Posted by
Jacqueline Ross on
Mar 17, 2015; 5:06am
URL: http://imagej.273.s1.nabble.com/FW-Directionality-plugin-getting-Directionality-analysis-output-values-tp5011976p5012006.html
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: 64 9 923 7438
Fax: 64 9 373 7484
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
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