[ImageJ-devel] Python script: z projection

[Hadrien Mary]

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.mary at 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