package com.github.celldynamics.quimp.plugin.ecmm;
   
   import java.io.File;
   import java.io.IOException;
   import java.util.ArrayList;
   // import java.util.Vector;
   import java.util.Random;
   
   import org.slf4j.Logger;
  import org.slf4j.LoggerFactory;
  
  import com.github.celldynamics.quimp.Nest;
  import com.github.celldynamics.quimp.Outline;
  import com.github.celldynamics.quimp.OutlineHandler;
  import com.github.celldynamics.quimp.QParams;
  import com.github.celldynamics.quimp.QParamsQconf;
  import com.github.celldynamics.quimp.QuimP;
  import com.github.celldynamics.quimp.QuimpException;
  import com.github.celldynamics.quimp.QuimpException.MessageSinkTypes;
  import com.github.celldynamics.quimp.SnakeHandler;
  import com.github.celldynamics.quimp.Vert;
  import com.github.celldynamics.quimp.filesystem.DataContainer;
  import com.github.celldynamics.quimp.filesystem.FileExtensions;
  import com.github.celldynamics.quimp.filesystem.OutlinesCollection;
  import com.github.celldynamics.quimp.filesystem.QconfLoader;
  import com.github.celldynamics.quimp.filesystem.converter.FormatConverter;
  import com.github.celldynamics.quimp.geom.ExtendedVector2d;
  import com.github.celldynamics.quimp.plugin.AbstractPluginQconf;
  import com.github.celldynamics.quimp.plugin.QuimpPluginException;
  
  import ij.IJ;
  import ij.WindowManager;
  import ij.gui.YesNoCancelDialog;
  import ij.process.ImageProcessor;
  
  /*
   * //!>
   * @startuml doc-files/ECMM_Mapping_1_UML.png
   * start
   * :Check registration;
   * if (input file given) then (no) 
   * :ask user; 
   * endif
   * :Load config file;
   * if (QUIMP_11 file) then (yes)
   * :process it;
   * :scan for other files;
   * repeat 
   * :process other file;
   * repeat while(more files?) else (no)
   * if(BOA data) then (no)
   * stop
   * endif
   * if(ECMM data) then (yes)
   * if(overwrite?) then (no)
   * end
   * endif
   * endif
   * :process it;
   * endif
   * end
   * @enduml
   * 
   * //!< 
   */
  /**
   * Main ECMM implementation class.
   * 
   * <p>To disable plotting hide {@link ECMplot#imPlus} by accessing {@link #plot}.
   * 
   * @author Richard Tyson. 23/09/2009. ECM Mapping Systems Biology DTC, Warwick University.
   * @author p.baniukiewicz
   *
   */
  public class ECMM_Mapping extends AbstractPluginQconf {
  
    private static String thisPluginName = "ECMM Mapping";
  
    private File fileToLoad = null; // file to load paQP/QCONF
    /**
     * The Constant LOGGER.
     */
    static final Logger LOGGER = LoggerFactory.getLogger(ECMM_Mapping.class.getName());
    private OutlineHandler oh;
    private OutlineHandler outputH;
    private OutlinesCollection outputOutlineHandlers; // output for new data file
  
    /**
     * The plot.
     */
    public static ECMplot plot;
  
    /**
     * Default constructor called on plugin run from IJ GUI.
     */
    public ECMM_Mapping() {
      super(new EcmmOptions(), thisPluginName);
    }
  
   /**
    * Constructor called by ANA.
    * 
    * @param frames frame
    */
   public ECMM_Mapping(int frames) { // work around. b is nothing
     this();
     if (ECMp.plot) {
       plot = new ECMplot(frames);
     }
   }
 
   /**
    * Constructor that allows to provide own parameters. Set apiCall to true.
    * 
    * @param paramString it can be null to ask user for file or it can be parameters string like that
    *        passed in macro.
    * @throws QuimpPluginException on any error
    */
   public ECMM_Mapping(String paramString) throws QuimpPluginException {
     super(paramString, new EcmmOptions(), thisPluginName); // will parse and fill options
   }
 
