void loadParticleResults(String filename, ResultsTable res) {
try {
String line;
FileReader fr = new FileReader(filename);
BufferedReader br = new BufferedReader(fr);
java.lang.String header =
" Intensity X (px) Y (px) X (nm) Y (nm) Z (nm) Left-Width(px) Right-Width (px) Up-Height (px) Down-Height (px) X Symmetry (%) Y Symmetry (%) Width minus Height (px) Frame Number";
java.lang.String firstline = br.readLine();
if (!firstline.contains("X (px) Y (px) X (nm) Y (nm) Z (nm)")) {
IJ.error("File does not seam to be a Particles Table file");
IJ.log("Found header: " + firstline);
IJ.log("Expecting: " + header);
return;
}
res.reset();
int counter = 1;
java.util.concurrent.locks.Lock lock = new java.util.concurrent.locks.ReentrantLock();
ThreadedLoader tloader = new ThreadedLoader();
// java.lang.String txt = fr.read();
while ((line = br.readLine()) != null) {
tloader = new ThreadedLoader();
tloader.mysetup(res, lock, line);
tloader.start();
IJ.showStatus("Loading particle " + counter + "... sit back and relax.");
counter++;
}
try {
tloader.join();
} catch (Exception e) {
IJ.error("" + e);
}
if (res.getCounter() < 5000000) {
IJ.showStatus("Creating particle table, this should take a few seconds...");
res.show("Results");
} else
IJ.showMessage(
"Warning",
"Results table has too many particles, they will not be shown but the data still exists within it\nyou can still use all the plugin functionality or save table changes though the 'Save Particle Table' command.");
fr.close();
IJ.showStatus("Done loading table...");
} catch (FileNotFoundException e) {
IJ.error("File not found exception" + e);
return;
} catch (IOException e) {
IJ.error("IOException exception" + e);
return;
} catch (NumberFormatException e) {
IJ.error("Number format exception" + e);
return;
}
}
/** Handle menu events. */
public void actionPerformed(ActionEvent e) {
if ((e.getSource() instanceof MenuItem)) {
MenuItem item = (MenuItem) e.getSource();
String cmd = e.getActionCommand();
commandName = cmd;
ImagePlus imp = null;
if (item.getParent() == Menus.getOpenRecentMenu()) {
new RecentOpener(cmd); // open image in separate thread
return;
} else if (item.getParent() == Menus.getPopupMenu()) {
Object parent = Menus.getPopupMenu().getParent();
if (parent instanceof ImageCanvas) imp = ((ImageCanvas) parent).getImage();
}
int flags = e.getModifiers();
hotkey = false;
actionPerformedTime = System.currentTimeMillis();
long ellapsedTime = actionPerformedTime - keyPressedTime;
if (cmd != null && (ellapsedTime >= 200L || !cmd.equals(lastKeyCommand))) {
if ((flags & Event.ALT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_ALT);
if ((flags & Event.SHIFT_MASK) != 0) IJ.setKeyDown(KeyEvent.VK_SHIFT);
new Executer(cmd, imp);
}
lastKeyCommand = null;
if (IJ.debugMode) IJ.log("actionPerformed: time=" + ellapsedTime + ", " + e);
}
}
void enlargeArrays() {
if (xp != null) {
int[] xptemp = new int[maxPoints * 2];
int[] yptemp = new int[maxPoints * 2];
System.arraycopy(xp, 0, xptemp, 0, maxPoints);
System.arraycopy(yp, 0, yptemp, 0, maxPoints);
xp = xptemp;
yp = yptemp;
}
if (xpf != null) {
float[] xpftemp = new float[maxPoints * 2];
float[] ypftemp = new float[maxPoints * 2];
System.arraycopy(xpf, 0, xpftemp, 0, maxPoints);
System.arraycopy(ypf, 0, ypftemp, 0, maxPoints);
xpf = xpftemp;
ypf = ypftemp;
}
int[] xp2temp = new int[maxPoints * 2];
int[] yp2temp = new int[maxPoints * 2];
System.arraycopy(xp2, 0, xp2temp, 0, maxPoints);
System.arraycopy(yp2, 0, yp2temp, 0, maxPoints);
xp2 = xp2temp;
yp2 = yp2temp;
if (IJ.debugMode) IJ.log("PolygonRoi: " + maxPoints + " points");
maxPoints *= 2;
}
boolean setProperties(String title, Roi roi) {
Frame f = WindowManager.getFrontWindow();
if (f != null && f.getTitle().indexOf("3D Viewer") != -1) return false;
if (roi == null) {
IJ.error("This command requires a selection.");
return false;
}
RoiProperties rp = new RoiProperties(title, roi);
boolean ok = rp.showDialog();
if (IJ.debugMode) IJ.log(roi.getDebugInfo());
return ok;
}
public void keyTyped(KeyEvent e) {
char keyChar = e.getKeyChar();
int flags = e.getModifiers();
if (IJ.debugMode)
IJ.log(
"keyTyped: char=\""
+ keyChar
+ "\" ("
+ (int) keyChar
+ "), flags= "
+ Integer.toHexString(flags)
+ " ("
+ KeyEvent.getKeyModifiersText(flags)
+ ")");
if (keyChar == '\\' || keyChar == 171 || keyChar == 223) {
if (((flags & Event.ALT_MASK) != 0)) doCommand("Animation Options...");
else doCommand("Start Animation [\\]");
}
}
/*
if selection is closed shape, create a circle with the same area and centroid, otherwise use<br>
the Pratt method to fit a circle to the points that define the line or multi-point selection.<br>
Reference: Pratt V., Direct least-squares fitting of algebraic surfaces", Computer Graphics, Vol. 21, pages 145-152 (1987).<br>
