developers

BRAPH 2 — For Developers

This section provides instructions and examples for developers who want to extend and enhance BRAPH 2 with new functionalities, for example, by adapting existing pipelines, modifying example scripts, or implementing completely new features.

The software architecture of BRAPH 2 provides a clear structure for developers to understand and extend its functionalities. All objects in BRAPH 2 are derived from a base object called Element. The core code includes the compiler (genesis), the essential source code (src), and the GUI functionalities (gui). Developers can easily add new elements such as brain surfaces, atlases, example scripts, GUI pipelines, graphs, measures, data types, data importers, data exporters, and analyses. By writing new elements and recompiling the code, the new elements and their functionalities are immediately integrated into the GUI.

BRAPH 2 software architecture. Directory structure of BRAPH 2 GENESIS (left) and BRAPH 2 (right). All objects are derived from a base object called Element and written in a simplified pseudocode (files *.gen.m) that is compiled into the actual elements (files *.m) by the command braph2genesis (some examples of these elements are shown). The compiled code can be launched by the command braph2. The core of BRAPH 2 (gray shaded area) includes the compiler (genesis), the essential source code (src), and the essential functionalities for the GUI (gui, yellow-shaded area). The users can easily add new brain surfaces (brainsurfs), atlases (atlases), example scripts and GUI pipelines (in the corresponding folder under pipelines). Furthermore, the users can add new elements such as new graphs (e.g., GraphWU in graphs), measures (e.g., Strength in measures), data types (e.g., SubjectCON in pipelines/connectivity), data importers (e.g., ImporterGroupSubjectCON_XLS in pipelines/connectivity), data exporters (e.g., ExporterGroupSubjectCON_XLS in pipelines/connectivity), and analyses (e.g., AnalyzeEnsemble_CON_WU in pipelines/connectivity) by writing new elements and recompiling the whole code: the new elements and their functionalities will be immediately available also in the GUI. Finally, BRAPH 2 is provided with a set of unit tests (executable by the command test_braph2) that ensure the formal correctness of the code, including that of any newly added elements.

Adapting a Pipeline Script

The simplest way to customize BRAPH 2 is by modifying a .braph2 pipeline script. This permits you to define parameters and adjust the analysis steps according to their specific requirements. The Developer Tutorial to Adapt a Pipeline Script provides guidance on adapting pipeline scripts.

Editing an Example Script

You can also edit the example scripts provided with the software to have more control over the analysis workflow and take advantage of parallel computing for faster calculations. For example, these scripts can be used to run calculations on a cluster. The developer tutorial Developer Tutorial to Adapt an Example Script demonstrates how to modify example scripts.

Expanding BRAPH 2 with New Functionalities

BRAPH 2 object-oriented programming architecture makes it easy to expand its capabilities by introducing new elements and features. An overview of the software architecture can be found in General Developer Tutorial for BRAPH 2

Here are some of the specific ways you can extend BRAPH 2:

• Graphs: You can implement new graph types by extending the Graph element. The Developer Tutorial to Implement a New Graph provides a step-by-step guide on how to create new graph types.

• Measures: You can add new measures to BRAPH 2 by extending the Measure element. The Developer Tutorial to Implement a New Measure explains the process of implementing custom measures.

• Subjects: You can introduce new data types by extending the Subject element. The tutorial Developer Tutorial to Implement a New Subject provides guidance on creating new data types for subjects.

• Group-based and Ensemble-based Analyses: You can add new analysis pipelines to BRAPH 2 by extending the AnalysisGroup or AnalysisEnsemble elements. The tutorials in this category demonstrate the process of implementing new analysis pipelines:

  • Developer Tutorial to Implement a New Group Analysis
  • Developer Tutorial to Implement a New Ensemble Analysis

• Deep-learning Functionalities: You can ntegrate new functionalities for deep-learning analyses into BRAPH 2 as well. Here are the tutorials for expanding BRAPH 2 with deep-learning features:

  • Developer Tutorial to Implement a New Neural Network Data Point
  • Developer Tutorial to Implement a New Neural Network Classifier
  • Developer Tutorial to Implement a New Neural Network Regressor
  • Developer Tutorial to Implement a New Neural Network Cross Validation

• Analysis Pipelines: Developers can also contribute to the evolution of BRAPH 2 by introducing new analysis pipelines tailored to specific research requirements. The Developer Tutorial to Implement a New Analysis Pipeline provides a comprehensive guide on creating custom analysis pipelines within the BRAPH 2 framework. This tutorial covers the entire pipeline development process, including data handling, calculation of measures, statistical analysis, and results visualization. By developing new analysis pipelines, users can enhance the capabilities of BRAPH 2 and enable the exploration of novel analytical approaches.

Expanding BRAPH 2 with New Graphical Elements

BRAPH 2's object-oriented programming architecture also simplifies the process of designing your own panels to visualize new properties and figures. Here are some ways by which you can expand the graphical capabilities of BRAPH 2:

• Property Panels: New property panels can be implemented by extending the PanelProp element. The Developer Tutorial to Implement a New Property Panel provides a step-by-step guide on creating new property panel.

• Figure Panels: New figure panels can be added to BRAPH 2 by extending the GUIFig element. The Developer Tutorial to Implement a New Figure Panel explains the process of implementing custom figures.

These tutorials provide step-by-step instructions and examples to guide developers in expanding BRAPH 2 with new functionalities and graphical elements. We encourage developers to contribute to the growth and improvement of BRAPH 2 by introducing new elements, measures, and analyses. Feel free to share your implementations, ask questions, and engage with the BRAPH 2 community through the BRAPH forum and GitHub page.