public void run(String arg) {
ImageWindow iw = WindowManager.getCurrentWindow();
pw = jutils.getPW4SelCopy(iw);
String title = pw.getTitle();
float[][] yvals = pw.getYValues();
float[][] xvals = pw.getXValues();
int length = yvals[0].length;
if (pw.getShowErrors()) errs = pw.getErrors(0, false);
int[] colors = pw.getColors();
colors[0] = 0;
ScriptEngineManager manager = new ScriptEngineManager();
engine = manager.getEngineByName("js");
ce = (Compilable) engine;
// hitcounter=0;
c2 = 0.0f;
iterations = 0;
checkc2 = false;
double[] stats = new double[3];
tempx = new float[length];
tempdata = new float[length];
System.arraycopy(xvals[0], 0, tempx, 0, length);
System.arraycopy(yvals[0], 0, tempdata, 0, length);
pw.addPoints(tempx, new float[tempx.length], false);
series = pw.getNpts().length - 1;
double[] params = new double[10];
int[] fixes = {0, 0, 0, 1, 1, 1, 1, 1, 1, 1};
init_options(params, fixes);
if (!init_functions()) {
return;
}
while (showoptions(params, fixes)) {
NLLSfit_v2 fitclass;
if (checkc2) {
fitclass = new NLLSfit_v2(this, 0);
} else {
fitclass = new NLLSfit_v2(this, 0.0001, 50, 0.1);
}
float[] fit = fitclass.fitdata(params, fixes, constraints, yvals[0], weights, stats, true);
pw.updateSeries(fit, series, false);
c2 = (float) stats[1];
iterations = (int) stats[0];
}
IJ.log("Chi Squared = " + (float) stats[1]);
IJ.log("Iterations = " + (int) stats[0]);
for (int i = 0; i < 10; i++) {
IJ.log("P" + (i + 1) + " = " + (float) params[i] + " fixed = " + fixes[i]);
}
IJ.log("AIC = " + (float) stats[2]);
// IJ.log("hits = "+hitcounter);
set_options(params, fixes);
}
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;
}
}
boolean init_functions() {
GenericDialog gd = new GenericDialog("Fitting Options");
gd.addStringField("Extra Definitions", exdef, 50);
gd.addCheckbox("Weight Using Plot Errors", false);
gd.addStringField("Weighting Equation (y is for data)", weightfunction, 50);
gd.addStringField("Fit_Equation", function, 50);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
exdef = gd.getNextString();
boolean errweights = gd.getNextBoolean();
weightfunction = gd.getNextString();
function = gd.getNextString();
// first initialize the weights
weights = new float[tempdata.length];
if (errweights
|| weightfunction.equals("")
|| weightfunction == null
|| weightfunction == "1.0") {
if (errweights) {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f / (errs[i] * errs[i]);
} else {
for (int i = 0; i < tempdata.length; i++) weights[i] = 1.0f;
}
} else {
for (int i = 0; i < tempdata.length; i++) {
String script =
"y =" + tempdata[i] + "; " + "x =" + tempx[i] + "; " + "retval=" + weightfunction + ";";
Double temp = new Double(0.0);
try {
temp = (Double) engine.eval(script);
} catch (Exception e) {
IJ.log(e.getMessage());
}
if (!(temp.isInfinite() || temp.isNaN())) {
weights[i] = temp.floatValue();
}
}
}
// now compile the function script
try {
String script1 = exdef + "; retval=" + function + ";";
cs = ce.compile(script1);
} catch (Exception e) {
IJ.log(e.toString());
return false;
}
return true;
}
/** 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);
}
}
public double[] fitfunc(double[] fitparams) {
Bindings b = engine.createBindings();
for (int i = 0; i < 10; i++) b.put("P" + (i + 1), fitparams[i]);
/*String script1="P1="+fitparams[0]+"; "+
"P2="+fitparams[1]+"; "+
"P3="+fitparams[2]+"; "+
"P4="+fitparams[3]+"; "+
"P5="+fitparams[4]+"; "+
"P6="+fitparams[5]+"; "+
"P7="+fitparams[6]+"; "+
"P8="+fitparams[7]+"; "+
"P9="+fitparams[8]+"; "+
"P10="+fitparams[9]+"; "+
exdef+"; x=";
String script2="; retval="+function+";";*/
try {
double[] temp = new double[tempx.length];
for (int i = 0; i < tempx.length; i++) {
// temp[i]=((Double)engine.eval(script1+(double)tempx[i]+script2)).doubleValue();
b.put("x", tempx[i]);
b.put("y", tempdata[i]);
temp[i] = (Double) cs.eval(b);
}
return temp;
} catch (Exception e) {
IJ.log(e.getMessage());
return null;
}
}
void Bernsen(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
// Bernsen recommends WIN_SIZE = 31 and CONTRAST_THRESHOLD = 15.
