コード例 #1
0
  public boolean doSelectCoord() throws HeadlessException {

    SingleCoordSelectionPanel pan = new SingleCoordSelectionPanel();
    // pan.setMaxX(this.expContext.getNrcols());
    // pan.setMaxY(this.expContext.getNrrows());
    if (maincont.getAbsDataAreaCoord() != null) {
      pan.setCoord1(maincont.getAbsDataAreaCoord());
    }
    int ans =
        JOptionPane.showConfirmDialog(
            this, pan, "Enter a selection:", JOptionPane.OK_CANCEL_OPTION);
    if (ans == JOptionPane.CANCEL_OPTION) {
      return true;
    }
    // RELATIVE to current sub experiment
    WellCoordinate c1 =
        new WellCoordinate(
            pan.getCoord1().getCol() - maincont.getExp().getColOffset(),
            pan.getCoord1().getRow() - maincont.getExp().getRowOffset());
    WellCoordinate c2 = c1.add(100, 100);
    WellSelection sel = new WellSelection(c1, c2);
    WellCoordinate abs = pan.getCoord1();
    if (maincont.getAbsDataAreaCoord() != null && abs.equals(maincont.getAbsDataAreaCoord())) {
      GuiUtils.showNonModalMsg("Same coordinates, I won't to anything", "Process");
      return true;
    }
    maincont.setAbsDataAreaCoord(abs);

    LookupUtils.publish(wellSelectionContent, sel);

    return false;
  }
コード例 #2
0
/** Top component which displays something. */
@ConvertAsProperties(
    dtd = "-//com.iontorrent.torrentscout.explorer//Process//EN",
    autostore = false)
@TopComponent.Description(
    preferredID = "ProcessTopComponent",
    iconBase = "com/iontorrent/torrentscout/explorer/chart-curve-edit.png",
    persistenceType = TopComponent.PERSISTENCE_NEVER)
@TopComponent.Registration(mode = "table_mode", openAtStartup = false)
@ActionID(category = "Window", id = "com.iontorrent.torrentscout.explorer.ProcessTopComponent")
@ActionReference(path = "Menu/Window" /*, position = 333 */)
@TopComponent.OpenActionRegistration(
    displayName = "#CTL_ProcessAction",
    preferredID = "ProcessTopComponent")
public final class ProcessTopComponent extends TopComponent
    implements TaskListener, FlowListener, FiletypeListener {

  ExperimentContext expContext;
  private final transient Lookup.Result<ExperimentContext> expContextResults =
      LookupUtils.getSubscriber(ExperimentContext.class, new SubscriberListener());
  //    private transient final Lookup.Result<WellSelection> selectionSelection =
  //            LookupUtils.getSubscriber(WellSelection.class, new WellSelectionListener());
  private final transient InstanceContent wellSelectionContent =
      LookupUtils.getPublisher(WellSelection.class);
  ExplorerContext maincont;
  WellSelection selection;
  CurveView cview;
  private RawType subtract_type;
  private int subtract_flow;
  RasterView raster;
  private FlowNrPanel flowPanel;
  private FiletypePanel typePanel;
  private RasterData data;
  boolean DOACTION;
  private boolean automatic_nn;

  public ProcessTopComponent() {
    initComponents();
    setName(NbBundle.getMessage(ProcessTopComponent.class, "CTL_ProcessTopComponent"));
    setToolTipText(NbBundle.getMessage(ProcessTopComponent.class, "HINT_ProcessTopComponent"));

    flowPanel = new FlowNrPanel(this);

    if (maincont == null) {
      flowPanel.setFlow(0);
    } else {
      flowPanel.setFlow(maincont.getFlow());
      typePanel.setType(maincont.getFiletype());
    }
    typePanel = new FiletypePanel(this);

    this.toolbar.add(this.flowPanel, null, 0);
    toolbar.add(this.typePanel, null, 0);
  }

  @Override
  public void flowChanged(ArrayList<Integer> flows) {
    int f = flows.get(0);
    if (maincont == null) {
      return;
    }
    if (f == maincont.getFlow()) {
      return;
    }
    p("flow changed");
    maincont.setFlow(f);
    // this.rasterViewCreate(true, null);
    // recomputeChart();
  }

