unstacking .eer movies

[Paul Sauer]

Dear experts,

I wish to 'unstack' a .eer movie to create individual frames, each one of them containing 28 eer frames (a total of 1176 eer frames per movie grouped by 28 should give 42 actual frames). I would like these 42 frames to be written out as .mrc files. The purpose is to perform an image processing step on each of these frames before combining them again and performing motion correction. My workflow would look something like that: convert eer. to .mrcs (with 28 raw eer frames per movie frame), unstack the resulting .mrcs movie, perform my image operation, make a new stack, motion correction. 

However already the fist step fails. Now my question is whether you could help me with the error (see below, it's probably something very trivial) but also whether the suggested workflow makes sense and if there is an easy/easier way to do it. I doubt I could do the converting and unstacking in one command? Are there obvious simplifications I  didn't think of?

Thank you very much for your help

Best

Paul

[psauer@shark test]$ e2version.py

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

Your Python version is: 3.7.9

[psauer@shark test]$ e2proc2d.py FoilHole_8895352_Data_8875556_8875558_20210711_010516_EER.eer mymovie.mrcs --avgseq 28

Traceback (most recent call last):

  File "/programs/x86_64-linux/eman2/2.91/eman2_extlib/eman2-2.91-nga4/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count

    ret = EMUtil.get_image_count_c(fsp)

ValueError: stoi

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "/programs/x86_64-linux/eman2/2.91/bin/e2proc2d.py", line 1214, in <module>

    main()

  File "/programs/x86_64-linux/eman2/2.91/bin/e2proc2d.py", line 452, in main

    nimg = EMUtil.get_image_count(infile)

  File "/programs/x86_64-linux/eman2/2.91/eman2_extlib/eman2-2.91-nga4/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count

    raise Exception(fsp)

Exception: FoilHole_8895352_Data_8875556_8875558_20210711_010516_EER.eer

Paul Sauer, PhD

Eva Nogales Lab

742 Stanley Hall, MS 3220

UC Berkeley

94720-3220 Berkeley, CA, USA

Phone: +1 510 666 3335

http://cryoem.berkeley.edu

[Ludtke, Steven J.]

Just to double-check, I tried this myself just now on one of my own EER files and it worked fine. I don't recall there being any intrinsic EER issues with the last release version (I'm using a current snapshot). Have you tried it on another file?  I do get a bunch of:

TIFFReadDirectory: Unknown field with tag 65001 (0xfde9) encountered

warnings, likely due to TF adding some new metadata item to the header we haven't dealt with, but these are just warnings, not errors.

If it fails in a similar way on another file, then we may need to find some way to take a look at one of your files. The error your getting seems to indicate a corrupt header in the EER file...

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <slu...@bcm.edu>                      Baylor College of Medicine 

Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)

Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)

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