swaptomostacks(1) General Commands Manual swaptomostacks(1)
NAME
swaptomostacks - Exchange tilt series files for making tomogram with
same parameters
SYNOPSIS
swaptomostacks -from otherRoot -to saveRoot [options] rootname
DESCRIPTION
Swaptomostacks will safely rename files in a tilt series data set in
order to substitute a different raw stack and make a new tomogram using
the same alignment parameters. This is useful for STEM data taken
simultaneously with multiple detectors, or when experimenting with a
different pre-processing of the raw stack. In addition to the raw
stack, the program renames a set of other files by default: "root-
name_orig.st", "rootname_xray.st.gz", "rootname.ali", "root-
name_full.rec", "rootnamea.rec", "rootnameb.rec", and "rootname .rec".
As arguments, it requires the rootname of the alternate stack to be
moved into place for processing (with the -from option) and the root-
name to which to rename existing data set files (with the -to option).
The program will detect the current naming style of the data set and
make changes in accordance with that. If the old naming style is being
used, the alternative stack may still be named with the extension
".mrc"; this will be detected and it will be renamed to ".st". How-
ever, when files are swapped back, the original extension will be lost.
OPTIONS
Swaptomostacks 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.
-from (-f) OR -FromRootname Text string
Root name of the stack file (and other possible files) to rename
as data set files. The name should not include "a" or "b" for a
dual-axis set, unless you want to rename files only for one
axis. If this option is not entered, the first non-option argu-
ment will be taken for this root name. One way or another, the
entry is required.
-to (-t) OR -ToRootname Text string
Root name to rename current data set file(s) to. Again, the
name should not include "a" or "b" for a dual-axis set, unless
swapping only one axis. If this option is not entered, the sec-
ond non-option argument will be taken for this root name. One
way or another, the entry is required.
-root (-r) OR -SetRootname Text string
Root name of the data set (excluding "a" or "b" for a dual-axis
set. This option should not ordinarily be needed because the
root name is determined by analyzing the command file for run-
ning Tilt. The option would be needed if the command file is
not present, or if you want to swap stacks for only one axis of
a dual-axis data set. The latter can be done by entering this
option (plus -from and -to) with the rootname including "a" or
"b", and also entering the -single option.
-single (-s) OR -SingleAxisSet
This option can be used to force the program to consider the
data set as being single-axis. There are two reasons the option
might be needed: 1) to swap files only for one axis of a dual
axis set, as described above; 2) if your alternative stack was
named with the same rootname followed by "a" or "b".
-excl (-e) OR -ExcludeType Integer
Enter 1 to exclude intermediate files (currently just the "root-
name.ali") or 2 to exclude the tomogram files also (including
the tomograms before post-processing, even if the final pro-
cessed volume is present).
-check (-c) OR -CheckForExcludingViews
Check whether the size of the current stack in Z matches that of
the stack being swapped in. An error is generated if the cur-
rent stack is larger, or if it is smaller and there is no
_cutviews0.info file indicating that Excludeviews was run on
the current stack. Otherwise, if the current stack is smaller,
Excludeviews is run with the -altstack option to obtain a
stack whose exclusions should match that of the main stack.
This option should be included only when swapping a stack in,
not when swapping it back out after processing.
-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
swaptomostacks series1-DF series1-BF
to save the existing files as series1-BF and move the series1-DF files
into place. After making the aligned stack and tomogram for the dark-
field series, one can run
swaptomostacks series1-HAADF series1-DF
then process the HAADF stack, and at the end run
swaptomostacks series1-BF series1-HAADF
to bring the bright-field data back to their original names.
AUTHOR
David Mastronarde <mast at colorado dot edu>
IMOD 5.0.2 swaptomostacks(1)