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.)

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, bilinear interpolation ||]

USAGE

.OPERATION: AP SCC

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

.ENTER FILE NUMBERS OR SELECTION DOC. FILE NAME: 1-21
[Enter numbers of reference 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).]

.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 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 EXPERIMENTAL IMAGE SERIES: REF***
[Give the template name of the existing file series of experimental images/volumes.]

.ENTER FILE NUMBERS OR SELECTION DOC. FILE NAME: SELECTREF
[Enter numbers of experimental 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).]

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

   1. Number of the sample 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 will give a peak 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, APCC

CALLER

UTIL4