# # This example Jython script shows how to # reslice an image in the GPU. # # # Author: Robert Haase, [email protected] # October 2019 ########################################## from net.haesleinhuepf.clij import CLIJ; from ij import IJ; IJ.run("Close All"); # init CLIJ and GPU clij = CLIJ.getInstance(); # get an example data set imp = IJ.openImage("http://imagej.nih.gov/ij/images/t1-head.zip"); imp.show(); imp.setRoi(86,3,100,250); imp = imp.crop("25-74"); imp.show(); # push it to the GPU src = clij.push(imp); # generate the output-image on the GPU with thee right size dst = clij.create([src.getWidth(), src.getDepth(), src.getHeight()], src.getNativeType()); # Reslice on GPU clij.op().resliceTop(src, dst);
# load single image
#imp = IJ.openImage("C:/structure/data/florence/000300.raw.tif");
#IJ.run(imp, "32-bit", "");
#imp.show();
# load sequence
IJ.run("Image Sequence...", "open=[" + data_folder + "] sort use")
IJ.run(
"Stack to Hyperstack...",
"order=xyczt(default) channels=1 slices=" + str(number_of_z_planes) +
" frames=" + str(number_of_images) + " display=Color")
imp = IJ.getImage()
# init GPU
clij = CLIJ.getInstance("1070")
# configure initial scaling step
calib = imp.getCalibration()
scaleX = calib.pixelWidth / calib.pixelDepth * zoom
scaleY = calib.pixelHeight / calib.pixelDepth * zoom
scaleZ = 1.0 * zoom
# initialize state
input = None
formerT = None
resultCylinderMaxProjection = None
resultMaxProjection = None
spots = None
circles = None
blobs = None