|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 REF||[Alignment - multi-reference, 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" pixel.
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 FOR PROJECTIONS: 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.
When this number is negative, the most similar is the mirrored projection (see note 1).
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.
7. Angular change for projection.]