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imagej / pyimagej

Use ImageJ from Python
https://pyimagej.readthedocs.io/
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"Failed to bootstrap the artifact" #206

Closed somsubhro88 closed 1 year ago

somsubhro88 commented 2 years ago

Hello @ctrueden ,

Hello again!

I'm the same guy from https://github.com/imagej/pyimagej/issues/176

I put a comment there, but I guess because that issue has been resolved, it did not get highlighted.

I tried install pyimagej (using the steps on Wiki) on a Windows 10 server PC (without admin rights) for a new user, but I faced an issue. I followed the same steps above and the recommended fix you suggested, but I now get the following error below. Could you please help? I tried a few more steps, but just can't make it work.

Failed to bootstrap the artifact.

Possible solutions:

  • Double check the endpoint for correctness (https://search.maven.org/).
  • Add needed repositories to ~/.jgorc [repositories] block (see README).
  • Try with an explicit version number (release metadata might be wrong).

Full Maven error output:

Traceback (most recent call last):

File "C:\Users\ldpue.UGENT.conda\envs\pyimagej\lib\site-packages\spyder_kernels\py3compat.py", line 356, in compat_exec exec(code, globals, locals)

File "g:\fluxys\for_laura\fluxys\python_wd\hydrogen_emb\image_processing\fluxys_imagej_postprocess.py", line 74, in ij = imagej.init(fiji_path, headless=False)

File "C:\Users\ldpue.UGENT.conda\envs\pyimagej\lib\site-packages\imagej__init__.py", line 1498, in init raise RuntimeError("Failed to create a JVM with the requested environment.")

RuntimeError: Failed to create a JVM with the requested environment.

ctrueden commented 2 years ago

@somsubhro88 Sorry to hear you're still encountering problems, and happy to help figure it out.

Have you seen the Debugging Tips from the troubleshooting guide? There are two things to try there: the PyImageJ doctor, and then enabling debug logging before you call imagej.init. If you enable debug logging you should see much more detail on why the mvn tool is unable to build a Java environment. Can you please give it a try, and paste your output here?

somsubhro88 commented 2 years ago

@ctrueden Sorry, I hadn't see this page yet. I will try it and let you know asap. Please give me a couple of days. It's a long weekend here in Belgium, I won't be able to try this until Monday 30/05.

ctrueden commented 2 years ago

@somsubhro88 No rush! Happy to help whenever you have time to follow up.

somsubhro88 commented 2 years ago

Hello @ctrueden,

Thank you for waiting :)

Important point to note before: For ImageJ, I simply copy-pasted the ImageJ folder from my user account folder (where it works) to this user account folder.

The trial code is:

import imagej  # https://pypi.org/project/pyimagej/

import os

import imagej.doctor
imagej.doctor.debug_to_stderr(debug_maven=True)

#define JAVA_HOME environment location. Specific to user
# os.environ["JAVA_HOME"] = 'C:\\Users\\schaudhu\\.conda\\envs\\pyimagej'
os.environ['JAVA_HOME'] = 'C:\\Users\\ldpue.UGENT\\.conda\\envs\\pyimagej2'

# fiji_path = 'C:/Users/schaudhu/Documents/Fiji.app'  # should be a folder
fiji_path = 'C:/Users/ldpue.UGENT/Documents/Fiji.app'  # should be a folder

print('initialising ImageJ ...')
ij = imagej.init(fiji_path, headless=False)
ij.ui().showUI()  # gives the imageJ ui for manual usage, if headless=False
print('ImageJ initialised')

So, first I tried - 


import imagej.doctor
imagej.doctor.checkup()

Result - 


Checking Python:
--> Python executable = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\python.exe

Checking environment:
--> CONDA_PREFIX = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2
--> Python executable matches Conda environment.

Checking Python dependencies:
--> jgo: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\jgo\__init__.py
--> scyjava: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\scyjava\__init__.py
--> imglyb: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\imglyb\__init__.py
--> pyimagej: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\imagej\__init__.py

Checking Maven:
--> Maven executable = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\Library\bin\mvn.CMD
$ mvn -v
Apache Maven 3.8.5 (3599d3414f046de2324203b78ddcf9b5e4388aa0)
Maven home: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\Library
Java version: 1.8.0_312, vendor: Azul Systems, Inc., runtime: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\Library\jre
Default locale: en_US, platform encoding: Cp1252
OS name: "windows server 2016", version: "10.0", arch: "amd64", family: "windows"

Checking Java:
--> JAVA_HOME is NOT set!
--> Java executable = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\Library\bin\java.EXE
$ java -version
openjdk version "1.8.0_312"
OpenJDK Runtime Environment (Zulu 8.58.0.13-CA-win64) (build 1.8.0_312-b07)
OpenJDK 64-Bit Server VM (Zulu 8.58.0.13-CA-win64) (build 25.312-b07, mixed mode)

Questions and advice for you:
--> Activate a conda environment with openjdk installed, or set JAVA_HOME manually.

I set the JAVA_HOME and then run Checkup again:

os.environ['JAVA_HOME'] = 'C:\\Users\\ldpue.UGENT\\.conda\\envs\\pyimagej2'

Result - 


Checking Python:
--> Python executable = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\python.exe

Checking environment:
--> CONDA_PREFIX = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2
--> Python executable matches Conda environment.

