AP MR - Alignment Program - Multi-reference alignment ||

PURPOSE

Multi-reference alignment of an image series with both shift and rotation.
NOTE: This operation has been superseded by 'AP MQ' .

SEE ALSO

AP CA	[Alignment Program - Classification and Alignment ||]
AP MQ	[Alignment Program - 3D, rot. & trans., multi reference ||]
AP MD	[Alignment Program - 3D, rotation, multi reference ||]
AP RA	[Alignment Program - Rotational Alignment ||]
AP SA	[Alignment Program - Shift Alignment ||]

USAGE

.OPERATION: AP MR

.ENTER TEMPLATE FOR 2-D REFERENCE IMAGE NAME: REF****
[Give the template of the existing files of the reference image series.]

.ENTER FILE NUMBERS OR SELECTION DOC. FILE NAME:1-700 OR SELECT001
[Enter file numbers or the name of the document file containing file numbers in the first column.]

.EXPECTED SIZE OF THE OBJECT: 25
[Expected size of the object in pixels should not exceed image size.]

.FIRST AND LAST RING: 5,15
[In the rotational alignment, only rings with the radii in the range 5-15 (in pixel units) will be analyzed.]

.ENTER TEMPLATE FOR 2-D IMAGE NAME: IMG****
[Give the template of the existing files to be aligned.]

.SELECTION DOC FILE: SELECTIMG
[Enter selection document file name containing the numbers of the input images in the first column.]

.DOCUMENT FILE: PRM101
[The document files will contain three alignment parameters: rotation angle and x- and y-shifts. These parameters can be used directly in the RT SQ operation to produce an aligned image series from the input image series. When used in conjunction with the Random Conical 3D reconstruction, the rotation angle (phi) has to have its sign changed. The fourth column contains value of the correlation coefficient between the image and the most similar reference image. The fifth column contains number of the most similar reference image. The sixth column contains number of the current aligned image.]

NOTES

1. In this operation every input image (IMG****) is aligned (both translation and rotation are found) with respect to all reference images and the highest correlation coefficient determines the most similar reference image.

2. Images do not have to have power-of-two dimensions, but mixed radix FFT is used in the program, so please consult 'FT' manual for the restrictions.

3. The internal accuracy of the search is set to 0.25 pixel.

4. Please note that the parameters produced by this program, rotation and shift, are given with the proper signs. It means that to rotate and shift the images (using 'RT SQ', for example) this parameters should be applied directly (without sign reversion). To combine parameters given by repeated alignment 'SA P' operation has to be used.

5. Implemented by Paul Penczek.

SUBROUTINES

MRALI, ALPRBS_Q, NRML_Q, ALRQ_Q, FOURING_Q, FMRS_2, ALROSR, COP, RTQS_Q, SUMAP, FINDMX_Q, CROSRNG_Q

CALLER

UTIL4

;b11.alm

;rotate and shift images according to the parameters found by AP MR
;Register x25 represents the corresponding reference projection to which
;that particle is matched.  Since the reference projections 88-174 are 
;mirror images of the first 87, those particles that correspond to the 
;mirrored reference projections are mirrored back to correspond to the
;first 87 projections.

MD
VB OFF

DO LB1 I=1,900
   X55=X0
   UD IC,X55,X21,X22,X23,X24,X25,X26
   docali
   IF(X25.GT.87) GOTO LB2
   RT SQ
   win/ser00x26
   ali/sar00x26
   x21
   x22,x23
   GOTO LB1

   LB2
   RT SQ
   win/ser00x26
   _1
   x21
   x22,x23
   MR
   _1
   ali/sar00x26
Y
LB1
EN