vmstopy(1) vmstopy(1)
NAME
vmstopy - converts IMOD command file to Python script
SYNOPSIS
vmstopy [-x | -q] com_filename log_filename [output_file]
DESCRIPTION
Vmstopy is a Python program for converting an IMOD command file into a
Python script that will run commands in the file and direct output to a
log file. Commands can consist of a single line running a program with
command line arguments, or a line running a program followed by entries
that the program will read from standard input. Python statements can
also be included in the file, and variables can be defined in Python
then used in the command or standard input lines. A small number of C-
shell commands will also be recognized and translated to the appropri-
ate Python statements.
The easiest way to use this program is through the submfg script
together with an alias to run submfg in the background, which is pro-
vided in the IMOD startup scripts as the alias subm. If you command
file is named "stuff.pcm", you can give the command "subm stuff". If
it is named with a different extension, such as the traditional ".com",
you need to indicate that the command file is to be run into vmstopy by
using "subm -p stuff". In either case, the file will be executed in
background, a log file stuff.log will be created, and you will be noti-
fied when the job is completed. Type "submfg" to see the usage state-
ment for more details.
Special Characters
Four special characters are used:
$ at the start of a command line. Commands may be continued on multi-
ple lines by ending each line except the last one with a backslash (\).
The continuation lines should not start with a $
> at the start of a Python statement
% for a variable to be substituted; this may occur anywhere in a com-
mand line or a standard input line. Variable substitution will always
convert the variable to a string, so the value can be an unquoted
string or a simple numeric value. Lists of numbers should be quoted
(e.g., ’1-5’).
# at the start of a line with a comment. A # later in a line will not
be recognized as starting a comment.
Standard input lines do not start with a special character. The pro-
gram will consider any lines between a command line and the next com-
mand line or Python statement as lines to be fed to the command’s stan-
dard input.
Indentation and Quoting
Indentation is significant, not only in the Python statements but also
in the command lines. Any commands that occur in a Python block must
have the appropriate indentation; i.e., with extra indentation if they
follow a statement that starts a block; with the same indentation as
the last statement if it is part of the same block, or with less inden-
tation if it ends a block. If you use no Python at all, all command
lines must have the same amount of space between the $ and the command.
Standard input lines need not be indented.
The program will enclose text, such as that used to run a command, in
single quotes (’). If you need to pass a command line argument con-
taining spaces to a program, enclose it in double quotes (").
Translations
The following translations will occur:
$goto label
will skip forward to the next command line starting with
$label:
Unlike in C-shell, the goto can be used only to skip forward, and it
cannot be part of a conditional statement. The goto’s and labels are
recognized and removed in a first pass through the command file. Any
more complicated conditional execution must be coded with Python state-
ments.
$if (-e file) command
will be converted to
> if os.path.exists(file):
$ command
$set variable = value becomes >variable = value
If "$set" has been used at all, $variable will be substituted just like
%variable.
\rm becomes rm -f
\mv becomes mv -f
$echo text becomes >print "text"
$exit
will cause the rest of the command file to be skipped.
>print "text" becomes >print >> log, "text"
In other words, in Python statements, print commands not directed to a
file will be redirected to the log file.
Options
-x Execute the script with execfile() in the same Python inter-
preter that is doing the conversion. This throws an exception
for no discernable reason so it is not possible to detect errors
in execution. Piping to a second Python interpreter is more
useful.
-q Suppress output messages about the progress of running the
script.
EXAMPLES
# Example 1: Command file to align an image stack
# Note the comments embedded in the input to xftoxg
#
$xftoxg
0 global fit
# Name of input file
g5a.prexf
# Name of output file
g5a.prexg
$newstack -fl 2 -mo 0 -xf g5a.prexg g5a.st g5a.preali
# Example 2: Command file to split a stack into two sets of files
# Note the indentation for Python and command lines
#
>for i in range(100):
> if i % 2:
$ newstack -sec %i data.st oddsec.%i
> else:
$ newstack -sec %i data.st evensec.%i
$header data.st
>print "Splitting done"
AUTHOR
David Mastronarde, mast at colorado dot edu
SEE ALSO
vmstocsh
HISTORY
Why vms and subm? Parts of IMOD started under the VMS operating sys-
tem. The ability to submit command files in this kind of format to a
queue and get a log file with the output was the one good feature of
VMS.
BL3DEMC 3.13.2 vmstopy(1)