View source for Refactoring itk::FEM framework - V4

This page outlines the proposed changes to the itk::FEM framework. A number of these changes will break backwards compatibility. 

=Submission Of Code=

http://review.source.kitware.com/#change,1993


=Authors=
The proposed changes for the itk::FEM framework are being proposed by the University of Iowa. This group is made up of investigators from the Departments of Radiology, Biomedical Engineering, and Psychiatry. Questions and comments regarding these changes should be sent to
*'''Vincent Magnotta (vincent-magnotta -at- uiowa.edu)''' - [http://mri.radiology.uiowa.edu Radiology]
Other team members include
*Nicole Grosland - [http://www.bme.engineering.uiowa.edu/ Biomedical Engineering], [http://www.ccad.uiowa.edu/mimx MIMX]
*Kiran Shivanna - [http://www.ccad.uiowa.edu/mimx MIMX]
*Hans Johnson - [http://www.psychiatry.uiowa.edu Psychiatry]
*Kent Williams - [http://www.psychiatry.uiowa.edu Psychiatry]

= Changes to the FEM Framework Classes=

==itk::fem::FEMLightObject==
This class has been updated to remove public access to the class variables. All fem classes derive from this class. This class was also converted to support smart pointers.
*Move the following class variables from public to protected: 
**'''GN''' - This variable was renamed to m_GlobalNumber
*The following member functions were added to support setting the global number for fem objects
**void '''SetGlobalNumber'''(int)
**int '''GetGlobalNumber'''()

==itk::FEMObject==
Currently the itk::fem framework offers a complicated interface for specifying mesh to be used for analysis. We will create a new ITK object called itk::FEMObject which will define the entire FE model. The itk::FEMObject will inherit from itk::DataObject. This object will allow the user to completely specify the Nodes, Elements, Loads, and Materials for the problem. This decision was based on the decision to make a parallel structure to itk::Mesh without a complete refactoring of the mesh data structure. This also removes the specification of the FE simulation from the solver.

In order to support input/output, we have decided to use SpatialObjects. To support the new FEMObject, a new FEMSpatialObject was created. This also required that additions be added to the metaIO library to support this new spatial object type. The minor disadvantage of this implementation is that new element, load, and material types will require additions in multiple locations. We have decided to use the same FEM model specification that was used previously, but it is now encoded in a spatial object.


=== Migration Guide ===
The [http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html itk::fem::FEMObject] was created to provide support for a first class object in ITK that will define the finite element problem being used for analysis. This used to be defined only in the itk::fem::Solver. All support for file I/O was removed from this class. The user would now define a FEMObject object and use this an input into the solver. Here is an outline on how to define a new problem.
   
  itk::fem::FEMObject::Pointer fem = itk::fem::FEMObject::New();
  .
  .
  .
  itk::fem::Solver::Pointer solver = itk::fem::Solver::New();
  solver->SetInput( fem );
  solver->Update( );
  
  itk::fem::FEMObject::Pointer result = solver->GetOutput();

The FEMObject has interfaces to define the nodes, elements, materials, and loads used to define the finite element problem. Here are the public member functions used to manipulate the various portions of the FEM problem.

*'''Nodes:'''
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods AddNextNode (Element::Node::Pointer e)] - Add another node to the FEM problem. This will be added as the last node in the node container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods InsertElement (Element::Pointer e, ElementIdentifier index)] - Add another node at the specified position in the node container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNode (NodeIdentifier index)]  - Get the node at the specified index of the node container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNodeWithGlobalNumber (int globalNumber)] - Get the node with the specified global number. This is independent of the order in the node container, and is defined by the user when defining the FEM problem.
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNumberOfElements (void) ] - Get number of nodes in the FEM problem
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNodeContainer ()] - Get the entire node container

*'''Elements:'''
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods AddNextElement (Element::Pointer e)] - Add another element to the FEM problem. This will be added as the last element in the element container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetElementContainer ()] - Get the entire element container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNumberOfElements (void)] - Get number of elements in the FEM problem
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods InsertElement (Element::Pointer e, ElementIdentifier index)] - Add another element at the specified position in the element container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetElement (ElementIdentifier index)] - Get the element at the specified index of the element container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetElementWithGlobalNumber (int globalNumber)] - Get the element with the specified global number. This is independent of the order in the element container, and is defined by the user when defining the FEM problem.

