/**
* 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();
}
}