   /**
    * Create object and fill options with specified file.
    * 
    * <p>Set apiCall to true and errors redirects to console.
    * 
    * @param file file to process.
    */
   public ECMM_Mapping(File file) {
     super(new EcmmOptions(file), thisPluginName);
     apiCall = true;
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.PluginTemplate#run(java.lang.String)
    */
   @Override
   public void run(String arg) {
     super.run(arg);
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.AbstractPluginQconf#loadFile(java.lang.String)
    */
   @Override
   protected void loadFile(String paramFile) throws QuimpException {
     if (options.paramFile == null || options.paramFile.isEmpty()) {
       fileToLoad = null;
     } else {
       fileToLoad = new File(options.paramFile);
     }
 
     qconfLoader = new QconfLoader(fileToLoad); // load file
     if (qconfLoader == null || qconfLoader.getQp() == null) {
       return; // failed to load exit
     }
     if (qconfLoader.isFileLoaded() == QParams.QUIMP_11) { // old path
       QParams qp;
       runFromPaqp();
       // old flow with paQP files - detect other paQP
       File[] otherPaFiles = qconfLoader.getQp().findParamFiles();
       if (otherPaFiles.length > 0) {
         YesNoCancelDialog yncd = new YesNoCancelDialog(IJ.getInstance(), "Batch Process?",
                 "\tBatch Process?\n\n" + "Process other " + FileExtensions.configFileExt
                         + " files in the same folder with ECMM?\n"
                         + "[Files already run through ECMM will be skipped!]");
         if (yncd.yesPressed()) {
           ArrayList<String> runOn = new ArrayList<String>(otherPaFiles.length);
           ArrayList<String> skipped = new ArrayList<String>(otherPaFiles.length);
 
           for (int j = 0; j < otherPaFiles.length; j++) {
             plot.close();
             qconfLoader = new QconfLoader(otherPaFiles[j]); // load file
             if (qconfLoader == null || qconfLoader.getQp() == null) {
               return; // failed to load exit
             }
             qp = qconfLoader.getQp();
             if (!qp.isEcmmHasRun()) {
               IJ.log("Running on " + otherPaFiles[j].getAbsolutePath());
               runFromPaqp();
               runOn.add(otherPaFiles[j].getName());
             } else {
               IJ.log("Skipped " + otherPaFiles[j].getAbsolutePath());
               skipped.add(otherPaFiles[j].getName());
             }
 
           }
           IJ.log("\n\nBatch - Successfully ran ECMM on:");
           for (int i = 0; i < runOn.size(); i++) {
             IJ.log(runOn.get(i));
           }
           IJ.log("\nSkipped:");
           for (int i = 0; i < skipped.size(); i++) {
             IJ.log(skipped.get(i));
           }
         } else {
           return; // no batch processing
         }
       }
     } else if (qconfLoader.isFileLoaded() == QParams.NEW_QUIMP) { // new path
       // validate in case new format
       validate();
       if (qconfLoader.isECMMPresent() && apiCall == false && errorSink == MessageSinkTypes.GUI) {
         YesNoCancelDialog ync;
         ync = new YesNoCancelDialog(IJ.getInstance(), "Overwrite",
                 "You are about to override previous ECMM results. Is it ok?");
         if (!ync.yesPressed()) { // if no or cancel
           IJ.log("No changes done in input file.");
           return; // end}
         }
       }
       runFromQconf();
       IJ.log("The new data file " + qconfLoader.getQp().getParamFile().toString()
               + " has been updated by results of ECMM analysis.");
     } else {
       throw new QuimpPluginException("QconfLoader returned unknown version of QuimP or error: "
               + qconfLoader.isFileLoaded());
     }
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.AbstractPluginQconf#executer()
    */
   @Override
   protected void executer() throws QuimpException {
     // we need to use different handling for multiple paQP files, so use own loader
     if (apiCall == true) { // if run from other constructor, override sink
       errorSink = MessageSinkTypes.CONSOLE;
     }
     super.executer();
   }
 