  @Override
  public void fileTypeChanged(RawType filetype) {
    if (maincont == null) {
      return;
    }

    if (maincont != null) {
      maincont.setFiletype(filetype);
    }
    p("filetypechanged");

    //    this.rasterViewCreate(true, null);

  }

  public boolean doSaveChartAction() {

    String file = Export.getFile("Save chart data into file", "*.csv", true);
    if (file == null) {
      return true;
    }
    boolean ok = cview.export(file);
    // mask.write(file);
    if (!ok) {
      GuiUtils.showNonModalMsg("Problem writing chart to file...");
    } else {
      GuiUtils.showNonModalMsg("Wrote chart to file " + file);
    }
    return false;
  }

  public boolean doSelectCoord() throws HeadlessException {

    SingleCoordSelectionPanel pan = new SingleCoordSelectionPanel();
    // pan.setMaxX(this.expContext.getNrcols());
    // pan.setMaxY(this.expContext.getNrrows());
    if (maincont.getAbsDataAreaCoord() != null) {
      pan.setCoord1(maincont.getAbsDataAreaCoord());
    }
    int ans =
        JOptionPane.showConfirmDialog(
            this, pan, "Enter a selection:", JOptionPane.OK_CANCEL_OPTION);
    if (ans == JOptionPane.CANCEL_OPTION) {
      return true;
    }
    // RELATIVE to current sub experiment
    WellCoordinate c1 =
        new WellCoordinate(
            pan.getCoord1().getCol() - maincont.getExp().getColOffset(),
            pan.getCoord1().getRow() - maincont.getExp().getRowOffset());
    WellCoordinate c2 = c1.add(100, 100);
    WellSelection sel = new WellSelection(c1, c2);
    WellCoordinate abs = pan.getCoord1();
    if (maincont.getAbsDataAreaCoord() != null && abs.equals(maincont.getAbsDataAreaCoord())) {
      GuiUtils.showNonModalMsg("Same coordinates, I won't to anything", "Process");
      return true;
    }
    maincont.setAbsDataAreaCoord(abs);

    LookupUtils.publish(wellSelectionContent, sel);

    return false;
  }

  public void getUserPreferences() {
    if (maincont == null) {
      return;
    }
    Preferences p =
        NbPreferences.forModule(
            com.iontorrent.torrentscout.explorer.options.TorrentExplorerPanel.class);
    int span = p.getInt("span", 8);
    int size = p.getInt("masksize", 100);
    automatic_nn = p.getBoolean("automatic_nn", true);
    maincont.setRasterSize(size);
    maincont.setSpan(span);
    maincont.setMedianFunction("median");
  }

  protected boolean getExpContext() {
    //  Exception e = new Exception("showing stack trace");
    //   p(ErrorHandler.getString(e));
    if (expContext == null) {
      expContext = GlobalContext.getContext().getExperimentContext();
    }
    if (expContext == null) {
      GuiUtils.showNonModalMsg("Got no experiment context from global contexet");
      return false;
    }
    maincont = ExplorerContext.getCurContext(expContext);
    info.setText(expContext.getRawDir());
    this.btnreload.setToolTipText(
        "Reload data from dir " + expContext.getRawDir() + " at " + maincont.getAbsDataAreaCoord());
    return true;
  }

  //    private class WellSelectionListener implements LookupListener {
  //
  //        @Override
  //        public void resultChanged(LookupEvent ev) {
  //            //ask
  //            int ans = JOptionPane.showConfirmDialog(ProcessTopComponent.this, "Would you like to
  // reload the data with the updated coordinate?");
  //            if (ans == JOptionPane.OK_OPTION) getLatestSelection();
  //        }
  //    }
  //    private void getLatestSelection() {
  //        final Collection<? extends WellSelection> selections =
  // selectionSelection.allInstances();
  //        if (!selections.isEmpty()) {
  //            //  p("Getting last selection");
  //            selection = null;
  //            Iterator<WellSelection> it = (Iterator<WellSelection>) selections.iterator();
  //            while (it.hasNext()) {
  //                selection = it.next();
  //            }
  //            p("Got a selection: " + selection);
  //            maincont.setDataAreaCoord(selection.getCoord1());
  //            maincont.getExp().getWellContext().setSelection(selection);
  //
  //            //   p("SubscriberListener Got WellSelection:" + cur_context);
  //            GuiUtils.showNonModalMsg("Process: Got a well selection: " + selection);
  //            // rasterViewUpdate(true);
  //        }
  //
  //    }
  private void addGui() {

