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Add plain text conversions of .tex files
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For simplicity, we used detex (`brew install detex` on the mac):
`detex -n ./tex/01-intro.tex > ./plain/01-intro.txt`
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tferr committed Sep 16, 2015
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Extending ImageJsec:Extending-ImageJ

ImageJ capabilities can be extended by loadable code modules in the
form of macros, scripts or plugins. 300 macros, 500 plugins
and 20 scripts are available through the ImageJ web site. Below
is a short description of these three type of ImageJ add-ons:
lyxlistmacrosss
[sub:Macros-ExtendingIJ] The easiest way to
execute a series of ImageJ commands. The ImageJ Macrosmacro
language - a Java-like language - contains a set of control
structures, operators and built-in functions and can be used to call
built-in commands and other macros. Macro code is stored in text files
(.txt and .ijm extensions).
[sub:Plugins] Much more powerful, flexible and faster
than macros (most of ImageJ's built-in menu commands are actually
Pluginsplugins) but harder to write and debug. Plugins are
written in the JavaJava programming language (.java source
files) and compiled to .class files.
[sub:Scripts] ImageJ uses the Mozilla Rhino interpreter
to run JavaScriptJavaScripts. Similarly to plugins, scripts
have full access to all ImageJ and Java APIs but do not need to be
compiled (scripts and macros run interpretively). On the other hand,
scripts lack the simplicity of macro language and feel less integrated
in ImageJ.
lyxlist

Macrossub:Macros-ExtendingIJ

A Macrosmacro is a simple program that automates a series
of ImageJ commands. The easiest way to create a macro is to record
a sequence of commands using the command recorder (PluginsMacrossub:Record...).

A macro is saved as a text file (.txt or .ijm extension) and once
installed executed by selecting the macro name in the Pluginssub:Macros
submenu, by http://imagej.nih.gov/ij/developer/macro/macros.htmlshortcutspressing a key
or, in the case of http://imagej.nih.gov/ij/developer/macro/macros.htmltoolsMacro tools,
by clicking on an icon in the ImageJ toolbar. In addition, any macro
file placed in ImageJ/plugins with an .ijm extension will be installed
in the Plugins menu like any other plugin
(before version1.41 only files with an underscore in the name would
be listed).

There are more than 300example macros, on the ImageJ Web site.
To try one, open it in a browser window and drag it directly to the
fig:The-ImageJ-window or, copy it to the clipboard (Ctrl
A, Ctrl C), switch to IJ, and run FileNewsub:SystemClipboard=00005BV=00005D
(Ctrl Shift V), pasting the macro into a new sub:ImageJ-Macro-Editor
window. Run it using the editor's MacrosRun Macro
command (Ctrl R). Most of the example macros are also available
in the macros folder, inside the ImageJ folder.


Macro Programmingsub:Macro-Programming

The ImageJ community has created excellent tutorials on macro programming.
These resources are indispensable guides to the ImageJ macro language:
enumerate
The ImageJ Macro Language - Programmer's Reference Guide
by J�r�me Mutterer and Wayne Rasband. This booklet compiles most of
the documentation dispersed throughout the web related to ImageJ's
macro programming. It provides an up to date printable manual for
the ImageJ macro language:

http://imagej.nih.gov/ij/docs/macro_reference_guide.pdf
Fourtneen new macro functionsThe Built-in Macro Functions
webpage (Helpsub:Macro-Functions...
and MacrosFunctionFinder=00005BF=00005D
in the sub:ImageJ-Macro-Editor) is the indispensable guide
to the built-in functions that can be called from the ImageJ macro
language. It is thoroughly documented and constantly updated:

http://imagej.nih.gov/ij/developer/macro/functions.html
Tutorials on the FijiFiji webpage:

http://fiji.sc/wiki/index.php/Introduction_into_Macro_Programming
How-tos and tutorials on the ImageJ Documentation Portal

http://imagejdocu.tudor.lu/
enumerate
sub:Scripts, sub:Plugins, sub:ImageJ-Macro-Editor,
sub:Fiji-Scrip-Editor


Scriptssub:Scripts

JavaScriptJavaScript scripting was introduced in ImageJ1.41
in order to bring full access to ImageJ and Java APIs (see
tab:Advantages-JavaScript). ImageJ uses the Mozilla Rhino
interpreter built into Java1.6 for Linux and Windows to run JavaScript.
Mac users, and users of earlier versions of Java, must download JavaScript.jar
into the plugins folder. This JARJARJava ARchive
file is available on the http://imagej.nih.gov/ij/download/tools/JavaScript.jarImageJ website
and is included with the Mac version of ImageJ in ImageJ/plugins/jars.

Example JavaScript programs are available at http://imagej.nih.gov/ij/macros/js/imagej.nih.gov/ij/macros/js/.
Thread safe JavaScript code can be generated using the Recorder (PluginsMacrossub:Record...).
Scripts can be opened in the editor as any other macro. Scripts with
the extension .js can be run using MacrosRun Macro otherwise
MacrosEvaluate JavaScript (Ctrl J) must be used.


JavaScript Programming

Resources on ImageJ JavaScript scripting include:
enumerate
The ImageJ web site, with growing documentation:

http://imagej.nih.gov/ij/developer/javascript.html
Tutorials on the FijiFiji webpage:

http://fiji.sc/wiki/index.php/Javascript_Scripting
Online scripts repository:

http://imagej.nih.gov/ij/macros/js/
enumerate
american
table
[Advantages and disadvantages of JavaScript]english
tab:Advantages-JavaScriptAdvantages and disadvantages
of JavaScript in ImageJ. ActionBarCodeBar A thorough
comparison between different scripting languages is available on the
http://fiji.sc/wiki/index.php/Scripting_comparisonsFiji webpage.english




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