   /**
    * Called by ANA if no ECCM results are in file (old path).
    * 
    * @param m OutlineHandler
    * @param ipr ImageProcessor
    * @param d cortex?
    * @return Processed outline
    */
   public OutlineHandler./../../../com/github/celldynamics/quimp/OutlineHandler.html#OutlineHandler">OutlineHandler runByANA(OutlineHandler m, ImageProcessor ipr, double d) {
     oh = m;
     ECMp.image = ipr;
     ECMp.setParams(oh.maxLength);
     ECMp.startFrame = oh.getStartFrame();
     ECMp.endFrame = oh.getEndFrame();
     ECMp.plot = false;
     ECMp.ANA = true;
     ECMp.anaMigDist = d;
     ECMp.migQ = 1.5E-5; //
     ECMp.tarQ = -1.5E-5; // use same charge
 
     if (ECMp.plot) {
       plot = new ECMplot(oh.getSize() - 1);
     }
 
     // ECMp.setParams(m.indexGetOutline(0));
 
     // *******adjust params for ana***********
     ECMp.h = 0.9;
     ECMp.chargeDensity = 4;
     ECMp.d = 0.4;
     ECMp.maxVertF = 0.7;
     // *************************
     runPlugin();
     // IJ.log("ECM Mapping FINISHED");
     return outputH;
   }
 
   /**
    * Main executive for ECMM plugin.
    * 
    * @see #runFromQconf()
    * @see #runFromPaqp()
    */
   private void runPlugin() {
     long time = System.currentTimeMillis();
     if (!ECMp.ANA) {
       IJ.log("ECMM resolution: " + ECMp.markerRes + "(av. spacing)\n");
     }
 
     outputH = new OutlineHandler(oh);
     ECMp.unSnapped = 0;
     // int skippedFrames = 0; // if a frame is skipped need to divide next
     // time point migration by 2, etc...
 
     Mapping map1;
     int f = ECMp.startFrame; // now in frames
     Outline o1 = oh.getStoredOutline(f);
     // resolution is always as in segmentation - not now
     if (!ECMp.ANA) {
       if (Math.abs(ECMp.markerRes) > 0) {
         o1.setResolution(Math.abs(ECMp.markerRes));
       }
     }
     // LOGGER.trace("Outline o1:head =[" + o1.getHead().getX() + "," + o1.getHead().getY() +
     // "]");
     o1.resetAllCoords();
     o1.clearFluores();
     o1.calcCentroid(); // TODO this should be called as in case of Snakes
 
     outputH.save(o1, f);
     Outline o2;
 
     int stopAt = -1; // debug break
 
     for (; f <= oh.getEndFrame() - 1; f++) {
       if (f == stopAt) {
         ECMp.plot = true;
       }
       if (o1.checkCoordErrors()) {
         IJ.error("There was an error in tracking due to a bug (frame " + (f) + ")"
                 + "\nPlease try again");
         break;
       }
 
       if (!ECMp.ANA) {
         IJ.showStatus("Running ECMM");
         IJ.showProgress(f, oh.getEndFrame());
         IJ.log("Mapping " + f + " to " + (f + 1));
       }
 
       o2 = oh.getStoredOutline(f + 1);
       // o2 left as seen in the segmentation - i.e. marker res unchanged
       if (!ECMp.ANA && ECMp.markerRes > 0) {
         o2.setResolution(ECMp.markerRes); // must be done b4 intersects are calculated
       }
       o2.resetAllCoords();
       o2.clearFluores();
 
       if (!ECMp.ANA) {
         this.nudgeOverlaps(o1, o2); // ensure no points/edges lie directly on each other (to 1e-4)/
       }
 
       if (ECMp.plot) {
         plot.setDrawingFrame(f);
         o1.calcCentroid(); // calc it again as it is broken in loop by migrate() where Outline is
         // initialzied from one vertex
         plot.centre = o1.getCentroid();
 
         if (ECMp.drawInitialOutlines) {
           plot.setColor(0d, 0d, 1d);
           plot.drawOutline(o1);
           plot.setColor(0d, 1d, 0d);
           plot.drawOutline(o2);
           plot.setSlice(f);
         }
       }
 
       // OutlineHandler.writeSingle("o2.snQP", o2);
       // OutlineHandler.writeSingle("o1.snQP", o1);
 
       map1 = new Mapping(o1, o2);
 
