OR Q - ORientation search - 2D, multireference, rotation & translation, uses self-correlation ||

(05/22/08)

PURPOSE

Performs multireference alignment between a series of images and a set of reference images (templates) using self-correlation functions.   Example.

SEE ALSO

OR A [ORientation search - 2D, uses self-correlation ||]
AP SH [Alignment - multi-reference, exhaustive rotation & shift ||*]

USAGE

.OPERATION: OR Q

.TEMPLATE FOR REFERENCE IMAGE SERIES: REF***
[Give the template name of the existing file series of 2D reference images (typically projections).]

.FILE NUMBERS OR SELECTION DOC. FILE NAME: SELECTREF
[Enter numbers of reference files. The file numbers can also be read from a selection document file where file numbers are contained in the first register (not the keys).]

.REAL SPACE MASK RADIUS FOR EXP. AND REF. IMAGES: 25,15
[The radii applied in real space to the input and reference images, respectively.]

.RADIUS OF ACF, MAXIMUM SHIFT: 20,5
[Enter the maximum radius of the self-correlation function to be used in angle determination and the maximum shift to be considered.]

.CHECK MIRRORED POSITIONS? (Y/N) : Y
[Check mirrored image when using 1/2 coverage of projection space.]

.TEMPLATE FOR IMAGE SERIES TO BE ALIGNED: DAT***
[Give the template name of the existing file series of experimental images. These images will be checked for alignment versus the reference images.]

.FILE NUMBERS OR SELECTION DOC. FILE NAME: 1-21
[Enter numbers of experimental files. The file numbers can also be read from a selection document file where file numbers are contained in the first register (not the keys).]

.DOCUMENT FILE NAME: PARM101
[This is the only output produced by this program. It contains 6 columns:

1. Number of the most similar reference projection.
When this number is negative, the most similar is the mirrored projection.

2. Not-normalized correlation coefficient.
Can be used as a similarity measure.

3. Angle.
In-plane rotation angle determined.

4. X-shift.
X translation determined.

5. Y-shift.
Y translation determined.

6. Experimental projection number.]

NOTES

  1. This operation employs the same method as 'AP SH' except it uses self-correlation for determining the angular rotation. For details see:
    Joyeux, L. and P.A. Penczek. Efficiency of 2D alignment methods. Ultramicroscopy, 92, 33-46 (2002).

  2. Implemented by: Paul Penczek

  3. WARNING, the sub-pixel location seems to have a systematic shift error of 0.3 pixel when checked versus known image displacements. al

SUBROUTINES

ORACFMSKM, FRNG, CROSRNG_MS, CROSRNG_DS, RTQ_Q, FMRS_2, CCRS_2, FINDMX_Q, FMRS_2R

CALLER

UTIL3

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