AP SR - Alignment - reference free, Shift & Rotation ||

PURPOSE

Reference-free alignment shift and rotational alignment of an image series.
(See align_overview.html Note: This operation reportedly sometimes seg faults in threading - Oct 2019'   Example.

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 RA	[Alignment - Reference free, Rotation ||]
AP SA	[Alignment - reference free, Shift ||]
AP SH	[Alignment - multi-reference, exhaustive rotation & shift ||*]

USAGE

.OPERATION: AP SR

.INPUT FILE TEMPLATE (E.G. PIC****): img***
[Give the template name of the existing file series to be aligned.]

.FILE NUMBERS OR SELECTION DOC. FILE NAME: 1-34
[Enter selection document file name containing the numbers of the input images in the first column or file numbers.]

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

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

.IMAGE TO BE USED TO CENTER THE AVERAGE: *
[Give either the name of an image (reference pattern) that should be used to center averges during iterations, or enter an '*'. In the latter case a default procedure will be used, that is, initially a blob will be used to center all the images, and during the iterations phase approximation of a center of gravity will be used to center each average.]

.TEMPLATE FOR AVERAGE FILES: avg***
[The output files will contain averages produced by the alignment program after each iteration step.]

.TEMPLATE FOR ALIGNMENT DOC FILES: align_doc_***
[These document files will contain the alignment parameters after each iteration. They contain 3 register columns:

Register	Contents
1	Rotation angle
2	X shift
3	Y Shift

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.]

NOTES

1. This command implements a reference-free strategy for alignment of a image series. The theory is described in "Three-dimensional reconstruction of single particles embedded in ice", P. Penczek et al., Ultramicroscopy 40 (1992) 33-53. The search for rotation and shift parameters is not separated.

2. The operation will work for images with positive contrast (bright images on dark background) ONLY. Dark images on the bright should first have the contrast inverted (for example using 'AR' to do multiplication by -1).

3. The internal accuracy of the search is set to 0.5 pixel.

4. Note that the rotation parameters produced by this operation are given with the proper signs. This means that to rotate the images afterwards, these parameters should be applied directly (without sign reversal). To combine parameters given by repeated alignments, the 'SA P' operation can be used. (Only the angle signs used for 3-D reconstruction from tilted series need to be reversed.)

5. Should the program not give good results use operations 'AP SA' and 'AP RA' instead.

6. Usage example: ref-free-apsr-ali

7. Implemented by Paul Penczek.

SUBROUTINES

GALI, GETIMA_Q, ALROSI_Q, ALROSF_Q, RTQS_Q, CROSRNG_Q, SHFI_2, SUMAP, BLOB_Q, ALRQ_Q, ALPRBS_Q, FOURING_Q, RTQ_Q, CENT_Q, FMRS_2R, FMRS_2, COP, FINDMX_Q, OUTIM_Q, QUADRI_Q, OUTPR, UPDF, FNRM

CALLER

UTIL4