Error in find particles from segmentation

[Ziao]

Hi Steve,

I run into this error when I tried to find particles from a segmentation results.

NOT Writing notes, ppid=-2
Traceback (most recent call last):
  File "/opt/EMAN2/2.91/bin/e2spt_extractfromseg.py", line 154, in <module>
    main()
  File "/opt/EMAN2/2.91/bin/e2spt_extractfromseg.py", line 141, in main
    js["class_list"]=clst
  File "/opt/EMAN2/2.91/lib/python3.7/site-packages/EMAN2jsondb.py", line 905, in setval
    if not deferupdate : self.sync()
  File "/opt/EMAN2/2.91/lib/python3.7/site-packages/EMAN2jsondb.py", line 747, in sync
    jss=json.dumps(self.data,indent=0,sort_keys=True,default=obj_to_json)            # write the whole dictionary back to disk
  File "/opt/EMAN2/2.91/lib/python3.7/json/__init__.py", line 238, in dumps
    **kw).encode(obj)
  File "/opt/EMAN2/2.91/lib/python3.7/json/encoder.py", line 201, in encode
    chunks = list(chunks)
  File "/opt/EMAN2/2.91/lib/python3.7/json/encoder.py", line 431, in _iterencode
    yield from _iterencode_dict(o, _current_indent_level)
  File "/opt/EMAN2/2.91/lib/python3.7/json/encoder.py", line 405, in _iterencode_dict
    yield from chunks
  File "/opt/EMAN2/2.91/lib/python3.7/json/encoder.py", line 353, in _iterencode_dict
    items = sorted(dct.items(), key=lambda kv: kv[0])
TypeError: '<' not supported between instances of 'int' and 'str'

Any idea what I should do?

Let me know if you need more information.

Best,

Ziao

[Muyuan Chen]

I heard reports of the bug a few times lately but cannot reproduce this myself. According to the message, it seems that there are some particle classes in this tomogram that are labeled as numbers instead of strings. It may be solved if you specify something in --featurename, but I am not too sure. Also check if the error goes away if you clear all particles in the same tomogram before running the program. You can also look at the json file corresponding to the tomogram in the info directory and see if there is anything odd in the "class_lst" key. 

Just noticed this email is directed to Steve, which might be why it got classified as spam in my gmail... Anyway, feel free to comment if you have insight on this.

Muyuan

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