// 1) Bernsen J. (1986) "Dynamic Thresholding of Grey-Level Images"
// Proc. of the 8th Int. Conf. on Pattern Recognition, pp. 1251-1255
// 2) Sezgin M. and Sankur B. (2004) "Survey over Image Thresholding
// Techniques and Quantitative Performance Evaluation" Journal of
// Electronic Imaging, 13(1): 146-165
// http://citeseer.ist.psu.edu/sezgin04survey.html
// Ported to ImageJ plugin from E Celebi's fourier_0.8 routines
// This version uses a circular local window, instead of a rectagular one
ImagePlus Maximp, Minimp;
ImageProcessor ip = imp.getProcessor(), ipMax, ipMin;
int contrast_threshold = 15;
int local_contrast;
int mid_gray;
byte object;
byte backg;
int temp;
if (par1 != 0) {
IJ.log("Bernsen: changed contrast_threshold from :" + contrast_threshold + " to:" + par1);
contrast_threshold = (int) par1;
}
if (doIwhite) {
object = (byte) 0xff;
backg = (byte) 0;
} else {
object = (byte) 0;
backg = (byte) 0xff;
}
Maximp = duplicateImage(ip);
ipMax = Maximp.getProcessor();
RankFilters rf = new RankFilters();
rf.rank(ipMax, radius, rf.MAX); // Maximum
// Maximp.show();
Minimp = duplicateImage(ip);
ipMin = Minimp.getProcessor();
rf.rank(ipMin, radius, rf.MIN); // Minimum
// Minimp.show();
byte[] pixels = (byte[]) ip.getPixels();
byte[] max = (byte[]) ipMax.getPixels();
byte[] min = (byte[]) ipMin.getPixels();
for (int i = 0; i < pixels.length; i++) {
local_contrast = (int) ((max[i] & 0xff) - (min[i] & 0xff));
mid_gray = (int) ((min[i] & 0xff) + (max[i] & 0xff)) / 2;
temp = (int) (pixels[i] & 0x0000ff);
if (local_contrast < contrast_threshold)
pixels[i] = (mid_gray >= 128) ? object : backg; // Low contrast region
else pixels[i] = (temp >= mid_gray) ? object : backg;
}
// imp.updateAndDraw();
return;
}
void MidGrey(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
// See: Image Processing Learning Resourches HIPR2
// http://homepages.inf.ed.ac.uk/rbf/HIPR2/adpthrsh.htm
ImagePlus Maximp, Minimp;
ImageProcessor ip = imp.getProcessor(), ipMax, ipMin;
int c_value = 0;
int mid_gray;
byte object;
byte backg;
if (par1 != 0) {
IJ.log("MidGrey: changed c_value from :" + c_value + " to:" + par1);
c_value = (int) par1;
}
if (doIwhite) {
object = (byte) 0xff;
backg = (byte) 0;
} else {
object = (byte) 0;
backg = (byte) 0xff;
}
Maximp = duplicateImage(ip);
ipMax = Maximp.getProcessor();
RankFilters rf = new RankFilters();
rf.rank(ipMax, radius, rf.MAX); // Maximum
// Maximp.show();
Minimp = duplicateImage(ip);
ipMin = Minimp.getProcessor();
rf.rank(ipMin, radius, rf.MIN); // Minimum
// Minimp.show();
byte[] pixels = (byte[]) ip.getPixels();
byte[] max = (byte[]) ipMax.getPixels();
byte[] min = (byte[]) ipMin.getPixels();
for (int i = 0; i < pixels.length; i++) {
pixels[i] =
((int) (pixels[i] & 0xff) > (int) (((max[i] & 0xff) + (min[i] & 0xff)) / 2) - c_value)
? object
: backg;
}
// imp.updateAndDraw();
return;
}
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 [\\]");
}
}
void Mean(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
// See: Image Processing Learning Resourches HIPR2
// http://homepages.inf.ed.ac.uk/rbf/HIPR2/adpthrsh.htm
ImagePlus Meanimp;
ImageProcessor ip = imp.getProcessor(), ipMean;