Checking Python dependencies:
--> jgo: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\jgo\__init__.py
--> scyjava: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\scyjava\__init__.py
--> imglyb: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\imglyb\__init__.py
--> pyimagej: C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\imagej\__init__.py

Checking Maven:
--> Maven executable = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\Library\bin\mvn.CMD
$ mvn -v
Command '['C:\\Users\\ldpue.UGENT\\.conda\\envs\\pyimagej2\\Library\\bin\\mvn.CMD', '-v']' returned non-zero exit status 1.

Checking Java:
--> JAVA_HOME = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2
--> Java executable = C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\Library\bin\java.EXE
$ java -version
openjdk version "1.8.0_312"
OpenJDK Runtime Environment (Zulu 8.58.0.13-CA-win64) (build 1.8.0_312-b07)
OpenJDK 64-Bit Server VM (Zulu 8.58.0.13-CA-win64) (build 25.312-b07, mixed mode)

Great job! All looks good.

Next, I try the code below. I run this before initialising imagej.

import imagej.doctor
imagej.doctor.debug_to_stderr()

Result - 

runfile('C:/Users/ldpue.UGENT/.spyder-py3/temp.py', wdir='C:/Users/ldpue.UGENT/.spyder-py3')
The headless flag of imagej.init is deprecated. Use the mode argument instead.
initialising ImageJ ...
Local path to ImageJ2 installation given: C:\Users\ldpue.UGENT\Documents\Fiji.app
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/ahocorasick-0.2.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/alphanumeric-comparator-1.4.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/annotations-13.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/ant-1.9.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/ant-launcher-1.9.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/antlr-3.5.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/antlr-runtime-3.5.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/api-common-1.9.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/args4j-2.0.25.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/asm-7.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/asm-analysis-7.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/asm-commons-7.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/asm-tree-7.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/asm-util-7.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/auto-value-annotations-1.7.jar
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Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/aws-java-sdk-kms-1.11.796.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/aws-java-sdk-s3-1.11.796.jar
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Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/fiji-compat-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/fiji-lib-2.1.3.jar
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Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/ij1-patcher-1.2.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/image4j-0.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/imagej-2.3.0.jar
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Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/j3dcore-1.6.0-scijava-2.jar
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Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jackrabbit-webdav-2.21.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jackson-annotations-2.12.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jackson-core-2.12.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jackson-databind-2.12.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jackson-dataformat-cbor-2.12.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jackson-jq-1.0.0-preview.20191208.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jai-codec-1.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jai-core-1.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jakarta.activation-api-1.2.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jakarta.xml.bind-api-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jama-1.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/java-cup-11b-20160615.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/java-sizeof-0.0.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/javacpp-1.4.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/javaGeom-0.11.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/javassist-3.27.0-GA.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/javax.annotation-api-1.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/javax.servlet-api-3.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jaxb-runtime-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jblosc-1.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jclipboardhelper-0.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jcodings-1.0.55.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jcommander-1.48.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jcommon-1.0.24.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jdatepicker-1.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jdom2-2.0.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jep-2.4.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jffi-1.2.19-native.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jffi-1.2.20.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jfilechooser-bookmarks-0.1.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jfreechart-1.5.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jfreesvg-3.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jgoodies-common-1.7.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jgoodies-forms-1.7.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jgrapht-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jgrapht-core-1.4.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jgraphx-4.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jhdf5-14.12.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jheaps-0.11.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jhotdraw-7.6.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jitk-tps-3.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jline-2.14.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jmespath-java-1.11.796.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jna-4.5.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-a64asm-1.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-constants-0.9.12.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-enxio-0.16.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-ffi-2.1.10.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-netdb-1.1.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-posix-3.0.50.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-unixsocket-0.17.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jnr-x86asm-1.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/joal-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/joal-main-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jocl-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jocl-main-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/joda-time-2.10.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jogl-all-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jogl-all-main-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/joml-1.9.25.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/joni-2.1.29.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jpedalSTD-2.80b11.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jply-0.2.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jruby-core-9.1.17.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jruby-stdlib-9.1.17.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jsch-0.1.55.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/json-20090211.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jsoup-1.7.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jsr166y-1.7.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jsr305-3.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jtransforms-2.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jung-api-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jung-graph-impl-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/JWlz-1.4.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jython-shaded-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jython-slim-2.7.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/jzlib-1.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/Kappa-2.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/kotlin-stdlib-1.4.21.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/kotlin-stdlib-common-1.4.21.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/kryo-4.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/languagesupport-3.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/lapack-0.8.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/legacy-imglib1-1.1.9.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/log4j-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/logback-classic-1.2.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/logback-core-1.2.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/lz4-java-1.7.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/mapdb-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/markdownj-0.3.0-1.0.2b4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/maven-scm-api-1.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/maven-scm-provider-svn-commons-1.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/maven-scm-provider-svnexe-1.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/mchange-commons-java-0.2.15.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/metadata-extractor-2.11.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/methods-0.8.1906.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/miglayout-core-5.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/miglayout-swing-5.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/mines-jtk-20151125.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/minimaven-2.2.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/minio-5.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/minlog-1.3.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/modulator-1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/mpicbg-1.4.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/mtj-1.0.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/multiverse-core-0.7.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-2.5.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-aws-s3-3.2.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-blosc-1.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-google-cloud-3.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-hdf5-1.4.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-ij-3.2.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-imglib2-4.3.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/n5-zarr-0.0.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/nailgun-server-0.9.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/native-lib-loader-2.3.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netcdf-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netlib-java-0.9.3-renjin-patched-2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netty-buffer-4.1.45.Final.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netty-codec-4.1.45.Final.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netty-common-4.1.45.Final.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netty-handler-4.1.45.Final.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netty-resolver-4.1.45.Final.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/netty-transport-4.1.45.Final.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/object-inspector-0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/objenesis-2.5.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/ojalgo-45.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/okhttp-4.7.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/okio-2.6.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/OMEVisual-2.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/op-finder-0.1.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/opencensus-api-0.24.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/opencensus-contrib-http-util-0.24.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/opencsv-5.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/options-1.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/pal-optimization-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/parsington-2.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/perf4j-0.9.16.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/plexus-utils-1.5.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/postgresql-42.2.12.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/prettytime-4.0.1.Final.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/proto-google-common-protos-1.17.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/proto-google-iam-v1-0.13.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/protobuf-java-3.11.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/protobuf-java-util-3.11.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/reflectasm-1.11.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/regexp-1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/reload4j-1.2.18.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/renjin-appl-0.8.1906.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/renjin-core-0.8.1906.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/renjin-gnur-runtime-0.8.1906.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/renjin-script-engine-0.8.1906.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/rhino-1.7.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/rsyntaxtextarea-3.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scala-compiler-2.12.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scala-library-2.12.