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 5.0.2 alttomosetup(1)