Macro without windows?

[Jennifer Cass]

hi everyone
We're having trouble with a macro that we created to analyze and give us histograms of each of the following red dots


The scripts runs fine in MSWindows and Linux but in order to have it run in a headless environment or in a Raspberry Pi (we got close) it runs into the issue that it can't deal with the different windows. Essentially ImageJ can't address Windows in certain Linux or headless environments it seems.

So my question is: Is there an way to convert this into something else, a plugin perhaps and AVOID opening ImageJ windows to create our processing?  

Would you recommend trying to convert this into something else like Matlab? Would there be an ImageJ->Matlab converter?

Thanks
Jenn

[Herbie]

Good day Jennifer,

although I'm not perfectly clear about your wish, I'll propose two hints:

1.
You may have a look at the IJ-macro command "setBatchMode(arg)" and its
companions: <https://imagej.nih.gov/ij/developer/macro/functions.html>
In "BatchMode" processed images aren't shown and you can avoid showing
resulting windows by closing them before the end of your macro.

2.
For command line processing you may have a look at:
<https://imagej.nih.gov/ij/developer/macro/macros.html#cli>
and
<https://imagej.nih.gov/ij/docs/guide/146-18.html#sub:IJ-cmd-line>

HTH

Herbie

:::::::::::::::::::::::::::::::::::::::::::
Am 10.07.16 um 00:10 schrieb Jennifer Cass:

> hi everyone
> We're having trouble with a macro that we created to analyze and give us
> histograms of each of the following red dots
> <http://imagej.1557.x6.nabble.com/file/n5016836/Screenshot_2016-07-09_18.png>
>
> The scripts runs fine in MSWindows and Linux but in order to have it run in
> a headless environment or in a Raspberry Pi (we got close) it runs into the
> issue that it can't deal with the different windows. Essentially ImageJ
> can't address Windows in certain Linux or headless environments it seems.
>
> So my question is: Is there an way to convert this into something else, a
> plugin perhaps and AVOID opening ImageJ windows to create our processing?
>
> Would you recommend trying to convert this into something else like Matlab?
> Would there be an ImageJ->Matlab converter?
>
> Thanks
> Jenn
>
>
>
>
> --
> View this message in context: http://imagej.1557.x6.nabble.com/Macro-without-windows-tp5016836.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Jennifer,

If you truly need to run headless (i.e.: on a computer with no display),
then you will need ImageJ2, since plain ImageJ 1.x cannot be used headless
(at least: not without xvfb).

For further details, see:
http://imagej.net/Headless

Regards,
Curtis

--
Curtis Rueden
LOCI software architect - http://loci.wisc.edu/software
ImageJ2 lead, Fiji maintainer - http://imagej.net/User:Rueden
Did you know ImageJ has a forum? http://forum.imagej.net/


On Sat, Jul 9, 2016 at 5:10 PM, Jennifer Cass <[hidden email]> wrote:

> hi everyone
> We're having trouble with a macro that we created to analyze and give us
> histograms of each of the following red dots
> <
> http://imagej.1557.x6.nabble.com/file/n5016836/Screenshot_2016-07-09_18.png
> >
>
> The scripts runs fine in MSWindows and Linux but in order to have it run in
> a headless environment or in a Raspberry Pi (we got close) it runs into the
> issue that it can't deal with the different windows. Essentially ImageJ
> can't address Windows in certain Linux or headless environments it seems.
>
> So my question is: Is there an way to convert this into something else, a
> plugin perhaps and AVOID opening ImageJ windows to create our processing?
>
> Would you recommend trying to convert this into something else like Matlab?
> Would there be an ImageJ->Matlab converter?
>
> Thanks
> Jenn
>
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/Macro-without-windows-tp5016836.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html