    if (expContext == null) {
      expContext = GlobalContext.getContext().getExperimentContext();
    }
    if (expContext == null) {
      //  GuiUtils.showNonModalMsg("Got no experiment context");
      return;
    }
    maincont = ExplorerContext.getCurContext(expContext);
    getUserPreferences();

    rasterViewCreate(true, null);

    maincont.addListener(
        new ContextChangeAdapter() {

          @Override
          public void fileTypeChanged(RawType t) {
            p("RawType chnaged: " + t);
            typePanel.setType(t);
            // rasterViewCreate(true, null);
          }

          @Override
          public void flowChanged(int flow) {
            p("flow changed: " + flow);
            rasterViewCreate(true, "Raw data");
          }

          @Override
          public void dataChanged(
              RasterData data,
              int startrow,
              int startcol,
              int startflow,
              int endrow,
              int endcol,
              int endflow) {
            p(
                "RasterData chnged: "
                    + startrow
                    + "/"
                    + startcol
                    + "/"
                    + startflow
                    + ", NOT reloading automatically");
            // rasterViewUpdate();
          }

          @Override
          public void coordChanged(WellCoordinate coord) {
            // p("coord chnged: " + coord);
            chartViewUpdate();
          }

          @Override
          public void dataAreaCoordChanged(WellCoordinate coord) {
            p("data area coord changed: " + coord);
            btnreload.setToolTipText("Reload data from at " + maincont.getAbsDataAreaCoord());
            // rebuildMaskComboBoxes();
            rasterViewCreate(true, "Raw data");
          }

          @Override
          public void widgetChanged(Widget w) {
            p("widget chnged: " + w);
            chartViewUpdate();
          }
        });
    if (expContext.getWellContext().getCoordinate() == null) {
      expContext.getWellContext().setCoordinate(new WellCoordinate(100, 100));
    }
  }

  private RasterData computeNN(ProgressListener prog) {
    return computeNN(prog, maincont.getData());
  }

  private RasterData computeNN(ProgressListener prog, RasterData rawdata) {
    //   p("computeNN. Maincont is: " + maincont);
    if (rawdata == null) {
      GuiUtils.showNonModalDialog(
          "<html>I see no data yet - did you already pick a region?<br>"
              + "(Even if you see something somewhere, if you didn't actually select a region, it might just show some sample data)</html>",
          "No data - region selected?");
      return null;
    }
    RasterData nndata = null;
    try {
      if (maincont == null) {
        maincont = ExplorerContext.getCurContext(expContext);
      }
      int span = Math.max(1, this.maincont.getSpan());
      NearestNeighbor nn = new NearestNeighbor(span, maincont.getMedianFunction());
      BitMask ignore = maincont.getIgnoreMask();
      BitMask take = maincont.getBgMask();

      if (take != null && take == ignore) {
        JOptionPane.showMessageDialog(
            this,
            "You select the same mask for ignore and bg :-). \nYou should select another mask for the bg (or you get a null result. I will just return the old data.");
        return rawdata;
      }
      if (take != null && take.computePercentage() < 1) {
        int ans =
            JOptionPane.showConfirmDialog(
                this,
                "<html>The bg mask only has "
                    + take.computePercentage()
                    + "% wells, do you want to still use it?"
                    + "<br><b>Did you already select a region?</b>"
                    + "<br>You might want to use the MaskEditor (and <b>refresh</b> the masks possibly) to check them</html>",
                "Few wells",
                JOptionPane.OK_CANCEL_OPTION);
        if (ans == JOptionPane.CANCEL_OPTION) {
          return rawdata;
        }
      }
      maincont.setBgMask(take);
      maincont.setIgnoreMask(ignore);
      if (prog != null)
        prog.setMessage(
            "Masked neighbor subtraction: ignore mask " + ignore + " and empty mask " + take);
      // RasterData nndata = nn.compute(rawdata, mask, prog, span);

      //   p("calling computebetter");
      // if (boxslow.isSelected()) nndata =nn.computeSlow(rawdata, ignore, take, prog, span);
      nndata = nn.computeBetter(rawdata, ignore, take, prog, span);

