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Use ImageJ from Python
https://pyimagej.readthedocs.io/
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Cannot run installation test #103

Closed davidsean closed 2 years ago

davidsean commented 3 years ago

I am trying pyimagej for the first time, and cannot get it to work. I have tried numerous installations methods, including the recommended ones using conda.

(from README.md):

conda create -n pyimagej -c conda-forge pyimagej openjdk=8

or (from install.md):

conda config --add channels conda-forge
conda config --set channel_priority strict
conda create -n pyimagej pyimagej openjdk=8

Now the environment creation seem to work, and (after activating them) I can import imagej without a problem. The problem arises when I run ij = imagej.init('2.1.0')

log4j:WARN No appenders could be found for logger (org.bushe.swing.event.EventService).
log4j:WARN Please initialize the log4j system properly.
log4j:WARN See http://logging.apache.org/log4j/1.2/faq.html#noconfig for more info.
Traceback (most recent call last):
  File "AbstractGateway.java", line 135, in org.scijava.AbstractGateway.get
  File "Context.java", line 324, in org.scijava.Context.service
  File "Types.java", line 155, in org.scijava.util.Types.load
  File "Types.java", line 226, in org.scijava.util.Types.load
  File "ClassLoader.java", line 351, in java.lang.ClassLoader.loadClass
  File "Launcher.java", line 352, in sun.misc.Launcher$AppClassLoader.loadClass
  File "ClassLoader.java", line 418, in java.lang.ClassLoader.loadClass
  File "URLClassLoader.java", line 382, in java.net.URLClassLoader.findClass
java.lang.ClassNotFoundException: java.lang.ClassNotFoundException: net.imagej.legacy.LegacyService

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "AbstractGateway.java", line 135, in org.scijava.AbstractGateway.get
  File "Context.java", line 324, in org.scijava.Context.service
  File "Types.java", line 155, in org.scijava.util.Types.load
  File "Types.java", line 234, in org.scijava.util.Types.load
  File "Types.java", line 975, in org.scijava.util.Types.iae
Exception: Java Exception

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "<string>", line 1, in <module>
  File "/Users/davidsean/miniconda3/envs/pyimagej/lib/python3.8/site-packages/imagej/__init__.py", line 194, in init
    legacyServiceObj = ij.get('net.imagej.legacy.LegacyService')
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: Cannot load class: net.imagej.legacy.LegacyService

Any tips ?

elevans commented 3 years ago

@davidsean Right now there is a bug in selecting imagej versions that tracks back to one of the supporting packages, in this case jgo. @hinerm linked the relevant issue if you'd like more details.

Until this is resolved I'd recommend using ij = imagej.init() to get the latest version of imagej or ij = imagej.init('sc.fiji:fiji') if you'd like the latest version of Fiji and the plugins. Right now the latest version is 2.1.0 which is what you want anyways.

Note that running ij = imagej.init('sc.fiji:fiji') will return some java errors to the console. Its safe to ignore those errors. If you're not sure your initialization worked, check the imagej version with ij.getVersion().

ZhenhongDu commented 3 years ago

Is this error negligible? 

(pyimagej) C:\Users\admin2>python -c "import imagej; ij=imagej.init('sc.fiji:fiji');print(ij.getVersion()); ij.dispose()"
Error in `D:\Anaconda3\envs\pyimagej\Library\bin\mvn.CMD -B -f C:\Users\admin2\.jgo\net.imglib2\imglib2-imglyb\1.0.0+net.imagej-imagej-legacy-RELEASE+sc.fiji-fiji-RELEASE\pom.xml dependency:resolve': 1
elevans commented 3 years ago

@ddddg929 Sorry for the late reply here. There is currently an issue with the latest fiji release thats causing this issue. We're aware of it and working on it.

ctrueden commented 3 years ago

@elevans Is there an issue in the issue tracker here with more technical details? If not, should we file one? Do you think this is the FilamentDetector 1.0.0 problem? Or something else?

A couple of additional thoughts:

elevans commented 3 years ago

@ctrueden No there isn't one, but I'll file one for it. FilamentDetector made it into 2.2.0 core and the conda openjdk doesn't ship with JavaFX which FilamentDetector needs. JPype will refuse to initialize imagej and errors out with:

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "/home/edward/Documents/software/anaconda/envs/pyij/lib/python3.8/site-packages/imagej/__init__.py", line 168, in init
    ij = ImageJ()
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: Invalid service: sc.fiji.filamentdetector.gui.GUIStatusService

In my case I had the same error as @ddddg929. I cleared my .jgo cache and now I get the more specific FilamentDetector error.

