imagej / imagej/imagej-matlab

Failed using ImageJ-Matlab to start ImageJ in headless mode

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Dominant language
Java
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Description

Hi, I am using ImageJ-Matlab to start ImageJ2 from matlab by the matlab code

```
open_imageJ = false; % = true works and shows a Fiji panel, but false does not work
ImageJ(open_imageJ)
```
The non-headless mode runs OK when open_imageJ = true. .Although it shows a message box saying “cannot find java script engine”, the Fiji panel shows afterwards.

But if change open_imageJ to false, it shows the error after the same message box was shown :

```
[ERROR] Cannot create plugin: org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage

Error using ImageJ2 (line 99)
Java exception occurred:
java.lang.NullPointerException

at net.imagej.matlab.ImageJMATLAB.disableIJExit(ImageJMATLAB.java:247)

at net.imagej.matlab.ImageJMATLAB.launch(ImageJMATLAB.java:156)

at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:105)

log4j:WARN No appenders could be found for logger (loci.formats.ClassList).
log4j:WARN Please initialize the log4j system properly.
```

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the headless and non-headless calls in the issue, then inspect ImageJMATLAB.java at lines 99, 105, 156, and 247. Trace the JavaScriptScriptLanguage plugin error and the NullPointerException in disableIJExit; done means headless startup completes without the reported exception.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, javascript, matlab
Domain
tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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