int c_value = 0;
byte object;
byte backg;
if (par1 != 0) {
IJ.log("Mean: changed c_value from :" + c_value + " to:" + par1);
c_value = (int) par1;
}
if (doIwhite) {
object = (byte) 0xff;
backg = (byte) 0;
} else {
object = (byte) 0;
backg = (byte) 0xff;
}
Meanimp = duplicateImage(ip);
ImageConverter ic = new ImageConverter(Meanimp);
ic.convertToGray32();
ipMean = Meanimp.getProcessor();
RankFilters rf = new RankFilters();
rf.rank(ipMean, radius, rf.MEAN); // Mean
// Meanimp.show();
byte[] pixels = (byte[]) ip.getPixels();
float[] mean = (float[]) ipMean.getPixels();
for (int i = 0; i < pixels.length; i++)
pixels[i] = ((int) (pixels[i] & 0xff) > (int) (mean[i] - c_value)) ? object : backg;
// imp.updateAndDraw();
return;
}
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();
}
void Niblack(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
// Niblack recommends K_VALUE = -0.2 for images with black foreground
// objects, and K_VALUE = +0.2 for images with white foreground objects.
// Niblack W. (1986) "An introduction to Digital Image Processing" Prentice-Hall.
// Ported to ImageJ plugin from E Celebi's fourier_0.8 routines
// This version uses a circular local window, instead of a rectagular one
ImagePlus Meanimp, Varimp;
ImageProcessor ip = imp.getProcessor(), ipMean, ipVar;
double k_value;
int c_value = 0;
byte object;
byte backg;
if (doIwhite) {
k_value = 0.2;
object = (byte) 0xff;
backg = (byte) 0;
} else {
k_value = -0.2;
object = (byte) 0;
backg = (byte) 0xff;
}
if (par1 != 0) {
IJ.log("Niblack: changed k_value from :" + k_value + " to:" + par1);
k_value = par1;
}
if (par2 != 0) {
IJ.log(
"Niblack: changed c_value from :"
+ c_value
+ " to:"
+ par2); // requested feature, not in original
c_value = (int) par2;
}
Meanimp = duplicateImage(ip);
ImageConverter ic = new ImageConverter(Meanimp);
ic.convertToGray32();
ipMean = Meanimp.getProcessor();
RankFilters rf = new RankFilters();
rf.rank(ipMean, radius, rf.MEAN); // Mean
// Meanimp.show();
Varimp = duplicateImage(ip);
ic = new ImageConverter(Varimp);
ic.convertToGray32();
ipVar = Varimp.getProcessor();
rf.rank(ipVar, radius, rf.VARIANCE); // Variance
// Varimp.show();
byte[] pixels = (byte[]) ip.getPixels();
float[] mean = (float[]) ipMean.getPixels();
float[] var = (float[]) ipVar.getPixels();
for (int i = 0; i < pixels.length; i++)
pixels[i] =
((int) (pixels[i] & 0xff) > (int) (mean[i] + k_value * Math.sqrt(var[i]) - c_value))
? object
: backg;
// imp.updateAndDraw();
return;
}
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();
}
}
void Phansalkar(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
// This is a modification of Sauvola's thresholding method to deal with low contrast images.
// Phansalskar N. et al. Adaptive local thresholding for detection of nuclei in diversity
// stained
// cytology images.International Conference on Communications and Signal Processing (ICCSP),
// 2011,
// 218 - 220.
// In this method, the threshold t = mean*(1+p*exp(-q*mean)+k*((stdev/r)-1))
// Phansalkar recommends k = 0.25, r = 0.5, p = 2 and q = 10. In this plugin, k and r are the
// parameters 1 and 2 respectively, but the values of p and q are fixed.