    } catch (Exception e) {
      p("Error with nn: " + ErrorHandler.getString(e));
      JOptionPane.showMessageDialog(
          this,
          "I was not able to do the masked neighbor subtraction:\n" + ErrorHandler.getString(e));
      return null;
    }
    if (nndata == null) {
      JOptionPane.showMessageDialog(
          this,
          "I was not able to do the masked neighbor subtraction - I got no error but also no result :-) ");
    }
    return nndata;
  }

  private void doHintAction() {
    String msg = "<html>You can do the following things here:<ul>";
    msg += "<li><b>Pick the masks for NN subtraction in the Mask Editor Component</b></li>";
    msg +=
        "<li>You can change the automatic NN subtraction in the <b>Options/Explorer options tab</b></li>";
    msg += "<li>drag the cursors around in the left view with the <b>left</b> mouse button </li>";
    msg +=
        "<li>overlay masks by selecting them in the drop down box and checking one of the 3 check boxes </li>";
    msg += "<li>move the yellow cursor (main cursor) around:";
    msg += "<ul><li>First, click on it (or the image)</li>";
    msg += "<li>the <b>cursor keys</b> will move it around</li>";
    msg +=
        "<li>the <b>space or tab key</b> will move it to the next flagged coordinate (if a mask is overlayed)</li>";
    msg += "<li>the <b>delete key</b> will delete a flag (if a mask is overlayed)</li>";
    msg += "<li>the <b>insert key</b> will add a flag (if a mask is overlayed)</li>";
    msg += "</ul></li>";
    msg += "<li>change the number of cursors (text field) </li>";
    msg +=
        "<li>do a <b>masked neighbor subtraction</b> by picking a bg and ingore mask and then clicking the wheels icon"
            + "<br>(it will compute the average signal using bg wells, excluding ignore wells, with the given radius around a well (span))"
            + "<br>(the span can ge changed in Tools, Options, Explorer Options)</li>";
    msg += "<li>move the image around with the right mouse button</li>";
    msg += "<li>zoom in or out of the image  with a mouse wheel</li>";
    msg +=
        "<li>to change the size (100x100 is default), go to Tools, Options, Explorer Options</li>";
    msg += "</ul></html>";
    JOptionPane.showMessageDialog(this, msg);
  }

  @Override
  public void taskDone(Task t) {
    p("Task " + t + " is done");
    setCursor(null);
    // if (t.isSuccess()) {
    this.data = ((ComputeNN) t).getData();

    p("Got nndata " + data);
    if (data == null) {
      JOptionPane.showMessageDialog(this, "There was a problem in nn compute, I got no result");
    } else {
      maincont.setData(data);
      rasterViewCreate(
          false,
          "After masked neighbor subtraction, span="
              + maincont.getSpan()
              + ", BG mask="
              + maincont.getBgMask());
    }
  }

  private class ComputeNN extends Task {

    boolean ok;

    public ComputeNN(TaskListener tlistener) {

      super(tlistener, ProgressHandleFactory.createHandle("Computing NN..."));
    }

    public RasterData getData() {
      return data;
    }

    @Override
    public Void doInBackground() {
      data = computeNN(this);
      return null;
    }

    public boolean isSuccess() {
      return ok;
    }
  }

  private class SubscriberListener implements LookupListener {

    @Override
    public void resultChanged(LookupEvent ev) {
      getLatestExperimentContext();
    }
  }

  private void getLatestExperimentContext() {
    final Collection<? extends ExperimentContext> items = expContextResults.allInstances();
    if (!items.isEmpty()) {
      ExperimentContext data = null;
      Iterator<ExperimentContext> it = (Iterator<ExperimentContext>) items.iterator();
      while (it.hasNext()) {
        data = it.next();
      }

      expContext = data;
      update(expContext);
    }
  }

  @Override
  public Action[] getActions() {
    return OpenWindowAction.getActions(this);
  }

