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)