[ImageJ-devel] Python script: z projection

[Curtis Rueden]

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.mary at 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.mary at 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.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
>
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