  @Override
  public void componentOpened() {

    getLatestExperimentContext();
  }

  private void p(String msg) {
    System.out.println("Process: " + msg);
  }

  private void update(ExperimentContext result) {
    if (result == null) {
      result = GlobalContext.getContext().getExperimentContext();
    }
    if (result == null) {
      // GuiUtils.showNonModalMsg("Got no experiment context");
      return;
    }
    if (result != null) {
      this.expContext = result;
      maincont = ExplorerContext.getCurContext(result);
      getUserPreferences();
      addGui();
    }
  }

  public void rasterViewUpdate() {
    p("rasterviewupdate called");
    raster.update(false, maincont);

    cview.repaint();
  }

  public void rasterViewCreate(boolean load, String title) {
    p("=========rasterViewCreate called: load=" + load);
    // if (load) {
    //  Exception e = new Exception("Tracing call");
    //   p(ErrorHandler.getString(e));
    //  }
    if (!getExpContext()) {
      return;
    }
    if (load) {
      if (selection != null)
        GuiUtils.showNonModalMsg(
            "Loading "
                + selection
                + " for "
                + maincont.getFiletype()
                + ", flow "
                + maincont.getFlow(),
            "Process");
    }

    String base = "?";
    if (maincont.getFiletype() == RawType.ACQ) {
      base = "" + maincont.getExp().getWellContext().getBase(maincont.getFlow());
    }
    this.flowPanel.setToolTipText(
        "<html>Base for flow "
            + maincont.getFlow()
            + ":"
            + base
            + "<br>Flow order: "
            + maincont.getExp().getFlowOrder()
            + "</html>");

    raster = new RasterView(maincont, load);

    this.panImage.removeAll();
    panImage.add(raster);
    // repaint();
    //  p("adding raster view");
    if (load) {
      this.getUserPreferences();
    }
    raster.update(load, maincont);

    // paintImmediately(0,0,1000,1000);
    panImage.repaint();
    raster.repaint();

    if (load) {
      title = "Raw data";
    }
    title += " flow " + maincont.getFlow() + "=" + base;
    chartViewCreate(title);

    invalidate();
    revalidate();
    // this.paintAll(getGraphics());
    repaint();
    if (load) {
      if (this.automatic_nn) {
        p("also doing nn - disable nn");
        this.btnNN.setEnabled(false);
        btnNN.setText("");
        btnNN.setToolTipText(
            "Automatically computing NN - check Explorer Options if you wish to change it!");
        RasterData data = computeNN(null);
        maincont.setData(data);
        rasterViewCreate(
            false,
            "After masked neighbor subtraction, span="
                + maincont.getSpan()
                + ", BG mask="
                + maincont.getBgMask());
      } else {
        this.btnNN.setEnabled(true);
        btnNN.setText("Compute NN");
        btnNN.setToolTipText(
            "Click to compute NN bg subtraction - check Explorer Options if you wish <b>automate</b> this!");
      }
    }
  }

  public void chartViewCreate(String title) {
    cview = new CurveView(maincont, title);
    this.panChart.removeAll();
    this.panChart.add("Center", cview);
    panChart.repaint();
    cview.repaint();
  }

  public void chartViewUpdate() {

    cview.repaint();
  }

  /**
   * This method is called from within the constructor to initialize the form. WARNING: Do NOT
   * modify this code. The content of this method is always regenerated by the Form Editor.
   */
  // <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
  private void initComponents() {

    toolbar = new javax.swing.JToolBar();
    btnNN = new javax.swing.JButton();
    btnreload = new javax.swing.JButton();
    subtract = new javax.swing.JButton();
    btnSelect = new javax.swing.JButton();
    btnSave = new javax.swing.JButton();
    hint = new javax.swing.JButton();
    refresh = new javax.swing.JButton();
    info = new javax.swing.JLabel();
    jScrollPane1 = new javax.swing.JScrollPane();
    panChart = new javax.swing.JPanel();
    panImage = new javax.swing.JPanel();

    toolbar.setRollover(true);
    toolbar.setOpaque(false);

    btnNN.setIcon(
        new javax.swing.ImageIcon(
            getClass()
                .getResource("/com/iontorrent/torrentscout/explorer/system-run-3.png"))); // NOI18N
    org.openide.awt.Mnemonics.setLocalizedText(
        btnNN,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnNN.text")); // NOI18N
    btnNN.setToolTipText(
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnNN.toolTipText")); // NOI18N
    btnNN.setFocusable(false);
    btnNN.setHorizontalTextPosition(javax.swing.SwingConstants.LEFT);
    btnNN.setMargin(new java.awt.Insets(1, 1, 1, 1));
    btnNN.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(java.awt.event.ActionEvent evt) {
            btnNNActionPerformed(evt);
          }
        });
    toolbar.add(btnNN);