Original code: Nikolai Chernov's MATLAB script for Newton-based Pratt fit.<br>
(http://www.math.uab.edu/~chernov/cl/MATLABcircle.html)<br>
Java version: https://github.com/mdoube/BoneJ/blob/master/src/org/doube/geometry/FitCircle.java<br>
@authors Nikolai Chernov, Michael Doube, Ved Sharma
*/
void fitCircle(ImagePlus imp) {
Roi roi = imp.getRoi();
if (roi == null) {
noRoi("Fit Circle");
return;
}
if (roi.isArea()) { // create circle with the same area and centroid
ImageProcessor ip = imp.getProcessor();
ip.setRoi(roi);
ImageStatistics stats =
ImageStatistics.getStatistics(ip, Measurements.AREA + Measurements.CENTROID, null);
double r = Math.sqrt(stats.pixelCount / Math.PI);
imp.killRoi();
int d = (int) Math.round(2.0 * r);
IJ.makeOval(
(int) Math.round(stats.xCentroid - r), (int) Math.round(stats.yCentroid - r), d, d);
return;
}
Polygon poly = roi.getPolygon();
int n = poly.npoints;
int[] x = poly.xpoints;
int[] y = poly.ypoints;
if (n < 3) {
IJ.error("Fit Circle", "At least 3 points are required to fit a circle.");
return;
}
// calculate point centroid
double sumx = 0, sumy = 0;
for (int i = 0; i < n; i++) {
sumx = sumx + poly.xpoints[i];
sumy = sumy + poly.ypoints[i];
}
double meanx = sumx / n;
double meany = sumy / n;
// calculate moments
double[] X = new double[n], Y = new double[n];
double Mxx = 0, Myy = 0, Mxy = 0, Mxz = 0, Myz = 0, Mzz = 0;
for (int i = 0; i < n; i++) {
X[i] = x[i] - meanx;
Y[i] = y[i] - meany;
double Zi = X[i] * X[i] + Y[i] * Y[i];
Mxy = Mxy + X[i] * Y[i];
Mxx = Mxx + X[i] * X[i];
Myy = Myy + Y[i] * Y[i];
Mxz = Mxz + X[i] * Zi;
Myz = Myz + Y[i] * Zi;
Mzz = Mzz + Zi * Zi;
}
Mxx = Mxx / n;
Myy = Myy / n;
Mxy = Mxy / n;
Mxz = Mxz / n;
Myz = Myz / n;
Mzz = Mzz / n;
// calculate the coefficients of the characteristic polynomial
double Mz = Mxx + Myy;
double Cov_xy = Mxx * Myy - Mxy * Mxy;
double Mxz2 = Mxz * Mxz;
double Myz2 = Myz * Myz;
double A2 = 4 * Cov_xy - 3 * Mz * Mz - Mzz;
double A1 = Mzz * Mz + 4 * Cov_xy * Mz - Mxz2 - Myz2 - Mz * Mz * Mz;
double A0 = Mxz2 * Myy + Myz2 * Mxx - Mzz * Cov_xy - 2 * Mxz * Myz * Mxy + Mz * Mz * Cov_xy;
double A22 = A2 + A2;
double epsilon = 1e-12;
double ynew = 1e+20;
int IterMax = 20;
double xnew = 0;
int iterations = 0;
// Newton's method starting at x=0
for (int iter = 1; iter <= IterMax; iter++) {
iterations = iter;
double yold = ynew;
ynew = A0 + xnew * (A1 + xnew * (A2 + 4. * xnew * xnew));
if (Math.abs(ynew) > Math.abs(yold)) {
if (IJ.debugMode) IJ.log("Fit Circle: wrong direction: |ynew| > |yold|");
xnew = 0;
break;
}
double Dy = A1 + xnew * (A22 + 16 * xnew * xnew);
double xold = xnew;
xnew = xold - ynew / Dy;
if (Math.abs((xnew - xold) / xnew) < epsilon) break;
if (iter >= IterMax) {
if (IJ.debugMode) IJ.log("Fit Circle: will not converge");
xnew = 0;
}
if (xnew < 0) {
if (IJ.debugMode) IJ.log("Fit Circle: negative root: x = " + xnew);
xnew = 0;
}
}
if (IJ.debugMode)
IJ.log("Fit Circle: n=" + n + ", xnew=" + IJ.d2s(xnew, 2) + ", iterations=" + iterations);
// calculate the circle parameters
double DET = xnew * xnew - xnew * Mz + Cov_xy;
double CenterX = (Mxz * (Myy - xnew) - Myz * Mxy) / (2 * DET);
double CenterY = (Myz * (Mxx - xnew) - Mxz * Mxy) / (2 * DET);
double radius = Math.sqrt(CenterX * CenterX + CenterY * CenterY + Mz + 2 * xnew);
if (Double.isNaN(radius)) {
IJ.error("Fit Circle", "Points are collinear.");
return;
}
CenterX = CenterX + meanx;
CenterY = CenterY + meany;
imp.killRoi();
IJ.makeOval(
(int) Math.round(CenterX - radius),
(int) Math.round(CenterY - radius),
(int) Math.round(2 * radius),
(int) Math.round(2 * radius));
}
public static void main(String args[]) {
if (System.getProperty("java.version").substring(0, 3).compareTo("1.5") < 0) {
javax.swing.JOptionPane.showMessageDialog(
null, "ImageJ " + VERSION + " requires Java 1.5 or later.");
System.exit(0);
}
boolean noGUI = false;
int mode = STANDALONE;
arguments = args;
// System.setProperty("file.encoding", "UTF-8");
int nArgs = args != null ? args.length : 0;
boolean commandLine = false;
for (int i = 0; i < nArgs; i++) {
String arg = args[i];
if (arg == null) continue;
if (args[i].startsWith("-")) {
if (args[i].startsWith("-batch")) noGUI = true;
else if (args[i].startsWith("-debug")) IJ.setDebugMode(true);
else if (args[i].startsWith("-ijpath") && i + 1 < nArgs) {
if (IJ.debugMode) IJ.log("-ijpath: " + args[i + 1]);
Prefs.setHomeDir(args[i + 1]);
commandLine = true;
args[i + 1] = null;
} else if (args[i].startsWith("-port")) {
int delta = (int) Tools.parseDouble(args[i].substring(5, args[i].length()), 0.0);
commandLine = true;
if (delta == 0) mode = EMBEDDED;
else if (delta > 0 && DEFAULT_PORT + delta < 65536) port = DEFAULT_PORT + delta;
}
}
}
// If existing ImageJ instance, pass arguments to it and quit.