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scala-reflect-2.12.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scala-xml_2.12-1.0.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scifio-0.42.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scifio-bf-compat-4.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scifio-cli-0.6.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scifio-hdf5-0.2.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scifio-jai-imageio-1.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scifio-lifesci-0.9.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scifio-ome-xml-0.16.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-common-2.87.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-config-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-io-http-0.2.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-listeners-1.0.0-beta-3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-optional-1.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-plugins-commands-0.2.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-plugins-io-table-0.4.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-plugins-platforms-0.3.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-plugins-text-markdown-0.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-plugins-text-plain-0.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-search-0.7.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-table-0.7.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-ui-awt-0.1.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scijava-ui-swing-0.13.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/script-editor-0.6.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/script-editor-jython-0.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-beanshell-0.3.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-clojure-0.1.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-groovy-0.3.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-java-0.4.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-javascript-0.5.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-jruby-0.3.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-jython-1.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-renjin-0.2.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/scripting-scala-0.2.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/serializer-2.7.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/slf4j-api-1.7.30.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/snakeyaml-1.26.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/spim_data-2.2.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/sqlite-jdbc-3.28.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/ST4-4.0.8.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/stats-0.8.1906.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/stax-ex-1.8.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/swing-checkbox-tree-1.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/swing-worker-1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/swingx-1.6.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/T2-NIT-1.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/T2-TreelineGraph-1.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/threetenbp-1.4.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/TrackMate-7.6.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/trakem2-transform-1.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/trove4j-3.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/txw2-2.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/udunits-4.3.18.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/ui-behaviour-2.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/unsafe-fences-1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/utils-0.8.1906.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/vecmath-1.6.0-scijava-2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/VectorGraphics2D-0.13.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/VectorString-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/VIB-lib-2.2.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/weave_jy2java-2.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/weka-dev-3.9.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xalan-2.7.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xchart-3.5.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xerbla-0.8.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xercesImpl-2.8.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xml-apis-ext-1.3.04.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xmlgraphics-commons-2.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xmpcore-5.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xpp3-1.1.4c.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/xz-1.8.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars/yecht-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/formats-api-6.8.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/formats-bsd-6.8.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/formats-gpl-6.8.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/jai_imageio-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/jxrlib-all-0.2.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/metakit-5.3.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/ome-codecs-0.3.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/ome-common-6.0.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/ome-jai-0.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/ome-mdbtools-5.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/ome-poi-5.3.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/ome-xml-6.2.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/specification-6.2.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\bio-formats/turbojpeg-6.8.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\win64/ffmpeg-4.1-1.4.4-windows-x86_64.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\win64/gluegen-rt-2.3.2-natives-windows-amd64.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\win64/joal-2.3.2-natives-windows-amd64.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\win64/jocl-2.3.2-natives-windows-amd64.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/jars\win64/jogl-all-2.3.2-natives-windows-amd64.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/3D_Blob_Segmentation-3.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/3D_Objects_Counter-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/3D_Viewer-4.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/AnalyzeSkeleton_-3.4.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Anisotropic_Diffusion_2D-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Archipelago_Plugins-0.5.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Arrow_-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Auto_Local_Threshold-1.10.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Auto_Threshold-1.17.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/BalloonSegmentation_-3.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/bigdataviewer_fiji-6.2.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/bigwarp_fiji-7.0.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/bio-formats_plugins-6.8.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/blockmatching_-2.1.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Bug_Submitter-2.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/bUnwarpJ_-2.6.13.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Calculator_Plus-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Cell_Counter-3.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Colocalisation_Analysis-3.0.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Color_Histogram-2.0.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Color_Inspector_3D-2.5.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Colour_Deconvolution-3.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/CorrectBleach_-2.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Correct_3D_Drift-1.0.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/CPU_Meter-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Descriptor_based_registration-2.1.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Dichromacy_-2.1.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Directionality_-2.3.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Feature_Detection-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Fiji_Archipelago-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Fiji_Developer-2.0.7.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Fiji_Package_Maker-2.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Fiji_Plugins-3.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/FlowJ_-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/FS_Align_TrakEM2-2.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Graph_Cut-1.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Gray_Morphology-2.3.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/H5J_Loader_Plugin-1.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/HDF5_Vibez-1.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Helmholtz_Analysis-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/ij_ridge_detect-1.4.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/IJ_Robot-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Image_5D-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Image_Expression_Parser-3.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Interactive_3D_Surface_Plot-3.0.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/IO_-4.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/IsoData_Classifier-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Kuwahara_Filter-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/KymographBuilder-2.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Lasso_and_Blow_Tool-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/level_sets-1.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Linear_Kuwahara-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/LocalThickness_-4.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/LSM_Reader-4.1.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/LSM_Toolbox-4.1.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Manual_Tracking-2.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/mpicbg_-1.4.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/MTrack2_-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Multi_Kymograph-3.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/M_I_P-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/n5-viewer_fiji-4.5.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/panorama_-3.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/PIV_analyser-1.1.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/QuickPALM_-1.1.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/RATS_-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Reconstruct_Reader-2.0.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/register_virtual_stack_slices-3.0.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/registration_3d-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Samples_-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Series_Labeler-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Sholl_Analysis-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Simple_Neurite_Tracer-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Siox_Segmentation-1.0.5.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Skeletonize3D_-2.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/SPIM_Opener-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/SPIM_Registration-5.0.22.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/SplineDeformationGenerator_-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Stack_Manipulation-2.1.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Statistical_Region_Merging-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Stitching_-3.1.8.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Sync_Win-1.7-fiji4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Thread_Killer-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Time_Lapse-2.1.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Time_Stamper-2.1.0.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/ToAST_-25.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/TopoJ_-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/TrackMate_-0.0.0-STUB.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Trainable_Segmentation-3.3.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/TrakEM2_-1.3.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/TrakEM2_Archipelago-2.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/trakem2_tps-1.1.4.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Vaa3d_Reader-2.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Vaa3d_Writer-1.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/VIB_-3.0.3.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Video_Editing-2.0.1.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/View5D_-2.3.6.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Volume_Calculator-2.0.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/Volume_Viewer-2.01.2.jar
Added C:\Users\ldpue.UGENT\Documents\Fiji.app/plugins/z_spacing-1.1.1.jar
Added 504 JARs to the Java classpath.
Adding jars from endpoints ['io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.0.1']
Using endpoints ['io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.0.1']
Getting verbose level: 0
Getting verbose level: 0
Returning expanded coordinate io.scif:scifio-labeling:0.3.1.
Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1.
First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions.
Executing: ('C:\\Users\\ldpue.UGENT\\.conda\\envs\\pyimagej2\\Library\\bin\\mvn.CMD', '-B', '-f', 'C:\\Users\\ldpue.UGENT\\.jgo\\io.scif\\scifio-labeling\\0.3.1\\eb3228841e43c0aa0cffa924ea6aa524384a3685113d54510c0ed985c20d2ab0\\pom.xml', 'dependency:resolve')
Failed to bootstrap the artifact.

