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Add plain text conversions of .tex files
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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Extending ImageJsec:Extending-ImageJ | ||
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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 | ||
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Macrossub:Macros-ExtendingIJ | ||
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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...). | ||
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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). | ||
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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. | ||
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Macro Programmingsub:Macro-Programming | ||
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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: | ||
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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: | ||
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http://imagej.nih.gov/ij/developer/macro/functions.html | ||
Tutorials on the FijiFiji webpage: | ||
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http://fiji.sc/wiki/index.php/Introduction_into_Macro_Programming | ||
How-tos and tutorials on the ImageJ Documentation Portal | ||
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http://imagejdocu.tudor.lu/ | ||
enumerate | ||
sub:Scripts, sub:Plugins, sub:ImageJ-Macro-Editor, | ||
sub:Fiji-Scrip-Editor | ||
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Scriptssub:Scripts | ||
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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. | ||
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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. | ||
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JavaScript Programming | ||
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Resources on ImageJ JavaScript scripting include: | ||
enumerate | ||
The ImageJ web site, with growing documentation: | ||
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http://imagej.nih.gov/ij/developer/javascript.html | ||
Tutorials on the FijiFiji webpage: | ||
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http://fiji.sc/wiki/index.php/Javascript_Scripting | ||
Online scripts repository: | ||
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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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