boolean passArgs = mode == STANDALONE && !noGUI;
if (IJ.isMacOSX() && !commandLine) passArgs = false;
if (passArgs && isRunning(args)) return;
ImageJ ij = IJ.getInstance();
if (!noGUI && (ij == null || (ij != null && !ij.isShowing()))) {
ij = new ImageJ(null, mode);
ij.exitWhenQuitting = true;
}
int macros = 0;
for (int i = 0; i < nArgs; i++) {
String arg = args[i];
if (arg == null) continue;
if (arg.startsWith("-")) {
if ((arg.startsWith("-macro") || arg.startsWith("-batch")) && i + 1 < nArgs) {
String arg2 = i + 2 < nArgs ? args[i + 2] : null;
Prefs.commandLineMacro = true;
if (noGUI && args[i + 1].endsWith(".js")) Interpreter.batchMode = true;
IJ.runMacroFile(args[i + 1], arg2);
break;
} else if (arg.startsWith("-eval") && i + 1 < nArgs) {
String rtn = IJ.runMacro(args[i + 1]);
if (rtn != null) System.out.print(rtn);
args[i + 1] = null;
} else if (arg.startsWith("-run") && i + 1 < nArgs) {
IJ.run(args[i + 1]);
args[i + 1] = null;
}
} else if (macros == 0 && (arg.endsWith(".ijm") || arg.endsWith(".txt"))) {
IJ.runMacroFile(arg);
macros++;
} else if (arg.length() > 0 && arg.indexOf("ij.ImageJ") == -1) {
File file = new File(arg);
IJ.open(file.getAbsolutePath());
}
}
if (IJ.debugMode && IJ.getInstance() == null) new JavaProperties().run("");
if (noGUI) System.exit(0);
}
public void keyPressed(KeyEvent e) {
// if (e.isConsumed()) return;
int keyCode = e.getKeyCode();
IJ.setKeyDown(keyCode);
hotkey = false;
if (keyCode == KeyEvent.VK_CONTROL || keyCode == KeyEvent.VK_SHIFT) return;
char keyChar = e.getKeyChar();
int flags = e.getModifiers();
if (IJ.debugMode)
IJ.log(
"keyPressed: code="
+ keyCode
+ " ("
+ KeyEvent.getKeyText(keyCode)
+ "), char=\""
+ keyChar
+ "\" ("
+ (int) keyChar
+ "), flags="
+ KeyEvent.getKeyModifiersText(flags));
boolean shift = (flags & KeyEvent.SHIFT_MASK) != 0;
boolean control = (flags & KeyEvent.CTRL_MASK) != 0;
boolean alt = (flags & KeyEvent.ALT_MASK) != 0;
boolean meta = (flags & KeyEvent.META_MASK) != 0;
String cmd = null;
ImagePlus imp = WindowManager.getCurrentImage();
boolean isStack = (imp != null) && (imp.getStackSize() > 1);
if (imp != null
&& !control
&& ((keyChar >= 32 && keyChar <= 255) || keyChar == '\b' || keyChar == '\n')) {
Roi roi = imp.getRoi();
if (roi instanceof TextRoi) {
if ((flags & KeyEvent.META_MASK) != 0 && IJ.isMacOSX()) return;
if (alt) {
switch (keyChar) {
case 'u':
case 'm':
keyChar = IJ.micronSymbol;
break;
case 'A':
keyChar = IJ.angstromSymbol;
break;
default:
}
}
((TextRoi) roi).addChar(keyChar);
return;
}
}
// Handle one character macro shortcuts
if (!control && !meta) {
Hashtable macroShortcuts = Menus.getMacroShortcuts();
if (macroShortcuts.size() > 0) {
if (shift) cmd = (String) macroShortcuts.get(new Integer(keyCode + 200));
else cmd = (String) macroShortcuts.get(new Integer(keyCode));
if (cmd != null) {
// MacroInstaller.runMacroCommand(cmd);
commandName = cmd;
MacroInstaller.runMacroShortcut(cmd);
return;
}
}
}
if ((!Prefs.requireControlKey || control || meta) && keyChar != '+') {
Hashtable shortcuts = Menus.getShortcuts();
if (shift) cmd = (String) shortcuts.get(new Integer(keyCode + 200));
else cmd = (String) shortcuts.get(new Integer(keyCode));
}
if (cmd == null) {
switch (keyChar) {
case '<':
case ',':
if (isStack) cmd = "Previous Slice [<]";
break;
case '>':
case '.':
case ';':
if (isStack) cmd = "Next Slice [>]";
break;
case '+':
case '=':
cmd = "In [+]";
break;
case '-':
cmd = "Out [-]";
break;
case '/':
cmd = "Reslice [/]...";
break;
default:
}
}
if (cmd == null) {
switch (keyCode) {
case KeyEvent.VK_TAB:
WindowManager.putBehind();
return;
case KeyEvent.VK_BACK_SPACE: // delete
if (deleteOverlayRoi(imp)) return;
cmd = "Clear";
hotkey = true;
break;
// case KeyEvent.VK_BACK_SLASH: cmd=IJ.altKeyDown()?"Animation Options...":"Start
// Animation"; break;
case KeyEvent.VK_EQUALS:
cmd = "In [+]";
break;
case KeyEvent.VK_MINUS:
cmd = "Out [-]";
break;
case KeyEvent.VK_SLASH:
case 0xbf:
cmd = "Reslice [/]...";
break;
case KeyEvent.VK_COMMA:
case 0xbc:
if (isStack) cmd = "Previous Slice [<]";
break;
case KeyEvent.VK_PERIOD:
case 0xbe:
if (isStack) cmd = "Next Slice [>]";
break;
case KeyEvent.VK_LEFT:
case KeyEvent.VK_RIGHT:
case KeyEvent.VK_UP:
case KeyEvent.VK_DOWN: // arrow keys
if (imp == null) return;
Roi roi = imp.getRoi();
if (IJ.shiftKeyDown() && imp == Orthogonal_Views.getImage()) return;
boolean stackKey = imp.getStackSize() > 1 && (roi == null || IJ.shiftKeyDown());
