex);
//	    	  int cachekey = Integer.valueOf(theCacheKey);
	    	  
//Get the data values using the cache-key
//IJTimeSeriesJobResults getTimeSeries(String[] variableNames, int[] indices, double startTime, int step, double endTime,boolean calcSpaceStats, boolean calcTimeStats, int jobid, int cachekey) throws Exception{
//ijTimeSeriesJobResults = vh.getTimeSeries(vars, dataIndexes, 22 as double, 1, 22 as double, false, false, 0/*jobid, if parameter scan can be non-zero*/, theCacheKey as int)
//ijTimeSeriesJobResults.data[numVars][numDataPoints+1][numTimes] structure of ijTimeSeriesJobResults.data
//ijTimeSeriesJobResults.data[varIndex][0][0...numTimes-1] contains the timePoints
//ijTimeSeriesJobResults.data[varIndex][1...numDataPoints][0...numTimes-1] contains the data values at each index for each timePoint
//Demo TimePoints ijTimeSeriesJobResults.data[0][0] == array of timePoints for var="r", array has 1 value for timePoint=22.0
//Demo DataPoints ijTimeSeriesJobResults.data[0][1..numDataPoints][0] iterate over dataPoints at each timePoint for each var to get data for var,times

//double[] chartTheseDataPoints = new double[dataIndexes.length]
//for(int i=0;i<dataIndexes.length;i++){
//	chartTheseDataPoints[i] =
//		ijTimeSeriesJobResults.data[0/*index of "r"*/][i+1/*data, skip 0 because it holds copy of times*/][0/*0 always because we had only 1 timePoint=22.0*/]
//}
//Create JFreechart x,y axis arrays for plotting x=data indexes, y=dataPoint values
//double[][] data = [dataIndexes,chartTheseDataPoints];	    	  

/*	public IJTimeSeriesJobResults getTimeSeries(String[] variableNames, int[] indices, double startTime, int step, double endTime,
			boolean calcSpaceStats, boolean calcTimeStats, int jobid, int cachekey) throws Exception{
*/	    	  

//ijTimeSeriesJobResults = vh.getTimeSeries(vars, dataIndexes, 22 as double, 1, 22 as double, false, false, 0/*jobid, if parameter scan can be non-zero*/, theCacheKey as int)

	    		//Get data at single time for a single variable
	    		//TimePointData getTimePointData(String simulationDataCacheKey,String variableName,int[] timePointIndexes,int simulationJobIndex)
	//    		ijDataList = vcHelper.getTimePointData(theCacheKey as String,var,VARTYPE_POSTPROC.NotPostProcess,timeIndex,0)
	//    		bsd = ijDataList.ijData[0].stackInfo
	//    		println(bsd.xsize+" "+bsd.ysize+" "+bsd.zsize)
	  //  		data = ijDataList.ijData[0].getDoubleData()
	 //   		notInDomainVal = ijDataList.ijData[0].notInDomainValue
	    		//println(bsd.xsize+" "+bsd.ysize+" "+bsd.zsize)
	    		//ds = imagej.dataset().create(new FloatType(),[5,5,5] as long[],"hello", [Axes.X,Axes.Y,Axes.Z] as AxisType[])
	    		//imagej.display().createDisplay("dsimg",ds)	   
//ijDataList = vcHelper.getTimePointData(theCacheKey as String,var,VARTYPE_POSTPROC.NotPostProcess,timeIndex,0)	    	  
//	public IJDataList getTimePointData(String simulationDataCacheKey,String variableName,VARTYPE_POSTPROC varTypePostProcess,int[] timePointIndexes,int simulationJobIndex)	    	  
	    	  IJDataList tpd = vcellHelper.getTimePointData(theCacheKey, variableName, VCellHelper.VARTYPE_POSTPROC.NotPostProcess, timePointIndexes, 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,variable,VCellHelper.VARTYPE_POSTPROC.NotPostProcess,time,0\n"+e.getMessage(), "getTimePoint(...) failed", MessageType.ERROR_MESSAGE);
			displayProgressBar(false, null, null);

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