Posted by
bnorthan on
Feb 11, 2016; 5:34pm
URL: http://imagej.273.s1.nabble.com/error-in-Fiji-headless-mode-at-convolve-step-tp5015595p5015607.html
Hi
I agree with Marc's suggestion, using ops may help. Of course you
mentioned that the convolution is just part of a larger macro.
IJ1 code and ops can actually be run in the same script... though I don't
think you could run ops in an IJ1 macro (Mark: correct me if I am wrong).
So if you wanted to start using ops, you might have to convert your Macro
to a script (for example using Jython, Groovy or another scripting
language).
Then you could convert small pieces to ops, if ops had an advantage (like
running headless).
I tried to convert your processing steps to ops and opened up a topic about
it in the Discourse Forum -
http://forum.imagej.net/t/translating-filter-macro-to-imagej2/831Below is the 'ops' version of your processing steps... I appreciate that it
is (currently) a little more intimidating then the macro version... maybe
some people on the forum will have some ideas regarding how to streamline
it.
# @OpService ops
# @UIService ui
# @Dataset inputData
from net.imglib2.img.display.imagej import ImageJFunctions
from ij import IJ
from java.lang import Integer
from net.imagej.ops import Ops
from net.imglib2.type.numeric.real import FloatType
from net.imglib2.type.numeric.integer import IntType
from net.imglib2.outofbounds import OutOfBoundsMirrorFactory
from net.imglib2.outofbounds.OutOfBoundsMirrorFactory import Boundary
img=inputData.getImgPlus();
# convert to 32 bit
img32=ops.create().img(img, FloatType());
convertOp=ops.op(Ops.Convert.Copy, FloatType, IntType);
ops.map(img32, inputData, convertOp)
# create horizontal edge filter ###################################
kernel=ops.create().img([3,3])
kernelList=[0,1,0,1,-4,1,0,1,0]
kernelCursor=kernel.cursor()
i=0
for t in kernel:
t.setReal(kernelList[i])
i=i+1
# end create horizontal edge filter ###################################
gaussFiltered=ops.filter().gauss(img32, [4.0,4.0]);
ui.show(gaussFiltered)
# convolve with edge filter
filtered=ops.filter().convolve(gaussFiltered, kernel)
# display log filter result
ui.show("filtered", filtered)
On Thu, Feb 11, 2016 at 10:39 AM, Mark Hiner <
[hidden email]> wrote:
> Hello,
>
> >It makes me think the convolve step is failing. Thoughts?
>
> Based on the line number, it looks like the kernel is null[1]. The kernel
> is only set in the dialogItemChanged method[2] - which means I do not think
> there is a way to perform convolution headlessly with this class.
>
> If you open up the Script Editor[3] in Fiji, under "Templates > Tutorials >
> Create and Convolve Points" there is actually an example of convolution
> using ImageJ Ops - part of the ImageJ2 framework, which emphasizes
> decoupling algorithms from user interface.
>
> If you give it a try and have any questions, most Ops discussion takes
> place on the ImageJ forum.[4]
>
> Hope that helps.
>
> Regards,
> Mark Hiner
> ImageJ2 developer
> LOCI, UW-Madison
>
>
> [1]
>
>
https://github.com/imagej/ImageJA/blob/40afa1d8cf4b4ca74a16f25fba711dd7fd4d2142/src/main/java/ij/plugin/filter/Convolver.java#L177> [2]
>
>
https://github.com/imagej/ImageJA/blob/40afa1d8cf4b4ca74a16f25fba711dd7fd4d2142/src/main/java/ij/plugin/filter/Convolver.java#L83> [3]
http://imagej.net/Using_the_Script_Editor> [4]
http://forum.imagej.net/>
>
>
> On Wed, Feb 10, 2016 at 2:20 PM, samjlord <
[hidden email]> wrote:
>
> > Hi all,
> >
> > I have a macro that at one step convolves the image with a kernel. When I
> > run the macro from Fiji, everything works fine. When I run it in headless
> > mode, something goes wrong: instead of convolving like it does in normal
> > mode, it seems to skip that step.
