NoSuchMethodError: setLevel

[Benny-Github]

I am trying to convert VSI files to TIFF, and I found that your microscoper should be helpful.

When I trying to use command: microscoper, there are some error occurred:

---

C:\Users\ABC\Desktop\ABC\Image\VSI-Test\2007>python -m microscoper
Exception in thread "Thread-0" java.lang.NoSuchMethodError: setLevel
Traceback (most recent call last):
File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\runpy.py", line 193, in _run_module_as_main
"main", mod_spec)
File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\runpy.py", line 85, in run_code
exec(code, run_globals)
File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\microscoper_main.py", line 3, in
run()
File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\microscoper\io.py", line 185, in run
logger = _init_logger()
File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\microscoper\io.py", line 162, in _init_logger
logLevel)
File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\javabridge\jutil.py", line 883, in call
fn = make_call(o, method_name, sig)
File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\javabridge\jutil.py", line 846, in make_call
raise JavaException(jexception)
javabridge.jutil.JavaException: setLevel

Here are the packages version:

---

Package Version

boto3 1.12.35
botocore 1.15.35
docutils 0.15.2
future 0.18.2
imagecodecs 2020.2.18
javabridge 1.0.18
jmespath 0.9.5
microscoper 0.3.1
numpy 1.18.2
pip 20.0.2
python-bioformats 1.5.2
python-dateutil 2.8.1
s3transfer 0.3.3
setuptools 41.2.0
six 1.14.0
tifffile 2020.2.16
tqdm 4.45.0
urllib3 1.25.8

I think the problem should be on the [NoSuchMethodError: setLevel], but I googled a lot and still cannot solve it.
Could you help me to make a check?
Thank you so much!

[pskeshu]

try with python-bioformats==1.2.0

…

On Fri, 3 Apr 2020 at 23:31, Benny-Github ***@***.***> wrote: I am trying to convert VSI files to TIFF, and I found that your microscoper should be helpful. When I trying to use command: microscoper, there are some error occurred: ------------------------------ C:\Users\ABC\Desktop\ABC\Image\VSI-Test\2007>python -m microscoper Exception in thread "Thread-0" java.lang.NoSuchMethodError: setLevel Traceback (most recent call last): File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\runpy.py", line 193, in _run_module_as_main "*main*", mod_spec) File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\runpy.py", line 85, in *run_code exec(code, run_globals) File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\microscoper_main*.py", line 3, in run() File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\microscoper\io.py", line 185, in run logger = _init_logger() File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\microscoper\io.py", line 162, in _init_logger logLevel) File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\javabridge\jutil.py", line 883, in call fn = make_call(o, method_name, sig) File "C:\Users\ABC\AppData\Local\Programs\Python\Python37\lib\site-packages\javabridge\jutil.py", line 846, in make_call raise JavaException(jexception) javabridge.jutil.JavaException: setLevel Here are the packages version: ------------------------------ Package Version boto3 1.12.35 botocore 1.15.35 docutils 0.15.2 future 0.18.2 imagecodecs 2020.2.18 javabridge 1.0.18 jmespath 0.9.5 microscoper 0.3.1 numpy 1.18.2 pip 20.0.2 python-bioformats 1.5.2 python-dateutil 2.8.1 s3transfer 0.3.3 setuptools 41.2.0 six 1.14.0 tifffile 2020.2.16 tqdm 4.45.0 urllib3 1.25.8 I think the problem should be on the [NoSuchMethodError: setLevel], but I googled a lot and still cannot solve it. Could you help me to make a check? Thank you so much! — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#4>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABVNN4F5WTTW74DKF6TBRE3RKYQARANCNFSM4L4K2JIQ> .

-- Kesavan

[Benny-Github]

try with python-bioformats==1.2.0
Kesavan

Thank you so much!
Python-bioformats==1.2.0 is working.
A .vsi file can be converted into 3 .tif files.
But unfortunately, all these 3 .tif files cannot be opened by Openslide.
[Openslide] https://openslide.org/
If you have any good idea, please let me know.
So appreciate for you help!

[fengkh]

try with python-bioformats==1.2.0
Kesavan

Thank you so much! Python-bioformats==1.2.0 is working. A .vsi file can be converted into 3 .tif files. But unfortunately, all these 3 .tif files cannot be opened by Openslide. [Openslide] https://openslide.org/ If you have any good idea, please let me know. So appreciate for you help!

Did you find the method of converting .vsi file to the format which openslide can open?

[pskeshu]

It would help to know what kind of errors you're getting with openslide. I've not used that tool, but based on the description in the website, my guess would be that it's looking for some metadata, such as XYZTC embedded in the image to project it correctly.

…

On Thu, 4 Jan 2024, 08:29 Feng Kanghui, ***@***.***> wrote: try with python-bioformats==1.2.0 Kesavan Thank you so much! Python-bioformats==1.2.0 is working. A .vsi file can be converted into 3 .tif files. But unfortunately, all these 3 .tif files cannot be opened by Openslide. [Openslide] https://openslide.org/ If you have any good idea, please let me know. So appreciate for you help! Did you find the method of converting .vsi file to the format which openslide can open? — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABVNN4ANJGDPMZYO6X4FBZLYMZK4LAVCNFSM4L4K2JI2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBXGY2TSOBXHE3A> . You are receiving this because you commented.Message ID: ***@***.***>

[fengkh]

It would help to know what kind of errors you're getting with openslide. I've not used that tool, but based on the description in the website, my guess would be that it's looking for some metadata, such as XYZTC embedded in the image to project it correctly.
…
On Thu, 4 Jan 2024, 08:29 Feng Kanghui, @.> wrote: try with python-bioformats==1.2.0 Kesavan Thank you so much! Python-bioformats==1.2.0 is working. A .vsi file can be converted into 3 .tif files. But unfortunately, all these 3 .tif files cannot be opened by Openslide. [Openslide] https://openslide.org/ If you have any good idea, please let me know. So appreciate for you help! Did you find the method of converting .vsi file to the format which openslide can open? — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABVNN4ANJGDPMZYO6X4FBZLYMZK4LAVCNFSM4L4K2JI2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBXGY2TSOBXHE3A . You are receiving this because you commented.Message ID: @.>

I have some pathological tissue section data in vsi format, but if I directly open these data with openslide, I can only get images with very small resolution and cannot read data of other levels