Possible solutions:
* Double check the endpoint for correctness (https://search.maven.org/).
* Add needed repositories to ~/.jgorc [repositories] block (see README).
* Try with an explicit version number (release metadata might be wrong).

Full Maven error output:
    The JAVA_HOME environment variable is not defined correctly, 
    this environment variable is needed to run this program. 

Traceback (most recent call last):

  File "C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\spyder_kernels\py3compat.py", line 356, in compat_exec
    exec(code, globals, locals)

  File "c:\users\ldpue.ugent\.spyder-py3\temp.py", line 23, in <module>
    ij = imagej.init(fiji_path, headless=False)

  File "C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\imagej\__init__.py", line 1498, in init
    raise RuntimeError("Failed to create a JVM with the requested environment.")

RuntimeError: Failed to create a JVM with the requested environment.

Next I tried this to get more information:

import imagej.doctor
imagej.doctor.debug_to_stderr(debug_maven=True)

Result (after the loading of JAR files) - 

Adding jars from endpoints ['io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.0.1']
Using endpoints ['io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.0.1']
Getting verbose level: 2
Getting verbose level: 2
Returning expanded coordinate io.scif:scifio-labeling:0.3.1.
Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1.
First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions.
Executing: ('C:\\Users\\ldpue.UGENT\\.conda\\envs\\pyimagej2\\Library\\bin\\mvn.CMD', '-B', '-f', 'C:\\Users\\ldpue.UGENT\\.jgo\\io.scif\\scifio-labeling\\0.3.1\\eb3228841e43c0aa0cffa924ea6aa524384a3685113d54510c0ed985c20d2ab0\\pom.xml', 'dependency:resolve', '-X')
Failed to bootstrap the artifact.

Possible solutions:
* Double check the endpoint for correctness (https://search.maven.org/).
* Add needed repositories to ~/.jgorc [repositories] block (see README).
* Try with an explicit version number (release metadata might be wrong).

Full Maven error output:
    The JAVA_HOME environment variable is not defined correctly, 
    this environment variable is needed to run this program. 

Traceback (most recent call last):

  File "C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\spyder_kernels\py3compat.py", line 356, in compat_exec
    exec(code, globals, locals)

  File "c:\users\ldpue.ugent\.spyder-py3\temp.py", line 23, in <module>
    ij = imagej.init(fiji_path, headless=False)

  File "C:\Users\ldpue.UGENT\.conda\envs\pyimagej2\lib\site-packages\imagej\__init__.py", line 1498, in init
    raise RuntimeError("Failed to create a JVM with the requested environment.")

RuntimeError: Failed to create a JVM with the requested environment.

This is a lot information :) I don't understand why Maven says JAVA_HOME is not defined. The script contains a line which defines JAVA_HOME. This is reflected in the PyDoctor checkup as well. :(

ctrueden commented 2 years ago

@somsubhro88 Thank you for the more verbose debugging output.

