AP SCC - Alignment - multi-reference, translation alignment ||

PURPOSE

Calculates translational differences between experimental image/volume(s) and a series of reference image/volumes(s). Determines translational parameters to align the experimental image/volume with the given reference images/volumes.
(See align_overview.html for comparison of 'AP' operations.)   Example.

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 ||]
SH F	[Shift - using Fourier interpolation ||]
CC	[Cross Correlation ||]
PK M	[Peak search - Maximum]

USAGE

.OPERATION: AP SCC [exp],[ref],[xsh],[ysh],[zsh],[pk]

[This operation can return up to six optional register variables for the last experimental image/ reference image pair analyzed:

Variable	Example	Receives
First	[exp]	Experimental image number
Second	[ref]	Reference image number
Third	[xsh]	Xshift
Fourth	[ysh]	Y shift
Fifth	[zsh]	Z shift
Sixth	[pk]	Peak height

.REFERENCE IMAGE FILE NAME OR TEMPLATE (E.G. STK@**): REF***
[Give the template name of the existing file or series of reference image/volume(s). Each of the experimental image/volume(s) will be checked for alignment versus all of these reference image/volume(s).]

If the reference file name contains a template for a set of images SPIDER asks:

.FILE NUMBERS OR SELECTION DOC. FILE NAME: select_ref
[Enter the file numbers to be substituted into the file name template or name of a selection document file that contains the file numbers in the first register column.]

.TRANSLATION SEARCH RANGE IN X, Y, & Z (ZERO FOR ALL): 0 ,0
[The search for translation parameters will be restricted to +/- search range.' If the input is zero the whole image/volume is searched. If an input is <0, then that dimension is not searched. This allows for a one dimensional search of image shift. Note: Increasing range does NOT slow this operation.]

.NORMALIZE PEAK HEIGHT, PAD IMAGE (Y/N): N
[Normalize peak height output to range: 0...1. Normalization does not slow the calculation nor improve of accuracy. Unless specified all images/volumes will be padded to twice their original dimesions with average of the image. Padding is said to improve the alignment values depending on the structure present in the image and any periodicity within the structure. It may not help your specific image.]

.EXPERIMENTAL IMAGE FILE NAME OR TEMPLATE (E.G. STK@****): EXP***
[Give the template name of the existing file or series of experiment image/volume(s). Each of the experimental image/volume(s) will be checked for alignment versus all of the reference image/volume(s).]

If the experimental image file name contains a template for a set of images SPIDER asks:

.FILE NUMBERS OR SELECTION DOC. FILE NAME: select_exp
[Enter the file numbers to be substituted into the file name template or name of a selection document file that contains the file numbers in the first register column.]

.OUTPUT ALIGNMENT DOCUMENT FILE: align_param
[This is the only output produced by this operation. It contains 5 register columns for each aligned image pair:

   1. Number of the experimental image/volume.
   2. Number of the reference image/volume.
   3. X-shift. (X translation determined.)
   4. Y-shift. (Y translation determined.)
   5. Z-shift. (If a volume.)
   6. Peak height.
     Can be used as a similarity measure.
     If normalized, a self correlation should give a peak height of: 1.0

NOTES

1. Translation alignment parameters in columns 3-5 of the output document file) can be used with operation 'SH' or 'SH F' to align images.

2. This operation is equivalent to 'CC' followed by 'PK M'.

3. Implemented by: ArDean Leith.

SUBROUTINES

APSCC, APCC

CALLER

UTIL4