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()
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() )