Re: using eman2 to mask layer lines in Fourier space

[Steven Ludtke]

Hi Rui. EMAN2 uses FFTW convention (which is the same for pretty much all other FFT libraries out there). If you just say

fft=image.do_fft()

then the phase origin in real-space is at (0,0), the corner of the image, not the center. In Fourier space, the Fourier origin (0 in x and y) is also at (0,0). 

In most cases the phase-origin is more intuitive if it's at the center of the image. This can be accomplished with:

image.process_inplace("xform.phaseorigin.tocorner")

fft=image.do_fft()

The complex origin will still be at the origin of the image, however. There are two solutions to this issue. From Python, if you access the complex pixel values as:

fft[x,y]

or

fft[x,y]=newcomplex

it will properly handle all periodic boundary conditions, and x and y can range from -box_size/2 to +box_size/2. That is

fft[0,0] will be at the Fourier origin.

fft[4,0] will be 4 complex pixels away from the origin in the x direction

To convert these pixel locations in the FFT to 1/Å,  ds=1.0/(Apix*box_size)

for example location fft[0,4] is 4 pixels from the origin. with a box size of 100 and 2.0 A/pix, this would 

correspond to 1/50 1/Å. 

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

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

On Oct 23, 2013, at 3:30 PM, Rui Zhang <ru...@lbl.gov> wrote:

Hi, Steve,

I am trying to write a python script to mask out a certain layer line (say 40 Angstrom) for a microtubule image in Fourier space, but I am not sure I understand how FT is stored/displayed in EMAN2. The fourier origin and mirror things are confusing to me.

Can you or someone help me out?

Basically I want to do:

a = EMData('MT.hed',0)

f = a.do_fft()

# to set some pixels in Fourier space to zero

b = f.do_ift()

Thank you!

Rui

[Rui Zhang]

Hi, Steve,

Thanks for the explanation!

Now my python script works, although I found for fft[x,y], the x and y cannot be negative.

here is my script, please let me know if I did something wrong.

a = EMData('helical.hed',0)

# I found I can skip this step because I am just going to set the complex pixel to zero

#a.process_inplace("xform.phaseorigin.tocorner")

fft = a.do_fft()

nx = fft.get_xsize()

ny = fft.get_ysize()

for x in range(0,nx):

fft[x,16] = 0

fft[x,17] = 0

fft[x,ny-1-16] = 0

fft[x,ny-1-17] = 0

#display(fft)

b = fft.do_ift()

display(b)

[Steven Ludtke]

Hmm, I thought the direct coordinate access would handle the wraparound. You can use the explicit function call instead:

In [3]: a=test_image()

In [4]: b=a.do_fft()

In [5]: b.get_complex_at(-2,-2)

Out[5]: (1489.08056640625-144.55996704101562j)

In [6]: b.get_complex_at(2,2)

Out[6]: (1489.08056640625+144.55996704101562j)

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