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\newtheorem{definition}{تعریف}[section]
\theoremstyle{theorem}
\newtheorem{theorem}{قضیه}[section]
\newtheorem{lemma}{لم}[section]
\newtheorem{proposition}{گزاره}[section]
\newtheorem{corollary}{نتیجه}[section]
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\usepackage{xepersian}
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\begin{document}

\section{فرضیات حاکم بر مساله} 
با توجه به فرضیات بخ ماتریس کسینوس‌های هادی\footnote{ Matrix(DCM) Cosine Direction}  از رابطه زیر بدست خواهد آمد:

\begin{equation} \label{DCM}
\begin{split}
DCM=
&  \left[ 
\begin {array}{ccc} 1&0&0\\ \noalign{\medskip}0&\cos \left( \phi
 \right) &\sin \left( \phi \right) \\ \noalign{\medskip}0&-\sin
 \left( \phi \right) &\cos \left( \phi \right) \end {array} \right].
 \left[ \begin {array}{ccc} \cos \left( \theta \right) &0&-\sin
 \left( \theta \right) \\ \noalign{\medskip}0&1&0\\ \noalign{\medskip}
\sin \left( \theta \right) &0&\cos \left( \theta \right) \end {array}
 \right]   . \left[ \begin {array}{ccc} \cos \left( \psi
 \right) &\sin \left( \psi \right) &0\\ \noalign{\medskip}-\sin
 \left( \psi \right) &\cos \left( \psi \right) &0\\ \noalign{\medskip}0
&0&1\end {array} \right]  \\
=& \left[ \begin {array}{ccc} \cos \left( \theta \right) \cos \left( 
\psi \right) &\cos \left( \theta \right) \sin \left( \psi \right) &-
\sin \left( \theta \right) \\ \noalign{\medskip}\sin \left( \phi
 \right) \sin \left( \theta \right) \cos \left( \psi \right) -\cos
 \left( \phi \right) \sin \left( \psi \right) &\sin \left( \phi
 \right) \sin \left( \theta \right) \sin \left( \psi \right) +\cos
 \left( \phi \right) \cos \left( \psi \right) &\sin \left( \phi
 \right) \cos \left( \theta \right) \\ \noalign{\medskip}\cos \left( 
\phi \right) \sin \left( \theta \right) \cos \left( \psi \right) +\sin
 \left( \phi \right) \sin \left( \psi \right) &\cos \left( \phi
 \right) \sin \left( \theta \right) \sin \left( \psi \right) -\sin
 \left( \phi \right) \cos \left( \psi \right) &\cos \left( \phi
 \right) \cos \left( \theta \right) \end {array} \right]
\end{split}
\end{equation}

\end{document}