Name: scifio-cli
Owner: SCIFIO
Description: SCIFIO command line tools
Created: 2014-06-23 19:25:38.0
Updated: 2016-04-07 00:47:28.0
Pushed: 2017-10-06 02:28:27.0
Homepage: null
Size: 161
Language: Java
GitHub Committers
| User | Most Recent Commit | # Commits |
|---|
Other Committers
| User | Most Recent Commit | # Commits |
|---|
An extensible application for using SCIFIO components from the command line.
The easiest way to run the SCIFIO command line tools is via the jrun launcher.
Add the following to your .jrunrc:
rtcuts]
io = io.scif:scifio-cli
ositories]
ej.public = https://maven.imagej.net/content/groups/public
And then run:
scifio
The first time you run it, it will bootstrap the libraries into your Maven
local repository cache (typically in ~/.m2/repository) and symlinked them
into the jrun cache (typically at ~/.jrun/io.scif/scifio-cli).
Subsequent invocations will be much faster.
If you would like to build the SCIFIO command-line tools from scratch, simply run:
the top-level SCIFIO directory. You should see three projects completed: "SCIFIO projects", "SCIFIO Core" and "SCIFIO Tools." After installation, the tools will be installed to ```tools/target/appassembler/```. Here you will find the directory structure detailed in the [installation](#installation) section.
that there is one caveat in using these tools on *nix operating systems: by default, they will not be created witih execute permissions (per [this issue](http://jira.codehaus.org/browse/MAPPASM-54). So, instead of running ```scifio ...``` commands as in the [usage](#usage) section, you will have two options:
n ```bash scifio ...``` instead
d execution permissions to the scifio script, using ```chmod a+x tools/target/appassembler/bin/scifio```
also that the zipped scripts (which will also be created as part of the install, in ```tools/target```) will unzip with execute permission already set.
e
-
SCIFIO command-line tools were designed to be syntactically similar to [git](http://git-scm.com/docs/gittutorial). So if you already know git, this should feel familiar.
ming you have the scripts on your ```PATH``` (per [installation](#installation) instructions) executing a command will always take the form of:
NB: in all these examples, use `scifio.bat` if running in a Windows environment.
The `<command>option is the simple lowercase name of the command you want to run. For example, if you wanted to view (using the ``Show.java``` command) a picture of a kraken, you would use:
ou want to see a list of all available commands, just run the script with no arguments.
ands may have a set of flags or options available to modify their behavior. All command options are designed to work like [unix flags or switches](http://www.cs.bu.edu/teaching/unix/reference/vocab.html#flag), and typically will have a short (```-x```) and explicit (```--exterminate-kraken```) version. You can combine as many of these options as you want. For example, to print an ascii version of the top left 128x128 square of your kraken picture, you could use:
If you ever need to see the list of options a command has, and parameters a command requires, each command has a help flag:
can also run the ```help``` meta-command:
Don't worry about making mistakes with the command invocation - commands will always print their usage on failure.
If you run into any problems or have questions about the commands, or adding new commands, please use the scifio tag on the ImageJ Forum.
Thank you for using the SCIFIO command-line tools!