restrictalign(1)                                              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 tilt angles fixed, then magnifications grouped,
              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                                 4.9.5                    restrictalign(1)