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

PURPOSE

Compares a series of experimental images with a series of reference images. For each experimental image, it finds the in-plane Euler rotation angle and X,Y shifts which align the image with the most-similar reference image. Only checks reference images within a restricted rotation angle from the current image posistion. The only difference between this operation and 'AP RQ' is that this operation does not check mirrored images.
(See align_overview.html for comparison of 'AP' operations.)

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 I	[Alignment - Initialize Rings File ||]
AP MD	[Alignment - Multi reference, rotation ||]
AP RA	[Alignment - Reference free, Rotation ||]
AP RD	[Alignment - multireference, restricted projections ||]
AP RN	[Alignment - multi-reference, restricted projections, no mirror check ||]
PJ 3Q	[Project - volume, Eulerian angles, trilinear interpolation ||]

USAGE

.OPERATION: AP RQN

.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" pixel.
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 IMAGES ANGLES DOCUMENT FILE: Refangles
[Enter the name of the angular document file containing Eulerian angles of reference images (projections): psi, theta, phi.]

.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).]

.EXPERIMENTAL IMAGES ANGLES DOCUMENT FILE: angles001
[Enter the name of the angular document file containing Eulerian angles of experimental images (projections: psi, theta, phi. Experimental images will be compared with only these reference images whose normal is within a specified range from this angular value.]

.RANGE OF ANGULAR SEARCH: 20.0
[Experimental projections will be compared with only these reference projections whose normal is within 20 degrees range.]

.OUTPUT ANGLES DOCUMENT FILE: 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.

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 MQ' 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'.

SUBROUTINES

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

CALLER

UTIL4