AP MS - Alignment - multi reference, shift ||

PURPOSE

Calculates translational differences with additional check of 180 degrees rotation between experimental images and a series of reference images. Determines translational parameters to align the experimental image with the "most similar" reference image.
(See align_overview.html for comparison of 'AP' operations.) Warning: This operation gives incorrect sub-pixel shifts, (the pixel shifts are OK). I suggest that you do not use the operation, AL Feb 2008).

SEE ALSO

AP C	[Rotation Alignment - classification, unknown references ||]
AP RA	[Alignment - Reference free, Rotation ||]
AP SA	[Alignment - reference free, Shift ||]
AP SR	[Alignment - reference free, Shift & Rotation ||]
PJ 3Q	[Project - 3D volume using Eulerian angles, trilinear interpolation ||]

USAGE

.OPERATION: AP MS

.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).]

.TRANSLATION SEARCH RANGE X and Y: 6,2
[The search for translation parameters will be restricted to +/- search range.

.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 images. The file numbers can also be read from a selection document file where file numbers are contained in the first register (not the keys).]

.OUTPUT DOCUMENT FILE NAME: PARM101
[This is the only output produced by this program. It contains 5 columns for each aligned image:

Register	Contents
1	Most similar reference file number
3	Normalized correlation coefficient (similarity measure)
2	Rotation angle (Either 0 or 180 degrees)
4	X shift
3	Y Shift
5	Classification group number
6	Experimental image number

NOTES

1. This program performs the following sequence of operations for each image:
   - Ramp (2D linear trend) is subtracted
   - Image is normalized (average is set to zero and Std. Dev to one).
   - Image is padded with zeroes to twice its size.
   - Cross-correlation is calculated and normalized by factors (image size - lag).
   If the best match was for an image rotated by 180 degrees, then the number stored in the first column of the document file is negative.

2. Alignment parameters (angle and translation included in columns 3-4 of the output document file) can be used in command 'RT SQ' to align images.

3. Implemented by: Paul Penczek.

SUBROUTINES

MULTISHIFT

CALLER

UTIL4

Example of SPIDER procedure implementing alignment of 
projections following use of 'AP MS'

;Rotate/ shift images according to the parameters from 'AP MS' alignment

DO [i]=1,200
   UD IC [i],[n],[cc],[ang],[x],[y]
     docapmq

   RT SF
     win/ser{****[i]}
     ali/ser{****[i]}
     [ang]
     [x],[y]
ENDDO
EN