/**
* 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);
}
}
@Override
public void keyTyped(final KeyEvent e) {
if (undo == null || control(e) || DELNEXT.is(e) || DELPREV.is(e) || ESCAPE.is(e)) return;
text.pos(text.cursor());
// string to be added
String ch = String.valueOf(e.getKeyChar());
// remember if marked text is to be deleted
boolean del = true;
final byte[] txt = text.text();
if (TAB.is(e)) {
if (text.marked()) {
// check if lines are to be indented
final int s = Math.min(text.pos(), text.start());
final int l = Math.max(text.pos(), text.start()) - 1;
for (int p = s; p <= l && p < txt.length; p++) del &= txt[p] != '\n';
if (!del) {
text.indent(s, l, e.isShiftDown());
ch = null;
}
} else {
boolean c = true;
for (int p = text.pos() - 1; p >= 0 && c; p--) {
final byte b = txt[p];
c = ws(b);
if (b == '\n') break;
}
if (c) ch = " ";
}
}
// delete marked text
if (text.marked() && del) text.delete();
if (ENTER.is(e)) {
// adopt indentation from previous line
final StringBuilder sb = new StringBuilder(1).append(e.getKeyChar());
int s = 0;
for (int p = text.pos() - 1; p >= 0; p--) {
final byte b = txt[p];
if (b == '\n') break;
if (b == '\t') {
s += 2;
} else if (b == ' ') {
s++;
} else {
s = 0;
}
}
for (int p = 0; p < s; p++) sb.append(' ');
ch = sb.toString();
}
if (ch != null) text.add(ch);
text.setCaret();
rend.calc();
showCursor(2);
e.consume();
}
/**
* Ensures that the caret is visible by scrolling the text area if necessary.
*
* @return True if scrolling was actually performed, false if the caret was already visible
*/
public boolean scrollToCaret() {
int line = getCaretLine();
int lineStart = getLineStartOffset(line);
int offset = Math.max(0, Math.min(getLineLength(line) - 1, getCaretPosition() - lineStart));
return scrollTo(line, offset);
}
/**
* Ensures that the specified line and offset is visible by scrolling the text area if necessary.
*
* @param line The line to scroll to
* @param offset The offset in the line to scroll to
* @return True if scrolling was actually performed, false if the line and offset was already
* visible
*/
public boolean scrollTo(int line, int offset) {
// visibleLines == 0 before the component is realized
// we can't do any proper scrolling then, so we have
// this hack...
if (visibleLines == 0) {
setFirstLine(Math.max(0, line - electricScroll));
return true;
}
int newFirstLine = firstLine;
int newHorizontalOffset = horizontalOffset;
if (line < firstLine + electricScroll) {
newFirstLine = Math.max(0, line - electricScroll);
} else if (line + electricScroll >= firstLine + visibleLines) {
newFirstLine = (line - visibleLines) + electricScroll + 1;
if (newFirstLine + visibleLines >= getLineCount())
newFirstLine = getLineCount() - visibleLines;
if (newFirstLine < 0) newFirstLine = 0;
}
int x = _offsetToX(line, offset);
int width = painter.getFontMetrics().charWidth('w');
if (x < 0) {
newHorizontalOffset = Math.min(0, horizontalOffset - x + width + 5);
} else if (x + width >= painter.getWidth()) {
newHorizontalOffset = horizontalOffset + (painter.getWidth() - x) - width - 5;
}
return setOrigin(newFirstLine, newHorizontalOffset);
}
private void getintbright() {
weights = new float[ncurves][xpts][ypts];
for (int i = 0; i < ncurves; i++) {
nmeas[i] = 0;
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
nmeas[i] += (int) pch[i][j][k];
}
}
double tempavg = 0.0;
double tempavg2 = 0.0;
double temp2avg = 0.0;
double temp2avg2 = 0.0;
double tempccavg = 0.0;
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