boolean zoomKey = roi == null || IJ.shiftKeyDown() || IJ.controlKeyDown();
if (stackKey && keyCode == KeyEvent.VK_RIGHT) cmd = "Next Slice [>]";
else if (stackKey && keyCode == KeyEvent.VK_LEFT) cmd = "Previous Slice [<]";
else if (zoomKey
&& keyCode == KeyEvent.VK_DOWN
&& !ignoreArrowKeys(imp)
&& Toolbar.getToolId() < Toolbar.SPARE6) cmd = "Out [-]";
else if (zoomKey
&& keyCode == KeyEvent.VK_UP
&& !ignoreArrowKeys(imp)
&& Toolbar.getToolId() < Toolbar.SPARE6) cmd = "In [+]";
else if (roi != null) {
if ((flags & KeyEvent.ALT_MASK) != 0) roi.nudgeCorner(keyCode);
else roi.nudge(keyCode);
return;
}
break;
case KeyEvent.VK_ESCAPE:
abortPluginOrMacro(imp);
return;
case KeyEvent.VK_ENTER:
WindowManager.toFront(this);
return;
default:
break;
}
}
if (cmd != null && !cmd.equals("")) {
commandName = cmd;
if (cmd.equals("Fill") || cmd.equals("Draw")) hotkey = true;
if (cmd.charAt(0) == MacroInstaller.commandPrefix) MacroInstaller.runMacroShortcut(cmd);
else {
doCommand(cmd);
keyPressedTime = System.currentTimeMillis();
lastKeyCommand = cmd;
}
}
}
public void mousePressed(MouseEvent e) {
Undo.reset();
if (!Prefs.noClickToGC) System.gc();
IJ.showStatus(version() + IJ.freeMemory());
if (IJ.debugMode) IJ.log("Windows: " + WindowManager.getWindowCount());
}
/**
* If 'applet' is not null, creates a new ImageJ frame that runs as an applet. If 'mode' is
* ImageJ.EMBEDDED and 'applet is null, creates an embedded (non-standalone) version of ImageJ.
*/
public ImageJ(java.applet.Applet applet, int mode) {
super("ImageJ");
if ((mode & DEBUG) != 0) IJ.setDebugMode(true);
mode = mode & 255;
if (IJ.debugMode) IJ.log("ImageJ starting in debug mode: " + mode);
embedded = applet == null && (mode == EMBEDDED || mode == NO_SHOW);
this.applet = applet;
String err1 = Prefs.load(this, applet);
setBackground(backgroundColor);
Menus m = new Menus(this, applet);
String err2 = m.addMenuBar();
m.installPopupMenu(this);
setLayout(new BorderLayout());
// Tool bar
toolbar = new Toolbar();
toolbar.addKeyListener(this);
add("Center", toolbar);
// Status bar
statusBar = new Panel();
statusBar.setLayout(new BorderLayout());
statusBar.setForeground(Color.black);
statusBar.setBackground(backgroundColor);
statusLine = new JLabel();
statusLine.setFont(new Font("SansSerif", Font.PLAIN, 13));
statusLine.addKeyListener(this);
statusLine.addMouseListener(this);
statusBar.add("Center", statusLine);
progressBar = new ProgressBar(120, 20);
progressBar.addKeyListener(this);
progressBar.addMouseListener(this);
statusBar.add("East", progressBar);
add("South", statusBar);
IJ.init(this, applet);
addKeyListener(this);
addWindowListener(this);
setFocusTraversalKeysEnabled(false);
m.installStartupMacroSet(); // add custom tools
runStartupMacro();
Point loc = getPreferredLocation();
Dimension tbSize = toolbar.getPreferredSize();
setCursor(Cursor.getDefaultCursor()); // work-around for JDK 1.1.8 bug
if (mode != NO_SHOW) {
if (IJ.isWindows())
try {
setIcon();
} catch (Exception e) {
}
setLocation(loc.x, loc.y);
setResizable(!IJ.isMacOSX());
pack();
setVisible(true);
}
if (err1 != null) IJ.error(err1);
if (err2 != null) {
IJ.error(err2);
IJ.runPlugIn("ij.plugin.ClassChecker", "");
}
if (IJ.isMacintosh() && applet == null) {
Object qh = null;
qh = IJ.runPlugIn("MacAdapter", "");
if (qh == null) IJ.runPlugIn("QuitHandler", "");
}
if (applet == null) IJ.runPlugIn("ij.plugin.DragAndDrop", "");
String str = m.getMacroCount() == 1 ? " macro" : " macros";
IJ.showStatus(version() + m.getPluginCount() + " commands; " + m.getMacroCount() + str);
configureProxy();
if (applet == null) loadCursors();
}
public void build_bricks() {
ImagePlus imp;
ImagePlus orgimp;
ImageStack stack;
FileInfo finfo;
if (lvImgTitle.isEmpty()) return;
orgimp = WindowManager.getImage(lvImgTitle.get(0));
imp = orgimp;
finfo = imp.getFileInfo();
if (finfo == null) return;
int[] dims = imp.getDimensions();
int imageW = dims[0];
int imageH = dims[1];
int nCh = dims[2];
int imageD = dims[3];
int nFrame = dims[4];
int bdepth = imp.getBitDepth();
double xspc = finfo.pixelWidth;
double yspc = finfo.pixelHeight;
double zspc = finfo.pixelDepth;
double z_aspect = Math.max(xspc, yspc) / zspc;
int orgW = imageW;
int orgH = imageH;
int orgD = imageD;
double orgxspc = xspc;
double orgyspc = yspc;
double orgzspc = zspc;
lv = lvImgTitle.size();
if (filetype == "JPEG") {
for (int l = 0; l < lv; l++) {
if (WindowManager.getImage(lvImgTitle.get(l)).getBitDepth() != 8) {
IJ.error("A SOURCE IMAGE MUST BE 8BIT GLAYSCALE");