    btnreload.setIcon(
        new javax.swing.ImageIcon(
            getClass()
                .getResource(
                    "/com/iontorrent/torrentscout/explorer/database-refresh.png"))); // NOI18N
    org.openide.awt.Mnemonics.setLocalizedText(
        btnreload,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnreload.text")); // NOI18N
    btnreload.setToolTipText(
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnreload.toolTipText")); // NOI18N
    btnreload.setFocusable(false);
    btnreload.setHorizontalTextPosition(javax.swing.SwingConstants.LEFT);
    btnreload.setMargin(new java.awt.Insets(1, 1, 1, 1));
    btnreload.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
    btnreload.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(java.awt.event.ActionEvent evt) {
            btnreloadActionPerformed(evt);
          }
        });
    toolbar.add(btnreload);

    subtract.setIcon(
        new javax.swing.ImageIcon(
            getClass().getResource("/com/iontorrent/torrentscout/explorer/minus.png"))); // NOI18N
    org.openide.awt.Mnemonics.setLocalizedText(
        subtract,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.subtract.text")); // NOI18N
    subtract.setToolTipText(
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.subtract.toolTipText")); // NOI18N
    subtract.setFocusable(false);
    subtract.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
    subtract.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
    subtract.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(java.awt.event.ActionEvent evt) {
            subtractActionPerformed(evt);
          }
        });
    toolbar.add(subtract);

    btnSelect.setIcon(
        new javax.swing.ImageIcon(getClass().getResource("/select-rectangular.png"))); // NOI18N
    org.openide.awt.Mnemonics.setLocalizedText(
        btnSelect,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnSelect.text")); // NOI18N
    btnSelect.setToolTipText(
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnSelect.toolTipText")); // NOI18N
    btnSelect.setFocusable(false);
    btnSelect.setHorizontalTextPosition(javax.swing.SwingConstants.LEFT);
    btnSelect.setMargin(new java.awt.Insets(1, 1, 1, 1));
    btnSelect.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(java.awt.event.ActionEvent evt) {
            btnSelectActionPerformed(evt);
          }
        });
    toolbar.add(btnSelect);

    btnSave.setIcon(
        new javax.swing.ImageIcon(
            getClass().getResource("/com/iontorrent/maskview/document-export.png"))); // NOI18N
    org.openide.awt.Mnemonics.setLocalizedText(
        btnSave,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnSave.text")); // NOI18N
    btnSave.setToolTipText(
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.btnSave.toolTipText")); // NOI18N
    btnSave.setMargin(new java.awt.Insets(1, 1, 1, 1));
    btnSave.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(java.awt.event.ActionEvent evt) {
            btnSaveActionPerformed(evt);
          }
        });
    toolbar.add(btnSave);

    hint.setIcon(
        new javax.swing.ImageIcon(
            getClass()
                .getResource("/com/iontorrent/torrentscout/explorer/help-hint.png"))); // NOI18N
    org.openide.awt.Mnemonics.setLocalizedText(
        hint,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.hint.text")); // NOI18N
    hint.setToolTipText(
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.hint.toolTipText")); // NOI18N
    hint.setFocusable(false);
    hint.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
    hint.setMargin(new java.awt.Insets(0, 0, 0, 0));
    hint.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
    hint.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(java.awt.event.ActionEvent evt) {
            hintActionPerformed(evt);
          }
        });
    toolbar.add(hint);

    refresh.setIcon(
        new javax.swing.ImageIcon(
            getClass()
                .getResource(
                    "/com/iontorrent/torrentscout/explorer/view-refresh-3.png"))); // NOI18N
    org.openide.awt.Mnemonics.setLocalizedText(
        refresh,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.refresh.text")); // NOI18N
    refresh.setToolTipText(
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.refresh.toolTipText")); // NOI18N
    refresh.setFocusable(false);
    refresh.setHorizontalTextPosition(javax.swing.SwingConstants.CENTER);
    refresh.setVerticalTextPosition(javax.swing.SwingConstants.BOTTOM);
    refresh.addActionListener(
        new java.awt.event.ActionListener() {
          public void actionPerformed(java.awt.event.ActionEvent evt) {
            refreshActionPerformed(evt);
          }
        });
    toolbar.add(refresh);