double normed = (double) pch[i][j][k] / (double) nmeas[i];
if (pch[i][j][k] > 0.0f) {
weights[i][j][k] = (float) ((double) nmeas[i] / (normed * (1.0f - normed)));
} else {
weights[i][j][k] = 1.0f;
}
tempavg += normed * (double) j;
tempavg2 += normed * (double) j * (double) j;
temp2avg += normed * (double) k;
temp2avg2 += normed * (double) k * (double) k;
tempccavg += normed * (double) k * (double) j;
}
}
tempccavg -= tempavg * temp2avg;
brightcc[i] = tempccavg / Math.sqrt(tempavg * temp2avg);
tempavg2 -= tempavg * tempavg;
tempavg2 /= tempavg;
bright1[i] = (tempavg2 - 1.0);
temp2avg2 -= temp2avg * temp2avg;
temp2avg2 /= temp2avg;
bright2[i] = (temp2avg2 - 1.0);
intensity1[i] = tempavg;
intensity2[i] = temp2avg;
if (psfflag == 0) {
bright1[i] /= 0.3536;
bright2[i] /= 0.3536;
brightcc[i] /= 0.3536;
} else {
if (psfflag == 1) {
bright1[i] /= 0.078;
bright2[i] /= 0.078;
brightcc[i] /= 0.078;
} else {
bright1[i] /= 0.5;
bright2[i] /= 0.5;
brightcc[i] /= 0.5;
}
}
number1[i] = intensity1[i] / bright1[i];
number2[i] = intensity2[i] / bright2[i];
brightmincc[i] = (bright1[i] * beta) * Math.sqrt(intensity1[i] / intensity2[i]);
}
}
@Override
public final void mouseDragged(final MouseEvent e) {
if (!SwingUtilities.isLeftMouseButton(e)) return;
// selection mode
select(e.getPoint(), false);
final int y = Math.max(20, Math.min(e.getY(), getHeight() - 20));
if (y != e.getY()) scroll.pos(scroll.pos() + e.getY() - y);
}
/**
* Draw every char in separate terminal cell to guaranty equal width for different lines.
* Nevertheless to improve kerning we draw word characters as one block for monospaced fonts.
*/
private void drawChars(int x, int y, CharBuffer buf, TextStyle style, Graphics2D gfx) {
final int blockLen = 1;
int offset = 0;
int drawCharsOffset = 0;
// workaround to fix Swing bad rendering of bold special chars on Linux
// TODO required for italic?
CharBuffer renderingBuffer;
if (mySettingsProvider.DECCompatibilityMode() && style.hasOption(TextStyle.Option.BOLD)) {
renderingBuffer = CharUtils.heavyDecCompatibleBuffer(buf);
} else {
renderingBuffer = buf;
}
while (offset + blockLen <= buf.length()) {
if (renderingBuffer.getBuf()[buf.getStart() + offset] == CharUtils.DWC) {
offset += blockLen;
drawCharsOffset += blockLen;
continue; // dont' draw second part(fake one) of double width character
}
Font font = getFontToDisplay(buf.charAt(offset + blockLen - 1), style);
// while (myMonospaced && (offset + blockLen < buf.getLength()) &&
// isWordCharacter(buf.charAt(offset + blockLen - 1))
// && (font == getFontToDisplay(buf.charAt(offset + blockLen - 1), style))) {
// blockLen++;
// }
gfx.setFont(font);
int descent = gfx.getFontMetrics(font).getDescent();
int baseLine = (y + 1) * myCharSize.height - descent;
int xCoord = (x + drawCharsOffset) * myCharSize.width;
int textLength =
CharUtils.getTextLengthDoubleWidthAware(
buf.getBuf(),
buf.getStart() + offset,
blockLen,
mySettingsProvider.ambiguousCharsAreDoubleWidth());
int yCoord = y * myCharSize.height;
gfx.setClip(
xCoord,
yCoord,
Math.min(textLength * myCharSize.width, getWidth() - xCoord),
Math.min(myCharSize.height, getHeight() - yCoord));
gfx.setColor(getPalette().getColor(myStyleState.getForeground(style.getForegroundForRun())));
gfx.drawChars(renderingBuffer.getBuf(), buf.getStart() + offset, blockLen, xCoord, baseLine);
drawCharsOffset += blockLen;
offset += blockLen;
}
gfx.setClip(null);
}
/**
* 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));
}
/**
* Draws the specified string.
