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 -):

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

       -dual OR -DualAxis
              Dual-axis data set

       -montage OR -MontagedImages
              Data are montaged

       -backup 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 OR -PixelSize      Floating point
              Pixel size of images in nanometers.  This entry is required.

       -gold OR -GoldBeadSize    Unknown argument type
              Size of gold beads in nanometers.  This entry is required.
              Enter an arbitrary number like 1 if you are not going to track
              fiducials.

       -rotation 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 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 OR -FirstAndIncAngle      Two floats
              First tilt angle and tilt angle increment for the A axis or only
              axis.

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

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

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

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

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

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

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

       -skip 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 OR -BViewsToSkip   List of integer ranges
              List of views to exclude from processing for B axis

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

       -binning 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 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 OR -FocusWasAdjusted
              Focus was adjusted between frames when acquiring montage for the
              A axis or the only axis

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

       -voltage OR -VoltageInKV       Integer
              Microscope voltage in kV

       -Cs OR -SphericalAberration    Floating point
              Spherical aberration

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

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

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

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

       -ysize 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                              4.3.7                     copytomocoms(1)