About Spyder: you are not the first person who has had trouble with e.g. conda environments with Spyder. Do things work if you run PyImageJ outside of Spyder, from the command line? When you start Spyder, do you start it from the command line, from the conda environment where JAVA_HOME is already set? To me it looks like the os.environ call is not actually setting the variable when Python is run from Spyder. Apparently you can set environment variables explicitly in Spyder via the Tools → Current user environment variables... menu item; see this SO answer. Does doing that make any difference?

@CanYing0913 Might it be the case that you are also using Spyder? Or no?

I also found this article about combining conda and Spyder which might be interesting.

Ultimately, to figure this out, I probably need to try to reproduce the issue on a Windows machine. If you continue to be stuck, let me know and I can try to spend some time on it.

CanYing0913 commented 2 years ago

I was using PyCharm with conda environment when facing this problem. To me the os.environ['JAVA_HOME'] successfully prints out the corresponding conda env name, so I assume that's not a unique thing for Spyder.

ctrueden commented 2 years ago

Thanks @CanYing0913. Does your Python script work from the command line in your conda environment? I.e. is it an IDE-specific thing? Or do you see the same behavior outside of PyCharm?

CanYing0913 commented 2 years ago

Thanks @CanYing0913. Does your Python script work from the command line in your conda environment? I.e. is it an IDE-specific thing? Or do you see the same behavior outside of PyCharm?

Just tried outside of PyCharm, and it behaved the same, it didn't appear to be the IDE-specific bug.

ctrueden commented 2 years ago

@CanYing0913 Huh. So from the command line, when you type:

echo "$JAVA_HOME"

You see that JAVA_HOME is set correctly, but then when you run the Python script, it fails to bootstrap the environment with the error about JAVA_HOME not being set? (Are you calling import imagej.doctor; imagej.doctor.debug_to_stderr(debug_maven=True) before initializing PyimageJ as mentioned above to verify that?) If not, it is possible that Maven is failing on your system for some other reason besides the JAVA_HOME problem.

CanYing0913 commented 2 years ago

@CanYing0913 Huh. So from the command line, when you type:

echo "$JAVA_HOME"

You see that JAVA_HOME is set correctly, but then when you run the Python script, it fails to bootstrap the environment with the error about JAVA_HOME not being set? (Are you calling import imagej.doctor; imagej.doctor.debug_to_stderr(debug_maven=True) before initializing PyimageJ as mentioned above to verify that?) If not, it is possible that Maven is failing on your system for some other reason besides the JAVA_HOME problem.

echo is not showing anything from terminal but when I try to do os.environ['JAVA_HOME'], it prints out the right thing. Is it the possible reason? image

After adding the import imagej.doctor; imagej.doctor.debug_to_stderr(debug_maven=True), I got:

C:\Users\wyari\.conda\envs\caiman  # This is the print(os.environ['JAVA_HOME'])
Setting verbose level to 2 (was 0)
Setting verbose level to 2 (was 0)
Maven coordinate given: sc.fiji:fiji
Adding jars from endpoints ['sc.fiji:fiji', 'net.imagej:imagej-legacy:MANAGED', 'io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.0.1']
Using endpoints ['sc.fiji:fiji', 'io.scif:scifio-labeling:0.3.1', 'net.imagej:imagej-legacy:MANAGED', 'net.imglib2:imglib2-imglyb:1.0.1']
Getting verbose level: 2
Getting verbose level: 2
Returning expanded coordinate sc.fiji:fiji.
Returning expanded coordinate io.scif:scifio-labeling:0.3.1.
Returning expanded coordinate net.imagej:imagej-legacy:MANAGED.
Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1.
First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions.
Executing: ('C:\\Users\\wyari\\.conda\\envs\\caiman\\Library\\bin\\mvn.CMD', '-B', '-f', 'C:\\Users\\wyari\\.jgo\\sc.fiji\\fiji\\RELEASE\\756695f0b00b18ae43e78d2530dbf214204907cf4a15388bef762a92c2ee73bf\\pom.xml', 'dependency:resolve', '-X')
ctrueden commented 2 years ago

echo is not showing anything from terminal

On Windows, I think the syntax is:

echo "%JAVA_HOME%"

It probably also works to type set and hit enter and then it lists all the environment variables and their values, if I recall correctly.

Executing: ('C:\\Users\\wyari\\.conda\\envs\\caiman\\Library\\bin\\mvn.CMD', '-B', '-f', 'C:\\Users\\wyari\\.jgo\\sc.fiji\\fiji\\RELEASE\\756695f0b00b18ae43e78d2530dbf214204907cf4a15388bef762a92c2ee73bf\\pom.xml', 'dependency:resolve', '-X')

There should be more output after that: the result of that command execution. Is it hanging? If so, wait a minute or two; it may be downloading dependencies and such. If it hangs for many minutes, then it might be a firewall issue; see this troubleshooting tip for info on how to configure a proxy in that case.

CanYing0913 commented 2 years ago

echo is not showing anything from terminal

On Windows, I think the syntax is:

echo "%JAVA_HOME%"

It probably also works to type set and hit enter and then it lists all the environment variables and their values, if I recall correctly.

Executing: ('C:\\Users\\wyari\\.conda\\envs\\caiman\\Library\\bin\\mvn.CMD', '-B', '-f', 'C:\\Users\\wyari\\.jgo\\sc.fiji\\fiji\\RELEASE\\756695f0b00b18ae43e78d2530dbf214204907cf4a15388bef762a92c2ee73bf\\pom.xml', 'dependency:resolve', '-X')

There should be more output after that: the result of that command execution. Is it hanging? If so, wait a minute or two; it may be downloading dependencies and such. If it hangs for many minutes, then it might be a firewall issue; see this troubleshooting tip for info on how to configure a proxy in that case.

