Merge pull request #237 from hjmjohnson/remove-fem-references

DOC: Remove FEM registration content retired to the ITKFEM remote module

Author: thewtex

SoftwareGuide/Art/DeformableRegistration1CheckerboardAfter.jpg

@@ -1403,12 +1403,12 @@ \section{Namespaces}%
 \begin{minted}[baselinestretch=1,fontsize=\footnotesize,linenos=false,bgcolor=ltgray]{cpp}
 namespace itk
 {
-namespace fem
+namespace Statistics
 {
 
 ...
 
-} // end namespace fem
+} // end namespace Statistics
 } // end namespace itk
 \end{minted}
 \normalsize

SoftwareGuide/Art/DeformableRegistration1CheckerboardBefore.jpg

@@ -27,7 +27,7 @@ \section{Introduction}%
 
   \item[Model-to-model registration.] Iterative closest point, landmark, and
   surface distance minimization methods can be used with any ITK transform,
-  to rigidly and non-rigidly register image, FEM, and Fourier
+  to rigidly and non-rigidly register image and Fourier
   descriptor-based representations of objects as SpatialObjects.
 
   \item[Atlas formation.] Collections of images or SpatialObjects can be

SoftwareGuide/Art/DeformableRegistration1Output.jpg

@@ -58,14 +58,8 @@ \section{System Organization}%
         anatomical priors in both segmentation and registration methods.
 
   \item[Registration Framework.] A flexible framework for registration
-        supports four different types of registration: image registration,
-        multiresolution registration, PDE-based registration, and FEM (finite
-        element method) registration.
-
-  \item[FEM Framework.] ITK includes a subsystem for solving general
-        FEM problems, in particular non-rigid registration. The FEM package
-        includes mesh definition (nodes and elements), loads, and boundary
-        conditions.
+        supports several different types of registration: image registration,
+        multiresolution registration, and PDE-based registration.
 
   \item[Level Set Framework.] The level set framework is a set of
         classes for creating filters to solve partial differential equations
@@ -549,8 +543,7 @@ \section{Numerics}%
 use VNL under the hood and integrate with the registration framework
 are available. A large collection of statistics functions---not available from
 VNL---are also provided in the \code{Insight/Numerics/Statistics}
-directory. In addition, a complete finite element (FEM) package is available,
-primarily to support the deformable registration in ITK.
+directory.
 
 
 \section{Data Representation}%

SoftwareGuide/Latex/Appendices/CodingStyleGuide.tex

@@ -10,42 +10,6 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 
 
-\subsection{FEM-Based Image Registration}%
-\label{sec:FEMBasedImageRegistration}
-
-\begin{figure}
-\centering
-\includegraphics[width=0.44\textwidth]{DeformableRegistration1CheckerboardBefore.eps}
-\includegraphics[width=0.44\textwidth]{DeformableRegistration1CheckerboardAfter.eps}
-\itkcaption[FEM-based deformable registration results]{Checkerboard comparisons
-before and after FEM-based deformable registration.}%
-\label{fig:DeformableRegistration1Output}
-\end{figure}
-
-\input{DeformableRegistration1.tex}
-
-Figure~\ref{fig:DeformableRegistration1Output} presents the results of
-the FEM-based deformable registration applied to two time-separated
-slices of a living rat dataset.  Checkerboard comparisons of the two
-images are shown before registration (left) and after registration
-(right).  Both images were acquired from the same living rat, the
-first after inspiration of air into the lungs and the second after
-exhalation.  Deformation occurs due to the relaxation of the diaphragm
-and the intercostal muscles, both of which exert force on the lung tissue
-and cause air to be expelled.
-
-The following is a documented sample parameter file that can be used with this
-deformable registration example.  This example demonstrates the setup of a
-basic registration problem that does not use multi-resolution strategies.  As a
-result, only one value for the parameters between \texttt{(\# of pixels per
-element)} and \texttt{(maximum iterations)} is necessary.  In order to use a
-multi-resolution strategy, you would have to specify values for those
-parameters at each level of the pyramid.
-
-\small
-\verbatiminput{FiniteElementRegistrationParameters1.txt}
-\normalsize
-
 \subsection{BSplines Image Registration}%
 \label{sec:BSplinesImageRegistration}
 \input{DeformableRegistration4.tex}

SoftwareGuide/Latex/Architecture/SpatialObjects.tex

@@ -399,8 +399,8 @@ \subsection{Advanced Module Configuration}%
 \end{minted}
 \normalsize
 
-where \code{Module\_{Module1}} could be, for example, \code{Module\_ITKFEM} for
-the non-default, built-in \code{FEM} module, or \code{Module\_Cuberille} for
+where \code{Module\_{Module1}} could be, for example, \code{Module\_ITKReview} for
+the non-default, built-in \code{Review} module, or \code{Module\_Cuberille} for
 the \code{Cuberille} remote module.
 
 \item \textbf{Example 4}: Enable examples.

SoftwareGuide/Latex/Architecture/SystemOverview.tex

@@ -153,7 +153,7 @@ \section{Software Organization}%
         \item \code{ITK/Modules/IO} --- classes that support the reading
         and writing of images, transforms, and geometry.
         \item \code{ITK/Modules/Numerics} --- a collection of numeric modules, including
-        FEM, Optimization, Statistics, Neural Networks, etc.
+        Optimization, Statistics, Neural Networks, etc.
         \item \code{ITK/Modules/Registration} --- classes for registration of
         images or other data structures to each other.
         \item \code{ITK/Modules/Remote} --- a group of modules distributed outside