AP MQ R - Alignment - multi-reference, shift & rot., use rings file ||

PURPOSE

This sub-operation only differs from 'AP MQ' in that it uses a precalculated copy of the reference-rings which has been stored in a file. Use 'AP I' to create the precalculated copy of the reference-rings.

SEE ALSO

AP I	[Alignment - Initalize Rings File ||]
AP MQ	[Alignment - multi-reference, shift & rotation ||]

USAGE

.OPERATION: AP MQ R

.ENTER TEMPLATE FOR REFERENCE IMAGE SERIES: REF***
[Give the template name of the existing file series of reference images (typically projections).]

.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, STEP SIZE: 6,2
[The search for translation parameters will be restricted to +/- search range, performed every "step size" pixels.
Restrictions:
1. Search range + last ring <=NSAM/2-2
2. Search range has to be divisible by step size.]

.FIRST AND LAST RING: 5,15
[Only rings with radii in the range 5-15 will be analyzed.]

.REFERENCE-RINGS FILE: REF001
[Give name for reference-rings file. SPIDER will read the reference-rings data from this file (not from the reference images themselves). More than one SPIDER run can use the same reference-rings file. Use operation 'AP I' to create this file.

.ENTER 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.]

.ENTER FILE NUMBERS OR SELECTION DOC. FILE NAME:1-21
[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).]

.DOCUMENT FILE NAME: PARM101
[This is the only output produced by this program. It contains 6 columns for each aligned image:

1. Number of the most similar reference projection.
When this number is negative, the most similar is the mirrored projection (see note 1).

2. Not-normalized correlation coefficient.
Can be used as a similarity measure.

3. Angle.
In-plane rotation angle determined.

4. X-shift.
X translation determined.

5. Y-shift.
Y translation determined.

6. Experimental projection number.]

NOTES

1. See 'AP MQ' for all details

SUBROUTINES

APMASTER, MRQLI_PS, MRQLI_SS, NORMAS, NORMASC, ALRQ_M, ALRQ_MS, CROSRNG_MS, CROSRMG_DS, CROSRNG_DS, FRNG, FRNGS, APPLYWS, ALRQS, PARABLD, RINGWE

CALLER

UTIL4