       /*
        * if (map1.invalid) { //Use no sectors IJ.log(" invalid outline intersection,
        * attempting non-intersect mapping..."); plot.writeText("Non-intersect mapping");
        * ECMp.noSectors = true; map1 = new Mapping(o1, o2); ECMp.noSectors = false; }
        */
 
       o1 = map1.migrate();
       // System.out.println("num nodes: "+o1.getVerts());
 
       if (!ECMp.ANA) {
         // System.out.println("\n check final intersects");
         if (!ECMp.disableDensityCorrections) {
           if (o1.removeNanoEdges()) {
             // IJ.log(" result had some v.small edges- removed");
           }
           if (o1.cutSelfIntersects()) {
             IJ.log("    result self intersected - fixed");
             if (ECMp.plot) {
               plot.writeText("Fixed self intersection");
             }
           }
 
           if (ECMp.markerRes == 0) {
             o1.correctDensity(2 * 1.6, 2 / 1.6);
           } else {
             o1.correctDensity(ECMp.markerRes * 1.6, ECMp.markerRes / 1.6);
           }
         }
         if (ECMp.plot && ECMp.drawSolutionOutlines) {
           plot.setColor(1d, 0d, 0d);
           plot.drawOutline(o1);
         }
       }
 
       if (ECMp.ANA && ECMp.plot) {
         plot.setColor(0d, 0.7d, 0.7d);
         plot.drawOutline(o1);
       }
 
       // OutlineHandler.writeSingle("o2.snQP", o2);
       // OutlineHandler.writeSingle("o1.snQP", o1);
 
       o1.coordReset(); // reset the frame Coordinate system
 
       outputH.save(o1, f + 1);
       if (f == stopAt) {
         break;
       }
     }
 
     // IJ.log("Total iterations = " + ECMp.its);
     if (ECMp.plot) {
       plot.repaint();
     }
 
     if (!ECMp.ANA) {
       double timeSec = (System.currentTimeMillis() - time) / 1000d;
       IJ.showStatus("ECMM finished");
       IJ.log("ECMM finished in " + timeSec + " seconds.");
     }
     return;
   }
 
   private void nudgeOverlaps(Outlineref="../../../../../../com/github/celldynamics/quimp/Outline.html#Outline">Outline o1, Outline o2) {
 
     int state;
     double[] intersect = new double[2];
     Random rg = new Random();
 
     Vert na = o1.getHead();
     Vert nb;
     do {
       nb = o2.getHead();
       do {
         // check if points on top of each other
         if (nb.getX() == na.getX() && nb.getY() == na.getY()) {
           // use a minimum nudge of 0.01 (imageJ pixel accurracy
           na.setX(na.getX() + (rg.nextDouble() * 0.5) + 0.01);
           na.setY(na.getY() + (rg.nextDouble() * 0.5) + 0.01);
         }
 
         // check if lines are parallel
         state = ExtendedVector2d.segmentIntersection(na.getX(), na.getY(), na.getNext().getX(),
                 na.getNext().getY(), nb.getX(), nb.getY(), nb.getNext().getX(), nb.getNext().getY(),
                 intersect);
         if (state == -1 || state == -2) {
           // IJ.log(" outline parrallel -fixed");
           na.setX(na.getX() + (rg.nextDouble() * 0.5) + 0.01);
           na.setY(na.getY() + (rg.nextDouble() * 0.5) + 0.01);
         }
 
         nb = nb.getNext();
       } while (!nb.isHead());
       na = na.getNext();
 
     } while (!na.isHead());
 
