from net.imglib2.img.display.imagej import ImageJFunctions as IL
from net.imglib2.view import Views
from ij import IJ, ImagePlus
# Fetch an RGB image stack (or any RGB image with more than 1 dimension)
imp_rgb = IJ.getImage(
) # IJ.openImage("http://imagej.nih.gov/ij/images/flybrain.zip")
img = IL.wrap(imp_rgb) # an ARGBType Img
red = Converters.argbChannel(img, 1) # a view of the ARGB red channel
# Project the last dimension using the max function
last_d = red.numDimensions() - 1
op = maximum(
[Views.hyperSlice(red, last_d, i) for i in xrange(red.dimension(last_d))])
img_max_red = compute(op).intoArrayImg()
IL.wrap(img_max_red, "max projection of the red channel)").show()
# Now project all 3 color channels and compose an RGB image
last_dim_index = img.numDimensions() - 1
channel_stacks = [[
Views.hyperSlice(Converters.argbChannel(img, channel_index),
last_dim_index, slice_index)
for slice_index in xrange(img.dimension(last_dim_index))
] for channel_index in [1, 2, 3]] # 1: red, 2: green, 3: blue
channels = Views.stack([maximum(cs).view() for cs in channel_stacks])
max_rgb = Converters.mergeARGB(channels, ColorChannelOrder.RGB)
IL.wrap(max_rgb, "max RGB").show()
from net.imglib2.img.array import ArrayImgs
from net.imglib2.img.display.imagej import ImageJFunctions as IL
from net.imglib2.view import Views
# Fetch an RGB image stack
imp_rgb = IJ.getImage(
) # IJ.openImage("http://imagej.nih.gov/ij/images/flybrain.zip")
img = IL.wrap(imp_rgb) # an ARGBType Img
# Color channel views
red, green, blue = (Converters.argbChannel(img, c) for c in [1, 2, 3])
# ImgLib1 scripting gamma function
# return Min(255, Max(0, Multiply(Exp(Multiply(gamma, Log(Divide(channel, 255)))), 255)))
gamma = 0.5
def op(channel):
return minimum(
255, maximum(0, mul(exp(mul(gamma, log(div(channel, 255)))), 255)))
img_gamma = Converters.mergeARGB(
Views.stack(
op(red).viewDouble(),
op(green).viewDouble(),
op(blue).viewDouble()), ColorChannelOrder.RGB)
IL.wrap(img_gamma, "gamma 0.5").show()
sliceInterval = FinalInterval([interval2.dimension(0), interval2.dimension(1)])
slices2 = []
for index in xrange(img1.dimension(2)):
# One single 2D RGB slice
imgSlice1 = Views.hyperSlice(img1, 2, index)
# Views of the 3 color channels, as extended and interpolatable
channels = [
Views.interpolate(
Views.extendZero(Converters.argbChannel(imgSlice1, i)),
NLinearInterpolatorFactory()) for i in [1, 2, 3]
]
# ARGBType 2D view of the transformed color channels
imgSlice2 = Converters.mergeARGB(
Views.stack(
Views.interval(RealViews.transform(channel, transform),
sliceInterval)
for channel in channels), ColorChannelOrder.RGB)
slices2.append(imgSlice2)
# Transformed view
viewImg2 = Views.stack(slices2)
# Materialized image
img2 = ArrayImgs.argbs(Intervals.dimensionsAsLongArray(interval2))
ImgUtil.copy(viewImg2, img2)
imp4 = IL.wrap(img2, "imglib2-transformed RGB (pull)")
imp4.show()
# Fourth approach: pull (CORRECT!), and much faster (delegates pixel-wise operations
# to java libraries and delegates RGB color handling altogether)