This time the terminal prints the correct JAVA_HOME value. The output from imagej.doctor is not hanging. the following print-outs are the same as I sent above:

Setting verbose level to 2 (was 0)
Setting verbose level to 2 (was 0)
Maven coordinate given: sc.fiji:fiji
Adding jars from endpoints ['sc.fiji:fiji', 'net.imagej:imagej-legacy:MANAGED', 'io.scif:scifio-labeling:0.3.1', 'net.imglib2:imglib2-imglyb:1.0.1']
Using endpoints ['sc.fiji:fiji', 'io.scif:scifio-labeling:0.3.1', 'net.imagej:imagej-legacy:MANAGED', 'net.imglib2:imglib2-imglyb:1.0.1']
Getting verbose level: 2
Getting verbose level: 2
Returning expanded coordinate sc.fiji:fiji.
Returning expanded coordinate io.scif:scifio-labeling:0.3.1.
Returning expanded coordinate net.imagej:imagej-legacy:MANAGED.
Returning expanded coordinate net.imglib2:imglib2-imglyb:1.0.1.
First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions.
Executing: ('C:\\Users\\wyari\\.conda\\envs\\caiman\\Library\\bin\\mvn.CMD', '-B', '-f', 'C:\\Users\\wyari\\.jgo\\sc.fiji\\fiji\\RELEASE\\756695f0b00b18ae43e78d2530dbf214204907cf4a15388bef762a92c2ee73bf\\pom.xml', 'dependency:resolve', '-X')
Failed to bootstrap the artifact.

Possible solutions:
* Double check the endpoint for correctness (https://search.maven.org/).
* Add needed repositories to ~/.jgorc [repositories] block (see README).
* Try with an explicit version number (release metadata might be wrong).

Full Maven error output:
    The JAVA_HOME environment variable is not defined correctly, 
    this environment variable is needed to run this program. 

Traceback (most recent call last):
  File "D:\CanYing\Code\pyimgj.py", line 29, in <module>
    ij = imagej.init('sc.fiji:fiji')
  File "C:\Users\wyari\.conda\envs\caiman\lib\site-packages\imagej\__init__.py", line 1498, in init
    raise RuntimeError("Failed to create a JVM with the requested environment.")
RuntimeError: Failed to create a JVM with the requested environment.
ctrueden commented 2 years ago

@CanYing0913 Thanks. The key part of the output is this:

Full Maven error output:
  The JAVA_HOME environment variable is not defined correctly, 
  this environment variable is needed to run this program.

Which indeed confirms that it's an issue with the JAVA_HOME environment variable, same as @somsubhro88.

So then, the question is: why does Maven not think this variable is set?

Could you now, from within your conda environment, please try this command?

mvn -v

 Does it work, listing the intended Java installation in the output?

If it does not work: I wonder if it's related to this note from the JPype documentation? In that case, you could try also appending the bin or jre\bin directory of your Java installation to the PATH variable, to see whether that makes any difference.

But if the mvn -v command does work from the command line from the conda environment, then... maybe it's an issue with way jgo is invoking mvn: using subprocess.check_output. Is it possible that approach has limitations or differences on Windows, I wonder?

CanYing0913 commented 2 years ago

This is what I got after mvn -v:

Maven home: C:\Users\wyari\.conda\envs\caiman\Library
Java version: 1.8.0_312, vendor: Azul Systems, Inc., runtime: C:\Users\wyari\.conda\envs\caiman\Library\jre
Default locale: en_US, platform encoding: GBK
OS name: "windows 10", version: "10.0", arch: "amd64", family: "windows"
ctrueden commented 2 years ago

@CanYing0913 Hmm, OK, how about this:

$ python -c 'import jgo; jgo.main(["-v", "net.imagej:imagej:2.5.0", "--headless"])'
DEBUG 2022-06-13 21:33:44,251: Using settings:      {'m2repo': '/home/curtis/.m2/repository', 'cachedir': '/home/curtis/mambaforge/envs/pyimagej-dev/jgo', 'links': 'soft'}
DEBUG 2022-06-13 21:33:44,251: Using respositories: {'scijava.public': 'https://maven.scijava.org/content/groups/public'}
DEBUG 2022-06-13 21:33:44,251: Using shortcuts:     {'repl': 'imagej:org.scijava.script.ScriptREPL', 'fiji': 'sc.fiji:fiji:LATEST', 'imagej': 'net.imagej:imagej', 'scifio': 'io.scif:scifio-cli', 'scijava': 'org.scijava:scijava-common', 'ij': 'net.imagej:ij', 'bfconvert': 'ome:bio-formats-tools:loci.formats.tools.ImageConverter', 'formatlist': 'ome:bio-formats-tools:loci.formats.tools.PrintFormatTable', 'showinf': 'ome:bio-formats-tools:loci.formats.tools.ImageInfo', 'tiffcomment': 'ome:bio-formats-tools:loci.formats.tools.TiffComment', 'xmlindent': 'ome:bio-formats-tools:loci.formats.tools.XMLIndent', 'xmlvalid': 'ome:bio-formats-tools:loci.formats.tools.XMLValidate', 'jython': 'org.python:jython-standalone', 'groovy': 'org.codehaus.groovy:groovy-groovysh:org.codehaus.groovy.tools.shell.Main+commons-cli:commons-cli:1.3.1', 'jd-cli': 'com.github.kwart.jd:jd-cli'}
DEBUG 2022-06-13 21:33:44,251: Returning expanded coordinate net.imagej:imagej:2.5.0.
DEBUG 2022-06-13 21:33:44,251: class path: /home/curtis/mambaforge/envs/pyimagej-dev/jgo/net.imagej/imagej/2.5.0/5eaefb2ee4ee2c6254e587f673ab0b31146006e43806860b75b2602c18859375/*
SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.