What about using imagej.init('sc.fiji:fiji:2.1.1')? Does that work around the problem?

imagej.init('sc.fiji:fiji:2.1.1') works! But for now imagej.init('2.1.1') does not (for me at least, https://github.com/scijava/scyjava/issues/23).

I want to improve the debugging output of jgo, so that it can print what goes wrong with the mvn dependency:resolve operation. It's often helpful to see that detailed error message, for understanding problems with endpoints. I filed scijava/jgo#61.

That would be great!

ctrueden commented 2 years ago

Fiji 2.3.1 has been released, which no longer suffers from the FilamentDetector initialization issue, because it includes FilamentDetector 1.0.1 now with that bug fixed.

However: PyImageJ will continue to have issues initializing the desired versions of things, until #140 is fixed. We are working on it.

hinerm commented 2 years ago

With the 1.0.2 release, pyimagej should now be compatible with Fiji 2.3.1 to get the fixed FilamentDetector.

ss8319 commented 2 years ago

@hinerm It seems like I am getting the same problem still with Fiji 2.3.1.

This is the code I am running.

from scyjava import  config, jimport
import imagej
config.add_option('-Xmx6g') # increase heap size in Java

ij = imagej.init('sc.fiji:fiji:2.3.1')

Terminal Output:

 "C:\Users\USER\Desktop\Year 3\StemCell\venv\Scripts\python.exe" "C:/Users/USER/Desktop/Year 3/StemCell/venv/Scripts/pyimagej.py"
22:38:40.385 [SciJava-3bbcc7ce-Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.URLReader
java.lang.ClassNotFoundException: loci.formats.in.URLReader
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at java.base/java.lang.Class.forName0(Native Method)
    at java.base/java.lang.Class.forName(Class.java:375)
    at loci.formats.ClassList.parseLine(ClassList.java:196)
    at loci.formats.ClassList.parseFile(ClassList.java:258)
    at loci.formats.ClassList.<init>(ClassList.java:138)
    at loci.formats.ClassList.<init>(ClassList.java:122)
    at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80)
    at io.scif.bf.BioFormatsFormat.cacheReaderClasses(BioFormatsFormat.java:538)
    at io.scif.bf.BioFormatsFormat.<init>(BioFormatsFormat.java:139)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)
    at java.base/jdk.internal.reflect.ReflectionFactory.newInstance(ReflectionFactory.java:347)
    at java.base/java.lang.Class.newInstance(Class.java:645)
    at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:304)
    at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:234)
    at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:223)
    at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:214)
    at io.scif.services.DefaultFormatService.lambda$initialize$0(DefaultFormatService.java:459)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:211)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)
22:38:40.394 [SciJava-3bbcc7ce-Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.SlideBook6Reader
java.lang.ClassNotFoundException: loci.formats.in.SlideBook6Reader
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at java.base/java.lang.Class.forName0(Native Method)
    at java.base/java.lang.Class.forName(Class.java:375)
    at loci.formats.ClassList.parseLine(ClassList.java:196)
    at loci.formats.ClassList.parseFile(ClassList.java:258)
    at loci.formats.ClassList.<init>(ClassList.java:138)
    at loci.formats.ClassList.<init>(ClassList.java:122)
    at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80)
    at io.scif.bf.BioFormatsFormat.cacheReaderClasses(BioFormatsFormat.java:538)
    at io.scif.bf.BioFormatsFormat.<init>(BioFormatsFormat.java:139)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)
    at java.base/jdk.internal.reflect.ReflectionFactory.newInstance(ReflectionFactory.java:347)
    at java.base/java.lang.Class.newInstance(Class.java:645)
    at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:304)
    at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:234)
    at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:223)
    at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:214)
    at io.scif.services.DefaultFormatService.lambda$initialize$0(DefaultFormatService.java:459)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:211)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)
22:38:40.395 [SciJava-3bbcc7ce-Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.ScreenReader
java.lang.ClassNotFoundException: loci.formats.in.ScreenReader
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at java.base/java.lang.Class.forName0(Native Method)
    at java.base/java.lang.Class.forName(Class.java:375)
    at loci.formats.ClassList.parseLine(ClassList.java:196)
    at loci.formats.ClassList.parseFile(ClassList.java:258)
    at loci.formats.ClassList.<init>(ClassList.java:138)
    at loci.formats.ClassList.<init>(ClassList.java:122)
    at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80)
    at io.scif.bf.BioFormatsFormat.cacheReaderClasses(BioFormatsFormat.java:538)
