AP NQ - Alignment - multi-reference, shift & rotation, no mirror check ||

(8/28/03)

PURPOSE

Compares a series of experimental images with a series of reference images. For each experimental image it finds the in-plane Euler rotation and X,Y shifts which align the image with the most similar reference image. Mirrored posistions are not checked. The only difference between this operation and 'AP MQ' is the lack of mirroring.
(See align_overview.html for comparison of 'AP' operations.)
OBSOLETE! USE 'AP SH' INSTEAD!

SEE ALSO

VO EA [Vector Operation - Create Doc File Containing Evenly Spaced Angles]
VO MD [Vector Operation - angular Document file from 'AP MD' output]
AP C [Rotation Alignment - classification, unknown references ||]
AP SA [Alignment - reference free, Shift ||]
AP SR [Alignment - reference free, Shift & Rotation ||]
AP SH [Alignment - multi-reference, exhaustive rotation & shift ||*]

USAGE

.OPERATION: AP NQ

.ENTER TEMPLATE FOR REFERENCE IMAGE SERIES: REF***
[Give the template name of the existing file series of 2D 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 <=NX/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.]

.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).]

.OUTPUT ANGLES DOCUMENT FILE: PARM101
[This is the only output produced by this program. It contains 6 columns:

1. Number of the most similar reference projection.

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. Images need not have power-of-two dimensions.

  2. The reference projections (of the existing structure) can be created using 'VO EA' and 'PJ 3Q' commands. 'VO EA' creates an angular document file with quasi-evenly spaced projection directions and 'PJ 3Q' creates projections of the volume according to this doc file.

  3. The output document file created by 'AP NQ' can be converted to the angular document file using 'VO MD' command. Please note that in this case the angular document file created by 'VO EA' is required.

  4. Alignment parameters (angle and translation included in columns 3-5 of the output document file) can be used in command 'RT SQ' to align images.

  5. An example of the Spider batch program which can be used to produce an angular document file from the output document file of this command is included in the manual chapter for the command 'VO MD'.

  6. Implemented by: Paul Penczek.

SUBROUTINES

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

CALLER

UTIL4
Example of the Spider batch program implementing 3D alignment of projections
procedure:

;b12.alq
;Rotate and shift images according to the parameters from 'AP NQ' alignment

; NUMBER OF REFERENCE IMAGES IS 83
X87=83
DO LB1 I=1,900
   X55=X0
   UD IC,X55,X21,X22,X23,X24,X25,X26
   docapmq
   RT SQ
   win/ser00x26
   ali/sar00x26
   X23
   X24,X25
LB1
EN 

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