AP RA - Alignment - Reference free, Rotation ||

(3/21/12)

PURPOSE

Reference-free rotational alignment of an image series.
(See align_overview.html for comparison of 'AP' operations.)   Example.

SEE ALSO

VO EA [Vector Operation - Create Doc File Containing Evenly Spaced Angles]
VO MD [Vector Operation - angular Document file from 'AP MD' output]
AP C [Rotation Alignment - classification, unknown references ||]
AP SA [Alignment - reference free, Shift ||]
AP SR [Alignment - reference free, Shift & Rotation ||]
AP SH [Alignment - multi-reference, exhaustive rotation & shift ||*]

USAGE

.OPERATION: AP RA

.INPUT FILE TEMPLATE (E.G. PIC****): IMG****
[Give the template name of the existing image file series to be aligned.]

.FILE NUMBERS OR SELECTION DOC. FILE NAME:1-700
[Enter file numbers or the name of the document file containing file numbers in the first column of registers (not keys).]

.FIRST, LAST RING, & RING SKIP: 5, 15, 1
[Only polar rings with the radii in the range 5-15 (in pixel units) will be analyzed. If skip=0 or 1 then each ring between 5 and 15 will be taken; for skip=2 each second, and so on.]

.ANALYZE FULL OR HALF RING? (F/H): H
[Use 'F' for analyzing complete ring with real data. Use 'H' for analyzing half ring containing autocorrelation function.]

.ROTATIONAL ALIGNMENT DOCUMENT FILE: aligndoc
[Document file with rotational alignment results. This is the only output produced by this operation It contains 4 register columns:

Register    Contents
1    Image file number (May have gaps)
2    Rotation angle
3    Distance from total average (similarity measure)
4    Classification group number (=1 for consistency with 'AP C'

NOTES

  1. Note that the rotation parameters produced by this operation are given with the proper signs. This means that to rotate the images afterwards, these parameters should be applied directly (without sign reversal). To combine parameters given by repeated alignments, the 'SA P' operation can be used. (Only the angle signs used for 3-D reconstruction from tilted series need to be reversed.)

  2. Usage example: ref-free-apra-ali.spi

  3. Implemented by Paul Penczek

SUBROUTINES

FALB, ANG, ENER, ALPRBS, ALRQ, UPDTC, OUTRNG, CROSRNG, FOURING, PRB1D, FFTR_D, FFTC_D

CALLER

UTIL4

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