    org.openide.awt.Mnemonics.setLocalizedText(
        info,
        org.openide.util.NbBundle.getMessage(
            ProcessTopComponent.class, "ProcessTopComponent.info.text")); // NOI18N
    toolbar.add(info);

    panChart.setBorder(javax.swing.BorderFactory.createEtchedBorder());
    panChart.setOpaque(false);
    panChart.setLayout(new java.awt.BorderLayout());

    panImage.setBorder(javax.swing.BorderFactory.createEtchedBorder());
    panImage.setLayout(new java.awt.BorderLayout());

    javax.swing.GroupLayout layout = new javax.swing.GroupLayout(this);
    this.setLayout(layout);
    layout.setHorizontalGroup(
        layout
            .createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addComponent(toolbar, javax.swing.GroupLayout.DEFAULT_SIZE, 1090, Short.MAX_VALUE)
            .addGroup(
                layout
                    .createSequentialGroup()
                    .addComponent(
                        panImage,
                        javax.swing.GroupLayout.PREFERRED_SIZE,
                        546,
                        javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                    .addComponent(
                        panChart, javax.swing.GroupLayout.DEFAULT_SIZE, 528, Short.MAX_VALUE)
                    .addContainerGap())
            .addGroup(
                layout
                    .createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(
                        layout
                            .createSequentialGroup()
                            .addGap(0, 544, Short.MAX_VALUE)
                            .addComponent(
                                jScrollPane1,
                                javax.swing.GroupLayout.PREFERRED_SIZE,
                                javax.swing.GroupLayout.DEFAULT_SIZE,
                                javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addGap(0, 544, Short.MAX_VALUE))));
    layout.setVerticalGroup(
        layout
            .createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
            .addGroup(
                layout
                    .createSequentialGroup()
                    .addComponent(
                        toolbar,
                        javax.swing.GroupLayout.PREFERRED_SIZE,
                        25,
                        javax.swing.GroupLayout.PREFERRED_SIZE)
                    .addPreferredGap(javax.swing.LayoutStyle.ComponentPlacement.RELATED)
                    .addGroup(
                        layout
                            .createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                            .addComponent(
                                panChart,
                                javax.swing.GroupLayout.DEFAULT_SIZE,
                                382,
                                Short.MAX_VALUE)
                            .addComponent(
                                panImage,
                                javax.swing.GroupLayout.DEFAULT_SIZE,
                                382,
                                Short.MAX_VALUE)))
            .addGroup(
                layout
                    .createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
                    .addGroup(
                        layout
                            .createSequentialGroup()
                            .addGap(0, 208, Short.MAX_VALUE)
                            .addComponent(
                                jScrollPane1,
                                javax.swing.GroupLayout.PREFERRED_SIZE,
                                javax.swing.GroupLayout.DEFAULT_SIZE,
                                javax.swing.GroupLayout.PREFERRED_SIZE)
                            .addGap(0, 203, Short.MAX_VALUE))));
  } // </editor-fold>//GEN-END:initComponents

  private void btnNNActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_btnNNActionPerformed
    p(" about to compute nn. Maincont is: " + maincont + ", data is: " + maincont.getData());
    ComputeNN task = new ComputeNN(this);
    task.execute();
  } // GEN-LAST:event_btnNNActionPerformed

  private void btnreloadActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_btnreloadActionPerformed
    rasterViewCreate(true, "Raw data");
  } // GEN-LAST:event_btnreloadActionPerformed

  private void btnSelectActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_btnSelectActionPerformed
    doSelectCoord();
  } // GEN-LAST:event_btnSelectActionPerformed

  private void btnSaveActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_btnSaveActionPerformed
    doSaveChartAction();
  }
  // GEN-LAST:event_btnSaveActionPerformed

  private void refreshActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_refreshActionPerformed

    this.raster.redrawImages();
  } // GEN-LAST:event_refreshActionPerformed

  private void subtractActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_subtractActionPerformed

