finishjoin(1) General Commands Manual finishjoin(1)
NAME
finishjoin - Join serial section tomograms after finding alignments
SYNOPSIS
finishjoin [options] rootname
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.
"rootname" is the root name for various intermediate files and the
joined tomogram, as already specified to "makejoincom".
OPTIONS
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-
tation.
-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
left.
-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-
name"_trial.join.
-binning (-b) OR -BinningForTrial Integer
Bin images by the given value when building a trial joined tomo-
gram.
-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
-StandardInput
Read parameter entries from standard input
FILES
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.
AUTHOR
David Mastronarde <mast at colorado dot edu>
SEE ALSO
newstack, xftoxg, xfjointomo
HISTORY
Makejoincom was a originally a C-shell script. In June 2011 it was
converted to Python.
IMOD 5.2.0 finishjoin(1)