Hi Hadrien, > I am trying to write a small script to perform z projection on an > image.
Thanks for playing with Ops, and sorry that no one replied to this thread until now! I just wanted to let you know that based on your attempts, we are preparing a Z projection example with Ops for the upcoming 2015 ImageJ conference. Preliminary work can be seen at: https://github.com/imagej/imagej-tutorials/pull/16 It will merge to master within the next few days, and become available in ImageJ's Script Editor in the Templates > Tutorials menu by the conference. Regards, Curtis On Sat, Jan 24, 2015 at 4:29 PM, Hadrien Mary <hadrien.m...@gmail.com> wrote: > 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 >
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