OR SH - Orientation Search - 2D, rotation & shift, uses polar coords. ||

PURPOSE

Determines rotational and translational orientation using cross correlation between two images after remappingg into polar coordinates with optional additional check of mirror transformation. This is eqivalent to: 'AP SH' but this operation processes a single pair of images.
(See align_overview.html for comparison of 'AP' and 'OR' operations.)   Example.

SEE ALSO

AP SH	[Alignment - multi-reference, exhaustive rotation & shift ||*]
OR R	[ORientation Search - 2D, rotation, uses polar coords. ||]
OR MAP	[ORientation MAP - 2D, rotational cross correlation plot ||]

USAGE

.OPERATION: OR SH [rot],[xs],[ys],[mir],[cc]

[This operation can return up to five optional register variables:

Variable	Example	Receives
First	[rot]	Rotation angle
Second	[xs]	X shift
Third	[ys]	Y shift
Fourth	[mir]	1 = mirroring required, 0= no mirroring
Fifth	[cc]	Not-normalized correlation coefficient

This is the only output from the operation!]

.REFERENCE IMAGE: REF002
[Enter the name of the file containing the reference image; dimensions must be same as the input image.]

.TRANSLATION SEARCH RANGE IN X, IN Y (OPTIONAL), STEP SIZE': 6, 2
[The search for translation parameters will be restricted to +/- search range, performed every "step size" pixel.
Restrictions:
1. Search range + last ring <= NX/2-2
2. Search range has to be divisible by step size.]
Speed will depend on square of the number of positions searched. Use of 'step size' greater than one can speed up alignment determination with little effect on final reconstruction resolution. The input for Y shift is optional, if only two inputs are present the second one is interpreted as the step size. ]

.FIRST & LAST RING: 2, 15
[Only polar coordinate radial rings with radii in the range 2-15 will be analyzed for rotational alignment.]

.EXPERIMENTAL IMAGE: IMG001
[Enter name of the file.]

.CHECK MIRRORED POSITIONS? (Y/N): Y
[Can also check mirror image of the reference file.]

NOTES

1. This operation uses the same method as 'AP SH'. 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. Previously this operation was called 'OR MQ' or 'OR NQ'.

SUBROUTINES

APMASTER, APRINGS, AP_GETDATA, APSH_SS, AP_END

CALLER

UTIL3