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. $! at the start of a line is also recognized as 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 the text that used to run a command, in single quotes (' ') and text that is input to programs in triple quotes (""" """). If you need to pass a command line argument containing spaces to a program, enclose it in double quotes (" "). Translations The following translations will occur. Some of these are generally useful, some are needed to support constructs in existing command files for tomogram processing. $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 $if (! -e file) command will be converted to > if not os.path.exists(file): $ command $set tmpdir = and the 1-3 following lines will replaced by > tmpdir = imodTempDir() provided that either the following line contains "settmpdir", or the next three lines contain "if", "settmpdir", and "endif" $set variable = value becomes >variable = value and "value" is quoted unless it can be assigned to a numeric variable If "$set" has been used at all, $variable will be substituted just like %variable. $setenv variable value becomes >os.environ['variable'] = 'value' This is generally to set the environment for programs that will be run, but these and other environment variables may be accessed within the command file provided that they are all upper case (A-Z, 0-9, and underscore are allowed) and enclosed in braces. In other words, ${ENV_VAR} becomes os.environ('ENV_VAR'). \rm, \rm -f, rm, and rm -f all become b3dremove -g cp or \cp become b3dcopy, and if the following line has a chmod, -p is added to the b3dcopy \rm -r, \rm -rf, rm -r and rm -rf are all replaced by a call to shutil.rmtree mkdir is replaced by a call to os.mkdir \mv becomes mv -f $if (-e file) mv file file~ is replaced by a call to the makeBackup- File function $echo text becomes >print "text" after substituting variables in "text" $exit will cause the rest of the command file to be skipped, whereas $exit n will result in calling a function that terminates with sys.exit(n), but further lines will be processed. >print "text" becomes >prnstr("text", file=log) In other words, in Python statements, print commands not directed to a file will be redirected to the log file. prnstr is function that works for printing with both Python 2.x and Python 3.x. b3dremove becomes b3dremove -g on Windows On other systems, wildcards in the filename list are expanded by the shell that runs the command, but on Windows, b3dremove needs to glob the filenames. $if ($status) goto label When this construct is present, the program will collect lines between "label:" and "exit n" and move them into a function. When the con- struct is encountered after running a command, a call to the function is inserted in the exception handler for the command. $vmstocsh com.log < com.com When this construct is encountered, the line containing it, through a line containing "csh -ef", are replaced with commands to run vmstopy and to run the resulting script. `hostname` is substituted with the computer hostname upon execution; Note that "hostname" must be enclosed in back-quotes (as for command execution in a shell); this character may not appear properly here. $$ is replaced by the PID of the Python running the command file Certain commands are eliminated from the command file: $set nonomatch $matchshifts $sync (on Windows) Options -x Execute the script with a new Python instance. -q Suppress output messages about the progress of running the script. -c Output "CHUNK DONE" to the log file after successful execution. 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 4.3.7 vmstopy(1)