makejoincom(1) General Commands Manual 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 (-sr) 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.
-style (-st) OR -NamingStyle Integer
0 for output image files to have descriptive extensions like
".sample", 1 for extension ".mrc", 2 for extension ".hdf", or 3
for extension "tif". In the latter three cases the usual
descriptive text is put before the extension, and the command
file will contain an environment variable setting to make pro-
grams generate files of the corresponding type.
-pcm (-p) OR -MakeComExtensionPcm Integer
0 or 1 to name the output command file with extension ".com" or
".pcm". The latter is not yet supported by Etomo.
-test (-te) OR -TestMode
Do not run anything that requires complete image files, specifi-
cally, Densmatch.
-help (-h) OR -usage
Print help output
-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.
IMOD 4.11.0 makejoincom(1)