Exception in thread "Thread-0" java.lang.NoSuchMethodError: setLevel

[n0542344]

I'm trying to use microscoper (which sounds exactly like the tool I'd need, since I have to convert multiple .vsi-files into a usable image-format like .tiff or .png or .jpg) but have to admit that I'm unable to do so.

I'm running microscoper -f . -k .vsi in a directory where only the image files are present.

The output of ls -l is:

total 596K
drwx------ 1 me me   12 2020-07-22 13:23 _30-005 cre_
-rw------- 1 me me 596K 2020-07-22 13:23 30-005 cre.vsi

The output of tree -a is:
.
├── 30-005 cre
│ └── stack1
│ └── frame_t.ets
└── 30-005 cre.vsi

2 directories, 2 files


Exception in thread "Thread-0" java.lang.NoSuchMethodError: setLevel
Traceback (most recent call last):
  File "/home/x0ff/.local/bin/microscoper", line 10, in <module>
    sys.exit(run())
  File "/home/x0ff/.local/lib/python3.7/site-packages/microscoper/io.py", line 185, in run
    logger = _init_logger()
  File "/home/x0ff/.local/lib/python3.7/site-packages/microscoper/io.py", line 162, in _init_logger
    logLevel)
  File "/home/x0ff/.local/lib/python3.7/site-packages/javabridge/jutil.py", line 888, in call
    fn = make_call(o, method_name, sig)
  File "/home/x0ff/.local/lib/python3.7/site-packages/javabridge/jutil.py", line 851, in make_call
    raise JavaException(jexception)
javabridge.jutil.JavaException: setLevel

Then the process hangs and I have to Ctrl-C out of it.

Do you have any ideas why that happens and what I could do to get the program to work properly?

Thanks, Alex

[pskeshu]

Can you tell me which version of python-bioformats and python-javabridge you have in your system?

…

On Wed 22 Jul, 2020, 5:39 PM n0542344, ***@***.***> wrote: I'm trying to use microscoper (which sounds exactly like the tool I'd need, since I have to convert multiple .vsi-files into a usable image-format like .tiff or .png or .jpg) but have to admit that I'm unable to do so. I'm running microscoper -f . -k .vsi in a directory where only the image files are present. The output of ls -l is: total 596K drwx------ 1 me me 12 2020-07-22 13:23 _30-005 cre_ -rw------- 1 me me 596K 2020-07-22 13:23 30-005 cre.vsi The output of tree -a is: . ├── *30-005 cre* │ └── stack1 │ └── frame_t.ets └── 30-005 cre.vsi 2 directories, 2 files Exception in thread "Thread-0" java.lang.NoSuchMethodError: setLevel Traceback (most recent call last): File "/home/x0ff/.local/bin/microscoper", line 10, in <module> sys.exit(run()) File "/home/x0ff/.local/lib/python3.7/site-packages/microscoper/io.py", line 185, in run logger = _init_logger() File "/home/x0ff/.local/lib/python3.7/site-packages/microscoper/io.py", line 162, in _init_logger logLevel) File "/home/x0ff/.local/lib/python3.7/site-packages/javabridge/jutil.py", line 888, in call fn = make_call(o, method_name, sig) File "/home/x0ff/.local/lib/python3.7/site-packages/javabridge/jutil.py", line 851, in make_call raise JavaException(jexception) javabridge.jutil.JavaException: setLevel Then the process hangs and I have to Ctrl-C out of it. Do you have any ideas why that happens and what I could do to get the program to work properly? Thanks, Alex — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABVNN4AMAGX2IOQ2JSPUDETR43JGZANCNFSM4PEUPHNQ> .

[n0542344]

Can you tell me which version of python-bioformats and python-javabridge
you have in your system?

The result of pip3 show python-bioformats yields Version: 1.5.2.

pip3 show python-javabridge gets no results, but pip3 show javabridge gives as output Version: 1.0.19.

In the meantime I also installed bioformats (without the 'python-'-part), pip3 show bioformats shows Version: 0.1.15. Now my error output of microscoper -f . -k .vsi changed:

Traceback (most recent call last):
  File "/home/x0ff/.local/bin/microscoper", line 10, in <module>
    sys.exit(run())
  File "/home/x0ff/.local/lib/python3.7/site-packages/microscoper/io.py", line 184, in run
    jb.start_vm(class_path=bf.JARS, max_heap_size="2G")
AttributeError: module 'bioformats' has no attribute 'JARS'

and the program exits with an echo $? of 1.

ps.: I just re-wrote my answer because I realized that email-replies do not support markdown formatting.