Automatic tomogram segmentation error

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Nikolai Petrosian

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Nov 17, 2020, 9:25:18 AM11/17/20
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Hallo everyone,

Sorry for such a question, I am a new in this field and in using EMAN2..
I tried to use EMAN2 automatic tomogram segmentation, which uses CNN, in order to segment and extract ribosome densities from  the tomogram. It worked well until last step of finding and extracting particles, seems calculation worked, but I didn't find any output file which includes list of coordinates of extracted particles, which I could use for Subtomogram averaging..
result:

NOT Writing notes, ppid=-2

706 boxes found..


After that I got a problem with launching files if I run e2projectmanmager.py from other folders

Result after launching a new tomogram (.rec or .mrc) using e2projectmanager.py GUI:

NOT Writing notes, ppid=-2

1/1Traceback (most recent call last):

File "/Users/nikolaipetrosian/EMAN2/bin/e2tomoseg_preproc.py", line 89, in <module>

main()

File "/Users/nikolaipetrosian/EMAN2/bin/e2tomoseg_preproc.py", line 86, in main

im.write_image(procout[0],0)

File "/Users/nikolaipetrosian/EMAN2/lib/python2.7/site-packages/EMAN2db.py", line 509, in db_write_image

return self.write_image_c(fsp,*parms)

RuntimeError: FileAccessException at /Users/eman/anaconda/conda-bld/eman2_1569858044896/work/libEM/hdfio2.cpp:514: error with 'tomograms/DBla35_ts19_ali_32b_05_preproc.hdf': 'cannot access file 'tomograms/DBla35_ts19_ali_32b_05_preproc.hdf'' caught

Do you know how to correct these errors and make e2projectmanager.py working properly again? I can't start other projects..

Version of eman2:

e2version.py     

EMAN 2.31 final (GITHUB: 2019-09-30 10:43 - commit: 194df95 )

Your EMAN2 is running on: Mac OS 10.15.6 x86_64

Your Python version is: 2.7.14


Thank you

Nick


Muyuan Chen

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Nov 17, 2020, 11:00:49 AM11/17/20
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Particles should be found by going to the manual particles boxing program and look for the specified new label. You can then modify them and save through the extract particles step.

Running program inside other folders than the project folder is not recommended and will cause problems all over the place...

Also, if you just want to automatically pick particles, in later versions now we offer more specialized cnn based tool for it.
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Петросян, Николай Степанович

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Nov 17, 2020, 11:43:54 AM11/17/20
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Dear Chen,

Thank you very much for the help!
I tried to do extraction:

e2spt_extract.py tomograms/DBla35_ts06_ali_32b_05_preproc.hdf --boxsz_unbin=-1 --threads=12 --maxtilt=100 --padtwod=2.0 --shrink=1.0 --tltkeep=1.0 --rmbeadthr=-1.0 --curves=-1 --curves_overlap=0.5


but got errors:

NOT Writing notes, ppid=-2

Reading from tomograms/DBla35_ts06_ali_32b_05_preproc.hdf...

Traceback (most recent call last):

  File "/Users/nikolaipetrosian/EMAN2/bin/e2spt_extract.py", line 782, in <module>

    main()

  File "/Users/nikolaipetrosian/EMAN2/bin/e2spt_extract.py", line 110, in main

    do_extraction(args[0], options)

  File "/Users/nikolaipetrosian/EMAN2/bin/e2spt_extract.py", line 135, in do_extraction

    ttparams=np.array(js["tlt_params"])

  File "/Users/nikolaipetrosian/EMAN2/lib/python2.7/site-packages/EMAN2jsondb.py", line 856, in get

    raise KeyError(key)

KeyError: 'tlt_params'


Do I understand correctly, I can't have different folders for different projects (different tomograms) and run the program in each of them? Should I create one EMAN folder and always run all different projects only in that folder? 

Thank you
Nick



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Steve Ludtke

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Nov 17, 2020, 11:47:44 AM11/17/20
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You should never, ever, run EMAN commands from inside the EMAN software folders. This will create a massive mess. Each project should have a project folder, and all EMAN2 commands should be executed from within that folder. Frequently there will be subfolders within the project folder, but you should always run the EMAN2 commands from the main project folder.

