e2proc2d.py fftavg option

[Rui Zhang]

Hi, Steve,

I tried the command e2proc2d.py test.hed 1.hed --fftavg=test.tnf

If I use the EMAN1 "v2" viewer to open the resulting test.tnf file, it says "Error: Incomplete data read 0/512 blocks"

and the image looks like the one in the attachment.

Did I miss something here?

P.S. the eman1 command proc2d test.hed 1.hed fftavg=test.tnf works fine.

Thanks!

Rui

[Steven Ludtke]

Hi Rui. The TNF file you sent is square, and not complex.  I just tried an equivalent e2proc2d.py command with the current CVS version of EMAN2, and it produced an appropriate TNF file (complex with 2 more pixels in x than y, as it should be).   What version are you using ?  It is possible it was broken at some point in the past...

----------------------------------------------------------------------------

Steven Ludtke, Ph.D.

Professor, Dept of Biochemistry and Mol. Biol.         (www.bcm.edu/biochem)

Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)

Co-Director CIBR Center                          (www.bcm.edu/research/cibr)

Baylor College of Medicine                             

slu...@bcm.edu

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<test.tnf>

[Rui Zhang]

Hi, Steve,

I am using eman2.05. 

Sorry, it was just a png image in my previous email. Please see the real TNF file in the attachment.

Rui

[Steven Ludtke]

Hi Rui. Sorry, I wasn't really paying attention to the first message. The only 2 formats we really support writing FFTs to are HDF and (pre 2.1) BDB. Even if the format supports it, there are a lot of annoying issues with varying FFT conventions, so we made a conscious decision not to support writing FFTs to disk in any broad way. You are correct, that it looks like TNF's should work, but clearly the files don't get written properly. 

<test2.tnf>

[Rui Zhang]

Hi, Steve,

Thank you for clarifying that!

What I really want is to sum up a bunch of power spectra of aligned helical images.

Which eman2 function can I use at the python level?

Thanks!

Rui 

[Steven Ludtke]

If they are aligned, then shouldn't you be doing a coherent average (or average in real-space) before computing the power-spectrum ?

This is the code from the --fftavg option, which works correctly (it's just the file-saving you were having issues with):

if not fftavg:

fftavg = EMData()

fftavg.set_size(nx+2, ny)

fftavg.set_complex(1)

fftavg.to_zero()

d.process_inplace("mask.ringmean")

d.process_inplace("normalize")

df = d.do_fft()

df.mult(df.get_ysize())

fftavg.add_incoherent(df)

Most of what the above code does should be pretty obvious. You can display the results easily in e2.py with:

display(image)

If you're writing your own script and want to bring up a GUI, it takes a notch or two more effort. You can use display() there too for a quick solution, but you'll have to close the display window before the script will continue. 

Also note that the script above assumes unaligned images, ie - the averaging is incoherent.

[Rui Zhang]

Hi, Steve,

Thanks!

My particles are helical particles (microtubules) with 90% overlap, so averaging a few aligned overlapping particles in real space will cause the same noise pattern to repeat in my final average, this will leads to artificial layer lines. That's why I am sending this email : >

For this reason, sum of power spectra of aligned images ≠ power spectrum of sum of aligned images.