> >
> > I see the following message when I run in headless mode:
> >
> >
> > > ERROR: java.lang.NullPointerException
> > > in Convolve... 600-899
> > > at ij.plugin.filter.Convolver.convolve(Convolver.java:177)
> > > from ij.plugin.filter.Convolver.run(Convolver.java:63)
> > > java.lang.NullPointerException
> > > at ij.plugin.filter.Convolver.convolve(Convolver.java:177)
> > > at ij.plugin.filter.Convolver.run(Convolver.java:63)
> > > at
> > >
> >
> ij.plugin.filter.PlugInFilterRunner.processChannelUsingThreads(PlugInFilterRunner.java:330)
> > > at
> > >
> >
> ij.plugin.filter.PlugInFilterRunner.processImageUsingThreads(PlugInFilterRunner.java:299)
> > > at
> > >
> >
> ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:234)
> > > at ij.plugin.filter.PlugInFilterRunner.
> > > <init>
> > > (PlugInFilterRunner.java:112)
> > > at ij.IJ.runPlugIn(IJ.java:184)
> > > at ij.Executer.runCommand(Executer.java:136)
> > > at ij.Executer.run(Executer.java:65)
> > > at ij.IJ.run(IJ.java:292)
> > > at ij.macro.Functions.doRun(Functions.java:601)
> > > at ij.macro.Functions.doFunction(Functions.java:96)
> > > at ij.macro.Interpreter.doStatement(Interpreter.java:230)
> > > at ij.macro.Interpreter.doBlock(Interpreter.java:608)
> > > at ij.macro.Interpreter.doStatement(Interpreter.java:272)
> > > at ij.macro.Interpreter.doFor(Interpreter.java:530)
> > > at ij.macro.Interpreter.doStatement(Interpreter.java:254)
> > > at ij.macro.Interpreter.doStatements(Interpreter.java:218)
> > > at ij.macro.Interpreter.run(Interpreter.java:115)
> > > at ij.macro.Interpreter.run(Interpreter.java:85)
> > > at ij.macro.Interpreter.run(Interpreter.java:96)
> > > at ij.plugin.Macro_Runner.runMacro(Macro_Runner.java:153)
> > > at ij.plugin.Macro_Runner.runMacroFile(Macro_Runner.java:137)
> > > at ij.IJ.runMacroFile(IJ.java:143)
> > > at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:952)
> > > at net.imagej.legacy.IJ1Helper$4.call(IJ1Helper.java:949)
> > > at
> net.imagej.legacy.IJ1Helper.runMacroFriendly(IJ1Helper.java:899)
> > > at net.imagej.legacy.IJ1Helper.runMacroFile(IJ1Helper.java:949)
> > > at
> > >
> >
> net.imagej.legacy.LegacyCommandline$Macro.handle(LegacyCommandline.java:188)
> > > at
> > >
> >
> org.scijava.console.DefaultConsoleService.processArgs(DefaultConsoleService.java:93)
> > > at
> > >
> >
> net.imagej.legacy.LegacyConsoleService.processArgs(LegacyConsoleService.java:76)
> > > at net.imagej.Main.launch(Main.java:64)
> > > at net.imagej.Main.main(Main.java:73)
> > > at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
> > > at
> > >
> >
> sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
> > > at
> > >
> >
> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
> > > at java.lang.reflect.Method.invoke(Method.java:497)
> > > at
> net.imagej.launcher.ClassLauncher.launch(ClassLauncher.java:279)
> > > at net.imagej.launcher.ClassLauncher.run(ClassLauncher.java:186)
> > > at net.imagej.launcher.ClassLauncher.main(ClassLauncher.java:77)
> >
> > It makes me think the convolve step is failing. Thoughts? (This is on a
> > Mac,
> > but also fails on a PC. Fiji updated.)
> >
> > Here's a shortened version of the macro that also fails the same way with
> > some comparative images:
> >
>
https://www.dropbox.com/sh/gaf2hgvnjlge53y/AAAucdebIHDfjwC56W5iysjIa?dl=0> >
> >
> >
> > --
> > View this message in context:
> >
>
http://imagej.1557.x6.nabble.com/error-in-Fiji-headless-mode-at-convolve-step-tp5015595.html> > Sent from the ImageJ mailing list archive at Nabble.com.
> >
> > --
> > ImageJ mailing list:
http://imagej.nih.gov/ij/list.html> >
>
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