From your conda environment, of course. That's a direct call to jgo, which is what's failing from PyImageJ. The above is the output I see on my Linux machine. If you remove the --headless item from the input list, you should even see the ImageJ user interface pop up.

If it doesn't work, you could try deleting your .jgo cache folder (indicated by the cachedir value in the debug output) and trying again.

CanYing0913 commented 2 years ago

hmmm I am getting a strange error:

  File "<string>", line 1
    'import
           ^
SyntaxError: EOL while scanning string literal

It seems my string source file is somehow modified? But there is no differences after I compare them.

somsubhro88 commented 2 years ago

@ctrueden On the same Windows machine (for a different user), pyimagej works perfectly well. If you would like, I could run any debugging script/code there and copy-paste it here for comparison.

PS - I am travelling again, so might be a bit slow in responding.

Thanks, Som

CanYing0913 commented 2 years ago

@ctrueden Just want to let you know today it works fine. I assume a complete restart of the computer instead of signing out and back in is required after configuring JAVA_HOME.

ctrueden commented 2 years ago

@CanYing0913 wrote:

It seems my string source file is somehow modified?

Ahh, I forgot that single quotation marks do not work on Windows shells. You need to use double quotation marks.

Just want to let you know today it works fine. I assume a complete restart of the computer instead of signing out and back in is required after configuring JAVA_HOME.

Hmm, I thought logging out and in would be sufficient, assuming you change the value in your System properties of Control Panel. But... did you do that? We didn't talk about doing that. And I would prefer for PyImageJ to work on Windows even without configuring any environment variables in Control Panel.

@somsubhro88 wrote:

If you would like, I could run any debugging script/code there and copy-paste it here for comparison.

It is up to you. If you have time, that's great, we can try to understand what's happening. But how impactful it is for us to use our time like that... depends on the percentage of Windows users out there who are having such problems. We could wait until someone else comes along and comments on this issue having the same problem?

CanYing0913 commented 2 years ago

@ctrueden

assuming you change the value in your System properties of Control Panel

Yes I added it way before this problem raised.

You need to use double quotation marks.

so $ python -c "import jgo; jgo.main(["-v", "net.imagej:imagej:2.5.0", "--headless"])"? It throws

D:\CanYing\Code>python -c "import jgo; jgo.main(["-v", "net.imagej:imagej:2.5.0", "--headless"])"
  File "<string>", line 1
    import jgo; jgo.main([-v, net.imagej:imagej:2.5.0, --headless])
                                        ^
SyntaxError: invalid syntax
ctrueden commented 2 years ago

@CanYing0913 The double quotes cannot be nested, so try this:

python -c "import jgo; jgo.main(['-v', 'net.imagej:imagej:2.5.0', '--headless'])"
CanYing0913 commented 2 years ago

@ctrueden This is what I got:

