imagej / imagej/pyimagej

Testing your installation - failed

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Description

Hi,
I have just followed the instructions for installing PyImageJ using mamba.
running the complete test command gave the following syntax error:
`(pyimagej) C:\Windows\system32>python -c "import imagej; ij = imagej.init("2.14.0"); print(ij.getVersion())"
File "", line 1
import imagej; ij = imagej.init(2.14.0); print(ij.getVersion())
^
SyntaxError: invalid syntax

(pyimagej) C:\Windows\system32>python -c "import imagej; ij = imagej.init('2.14.0'); print(ij.getVersion())"
Failed to guess the Java version.
#
# A fatal error has been detected by the Java Runtime Environment:
#
# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x00007fff25f764f9, pid=31756, tid=12988
#
# JRE version: (11.0.13+7) (build )
# Java VM: OpenJDK 64-Bit Server VM (11.0.13+7-b1751.21, mixed mode, sharing, tiered, compressed oops, g1 gc, windows-amd64)
# Problematic frame:
# C 0x00007fff25f764f9
#
# No core dump will be written. Minidumps are not enabled by default on c`

When I have run the test command sequentially I got the following error:
`(pyimagej) C:\Windows\system32>python
Python 3.8.18 (default, Sep 11 2023, 13:39:12) [MSC v.1916 64 bit (AMD64)] :: Anaconda, Inc. on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import imagej
>>> ij = imagej.init("2.14.0")
Failed to guess the Java version.
#
# A fatal error has been detected by the Java Runtime Environment:
#
# EXCEPTION_ACCESS_VIOLATION (0xc0000005) at pc=0x00007fff25f764f9, pid=32360, tid=14892
#
# JRE version: (11.0.13+7) (build )
# Java VM: OpenJDK 64-Bit Server VM (11.0.13+7-b1751.21, mixed mode, sharing, tiered, compressed oops, g1 gc, windows-amd64)
# Problematic frame:
# C 0x00007fff25f764f9
#
# No core dump will be written. Minidumps are not enabled by default on client versions of Windows`

I'm using win10 pro OS.

pip freeze:
`(pyimagej) C:\Windows\system32>pip freeze
Bottleneck @ file:///C:/b/abs_f05kqh7yvj/croot/bottleneck_1707864273291/work
Brotli @ file:///C:/Windows/Temp/abs_63l7912z0e/croots/recipe/brotli-split_1659616056886/work
certifi @ file:///C:/b/abs_35d7n66oz9/croot/certifi_1707229248467/work/certifi
charset-normalizer @ file:///tmp/build/80754af9/charset-normalizer_1630003229654/work
contourpy @ file:///C:/b/abs_d5rpy288vc/croots/recipe/contourpy_1663827418189/work
cycler @ file:///tmp/build/80754af9/cycler_1637851556182/work
fonttools==4.25.0
idna @ file:///C:/b/abs_bdhbebrioa/croot/idna_1666125572046/work
imagecodecs @ file:///C:/b/abs_e2g5zbs1q0/croot/imagecodecs_1695065012000/work
imglyb @ file:///home/conda/feedstock_root/build_artifacts/imglyb_1678677411834/work
importlib-resources @ file:///C:/b/abs_d0dmp77t95/croot/importlib_resources-suite_1704281892795/work
jgo @ file:///home/conda/feedstock_root/build_artifacts/jgo_1685135883509/work
JPype1 @ file:///C:/b/abs_1f92quvzzn/croot/jpype1_1674515186799/work
kiwisolver @ file:///C:/b/abs_88mdhvtahm/croot/kiwisolver_1672387921783/work
labeling @ file:///home/conda/feedstock_root/build_artifacts/labeling_1651082750833/work
matplotlib @ file:///C:/b/abs_085jhivdha/croot/matplotlib-suite_1693812524572/work
mkl-fft @ file:///C:/b/abs_19i1y8ykas/croot/mkl_fft_1695058226480/work
mkl-random @ file:///C:/b/abs_edwkj1_o69/croot/mkl_random_1695059866750/work
mkl-service==2.4.0
munkres==1.1.4
numexpr @ file:///C:/b/abs_afm0oewmmt/croot/numexpr_1683221839116/work
numpy @ file:///C:/Users/dev-admin/mkl/numpy_and_numpy_base_1682982345978/work
packaging @ file:///C:/b/abs_28t5mcoltc/croot/packaging_1693575224052/work
pandas @ file:///C:/miniconda3/conda-bld/pandas_1692299636855/work
Pillow @ file:///C:/b/abs_153xikw91n/croot/pillow_1695134603563/work
platformdirs @ file:///C:/b/abs_b6z_yqw_ii/croot/platformdirs_1692205479426/work
pooch @ file:///C:/b/abs_a8nmng7d_x/croot/pooch_1695850149827/work
psutil @ file:///C:/Windows/Temp/abs_b2c2fd7f-9fd5-4756-95ea-8aed74d0039flsd9qufz/croots/recipe/psutil_1656431277748/work
pyimagej @ file:///D:/bld/pyimagej_1678737117317/work
pyparsing @ file:///C:/Users/BUILDE~1/AppData/Local/Temp/abs_7f_7lba6rl/croots/recipe/pyparsing_1661452540662/work
PySocks @ file:///C:/ci/pysocks_1605287845585/work
python-dateutil @ file:///tmp/build/80754af9/python-dateutil_1626374649649/work
pytz @ file:///C:/b/abs_19q3ljkez4/croot/pytz_1695131651401/work
requests @ file:///C:/b/abs_474vaa3x9e/croot/requests_1707355619957/work
scipy==1.10.1
scyjava @ file:///home/conda/feedstock_root/build_artifacts/scyjava_1689084809566/work
six @ file:///tmp/build/80754af9/six_1644875935023/work
tifffile @ file:///C:/b/abs_45o5chuqwt/croot/tifffile_1695107511025/work
tzdata @ file:///croot/python-tzdata_1690578112552/work
urllib3 @ file:///C:/b/abs_4etpfrkumr/croot/urllib3_1707770616184/work
win-inet-pton @ file:///C:/ci/win_inet_pton_1605306167264/work
xarray @ file:///C:/b/abs_2fi_umrauo/croot/xarray_1668776806973/work
zipp @ file:///C:/b/abs_b0beoc27oa/croot/zipp_1704206963359/work`

I have used JAVA version "JavaSetup8u401.exe"

Please assist.

Thanks,

- Dean

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by reproducing the installation test on Windows 10 with the reported Python, Java, PyImageJ, JPype1, and scyjava versions. Inspect the imagej.init entry point and the Java-version detection path after the syntax issue is corrected. Done means the documented test command completes without the JVM access violation or clearly reports an unsupported environment.

Written by the indexing model from the issue text.

Assessment

Tech stack
java, python
Domain
backend, tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
25/100

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