| VO EA | [Vector Operation - Create Evenly Spaced Angles Document file] |
| VO MD | [Vector Operation - angular Document file from 'AP MD' output] |
| AP REF | [Alignment - multi-reference, rotation & shift ||*] |
| OR SH | [ORientation search - 2D, rotation & shift, uses polar coords. ||] |
| PJ 3Q | [Project - 3D volume using Eulerian angles ||] |
| AP SHC | [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 IN X, IN Y (OPTIONAL), STEP SIZE': 6,2
[The search for translation parameters will be restricted to
+/- search range, performed every "step size" pixel.
Restrictions:
1. Search range + last ring <= NX/2-2
2. Search range has to be divisible by step size.]
Speed will depend on square of the number of positions searched.
Use of 'step size' greater than one can speed up
alignment determination with minimal effect on
final reconstruction resolution. The input for Y shift is
optional, if only two inputs are present the second one is
interpreted as the step size. ]
.FIRST, LAST RING, RING STEP, & RAY STEP: 5,15,1,1
[The search for rotational alignment will be restricted to
pixels with radii in the specified range (here: 5-15), performed
every 'ring step' radius and on every 'ray step' radial ray.
Restrictions on 'ray' search, every: 1,2,4,8,16 'th radial
ray can be included in search.
Use of 'ring step' and 'ray step' greater than one can speed up
alignment determination on large images with minimal effect on
final reconstruction resolution.]
.REFERENCE IMAGES ANGLES DOCUMENT FILE: Refangles
[Optional input file. Enter name of the doc file containing
Eulerian angles (psi, theta, phi) for the reference images.
Enter '*' if you do not have any reference angles doc file.
.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: 1-2100
[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 ALIGNMENT DOCUMENT FILE: angles001
[Optional input file. If '*' is given then this operation is
similar to old 'AP MQ'. If you desire to restrict the range of
angular search for projections then this file is necessary. It
must contain the current Eulerian angles of experimental images
(projections: psi, theta, phi) and optionally the current
inplane rotation, shifts and other alignment parameters.
The output files from 'AP SH' and 'AP REF' contain this info.]
.RANGE OF PROJECTION ANGLE SEARCH & ANGLE CHANGE THRESHOLD: 20.0, 14.0
[Experimental images will be compared with only those
reference images whose normal is within specified range (in degrees).
If a 0.0
is entered, then there is NO restriction on which of the projections
are compared. The "angle change threshold" is only used to report what
percentage of the rotational changes exceed this specified threshold. This
value can later be used to halt the iterations. The value is placed in
a comment key at the end of the operations output file. It is
not used for any other purpose.]
.CHECK MIRRORED POSITIONS?, SHIFT/ROTATE INPUT? (Y/N): Y,Y
[Optional check of the mirrored reference image. By using this check and
only providing reference images from one hemisphere of projection
directions, speed can be doubled. See note: 1 below.
The second prompt
requests that the input files first be rotated/shifted by the alignment
parameters from the experimental images alignment document file before
use. This is equivalent to running the 'RT SQ' operation before using
'AP SH'. If this is 'Y' there is no need for 'dala' files. (For
backward compatibility the legacy '0/1' response is still accepted for
CHECK MIRRORED POSITIONS and second response defaults to 'N'.)]
.OUTPUT ALIGNMENT DOCUMENT FILE: align_doc_001
[This is the only output produced by this operation. (Will append to
existing output file of same name).
It contains 15 register columns:
1. Eulerian angle (psi) of nearest reference image.
When no matching projection was found within
the angular range specified, this column will contain
the experimental
image's previous Eulerian angle (if any) or 0.0.
2. Eulerian angle (theta) of nearest reference image.
When no matching projection was found within
the angular range specified, this column will contain
the experimental
image's previous Eulerian angle (if any) or 0.0.
3. Eulerian angle (phi) of nearest reference image.
When no matching projection was found within
the angular range specified, this column will contain
the experimental
image's previous Eulerian angle (if any) or 0.0.
4. Number of the most similar reference projection.
When no matching projection was found within
the angular range specified, this column will contain 0.
5. Experimental projection number.
6. Cumulative In-plane rotation angle (psi).
To use in 3D reconstruction programs invert the sign.
This is the sum of any rotation from the 'experimental
images align. document file' and the current rotation.
7. Cumulative X shift.
This is the sum of any shift from the 'experimental
images align. document file' and any current shift.
Note that the shifts reported here have been adjusted
to compensate for any rotation, so that they are
appropriate for use with SPIDER operations such as
'RT SQ'. For this reason the current shifts may be
greater than this shift range that you applied above.
8. Cumulative Y shift.
This is the sum of any shift from the 'experimental
images align. document file' and any current shift.
9. Number of reference projections searched.
This number can vary when an angular restriction
on search is used.
10. Angular change for projection.
Angular difference between previous and current
projection. This will be -1.0 if the previous
projection angles were not specified.
11. Not-normalized alignment correlation coefficient.
Can be used as a similarity measure. (Normalization
gives a significant time penalty and there are reports
that normalization decreases value of the statistic
in distinguishing best fit.)
Following values are seldom used by existing procedures:
13. Current X shift.
X shift necessary to align the experimental
image with the current reference projection.
Note that the shifts reported here have been adjusted
to compensate for any rotation, so that they are
appropriate for use with SPIDER operations such as
'RT SQ'. For this reason the current shifts may be
greater than this shift range that you applied above.
14. Current Y shift.
Y shift necessary to align the experimental
image with the current reference projection.
15. Current Mirroring.
This value is negative if mirroring was necessary to
align the experimental image with the reference
projection. Otherwise it is positive.
NOTES