I note from your earlier post that you are running EMAN2.31. There have been a number of important changes and improvements to the tomography software over the last year, so if you are trying to do subtomogram averaging we very strongly encourage you to use the current continuous build instead of the 2.31 release. We've been promising a new release for some months, but still haven't managed to push it out just yet, but the continuous builds should be quite stable.


Muyuan Chen

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Nov 17, 2020, 11:54:57 AM11/17/20
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Oh, if you reconstruct tomograms in imod or other softwares then import to Eman, many functionalities such as extract particles won’t work. You can instead save particles from the manual particle boxer window. 

No you should have one folder per project (which can have many tomograms). Just do not run programs anywhere other than the main project folders.

Петросян, Николай Степанович

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Nov 17, 2020, 12:53:20 PM11/17/20
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Thank you very much for all your help!

To view this discussion on the web visit https://groups.google.com/d/msgid/eman2/28F0A4A4-4DA8-4485-AB36-33B819459D7C%40gmail.com.

Петросян, Николай Степанович

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Nov 17, 2020, 1:30:23 PM11/17/20
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Excuse me again..
I tried to create new folders (outside of initial folder where I run EMAN before) for new projects and both copy a new tomogram there and run the program, or just run the program and give a link to the location of the tomogram, in both cases I still get errors when I try to do preprocessing of the tomogram:

e2tomoseg_preproc.py DBla35_ts19_ali_32b_05.mrc --proctag=preproc --proc1=filter.lowpass.gauss:cutoff_abs=.25 --proc2=filter.highpass.gauss:cutoff_pixels=5 --proc3=normalize --proc4=threshold.clampminmax.nsigma:nsigma=3


NOT Writing notes, ppid=-2


1/1Traceback (most recent call last):

  File "/Users/nikolaipetrosian/EMAN2/bin/e2tomoseg_preproc.py", line 89, in <module>

    main()

  File "/Users/nikolaipetrosian/EMAN2/bin/e2tomoseg_preproc.py", line 86, in main

    im.write_image(procout[0],0)

  File "/Users/nikolaipetrosian/EMAN2/lib/python2.7/site-packages/EMAN2db.py", line 509, in db_write_image

    return self.write_image_c(fsp,*parms)

RuntimeError: FileAccessException at /Users/eman/anaconda/conda-bld/eman2_1569858044896/work/libEM/hdfio2.cpp:514: error with 'tomograms/DBla35_ts19_ali_32b_05_preproc.hdf': 'cannot access file 'tomograms/DBla35_ts19_ali_32b_05_preproc.hdf'' caught



I think I somehow messed up the pathways of EMAN2, but how can I correct everything? 

Thank you
Nick

Muyuan Chen

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Nov 17, 2020, 1:49:33 PM11/17/20
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I suspect just manually creating a folder called tomograms will work, although it could be much messier than I imagined....

Steve Ludtke

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Nov 17, 2020, 1:56:39 PM11/17/20
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Did you import the tomogram into the project? Are you using e2projectmanager.py or just running from the command-line? Are you sure there weren't any other errors before this one?

Петросян, Николай Степанович

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Nov 17, 2020, 1:58:16 PM11/17/20
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Thanks! 
Seems it works. I guess, next time if something doesn't work in a new folder, I just can manually create the missing folder to correct pathway errors?

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MuyuanChen

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Nov 17, 2020, 2:05:32 PM11/17/20
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In theory if you go through the workflow in the correct way, the folders should be created automatically.

Петросян, Николай Степанович

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Nov 17, 2020, 2:09:31 PM11/17/20
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Yes, the project folder included the tomogram, I use e2projectmanager.py, during the day I had several errors, but it seems they all were similar to this pathway error.
I tried a few times, when I create a new folder and run the program - preprocessing doesn't work and only "info" folder is created, but if i manually create 'tomograms" folder it works well.


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