*
* @param g graphics reference
* @param s text
* @param x x coordinate
* @param y y coordinate
* @param w width
* @param fs font size
*/
public static void chopString(
final Graphics g, final byte[] s, final int x, final int y, final int w, final int fs) {
if (w < 12) return;
final int[] cw = fontWidths(g.getFont());
int j = s.length;
try {
int l = 0;
int fw = 0;
for (int k = 0; k < j; k += l) {
final int ww = width(g, cw, cp(s, k));
if (fw + ww >= w - 4) {
j = Math.max(1, k - l);
if (k > 1) fw -= width(g, cw, cp(s, k - 1));
g.drawString("..", x + fw, y + fs);
break;
}
fw += ww;
l = cl(s, k);
}
} catch (final Exception ex) {
Util.debug(ex);
}
g.drawString(string(s, 0, j), x, y + fs);
}
@Override
public void keyTyped(final KeyEvent e) {
if (!hist.active()
|| control(e)
|| DELNEXT.is(e)
|| DELPREV.is(e)
|| ESCAPE.is(e)
|| CUT2.is(e)) return;
final int caret = editor.pos();
// remember if marked text is to be deleted
final StringBuilder sb = new StringBuilder(1).append(e.getKeyChar());
final boolean indent = TAB.is(e) && editor.indent(sb, e.isShiftDown());
// delete marked text
final boolean selected = editor.selected() && !indent;
if (selected) editor.delete();
final int move = ENTER.is(e) ? editor.enter(sb) : editor.add(sb, selected);
// refresh history and adjust cursor position
hist.store(editor.text(), caret, editor.pos());
if (move != 0) editor.pos(Math.min(editor.size(), caret + move));
// adjust text height
scrollCode.invokeLater(true);
e.consume();
}
private static Color lighter(Color col) {
int hsl[] = new int[3];
Utils.rgb2hsl(col.getRed(), col.getGreen(), col.getBlue(), hsl);
hsl[1] = Math.round(0.7f * hsl[1]);
hsl[2] = 100;
int rgb[] = Utils.hsl2rgb(hsl);
return new Color(rgb[0], rgb[1], rgb[2]);
}
public void drop(DropTargetDropEvent dtde) {
dtde.acceptDrop(DnDConstants.ACTION_COPY);
DataFlavor[] flavors = null;
try {
Transferable t = dtde.getTransferable();
iterator = null;
flavors = t.getTransferDataFlavors();
if (IJ.debugMode) IJ.log("DragAndDrop.drop: " + flavors.length + " flavors");
for (int i = 0; i < flavors.length; i++) {
if (IJ.debugMode) IJ.log(" flavor[" + i + "]: " + flavors[i].getMimeType());
if (flavors[i].isFlavorJavaFileListType()) {
Object data = t.getTransferData(DataFlavor.javaFileListFlavor);
iterator = ((List) data).iterator();
break;
} else if (flavors[i].isFlavorTextType()) {
Object ob = t.getTransferData(flavors[i]);
if (!(ob instanceof String)) continue;
String s = ob.toString().trim();
if (IJ.isLinux() && s.length() > 1 && (int) s.charAt(1) == 0) s = fixLinuxString(s);
ArrayList list = new ArrayList();
if (s.indexOf("href=\"") != -1 || s.indexOf("src=\"") != -1) {
s = parseHTML(s);
if (IJ.debugMode) IJ.log(" url: " + s);
list.add(s);
this.iterator = list.iterator();
break;
}
BufferedReader br = new BufferedReader(new StringReader(s));
String tmp;
while (null != (tmp = br.readLine())) {
tmp = java.net.URLDecoder.decode(tmp.replaceAll("\\+", "%2b"), "UTF-8");
if (tmp.startsWith("file://")) tmp = tmp.substring(7);
if (IJ.debugMode) IJ.log(" content: " + tmp);
if (tmp.startsWith("http://")) list.add(s);
else list.add(new File(tmp));
}
this.iterator = list.iterator();
break;
}
}
if (iterator != null) {
Thread thread = new Thread(this, "DrawAndDrop");
thread.setPriority(Math.max(thread.getPriority() - 1, Thread.MIN_PRIORITY));
thread.start();
}
} catch (Exception e) {
dtde.dropComplete(false);
return;
}
dtde.dropComplete(true);
if (flavors == null || flavors.length == 0) {
if (IJ.isMacOSX())
IJ.error(
"First drag and drop ignored. Please try again. You can avoid this\n"
+ "problem by dragging to the toolbar instead of the status bar.");
else IJ.error("Drag and drop failed");
}
}
/**
* Computes CPU usage (fraction of 1.0) between <code>start[1]</code> and <code>end[1]</code> time
* points [1.0 corresponds to 100% utilization of all processors].
*
* @throws IllegalArgumentException if start and end time points are less than #MIN_ELAPSED_TIME
* ms apart.
* @throws IllegalArgumentException if either argument is null
* @param start,end long[2]: [0] system time stamp, [1] process CPU time (as returned by
* makeCPUUsageSnapshot()).
