|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 ||*]|
.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.
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.
In-plane rotation angle determined.
X translation determined.
Y translation determined.
6. Experimental projection number.]
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