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 setStackDisplayRange(ImagePlus imp) {
ImageStack stack = imp.getStack();
double min = Double.MAX_VALUE;
double max = -Double.MAX_VALUE;
int n = stack.getSize();
for (int i = 1; i <= n; i++) {
if (!silentMode) IJ.showStatus("Calculating stack min and max: " + i + "/" + n);
ImageProcessor ip = stack.getProcessor(i);
ip.resetMinAndMax();
if (ip.getMin() < min) min = ip.getMin();
if (ip.getMax() > max) max = ip.getMax();
}
imp.getProcessor().setMinAndMax(min, max);
imp.updateAndDraw();
}
void borderstack(final ImageStack stack1, int nb, byte[] b) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final byte[][] bord = new byte[dimZ][nb];
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi < dimZ;
superi = ai.getAndIncrement()) {
int k = superi;
ImageProcessor ip = stack1.getProcessor(k + 1);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int val = (int) (ip.getPixelValue(i, j));
if ((val != 0)
&& (i == 0
|| j == 0
|| k == 0
|| i == dimX - 1
|| j == dimY - 1
|| k == dimZ - 1))
// bord[k][val-2]=1;
bord[k][val - 1] = 1;
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
b[j] *= (1 - bord[i][j]);
}
}
for (int j = 0; j < nb; j++) {
b[j] = (byte) (1 - b[j]);
}
}
public void showRois3D() {
registerActiveImage();
if (currentImage == null) return;
// verifier que l'image active a les memes dimentions
Object[] os = this.list.getSelectedValues();
if (os.length == 1) {
mcib3d.geom.Object3D o = ((Object3DGui) os[0]).getObject3D();
currentImage.setSlice((o.getZmax() + o.getZmin()) / 2 + 1);
}
int nSlices = currentImage.getNSlices();
currentROIs = new HashMap<Integer, Roi>(nSlices);
// stores the roi mask to save memory..
if (roiMask == null || !roiMask.sameDimentions(currentImage)) {
roiMask = new ImageByte("mask", currentImage.getWidth(), currentImage.getHeight(), nSlices);
} else {
roiMask.erase();
}
ImageStack maskStack = roiMask.getImageStack();
Object3DGui obj;
for (Object o : os) {
obj = (Object3DGui) o;
obj.getObject3D().draw(maskStack, 255);
}
// roiMask.show();
for (int i = 1; i <= nSlices; i++) {
ImagePlus im = new ImagePlus("mask", maskStack.getProcessor(i));
im.getProcessor().setThreshold(1, 255, ImageProcessor.NO_LUT_UPDATE);
ThresholdToSelection tts = new ThresholdToSelection();
tts.setup("", im);
tts.run(im.getProcessor());
Roi r = im.getRoi();
if (r != null) currentROIs.put(i, r);
}
updateRoi();
}
public int calculnb(final ImageStack stack1) {
final AtomicInteger ai = new AtomicInteger(1);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final int[] value = new int[dimZ];
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi <= dimZ;
superi = ai.getAndIncrement()) {
int current = superi;
ImageProcessor ip = stack1.getProcessor(current);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int val = (int) (ip.getPixelValue(i, j));
if (val > value[current - 1]) value[current - 1] = val;
}
}
}
}
};
}
startAndJoin(threads);
int val = 0;
for (int i = 0; i < dimZ; i++) {
if (val < value[i]) val = value[i];
}
return val;
}
void calculvolumestack(final ImageStack stack1, int nb, int v[]) {
