copytomocoms(1)                                                copytomocoms(1)



NAME
       copytomocoms - Create command files for generating tomograms

SYNOPSIS
       copytomocoms  [options]  -name rootname


DESCRIPTION
       Copytomocoms generates the command files needed for nearly all of the
       processing involved in generating a tomogram.  The program is run by
       the setup page of eTomo.

       There are several ways in which tilt angles can be entered: as a start-
       ing and increment tilt angle, in a file with a list of angles (which
       can be extracted from the image file or supplied separately), or
       directly as a list of angles.  For each axis, one of these option must
       be entered for the tilt angle entry, but only one way can be specified.

OPTIONS
       Copytomocoms 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 (-n) OR -RootName   File name
              Root name of data set (omit a or b for dual-axis set)

       -dual (-du) OR -DualAxis
              Dual-axis data set

       -montage (-m) OR -MontagedImages
              Data are montaged

       -backup (-bac) OR -BackupDirectory       File name
              Directory for backing up small files.  Commands to save such
              files are placed ina script named "savework", which is run at
              end of every command file.  The directory need not exist yet.

       -pixel (-p) OR -PixelSize      Floating point
              Pixel size of images in nanometers.  This entry is required.

       -gold (-go) OR -GoldBeadSize   Floating point
              Size of gold beads in nanometers.  This entry is required.
              Enter 0 if you are not going to track fiducials.

       -rotation (-r) OR -RotationAngle    Floating point
              Angle from the vertical to the tilt axis in raw images for the A
              axis or only axis.  This entry is required.

       -brotation (-br) OR -BRotationAngle      Floating point
              Angle from the vertical to the tilt axis for B axis.  This entry
              is required for a dual-axis set.

       -firstinc (-fi) OR -FirstAndIncAngle     Two floats
              First tilt angle and tilt angle increment for the A axis or only
              axis.

       -bfirstinc (-bfi) OR -BFirstAndIncAngle       Two floats
              First tilt angle and tilt angle increment for B axis

       -userawtlt (-u) OR -UseRawtltFile
              Take tilt angle from a .rawtlt file for the A axis or only axis.

       -buserawtlt (-bu) OR -BUseRawtltFile
              Take tilt angle from a .rawtlt file for B axis

       -extract (-e) OR -ExtractAngles
              Extract tilt angles from data file for the A axis or only axis.
              This entry implies -userawtlt.

       -bextract (-be) OR -BExtractAngles
              Extract tilt angles from data file for B axis

       -angles (-a) OR -TiltAngles    List of integer ranges
              Complete list of tilt angles for the A or only axis, on one line
              with no spaces.

       -bangles (-ban) OR -BTiltAngles     List of integer ranges
              Complete list of tilt angles for the B axis

       -twodir (-t) OR -TwoDirectionsAngle      Floating point
              The tilt series was taken in two directions starting at the
              given angle.  The first half of the series will be defined as a
              separate view group for Tiltalign and Beadtrack, from the
              first view through the first occurrence of the given angle.

       -btwodir (-bt) OR -BTwoDirectionsAngle   Floating point
              Tilt series for B axis was bi-directional from given starting
              angle

       -skip (-s) OR -ViewsToSkip     List of integer ranges
              List of views to exclude from processing for A or only axis.
              This entry and the next are fed into view exclusion lists in
              track*.com, align*.com, and tilt*.com.

       -bskip (-bs) OR -BViewsToSkip       List of integer ranges
              List of views to exclude from processing for B axis

       -distort (-di) OR -DistortionField       File name
              Correct image distortion with the given .idf file.  The file
              will be copied to the current directory.

       -binning (-bi) OR -BinningOfImages       Integer
              Binning of the raw images; this entry is needed for distortion
              correction unless there is no ambiguity about whether they are
              binned; i.e., unless the images are not binned and are too large
              to be considered binned.

       -gradient (-gr) OR -GradientTable   File name
              Correct for magnification gradients using the given .mgt file.
              Extractmagrad will be run to extract mag gradient files for
              each axis.

       -focus (-fo) OR -FocusWasAdjusted
              Focus was adjusted between frames when acquiring montage for the
              A axis or the only axis

       -bfocus (-bfo) OR -BFocusWasAdjusted
              Focus was adjusted between montage frames for the B axis

       -voltage (-v) OR -VoltageInKV       Integer
              Microscope voltage in kV

       -Cs OR -SphericalAberration    Floating point
              Spherical aberration

       -ctfnoise (-ct) OR -NoiseConfigFile      File name
              Configuration file listing noise files for ctfplotter

       -defocus (-de) OR -Defocus     Floating point
              Defocus in nanometers, with underfocus positive

       -CTFfiles (-CT) OR -CopyCTFfiles    Integer
              Just copy files for CTF plotting and correction (1 for plotting,
              2 for correction, 3 for both)

       -fei (-fe) OR -SetFEIPixelSize
              Set the standard pixel spacing in the header of each image file
              if it comes from FEI software.  The pixel size from the extended
              header will be multiplied by the binning of the images, if any,
              and placed in the standard header location, so that it will
              propagate through the processing.  If there is already a stan-
              dard pixel spacing not equal to 1, 2, 3, or 4, it will not be
              modified.

       -change (-ch) OR -ChangeParametersFile   File name
              Name of file with directives for changing parameters.  A direc-
              tive (Successive entries accumulate)

       -one (-o) OR -OneParameterChange    Text string
              One directive for changing parameters, in the format just
              described.  Entries with this option are processed after, and
              can override, ones entered from files, and later ones override
              earlier ones.  (Successive entries accumulate)

       -xsize (-x) OR -XImageSize     Integer
              X size of image data (needed if data file not present)

       -ysize (-y) OR -YImageSize     Integer
              Y size of image data (needed if data file not present)

       -StandardInput
              Read parameter entries from standard input


FILES
       All files are modified from the master files in the $IMOD_DIR/com
       directory.  Existing copies of the command 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
       extracttilts, extractpieces, extractmagrad

HISTORY
       Copytomocoms was a original a C-shell script.  In February 2011 it was
       converted to Python.



BL3DEMC                              4.7.3                     copytomocoms(1)