    RasterData data = maincont.getData();
    if (data == null) {
      JOptionPane.showMessageDialog(this, "I have no data yet to subtract anything from :-)");
      return;
    }
    if (subtract_type == null) {
      subtract_type = maincont.getFiletype();
    }
    FlowSelection pan =
        new FlowSelection(
            "Select the flow and file type you wish to subtract from the currently selected data");
    pan.setFlow(subtract_flow);
    pan.setFiletype(subtract_type);
    int ans =
        JOptionPane.showConfirmDialog(
            this,
            pan,
            "Data Subtraction",
            JOptionPane.OK_CANCEL_OPTION,
            JOptionPane.QUESTION_MESSAGE);
    if (ans != JOptionPane.OK_OPTION) {
      return;
    }

    subtract_flow = pan.getFlow();
    subtract_type = pan.getFiletype();
    // otherwise load the data and then subtract
    RasterData sub = null;
    DataAccessManager manager = DataAccessManager.getManager(maincont.getExp().getWellContext());
    try {
      p("Loading subregion, RELATIVE coord " + maincont.getRelativeDataAreaCoord());
      sub =
          manager.getRasterDataForArea(
              null,
              maincont.getRasterSize(),
              maincont.getRelativeDataAreaCoord(),
              pan.getFlow(),
              pan.getFiletype(),
              null,
              0,
              -1);
      // now subtract first frame
    } catch (Exception ex) {
      p("Error when loading: " + ErrorHandler.getString(ex));
    }
    if (sub == null) {
      JOptionPane.showMessageDialog(
          this,
          "I could not load flow "
              + pan.getFlow()
              + ", "
              + pan.getFiletype()
              + ", @ "
              + maincont.getAbsDataAreaCoord());
      return;
    }
    String what = "raw";
    if (this.automatic_nn) {
      GuiUtils.showNonModalMsg("Computing NN before subtraction");
      sub = computeNN(null, sub);
      what = "NN subtracted";
    }

    data.subtract(sub);
    JOptionPane.showMessageDialog(
        this,
        "I subtracted the "
            + what
            + " data from "
            + pan.getFlow()
            + ", "
            + pan.getFiletype()
            + ", @ "
            + maincont.getAbsDataAreaCoord());
    this.rasterViewUpdate();
  } // GEN-LAST:event_subtractActionPerformed

  private void hintActionPerformed(
      java.awt.event.ActionEvent evt) { // GEN-FIRST:event_hintActionPerformed

    doHintAction();
  } // GEN-LAST:event_hintActionPerformed

  // Variables declaration - do not modify//GEN-BEGIN:variables
  private javax.swing.JButton btnNN;
  private javax.swing.JButton btnSave;
  private javax.swing.JButton btnSelect;
  private javax.swing.JButton btnreload;
  private javax.swing.JButton hint;
  private javax.swing.JLabel info;
  private javax.swing.JScrollPane jScrollPane1;
  private javax.swing.JPanel panChart;
  private javax.swing.JPanel panImage;
  private javax.swing.JButton refresh;
  private javax.swing.JButton subtract;
  private javax.swing.JToolBar toolbar;
  // End of variables declaration//GEN-END:variables

  @Override
  public void componentClosed() {
    // TODO add custom code on component closing
  }

  void writeProperties(java.util.Properties p) {
    // better to version settings since initial version as advocated at
    // http://wiki.apidesign.org/wiki/PropertyFiles
    p.setProperty("version", "1.0");
    // TODO store your settings
  }

  void readProperties(java.util.Properties p) {
    String version = p.getProperty("version");
    // TODO read your settings according to their version
  }

  private void setStatus(String msg) {
    Message message =
        StatusDisplayer.getDefault()
            .setStatusText(
                "<html>Process: " + msg + "</html>", StatusDisplayer.IMPORTANCE_FIND_OR_REPLACE);
    message.clear(30000);
  }

  private void setStatusWarning(String msg) {
    Message message =
        StatusDisplayer.getDefault()
            .setStatusText(
                "<html>Process: " + msg + "</html>", StatusDisplayer.IMPORTANCE_ERROR_HIGHLIGHT);
    message.clear(120000);
  }

  private void setStatusError(String msg) {
    Message message =
        StatusDisplayer.getDefault()
            .setStatusText(
                "<html>Process: " + msg + "</html>", StatusDisplayer.IMPORTANCE_ERROR_HIGHLIGHT);
    message.clear(240000);
  }
}