Questions about Sub-tilt refinement

[黄振]

Hi,

I would like to know the solution to some problems about Sub-tilt refinement.

When following the steps in tutorial and launching e2spt_tiltrefine.py, it just make a new dictionary "spt_xx_00", and it seems that only 1 iteration has occurred(I had set niter=4) even though the program has running for a few days. 

For example, that's all in "spt_04_00" after I have run the e2spt_tiltrefine.py for a few days:

and weirdly, the "threed_00.hdf" is just the same as the "threed_10.hdf" in "spt_04", which is the result of 3drefinement! That is to say, it seems that my e2spt_tiltrefine.py actually has NO effect. :^(

Moreover, the final result cannot be found in "subtlt_00/" since it just does not make that folder as what tutorial has illustrated!

For example:

but tutorial says that:

In addition to the dilemma that I have mentioned above, I cannot see the result of Sub-tilt refinement using "evaluate SPT refinement" in EMAN2 since the "subtilt_xx" folder does not exist at all!

I would appreciate your help! :D

Best,

Zhen Huang

ZheJiang University

[黄振]

Hi everyone,

And I just find these error informations after running the e2spt_tiltrefine.py :

Error running task :  3
e2proc3d.py spt_06_02/threed_01_even.hdf spt_06_02/threed_raw_even.hdf
Traceback (most recent call last):
  File "/share/apps/eman2.91/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count
    ret = EMUtil.get_image_count_c(fsp)
RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/hdfio2.cpp:464: error with 'spt_06_02/threed_01_even.hdf': 'cannot access file 'spt_06_02/threed_01_even.hdf'' caught


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/share/apps/eman2.91/bin/e2proc3d.py", line 890, in <module>
    main()
  File "/share/apps/eman2.91/bin/e2proc3d.py", line 308, in main
    else : nimg = EMUtil.get_image_count(infile)
  File "/share/apps/eman2.91/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count
    raise Exception(fsp)
Exception: spt_06_02/threed_01_even.hdf
e2spt_tiltrefine_oneiter.py --ptclin spt_06_02/ali_ptcls_00_odd.lst --ptclout spt_06_02/ali_ptcls_01_odd.lst --ref spt_06_02/threed_00_odd.hdf --threedout spt_06_02/threed_01_odd.hdf --keep 0.7 --threads 20 --parallel thread:20 --refineastep 1.0 --refinentry 8 --maxshift 8 --padby 1.5 --sym c1
Initializing parallelism...
20 total CPUs available
42975 jobs
Error running task :  7
e2proc3d.py spt_06_02/threed_01_odd.hdf spt_06_02/threed_raw_odd.hdf
Traceback (most recent call last):
  File "/share/apps/eman2.91/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count
    ret = EMUtil.get_image_count_c(fsp)
RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/hdfio2.cpp:464: error with 'spt_06_02/threed_01_odd.hdf': 'cannot access file 'spt_06_02/threed_01_odd.hdf'' caught


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/share/apps/eman2.91/bin/e2proc3d.py", line 890, in <module>
    main()
  File "/share/apps/eman2.91/bin/e2proc3d.py", line 308, in main
    else : nimg = EMUtil.get_image_count(infile)
  File "/share/apps/eman2.91/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count
    raise Exception(fsp)
Exception: spt_06_02/threed_01_odd.hdf
e2refine_postprocess.py --even spt_06_02/threed_01_even.hdf --odd spt_06_02/threed_01_odd.hdf --output spt_06_02/threed_01.hdf --iter 1 --restarget 9.31554932862836 --threads 20 --sym c1 --mass 3000.0  --setsf None --tophat localwiener
Fri Aug 12 21:01:01 2022: e2proc3d.py spt_06_02/threed_01_even.hdf spt_06_02/fsc_unmasked_01.txt --calcfsc=spt_06_02/threed_01_odd.hdf
Traceback (most recent call last):
  File "/share/apps/eman2.91/lib/python3.7/site-packages/EMAN2db.py", line 657, in db_get_image_count
    ret = EMUtil.get_image_count_c(fsp)
RuntimeError: FileAccessException at /home/eman2/miniconda3/conda-bld/eman2_1615224802990/work/libEM/io/hdfio2.cpp:464: error with 'spt_06_02/threed_01_even.hdf': 'cannot access file 'spt_06_02/threed_01_even.hdf'' caught


During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/share/apps/eman2.91/bin/e2proc3d.py", line 890, in <module>
    main()
  File "/share/apps/eman2.91/bin/e2proc3d.py", line 308, in main
    else : nimg = EMUtil.get_image_count(infile)
  File "/share/apps/eman2.91/lib/python3.7/site-packages/EMAN2db.py", line 660, in db_get_image_count
    raise Exception(fsp)
Exception: spt_06_02/threed_01_even.hdf
Error running:  e2proc3d.py spt_06_02/threed_01_even.hdf spt_06_02/fsc_unmasked_01.txt --calcfsc=spt_06_02/threed_01_odd.hdf
Traceback (most recent call last):
  File "/share/apps/eman2.91/bin/e2spt_tiltrefine.py", line 539, in <module>
    main()
  File "/share/apps/eman2.91/bin/e2spt_tiltrefine.py", line 460, in main
    fsc=np.loadtxt(os.path.join(path, "fsc_masked_{:02d}.txt".format(itr+1)))
  File "/share/apps/eman2.91/lib/python3.7/site-packages/numpy/lib/npyio.py", line 968, in loadtxt
    fh = np.lib._datasource.open(fname, 'rt', encoding=encoding)
  File "/share/apps/eman2.91/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 269, in open
    return ds.open(path, mode, encoding=encoding, newline=newline)
  File "/share/apps/eman2.91/lib/python3.7/site-packages/numpy/lib/_datasource.py", line 623, in open
    raise IOError("%s not found." % path)
OSError: spt_06_02/fsc_masked_01.txt not found.

What's going wrong?

Thanks!

Zhen Huang

ZheJiang University

[Muyuan Chen]

It seems that you are on a quite old version of Eman. I would recommend upgrading to the continuous build and also try out the “new” refinement protocol mentioned in the tutorial online. It should be more stable and performs better.

Muyuan 

On Aug 12, 2022, at 9:11 AM, 黄振 <zhenhu...@gmail.com> wrote:



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[黄振]

Hi Muyuan,

Thanks a million. I'll try that.

I really appreciate your timely help!

Zhen Huang

ZheJiang University