dev_pipeline.tex

\documentclass{tufte-handout}
\usepackage{../braph2_dev}
%\geometry{showframe} % display margins for debugging page layout

\title{Adapt a Pipeline Script}

\author[The BRAPH~2 Developers]{The BRAPH~2 Developers}

\begin{document}

\maketitle

\begin{abstract}
\noindent
This is the developer tutorial for adapting a pipeline script. 
In this tutorial, you will learn how to edit a \fn{*.braph2} file to change the steps of a pipeline. Here, you will use as an example the pipeline \code{Pipeline Structural Multiplex Comparison BUD} in the file \fn{pipeline\_structural\_multiplex\_comparison\_bud.braph2} (the pipeline for comparing two groups of subjects using structural multiplex data and binary undirected graphs at fixed densities) and adapt it in order to add a third group for structural multiplex.
\end{abstract}

\tableofcontents

\clearpage

\section{Adaption of the pipeline}

You will adapt in \code{Pipeline Structural Multiplex Comparison BUD} in the file \fn{pipeline\_structural\_multiplex\_comparison\_bud.braph2} as shown in \Coderef{cd:m:P_SMCBUD:all}. The changes are highlighted in the comments.

\begin{lstlisting}[
	label=cd:m:P_SMCBUD:all,
	caption={
		Adapted pipeline to compare three groups of subjects using structural multiplex data and binary undirected graphs at fixed densities.
		}
]
%% Pipeline Structural Multiplex Comparison BUD ¥\circled{1}\circlednote{1}{ specifies the name of the pipeline. {\bf The name is changed to avoid conflicts.}}¥

% This is the pipeline script to compare two groups of subjects using structural multiplex data and binary undirected graphs at fixed densities. ¥\circled{2}\circlednote{2}{ provides descriptions for the overall pipeline as well as for each step. {\bf This is updated to reflect the updated pipeline.}}¥
% 1. It loads a brain atlas from an XLS file (e.g., desikan_atlas.xlsx).
% 2. It loads the data of two groups of subjects from two directories (e.g., ST_MP_group_1_XLS and ST_MP_group_2_XLS).
% 3. It analyzes the first group using structural multiplex analyses (ST_MP) based on binary unidrected graphs at fixed densities (BUD).
% 4. It analyzes the second group using the same parameters selected for the first group.
% 5. It compares the results of the two analyses.

% PDF: /tutorials/pipelines/tut_a_mp_st_bud/tut_a_mp_st_bud.pdf ¥\circled{3}\circlednote{3}{ provides the relative file paths for this pipeline’s tutorial, including both the PDF and README versions}¥
% README: /tutorials/pipelines/tut_a_mp_st_bud/readme.md

%% Brain Atlas
ba = ImporterBrainAtlasXLS('WAITBAR', true).get('GET_FILE').get('BA'); ¥\circled{4}\circlednote{4}{ loads the brain atlas.}¥

%% Groups
gr1 = ImporterGroupSubjectST_MP_XLS('BA', ba, 'WAITBAR', true).get('GET_DIR').get('GR'); ¥\circled{5}\circlednote{5}{ loads group 1 from XLS.}¥
gr2 = ImporterGroupSubjectST_MP_XLS('BA', ba, 'WAITBAR', true).get('GET_DIR').get('GR'); ¥\circled{6}\circlednote{6}{ loads group 2 from XLS.}¥
gr3 = ImporterGroupSubjectST_MP_XLS('BA', ba, 'WAITBAR', true).get('GET_DIR').get('GR'); ¥\circled{7}\circlednote{7}{ loads group 3 from XLS. {\bf This is added.}}¥

%% Analysis 1
a_BUD1 = AnalyzeGroup_ST_MP_BUD('GR', gr1, 'DENSITIES', [10 20 30 40 50]); ¥\circled{8}\circlednote{8}{ performs the graph analysis for group 1. The default value of \code{'DENSITIES'} is set to \code{[10 20 30 40 50]}.}¥

%% Analysis 2
a_BUD2 = AnalyzeGroup_ST_MP_BUD('GR', gr2, 'TEMPLATE', a_BUD1); ¥\circled{9}\circlednote{9}{ performs the graph analysis for group 2 with the same analysis template as with group 1.}¥

%% Analysis 3
a_BUD3 = AnalyzeGroup_ST_MP_BUD('GR', gr3, 'TEMPLATE', a_BUD1); ¥\circled{10}\circlednote{10}{ performs the graph analysis for group 3 with the same analysis template as with group 1. {\bf This is added.}}¥

%% Comparison
c_BUD1 = CompareGroup('P', 1000, 'A1', a_BUD1, 'A2', a_BUD2, 'MEMORIZE', true); ¥\circled{10}\circlednote{10}{ compares graph measures between groups 1 group 2. The default value of the number of permutations is \code{'P'} set to \code{1000}.}¥
c_BUD2 = CompareGroup('P', 1000, 'A1', a_BUD1, 'A3', a_BUD3, 'MEMORIZE', true); ¥\circled{12}\circlednote{12}{ compares graph measures between groups 1 and 3. {\bf This is added.}}¥
c_BUD3 = CompareGroup('P', 1000, 'A2', a_BUD2, 'A3', a_BUD3, 'MEMORIZE', true); ¥\circled{13}\circlednote{13}{ compares graph measures between groups 2 and 3. {\bf This is added.}}¥
\end{lstlisting}

\end{document}