final AtomicInteger ai = new AtomicInteger(1);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final int[][] vol = new int[dimZ][nb];
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi <= dimZ;
superi = ai.getAndIncrement()) {
int current = superi;
ImageProcessor ip = stack1.getProcessor(current);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int val = (int) (ip.getPixelValue(i, j));
// if (val!=0) vol[current-1][val-2]++;
if (val != 0) vol[current - 1][val - 1]++;
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
v[j] += vol[i][j];
}
}
}
/** Opens a stack of images. */
ImagePlus openStack(ColorModel cm, boolean show) {
ImageStack stack = new ImageStack(fi.width, fi.height, cm);
long skip = fi.getOffset();
Object pixels;
try {
ImageReader reader = new ImageReader(fi);
InputStream is = createInputStream(fi);
if (is == null) return null;
IJ.resetEscape();
for (int i = 1; i <= fi.nImages; i++) {
if (!silentMode) IJ.showStatus("Reading: " + i + "/" + fi.nImages);
if (IJ.escapePressed()) {
IJ.beep();
IJ.showProgress(1.0);
silentMode = false;
return null;
}
pixels = reader.readPixels(is, skip);
if (pixels == null) break;
stack.addSlice(null, pixels);
skip = fi.gapBetweenImages;
if (!silentMode) IJ.showProgress(i, fi.nImages);
}
is.close();
} catch (Exception e) {
IJ.log("" + e);
} catch (OutOfMemoryError e) {
IJ.outOfMemory(fi.fileName);
stack.trim();
}
if (!silentMode) IJ.showProgress(1.0);
if (stack.getSize() == 0) return null;
if (fi.sliceLabels != null && fi.sliceLabels.length <= stack.getSize()) {
for (int i = 0; i < fi.sliceLabels.length; i++) stack.setSliceLabel(fi.sliceLabels[i], i + 1);
}
ImagePlus imp = new ImagePlus(fi.fileName, stack);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (show) imp.show();
imp.setFileInfo(fi);
setCalibration(imp);
ImageProcessor ip = imp.getProcessor();
if (ip.getMin() == ip.getMax()) // find stack min and max if first slice is blank
setStackDisplayRange(imp);
if (!silentMode) IJ.showProgress(1.0);
silentMode = false;
return imp;
}
/** Opens the image. Displays it if 'show' is true. Returns an ImagePlus object if successful. */
public ImagePlus open(boolean show) {
ImagePlus imp = null;
Object pixels;
ProgressBar pb = null;
ImageProcessor ip;
ColorModel cm = createColorModel(fi);
if (fi.nImages > 1) {
return openStack(cm, show);
}
switch (fi.fileType) {
case FileInfo.GRAY8:
case FileInfo.COLOR8:
case FileInfo.BITMAP:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ByteProcessor(width, height, (byte[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.GRAY16_SIGNED:
case FileInfo.GRAY16_UNSIGNED:
case FileInfo.GRAY12_UNSIGNED:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ShortProcessor(width, height, (short[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.GRAY32_INT:
case FileInfo.GRAY32_UNSIGNED:
case FileInfo.GRAY32_FLOAT:
case FileInfo.GRAY24_UNSIGNED:
case FileInfo.GRAY64_FLOAT:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new FloatProcessor(width, height, (float[]) pixels, cm);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.RGB:
case FileInfo.BGR:
case FileInfo.ARGB:
