/**
  * Writes the <code>shape</code>, <code>coords</code>, <code>href</code>,
  * <code>nohref</code> Attribute for the specified figure and ellipse.
  *
  * @return Returns true, if the circle is inside of the image bounds.
  */
 private boolean writeCircleAttributes(IXMLElement elem, SVGFigure f, Ellipse2D.Double ellipse) {
     AffineTransform t = TRANSFORM.getClone(f);
     if (t == null) {
         t = drawingTransform;
     } else {
         t.preConcatenate(drawingTransform);
     }
     
     if ((t.getType() &
             (AffineTransform.TYPE_UNIFORM_SCALE | AffineTransform.TYPE_TRANSLATION)) ==
             t.getType() &&
             ellipse.width == ellipse.height
             ) {
         
         Point2D.Double start = new Point2D.Double(ellipse.x, ellipse.y);
         Point2D.Double end = new Point2D.Double(ellipse.x + ellipse.width, ellipse.y + ellipse.height);
         t.transform(start, start);
         t.transform(end, end);
         ellipse.x = Math.min(start.x, end.x);
         ellipse.y = Math.min(start.y, end.y);
         ellipse.width = Math.abs(start.x - end.x);
         ellipse.height = Math.abs(start.y - end.y);
         
         elem.setAttribute("shape", "circle");
         elem.setAttribute("coords",
                 (int) (ellipse.x + ellipse.width / 2d)+","+
                 (int) (ellipse.y + ellipse.height / 2d)+","+
                 (int) (ellipse.width / 2d)
                 );
         writeHrefAttribute(elem, f);
         return bounds.intersects(ellipse.getBounds());
     } else {
         return writePolyAttributes(elem, f, (Shape) ellipse);
     }
 }
  /**
   * Move the cursor <i>where</i> characters, withough checking the current buffer.
   *
   * @see #where
   * @param where the number of characters to move to the right or left.
   */
  private final void moveInternal(final int where) throws IOException {
    // debug ("move cursor " + where + " ("
    // + buf.cursor + " => " + (buf.cursor + where) + ")");
    buf.cursor += where;

    char c;

    if (where < 0) {
      int len = 0;
      for (int i = buf.cursor; i < buf.cursor - where; i++) {
        if (buf.getBuffer().charAt(i) == '\t') len += TAB_WIDTH;
        else len++;
      }

      char cbuf[] = new char[len];
      Arrays.fill(cbuf, BACKSPACE);
      out.write(cbuf);

      return;
    } else if (buf.cursor == 0) {
      return;
    } else if (mask != null) {
      c = mask.charValue();
    } else {
      printCharacters(buf.buffer.substring(buf.cursor - where, buf.cursor).toCharArray());
      return;
    }

    // null character mask: don't output anything
    if (NULL_MASK.equals(mask)) {
      return;
    }

    printCharacters(c, Math.abs(where));
  }
 /**
  * All other write methods delegate their work to here.
  */
 public void write(OutputStream out, java.util.List<Figure> figures) throws IOException {
     Rectangle2D.Double drawingRect = null;
     
     for (Figure f : figures) {
         if (drawingRect == null) {
             drawingRect = f.getBounds();
         } else {
             drawingRect.add(f.getBounds());
         }
     }
     
     AffineTransform drawingTransform = new AffineTransform();
     drawingTransform.translate(
             -Math.min(0, drawingRect.x),
             -Math.min(0, drawingRect.y)
             );
     
     write(out, figures, drawingTransform,
             new Dimension(
             (int) (Math.abs(drawingRect.x) + drawingRect.width),
             (int) (Math.abs(drawingRect.y) + drawingRect.height))
             );
 }
 /**
  * Writes the <code>shape</code>, <code>coords</code>, <code>href</code>,
  * <code>nohref</code> Attribute for the specified figure and rectangle.
  *
  * @return Returns true, if the rect is inside of the image bounds.
  */
 private boolean writeRectAttributes(IXMLElement elem, SVGFigure f, Rectangle2D.Double rect) {
     AffineTransform t = TRANSFORM.getClone(f);
     if (t == null) {
         t = drawingTransform;
     } else {
         t.preConcatenate(drawingTransform);
     }
     
     if ((t.getType() &
             (AffineTransform.TYPE_UNIFORM_SCALE | AffineTransform.TYPE_TRANSLATION)) ==
             t.getType()
             ) {
         
         Point2D.Double start = new Point2D.Double(rect.x, rect.y);
         Point2D.Double end = new Point2D.Double(rect.x + rect.width, rect.y + rect.height);
         t.transform(start, start);
         t.transform(end, end);
         Rectangle r = new Rectangle(
                 (int) Math.min(start.x, end.x),
                 (int) Math.min(start.y, end.y),
                 (int) Math.abs(start.x - end.x),
                 (int) Math.abs(start.y - end.y)
                 );
         
