Name

Currently disabled 05/15/08

sxssnr3d.py - Calculate variance and spectrum signal noise ratio (SSNR) of a 3D reconstruction on a set of data set.

Usage

Usage in command line:

sxssnr3d.py stack <output_volume> <ssnr_text_file> <reference_structure> <2Dmaskfile> --ou=outer_radius --rw=ring_width --npad=padding_times --CTF --MPI --sign=CTF_sign --sym=symmetry --random_angles=0

Usage in python programming:

ssnr3d(stack, output_volume = None, ssnr_text_file = None, mask = None, reference_structure = None, ou = -1, rw = 1.0, npad = 1, CTF = False, sign = 1, sym ="c1", MPI = False, random_angles = 0)

Input

data_stack

An image stack file (in hdf format) for SSNR calculation. The 3D refinement parameters ( three Eulerian angles and sx2, sy2) and CTF parameters are already written in the headers.

Output

ssnr01.txt

1D rotationally averaged SSNR and variance calculated using raw images

ssnr02.txt

1D rotationally averaged SSNR and variance calculated using projection images.

variance.txt

1D rotationally averaged variance file.

vol_ssnr1.spi

3D SSNR volume calculated from raw images, which is real image while has Fourier dimension. It can be used as a filter to multiply Fouerier 3D volumes.

vol_ssnr2.spi

3D SSNR volume calculated from projection images, which is real image while has Fourier dimension. It can be used as a filter to multiply Fouerier 3D volumes.

Options

ou

outer radius

npad

padding (increase the image size) for 3D SSNR calculation, default is 1.

ring_width

The thickness of the Fourier shell, default is 1.

CTF

if this flag is set, the program will use CTF information provided in file headers (default no CTF)

snr

signal noise ratio used for correcting CTF. Default is 1.

sign

sign used for correct CTF.

symmetry

point group symmetry used for the 3D SSNR calculation, default is c1

random_angles

randomize Euler angles: 0 - no, 1 - only psi, 2 - all three

Method

• The variance of a 3D reconstruction is calculated as following:
• Perform a 3D SSNR caclulation using raw images, calculate the variance of reconstruction.
• Perform 4nn reconstruction using raw images.
• project voume obtained in step 2 using orientation parameters in raw image of step 1.
• Perform 3D SSNR calculation using projections obtained in step 3, calculate variance of the 3D reconstruction.
• Subtract 4 from 1
• Turning on ctf flag will correct CTF with given snr during the 3D reconstruction.

• ATTENTION: The input raw image should not be pre-multiplied by CTF

Reference

• Penczek, P.A., Three-dimensional Spectral Signal-to-Noise Ratio for a class of reconstruction algorithms. J. Struct. Biol. 138:34-46, 2002.

Author / Maintainer

Zhong Huang

Keywords

category 1

APPLICATIONS

category 2

FOURIER

Files

applications.py

See also

References to relevant other routines.

Maturity

stable

works for most people, has been tested; test cases/examples available.

Bugs

None. It is perfect.