I need to run a Fiji(imageJ) script from terminal on a macOS. Using the code below.
/Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless -macro ~/desktop/testing.ijm.ijm
And the Fiji script I need to run is
dir = getDirectory("Where I need help");
run("Image Sequence...", "open=dir");
path=dir+"needsave.avi";
run("AVI... ", "compression=JPEG frame=5 save=&path");
close();
However I want the directory to be the current location in terminal.
For example:
MYs-MBP:~ csh;
[MYs-MBP:~] cd desktop/test/test2
[MYs-MBP:~/desktop/test/test2] /Applications/Fiji.app/Contents/MacOS/ImageJ-macosx --headless -macro ~/desktop/testing.ijm.ijm
and therefore I will process everything in test2 by using the Fiji script I write.
Use this macro command:
cwd = call("java.lang.System.getProperty", "user.dir");
Note that this question was cross-posted to the ImageJ mailing list (1) and to the ImageJ Forum (2).
In future, when cross-posting, please link to all other places you are asking the question, to protect the time of those answering your question.
Related
I'm thinking a hypothetical CMDOUTPUT would be useful:
locate -r 'regexp...' # locate finds a file: /myfile.
# Shell puts `/myfile' string into CMDOUTPUT
vim $CMDOUTPUT # No need to run locate again as with: vim `!!`
The locate command above is just an example. I want the output saved for all commands that I run so that if I need it I can access it quickly. (The output should still be printed by the command to stdout.) I don't want to do
CMDOUTPUT="$(...)"
or
command | tee /tmp/cmdoutput
or anything else that I have to do because that's more typing for me at the prompt for everything that I run: I want the shell to do it all in the background. Again, to make it clear: I am casually typing commands away and decide "Oh, I want to use the output of that last command in this command, let me just retrieve it...". Can I tell the shell to store the output somehow so that I can retrieve it.
If there's no option for it, is there some way that I can implement it that is as close to invisible as it can be, meaning exit codes from the command are not lost (...and that's all I can think of, but I'm sure there are other subtleties) etc. I'm primarily thinking of zsh, but answers for any shell would be useful.
I found a solution, not sure if this is exactly what you're looking for. But it should provide a start :)
zsh | tee log >&1
I can't find a man page or any help for ssft. I want to use it in my bash scripts to select either kdialog (if on KDE) or zenity (if on gnome).
See Shell Scripts Frontend Tool
Surely the help pages are somewhere, but I must be overlooking them.
I am running Debian 6.0 Squeeze stable right now, and it has a manpage for ssft.sh. Try man ssft.sh. If that doesn't do what you want, let me know and you and I will figure out what does.
Update: All right. You have tried the manpage, which doesn't tell you what you want to know. There does not appear to exist any more thorough documentation for Ssft (maybe, when this is all over, you will write and contribute that very documentation). However, in Ssft's source appears to be a test script that makes the software do the various things it is designed to do. Sometimes, a good example is even better than a manual. That test script may be just what you need.
To extract the test script, issue a sequence of commands like the following sequence.
$ cd /tmp
$ apt-get source ssft
$ ls
$ cd ssft-0.9.13 # (Your version number may differ from 0.9.13.)
$ ls
$ cd tests
$ ls
When I do the above, the last ls listing reveals a shell script named ssft-test.sh. Inside that script appear to be several examples of how to use ssft.sh correctly.
http://man.devl.cz/man/1/ssft.sh
ssft.sh(1)
SSFT
Name
ssft.sh - library of shell script frontend functions
Synopsis
. ssft.sh
Description
ssft.sh is a library of shell functions that must be sourced from other scripts. If the script is executed without arguments it prints an usage message and also supports the options --doc, --help and --version.
To get a list of available functions call the script with the --doc argument and to get a description of what a given function does call the script with --doc FUNCTION_NAME.
On the typical case the library must be sourced and the SSFT_FRONTEND variable must be set to the desired frontend (zenity, dialog or text); if the variable is not set the default frontend is noninteractive.
To choose the theorically best looking frontend use the function ssft_choose_frontend as follows:
. ssft.sh [ -n "$SSFT_FRONTEND" ] || SSFT_FRONTEND="$( ssft_choose_frontend )"
Written by Sergio Talens-Oliag .
$ /usr/bin/ssft.sh
Shell Script Frontend Tool (version 0.9.13)
Usage: . ssft.sh
When called directly the program supports the following options:
-d,--doc [FUNCTIONS] Prints the list of available functions. If function names are given prints functions' documentation.
