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.

       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 for each input file in the
       current directory.  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
       Excludeviews 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).

       -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".  The value can contain spaces if the whole entry
              is quoted.  Entries with this option are processed after a file
              entered wiuth -change, and later entries override earlier ones.
              For example, "-one BinByFactor=2" will produce output binned by
              2.  (Successive 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                                4.10.10                       justblend(1)