Re: running headless: Extended Depth of Field

Posted by dscho on Nov 16, 2012; 12:11am
URL: http://imagej.273.s1.nabble.com/Re-running-headless-Extended-Depth-of-Field-tp5000821p5000842.html

Hi Tischi,

On Thu, 15 Nov 2012, Christian Tischer wrote:

> in the meantime we (Kota Miura and me) hacked the EDF code ourselves in
> order to make it run headless.
>
> for those interested, here is how it works:
>
> 1) create a folder "edfgui" in the plugins folder
>
> 2) place the file at https://gist.github.com/4077617 into this folder
>
> 3) then, using FIJI, when you can use it via a jython script like so:
>
> from edfgui import ExtendedDepthOfFieldHeadless
> from edfgui import Parameters
>
> imp = ...some image stack...
>
> IJ.log("EDF: start...")
> parameters = Parameters()
> parameters.setQualitySettings(1)
> parameters.setTopologySettings(0)
> parameters.show3dView = False
> parameters.showTopology = False
> edfh = ExtendedDepthOfFieldHeadless(imp, parameters)
> impEDF = edfh.processHeadless()
> IJ.log("EDF: done.")
>
> # if you want to see the result in the GUI mode:
> impEDF.show()
> # of course you have to remove above line  in headless mode as it would
> crash otherwise
>
> 4) have fun, Tischi

It would be good if you could make this available on GitHub so that the
changes can be reviewed and hopefully even merged, in the worst case at
least ported from EDF version to the next.

Thanks,
Johannes

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