finishjoin(1)                                                    finishjoin(1)



NAME
       finishjoin - Join serial section tomograms after finding alignments

SYNOPSIS
       finishjoin [options] root_name  slice_range1  slice_range2  ...

DESCRIPTION
       finishjoin will complete the operations required to join serial section
       tomograms together, after one has made a command file with "makejoin-
       com", run the command file, and found alignments between the tomograms.
       "root_name" is the root name for various intermediate files and the
       joined tomogram, as already specified to "makejoincom".  The command
       line must also have a slice range to include from each individual tomo-
       gram.  Enter the starting and ending slice numbers of the desired
       ranges, separated by a comma.  Slices are numbered from 1.

   Options
       Options may be abbreviated to a single letter.


       -ref <tomogram #>
              Make the given tomogram be the reference for alignment, in which
              case slices from it will not be transformed, and other tomograms
              will be transformed into alignment with it.  By default, all
              tomograms will be transformed into alignment to a position aver-
              aged over all tomograms with similar orientations.

       -angle <range>
              Base the average alignment on tomograms whose rotation angles
              fall within the given range of each other (default 50 degrees).
              If a minority of the tomograms are rotated by large angles like
              90 or 180 degrees relative to the rest, then they will be
              excluded when determining the average alignment.  This prevents
              all of the sections from being rotated to an intermediate orien-
              tation.

       -size <X,Y>
              Set the size of the output slices to X by Y pixels.  The default
              size will be the maximum X size by the maximum Y size of the
              input tomograms.

       -offset <X,Y>
              Set the X and Y offsets for the output slices.  These follow the
              same sign convention as in newstack; namely, the numbers entered
              should be the offsets from the center of the current image to
              the image point which is intended to end up in the center of the
              output image.  A positive offset in X will thus shift the image
              to the left.

       -trial <interval>
              Build a trial joined tomogram using only slices at the given
              interval.  The first and last slice of each slice range will
              always be included.  The output file will be named
              "root_name"_trial.join.

       -bin # Bin images by the given value when building a trial joined tomo-
              gram.  The -size and -offset entries, if any, should be entered
              in unbinned pixels; i.e., they do not need to be changed when
              selecting binning.  This option has no effect if the -trial
              option is not entered.

       -xform <file>
              Use the refinement transforms contained in the given file to
              compute the transforms to apply to the tomograms.  The file
              should contain global transforms as computed by Xfjointomo.

       -maxsize
              Just compute the maximum size and offsets needed to contain the
              transformed images from all of the sections, given the current
              transformations.  No image file will be created.

       -gaps  Create blank slices when the slice ranges include values out of
              bounds (below 1 or above the number of slices in the file).
              This option can be used to make the gap between two sections
              bigger than what would be provided by simply stacking all the
              slices from each file.  Without this option, values out of
              bounds are not allowed.

       -P     Output process ID.

FILES
       The program assumes the existence of several files with the given root
       name, especially "root_name".info and "root_name".xf.

AUTHOR
       David Mastronarde  <mast at colorado dot edu>



BL3DEMC                             3.11.2                       finishjoin(1)