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https://github.com/sruffner/figurecomposer

FigureComposer is a standalone Java application originally developed to help researchers prepare and refine scientific figures for journal publication.
https://github.com/sruffner/figurecomposer

data-plotting data-visualization java matlab

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FigureComposer is a standalone Java application originally developed to help researchers prepare and refine scientific figures for journal publication.

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README 

        
# FigureComposer



**FigureComposer** is a standalone Java application for preparing, revising and reviewing detailed scientific figures 

intended for journal publication. It is a mature application that has been used by members of Stephen G.

Lisberger's laboratory at Duke University since 2007, as well as some others in the neuroscience commmunity.



**_NOTE: I am no longer actively developing FC. I have made this repo available for anyone in the neuroscience 

community that continues to use the application and might wish to fork the repo to adapt the program for their own 

use._**



## User Guide

An [online user's guide](https://sites.google.com/a/srscicomp.com/figure-composer/introduction) provides a thorough 

introduction to the program, a detailed format description of the application's figure document format (_FypML_), a

complete version history, and a downloads page where you can get the latest release.



## Installation

An (unsigned) application bundle is available for installation on MacOS, an installer EXE for Windows, and an executable

JAR for Linux. You must separately install a Java Runtime Environment compatible with your host operating system in 

order to run **FigureComposer**. As of version 5.2.0, a Java 8 runtime is required. For details, see the 

[online guide](https://sites.google.com/a/srscicomp.com/figure-composer/download-files).



**_NOTE: As of version 5.5.0, the code base is JDK11-compliant, and a Java 11 runtime is required. Recommend using

[Amazon Corretto 11](https://docs.aws.amazon.com/corretto/latest/corretto-11-ug/what-is-corretto-11.html)._**



### Related Matlab Utilities

Researchers in the Lisberger and other labs have used [_Matlab_](https://www.mathworks.com/products/matlab.html) 

extensively over the years to process their experimental data and prepare draft figures for journal publication. I have 

written a number of Matlab scripts to address the issue of how to conveniently get data into or out of a **FigureComposer**

figure (_FypML_ file). You will find these scripts in the `supporting` folder within the repo. These are probably of

limited use, since **FigureComposer** (as of version 4.2.3) can import many Matlab figure (`*.fig`) files directly.



The various utility scripts are described in details in the 

[online guide](https://sites.google.com/a/srscicomp.com/figure-composer/loading-data/matlab-utilities).



The `matfig2fyp()` script relies on JAR files `hhmi-ms-common.jar` and `hhmi-ms-datanav.jar`, which are included in the

**Figure Composer** download ZIP and must be installed in Matlab's Java class path. **_As of version 5.5.0, the

class files in these JARs are JDK11-compliant, so they require that Matlab be configured to use a Java 11 runtime_**. 

Matlab's default bundled JRE is still Java 8 as of R2024a, but it supports using OpenJDK 11 runtimes such as Amazon 

Corretto 11. To specify the JRE that Matlab should use, run `jenv()` from the Matlab command line (where 

`` is the installation path for the OpenJDK 11-compliant runtime environment), then restart Matlab.



## Building/Packaging

- The code base in this repository is set-up as an IntelliJ IDEA project, and the IDEA project settings are included in 

the repo.

- The `macosxdist` folder contains resource files for packaging FC as a MacOS application bundle, which is then archived

in a ZIP file for distribution. 

- The `windist` folder contains resource files for building a Windows installer EXE for FC. The installer is created on

a Windows workstation using [InnoSetup](https://jrsoftware.org/isinfo.php).

- An Ant build file, `release.xml`, semi-automates the build process: creating the source JARs for the three modules 

in the IDEA project (`common`, `jmatio`, and `figurecomposer`), packaging the class files in module JARS, and preparing 

ZIP archives for installing FC on MacOS, Windows, and Linux. **_Be sure to read through this file carefully before 

attempting to build your own release, and always rebuild the entire project before running the Ant build._**



## License

**Figure Composer** was created by [Scott Ruffner](mailto:[email protected]). It is licensed under the terms of 

the MIT license.



## Credits

**FigureComposer** was developed with funding provided by the Stephen G. Lisberger laboratory in the Department of

Neurobiology at Duke University.



As a full-featured Java Swing application, it relies heavily upon Oracle's Java Development Kit; as of June 2024, it is 

JDK11-compliant and built with Amazon Corretto 11. 



In addition, it makes use of a number of open-source software packages. Without these third-party packages, 

**FigureComposer** would have been a much more difficult endeavor. 

- _FypML_ figure documents have been read and written 

using [**MXP1**](https://github.com/codelibs/xpp3?tab=readme-ov-file), an open-source implementation of an XML pull 

parser. As of version 5.2.0, this library is no longer used; instead, FC relies on the Streaming API for XML Processing 

that is now part of the Java runtime environment.

- The JavaScript Object Notation (JSON) data interchange format is used heavily, and the application relies on the 

[org.json](https://www.json.org/json-en.html) package to read and write JSON data.

- _Matlab_ FIG files are read and parsed using a modified version of the 

[Java MAT-file IO (JMatIO)](https://sourceforge.net/projects/jmatio/) package.

- _FypML_ figures are exported to Portable Document Format (PDF) and Scalable Vector Graphics (SVG) files 

with the help of the [iText5 PDF](https://itextpdf.com/products/itext-5-legacy) and the 

[JFreeSVG](https://www.jfree.org/jfreesvg/index.html) libraries, respectively.