Error in "Find particles from segmentation"

[Genis Valentin]

Hello everyone!

I'm going through the tomography ribosome tutorial dataset and trying to perform the cnn-based segmentation and particle picking. 

I'm running using e2projectmanager.py

e2version.py reports 

EMAN 2.91 final ( GITHUB: 2021-03-08 11:36 - commit: 81caed2 )

Your Python version is: 3.7.9

I could train and apply the neural network, but the "Find particles from segmentation job" fails. This is the command that fails

/opt/eman2-sphire-sparx/bin/e2spt_extractfromseg.py segmentations/mixedCTEM_tomo1__cnn_good_apply.hdf tomograms/mixedCTEM_tomo1__bin4.hdf --thresh=1.0 --boxsz=32 --random=-1 --massthresh=20.0 --edge=4 --sort --ppid=-2

This is the terminal output of the failed job:

NOT Writing notes, ppid=-2

Traceback (most recent call last):

  File "/opt/eman2-sphire-sparx/bin/e2spt_extractfromseg.py", line 154, in <module>

    main()

  File "/opt/eman2-sphire-sparx/bin/e2spt_extractfromseg.py", line 141, in main

    js["class_list"]=clst

  File "/opt/eman2-sphire-sparx/lib/python3.7/site-packages/EMAN2jsondb.py", line 905, in setval

    if not deferupdate : self.sync()

  File "/opt/eman2-sphire-sparx/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-sphire-sparx/lib/python3.7/json/__init__.py", line 238, in dumps

    **kw).encode(obj)

  File "/opt/eman2-sphire-sparx/lib/python3.7/json/encoder.py", line 201, in encode

    chunks = list(chunks)

  File "/opt/eman2-sphire-sparx/lib/python3.7/json/encoder.py", line 431, in _iterencode

    yield from _iterencode_dict(o, _current_indent_level)

  File "/opt/eman2-sphire-sparx/lib/python3.7/json/encoder.py", line 405, in _iterencode_dict

    yield from chunks

  File "/opt/eman2-sphire-sparx/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'

The training and the segmentation results of the cnn look like this.

Thanks in advance for the help and for the great software!

Genis

[MuyuanChen]

Maybe putting something in the —featurename option will solve this. Also in 2.91, you can do automatic particle picking with a more dedicated CNN particle picker, bypassing the segmentation step. 

https://blake.bcm.edu/emanwiki/EMAN2/e2tomo_more#Automated_particle_selection

<cnn.png>

<segmentation.png>

Thanks in advance for the help and for the great software!

Genis

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<segmentation.png><cnn.png>

[Genis Valentin]

Thanks for the response!

Adding --featurename did not help, but the automatic particle picking cnn worked!

Best regards

Genis