    at io.scif.bf.BioFormatsFormat.<init>(BioFormatsFormat.java:139)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)
    at java.base/jdk.internal.reflect.ReflectionFactory.newInstance(ReflectionFactory.java:347)
    at java.base/java.lang.Class.newInstance(Class.java:645)
    at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:304)
    at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:234)
    at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:223)
    at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:214)
    at io.scif.services.DefaultFormatService.lambda$initialize$0(DefaultFormatService.java:459)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:211)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)
22:38:40.406 [SciJava-3bbcc7ce-Thread-0] DEBUG loci.formats.ClassList - Could not find loci.formats.in.ZarrReader
java.lang.ClassNotFoundException: loci.formats.in.ZarrReader
    at java.base/jdk.internal.loader.BuiltinClassLoader.loadClass(BuiltinClassLoader.java:641)
    at java.base/jdk.internal.loader.ClassLoaders$AppClassLoader.loadClass(ClassLoaders.java:188)
    at java.base/java.lang.ClassLoader.loadClass(ClassLoader.java:520)
    at java.base/java.lang.Class.forName0(Native Method)
    at java.base/java.lang.Class.forName(Class.java:375)
    at loci.formats.ClassList.parseLine(ClassList.java:196)
    at loci.formats.ClassList.parseFile(ClassList.java:258)
    at loci.formats.ClassList.<init>(ClassList.java:138)
    at loci.formats.ClassList.<init>(ClassList.java:122)
    at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:80)
    at io.scif.bf.BioFormatsFormat.cacheReaderClasses(BioFormatsFormat.java:538)
    at io.scif.bf.BioFormatsFormat.<init>(BioFormatsFormat.java:139)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)
    at java.base/jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:77)
    at java.base/jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
    at java.base/java.lang.reflect.Constructor.newInstanceWithCaller(Constructor.java:499)
    at java.base/java.lang.reflect.ReflectAccess.newInstance(ReflectAccess.java:128)
    at java.base/jdk.internal.reflect.ReflectionFactory.newInstance(ReflectionFactory.java:347)
    at java.base/java.lang.Class.newInstance(Class.java:645)
    at org.scijava.plugin.PluginInfo.createInstance(PluginInfo.java:304)
    at org.scijava.plugin.DefaultPluginService.createInstance(DefaultPluginService.java:234)
    at org.scijava.plugin.DefaultPluginService.createInstances(DefaultPluginService.java:223)
    at org.scijava.plugin.DefaultPluginService.createInstancesOfType(DefaultPluginService.java:214)
    at io.scif.services.DefaultFormatService.lambda$initialize$0(DefaultFormatService.java:459)
    at org.scijava.thread.DefaultThreadService.lambda$wrap$1(DefaultThreadService.java:211)
    at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:539)
    at java.base/java.util.concurrent.FutureTask.run(FutureTask.java:264)
    at java.base/java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1136)
    at java.base/java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:635)
    at java.base/java.lang.Thread.run(Thread.java:833)
Traceback (most recent call last):
  File "ImageJ.java", line 77, in net.imagej.ImageJ.<init>
  File "Context.java", line 160, in org.scijava.Context.<init>
  File "Context.java", line 174, in org.scijava.Context.<init>
  File "Context.java", line 234, in org.scijava.Context.<init>
  File "Context.java", line 285, in org.scijava.Context.<init>
  File "ServiceHelper.java", line 164, in org.scijava.service.ServiceHelper.loadServices
  File "ServiceHelper.java", line 192, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 229, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 267, in org.scijava.service.ServiceHelper.createExactService
  File "ServiceHelper.java", line 300, in org.scijava.service.ServiceHelper.createServiceRecursively
  File "Class.java", line 645, in java.lang.Class.newInstance
  File "ReflectionFactory.java", line 347, in jdk.internal.reflect.ReflectionFactory.newInstance
  File "ReflectAccess.java", line 128, in java.lang.reflect.ReflectAccess.newInstance
  File "Constructor.java", line 499, in java.lang.reflect.Constructor.newInstanceWithCaller
  File "DelegatingConstructorAccessorImpl.java", line 45, in jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance
  File "NativeConstructorAccessorImpl.java", line 77, in jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance
  File "NativeConstructorAccessorImpl.java", line -2, in jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0
  File "LegacyService.java", line 141, in net.imagej.legacy.LegacyService.<clinit>
  File "LegacyInjector.java", line 374, in net.imagej.patcher.LegacyInjector.preinit
  File "LegacyInjector.java", line 378, in net.imagej.patcher.LegacyInjector.preinit
  File "LegacyInjector.java", line 422, in net.imagej.patcher.LegacyInjector.alreadyPatched
  File "Class.java", line 2117, in java.lang.Class.getField
java.lang.NoSuchFieldException: java.lang.NoSuchFieldException: _hooks