return;
}
}
}
// calculate levels
/* int baseXY = 256;
int baseZ = 256;
if (z_aspect < 0.5) baseZ = 128;
if (z_aspect > 2.0) baseXY = 128;
if (z_aspect >= 0.5 && z_aspect < 1.0) baseZ = (int)(baseZ*z_aspect);
if (z_aspect > 1.0 && z_aspect <= 2.0) baseXY = (int)(baseXY/z_aspect);
IJ.log("Z_aspect: " + z_aspect);
IJ.log("BaseXY: " + baseXY);
IJ.log("BaseZ: " + baseZ);
*/
int baseXY = 256;
int baseZ = 128;
int dbXY = Math.max(orgW, orgH) / baseXY;
if (Math.max(orgW, orgH) % baseXY > 0) dbXY *= 2;
int dbZ = orgD / baseZ;
if (orgD % baseZ > 0) dbZ *= 2;
lv = Math.max(log2(dbXY), log2(dbZ)) + 1;
int ww = orgW;
int hh = orgH;
int dd = orgD;
for (int l = 0; l < lv; l++) {
int bwnum = ww / baseXY;
if (ww % baseXY > 0) bwnum++;
int bhnum = hh / baseXY;
if (hh % baseXY > 0) bhnum++;
int bdnum = dd / baseZ;
if (dd % baseZ > 0) bdnum++;
if (bwnum % 2 == 0) bwnum++;
if (bhnum % 2 == 0) bhnum++;
if (bdnum % 2 == 0) bdnum++;
int bw = (bwnum <= 1) ? ww : ww / bwnum + 1 + (ww % bwnum > 0 ? 1 : 0);
int bh = (bhnum <= 1) ? hh : hh / bhnum + 1 + (hh % bhnum > 0 ? 1 : 0);
int bd = (bdnum <= 1) ? dd : dd / bdnum + 1 + (dd % bdnum > 0 ? 1 : 0);
bwlist.add(bw);
bhlist.add(bh);
bdlist.add(bd);
IJ.log("LEVEL: " + l);
IJ.log(" width: " + ww);
IJ.log(" hight: " + hh);
IJ.log(" depth: " + dd);
IJ.log(" bw: " + bw);
IJ.log(" bh: " + bh);
IJ.log(" bd: " + bd);
int xyl2 = Math.max(ww, hh) / baseXY;
if (Math.max(ww, hh) % baseXY > 0) xyl2 *= 2;
if (lv - 1 - log2(xyl2) <= l) {
ww /= 2;
hh /= 2;
}
IJ.log(" xyl2: " + (lv - 1 - log2(xyl2)));
int zl2 = dd / baseZ;
if (dd % baseZ > 0) zl2 *= 2;
if (lv - 1 - log2(zl2) <= l) dd /= 2;
IJ.log(" zl2: " + (lv - 1 - log2(zl2)));
if (l < lv - 1) {
lvImgTitle.add(lvImgTitle.get(0) + "_level" + (l + 1));
IJ.selectWindow(lvImgTitle.get(0));
IJ.run(
"Scale...",
"x=- y=- z=- width="
+ ww
+ " height="
+ hh
+ " depth="
+ dd
+ " interpolation=Bicubic average process create title="
+ lvImgTitle.get(l + 1));
}
}
for (int l = 0; l < lv; l++) {
IJ.log(lvImgTitle.get(l));
}
Document doc = newXMLDocument();
Element root = doc.createElement("BRK");
root.setAttribute("version", "1.0");
root.setAttribute("nLevel", String.valueOf(lv));
root.setAttribute("nChannel", String.valueOf(nCh));
root.setAttribute("nFrame", String.valueOf(nFrame));
doc.appendChild(root);
for (int l = 0; l < lv; l++) {
IJ.showProgress(0.0);
int[] dims2 = imp.getDimensions();
IJ.log(
"W: "
+ String.valueOf(dims2[0])
+ " H: "
+ String.valueOf(dims2[1])
+ " C: "
+ String.valueOf(dims2[2])
+ " D: "
+ String.valueOf(dims2[3])
+ " T: "
+ String.valueOf(dims2[4])
+ " b: "
+ String.valueOf(bdepth));
bw = bwlist.get(l).intValue();
bh = bhlist.get(l).intValue();
bd = bdlist.get(l).intValue();
boolean force_pow2 = false;
/* if(IsPowerOf2(bw) && IsPowerOf2(bh) && IsPowerOf2(bd)) force_pow2 = true;
if(force_pow2){
//force pow2
if(Pow2(bw) > bw) bw = Pow2(bw)/2;
if(Pow2(bh) > bh) bh = Pow2(bh)/2;
if(Pow2(bd) > bd) bd = Pow2(bd)/2;
}
if(bw > imageW) bw = (Pow2(imageW) == imageW) ? imageW : Pow2(imageW)/2;
if(bh > imageH) bh = (Pow2(imageH) == imageH) ? imageH : Pow2(imageH)/2;
if(bd > imageD) bd = (Pow2(imageD) == imageD) ? imageD : Pow2(imageD)/2;
*/
if (bw > imageW) bw = imageW;
if (bh > imageH) bh = imageH;
if (bd > imageD) bd = imageD;
if (bw <= 1 || bh <= 1 || bd <= 1) break;
if (filetype == "JPEG" && (bw < 8 || bh < 8)) break;
Element lvnode = doc.createElement("Level");
lvnode.setAttribute("lv", String.valueOf(l));
lvnode.setAttribute("imageW", String.valueOf(imageW));
lvnode.setAttribute("imageH", String.valueOf(imageH));
lvnode.setAttribute("imageD", String.valueOf(imageD));
lvnode.setAttribute("xspc", String.valueOf(xspc));
lvnode.setAttribute("yspc", String.valueOf(yspc));
lvnode.setAttribute("zspc", String.valueOf(zspc));
lvnode.setAttribute("bitDepth", String.valueOf(bdepth));
root.appendChild(lvnode);
Element brksnode = doc.createElement("Bricks");
brksnode.setAttribute("brick_baseW", String.valueOf(bw));
brksnode.setAttribute("brick_baseH", String.valueOf(bh));
brksnode.setAttribute("brick_baseD", String.valueOf(bd));
lvnode.appendChild(brksnode);
ArrayList<Brick> bricks = new ArrayList<Brick>();
int mw, mh, md, mw2, mh2, md2;
double tx0, ty0, tz0, tx1, ty1, tz1;
double bx0, by0, bz0, bx1, by1, bz1;
for (int k = 0; k < imageD; k += bd) {
if (k > 0) k--;
for (int j = 0; j < imageH; j += bh) {
if (j > 0) j--;
for (int i = 0; i < imageW; i += bw) {
if (i > 0) i--;
mw = Math.min(bw, imageW - i);
mh = Math.min(bh, imageH - j);
