public void run(ImageProcessor ip) {
dimz = stack.getSize();
dimy = stack.getWidth();
dimx = stack.getHeight();
SaveDialog sd = new SaveDialog("Save Measurements as Text...", "res", ".dat");
String name = sd.getFileName();
if (name == null) return;
String directory = sd.getDirectory();
nb = calculnb(stack); // -1;
IJ.showStatus("Measure parameters for the " + nb + " objects ...");
if (nb < 1) {
IJ.showMessage("volume must be labeled");
} else {
double[] volume_m = new double[nb];
int[] volume_p = new int[nb];
double[] surface = new double[nb];
double[] surfacenb = new double[nb];
double[][][] I = new double[3][3][nb];
double[][] J = new double[3][nb];
double[][][] dir = new double[3][3][nb];
double[] xg = new double[nb];
double[] yg = new double[nb];
double[] zg = new double[nb];
byte[] bord = new byte[nb];
// double[] a = new double[nb];
// double[] b = new double[nb];
// double[] c = new double[nb];
// double[] Fab = new double[nb];
// double[] Fac = new double[nb];
// double[] Fbc = new double[nb];
// double[] sp = new double[nb];
double[][] lmin = new double[nb][3];
double[][] lmax = new double[nb][3];
IJ.showStatus("Measure surfaces ...");
calculmarchsurfstack(stack, nb, surface, volume_m);
calculmarchsurfstacknb(stack, nb, surfacenb);
// calculvolumestack(stack,nb,volume_p);
IJ.showStatus("Measure volumes and inertia ...");
calculcgstack(stack, nb, volume_p, xg, yg, zg);
calculinertiestack(stack, nb, xg, yg, zg, I);
inertie(nb, I, J, dir);
IJ.showStatus("Measure bounding boxes ...");
boitestack(stack, nb, xg, yg, zg, dir, lmin, lmax);
borderstack(stack, nb, bord);
IJ.showStatus("Save results ...");
sauvegarde(
volume_p, volume_m, surface, surfacenb, xg, yg, zg, J, dir, nb, bord, lmin, lmax,
directory, name);
volume_m = null;
volume_p = null;
surface = null;
xg = null;
yg = null;
zg = null;
}
}
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;
}
}
/** Ask for parameters and then execute. */
public void run(String arg) {
// 1 - Obtain the currently active image:
ImagePlus imp = IJ.getImage();
if (null == imp) {
IJ.showMessage("There must be at least one image open");
return;
}
if (imp.getBitDepth() != 8) {
IJ.showMessage("Error", "Only 8-bit images are supported");
return;
}
// 2 - Ask for parameters:
GenericDialog gd = new GenericDialog("Auto Local Threshold");
String[] methods = {
"Try all",
"Bernsen",
"Contrast",
"Mean",
"Median",
"MidGrey",
"Niblack",
"Otsu",
"Phansalkar",
"Sauvola"
};
gd.addMessage("Auto Local Threshold v1.5");
gd.addChoice("Method", methods, methods[0]);
gd.addNumericField("Radius", 15, 0);
gd.addMessage("Special paramters (if different from default)");
gd.addNumericField("Parameter_1", 0, 0);
gd.addNumericField("Parameter_2", 0, 0);
gd.addCheckbox("White objects on black background", true);
if (imp.getStackSize() > 1) {
gd.addCheckbox("Stack", false);
}
gd.addMessage("Thresholded result is always shown in white [255].");
gd.showDialog();
if (gd.wasCanceled()) return;
// 3 - Retrieve parameters from the dialog
String myMethod = gd.getNextChoice();
int radius = (int) gd.getNextNumber();
double par1 = (double) gd.getNextNumber();
double par2 = (double) gd.getNextNumber();
boolean doIwhite = gd.getNextBoolean();
boolean doIstack = false;
int stackSize = imp.getStackSize();
if (stackSize > 1) doIstack = gd.getNextBoolean();
// 4 - Execute!
// long start = System.currentTimeMillis();
if (myMethod.equals("Try all")) {
ImageProcessor ip = imp.getProcessor();
int xe = ip.getWidth();
int ye = ip.getHeight();
int ml = methods.length;
ImagePlus imp2, imp3;
ImageStack tstack = null, stackNew;
if (stackSize > 1 && doIstack) {
boolean doItAnyway = true;
if (stackSize > 25) {
YesNoCancelDialog d =
new YesNoCancelDialog(
IJ.getInstance(),
"Auto Local Threshold",
"You might run out of memory.\n \nDisplay "
+ stackSize
+ " slices?\n \n \'No\' will process without display and\noutput results to the log window.");
if (!d.yesPressed()) {
// doIlog=true; //will show in the log window
doItAnyway = false;
}
if (d.cancelPressed()) return;
}
for (int j = 1; j <= stackSize; j++) {
imp.setSlice(j);
ip = imp.getProcessor();
tstack = new ImageStack(xe, ye);
for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
imp2 = new ImagePlus("Auto Threshold", tstack);
imp2.updateAndDraw();
for (int k = 1; k < ml; k++) {
imp2.setSlice(k);
Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
}
// if (doItAnyway){
CanvasResizer cr = new CanvasResizer();
stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
imp3 = new ImagePlus("Auto Threshold", stackNew);
imp3.updateAndDraw();
MontageMaker mm = new MontageMaker();
mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true); // 3 columns and 3 rows
}
imp.setSlice(1);
// if (doItAnyway)
IJ.run("Images to Stack", "method=[Copy (center)] title=Montage");
return;
} else { // single image try all
tstack = new ImageStack(xe, ye);
for (int k = 1; k < ml; k++) tstack.addSlice(methods[k], ip.duplicate());
imp2 = new ImagePlus("Auto Threshold", tstack);
imp2.updateAndDraw();
for (int k = 1; k < ml; k++) {
imp2.setSlice(k);
// IJ.log("analyzing slice with "+methods[k]);
Object[] result = exec(imp2, methods[k], radius, par1, par2, doIwhite);
}
// imp2.setSlice(1);
CanvasResizer cr = new CanvasResizer();
stackNew = cr.expandStack(tstack, (xe + 2), (ye + 18), 1, 1);
imp3 = new ImagePlus("Auto Threshold", stackNew);
imp3.updateAndDraw();
MontageMaker mm = new MontageMaker();
mm.makeMontage(imp3, 3, 3, 1.0, 1, (ml - 1), 1, 0, true);
return;
}
} else { // selected a method
if (stackSize > 1 && doIstack) { // whole stack
// if (doIstackHistogram) {// one global histogram
// Object[] result = exec(imp, myMethod, noWhite, noBlack, doIwhite, doIset, doIlog,
// doIstackHistogram );
// }
// else{ // slice by slice
for (int k = 1; k <= stackSize; k++) {
imp.setSlice(k);
Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
}
// }
imp.setSlice(1);
} else { // just one slice
Object[] result = exec(imp, myMethod, radius, par1, par2, doIwhite);
}
// 5 - If all went well, show the image:
// not needed here as the source image is binarised
}
}