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "LegacyService.java", line 141, in net.imagej.legacy.LegacyService.<clinit>
  File "LegacyInjector.java", line 374, in net.imagej.patcher.LegacyInjector.preinit
  File "LegacyInjector.java", line 378, in net.imagej.patcher.LegacyInjector.preinit
  File "LegacyInjector.java", line 431, in net.imagej.patcher.LegacyInjector.alreadyPatched
  File "CodeHacker.java", line 826, in net.imagej.patcher.CodeHacker.javaAgentHint
java.lang.RuntimeException: java.lang.RuntimeException: No _hooks field found in ij.IJ
It appears that this class was already defined in the class loader!
Please make sure that you initialize the LegacyService before using
any ImageJ 1.x class. You can do that by adding this static initializer:

    static {
        LegacyInjector.preinit();
    }

To debug this issue, start the JVM with the option:

    -javaagent:/C:/Users/USER/.jgo/sc.fiji/fiji/cf5b9cfa780ed57120a6bfbf9ba822458a22ccc79d9a902d6a854c3f13849d4a/ij1-patcher-1.2.1.jar

To enforce pre-initialization, start the JVM with the option:

    -javaagent:/C:/Users/USER/.jgo/sc.fiji/fiji/cf5b9cfa780ed57120a6bfbf9ba822458a22ccc79d9a902d6a854c3f13849d4a/ij1-patcher-1.2.1.jar=init

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "ImageJ.java", line 77, in net.imagej.ImageJ.<init>
  File "Context.java", line 160, in org.scijava.Context.<init>
  File "Context.java", line 174, in org.scijava.Context.<init>
  File "Context.java", line 234, in org.scijava.Context.<init>
  File "Context.java", line 285, in org.scijava.Context.<init>
  File "ServiceHelper.java", line 164, in org.scijava.service.ServiceHelper.loadServices
  File "ServiceHelper.java", line 192, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 229, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 267, in org.scijava.service.ServiceHelper.createExactService
  File "ServiceHelper.java", line 300, in org.scijava.service.ServiceHelper.createServiceRecursively
  File "Class.java", line 645, in java.lang.Class.newInstance
  File "ReflectionFactory.java", line 347, in jdk.internal.reflect.ReflectionFactory.newInstance
  File "ReflectAccess.java", line 128, in java.lang.reflect.ReflectAccess.newInstance
  File "Constructor.java", line 499, in java.lang.reflect.Constructor.newInstanceWithCaller
  File "DelegatingConstructorAccessorImpl.java", line 45, in jdk.internal.reflect.DelegatingConstructorAccessorImpl.newInstance
  File "NativeConstructorAccessorImpl.java", line 77, in jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance
  File "NativeConstructorAccessorImpl.java", line -2, in jdk.internal.reflect.NativeConstructorAccessorImpl.newInstance0
java.lang.ExceptionInInitializerError: java.lang.ExceptionInInitializerError

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "ImageJ.java", line 77, in net.imagej.ImageJ.<init>
  File "Context.java", line 160, in org.scijava.Context.<init>
  File "Context.java", line 174, in org.scijava.Context.<init>
  File "Context.java", line 234, in org.scijava.Context.<init>
  File "Context.java", line 285, in org.scijava.Context.<init>
  File "ServiceHelper.java", line 164, in org.scijava.service.ServiceHelper.loadServices
  File "ServiceHelper.java", line 192, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 229, in org.scijava.service.ServiceHelper.loadService
  File "ServiceHelper.java", line 278, in org.scijava.service.ServiceHelper.createExactService
Exception: Java Exception

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "C:\Users\USER\Desktop\Year 3\StemCell\venv\Scripts\pyimagej.py", line 6, in <module>
    ij = imagej.init('sc.fiji:fiji:2.3.1')
  File "C:\Users\USER\Desktop\Year 3\StemCell\venv\lib\site-packages\imagej\__init__.py", line 171, in init
    ij = ImageJ()
java.lang.IllegalArgumentException: java.lang.IllegalArgumentException: Invalid service: net.imagej.legacy.LegacyService
hinerm commented 2 years ago

@ss8319 The initialization of fiji 2.3.1 works for me with pyimagej 1.0.2, so more info is needed to debug this:

  1. I'm assuming you're starting python from a command prompt/terminal. Can you run pip list from that same prompt and paste the output?
  2. What operating system are you on?
ss8319 commented 2 years ago

Hi @hinerm. Thanks for the help.

