finishjoin(1)               General Commands Manual              finishjoin(1)

       finishjoin - Join serial section tomograms after finding alignments

       finishjoin  [options]  rootname

       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.
       "rootname" is the root name for various intermediate files and the
       joined tomogram, as already specified to "makejoincom".

       Finishjoin 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.

       -name (-na) OR -RootName       Text string
              Rootname for info file, joined tomogram, and other intermediate
              files.  If this option is not entered, the first non-option
              argument will be taken as the root name.

       -use OR -UseSliceRange    Two integers
              Starting and ending slices to include from one tomogram.  This
              option must be entered for each tomogram if it is entered at
              all.  If the option is not entered, the second and following
              non-option arguments will be used for the entries.  Thus, the
              program may be run as
                 finishjoin [options]  root_name  slice_range1  slice_range2
              (Successive entries accumulate)

       -ref (-r) OR -ReferenceTomogram     Integer
              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 (-a) OR -AngleRange     Floating point
              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-

       -size (-s) OR -SizeInXandY     Two integers
              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.  Enter a size in unbinned pixels if binning is
              being used.

       -offset (-o) OR -OffsetInXandY      Two integers
              Set the X and Y offsets for the output slices, in unbinned pix-
              els if binning is being used.  These follow the same sign con-
              vention 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

       -trial (-t) OR -TrialInterval       Integer
              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-

       -binning (-b) OR -BinningForTrial   Integer
              Bin images by the given value when building a trial joined tomo-

       -local (-l) OR -LocalFits
              When running Xftoxg on the primary alignment transforms, run
              the program in its default mode, which does local fits to 7
              adjacent sections.  This option may eliminate unwanted trends in
              data sets with many sections.  When it is not entered, Xftoxg
              is run with "-nfit 0", which computes a global alignment.

       -xform (-x) OR -TransformFile       File name
              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 (-m) OR -MaximumSizeOnly
              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 (-g) OR -FillGaps
              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.

       -no OR -NoImage
              Do not run anything that requires complete image files, specifi-
              cally, Newstack, and output a file with the Newstack input.

       -PID   Print process ID

       -help (-h) OR -usage
              Print help output

              Read parameter entries from standard input

       The program assumes the existence of several files with the given root
       name, especially "rootname".info and "rootname".xf.  The final trans-
       formation file is named "rootname".tomoxg, regardless of whether refin-
       ing transformations are done.

       David Mastronarde  <mast at colorado dot edu>

       newstack, xftoxg, xfjointomo

       Makejoincom was a originally a C-shell script.  In June 2011 it was
       converted to Python.

IMOD                                4.11.0                       finishjoin(1)