restrictalign(1) General Commands Manual restrictalign(1)
NAME
restrictalign - Restrict tilt alignment parameters for low number of
fiducials
SYNOPSIS
restrictalign options tiltalign_command_file
DESCRIPTION
Restrictalign will modify the parameter settings in a command file for
running Tiltalign so that they are appropriate for the number of fidu-
cials available. It does this by applying a series of restrictions -
grouping a variable instead of solving at every tilt, or fixing it
instead of grouping - in a specified order until an appropriate ratio
of measured values to unknown variables is reached. That ratio is
picked based on two parameters, the minimum required ratio, and a tar-
get ratio. When two restrictions both give more than the minimum
ratio, the one closest to the target is chosen. To have the program
always pick the first restriction where the ratio is above the minimum,
set the target ratio equal to the minimum ratio.
The -order option controls the order in which restrictions will be
applied by changes in the magnification, rotation, and tilt solutions,
but these are not the only changes that can occur. Before applying any
of these restrictions, the stretching solution (X-stretch and skew),
local alignments, and variable X-axis tilt (except between two halves
of a tilt series) will be turned off. If these restrictions are suffi-
cient, no further changes are made. When there are fewer than 3 beads,
the beam tilt solution, projection stretch, and variable X-axis tilt
between two halves of a tilt series are turned off; all of these
involve solving for a single variable. The solution for one rotation
angle is turned off with only one bead. When the ratio of measurements
to unknowns falls below the minimum, robust fitting is turned off.
The program always changes parameters so as to solve for fewer vari-
ables than in the current file. If the ratio is already greater than
the minimum and closer to the target than with any restriction applied,
no change will be made.
To use the program with the default settings with a single-axis tilt
series, simply enter:
restrictalign align.com
The existing file will be renamed to align.com~ and the file with the
changed parameters will be written as align.com.
OPTIONS
Restrictalign uses the PIP package for input (see the manual page for
pip). Options can be specified either as command line arguments
(with the -) or one per line in a command file (without the -).
Options can be abbreviated to unique letters; the currently valid
abbreviations for short names are shown in parentheses.
-align (-a) OR -AlignCommandFile File name
Command file for running Tiltalign. If this option is not
entered, the first non-option argument will be used for the name
of the command file.
-fiducials (-f) OR -NumberOfFiducials Integer
Numbers of fiducial markers (beads) in the alignment model.
With this entry, he program will assume that each bead is marked
on every view. If this option is not entered, the program will
use the number of contours in the fiducial model with more than
one point, and count up the number of points in those contours.
The latter will give more accurate estimates of the ratio of
measurements to unknowns when there beads marked on only a sub-
set of views.
-views (-v) OR -NumberOfViews Integer
Number of views in the tilt series. If this option is not
entered, the program will use the number of views in the image
file listed in the command file.
-target (-t) OR -TargetMeasurementRatio Floating point
Target ratio of measurements to unknown values. If two succes-
sive restrictions give a ratio above the minimum required by the
-minimum option, the restriction that gives a ratio closest to
this value will be chosen. The default is 3.6.
-minimum (-m) OR -MinMeasurementRatio Floating point
Minimum ratio of measurements to unknown values. Restrictions
will be applied until at least one ratio rises above this value.
The default is 3.2.
-order (-o) OR -OrderOfRestrictions Multiple integers
Order in which possible restrictions should be applied to
achieve the target. The restrictions are numbered as follows:
1: Group rotations
2: Solve for one rotation
3: Fix tilt angles
4: Group magnifications
5: Fix magnifications
The default order is 1,4,3,2,5, which means rotations will be
grouped, then then magnifications grouped, tilt angles fixed,
then one rotation solved for, then magnifications fixed.
-skipbeam (-s) OR -SkipBeamTiltWithOneRot
By default, the program will add a solution for beam tilt if and
when it switches to solving for only one rotation angle. (If
parameters are already set to solve for only one rotation angle,
this switch does not occur and it will not add beam tilt.) With
this option, it will not add the beam tilt solution along with
this restriction.
-help (-h) OR -usage
Print help output
-StandardInput
Read parameter entries from standard input
FILES
The input file is renamed by adding a ~ to the end of its name and
replaced with the new file.
AUTHOR
David Mastronarde
SEE ALSO
tiltalign
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 4.11.0 restrictalign(1)