md = Math.min(bd, imageD - k);
if (force_pow2) {
mw2 = Pow2(mw);
mh2 = Pow2(mh);
md2 = Pow2(md);
} else {
mw2 = mw;
mh2 = mh;
md2 = md;
}
if (filetype == "JPEG") {
if (mw2 < 8) mw2 = 8;
if (mh2 < 8) mh2 = 8;
}
tx0 = i == 0 ? 0.0d : ((mw2 - mw + 0.5d) / mw2);
ty0 = j == 0 ? 0.0d : ((mh2 - mh + 0.5d) / mh2);
tz0 = k == 0 ? 0.0d : ((md2 - md + 0.5d) / md2);
tx1 = 1.0d - 0.5d / mw2;
if (mw < bw) tx1 = 1.0d;
if (imageW - i == bw) tx1 = 1.0d;
ty1 = 1.0d - 0.5d / mh2;
if (mh < bh) ty1 = 1.0d;
if (imageH - j == bh) ty1 = 1.0d;
tz1 = 1.0d - 0.5d / md2;
if (md < bd) tz1 = 1.0d;
if (imageD - k == bd) tz1 = 1.0d;
bx0 = i == 0 ? 0.0d : (i + 0.5d) / (double) imageW;
by0 = j == 0 ? 0.0d : (j + 0.5d) / (double) imageH;
bz0 = k == 0 ? 0.0d : (k + 0.5d) / (double) imageD;
bx1 = Math.min((i + bw - 0.5d) / (double) imageW, 1.0d);
if (imageW - i == bw) bx1 = 1.0d;
by1 = Math.min((j + bh - 0.5d) / (double) imageH, 1.0d);
if (imageH - j == bh) by1 = 1.0d;
bz1 = Math.min((k + bd - 0.5d) / (double) imageD, 1.0d);
if (imageD - k == bd) bz1 = 1.0d;
int x, y, z;
x = i - (mw2 - mw);
y = j - (mh2 - mh);
z = k - (md2 - md);
bricks.add(
new Brick(
x, y, z, mw2, mh2, md2, 0, 0, tx0, ty0, tz0, tx1, ty1, tz1, bx0, by0, bz0, bx1,
by1, bz1));
}
}
}
Element fsnode = doc.createElement("Files");
lvnode.appendChild(fsnode);
stack = imp.getStack();
int totalbricknum = nFrame * nCh * bricks.size();
int curbricknum = 0;
for (int f = 0; f < nFrame; f++) {
for (int ch = 0; ch < nCh; ch++) {
int sizelimit = bdsizelimit * 1024 * 1024;
int bytecount = 0;
int filecount = 0;
int pd_bufsize = Math.max(sizelimit, bw * bh * bd * bdepth / 8);
byte[] packed_data = new byte[pd_bufsize];
String base_dataname =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f);
String current_dataname = base_dataname + "_data" + filecount;
Brick b_first = bricks.get(0);
if (b_first.z_ != 0) IJ.log("warning");
int st_z = b_first.z_;
int ed_z = b_first.z_ + b_first.d_;
LinkedList<ImageProcessor> iplist = new LinkedList<ImageProcessor>();
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
// ImagePlus test;
// ImageStack tsst;
// test = NewImage.createByteImage("test", imageW, imageH, imageD,
// NewImage.FILL_BLACK);
// tsst = test.getStack();
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
if (ed_z > b.z_ || st_z < b.z_ + b.d_) {
if (b.z_ > st_z) {
for (int s = 0; s < b.z_ - st_z; s++) iplist.pollFirst();
st_z = b.z_;
} else if (b.z_ < st_z) {
IJ.log("warning");
for (int s = st_z - 1; s > b.z_; s--)
iplist.addFirst(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
st_z = b.z_;
}
if (b.z_ + b.d_ > ed_z) {
for (int s = ed_z; s < b.z_ + b.d_; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
ed_z = b.z_ + b.d_;
} else if (b.z_ + b.d_ < ed_z) {
IJ.log("warning");
for (int s = 0; s < ed_z - (b.z_ + b.d_); s++) iplist.pollLast();
ed_z = b.z_ + b.d_;
}
} else {
IJ.log("warning");
iplist.clear();
st_z = b.z_;
ed_z = b.z_ + b.d_;
for (int s = st_z; s < ed_z; s++)
iplist.add(stack.getProcessor(imp.getStackIndex(ch + 1, s + 1, f + 1)));
}
if (iplist.size() != b.d_) {
IJ.log("Stack Error");
return;
}
// int zz = st_z;
int bsize = 0;
byte[] bdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Iterator<ImageProcessor> ipite = iplist.iterator();
while (ipite.hasNext()) {
// ImageProcessor tsip = tsst.getProcessor(zz+1);
ImageProcessor ip = ipite.next();
ip.setRoi(b.x_, b.y_, b.w_, b.h_);
if (bdepth == 8) {
byte[] data = (byte[]) ip.crop().getPixels();
System.arraycopy(data, 0, bdata, bsize, data.length);
bsize += data.length;
} else if (bdepth == 16) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
short[] data = (short[]) ip.crop().getPixels();
for (short e : data) buffer.putShort(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
} else if (bdepth == 32) {
ByteBuffer buffer = ByteBuffer.allocate(b.w_ * b.h_ * bdepth / 8);
buffer.order(ByteOrder.LITTLE_ENDIAN);
float[] data = (float[]) ip.crop().getPixels();
for (float e : data) buffer.putFloat(e);
System.arraycopy(buffer.array(), 0, bdata, bsize, buffer.array().length);
bsize += buffer.array().length;
}
}
String filename =
basename
+ "_Lv"
+ String.valueOf(l)
+ "_Ch"
+ String.valueOf(ch)
+ "_Fr"
+ String.valueOf(f)
+ "_ID"
+ String.valueOf(i);
int offset = bytecount;
int datasize = bdata.length;
if (filetype == "RAW") {
int dummy = -1;
// do nothing
}
if (filetype == "JPEG" && bdepth == 8) {
try {
DataBufferByte db = new DataBufferByte(bdata, datasize);
