Hello Everybody,
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
On Wed, Oct 17, 2012 at 10:03 AM, Christian Tischer <
[hidden email]> wrote:
> Dear All,
>
> i am trying to run the Extended Depth of Field as headless (because we
> need to cluster batch process).
>
> but i am getting the error:
>
> ....
> Caused by: java.awt.HeadlessException
> at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:159)
> at java.awt.Window.<init>(Window.java:431)
> at java.awt.Frame.<init>(Frame.java:403)
> at java.awt.Frame.<init>(Frame.java:368)
> at javax.swing.JFrame.<init>(JFrame.java:158)
> at edfgui.AbstractDialog.<init>(AbstractDialog.java:66)
> at edfgui.BasicDialog.<init>(BasicDialog.java:81)
> at EDF_Easy_.run(EDF_Easy_.java:141)
> at ij.IJ.runUserPlugIn(IJ.java:185)
> at ij.IJ.runPlugIn(IJ.java:152)
>
>
> i am running:
>
>
> fiji --jython --headless edf.py
>
>
> where edf.py is:
>
> ###############
>
> from ij import IJ
> from ij import ImageStack
> from ij import ImagePlus
> from ij.plugin import Duplicator
>
> # make a stack
> imp = IJ.openImage("
http://imagej.nih.gov/ij/images/blobs.gif");
> stack = ImageStack(imp.width, imp.height)
> ip = imp.getProcessor()
> stack.addSlice("", ip)
> stack.addSlice("", ip)
> imp = ImagePlus("stack", stack)
> #imp.show()
>
> IJ.run(imp, "Extended Depth of Field (Easy mode)...", "");
>
> ################
>
> my problem is that i cannot figure out which java class and method to call
> directly in order to avoid the Run Method.
>
>
>
http://code.google.com/p/fiji-bi/source/browse/src-plugins/Extended_Depth_Field/EDF_Easy_.java?name=c610ac7a03&r=b08377b6e85f70e6ffe4fdb5c0276dbb711e180f>
> can someone help?
>
> Tischi
>
>
>
>
>
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