-h,--help This message
-v,--version File version
functions:
$ /usr/bin/ssft.sh -d
ssft_set_textdomain
ssft_reset_textdomain
ssft_choose_frontend
ssft_print_text_title
ssft_display_message
ssft_display_error
ssft_display_emsg
ssft_file_selection
ssft_directory_selection
ssft_progress_bar
ssft_read_string
ssft_read_password
ssft_select_multiple
ssft_select_single
ssft_yesno
ssft_show_file
I want to run a function - let's say test - inside my test.m file. I want to run this function using Octave from terminal. So, it should be something like:
$>/Users/me/octave/bin/octave test(param1,param2)?
How can I accomplish this? I can do that in Matlab. But I didn't find a way in Octave.
You can use octave --eval CODE
Octave's docs on this can be found here. To run a function with input args:
In Terminal cd to your working directory.
Type octave to open an interactive session.
ls to check that your function's file is in your working dir, cd to the dir if not.
Type the function's name immediately followed by the input args in brackets in the correct order, Eg: >foo(100). Your function will then run, spitting out whatever you print as well as all the results for lines of code not ending with ;.
The general idea is pretty simple, I want to make a script for a certain task, I do it in the shell (any shell), and then I want to copy the commands I have used.
If I copy all the stuff in the window, then I have a lot of stuff to delete and to correct. (and is not easy to copy from shell)
Resume: I want to take all the things I wrote...
Is there an easy way to do this easy task?
Update: Partial solution
In bash, the solution is pretty simple, there is a history command, and there are ports of the idea:
IRB: Tweaking IRB
Cmd: Use PowerShell -> Get-History (or use cygwin)
Another Update:
I found that doskey have a parameter history to do this:
cmd: Doskey /history >> history.cmd
Yes, you can use:
history -w filename.sh
This will save your command history to filename.sh. You may need to edit that to keep just the lines at the end that are part of your command sequence.
NOTE: This is a bash command and will not work with all shells.
script may help here. Typing script will throw you into a new shell and save
all input and output to a file called typescript. When you're done with your interaction,
exit the shell. The file typescript is then amenable to grep'ing. For example, you might
grep for your prompt and save the output to the file. If you're a clumsy typist like me, then you may need to do some cleanup work to remove backspaces. There used to be a program that did thisbut I don't seem to find it right now. Here is one I found on the
'net: http://www.cat.pdx.edu/tutors/files/fixts.cpp
This approach is especially useful if you want to track and post on the web an entire interactive session.
Update
Got it! See my solution (fifth comment)
Here is my problem:
I have created a small binary called "jail" and in /etc/password I have made it the default shell for a test user.
Here is the -- simplified -- source code:
#define HOME "/home/user"
#define SHELL "/bin/bash"
...
if(chdir(HOME) || chroot(HOME)) return -1;
...
char *shellargv[] = { SHELL, "-login", "-rcfile", "/bin/myscript", 0 };
execvp(SHELL, shellargv);
Well, no matter how hard I try, it seems that, when my test user logs in, /bin/myscript will never be sourced. Similarly, if I drop a .bashrc file in user's home directory, it will be ignored as well.
Why would bash snob these guys?
--
Some precisions, not necessarily relevant, but to clear out some of the points made in the comments:
The 'jail' binary is actually suid, thus allowing it to chroot() successfully.
I have used 'ln' to make the appropriate binaries available - my jail cell is nicely padded :)
The issue does not seem to be with chrooting the user...something else is remiss.
As Jason C says, the exec'ed shell isn't interactive.
His solution will force the shell to be interactive if it accepts -i to mean that (and bash does):
char *shellargv[] = { SHELL, "-i", "-login", ... };
execvp(SHELL, shellargv);
I want to add, though, that traditionally a shell will act as a login shell if ARGV[0] begins with a dash.
char *shellargv[] = {"-"SHELL, "-i", ...};
execvp(SHELL, shellargv);
Usually, though, Bash will autodetect whether it should run interactively or not. Its failure to in your case may be because of missing /dev/* nodes.
The shell isn't interactive. Try adding -i to the list of arguments.
I can identify with wanting to do this yourself, but if you haven't already, check out jail chroot project and jailkit for some drop in tools to create a jail shell.
By the time your user is logging in and their shell tries to source this file, it's running under their UID. The chroot() system call is only usable by root -- you'll need to be cleverer than this.
Also, chrooting to a user's home directory will make their shell useless, as (unless they have a lot of stuff in there) they won't have access to any binaries. Useful things like ls, for instance.
Thanks for your help, guys,
I figured it out:
I forgot to setuid()/setgid(), chroot(), setuid()/setgid() back, then pass a proper environment using execve()
Oh, and, if I pass no argument to bash, it will source ~/.bashrc
If I pass "-l" if will source /etc/profile
Cheers!