I am on Windows 10.

I ran my python script on PyCharm. Running pip list gives this. Package Version

argon2-cffi 21.3.0 argon2-cffi-bindings 21.2.0 asgiref 3.5.0 asttokens 2.0.5 atomicwrites 1.4.0 attrs 21.4.0 backcall 0.2.0 beautifulsoup4 4.10.0 black 22.1.0 bleach 4.1.0 certifi 2021.10.8 cffi 1.15.0 charset-normalizer 2.0.11 click 8.0.3 colorama 0.4.4 cycler 0.11.0 debugpy 1.5.1 decorator 5.1.1 defusedxml 0.7.1 Django 4.0.2 entrypoints 0.4 executing 0.8.2 fonttools 4.29.1 idna 3.3 image 1.5.33 imglyb 2.0.0 iniconfig 1.1.1 ipykernel 6.9.0 ipython 8.0.1 ipython-genutils 0.2.0 jedi 0.18.1 jgo 1.0.3 Jinja2 3.0.3 JPype1 1.3.0 jsonschema 4.4.0 jupyter-client 7.1.2 jupyter-core 4.9.1 jupyterlab-pygments 0.1.2 kiwisolver 1.3.2 lxml 4.7.1 MarkupSafe 2.0.1 matplotlib 3.5.1 matplotlib-inline 0.1.3 maven 0.0.6 mistune 0.8.4 mypy-extensions 0.4.3 nbclient 0.5.10 nbconvert 6.4.2 nbformat 5.1.3 nest-asyncio 1.5.4 notebook 6.4.8 numpy 1.22.2 opencv-python 4.5.5.62 packaging 21.3 pandas 1.4.0 pandocfilters 1.5.0 parso 0.8.3 pathspec 0.9.0 pickleshare 0.7.5 Pillow 9.0.1 pip 21.3.1 platformdirs 2.5.0 pluggy 1.0.0 prometheus-client 0.13.1 prompt-toolkit 3.0.27 psutil 5.9.0 pure-eval 0.2.2 py 1.11.0 pycparser 2.21 Pygments 2.11.2 pyimagej 1.0.2 pyjnius 1.4.1 pyparsing 3.0.7 pyrsistent 0.18.1 pytest 7.0.0 python-dateutil 2.8.2 pytz 2021.3 pywin32 303 pywinpty 2.0.2 pyzmq 22.3.0 requests 2.27.1 scyjava 1.4.1 Send2Trash 1.8.0 setuptools 60.1.0 six 1.16.0 soupsieve 2.3.1 sqlparse 0.4.2 stack-data 0.1.4 terminado 0.13.1 testpath 0.5.0 tomli 2.0.1 tornado 6.1 traitlets 5.1.1 typing_extensions 4.0.1 tzdata 2021.5 urllib3 1.26.8 wcwidth 0.2.5 webencodings 0.5.1 wheel 0.37.1 xarray 0.21.1 xlrd 2.0.1

hinerm commented 2 years ago

@ss8319 can you look in your /C:/Users/USER/.jgo/sc.fiji/fiji/cf5b9cfa780ed57120a6bfbf9ba822458a22ccc79d9a902d6a854c3f13849d4a/ directory and tell me what version of the ij-xxx.jar is in there? Is it ij-1.53f.jar?

ss8319 commented 2 years ago

@hinerm Sorry for getting back late. Yes it is ij-1.53f.jar

@ss8319 can you look in your /C:/Users/USER/.jgo/sc.fiji/fiji/cf5b9cfa780ed57120a6bfbf9ba822458a22ccc79d9a902d6a854c3f13849d4a/ directory and tell me what version of the ij-xxx.jar is in there? Is it ij-1.53f.jar?

ctrueden commented 2 years ago

@ss8319 Thanks for your patience debugging this. I don't have a complete answer, but here are some questions to check:

There are also patching issues with ImageJ >1.53f, which is why @hinerm asked about that. But 1.53f is known to work; it's what we currently ship with Fiji.