makejoincom(1)                                                  makejoincom(1)



NAME
       makejoincom - Create files for joining tomograms

SYNOPSIS
       makejoincom  [options]  rootname


DESCRIPTION
       Makejoincom generates a command file and an information file to start
       the process of joining (stacking) a set of serial tomograms into one
       volume.


OPTIONS
       Makejoincom 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.

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

       -input (-i) OR -InputTomogram       File name
              Input tomogram from one section.  If this option is used to
              enter any tomogram name, it must be used for all of them.  If
              the option is not entered, the first and following non-option
              arguments will be used for the entries.  (Successive entries
              accumulate)

   OPTIONS THAT APPLY TO INDIVIDUAL TOMOGRAMS
         These options apply only to a single tomogram.  All such options
       should be entered before the tomogram name is entered.  The name can be
       entered either with the -input option or as a non-option argument at
       the command line, but in either case it must be entered after all of
       the options that apply to it, and before the options that apply to the
       next tomogram.

       -top (-to) OR -TopSlices       Two integers
              Starting and ending slices of sample from top of section.  "Top"
              does not necessarily mean high Z; it is the end of the Z range
              that is contiguous to the next section.  This option must be
              entered for all but the last section.  (Multiple entries linked
              to a different option)

       -bottom (-b) OR -BottomSlices       Two integers
              Starting and ending slices of sample from bottom of section.
              "Bottom" means the end of the Z range that is contiguous to the
              previous section.  This option must be entered for all but the
              first section.  (Multiple entries linked to a different option)

       -flip (-fl) OR -FlipYandZ
              Flip Y and Z of tomogram to make X/Y be in plane of section.
              This option will invert handedness.  (Multiple entries linked to
              a different option)

       -rotate (-rot) OR -RotateByAngles   Three floats
              Run Rotatevol on tomogram with given rotation around X, Y, and Z
              axes, or just take account of this rotation if the -already
              option is entered.  (Multiple entries linked to a different
              option)

       -already (-a) OR -AlreadyRotated
              Rotatevol was already run with the rotations entered with
              -rotate (Multiple entries linked to a different option)

       -xyzsize (-x) OR -XYZsizeForRotation     Three integers
              Set output size from Rotatevol to given values in X, Y, Z for
              this section.  (Multiple entries linked to a different option)

       -fullsize (-fu) OR -FullSizeRotation
              Set Rotatevol output size to the maximum needed to hold the
              whole rotated section in X, Y, and Z (Multiple entries linked to
              a different option)

       -maxxysize (-ma) OR -MaxXYsizeForRotation
              Set Rotatevol output size in X and Y only to the maximum needed
              to hold this rotated section; some portions of the original
              tomogram will be out of range in Z, but those are probably por-
              tions that have no sectioned material in them.  (Multiple
              entries linked to a different option)

   GENERAL OPTIONS
         These options are entered only once and can appear anywhere among the
       other entries.

       -dir (-d) OR -DirectoryOfSource     File name
              Default directory for source tomograms.  If this option is
              entered, tomograms that do not include a directory in their path
              will be sought in the given directory instead of the current
              directory.

       -srcext (-s) OR -SourceExtension    Text string
              It is possible to enter filenames without extensions, in which
              case a default extension will be attached.  This option sets the
              default, which is otherwise "rec".  This is an unsafe option to
              use because no extension will be attached to a filename that has
              a dot in it before the extension.

       -tmpext (-tm) OR -TemporaryExtension     Text string
              When a flipped or rotated file is created, a different extension
              is attached to it, which is "tmp" by default.  Use this option
              to change the extension.

       -reference (-re) OR -ReferenceForDensity      Integer
              Tomogram to use as the reference for density scaling (numbered
              from 1).  This tomogram will be unscaled in the joined file and
              others will be scaled to match.  In addition, the mode of this
              tomogram will be used for the mode of the joined file.  The
              default is 1.

       -midaslim (-mi) OR -MidasSizeLimit       Integer
              Size to which sample slices will be squeezed for aligning in
              Midas, if they are larger than the given sizein X or Y.  The
              default is 1024.  Sampled slices will be scaled down with
              antialiasing using the -shrink option in Newstack.

       -test (-te) OR -TestMode
              Do not run anything that requires complete image files, specifi-
              cally, Densmatch.

       -StandardInput
              Read parameter entries from standard input


FILES
       The command file is always named "startjoin.com", the information file
       is "rootname".info, and transform files if sample images are shrunk are
       "rootname".sqzxf and "rootname".xpndxf.  Existing copies of files will
       be made into backup files by adding the extension ~.


AUTHOR
       David Mastronarde

BUGS
       Email bug reports to mast at colorado dot edu

SEE ALSO
       newstack, densmatch, midas

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



BL3DEMC                              4.7.3                      makejoincom(1)