Raster raster = Raster.createPackedRaster(db, b.w_, b.h_ * b.d_, 8, null);
BufferedImage img =
new BufferedImage(b.w_, b.h_ * b.d_, BufferedImage.TYPE_BYTE_GRAY);
img.setData(raster);
ByteArrayOutputStream baos = new ByteArrayOutputStream();
ImageOutputStream ios = ImageIO.createImageOutputStream(baos);
String format = "jpg";
Iterator<javax.imageio.ImageWriter> iter =
ImageIO.getImageWritersByFormatName("jpeg");
javax.imageio.ImageWriter writer = iter.next();
ImageWriteParam iwp = writer.getDefaultWriteParam();
iwp.setCompressionMode(ImageWriteParam.MODE_EXPLICIT);
iwp.setCompressionQuality((float) jpeg_quality * 0.01f);
writer.setOutput(ios);
writer.write(null, new IIOImage(img, null, null), iwp);
// ImageIO.write(img, format, baos);
bdata = baos.toByteArray();
datasize = bdata.length;
} catch (IOException e) {
e.printStackTrace();
return;
}
}
if (filetype == "ZLIB") {
byte[] tmpdata = new byte[b.w_ * b.h_ * b.d_ * bdepth / 8];
Deflater compresser = new Deflater();
compresser.setInput(bdata);
compresser.setLevel(Deflater.DEFAULT_COMPRESSION);
compresser.setStrategy(Deflater.DEFAULT_STRATEGY);
compresser.finish();
datasize = compresser.deflate(tmpdata);
bdata = tmpdata;
compresser.end();
}
if (bytecount + datasize > sizelimit && bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
filecount++;
current_dataname = base_dataname + "_data" + filecount;
bytecount = 0;
offset = 0;
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
} else {
System.arraycopy(bdata, 0, packed_data, bytecount, datasize);
bytecount += datasize;
}
Element filenode = doc.createElement("File");
filenode.setAttribute("filename", current_dataname);
filenode.setAttribute("channel", String.valueOf(ch));
filenode.setAttribute("frame", String.valueOf(f));
filenode.setAttribute("brickID", String.valueOf(i));
filenode.setAttribute("offset", String.valueOf(offset));
filenode.setAttribute("datasize", String.valueOf(datasize));
filenode.setAttribute("filetype", String.valueOf(filetype));
fsnode.appendChild(filenode);
curbricknum++;
IJ.showProgress((double) (curbricknum) / (double) (totalbricknum));
}
if (bytecount > 0) {
BufferedOutputStream fis = null;
try {
File file = new File(directory + current_dataname);
fis = new BufferedOutputStream(new FileOutputStream(file));
fis.write(packed_data, 0, bytecount);
} catch (IOException e) {
e.printStackTrace();
return;
} finally {
try {
if (fis != null) fis.close();
} catch (IOException e) {
e.printStackTrace();
return;
}
}
}
}
}
for (int i = 0; i < bricks.size(); i++) {
Brick b = bricks.get(i);
Element bricknode = doc.createElement("Brick");
bricknode.setAttribute("id", String.valueOf(i));
bricknode.setAttribute("st_x", String.valueOf(b.x_));
bricknode.setAttribute("st_y", String.valueOf(b.y_));
bricknode.setAttribute("st_z", String.valueOf(b.z_));
bricknode.setAttribute("width", String.valueOf(b.w_));
bricknode.setAttribute("height", String.valueOf(b.h_));
bricknode.setAttribute("depth", String.valueOf(b.d_));
brksnode.appendChild(bricknode);
Element tboxnode = doc.createElement("tbox");
tboxnode.setAttribute("x0", String.valueOf(b.tx0_));
tboxnode.setAttribute("y0", String.valueOf(b.ty0_));
tboxnode.setAttribute("z0", String.valueOf(b.tz0_));
tboxnode.setAttribute("x1", String.valueOf(b.tx1_));
tboxnode.setAttribute("y1", String.valueOf(b.ty1_));
tboxnode.setAttribute("z1", String.valueOf(b.tz1_));
bricknode.appendChild(tboxnode);
Element bboxnode = doc.createElement("bbox");
bboxnode.setAttribute("x0", String.valueOf(b.bx0_));
bboxnode.setAttribute("y0", String.valueOf(b.by0_));
bboxnode.setAttribute("z0", String.valueOf(b.bz0_));
bboxnode.setAttribute("x1", String.valueOf(b.bx1_));
bboxnode.setAttribute("y1", String.valueOf(b.by1_));
bboxnode.setAttribute("z1", String.valueOf(b.bz1_));
bricknode.appendChild(bboxnode);
}
if (l < lv - 1) {
imp = WindowManager.getImage(lvImgTitle.get(l + 1));
int[] newdims = imp.getDimensions();
imageW = newdims[0];
imageH = newdims[1];
imageD = newdims[3];
xspc = orgxspc * ((double) orgW / (double) imageW);
yspc = orgyspc * ((double) orgH / (double) imageH);
zspc = orgzspc * ((double) orgD / (double) imageD);
bdepth = imp.getBitDepth();
}
}
File newXMLfile = new File(directory + basename + ".vvd");
writeXML(newXMLfile, doc);
for (int l = 1; l < lv; l++) {
imp = WindowManager.getImage(lvImgTitle.get(l));
imp.changes = false;
imp.close();
}
}
public void run(String arg) {
Frame[] niframes = WindowManager.getNonImageWindows();
