headless: Extended Depth of Field

[Christian Tischer]

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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[Kota Miura]

Hi Tischi,

this might help
https://github.com/cmci/ijmacros/blob/master/tischi/EDF.py

Cheers,
Kota

On Wed, Oct 17, 2012 at 10:13 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
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

... [show rest of quote]

--

-------------------------------------------------------------*Dr. Kota Miura*

Scientist & IT Engineer
Centre for Molecular and Cellular Imaging,
European Molecular Biology Laboratory
Meyerhofstr. 1
69117 Heidelberg
GERMANY

Tel [phone]

Mobile [phone]

Fax [phone]

http://cmci.embl.de
-------------------------------------------------------------

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