*/
public static double getProcessCPUUsage(long[] start, long[] end) {
if (start == null) throw new IllegalArgumentException("null input: start");
if (end == null) throw new IllegalArgumentException("null input: end");
// if (end[0] < start[0] + MIN_ELAPSED_TIME) throw new IllegalArgumentException("end time must
// be at least " + MIN_ELAPSED_TIME + " ms later than start time");
end[0] = Math.max(end[0], start[0] + MIN_ELAPSED_TIME);
return ((double) (end[1] - start[1])) / (double) (end[0] - start[0]);
}
/**
* Draws a visualization tooltip.
*
* @param g graphics reference
* @param tt tooltip label
* @param x horizontal position
* @param y vertical position
* @param w width
* @param c color color depth
*/
public static void drawTooltip(
final Graphics g, final String tt, final int x, final int y, final int w, final int c) {
final int tw = width(g, tt);
final int th = g.getFontMetrics().getHeight();
final int xx = Math.min(w - tw - 8, x);
g.setColor(color(c));
g.fillRect(xx - 1, y - th, tw + 4, th);
g.setColor(BACK);
g.drawString(tt, xx, y - 4);
}
/** Returns the selected text, or null if no selection is active. */
public final String getSelectedText() {
if (selectionStart == selectionEnd) return null;
if (rectSelect) {
// Return each row of the selection on a new line
Element map = document.getDefaultRootElement();
int start = selectionStart - map.getElement(selectionStartLine).getStartOffset();
int end = selectionEnd - map.getElement(selectionEndLine).getStartOffset();
// Certain rectangles satisfy this condition...
if (end < start) {
int tmp = end;
end = start;
start = tmp;
}
StringBuffer buf = new StringBuffer();
Segment seg = new Segment();
for (int i = selectionStartLine; i <= selectionEndLine; i++) {
Element lineElement = map.getElement(i);
int lineStart = lineElement.getStartOffset();
int lineEnd = lineElement.getEndOffset() - 1;
int lineLen = lineEnd - lineStart;
lineStart = Math.min(lineStart + start, lineEnd);
lineLen = Math.min(end - start, lineEnd - lineStart);
getText(lineStart, lineLen, seg);
buf.append(seg.array, seg.offset, seg.count);
if (i != selectionEndLine) buf.append('\n');
}
return buf.toString();
} else {
return getText(selectionStart, selectionEnd - selectionStart);
}
}
/** Returns the offset where the selection ends on the specified line. */
public int getSelectionEnd(int line) {
if (line == selectionEndLine) return selectionEnd;
else if (rectSelect) {
Element map = document.getDefaultRootElement();
int end = selectionEnd - map.getElement(selectionEndLine).getStartOffset();
Element lineElement = map.getElement(line);
int lineStart = lineElement.getStartOffset();
int lineEnd = lineElement.getEndOffset() - 1;
return Math.min(lineEnd, lineStart + end);
} else return getLineEndOffset(line) - 1;
}
public final boolean replace(int num, String replacement) {
buf.buffer.replace(buf.cursor - num, buf.cursor, replacement);
try {
moveCursor(-num);
drawBuffer(Math.max(0, num - replacement.length()));
moveCursor(replacement.length());
} catch (IOException e) {
e.printStackTrace();
return false;
}
return true;
}
/**
* 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 drawCharacters(int x, int y, TextStyle style, CharBuffer buf, Graphics2D gfx) {
int xCoord = x * myCharSize.width;
int yCoord = y * myCharSize.height;
if (xCoord < 0 || xCoord > getWidth() || yCoord < 0 || yCoord > getHeight()) {
return;
}
gfx.setColor(getPalette().getColor(myStyleState.getBackground(style.getBackgroundForRun())));
int textLength =
CharUtils.getTextLengthDoubleWidthAware(
buf.getBuf(),
buf.getStart(),
buf.length(),
mySettingsProvider.ambiguousCharsAreDoubleWidth());
gfx.fillRect(
xCoord,
yCoord,
Math.min(textLength * myCharSize.width, getWidth() - xCoord),
Math.min(myCharSize.height, getHeight() - yCoord));
if (buf.isNul()) {
return; // nothing more to do
}
drawChars(x, y, buf, style, gfx);
gfx.setColor(getPalette().getColor(myStyleState.getForeground(style.getForegroundForRun())));
int baseLine = (y + 1) * myCharSize.height - myDescent;
if (style.hasOption(TextStyle.Option.UNDERLINED)) {
gfx.drawLine(xCoord, baseLine + 1, (x + textLength) * myCharSize.width, baseLine + 1);
}
}
/**
* Output the specified {@link Collection} in proper columns.
