Re: FW: Directionality plugin - getting Directionality analysis output values

Posted by Kenton Arkill on Mar 17, 2015; 8:09am
URL: http://imagej.273.s1.nabble.com/FW-Directionality-plugin-getting-Directionality-analysis-output-values-tp5011976p5012008.html

It is not much help to the discussion:
I did get the same window manager error last time I used this (with the
python script) after about 8months of not using it. However I used the
plugin on a stack without the script and I was able to 'get at' the output
table which I was not able to do previously (hence I used to use the
script). It did the job at the time so I did not worry about it.
Kenton

On 17 March 2015 at 05:06, Jacqui Ross <[hidden email]> wrote:

> Thanks Jean-Yves,
>
> I tried running the first macro directly and got the errors listed below -
> something to do with defining the WindowManager..? Is there something else
> I need to install for this to work?
>
> Traceback (most recent call last):
>   File
> "C:\Users\jros013\Desktop\Fiji.app\macros\Directionality_standard_.py",
> line 7, in <module>
>     dir.setImagePlus(WindowManager.getCurrentImage())
> NameError: name 'WindowManager' is not defined
>
>         at
> org.python.core.PyException.fillInStackTrace(PyException.java:70)
>         at java.lang.Throwable.<init>(Throwable.java:181)
>         at java.lang.Exception.<init>(Exception.java:29)
>         at java.lang.RuntimeException.<init>(RuntimeException.java:32)
>         at org.python.core.PyException.<init>(PyException.java:46)
>         at org.python.core.PyException.<init>(PyException.java:43)
>         at org.python.core.PyException.<init>(PyException.java:61)
>         at org.python.core.Py.NameError(Py.java:260)
>         at org.python.core.PyFrame.getname(PyFrame.java:257)
>         at
> org.python.pycode._pyx10.f$0(C:\Users\jros013\Desktop\Fiji.app\macros\Directionality_standard_.py:35)
>         at
> org.python.pycode._pyx10.call_function(C:\Users\jros013\Desktop\Fiji.app\macros\Directionality_standard_.py)
>         at org.python.core.PyTableCode.call(PyTableCode.java:165)
>         at org.python.core.PyCode.call(PyCode.java:18)
>         at org.python.core.Py.runCode(Py.java:1275)
>         at
> org.scijava.plugins.scripting.jython.JythonScriptEngine.eval(JythonScriptEngine.java:76)
>         at org.scijava.script.ScriptModule.run(ScriptModule.java:175)
>         at org.scijava.module.ModuleRunner.run(ModuleRunner.java:167)
>         at org.scijava.module.ModuleRunner.call(ModuleRunner.java:126)
>         at org.scijava.module.ModuleRunner.call(ModuleRunner.java:65)
>         at
> org.scijava.thread.DefaultThreadService$2.call(DefaultThreadService.java:164)
>         at
> java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:303)
>         at java.util.concurrent.FutureTask.run(FutureTask.java:138)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.runTask(ThreadPoolExecutor.java:886)
>         at
> java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:908)
>         at java.lang.Thread.run(Thread.java:662)
>
> If you have any further suggestions, I'd be very grateful. I've downloaded
> your example images to use to test the macros.
>
> Thanks to Herbie also for sending me the links to some interesting papers.
>
> Kind regards,
>
> Jacqui
>
> Jacqueline Ross
> Biomedical Imaging Microscopist
> Biomedical Imaging Research Unit
> School of Medical Sciences
> Faculty of Medical & Health Sciences
> The University of Auckland
> Private Bag 92019
> Auckland 1142, NEW ZEALAND
>
> Tel: [phone]
> Fax: [phone]
>
> http://www.fmhs.auckland.ac.nz/sms/biru/
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of
> Jean-Yves Tinevez
> Sent: Monday, 16 March 2015 9:29 p.m.
> To: [hidden email]
> Subject: Re: FW: Directionality plugin - getting Directionality analysis
> output values
>
> Hi Jaqui,The Python script you point to should do the work. But you don't
> have to run it after running the plugin. The python script itself runs the
> plugin. It would be the base on which you could build something that would
> allow you to process the 2000 images in batch. The 2nd plugin on the wiki
> page will show you how to get the analysis results.You mention that you get
> errors. Would you care to copy/paste them here, with a description on how
> they occur? But first, try to run it as mention above.Bestjy
>
>
>
> --
> View this message in context:
> http://imagej.1557.x6.nabble.com/FW-Directionality-plugin-getting-Directionality-analysis-output-values-tp5011976p5011979.html
> Sent from the ImageJ mailing list archive at Nabble.com.
>
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