Exemplo n.º 1
0
def thresholdStackW(imp, low, high):
    i = 1
    stack = imp.getStack()
    depth = imp.getNSlices()
    print "thresholdStackW: depth", depth
    width = stack.getProcessor(i).getWidth()
    height = stack.getProcessor(i).getHeight()
    winput = [None]
    w = Weaver.inline(
            """
            byte[] input = (byte[]) winput.get(0);
            byte[] output = new byte[input.length];
            for (int i=0; i<input.length; i++) {
                if (input[i] < low || input[i] > high){
                    output[i] = (byte)0;
                } else {
                    output[i] = (byte)255;
                }
            }
            return output;
            """,
            {"winput":winput, "low":low, "high":high})
    stackout = ImageStack(width, height)
    for k in range(1, depth+1):
        ip = stack.getProcessor(k)
        winput[0] = ip.getPixels()
        pixels = w.call()
        ipout = ByteProcessor(width, height)
        ipout.setPixels(pixels)
        stackout.addSlice(ipout)
        imp.setStack(stackout)
def Inline(arrays):
    return Weaver.inline(
        """
		int[] pixelst = (int[])arrays.get(0);
		int[] pixelsd = (int[])arrays.get(1);
		double sum = 0;
		for (int i=0; i<pixelst.length; i++) {
			int t = pixelst[i];
			int d = pixelsd[i];
			int red = ((t >> 16)&0xff) - ((d >> 16)&0xff);
			int green = ((t >> 8)&0xff) - ((d >> 8)&0xff);
			int blue = (t&0xff) - (d&0xff);
			//sum += Math.sqrt(red * red + green * green + blue * blue);
			sum += red * red + green * green + blue * blue;
		}
		return sum;
		""", {"arrays": arrays})
def Inline(arrays):
	return Weaver.inline(
		"""
		int[] pixelst = (int[])arrays.get(0);
		int[] pixelsd = (int[])arrays.get(1);
		double sum = 0;
		for (int i=0; i<pixelst.length; i++) {
			int t = pixelst[i];
			int d = pixelsd[i];
			int red = ((t >> 16)&0xff) - ((d >> 16)&0xff);
			int green = ((t >> 8)&0xff) - ((d >> 8)&0xff);
			int blue = (t&0xff) - (d&0xff);
			//sum += Math.sqrt(red * red + green * green + blue * blue);
			sum += red * red + green * green + blue * blue;
		}
		return sum;
		""",
		{"arrays" : arrays})
            imap(FloatType.getRealFloat,
                 hsc))  # ~1.5x faster than for t in hsc: s += t.getRealFloat
        #intensities2.append(float(s) / size)

t2 = System.currentTimeMillis()

print "Elapsed time:", (t2 - t1), "ms"

w = Weaver.inline(
    """
  double sum = 0;
  //final net.imglib2.Cursor<net.imglib2.type.numeric.real.FloatType> c = (net.imglib2.Cursor<net.imglib2.type.numeric.real.FloatType>) hsc;
  final Cursor<FloatType> c = (Cursor<FloatType>) hsc;
  while (c.hasNext()) {
  	c.fwd();
  	sum += c.get().getRealFloat();
  }
  // Fails, for some reason
  //for (final net.imglib2.type.numeric.real.FloatType t : c) {
  //  sum += t.getRealFloat();
  //}
  return sum;
  """, {"hsc": hsc}, Double, True, [FloatType, Cursor])

t3 = System.currentTimeMillis()

for i in xrange(100):
    for peak in peaks:
        hsc.updateCenter([int(peak[0]), int(peak[1]), int(peak[2])])
        #s = sum(imap(FloatType.getRealFloat, hsc))
        s = w.call()
Exemplo n.º 5
0
    print event


def update_roi_mappings():
    global roi_in
    global roi_ni
    for i in range(roimgr.getCount()):
        name = roimgr.getName(i)
        roi_in.append(name)
        roi_ni[name] = i

wcode = Weaver.inline(
	"""
javax.swing.AbstractListModel m = new javax.swing.AbstractListModel() {
    String[] strings = { "Item 1", "Item 2", "Item 3", "Item 4", "Item 5" };
    public int getSize() { return strings.length; }
    public Object getElementAt(int i) { return strings[i]; }
};
return m;
        """, {}, javax.swing.AbstractListModel)
print "Weaver created!"
listmodel = wcode.call()
print "Weaver called!"

roimgr = RoiManager.getInstance()
if roimgr is None:
  print "No ROIs defined."
  sys.exit(0)
roi_ni = {}
roi_in = []
update_roi_mappings()
from fiji.scripting import Weaver
from ij import IJ
from ij import ImagePlus
from ij import ImageStack
 
# The currently open image, an 8-bit stack
imp = IJ.openImage("http://imagej.net/images/bat-cochlea-volume.zip")
 
slices = [None, None]
 
w = Weaver.inline(
    """
    byte[] pix1 = (byte[]) slices.get(0);
    byte[] pix2 = (byte[]) slices.get(1);
 
    byte[] xor = new byte[pix1.length];
    for (int i=0; i<pix1.length; i++) {
        xor[i] = (byte)(pix1[i] ^ pix2[i]);
    }
    return xor;
    """,
    {"slices" : slices})
 
stack = imp.getStack()
stackXOR = ImageStack(stack.width, stack.height)
 
for i in range(2, imp.getNSlices()+1):
  # Put the pixel arrays into the pre-made list
  slices[0] = stack.getPixels(i-1)
  slices[1] = stack.getPixels(i)
  # Invoke native code
  stackXOR.addSlice( str(i-1), w.call() )