*
* @param stuff the stuff to print
*/
public void printColumns(final Collection stuff) throws IOException {
if ((stuff == null) || (stuff.size() == 0)) {
return;
}
int width = getTermwidth();
int maxwidth = 0;
for (Iterator i = stuff.iterator();
i.hasNext();
maxwidth = Math.max(maxwidth, i.next().toString().length())) {;
}
StringBuffer line = new StringBuffer();
int showLines;
if (usePagination) showLines = getTermheight() - 1; // page limit
else showLines = Integer.MAX_VALUE;
for (Iterator i = stuff.iterator(); i.hasNext(); ) {
String cur = (String) i.next();
if ((line.length() + maxwidth) > width) {
printString(line.toString().trim());
printNewline();
line.setLength(0);
if (--showLines == 0) { // Overflow
printString(loc.getString("display-more"));
flushConsole();
int c = readVirtualKey();
if (c == '\r' || c == '\n') showLines = 1; // one step forward
else if (c != 'q') showLines = getTermheight() - 1; // page forward
back(loc.getString("display-more").length());
if (c == 'q') break; // cancel
}
}
pad(cur, maxwidth + 3, line);
}
if (line.length() > 0) {
printString(line.toString().trim());
printNewline();
line.setLength(0);
}
}
private int clamp(int val, int min, int max) {
return Math.max(Math.min(val, max), min);
}
protected Point panelToCharCoords(final Point p) {
int x = Math.min(p.x / myCharSize.width, getColumnCount() - 1);
x = Math.max(0, x);
int y = Math.min(p.y / myCharSize.height, getRowCount() - 1) + myClientScrollOrigin;
return new Point(x, y);
}
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();
}
}
/**
* Replaces the selection with the specified text.
*
* @param selectedText The replacement text for the selection
*/
public void setSelectedText(String selectedText) {
if (!editable) {
throw new InternalError("Text component" + " read only");
}
document.beginCompoundEdit();
try {
if (rectSelect) {
Element map = document.getDefaultRootElement();
int start = selectionStart - map.getElement(selectionStartLine).getStartOffset();
int end = selectionEnd - map.getElement(selectionEndLine).getStartOffset();
// Certain rectangles satisfy this condition...
if (end < start) {
int tmp = end;
end = start;
start = tmp;
}
int lastNewline = 0;
int currNewline = 0;
for (int i = selectionStartLine; i <= selectionEndLine; i++) {
Element lineElement = map.getElement(i);
int lineStart = lineElement.getStartOffset();
int lineEnd = lineElement.getEndOffset() - 1;
int rectStart = Math.min(lineEnd, lineStart + start);
document.remove(rectStart, Math.min(lineEnd - rectStart, end - start));
if (selectedText == null) continue;
currNewline = selectedText.indexOf('\n', lastNewline);
if (currNewline == -1) currNewline = selectedText.length();
document.insertString(rectStart, selectedText.substring(lastNewline, currNewline), null);
lastNewline = Math.min(selectedText.length(), currNewline + 1);
}
if (selectedText != null && currNewline != selectedText.length()) {
int offset = map.getElement(selectionEndLine).getEndOffset() - 1;
document.insertString(offset, "\n", null);
document.insertString(offset + 1, selectedText.substring(currNewline + 1), null);
}
} else {
document.remove(selectionStart, selectionEnd - selectionStart);
if (selectedText != null) {
document.insertString(selectionStart, selectedText, null);
}
}
} catch (BadLocationException bl) {
bl.printStackTrace();
throw new InternalError("Cannot replace" + " selection");
}
// No matter what happends... stops us from leaving document
// in a bad state
finally {
document.endCompoundEdit();
}
setCaretPosition(selectionEnd);
}
private void updateavg() {
nmeas[ncurves] = 0;
avg = new float[xpts][ypts];
avgweights = new float[xpts][ypts];
for (int i = 0; i < ncurves; i++) {
if (include[i]) {
for (int j = 0; j < xpts; j++) {
for (int k = 0; k < ypts; k++) {
avg[j][k] += pch[i][j][k];
