k-dominik
commented
4 years ago Okay I want to give this a spin before merging. After the maven build I copied the jar to my fiji plugins. When starting fiji I then get the following error:
```java
[ERROR] Cannot create plugin: class='org.ilastik.ilastik4ij.util.StringToDatasetConverter', priority=10000.0, enabled=true, pluginType=Converter
org.scijava.InstantiableException: Class not found: org.ilastik.ilastik4ij.util.StringToDatasetConverter
at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:292)
at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:301)
at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:237)
at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:226)
at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:217)
at org.scijava.plugin.AbstractSingletonService.initInstances(AbstractSingletonService.java:138)
at org.scijava.plugin.AbstractSingletonService.getInstances(AbstractSingletonService.java:77)
at org.scijava.plugin.HandlerService.getHandler(HandlerService.java:59)
at org.scijava.util.ConversionUtils.handler(ConversionUtils.java:222)
at org.scijava.util.ConversionUtils.convert(ConversionUtils.java:91)
at org.scijava.command.CommandModuleItem.tValue(CommandModuleItem.java:257)
at org.scijava.command.CommandModuleItem.tValue(CommandModuleItem.java:251)
at org.scijava.command.CommandModuleItem.getMinimumValue(CommandModuleItem.java:143)
at org.scijava.module.DefaultMutableModuleItem.(DefaultMutableModuleItem.java:125)
at org.scijava.command.DynamicCommandInfo.copy(DynamicCommandInfo.java:314)
at org.scijava.command.DynamicCommandInfo.populateItems(DynamicCommandInfo.java:305)
at org.scijava.command.DynamicCommandInfo.(DynamicCommandInfo.java:74)
at org.scijava.command.DynamicCommand.getInfo(DynamicCommand.java:83)
at org.scijava.options.OptionsPlugin.load(OptionsPlugin.java:90)
at org.scijava.options.DefaultOptionsService.getInstances(DefaultOptionsService.java:84)
at org.scijava.plugin.SingletonService.lambda$initialize$0(SingletonService.java:97)
at org.scijava.object.ObjectIndex.resolvePending(ObjectIndex.java:388)
at org.scijava.object.ObjectIndex.get(ObjectIndex.java:133)
at org.scijava.object.DefaultObjectService.getObjects(DefaultObjectService.java:87)
at org.scijava.display.DefaultDisplayService.getDisplays(DefaultDisplayService.java:166)
at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:159)
at org.scijava.ui.DefaultUIService.showUI(DefaultUIService.java:142)
at org.scijava.AbstractGateway.launch(AbstractGateway.java:104)
at net.imagej.Main.main(Main.java:55)
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:498)
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)
Caused by: java.lang.IllegalArgumentException: Cannot load class: org.ilastik.ilastik4ij.util.StringToDatasetConverter
at org.scijava.util.Types.iae(Types.java:975)
at org.scijava.util.Types.load(Types.java:234)
at org.scijava.plugin.PluginInfo.loadClass(PluginInfo.java:286)
... 35 more
Caused by: java.lang.NoClassDefFoundError: org/scijava/convert/AbstractDelegateConverter
at java.lang.ClassLoader.defineClass1(Native Method)
at java.lang.ClassLoader.defineClass(ClassLoader.java:763)
at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
at java.net.URLClassLoader.defineClass(URLClassLoader.java:467)
at java.net.URLClassLoader.access$100(URLClassLoader.java:73)
at java.net.URLClassLoader$1.run(URLClassLoader.java:368)
at java.net.URLClassLoader$1.run(URLClassLoader.java:362)
at java.security.AccessController.doPrivileged(Native Method)
at java.net.URLClassLoader.findClass(URLClassLoader.java:361)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
at org.scijava.util.Types.load(Types.java:226)
... 36 more
Caused by: java.lang.ClassNotFoundException: org.scijava.convert.AbstractDelegateConverter
at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:349)
at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
... 49 more
```
any hint on how I would get this to work?
NicoKiaru
imagejan
Adds a converter needed for IJ1 macro scripting:
Converts a String (provided by an IJ1 macro script) to a Dataset by delegating the conversion to a String to ImagePlus converter chained to an {@link ImagePlus} to {@link Dataset} converter
This converter should be removed once this issue : https://github.com/imagej/imagej-legacy/issues/246 is resolved
See also : https://forum.image.sc/t/plugin-with-two-datasets-parameters-will-always-pop-up-gui-in-macro-runs/36637/11
https://forum.image.sc/t/object-classification-using-the-ilastik-plugin-for-fiji/32997
I did not try completely whether all issues were resolved with this - can you test whether that solves the batch issues you were mentioning @k-dominik ?
@imagejan I tried to put as much documentation as possible on the converter and also post on the issue in imagej-legacy. What do you think ? Does that sound reasonable for the moment ?