//
// Implemented from Phansalkar's paper description by G. Landini
// This version uses a circular local window, instead of a rectagular one
ImagePlus Meanimp, Varimp, Orimp;
ImageProcessor ip = imp.getProcessor(), ipMean, ipVar, ipOri;
double k_value = 0.25;
double r_value = 0.5;
double p_value = 2.0;
double q_value = 10.0;
byte object;
byte backg;
if (par1 != 0) {
IJ.log("Phansalkar: changed k_value from :" + k_value + " to:" + par1);
k_value = par1;
}
if (par2 != 0) {
IJ.log("Phansalkar: changed r_value from :" + r_value + " to:" + par2);
r_value = par2;
}
if (doIwhite) {
object = (byte) 0xff;
backg = (byte) 0;
} else {
object = (byte) 0;
backg = (byte) 0xff;
}
Meanimp = duplicateImage(ip);
ContrastEnhancer ce = new ContrastEnhancer();
ce.stretchHistogram(Meanimp, 0.0);
ImageConverter ic = new ImageConverter(Meanimp);
ic.convertToGray32();
ipMean = Meanimp.getProcessor();
ipMean.multiply(1.0 / 255);
Orimp = duplicateImage(ip);
ce.stretchHistogram(Orimp, 0.0);
ic = new ImageConverter(Orimp);
ic.convertToGray32();
ipOri = Orimp.getProcessor();
ipOri.multiply(1.0 / 255); // original to compare
// Orimp.show();
RankFilters rf = new RankFilters();
rf.rank(ipMean, radius, rf.MEAN); // Mean
// Meanimp.show();
Varimp = duplicateImage(ip);
ce.stretchHistogram(Varimp, 0.0);
ic = new ImageConverter(Varimp);
ic.convertToGray32();
ipVar = Varimp.getProcessor();
ipVar.multiply(1.0 / 255);
rf.rank(ipVar, radius, rf.VARIANCE); // Variance
ipVar.sqr(); // SD
// Varimp.show();
byte[] pixels = (byte[]) ip.getPixels();
float[] ori = (float[]) ipOri.getPixels();
float[] mean = (float[]) ipMean.getPixels();
float[] sd = (float[]) ipVar.getPixels();
for (int i = 0; i < pixels.length; i++)
pixels[i] =
((ori[i])
> (mean[i]
* (1.0
+ p_value * Math.exp(-q_value * mean[i])
+ k_value * ((sd[i] / r_value) - 1.0))))
? object
: backg;
// imp.updateAndDraw();
return;
}
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();
}
}
void Sauvola(ImagePlus imp, int radius, double par1, double par2, boolean doIwhite) {
// Sauvola recommends K_VALUE = 0.5 and R_VALUE = 128.
// This is a modification of Niblack's thresholding method.
// Sauvola J. and Pietaksinen M. (2000) "Adaptive Document Image Binarization"
// Pattern Recognition, 33(2): 225-236
// http://www.ee.oulu.fi/mvg/publications/show_pdf.php?ID=24
// Ported to ImageJ plugin from E Celebi's fourier_0.8 routines
// This version uses a circular local window, instead of a rectagular one
ImagePlus Meanimp, Varimp;
ImageProcessor ip = imp.getProcessor(), ipMean, ipVar;
double k_value = 0.5;
double r_value = 128;
byte object;
byte backg;
if (par1 != 0) {
IJ.log("Sauvola: changed k_value from :" + k_value + " to:" + par1);
k_value = par1;
}
if (par2 != 0) {
IJ.log("Sauvola: changed r_value from :" + r_value + " to:" + par2);
r_value = par2;
}
if (doIwhite) {
object = (byte) 0xff;
backg = (byte) 0;
} else {
object = (byte) 0;
backg = (byte) 0xff;
}
Meanimp = duplicateImage(ip);
ImageConverter ic = new ImageConverter(Meanimp);
ic.convertToGray32();
ipMean = Meanimp.getProcessor();
RankFilters rf = new RankFilters();
rf.rank(ipMean, radius, rf.MEAN); // Mean
// Meanimp.show();
Varimp = duplicateImage(ip);
ic = new ImageConverter(Varimp);
ic.convertToGray32();
ipVar = Varimp.getProcessor();
rf.rank(ipVar, radius, rf.VARIANCE); // Variance
// Varimp.show();
byte[] pixels = (byte[]) ip.getPixels();