nmeas[ncurves] += (int) pch[i][j][k];
}
}
}
}
double tempavg = 0.0;
double tempavg2 = 0.0;
double temp2avg = 0.0;
double temp2avg2 = 0.0;
double tempccavg = 0.0;
for (int i = 0; i < xpts; i++) {
for (int j = 0; j < ypts; j++) {
double normed = (double) avg[i][j] / (double) nmeas[ncurves];
avgweights[i][j] = (float) ((double) nmeas[ncurves] / (normed * (1.0f - normed)));
if (avg[i][j] > 0.0f) {
avgweights[i][j] = (float) ((double) nmeas[ncurves] / (normed * (1.0f - normed)));
} else {
avgweights[i][j] = 1.0f;
}
tempavg += (double) i * normed;
tempavg2 += (double) i * (double) i * normed;
temp2avg += (double) j * normed;
temp2avg2 += (double) j * (double) j * normed;
tempccavg += (double) i * (double) j * normed;
}
}
tempccavg -= tempavg * temp2avg;
brightcc[ncurves] = tempccavg / Math.sqrt(tempavg * temp2avg);
tempavg2 -= tempavg * tempavg;
tempavg2 /= tempavg;
bright1[ncurves] = (tempavg2 - 1.0);
temp2avg2 -= temp2avg * temp2avg;
temp2avg2 /= temp2avg;
bright2[ncurves] = (temp2avg2 - 1.0);
intensity1[ncurves] = tempavg;
intensity2[ncurves] = temp2avg;
if (psfflag == 0) {
bright1[ncurves] /= 0.3536;
bright2[ncurves] /= 0.3536;
brightcc[ncurves] /= 0.3536;
} else {
if (psfflag == 1) {
bright1[ncurves] /= 0.078;
bright2[ncurves] /= 0.078;
brightcc[ncurves] /= 0.078;
} else {
bright1[ncurves] /= 0.5;
bright2[ncurves] /= 0.5;
brightcc[ncurves] /= 0.5;
}
}
number1[ncurves] = intensity1[ncurves] / bright1[ncurves];
number2[ncurves] = intensity2[ncurves] / bright2[ncurves];
brightmincc[ncurves] =
(bright1[ncurves] * beta) * Math.sqrt(intensity1[ncurves] / intensity2[ncurves]);
}
public void updatebeta() {
for (int i = 0; i <= ncurves; i++) {
brightmincc[i] = (bright1[i] * beta) / Math.sqrt(intensity1[i] / intensity2[i]);
eminccarray[i].setText("" + (float) brightmincc[i]);
}
}
/**
* Converts a y co-ordinate to a line index.
*
* @param y The y co-ordinate
*/
public int yToLine(int y) {
FontMetrics fm = painter.getFontMetrics();
int height = fm.getHeight();
return Math.max(0, Math.min(getLineCount() - 1, y / height + firstLine));
}
private void doDoubleClick(MouseEvent evt, int line, int offset, int dot)
throws BadLocationException {
// Ignore empty lines
if (getLineLength(line) == 0) return;
try {
int bracket = TextUtilities.findMatchingBracket(document, Math.max(0, dot - 1));
if (bracket != -1) {
int mark = getMarkPosition();
// Hack
if (bracket > mark) {
bracket++;
mark--;
}
select(mark, bracket);
return;
}
} catch (BadLocationException bl) {
bl.printStackTrace();
}
// Ok, it's not a bracket... select the word
String lineText = getLineText(line);
char ch = lineText.charAt(Math.max(0, offset - 1));
String noWordSep = (String) document.getProperty("noWordSep");
if (noWordSep == null) noWordSep = "";
// If the user clicked on a non-letter char,
// we select the surrounding non-letters
boolean selectNoLetter = (!Character.isLetterOrDigit(ch) && noWordSep.indexOf(ch) == -1);
int wordStart = 0;
for (int i = offset - 1; i >= 0; i--) {
ch = lineText.charAt(i);
if (selectNoLetter ^ (!Character.isLetterOrDigit(ch) && noWordSep.indexOf(ch) == -1)) {
wordStart = i + 1;
break;
}
}
int wordEnd = lineText.length();
for (int i = offset; i < lineText.length(); i++) {
ch = lineText.charAt(i);
if (selectNoLetter ^ (!Character.isLetterOrDigit(ch) && noWordSep.indexOf(ch) == -1)) {
wordEnd = i;
break;
}
}
int lineStart = getLineStartOffset(line);
select(lineStart + wordStart, lineStart + wordEnd);
/*
String lineText = getLineText(line);
String noWordSep = (String)document.getProperty("noWordSep");
int wordStart = TextUtilities.findWordStart(lineText,offset,noWordSep);
int wordEnd = TextUtilities.findWordEnd(lineText,offset,noWordSep);
int lineStart = getLineStartOffset(line);
select(lineStart + wordStart,lineStart + wordEnd);
*/
}