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imagej / imagej-matlab

MATLAB integration with ImageJ data structures and runtime.
https://imagej.net/scripting/matlab
BSD 2-Clause "Simplified" License
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ImageJ cannot load the scripts #12

Open fmeyenhofer opened 7 years ago

fmeyenhofer commented 7 years ago

Hi

When launching ImageJ from MATLAB I get the errors bellow telling me that some scripts cannot be loaded. However I checked the paths and the files are there. Tjh IJM and MIJ objects are created though and they work.

I have the following setup: OsX sierra Java 1.8.0_40-b25 (as mentioned in the wiki) MATLAB 2016b

>> ImageJ
[ERROR] Cannot create plugin: class='org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage', name='JavaScript', priority=0.0, enabled=true, pluginType=ScriptLanguage
java.lang.IllegalArgumentException: No such script engine: javascript
    at org.scijava.script.AdaptedScriptLanguage.findFactory(AdaptedScriptLanguage.java:151)
    at org.scijava.script.AdaptedScriptLanguage.<init>(AdaptedScriptLanguage.java:73)
    at org.scijava.plugins.scripting.javascript.JavaScriptScriptLanguage.<init>(JavaScriptScriptLanguage.java:59)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
    at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.lang.reflect.Constructor.newInstance(Constructor.java:422)
    at java.lang.Class.newInstance(Class.java:442)
    at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:304)
    at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:236)
    at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:225)
    at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:216)
    at org.scijava.plugin.AbstractSingletonService.initInstances(AbstractSingletonService.java:92)
    at org.scijava.plugin.AbstractSingletonService.getInstances(AbstractSingletonService.java:75)
    at org.scijava.script.DefaultScriptService.initScriptLanguageIndex(DefaultScriptService.java:273)
    at org.scijava.script.DefaultScriptService.scriptLanguageIndex(DefaultScriptService.java:238)
    at org.scijava.script.DefaultScriptService.getIndex(DefaultScriptService.java:118)
    at org.scijava.script.ScriptService.canHandleFile(ScriptService.java:314)
    at org.scijava.script.ScriptFinder.createInfos(ScriptFinder.java:165)
    at org.scijava.script.ScriptFinder.scanResources(ScriptFinder.java:133)
    at org.scijava.script.ScriptFinder.findScripts(ScriptFinder.java:109)
    at org.scijava.script.DefaultScriptService.initScripts(DefaultScriptService.java:314)
    at org.scijava.script.DefaultScriptService.scripts(DefaultScriptService.java:256)
    at org.scijava.script.DefaultScriptService.getScripts(DefaultScriptService.java:153)
    at net.imagej.legacy.LegacyService.getScriptsAndNonLegacyCommands(LegacyService.java:628)
    at net.imagej.legacy.IJ1Helper.addMenuItems(IJ1Helper.java:744)
    at net.imagej.legacy.LegacyService.initialize(LegacyService.java:488)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:353)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
    at org.scijava.Context.<init>(Context.java:278)
    at org.scijava.Context.<init>(Context.java:234)
    at org.scijava.Context.<init>(Context.java:174)
    at org.scijava.Context.<init>(Context.java:160)
    at net.imagej.ImageJ.<init>(ImageJ.java:77)
    at net.imagej.Main.launch(Main.java:61)
    at net.imagej.matlab.ImageJMATLAB.launch(ImageJMATLAB.java:151)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:105)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:92)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:81)
[ERROR] Invalid script URL: file:/Users/turf/Applications/Fiji.app/plugins/Scripts/File/Open_Samples/Comparing_Lengths.ijm
java.io.FileNotFoundException: /Users/turf/Applications/Fiji.app/plugins/Scripts/File/Open_Samples/Comparing_Lengths.ijm (Too many open files)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at java.io.FileInputStream.<init>(FileInputStream.java:93)
    at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)
    at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188)
    at java.net.URL.openStream(URL.java:1038)
    at org.scijava.script.ScriptInfo.<init>(ScriptInfo.java:139)
    at org.scijava.script.ScriptFinder.createInfos(ScriptFinder.java:193)
    at org.scijava.script.ScriptFinder.scanDirectory(ScriptFinder.java:152)
    at org.scijava.script.ScriptFinder.findScripts(ScriptFinder.java:115)
    at org.scijava.script.DefaultScriptService.initScripts(DefaultScriptService.java:314)
