private ImagePlus findSurfaceVoxels(final ImagePlus imp) {
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getImageStackSize();
final ImageStack stack = imp.getImageStack();
final ImageStack surfaceStack = new ImageStack(w, h, d);
for (int z = 0; z < d; z++) {
IJ.showStatus("Finding surface voxels");
final byte[] pixels = (byte[]) stack.getPixels(z + 1);
surfaceStack.setPixels(pixels.clone(), z + 1);
final ImageProcessor surfaceIP = surfaceStack.getProcessor(z + 1);
for (int y = 0; y < h; y++) {
checkNeighbours:
for (int x = 0; x < w; x++) {
if (getPixel(stack, x, y, z, w, h, d) == (byte) 0) continue;
for (int nz = -1; nz < 2; nz++) {
final int znz = z + nz;
for (int ny = -1; ny < 2; ny++) {
final int yny = y + ny;
for (int nx = -1; nx < 2; nx++) {
final int xnx = x + nx;
final byte pixel = getPixel(stack, xnx, yny, znz, w, h, d);
if (pixel == (byte) 0) continue checkNeighbours;
}
}
}
// we checked all the neighbours for a 0
// but didn't find one, so this is not a surface voxel
surfaceIP.set(x, y, (byte) 1);
}
}
}
// turn all the 1's into 0's
final int wh = w * h;
for (int z = 0; z < d; z++) {
IJ.showStatus("Finding surface voxels");
final ImageProcessor ip = surfaceStack.getProcessor(z + 1);
for (int i = 0; i < wh; i++) {
if (ip.get(i) == (byte) 1) ip.set(i, (byte) 0);
}
}
final ImagePlus surfaceImp = new ImagePlus("Surface");
surfaceImp.setStack(surfaceStack);
surfaceImp.setCalibration(imp.getCalibration());
return surfaceImp;
}
@Override
public void putLineShort(short[] line, int k, int xdir) {
final int width = ip.getWidth();
final int height = ip.getHeight();
switch (xdir) {
case Ox:
{
if (debug) System.out.println("puting line in Ox");
final int lineno = height;
int offset = k * width;
int z = offset / (width * height);
if (z >= 0 && z < lineno) {
Object aux = ip.getPixels();
try {
System.arraycopy(line, 0, aux, offset, width);
// System.out.println(":"+(offset ));
} catch (Exception e) {
System.out.println("offset" + (offset));
e.printStackTrace();
}
}
break;
}
case Oy:
{
if (debug) System.out.println("puting line in Oy");
final int lineno = width;
k = k % width;
if (k >= 0 && k < lineno) {
try {
for (int y = 0; y < height; y++) {
ip.set(k, y, line[y]);
// System.out.print( "("+ k +" " +y +"),");
}
} catch (Exception e) {
// System.out.println("k "+ k );
e.printStackTrace();
}
}
break;
}
}
}
/**
* Reduce error in thickness quantitation by trimming the one pixel overhang in the thickness map
*
* @param imp Binary input image
* @param impLTC Thickness map
* @param inv true if calculating thickness of background, false for foreground
* @return Thickness map with pixels masked by input image
*/
private ImagePlus trimOverhang(ImagePlus imp, ImagePlus impLTC, boolean inv) {
final int w = imp.getWidth();
final int h = imp.getHeight();
final int d = imp.getImageStackSize();
final ImageStack stack = imp.getImageStack();
final ImageStack mapStack = impLTC.getImageStack();
final int keepValue = inv ? 0 : 255;
ImageProcessor ip = new ByteProcessor(w, h);
ImageProcessor map = new FloatProcessor(w, h);
for (int z = 1; z <= d; z++) {
IJ.showStatus("Masking thickness map...");
IJ.showProgress(z, d);
ip = stack.getProcessor(z);
map = mapStack.getProcessor(z);
for (int y = 0; y < h; y++) {
for (int x = 0; x < w; x++) {
if (ip.get(x, y) != keepValue) map.set(x, y, 0);
}
}
}
return impLTC;
}
public void run(ImageProcessor ip) {
// Ask the user for the sCol value (color saturation factor)
GenericDialog gd = new GenericDialog("sCol Value");
gd.addNumericField("sCol: ", 0.3, 3);
gd.showDialog();
if (gd.wasCanceled()) return;
sCol = gd.getNextNumber();
// Get the mask for the ROI (selected region)
ImageProcessor mask = ip.getMask();
Rectangle roi = ip.getRoi();
int x = (int) roi.getX();
int y = (int) roi.getY();
int w = (int) roi.getWidth();
int h = (int) roi.getHeight();
// IJ.write("mask w: "+mask.getWidth()+", mask h: "+mask.getHeight()+", roi w: "+w+", roi h:
// "+h);
// Create a new mask based on the selected region, but the size is equivalent to the original
// image
ColorProcessor temp = new ColorProcessor(ip.getWidth(), ip.getHeight());
for (int j = 0; j < ip.getHeight(); j++) {
for (int i = 0; i < ip.getWidth(); i++) {
if (j >= y && j < y + h && i >= x && i < x + w) {
// In the mask region
if (mask == null) // When ROI is Rectangle
temp.set(i, j, 1);
else {
if (mask.get(i - x, j - y) != 0) temp.set(i, j, 1);
else temp.set(i, j, 0);
}
} else {
temp.set(i, j, 0);
}
}
}
ip.setMask(temp); // not necessary
mask = temp;
// iterate over all pixels, and desaturate only pixels in ROI
for (int v = 0; v < ip.getHeight(); v++) {
for (int u = 0; u < ip.getWidth(); u++) {
if (mask.get(u, v) != 0) {
// get int-packed color pixel
int c = ip.get(u, v);
// extract RGB components from color pixel
int r = (c & 0xff0000) >> 16;
int g = (c & 0x00ff00) >> 8;
int b = (c & 0x0000ff);
// compute equivalent gray value
double yy = 0.299 * r + 0.587 * g + 0.114 * b;
// linearly interpolate $(yyy) --> (rgb)
r = (int) (yy + sCol * (r - yy));
g = (int) (yy + sCol * (g - yy));
b = (int) (yy + sCol * (b - yy));
// reassemble color pixel
c = ((r & 0xff) << 16) | ((g & 0xff) << 8) | b & 0xff;
ip.set(u, v, c);
}
}
}
imp.updateAndDraw();
}