AP SA - Alignment - reference free, Shift ||

(3/21/12)

PURPOSE

Reference free shift alignment of an image series. This operation together with operation 'AP RA' (rotational alignment) constitutes a reference-free approach to alignment of 2D images. A detailed description of the method can be found in "Three-dimensional reconstruction of single particles embedded in ice". P.Penczek et al., Ultramicroscopy, 40 (1992) 33-53. An example of the SPIDER procedure implementing the alignment is included below.   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 SR [Alignment - reference free, Shift & Rotation ||]
AP RA [Alignment - Reference free, Rotation ||]

USAGE

.OPERATION: AP SA

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

.DOCUMENT FILE CONTAINING GROUP ASSIGNMENT: FALDOC
[Document file name produced by 'AP RA' or 'AP C'.]

.GROUP NUMBER: 1
[Give 1 for output of 'AP RA' or give any valid group number coming from 'AP C'.]

.CHECK 180 DEGREE ROTATION? (Y/N): N
[Answer 'Y' should be given only if the images to be processed were on previous step aligned by 'AP RA' or 'AP C 'with option Half ring, which means that auto-correlation functions were aligned. Answer 'N' speeds up of this operation.]

.ALIGNMENT DOCUMENT FILE: aligndoc
[This is one of the the two outputs produced by this procedure. It contains 6 columns:

Register    Contents
1    Image file number (May have gaps)
2    Rotation angle
3    Distance from total rotational average (similarity measure)
4    X shift
3    Y Shift
5    Classification group number
6    Distance from the average found by 'AP SA'

The rotation angle is obtained from the input document file and 180 degrees is added if found to be needed by this operation.]

.OUTPUT AVERAGE FILE: avg_img_001
[Average image as found by the procedure.]

NOTES

  1. The less surrounding noise is included the faster operation runs and results are better.

  2. Note that shift parameters produced by this operation are given with the proper signs. To shift the images afterwards these parameters should be applied directly (without sign reversion). To combine parameters given by repeated alignment 'SA P' operation has to be used. The angle signs used for 3-D reconstruction from tilted series have to be reversed.

  3. Implemented by Paul Penczek.

  4. Usage example: ref-free-apsara-ali.spi

SUBROUTINES

SAQB, UPDTF, COP, MLC, SHFC_2, SH180_2, QUADRI, SHFM_2, CR180_2, FMRS_2, FMR_1, FFTMCF, FINDMX, ENFR_2, RTQ

CALLER

UTIL4

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