Unicode Error

[jawoll14]

I am currently trying to convert the following .vsi files into .tif files.

20180910_stimulated yfp_YFP-f_003_current
20180911_csf1after5min stimulated flms_PH_001_current
sad323-00a6ls04:untitled folder jared$ python -m microscoper --list
./20180910_stimulated yfp_YFP-f_003_current/stack1/20180910_stimulated yfp_YFP-f_003_current.vsi
./20180911_csf1after5min stimulated flms_PH_001_current/stack1/20180911_csf1after5min stimulated flms_PH_001_current.vsi

Total files found: 2

When I try to convert the following files into the tif format using the command python -m microscoper. I get the following output. One .tif file is created, but it gets stuck and doesn't process the rest of the files. I was able to get this working on my old macbook, but I recently got a new macbook and had to download it onto my new one, but I am having trouble getting it to work. I can open my files through imageJ using bioformats, but this can save me a lot of time to convert many files at once. Thanks

Traceback (most recent call last): | 0/2 [00:00<?, ?it/s]
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 174, in _run_module_as_main██████████| 100/100 [00:00<00:00, 102.77it/s]
"main", fname, loader, pkg_name)█████████| 1/1 [00:00<00:00, 127.46it/s]
File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/runpy.py", line 72, in _run_code
exec code in run_globals
File "/Users/jared/microscoper/microscoper/main.py", line 3, in
run()
File "/Users/jared/microscoper/microscoper/io.py", line 212, in run
save_metadata(metadata, save_directory)
File "/Users/jared/microscoper/microscoper/io.py", line 138, in save_metadata
xmlfile.write(pretty_xml_as_string)
UnicodeEncodeError: 'ascii' codec can't encode character u'\xb5' in position 565: ordinal not in range(128)

[pskeshu]

It's probably because you're running it on python2, and python-bioformats has some problem reading unicode characters from the metadata associated with .vsi files.

Installing the python3 version of microscoper will solve the problem.

[pskeshu]

BTW, you can also now run microscoper directly, without having to call it through python -m microscoper.

[jawoll14]

Hi, thanks for getting back to me so soon. So, I uninstalled python and reinstalled python 3 on my macbook, and then reinstalled microscoper, but now I have a new problem. I tried uninstalling both javabridge and microscoper and then reinstalling each of them after I got this error, but I still get the same error. Thanks

Traceback (most recent call last):
File "/Users/jared/miniconda3/lib/python3.6/runpy.py", line 183, in _run_module_as_main
mod_name, mod_spec, code = _get_module_details(mod_name, _Error)
File "/Users/jared/miniconda3/lib/python3.6/runpy.py", line 142, in _get_module_details
return _get_module_details(pkg_main_name, error)
File "/Users/jared/miniconda3/lib/python3.6/runpy.py", line 109, in _get_module_details
import(pkg_name)
File "/Users/jared/miniconda3/lib/python3.6/site-packages/microscoper/init.py", line 1, in
from .io import run
File "/Users/jared/miniconda3/lib/python3.6/site-packages/microscoper/io.py", line 13, in
import bioformats as bf
File "/Users/jared/miniconda3/lib/python3.6/site-packages/bioformats/init.py", line 21, in
import javabridge
File "/Users/jared/miniconda3/lib/python3.6/site-packages/javabridge/init.py", line 38, in
from .jutil import start_vm, kill_vm, vm, activate_awt, deactivate_awt
File "/Users/jared/miniconda3/lib/python3.6/site-packages/javabridge/jutil.py", line 157, in
import javabridge._javabridge as _javabridge
ImportError: dlopen(/Users/jared/miniconda3/lib/python3.6/site-packages/javabridge/_javabridge.cpython-36m-darwin.so, 2): Symbol not found: _kCFAllocatorDefault
Referenced from: /Users/jared/miniconda3/lib/python3.6/site-packages/javabridge/_javabridge.cpython-36m-darwin.so
Expected in: flat namespace
in /Users/jared/miniconda3/lib/python3.6/site-packages/javabridge/_javabridge.cpython-36m-darwin.so

[pskeshu]

Seems like a conda specific python-javabridge error. Can you try reinstalling python-javabridge or install the latest version from their github repo?

Similar problem was reported here: LeeKamentsky/python-javabridge#136