    at org.scijava.script.DefaultScriptService.scripts(DefaultScriptService.java:256)
    at org.scijava.script.DefaultScriptService.getScripts(DefaultScriptService.java:153)
    at net.imagej.legacy.LegacyService.getScriptsAndNonLegacyCommands(LegacyService.java:628)
    at net.imagej.legacy.IJ1Helper.addMenuItems(IJ1Helper.java:744)
    at net.imagej.legacy.LegacyService.initialize(LegacyService.java:488)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:353)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
    at org.scijava.Context.<init>(Context.java:278)
    at org.scijava.Context.<init>(Context.java:234)
    at org.scijava.Context.<init>(Context.java:174)
    at org.scijava.Context.<init>(Context.java:160)
    at net.imagej.ImageJ.<init>(ImageJ.java:77)
    at net.imagej.Main.launch(Main.java:61)
    at net.imagej.matlab.ImageJMATLAB.launch(ImageJMATLAB.java:151)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:105)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:92)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:81)
[ERROR] Invalid script URL: file:/Users/turf/Applications/Fiji.app/plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm
java.io.FileNotFoundException: /Users/turf/Applications/Fiji.app/plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm (Too many open files)
    at java.io.FileInputStream.open0(Native Method)
    at java.io.FileInputStream.open(FileInputStream.java:195)
    at java.io.FileInputStream.<init>(FileInputStream.java:138)
    at java.io.FileInputStream.<init>(FileInputStream.java:93)
    at sun.net.www.protocol.file.FileURLConnection.connect(FileURLConnection.java:90)
    at sun.net.www.protocol.file.FileURLConnection.getInputStream(FileURLConnection.java:188)
    at java.net.URL.openStream(URL.java:1038)
    at org.scijava.script.ScriptInfo.<init>(ScriptInfo.java:139)
    at org.scijava.script.ScriptFinder.createInfos(ScriptFinder.java:193)
    at org.scijava.script.ScriptFinder.scanDirectory(ScriptFinder.java:152)
    at org.scijava.script.ScriptFinder.findScripts(ScriptFinder.java:115)
    at org.scijava.script.DefaultScriptService.initScripts(DefaultScriptService.java:314)
    at org.scijava.script.DefaultScriptService.scripts(DefaultScriptService.java:256)
    at org.scijava.script.DefaultScriptService.getScripts(DefaultScriptService.java:153)
    at net.imagej.legacy.LegacyService.getScriptsAndNonLegacyCommands(LegacyService.java:628)
    at net.imagej.legacy.IJ1Helper.addMenuItems(IJ1Helper.java:744)
    at net.imagej.legacy.LegacyService.initialize(LegacyService.java:488)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:353)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.createServiceRecursively(ServiceHelper.java:340)
    at org.scijava.service.ServiceHelper.createExactService(ServiceHelper.java:269)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:231)
    at org.scijava.service.ServiceHelper.loadService(ServiceHelper.java:194)
    at org.scijava.service.ServiceHelper.loadServices(ServiceHelper.java:166)
    at org.scijava.Context.<init>(Context.java:278)
    at org.scijava.Context.<init>(Context.java:234)
    at org.scijava.Context.<init>(Context.java:174)
    at org.scijava.Context.<init>(Context.java:160)
    at net.imagej.ImageJ.<init>(ImageJ.java:77)
    at net.imagej.Main.launch(Main.java:61)
    at net.imagej.matlab.ImageJMATLAB.launch(ImageJMATLAB.java:151)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:105)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:92)
    at net.imagej.matlab.ImageJMATLAB.start(ImageJMATLAB.java:81)
ctrueden commented 7 years ago

java.lang.IllegalArgumentException: No such script engine: javascript

This is a more general problem with the fact that Java 8 ships the Nashorn JavaScript engine as a platform extension, and I guess in some cases the platform extensions are not initialized properly. I have seen this error outside the context of MATLAB as well. For now, I suggest ignoring it unless you need JavaScript scripting from MATLAB specifically.

(Too many open files)

From the Miji page:

There are over 300 jar and plugin files that ship with Fiji, and depending on your operating system and configuration, you may run into too many files open errors (for example, on OSX MATLAB seems to use the default soft limit for open files, which is typically 256). If this happens you will need to increase the open file limit per-session or system-wide. See this guide for helpful instructions on doing so for OSX and Linux.

Maybe that guide helps alleviate the issue for you?