def findPeaks(img4D, params):
"""
img4D: a 4D RandomAccessibleInterval
params["frames"]: the number of consecutive time points to average
towards detecting peaks with difference of Gaussian.
Returns a list of lists of peaks found, one list per time point.
"""
frames = params["frames"]
# Work image: the current sum
sum3D = ArrayImgs.unsignedLongs([img4D.dimension(d) for d in [0, 1, 2]])
peaks = []
# Sum of the first set of frames
compute(add([Views.hyperSlice(img4D, 3, i) for i in xrange(frames)])).into(sum3D)
# Extract nuclei from first sum3D
peaks.append(doGPeaks(sum3D, params))
# Running sums: subtract the first and add the last
for i in xrange(frames, img4D.dimension(3), 1):
compute(add(sub(sum3D,
Views.hyperSlice(img4D, 3, i - frames)),
Views.hyperSlice(img4D, 3, i))) \
.into(sum3D)
# Extract nuclei from sum4D
peaks.append(doGPeaks(sum3D, params))
return peaks
def testASMLongs():
img2 = ArrayImgs.unsignedLongs(dimensions)
ImgUtil.copy(
ImgView.wrap(
Converters.convertRandomAccessibleIterableInterval(
img1s, sampler_conv_longs), img1.factory()), img2)
from net.imglib2.algorithm.math.ImgMath import compute, block, div, offset, add
from net.imglib2.img.display.imagej import ImageJFunctions as IL
from net.imglib2.img.array import ArrayImgs
from net.imglib2.type.numeric.real import FloatType
from net.imglib2.view import Views
from net.imglib2.util import Intervals
from ij import IJ
imp = IJ.getImage() # an 8-bit image
img = IL.wrap(imp)
# Create the integral image of an 8-bit input, stored as 64-bit
target = ArrayImgs.unsignedLongs(Intervals.dimensionsAsLongArray(img))
# Copy input onto the target image
compute(img).into(target)
# Extend target with zeros, so that we can read at coordinate -1
imgE = Views.extendZero(target)
# Integrate every dimension, cummulatively by writing into
# a target image that is also the input
for d in xrange(img.numDimensions()):
coord = [0] * img.numDimensions() # array of zeros
coord[d] = -1
# Cummulative sum along the current dimension
# Note that instead of the ImgMath offset op,
# we could have used Views.translate(Views.extendZero(target), [1, 0]))
# (Notice though the sign change in the translation)
integral = add(target, offset(imgE, coord))
compute(integral).into(target)
# The target is the integral image
integralImg = target