case FileInfo.ABGR:
case FileInfo.BARG:
case FileInfo.RGB_PLANAR:
pixels = readPixels(fi);
if (pixels == null) return null;
ip = new ColorProcessor(width, height, (int[]) pixels);
imp = new ImagePlus(fi.fileName, ip);
break;
case FileInfo.RGB48:
case FileInfo.RGB48_PLANAR:
boolean planar = fi.fileType == FileInfo.RGB48_PLANAR;
Object[] pixelArray = (Object[]) readPixels(fi);
if (pixelArray == null) return null;
ImageStack stack = new ImageStack(width, height);
stack.addSlice("Red", pixelArray[0]);
stack.addSlice("Green", pixelArray[1]);
stack.addSlice("Blue", pixelArray[2]);
imp = new ImagePlus(fi.fileName, stack);
imp.setDimensions(3, 1, 1);
if (planar) imp.getProcessor().resetMinAndMax();
imp.setFileInfo(fi);
int mode = CompositeImage.COMPOSITE;
if (fi.description != null) {
if (fi.description.indexOf("mode=color") != -1) mode = CompositeImage.COLOR;
else if (fi.description.indexOf("mode=gray") != -1) mode = CompositeImage.GRAYSCALE;
}
imp = new CompositeImage(imp, mode);
if (!planar && fi.displayRanges == null) {
for (int c = 1; c <= 3; c++) {
imp.setPosition(c, 1, 1);
imp.setDisplayRange(minValue, maxValue);
}
imp.setPosition(1, 1, 1);
}
break;
}
imp.setFileInfo(fi);
setCalibration(imp);
if (fi.info != null) imp.setProperty("Info", fi.info);
if (fi.sliceLabels != null && fi.sliceLabels.length == 1 && fi.sliceLabels[0] != null)
imp.setProperty("Label", fi.sliceLabels[0]);
if (show) imp.show();
return imp;
}
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 boitestack(
final ImageStack stack1,
final int nb,
final double[] xg,
final double[] yg,
final double[] zg,
final double[][][] dir,
double[][] lmin,
double[][] lmax) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final double[][][] lmint = new double[dimZ][nb][3];
final double[][][] lmaxt = new double[dimZ][nb][3];
for (int k = 0; k < nb; k++) {
lmin[k][0] = 100000;
lmin[k][1] = 100000;
lmin[k][2] = 100000;
lmax[k][0] = -100000;
lmax[k][1] = -100000;
lmax[k][2] = -100000;
}
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi < dimZ;
superi = ai.getAndIncrement()) {
int k = superi;
ImageProcessor ip = stack1.getProcessor(k + 1);
for (int l = 0; l < nb; l++) {
lmint[k][l][0] = 100000;
lmint[k][l][1] = 100000;
lmint[k][l][2] = 100000;
lmaxt[k][l][0] = -100000;
lmaxt[k][l][1] = -100000;
lmaxt[k][l][2] = -100000;
}
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int pix = (int) (ip.getPixelValue(i, j));
if (pix != 0) {
// double v1 =
// (i-xg[pix-2])*dir[0][0][pix-2]+(j-yg[pix-2])*dir[1][0][pix-2]+(k-zg[pix-2])*dir[2][0][pix-2];
// double v2 =
// (i-xg[pix-2])*dir[0][1][pix-2]+(j-yg[pix-2])*dir[1][1][pix-2]+(k-zg[pix-2])*dir[2][1][pix-2];
// double v3 =
// (i-xg[pix-2])*dir[0][2][pix-2]+(j-yg[pix-2])*dir[1][2][pix-2]+(k-zg[pix-2])*dir[2][2][pix-2];
// if (v1<lmint[k][pix-2][0]) lmint[k][pix-2][0]=v1;
// if (v1>lmaxt[k][pix-2][0]) lmaxt[k][pix-2][0]=v1;
// if (v2<lmint[k][pix-2][1]) lmint[k][pix-2][1]=v2;
// if (v2>lmaxt[k][pix-2][1]) lmaxt[k][pix-2][1]=v2;
// if (v3<lmint[k][pix-2][2]) lmint[k][pix-2][2]=v3;
// if (v3>lmaxt[k][pix-2][2]) lmaxt[k][pix-2][2]=v3;
double v1 =
