I tried another approach without success neither : ----------------------------------- # @DatasetService data # @DisplayService display # @ImageJ ij
from net.imagej.ops.statistics import Max from net.imagej.ops.statistics import Sum from net.imglib2.type.numeric import RealType from jarray import array fname = "/home/hadim/test_small.ome.tif" ds = data.open(fname) # TODO : find dimensions in ds object dims = array([136, 65], 'l') out = ij.op().createimg(dims) # Find ndim for project on Z axis ndim = 2 op = ij.op().sum(RealType, out) ds2 = ij.op().project(out, ds, op, ndim) ij.ui().show(ds2.getName(), ds2) # TODO: should I delete out ? ------------------------------------- -- Hadrien Mary Ph.D student in Biology Tournier-Gachet Team CNRS - LBCMCP - UMR 5088 Université de Toulouse - Bât. 4R3B1 118, route de Narbonne - 31062 Toulouse On Sat, Jan 24, 2015 at 9:35 PM, Hadrien Mary <hadrien.m...@gmail.com> wrote: > Last thing : I would like to run this script in headless mode on > pretty big images (17GB), so I would like to be sure wether `img = > data.open(fname)` use SCIFIO to open them. > > If it does I guess virtual stack is used in case the opened image is > big. Am I correct ? > > -- > Hadrien Mary > > Ph.D student in Biology > Tournier-Gachet Team > CNRS - LBCMCP - UMR 5088 > > Université de Toulouse - Bât. 4R3B1 > 118, route de Narbonne - 31062 Toulouse > > > On Sat, Jan 24, 2015 at 9:25 PM, Hadrien Mary <hadrien.m...@gmail.com> wrote: >> Hi, >> >> I am trying to write a small script to perform z projection on an >> image. It seems that I use the wrong signature for ops.project() >> function. I tried many combinations without success... >> >> ------------------------------- >> # @DatasetService data >> # @DisplayService display >> # @OpService ops >> >> from net.imagej.ops.statistics import Max >> from net.imglib2.type.numeric import RealType >> >> fname = "/home/hadim/test_small.ome.tif" >> img = data.open(fname) >> display.createDisplay(img.getName(), img) >> >> #op = ops.sum(RealType, img) >> img2 = ops.project(img, Max, 1) >> display.createDisplay(img2.getName(), img2) >> >> data.save(img2, "/home/hadim/projected.ome.tif") >> ----------------------------------- >> >> I looked the doc, imagej-ops tests but I can't find the correct >> signature for python. Maybe you can help. >> >> Thank you >> >> -- >> Hadrien Mary >> >> Ph.D student in Biology >> Tournier-Gachet Team >> CNRS - LBCMCP - UMR 5088 >> >> Université de Toulouse - Bât. 4R3B1 >> 118, route de Narbonne - 31062 Toulouse _______________________________________________ ImageJ-devel mailing list ImageJ-devel@imagej.net http://imagej.net/mailman/listinfo/imagej-devel