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.IQuimpPlugin#about()
    */
   @Override
   public String about() {
     return "ECMM plugin.\n" + "Authors: Piotr Baniukiewicz\n"
             + "mail: p.baniukiewicz@warwick.ac.uk\n" + "Richard Tyson";
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.AbstractPluginQconf#runFromQconf()
    */
   @Override
   protected void runFromQconf() throws QuimpException {
     LOGGER.debug("Processing from new file format");
     Nest nest = ((QParamsQconf) qconfLoader.getQp()).getNest();
     outputOutlineHandlers = new OutlinesCollection(nest.size());
     for (int i = 0; i < nest.size(); i++) { // go over all snakes
       // For compatibility, all methods have the same syntax (assumes that there is only one
       // handler)
       ((QParamsQconf) qconfLoader.getQp()).setActiveHandler(i); // set current handler number.
       SnakeHandler sh = nest.getHandler(i);
       if (sh == null) {
         continue;
       }
       oh = new OutlineHandler(sh); // convert to outline, oh is global var
       ECMp.setup(qconfLoader.getQp());
       ECMp.setParams(oh.maxLength); // base params on outline in middle of
       // sequence
       if (ECMp.plot) {
         plot = new ECMplot(oh.getSize() - 1);
         plot.imPlus.setTitle(WindowManager.makeUniqueName(ECMplot.ECMM_TITLE + "_" + "cell_" + i));
       }
       runPlugin(); // fills outputH
       outputOutlineHandlers.oHs.add(i, new OutlineHandler(outputH)); // store actual result
     }
 
     DataContainer dc = ((QParamsQconf) qconfLoader.getQp()).getLoadedDataContainer();
     dc.ECMMState = outputOutlineHandlers; // assign ECMM container to global output
     try {
       qconfLoader.getQp().writeParams();
     } catch (IOException e) {
       throw new QuimpPluginException(e);
     } // save global container
     // generate additional OLD files, disabled #263, enabled GH228
     if (QuimP.newFileFormat.get() == false) {
       FormatConverterm/converter/FormatConverter.html#FormatConverter">FormatConverter foramtConvrter = new FormatConverter(qconfLoader);
       foramtConvrter.doConversion();
     }
 
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.AbstractPluginQconf#runFromPaqp()
    */
   @Override
   protected void runFromPaqp() throws QuimpException {
     oh = new OutlineHandler(qconfLoader.getQp());
     if (!oh.readSuccess) {
       throw new QuimpException("Could not read OutlineHandler");
     }
 
     ECMp.setup(qconfLoader.getQp());
     // System.out.println("sf " + ECMp.startFrame + ", ef " +
     // ECMp.endFrame);
     // System.out.println("outfile " + ECMp.OUTFILE.getAbsolutePath());
     ECMp.setParams(oh.maxLength); // base params on outline in middle of sequence
     if (ECMp.plot) {
       plot = new ECMplot(oh.getSize() - 1);
     }
     runPlugin();
 
     if (ECMp.saveTemp) {
       // ------ save a temporary version instead as to not over write the
       // old version
       File tempFile = new File(ECMp.OUTFILE.getAbsolutePath() + ".temp.txt");
       outputH.writeOutlines(tempFile, true);
       IJ.log("ECMM:137, saving to a temp file instead");
     } else {
       ECMp.INFILE.delete();
       outputH.writeOutlines(ECMp.OUTFILE, true);
     }
 
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.AbstractPluginQconf#validate()
    */
   @Override
   protected void validate() throws QuimpException {
     super.validate();
     boolean fail = false;
     String ver = IJ.getVersion();
     if (ver.indexOf("/") > -1) {
       ver = ver.substring(ver.indexOf("/") + 1);
     }
     LOGGER.info(ver);
     // assume letter code at the end
     try {
       if (Character.isLetter(ver.charAt(ver.length() - 1))) {
         String vern = ver.substring(0, ver.length() - 1); // should be 1.52 only
         if (Double.parseDouble(vern) < 1.52) {
           fail = true;
         } else {
           if (ver.charAt(ver.length() - 1) < 'n') {
             fail = true;
           }
         }
       } else {
         if (Double.parseDouble(ver) < 1.52) {
           fail = true;
         }
       }
       if (fail) {
         throw new QuimpException("IJ 1.52n version required (or above)");
       }
     } catch (NullPointerException | NumberFormatException e) {
       LOGGER.warn("Cannot process IJ version.");
     }
   }
 
   /*
    * (non-Javadoc)
    * 
    * @see com.github.celldynamics.quimp.plugin.AbstractPluginBase#showUi(boolean)
    */
   @Override
   public void showUi(boolean val) throws Exception {
     // no options given, no UI but load file and execute plugin
     executer();
 
     // in case user loaded the file
     if (qconfLoader != null && qconfLoader.getQp() != null) {
       options.paramFile = qconfLoader.getQp().getParamFile().getAbsolutePath();
     }
   }
 }