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 "most similar" reference image/volume.
(See align_overview.html for comparison of 'AP' operations.)

SEE ALSO

AP RA	[Alignment - Reference-free rotational alignment ||]
AP SA	[Alignment - Reference free, Shift ||]
AP SR	[Alignment - reference free, Shift & Rotation ||]
PJ 3Q	[Project - 3D volume using Eulerian angles ||]

USAGE

.OPERATION: AP SCC

.ENTER TEMPLATE FOR REFERENCE IMAGE SERIES: REF***
[Give the template name of the existing file series of reference images/volumes.]

.ENTER 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 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. Increasing range does NOT slow the operation.]

.NORMALIZE PEAK HEIGHT (Y/N) : N
[Normalize peak height output to range: 0...1. Normalization slows the calculation with no improvement of accuracy.]

.ENTER TEMPLATE FOR IMAGE SERIES TO BE ALIGNED: DAT***
[Give the template name of the existing file series of experimental image/volume(s). These image/volume(s) will be checked for alignment versus the reference image/volume(s).]

.ENTER 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:

1. Number of the sample image/volume.

2. Number of the most similar reference image/volume.

3. X-shift.
X translation determined.

4. Y-shift.
Y translation determined for an image.

5. Z-shift.
Y translation determined for a volume.

6. correlation coefficient.
Can be used as a similarity measure. If normalized a self correlation will lead to coefficient of: 1.0

NOTES

1. Image/volume is padded with zeroes to twice its size.
   Cross-correlation is calculated and normalized if requested.

2. Translation alignment parameters in columns 3-4 of the output document file) can be used in command 'RT SQ' to align images.

3. Implemented by: ArDean Leith.

SUBROUTINES

APSCC

CALLER

UTIL4