float[] mean = (float[]) ipMean.getPixels();
float[] var = (float[]) ipVar.getPixels();
for (int i = 0; i < pixels.length; i++)
pixels[i] =
((int) (pixels[i] & 0xff)
> (int) (mean[i] * (1.0 + k_value * ((Math.sqrt(var[i]) / r_value) - 1.0))))
? object
: backg;
// imp.updateAndDraw();
return;
}
public boolean get_errors(double[] params, int[] fixes) {
GenericDialog gd = new GenericDialog("Error Options");
String[] methods = {"Support Plane", "Monte Carlo"};
gd.addChoice("Method", methods, methods[0]);
float conf = 0.67f;
gd.addNumericField("SP_Confidence Limit (%)", (int) (conf * 100.0f), 5, 10, null);
String[] labels = {"P1", "P2", "P3", "P4", "P5", "P6", "P7", "P8", "P9", "P10"};
gd.addChoice("SP_Parameter", labels, labels[0]);
double spacing = 0.01;
gd.addNumericField("SP_Chi^2_plot_spacing (% of value)?", spacing * 100.0, 2, 10, null);
int ntrials = 100;
gd.addNumericField("MC_#_Trials", ntrials, 0);
gd.showDialog();
if (gd.wasCanceled()) {
return false;
}
int methodindex = gd.getNextChoiceIndex();
conf = 0.01f * (float) gd.getNextNumber();
int paramindex = gd.getNextChoiceIndex();
spacing = 0.01 * gd.getNextNumber();
ntrials = (int) gd.getNextNumber();
if (methodindex == 0) {
support_plane_errors_v2 erclass = new support_plane_errors_v2(this, 0.0001, 50, false, 0.1);
int errindex = paramindex;
int nfit = 0;
for (int i = 0; i < labels.length; i++) {
if (fixes[i] == 0) {
nfit++;
}
}
int npts = tempdata.length;
int dofnum = npts - (nfit - 1) - 1;
int dofden = npts - 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 false;
}
double truespacing = Math.abs(params[errindex] * spacing);
double[][] c2plot =
erclass.geterrors(
params, fixes, constraints, tempdata, weights, flim, truespacing, errindex);
IJ.log("upper limit = " + c2plot[1][0] + " lower limit = " + c2plot[0][0]);
IJ.log(
"upper error = "
+ (c2plot[1][0] - params[errindex])
+ " lower error = "
+ (params[errindex] - 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", labels[errindex], "Chi^2", c2plotf[0], c2plotf[1]).draw();
} else {
StringBuffer sb = new StringBuffer();
sb.append("Trial\t");
for (int i = 0; i < labels.length; i++) {
if (fixes[i] == 0) sb.append(labels[i] + "\t");
}
sb.append("chi^2");
tw = new TextWindow("Monte Carlo Results", sb.toString(), "", 400, 400);
redirect = true;
monte_carlo_errors_v2 erclass = new monte_carlo_errors_v2(this, 0.0001, 50, false, 0.1);
double[][] errors = erclass.geterrors(params, fixes, constraints, tempdata, weights, ntrials);
sb = new StringBuffer();
sb.append("StDev\t");
for (int i = 0; i < errors.length; i++) {
float[] ferr = new float[errors[0].length];
for (int j = 0; j < ferr.length; j++) ferr[j] = (float) errors[i][j];
float stdev = jstatistics.getstatistic("StDev", ferr, null);
sb.append("" + stdev);
if (i < (errors.length - 1)) sb.append("\t");
}
tw.append(sb.toString());
redirect = false;
}
return true;
}
public void run(String arg) {
GenericDialog gd = new GenericDialog("Options");
gd.addCheckbox("Acceptor_First", true);
gd.showDialog();
if (gd.wasCanceled()) return;
boolean a1 = gd.getNextBoolean();
int asp = 0;
int dsp = 1;
int aop = 2;
int dop = 3;
int atp = 4;
int dtp = 5;
if (!a1) {
asp = 1;
dsp = 0;
aop = 3;
dop = 2;
atp = 5;
dtp = 4;
}
ImageWindow iw = WindowManager.getCurrentWindow();
float[][] xvals = (float[][]) jutils.runPW4VoidMethod(iw, "getXValues");
float[][] yvals = (float[][]) jutils.runPW4VoidMethod(iw, "getYValues");
