justblend(1) General Commands Manual justblend(1)
NAME
justblend - Batch blending of montages with Blendmont
SYNOPSIS
justblend options inputFiles...
DESCRIPTION
Justblend allows one to run Blendmont to blend one or more 2-D mon-
taged images, namely ones that do not consist of serial sections or
tilts needing alignment. Multiple images files can be entered and pro-
cessing can be done in parallel. After an initial run, the program can
be run again to allow you to fix the displacements in the overlap zones
manually with Midas. To control the blending, the program has a few
simple options corresponding to those available in the Etomo interface
for blending montages, but it also allows arbitrary options to Blend-
mont to be entered. It makes a command file based on the file "sloppy-
blend.com" in the "IMOD/com" directory
Blendmont requires a file with a list of piece coordinates for each
montage. If the file is not already present, the program will run
Extractpieces, which will attempt to extract the piece coordinates
from the image file header, or from the associated ".mdoc" metadata
file produced by SerialEM. Montages with more than ~65000 pixels will
not have piece coordinates in the header, so be sure to provide the
.mdoc files for large area montages.
A Blendmont command file will be created in the current directory
for each input file The files to be processed do not need to be
located in the current directory; they can be specified by absolute
paths or paths relative to the current directory.
Blending can be run on multiple processors in one of two ways: by run-
ning Processchunks once with all of the command files, thus running
Blendmont once for each input file; or by splitting up the blending
operation into multiple chunks and running Processchunks on those
chunks for each input file. Because of the limitations on such paral-
lel blending explained in the Splitblend man page, it is likely to
be less significantly efficient than blending multiple files at once,
each in one operation. However, if there are only a few, large input
files, the parallel blending of individual files may be quicker.
OPTIONS
Justblend 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.
-input (-in) OR -InputFile File name
Montaged image input file to be blended. All non-option argu-
ments will also be taken as input files. (Successive entries
accumulate)
-distort (-d) OR -DistortionField File name
Image distortion field file to use for undistorting images. The
undistortion is applied when computing edge functions.
-imagebinned (-im) OR -ImagesAreBinned Floating point
The current binning of the images, so that the image distortion
field can be applied correctly. This entry is required when
doing image distortion corrections unless Blendmont can deter-
mine the binning unambiguously from the image size.
-very (-v) OR -VerySloppyMontage
Do correlations with parameters for finding very big displace-
ments. This option should generally be used for montages taken
with stage movement, unless stage movements are relatively pre-
cise (e.g., at very low magnification or with a very good
stage). The default is to have just the -sloppy option to
Blendmont.
-robust (-ro) OR -RobustFitCriterion Floating point
When solving for the piece shifts from the displacements between
pieces, Blendmont can give less weight to, or completely
ignore, displacements that appear to be outliers. This option
activates this robust fitting and specifies the criterion for
determining an outlier. A value of 1 will generally find nearly
all outliers but may downweight some edge displacements inappro-
priately and give a poor blend across those edges. Higher val-
ues, up to about 1.5, will avoid the latter problem but will
tend not to catch actual outliers. This option is ideal for
getting a higher quality blend quickly for a low-magnification
map where grid bars ruin some of the displacements. For data to
be analyzed, it is preferable to fix the bad displacements or
mark edges to be excluded in Midas. Robust fitting is avail-
able only with more than 10 pieces.
-cpus (-cp) OR -CPUMachineList Text string
List of machines to use for parallel processing, or simply a
number of cores to use on the local machine. The entry is
passed directly to Processchunks. Machines with multiple
processors can be entered as many times as the number of proces-
sors that you want to use, or a machine name can be entered with
a ":" and the number of processors to use. For example,
"tubule:4,eclipse:6" would use 4 processors on tubule and 6 on
eclipse.
-remote (-rem) OR -RemoteDirectory File name
Path on remote machines to the current directory, the one where
this program is being run. This would be determined by ssh'ing
to the machine, cd'ing to this directory, and running pwd.
-parallel (-p) OR -ParallelBlend Integer
This option causes the program to run Blendmont in parallel
for each individual input file. Splitblend is called with
the given number as the expected number of processors. If -cpus
is not entered, Processchunks is run with the same number of
processors; however, if -cpus is entered, it will be sent to
Processchunks and that determines how many processors are
actually used. It is best to make the number of processors be
consistent between the two entries.
-resume (-res) OR -ResumeProcessing
Resume processing uncompleted files instead of redoing all
files. This option cannot be used with parallel blending of
individual files.
-fix (-f) OR -FixEdgesInMidas
Open Midas for fixing alignments in overlap zones. This
option can be used only after an initial run has created the
command files. Midas will first be opened for each input file
in turn, then all files will be reblended using the existing
edge displacements but recomputing edge functions.
-check (-che) OR -CheckFile File name
File to check for quit and finish signals. The default is
"justblend.cmds" in the directory where this program is run.
This file should not have the same name as the file used to con-
trol Processchunks when it runs jobs, which is "process-
chunks-jb.cmds", also in the current directory. If a Q is
placed in this file, it will terminate any running jobs and stop
all processing. If an F is placed in the file, the program will
stop after finishing the current file. A P can be used instead
of F except when blending individual files in parallel.
-change (-cha) OR -ChangeParametersFile File name
Name of file with entries for changing Blendmont parameters.
Each entry has the form "option=value", where "option" can be
any Blendmont option that does not conflict with the ones man-
aged by this program. There can be spaces in the value. The
full name of the option should be used in case the option is
included in the stock command file.
-one (-o) OR -OneParameterChange Text string
One entry for changing a Blendmont parameter, in the format
"option=value". When entering options at the command line, the
whole entry must be quoted if the value contains spaces.
Entries with this option are processed after a file entered with
-change, and later entries override earlier ones. For example,
"-one BinByFactor=2" will produce output binned by 2. (Succes-
sive entries accumulate)
-help (-h) OR -usage
Print help output.
-StandardInput
Read parameter entries from standard input
FILES
For each file, a rootname is used that is either the filname without
extension if the extension is 4 characters or less, or the full file-
name otherwise. The command file is named rootname_blend.com and the
output file is named rootname_blend.mrc.
AUTHOR
David Mastronarde
SEE ALSO
blendmont, midas, processchunks
BUGS
Email bug reports to mast at colorado dot edu.
IMOD 5.0.2 justblend(1)