String[] titles = new String[niframes.length + 1];
for (int i = 0; i < niframes.length; i++) {
titles[i] = niframes[i].getTitle();
}
titles[niframes.length] = "Clipboard";
GenericDialog gd = new GenericDialog("Windows");
boolean importfile = false;
gd.addCheckbox("Import from file?", importfile);
gd.addChoice("Windows", titles, titles[0]);
boolean hasxvals = false;
gd.addCheckbox("X Vals Column?", hasxvals);
boolean multix = false;
gd.addCheckbox("Multi_X_Columns?", multix);
boolean skipendzeros = false;
gd.addCheckbox("Skip_end_zeros?", skipendzeros);
String[] delimiters = {"Tab", "Comma", "Space"};
gd.addChoice("Delimiter", delimiters, delimiters[0]);
gd.showDialog();
if (gd.wasCanceled()) {
return;
}
importfile = gd.getNextBoolean();
int index = gd.getNextChoiceIndex();
hasxvals = gd.getNextBoolean();
multix = gd.getNextBoolean();
skipendzeros = gd.getNextBoolean();
int delimindex = gd.getNextChoiceIndex();
if (multix) hasxvals = true;
String textdata = "";
if (importfile) {
OpenDialog od = new OpenDialog("Open File", "", ".txt");
String directory = od.getDirectory();
String name = od.getFileName();
if (name == null) {
return;
}
try {
File infile = new File(directory + name);
BufferedReader b = new BufferedReader(new FileReader(infile));
textdata = (new jdataio()).readstringfile(b);
b.close();
} catch (IOException e) {
return;
}
} else {
if (index == niframes.length) {
// here we get the data from the clipboard
Transferable t = Toolkit.getDefaultToolkit().getSystemClipboard().getContents(null);
try {
if (t != null && t.isDataFlavorSupported(DataFlavor.stringFlavor)) {
textdata = (String) t.getTransferData(DataFlavor.stringFlavor);
}
} catch (UnsupportedFlavorException e) {
} catch (IOException e) {
}
if (textdata.equals("")) {
IJ.error("Error copying from clipboard.");
return;
}
} else {
if (niframes[index] instanceof Editor) {
Editor tw = (Editor) niframes[index];
textdata = tw.getText();
} else {
if (niframes[index] instanceof TextWindow) {
TextWindow tw = (TextWindow) niframes[index];
textdata = tw.getTextPanel().getText();
} else {
IJ.showMessage("Not a valid text window");
return;
}
}
}
}
if (textdata == null) {
IJ.showMessage("Error in Obtaining String");
return;
}
if (textdata.indexOf("\r") >= 0) {
textdata = textdata.replace('\r', '\n');
}
char[] delims = {'\t', ',', ' '};
delimit_string ds = new delimit_string(delims[delimindex]);
String[] rows = ds.getrows(textdata);
int lines = rows.length;
int columns = ds.getnumcolumns(rows[0]);
int ycolumns = columns;
if (hasxvals) {
if (multix) {
ycolumns /= 2;
} else {
ycolumns--;
}
}
if (multix) {
float[][] ydata = new float[ycolumns][lines];
float[][] xdata = new float[ycolumns][lines];
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
for (int j = 0; j < ycolumns; j++) {
ydata[j][i] = temp[2 * j + 1];
xdata[j][i] = temp[2 * j];
}
}
int[] npts = new int[ycolumns];
for (int i = 0; i < ycolumns; i++) {
npts[i] = lines;
}
if (skipendzeros) {
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
while ((xdata[i][counter] == 0.0f || Float.isNaN(xdata[i][counter])) && counter > 0) {
xdata[i][counter] = 0.0f;
ydata[i][counter] = 0.0f;
npts[i]--;
counter--;
}
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
} else {
float[][] tempydata = new float[ycolumns][lines];
float[] tempxdata = new float[lines];
float[][] xdata = null;
float[][] ydata = null;
int startcolumn = 0;
if (hasxvals) startcolumn = 1;
for (int i = 0; i < lines; i++) {
float[] temp = ds.delim2float(rows[i], columns);
if (hasxvals) {
tempxdata[i] = temp[0];
} else {
tempxdata[i] = (float) (i + 1);
}
for (int j = 0; j < ycolumns; j++) {
tempydata[j][i] = temp[j + startcolumn];
}
}
int[] npts = new int[ycolumns];
npts[0] = lines;
if (skipendzeros) {
int maxpts = 0;
for (int i = 0; i < ycolumns; i++) {
int counter = lines - 1;
npts[i] = lines;
while ((tempydata[i][counter] == 0.0f || Float.isNaN(tempydata[i][counter]))
&& counter > 0) {
npts[i]--;
counter--;
}
if (npts[i] > maxpts) maxpts = npts[i];
IJ.log("" + npts[i]);
}
ydata = new float[ycolumns][maxpts];
xdata = new float[ycolumns][maxpts];
for (int i = 0; i < ycolumns; i++) {
// npts[i]=npts[0];
System.arraycopy(tempxdata, 0, xdata[i], 0, npts[i]);
System.arraycopy(tempydata[i], 0, ydata[i], 0, npts[i]);
}
} else {
ydata = tempydata;
xdata = new float[ycolumns][];
for (int i = 0; i < ycolumns; i++) {
npts[i] = npts[0];
xdata[i] = tempxdata.clone();
}
}
(new PlotWindow4("Text Plot", "x", "y", xdata, ydata, npts)).draw();
}
}