         elem.setAttribute("shape", "rect");
         elem.setAttribute("coords",
                 r.x + ","+
                 r.y + ","+
                 (r.x + r.width) + ","+
                 (r.y + r.height)
                 );
         writeHrefAttribute(elem, f);
         return bounds.intersects(r);
     } else {
         return writePolyAttributes(elem, f, (Shape) rect);
     }
 }
  private void geterrors() {
    GenericDialog gd = new GenericDialog("Options");
    float conf = 0.67f;
    gd.addNumericField("Confidence Limit", (int) (conf * 100.0f), 5, 10, null);
    gd.addChoice("Error Parameter", paramsnames, paramsnames[0]);
    double spacing = 0.01;
    gd.addNumericField("Chi^2 plot spacing (% of value)?", spacing * 100.0, 2, 10, null);
    boolean globalerror = false;
    gd.addCheckbox("Global Fit Error?", globalerror);
    int dataset = 0;
    gd.addNumericField("Data Set (for Global Error)", dataset, 0);
    gd.showDialog();
    if (gd.wasCanceled()) {
      return;
    }
    conf = 0.01f * (float) gd.getNextNumber();
    int paramindex = (int) gd.getNextChoiceIndex();
    spacing = 0.01 * gd.getNextNumber();
    globalerror = gd.getNextBoolean();
    dataset = (int) gd.getNextNumber();

    if (globalerror) {
      support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, true, 0.1);
      int[] erindeces = {paramindex, dataset};
      // need to set up all the matrices
      int nsel = 0;
      int nparams = 11;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          nsel++;
        }
      }
      double[][] params = new double[nsel][nparams];
      String[][] tempformulas = new String[nsel][nparams];
      double[][][] constraints = new double[2][nsel][nparams];
      int[][] vflmatrix = new int[nsel][nparams];

      float[][] tempdata = new float[nsel][xpts * ypts];
      float[][] tempweights = new float[nsel][xpts * ypts];

      int nfit = 0;
      int counter = 0;
      for (int i = 0; i < ncurves; i++) {
        if (include[i]) {
          for (int j = 0; j < nparams; j++) {
            params[counter][j] = globalparams[i][j];
            tempformulas[counter][j] = globalformulas[i][j];
            constraints[0][counter][j] = globalconstraints[0][i][j];
            constraints[1][counter][j] = globalconstraints[1][i][j];
            vflmatrix[counter][j] = globalvflmatrix[i][j];
            if (vflmatrix[counter][j] == 0 || (j == 0 && vflmatrix[counter][j] == 2)) {
              nfit++;
            }
          }
          for (int j = 0; j < xpts; j++) {
            for (int k = 0; k < ypts; k++) {
              tempdata[counter][j + k * xpts] = (float) ((double) pch[i][j][k] / (double) nmeas[i]);
              tempweights[counter][j + k * xpts] = weights[i][j][k];
            }
          }
          counter++;
        }
      }
      int dofnum = xpts * ypts * nsel - (nfit - 1) - 1;
      int dofden = xpts * ypts * nsel - nfit - 1;
      // double flim=FLimit(dofnum,dofden,(double)conf);
      double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
      IJ.log("FLimit = " + (float) flim);
      if (flim == Double.NaN && flim < 1.0) {
        IJ.showMessage("Invalid Limiting F Value");
        return;
      }
      double truespacing = Math.abs(params[erindeces[1]][erindeces[0]] * spacing);
      double[][] c2plot =
          erclass.geterrorsglobal(
              params,
              vflmatrix,
              tempformulas,
              paramsnames,
              constraints,
              tempdata,
              tempweights,
              flim,
              truespacing,
              erindeces);
      IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
      int templength = c2plot[0].length;
      float[][] c2plotf = new float[2][templength - 1];
      for (int i = 0; i < (templength - 1); i++) {
        c2plotf[0][i] = (float) c2plot[0][i + 1];
        c2plotf[1][i] = (float) c2plot[1][i + 1];
      }
      new PlotWindow4(
              "c2 plot",
              paramsnames[paramindex] + "[" + dataset + "]",
              "Chi^2",
              c2plotf[0],
              c2plotf[1])
          .draw();
    } else {
      support_plane_errors erclass = new support_plane_errors(this, 0.0001, 50, false, 0.1);
      int errindex = paramindex;

      float[] tempdata = new float[xpts * ypts];
      float[] tempweights = new float[xpts * ypts];
      for (int i = 0; i < xpts; i++) {
        for (int j = 0; j < ypts; j++) {
          tempdata[i + j * xpts] = (float) ((double) avg[i][j] / (double) nmeas[ncurves]);
          tempweights[i + j * xpts] = avgweights[i][j];
        }
      }

      int nfit = 0;
      for (int i = 0; i < 7; i++) {
        if (avgfixes[i] == 0) {
          nfit++;
        }
      }
      int dofnum = xpts * ypts - (nfit - 1) - 1;
      int dofden = xpts * ypts - nfit - 1;
      double flim = (new jdist()).FLimit(dofnum, dofden, (double) conf);
      IJ.log("FLimit = " + (float) flim);
      if (flim == Double.NaN && flim < 1.0) {
        IJ.showMessage("Invalid Limiting F Value");
        return;
      }
      double truespacing = Math.abs(avgparams[errindex] * spacing);
      double[][] c2plot =
          erclass.geterrors(
              avgparams,
              avgfixes,
              avgconstraints,
              tempdata,
              tempweights,
              flim,
              truespacing,
              errindex);
      IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
      int templength = c2plot[0].length;
      float[][] c2plotf = new float[2][templength - 1];
      for (int i = 0; i < (templength - 1); i++) {
        c2plotf[0][i] = (float) c2plot[0][i + 1];
        c2plotf[1][i] = (float) c2plot[1][i + 1];
      }
      new PlotWindow4("c2 plot", paramsnames[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
    }
  }