alttomosetup

alttomosetup(1) General Commands Manual alttomosetup(1)
NAME
 alttomosetup - Exchange tilt series files for making tomogram with same
 parameters
SYNOPSIS
 alttomosetup -from otherRoot -to saveRoot [options] rootname
DESCRIPTION
 Alttomosetup will set up command files for efficiently processing an
 alternative raw stack and making a new tomogram using the same align-
 ment parameters. This is useful for STEM data taken simultaneously
 with multiple detectors, and for sums of even and odd aligned frames.
 In addition to the essential commands for making the aligned stack and
 making a reconstruction, it can include optional steps, namely pre-pro-
 cessing to remove extreme values and all of the modifications of the
 aligned stack, and it can include a trimming step. It produces one set
 of command files to make the single-axis tomograms for one or both axes
 of a dual-axis data set, or for both the even and odd frame sums of a
 single-axis data set. The Swaptomostacks script is used to exchange
 the alternative stacks and other files for the current ones; see that
 man page for details and restrictions.
OPTIONS
 Alttomosetup 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.
 -rootname (-ro) OR -RootnameToProcess Text string
 Enter rootname of the alternative stack to process, omitting the
 extension, and omitting a or b for a dual-axis data set. Both
 axes of a dual-axis set are processed unless the -axis option is
 entered, but even in that case, omit a or b from this entry.
 -evenodd (-ev) OR -EvenAndOddPairs
 Process even and odd aligned sums from Alignframes, or any
 pair of stacks with the data set rootname followed by "_even"
 and "_odd". You cannot use this option for a dual-axis data
 set; in that case you would have to enter the -rootname option
 separately for the even or odd stacks and do two separate pro-
 cessing runs. Note that in order for the even and odd stacks to
 have valid dual-axis names, you should enter 2 for the -evenodd
 option to Alignframes.
 -axis (-a) OR -AxisToProcess Text string
 Axis of dual-axis data set to process. Enter a, A, b, or B to
 process just a single axis for a dual-axis set.
 -preproc (-pre) OR -PreprocessForExtremes Integer
 Enter 1 (or any non-zero value) to remove extreme values in the
 raw stack with the "eraser" command file; enter 2 to run
 Archiveorig afterwards to archive the original stack.
 -ctf (-ct) OR -CorrectCTF
 Correct CTF in aligned stack with the "ctfcorrection" command
 file. The choice of whether to use the GPU is determined from
 the "tilt" command file, which overrides the value in the "ctf-
 correction" command file.
 -erase (-er) OR -EraseFiducials
 Erase gold in aligned stack with the "golderaser" command file.
 -filter (-f) OR -FilterIn2D
 Filter images in 2-D using the command file for running Mtffil-
 ter(1).
 -trim (-t) OR -TrimVolume
 Run Trimvol on the reconstruction using parameters stored in
 the Etomo ".edf" file. If Postprocessing was just run in the
 Etomo interface, be sure to Postpone or otherwise close the
 Postprocessing panel so that current parameters are saved in the
 ".edf" file. This command should work even if the trimming was
 done in a batch run and the data set has not yet been opened in
 Etomo. This option cannot be used for a dual-axis data set.
 The full reconstruction file for the main data stack must still
 be present.
 -clean (-cl) OR -CleanUpIntermediates
 When the reconstruction is done, remove the aligned stack; and
 when trimming is done, remove the untrimmed reconstruction.
 -procs (-pro) OR -NumberOfProcessors Integer
 Use this option to specify the number of processors or GPUs that
 you expect to run the command files on. If it is 1, no process-
 ing is divided into chunks. A higher value is passed directly
 to Splittilt and used to determine the maximum number of
 views to pass to Splitcorrection. The default is 8 unless
 the Tilt command file contains the option to use the GPU, in
 which case it is 1.
 -restore (-re) OR -JustRestoreInitialSet
 When the processing is stopped or fails at some point, files
 will be left in a swapped state, with the alternate stack(s)
 having the regular set name. With this option, the program will
 restore files if they are in such a state, then exit without
 making any command files. Without this option, the program will
 detect whether files are swapped, swap them back, and make new
 command files.
 -help (-h) OR -usage
 Print help output
 -StandardInput
 Read parameter entries from standard input
EXAMPLE
 Suppose data are taken with bright-field, dark-field and HAADF detec-
 tors, the three stacks are named series1.mrc, series1-DF.mrc, and
 series1-HAADF.mrc. If the bright-field stack is processed first, then
 one can run
 alttomosetup -erase -filt -trim -root series1-DF -proc 6
 then run the resulting set of files in the Etomo Parallel Processing
 interface or use Processchunks directly to run it on 6 CPU cores
 with this command:
 processchunks 6 alttomo
 (This would not be a suitable command if running on GPUs; a more com-
 plex command would be needed in that case). When the processing is
 done, you would repeat these steps for series1-HAADF.
FILES
 The current files are renamed by adding "_primts" after their root
 names.
AUTHOR
 David Mastronarde <mast at colorado dot edu>
IMOD 5.2.0 alttomosetup(1)