(i - xg[pix - 1]) * dir[0][0][pix - 1]
+ (j - yg[pix - 1]) * dir[1][0][pix - 1]
+ (k - zg[pix - 1]) * dir[2][0][pix - 1];
double v2 =
(i - xg[pix - 1]) * dir[0][1][pix - 1]
+ (j - yg[pix - 1]) * dir[1][1][pix - 1]
+ (k - zg[pix - 1]) * dir[2][1][pix - 1];
double v3 =
(i - xg[pix - 1]) * dir[0][2][pix - 1]
+ (j - yg[pix - 1]) * dir[1][2][pix - 1]
+ (k - zg[pix - 1]) * dir[2][2][pix - 1];
if (v1 < lmint[k][pix - 1][0]) lmint[k][pix - 1][0] = v1;
if (v1 > lmaxt[k][pix - 1][0]) lmaxt[k][pix - 1][0] = v1;
if (v2 < lmint[k][pix - 1][1]) lmint[k][pix - 1][1] = v2;
if (v2 > lmaxt[k][pix - 1][1]) lmaxt[k][pix - 1][1] = v2;
if (v3 < lmint[k][pix - 1][2]) lmint[k][pix - 1][2] = v3;
if (v3 > lmaxt[k][pix - 1][2]) lmaxt[k][pix - 1][2] = v3;
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
for (int l = 0; l < 3; l++) {
if (lmint[i][j][l] < lmin[j][l]) lmin[j][l] = lmint[i][j][l];
if (lmaxt[i][j][l] > lmax[j][l]) lmax[j][l] = lmaxt[i][j][l];
}
}
lmint[i] = null;
lmaxt[i] = null;
}
}
void calculinertiestack(
final ImageStack stack1,
int nb,
final double[] xg,
final double[] yg,
final double[] zg,
double[][][] I) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final double[][][][] inert = new double[dimZ][nb][3][3];
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi < dimZ;
superi = ai.getAndIncrement()) {
int k = superi;
ImageProcessor ip = stack1.getProcessor(k + 1);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int pix = (int) (ip.getPixelValue(i, j));
if (pix != 0) {
//
// inert[k][pix-2][0][0]+=(i-yg[pix-2])*(i-yg[pix-2])+(k-zg[pix-2])*(k-zg[pix-2])+1.0/6.0;
// inert[k][pix-2][0][1]-=(j-xg[pix-2])*(i-yg[pix-2]);
// inert[k][pix-2][0][2]-=(j-xg[pix-2])*(k-zg[pix-2]);
//
// inert[k][pix-2][1][1]+=(j-xg[pix-2])*(j-xg[pix-2])+(k-zg[pix-2])*(k-zg[pix-2])+1.0/6.0;
// inert[k][pix-2][1][2]-=(i-yg[pix-2])*(k-zg[pix-2]);
//
// inert[k][pix-2][2][2]+=(j-xg[pix-2])*(j-xg[pix-2])+(i-yg[pix-2])*(i-yg[pix-2])+1.0/6.0;
inert[k][pix - 1][0][0] +=
(j - yg[pix - 1]) * (j - yg[pix - 1])
+ (k - zg[pix - 1]) * (k - zg[pix - 1])
+ 1.0 / 6.0;
inert[k][pix - 1][0][1] -= (i - xg[pix - 1]) * (j - yg[pix - 1]);
inert[k][pix - 1][0][2] -= (i - xg[pix - 1]) * (k - zg[pix - 1]);
inert[k][pix - 1][1][1] +=
(i - xg[pix - 1]) * (i - xg[pix - 1])
+ (k - zg[pix - 1]) * (k - zg[pix - 1])
+ 1.0 / 6.0;
inert[k][pix - 1][1][2] -= (j - yg[pix - 1]) * (k - zg[pix - 1]);
inert[k][pix - 1][2][2] +=
(i - xg[pix - 1]) * (i - xg[pix - 1])
+ (j - yg[pix - 1]) * (j - yg[pix - 1])
+ 1.0 / 6.0;
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
for (int l = 0; l < 3; l++) {
for (int m = 0; m <= l; m++) {
I[l][m][j] += inert[i][j][l][m];
}
}
}
inert[i] = null;
}
for (int j = 0; j < nb; j++) {
I[1][0][j] = I[0][1][j];
I[2][0][j] = I[0][2][j];
I[2][1][j] = I[1][2][j];
}
}
void calculcgstack(
final ImageStack stack1,
int nb,
final int[] v,
final double[] xg,
final double[] yg,
final double[] zg) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final int[][] vol = new int[dimZ][nb];
final int[][] tmpxg = new int[dimZ][nb];
final int[][] tmpyg = new int[dimZ][nb];
final int[][] tmpzg = new int[dimZ][nb];