(caiman) D:\CanYing\Code\Columbia\CaImAn>python -c "import jgo; jgo.main(['-v', 'net.imagej:imagej:2.5.0', '--headless'])"
DEBUG 2022-06-14 21:47:26,235: Using settings:      {'m2repo': 'C:\\Users\\wyari\\.m2\\repository', 'cachedir': 'C:\\Users\\wyari\\.jgo', 'links': 'auto'}
DEBUG 2022-06-14 21:47:26,235: Using respositories: {}
DEBUG 2022-06-14 21:47:26,237: Using shortcuts:     {}
DEBUG 2022-06-14 21:47:26,237: Returning expanded coordinate net.imagej:imagej:2.5.0.
INFO 2022-06-14 21:47:26,238: First time start-up may be slow. Downloaded dependencies will be cached for shorter start-up times in subsequent executions.
DEBUG 2022-06-14 21:47:26,254: Executing: ('C:\\Users\\wyari\\.conda\\envs\\caiman\\Library\\bin\\mvn.CMD', '-B', '-f', 'C:\\Users\\wyari\\.jgo\\net.imagej\\imagej\\2.5.0\\5eaefb2ee4ee2c6254e587f673ab0b31146006e43806860b75b2602c18859375\\pom.xml', 'dependency:resolve')
ERROR 2022-06-14 21:47:28,319: Failed to bootstrap the artifact.
ERROR 2022-06-14 21:47:28,319:
ERROR 2022-06-14 21:47:28,320: Possible solutions:
ERROR 2022-06-14 21:47:28,320: * Double check the endpoint for correctness (https://search.maven.org/).
ERROR 2022-06-14 21:47:28,320: * Add needed repositories to ~/.jgorc [repositories] block (see README).
ERROR 2022-06-14 21:47:28,321: * Try with an explicit version number (release metadata might be wrong).
ERROR 2022-06-14 21:47:28,321:
ERROR 2022-06-14 21:47:28,321: Full Maven error output:
DEBUG 2022-06-14 21:47:28,321:  [INFO] Scanning for projects...
DEBUG 2022-06-14 21:47:28,322:  [INFO]
DEBUG 2022-06-14 21:47:28,322:  [INFO] ------------< net.imagej-BOOTSTRAPPER:imagej-BOOTSTRAPPER >-------------
DEBUG 2022-06-14 21:47:28,322:  [INFO] Building imagej-BOOTSTRAPPER 0
DEBUG 2022-06-14 21:47:28,323:  [INFO] --------------------------------[ jar ]---------------------------------
DEBUG 2022-06-14 21:47:28,323:  [INFO] Downloading from central: https://repo.maven.apache.org/maven2/net/imagej/imagej/2.5.0/imagej-2.5.0.pom
DEBUG 2022-06-14 21:47:28,323:  [WARNING] The POM for net.imagej:imagej:jar:2.5.0 is missing, no dependency information available
DEBUG 2022-06-14 21:47:28,323:  [INFO] Downloading from central: https://repo.maven.apache.org/maven2/net/imagej/imagej/2.5.0/imagej-2.5.0.jar
DEBUG 2022-06-14 21:47:28,324:  [INFO] ------------------------------------------------------------------------
DEBUG 2022-06-14 21:47:28,324:  [INFO] BUILD FAILURE
DEBUG 2022-06-14 21:47:28,325:  [INFO] ------------------------------------------------------------------------
DEBUG 2022-06-14 21:47:28,325:  [INFO] Total time:  1.100 s
DEBUG 2022-06-14 21:47:28,325:  [INFO] Finished at: 2022-06-14T21:47:28-05:00
DEBUG 2022-06-14 21:47:28,325:  [INFO] ------------------------------------------------------------------------
ERROR 2022-06-14 21:47:28,326:  [ERROR] Failed to execute goal on project imagej-BOOTSTRAPPER: Could not resolve dependencies for project net.imagej-BOOTSTRAPPER:imagej-BOOTSTRAPPER:jar:0: Could not find artifact net.imagej:imagej:jar:2.5.0 in central (https://repo.maven.apache.org/maven2) -> [Help 1]
ERROR 2022-06-14 21:47:28,326:  [ERROR]
ERROR 2022-06-14 21:47:28,326:  [ERROR] To see the full stack trace of the errors, re-run Maven with the -e switch.
ERROR 2022-06-14 21:47:28,327:  [ERROR] Re-run Maven using the -X switch to enable full debug logging.
ERROR 2022-06-14 21:47:28,327:  [ERROR]
ERROR 2022-06-14 21:47:28,330:  [ERROR] For more information about the errors and possible solutions, please read the following articles:
ERROR 2022-06-14 21:47:28,330:  [ERROR] [Help 1] http://cwiki.apache.org/confluence/display/MAVEN/DependencyResolutionException
ERROR 2022-06-14 21:47:28,335:
ctrueden commented 2 years ago 
[WARNING] The POM for net.imagej:imagej:jar:2.5.0 is missing, no dependency information available

@CanYing0913 Hmm, that's because net.imagej:imagej (i.e. the top-level ImageJ2 artifact) lives in maven.scijava.org, and I guess we didn't configure jgo to look there. This may be a red herring, in that the PyImageJ project does configure jgo to look there...

Let's try something else: can you please delete the following folders:

And then try initializing PyImageJ again? That will ensure you are starting from clean caches.

CanYing0913 commented 2 years ago

@ctrueden output.pdf I am getting this amount of debugging info... The os.envrion['JAVA_HOME'] now becomes the Library under my python environment.

ctrueden commented 2 years ago

@CanYing0913 Unfortunately, I am not able to download the PDF. It appears to be 0 bytes. Can you please copy-paste the messages, rather than using a screenshot? At this point, I forgot what we are trying to solve... you have one computer where PyImageJ gives the "Failed to bootstrap the artifact" error, but other computers where it works? I would certainly try to create a fresh conda environment on the affected machine, with the latest PyImageJ installed, and see if the problem still occurs.

ptschanz commented 2 years ago

Hi @ctrueden

I was having similar issues ("Failed to bootstrap the artifact") when trying to install pyimagej both on Linux Mint and Windows. After many attempts I finally managed to make it work on both Linux and Windows. I do not fully understand the problem and why the steps solved the problem, but it might help in identifying the problem.

On Windows, I managed to solve the problem after installing JDK 18.0.2 and setting the environment variables. Then the problem disappeared. Below the steps in detail:

  1. Installation of JDK 18.0.2
  2. Set the environment variables as follows
    • JAVA_HOME = C:\Program Files\Java\jdk-18.0.2
    • Path = C:\Program Files\Java\jdk-18.0.2\bin
  3. When starting the pyimagej environment, Anaconda automatically runs the following commands before starting pyimagej
    • set JAVA_HOME_CONDA_BACKUP=C:\Program Files\Java\jdk-18.0.2
    • set JAVA_HOME=C:\Users\ptsch\mambaforge\envs\pyimagej\Library before starting the pyimagej envrionment

Hope this maybe helps to better understand the problem, but I don't know which of these steps were the critical ones. To make it work on Linux, I basically used the Windows solution above, which also solved the problem in Linux.

cmhulbert commented 1 year ago

I recently ran into this exact issue, using jgo with Paintera. It seems to be related to this issue: https://github.com/conda-forge/openjdk-feedstock/issues/107. The manual solution for me was to just remove the \lib\jvm from the end of %JAVA_PATH% before running Paintera.

ctrueden commented 1 year ago

Thanks @cmhulbert for the pointer to the OpenJDK feedstock issue. It sounds like it was now fixed upstream? I'm going to close this issue now with hope in my heart that everyone is now happy with it working on their systems. Please reopen, or maybe better, open a new issue, if anyone reading this continues to have problems along these lines with a fresh installation. Thanks!