def translate_single_stack_using_imglib2(imp, dx, dy, dz):
# wrap into a float imglib2 and translate
# conversion into float is necessary due to "overflow of n-linear interpolation due to accuracy limits of unsigned bytes"
# see: https://github.com/fiji/fiji/issues/136#issuecomment-173831951
img = ImagePlusImgs.from(imp.duplicate())
extended = Views.extendZero(img)
converted = Converters.convert(extended, RealFloatSamplerConverter())
interpolant = Views.interpolate(converted, NLinearInterpolatorFactory())
# translate
if imp.getNDimensions()==3:
transformed = RealViews.affine(interpolant, Translation3D(dx, dy, dz))
elif imp.getNDimensions()==2:
transformed = RealViews.affine(interpolant, Translation2D(dx, dy))
else:
IJ.log("Can only work on 2D or 3D stacks")
return None
cropped = Views.interval(transformed, img)
# wrap back into bit depth of input image and return
bd = imp.getBitDepth()
if bd==8:
return(ImageJFunctions.wrapUnsignedByte(cropped,"imglib2"))
elif bd == 16:
return(ImageJFunctions.wrapUnsignedShort(cropped,"imglib2"))
elif bd == 32:
return(ImageJFunctions.wrapFloat(cropped,"imglib2"))
else:
return None
def translate_single_stack_using_imglib2(imp, dx, dy, dz):
# wrap into a float imglib2 and translate
# conversion into float is necessary due to "overflow of n-linear interpolation due to accuracy limits of unsigned bytes"
# see: https://github.com/fiji/fiji/issues/136#issuecomment-173831951
img = ImagePlusImgs.from(imp.duplicate())
extended = Views.extendBorder(img)
converted = Converters.convert(extended, RealFloatSamplerConverter())
interpolant = Views.interpolate(converted, NLinearInterpolatorFactory())
# translate
if imp.getNDimensions()==3:
transformed = RealViews.affine(interpolant, Translation3D(dx, dy, dz))
elif imp.getNDimensions()==2:
transformed = RealViews.affine(interpolant, Translation2D(dx, dy))
else:
IJ.log("Can only work on 2D or 3D stacks")
return None
cropped = Views.interval(transformed, img)
# wrap back into bit depth of input image and return
bd = imp.getBitDepth()
if bd==8:
return(ImageJFunctions.wrapUnsignedByte(cropped,"imglib2"))
elif bd == 16:
return(ImageJFunctions.wrapUnsignedShort(cropped,"imglib2"))
elif bd == 32:
return(ImageJFunctions.wrapFloat(cropped,"imglib2"))
else:
return None
def translate_using_imglib2(imp, dx, dy, dz):
print "imp channels",imp.getNChannels()
# todo:
# if multiple channels use Duplicator to translate each channel individually
## wrap
# http://javadoc.imagej.net/ImgLib2/net/imglib2/img/imageplus/ImagePlusImg.html
img = ImagePlusImgs.from(imp.duplicate())
print "dimensions:",img.numDimensions()
print img.getChannels()
## prepare image
print "img",img
ddd
extended = Views.extendBorder(img)
#print "extended",extended
#print "extended",extended.dimension(1)
dims = zeros(4, 'l')
img.dimensions(dims)
print "dims",dims
converted = Converters.convert(extended, RealFloatSamplerConverter())
composite = Views.collapseReal(converted, imp.getNChannels())
print "composite",composite
interpolant = Views.interpolate(composite, NLinearInterpolatorFactory())
#print "interpolant",interpolant
transformed = RealViews.affine(interpolant, Translation3D(dx, dy, dz))
print "transformed", transformed
cropped = Views.interval(transformed, img)
print "cropped.numDimensions()", cropped.numDimensions()
print "cropped",cropped
## wrap back and return
bd = imp.getBitDepth()
# maybe simply wrap works?
if bd==8:
return(ImageJFunctions.wrapUnsignedByte(cropped,"imglib2"))
elif bd == 16:
return(ImageJFunctions.wrapUnsignedShort(cropped,"imglib2"))
elif bd == 32:
return(ImageJFunctions.wrapFloat(cropped,"imglib2"))
else:
return None
affine.rotate(angle_rad)
affine.translate(center)
# Get the interpolator
interpolator = LanczosInterpolatorFactory()
# Iterate over all frame in the stack
axis = Axes.TIME
output = []
for d in range(data.dimension(axis)):
# Get the current frame
frame = crop_along_one_axis(ops, data, [d, d], "TIME")
# Get the interpolate view of the frame
extended = ops.run("transform.extendZeroView", frame)
interpolant = ops.run("transform.interpolateView", extended, interpolator)
# Apply the transformation to it
rotated = RealViews.affine(interpolant, affine)
# Set the intervals
rotated = ops.transform().offsetView(rotated, frame)
output.append(rotated)
output = Views.stack(output)
# Create output Dataset
output = ds.create(output)
affine.rotate(angle_rad)
affine.translate(center)
# Get the interpolator
interpolator = LanczosInterpolatorFactory()
# Iterate over all frame in the stack
axis = Axes.TIME
output = []
for d in range(data.dimension(axis)):
# Get the current frame
frame = crop_along_one_axis(ops, data, [d, d], "TIME")
# Get the interpolate view of the frame
extended = ops.run("transform.extendZeroView", frame)
interpolant = ops.run("transform.interpolateView", extended, interpolator)
# Apply the transformation to it
rotated = RealViews.affine(interpolant, affine)
# Set the intervals
rotated = ops.transform().offset(rotated, frame)
output.append(rotated)
output = Views.stack(output)
# Create output Dataset
output = ds.create(output)
# create an empty image
phantom = ops.create().img([xSize, ySize, zSize])
# make phantom an ImgPlus
phantom = ops.create().imgPlus(phantom)
location = Point(phantom.numDimensions())
location.setPosition([xSize / 2, ySize / 2, zSize / 2])
hyperSphere = HyperSphere(phantom, location, 10)
for value in hyperSphere:
value.setReal(100)
phantom.setName("phantom")
affine = AffineTransform3D()
affine.scale(1, 1, 0.4)
interpolatedImg = Views.interpolate(Views.extendZero(phantom),
NLinearInterpolatorFactory())
phantom = Views.interval(
Views.raster(RealViews.affine(interpolatedImg, affine)),
Intervals.createMinMax(0, 0, 18, 255, 255, 82))
# make phantom an ImgPlus
phantom = ops.create().imgPlus(ops.copy().iterableInterval(
Views.zeroMin(phantom)))
phantom.setName('phantom')