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi < dimZ;
superi = ai.getAndIncrement()) {
int k = superi;
ImageProcessor ip = stack1.getProcessor(k + 1);
for (int j = 0; j < dimY; j++) {
for (int i = 0; i < dimX; i++) {
int pix = (int) (ip.getPixelValue(i, j));
if (pix != 0) {
// tmpxg[k][pix-2] += j;
// tmpyg[k][pix-2] += i;
// tmpzg[k][pix-2] += k;
// vol[k][pix-2]++;
tmpxg[k][pix - 1] += i;
tmpyg[k][pix - 1] += j;
tmpzg[k][pix - 1] += k;
vol[k][pix - 1]++;
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
v[j] += vol[i][j];
xg[j] += tmpxg[i][j];
yg[j] += tmpyg[i][j];
zg[j] += tmpzg[i][j];
}
}
for (int i = 0; i < nb; i++) {
xg[i] = (1.0 * xg[i] / v[i]);
yg[i] = (1.0 * yg[i] / v[i]);
zg[i] = (1.0 * zg[i] / v[i]);
}
}
void calculsurfacemarch3stack(final ImageStack stack1, int nb, final double[] tri, double[] s2) {
final AtomicInteger ai = new AtomicInteger(0);
final int dimX = stack1.getWidth();
final int dimY = stack1.getHeight();
final int dimZ = stack1.getSize();
final double[][] surf = new double[dimZ][nb];
for (int ithread = 0; ithread < threads.length; ithread++) {
// Concurrently run in as many threads as CPUs
threads[ithread] =
new Thread() {
public void run() {
for (int superi = ai.getAndIncrement();
superi < dimZ - 1;
superi = ai.getAndIncrement()) {
int k = superi;
ImageProcessor ip1, ip2;
ip1 = stack1.getProcessor(k + 1);
ip2 = stack1.getProcessor(k + 2);
for (int j = 0; j < dimY - 1; j++) {
for (int i = 0; i < dimX - 1; i++) {
int[] p = new int[8];
int p1, p2, p3, p4, p5, p6, p7, p8, ptot;
int[] nontab = new int[8];
ptot = (short) 0;
p[0] = (int) ip1.getPixelValue(i, j);
p[1] = (int) ip1.getPixelValue(i, j + 1);
p[2] = (int) ip2.getPixelValue(i, j);
p[3] = (int) ip2.getPixelValue(i, j + 1);
p[4] = (int) ip1.getPixelValue(i + 1, j);
p[5] = (int) ip1.getPixelValue(i + 1, j + 1);
p[6] = (int) ip2.getPixelValue(i + 1, j);
p[7] = (int) ip2.getPixelValue(i + 1, j + 1);
int pixcoul = 0;
for (int l = 0; l < 8; l++) nontab[l] = 0;
int cpt = 0;
// look for different colors
for (int l = 0; l < 8; l++) {
if (p[l] != 0 && appart(p[l], nontab, 8) == 1) {
nontab[cpt] = p[l];
cpt++;
}
}
for (int mm = 0; mm < cpt; mm++) {
p1 = 0;
p2 = 0;
p3 = 0;
p4 = 0;
p5 = 0;
p6 = 0;
p7 = 0;
p8 = 0;
if (p[0] != 0 && p[0] == nontab[mm]) {
pixcoul = nontab[mm];
p1 = 1;
}
if (p[1] != 0 && p[1] == nontab[mm]) {
pixcoul = nontab[mm];
p2 = 4;
}
if (p[2] != 0 && p[2] == nontab[mm]) {
pixcoul = nontab[mm];
p3 = 2;
}
if (p[3] != 0 && p[3] == nontab[mm]) {
pixcoul = nontab[mm];
p4 = 8;
}
if (p[4] != 0 && p[4] == nontab[mm]) {
pixcoul = nontab[mm];
p5 = 16;
}
if (p[5] != 0 && p[5] == nontab[mm]) {
pixcoul = nontab[mm];
p6 = 64;
}
if (p[6] != 0 && p[6] == nontab[mm]) {
pixcoul = nontab[mm];
p7 = 32;
}
if (p[7] != 0 && p[7] == nontab[mm]) {
pixcoul = nontab[mm];
p8 = 128;
}
ptot = (p1 + p2 + p3 + p4 + p5 + p6 + p7 + p8);
if (pixcoul != 0) {
surf[k][(int) (pixcoul - 1)] += tri[(int) (ptot)];
// surf[k][(int)(pixcoul-2)]+=tri[(int)(ptot)];
}
}
}
}
}
}
};
}
startAndJoin(threads);
for (int i = 0; i < dimZ; i++) {
for (int j = 0; j < nb; j++) {
s2[j] += surf[i][j];
}
}
}