int[] npts = (int[]) jutils.runPW4VoidMethod(iw, "getNpts");
int maxpts = (int) jstatistics.getstatistic("Max", npts, null);
int nsets = npts.length / 6;
float[][] rtxvals = new float[nsets][maxpts];
float[][] rtavals = new float[nsets][maxpts];
float[][] rtdvals = new float[nsets][maxpts];
int[] rtnpts = new int[nsets];
int fretlength = 10;
float[][] stfretvals = new float[nsets][fretlength];
float[][] offfretvals = new float[nsets][fretlength];
TextWindow tw = jutils.selectTable("DNA Damage FRET");
if (tw == null)
tw =
new TextWindow(
"DNA Damage FRET",
"title\tacceptor\tdonor\testripe\teoff\tmaxart\tmaxdrt",
"",
400,
200);
// note that st stands for stripe and off is for areas off the damage stripe
for (int i = 0; i < npts.length / 6; i++) {
int len = npts[i * 6];
int damageindex = findbleach(yvals[i * 6 + dsp], len);
int fretindex = findbleach(yvals[i * 6 + atp], len);
IJ.log("set " + i + " damage pos = " + damageindex + " , fret pos = " + fretindex);
int predamagestart = damageindex - 4;
int prefretstart = fretindex - 5;
float staccpredam = getavg(yvals[i * 6 + asp], len, predamagestart, damageindex - 1);
float stdonpredam = getavg(yvals[i * 6 + dsp], len, predamagestart, damageindex - 1);
float nucaccpredam = getavg(yvals[i * 6 + atp], len, predamagestart, damageindex - 1);
float nucdonpredam = getavg(yvals[i * 6 + dtp], len, predamagestart, damageindex - 1);
float stdonprefret = getavg(yvals[i * 6 + dsp], len, prefretstart, fretindex - 2);
float stdonafret = getavg(yvals[i * 6 + dsp], len, fretindex, fretindex + 3);
float offdonprefret = getavg(yvals[i * 6 + dop], len, prefretstart, fretindex - 2);
float offdonafret = getavg(yvals[i * 6 + dop], len, fretindex, fretindex + 3);
float estripe = 1.0f - stdonprefret / stdonafret;
float eoff = 1.0f - offdonprefret / offdonafret;
rtnpts[i] = len;
for (int j = 0; j < len; j++) {
rtxvals[i][j] = j - damageindex - 1;
rtavals[i][j] =
(yvals[i * 6 + asp][j] / staccpredam) / (yvals[i * 6 + atp][j] / nucaccpredam);
rtdvals[i][j] =
(yvals[i * 6 + dsp][j] / stdonpredam) / (yvals[i * 6 + dtp][j] / nucdonpredam);
}
float[] smart = (float[]) algutils.get_subarray(rtavals[i], 0, fretindex);
float[] smdrt = (float[]) algutils.get_subarray(rtdvals[i], 0, fretindex);
jsmooth.blur1D(smart, 2.0f);
jsmooth.blur1D(smdrt, 2.0f);
float maxart = 0.0f;
float maxdrt = 0.0f;
for (int j = 0; j < fretindex - 2; j++) {
if (smart[j] > maxart) maxart = smart[j];
if (smdrt[j] > maxdrt) maxdrt = smdrt[j];
}
stfretvals[i] = getregion(yvals[i * 6 + dsp], len, prefretstart, fretlength);
offfretvals[i] = getregion(yvals[i * 6 + dop], len, prefretstart, fretlength);
tw.append(
iw.getTitle()
+ "-"
+ (i + 1)
+ "\t"
+ staccpredam
+ "\t"
+ stdonpredam
+ "\t"
+ estripe
+ "\t"
+ eoff
+ "\t"
+ maxart
+ "\t"
+ maxdrt);
}
new PlotWindow4("Stripe_FRET_profiles", "time", "intensity", stfretvals, null).draw();
new PlotWindow4("OffStripe_FRET_profiles", "time", "intensity", offfretvals, null).draw();
new PlotWindow4("Acc_Rt_profiles", "time", "intensity", rtxvals, rtavals, rtnpts).draw();
new PlotWindow4("Don_Rt_profiles", "time", "intensity", rtxvals, rtdvals, rtnpts).draw();
}
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();
}
}
public void showresults(String results) {
IJ.showStatus(results);
IJ.log(results);
}
public void showresults(String results) {
if (redirect) tw.append(results);
else IJ.log(results);
}