*'''Loads:'''
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods AddNextLoad()] - Add another load to the FEM problem. This will be added as the last load in the load container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods InsertLoad()] - Add another load at the specified position in the load container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNumberOfLoads()] - Get number of loads in the FEM problem
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetLoadContainer()] - Get the entire load container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetLoadWithGlobalNumber()] - Get the load with the specified global number. This is independent of the order in the load container, and is defined by the user when defining the FEM problem.
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetLoad()] - Get the load at the specified index in the load container.

*'''Materials:'''
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetMaterialContainer ()] - Get the entire material container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods AddNextMaterial (MaterialLinearElasticity::Pointer mat)] - Add another material at the specified position in the material container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNumberOfMaterials (void)] - Get number of materials in the FEM problem
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods InsertMaterial (Material::Pointer e, MaterialIdentifier index)]  - Add another material at the specified position in the material container
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetMaterial (MaterialIdentifier index)]
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetMaterialWithGlobalNumber (int globalNumber)] - Get the material with the specified global number. This is independent of the order in the material container, and is defined by the user when defining the FEM problem.

*'''Other Public Membership Functions:'''
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods Clear ()] - Initialize the FEMObject 
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods DeepCopy (FEMObject *Copy)] - Copy the FEMObject into the current FEMObject
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods FinalizeMesh ()] - Finalize the mesh. This '''must''' be called before using this object in the itk::fem::Solver
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNumberOfDegreesOfFreedom (void)] - Get the degrees of freedom for the FEMObject 
*#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1FEMObject.html#pub-methods GetNumberOfMultiFreedomConstraints (void)] - Get the number of constraints for the FEMObject

==itk::fem::Node==
This class is defined in itkFEMElementBase.h and defines the degree of freedom and coordinate for the node. A node is essentially a point in space.

*'''Public Member Functions:'''
**VectorType & '''GetCoordinates(void)''' - get the spatial coordinates for the node
**void '''SetCoordinates(const VectorType & coords)''' - Set the spatial coordinates of the node
**DegreeOfFreedomIDType '''GetDegreeOfFreedom(unsigned int i)''' - Get the degree of freedom for the spatial coordinate (x,y,z)
**void '''SetDegreeOfFreedom(unsigned int i, DegreeOfFreedomIDType dof)''' - Set the degree of freedom for the spatial coordinate
**void '''ClearDegreesOfFreedom(void)''' - Remove all of the degrees of freedom



==itk::fem::Element==
This is the [http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element.html base class] and specific element types are defined below. This class did not change from its implementation in previous versions of ITK. The following changes were made to each of the specific element types.

#The following variables have been moved from public to protected: 
#*'''mat''' - This variable is now called m_mat
#The following variables have been moved from public to protected: 
#*Material::ConstPointer '''GetMaterial'''(void) - Get the material property used for the element
#*void '''SetMaterial'''(Material::ConstPointer mat_) - Set the material property for the element
#The following public membership functions have been removed: 
#*void '''Read'''(std::istream &, void *info)
#*void '''Write'''(std::ostream & f)


The specific element types available are defined below:
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC1Beam.html Element2DC1Beam]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0LinearQuadrilateralStress.html Element2DC0LinearQuadrilateralStress] 
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0LinearQuadrilateralStrain.html Element2DC0LinearQuadrilateralStrain]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0LinearQuadrilateralMembrane.html Element2DC0LinearQuadrilateralMembrane] 
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0LinearTriangularStress.html Element2DC0LinearTriangularStress] 
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0LinearTriangularStrain.html Element2DC0LinearTriangularStrain] 
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0LinearTriangularMembrane.html Element2DC0LinearTriangularMembrane] 
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0QuadraticTriangularStress.html Element2DC0QuadraticTriangularStress] 
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element2DC0QuadraticTriangularStrain.html Element2DC0QuadraticTriangularStrain]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element3DC0LinearHexahedronMembrane.html Element3DC0LinearHexahedronMembrane]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element3DC0LinearHexahedronStrain.html Element3DC0LinearHexahedronStrain]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element3DC0LinearTetrahedronMembrane.html Element3DC0LinearTetrahedronMembrane]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element3DC0LinearTetrahedronStrain.html Element3DC0LinearTetrahedronStrain]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element3DC0LinearTriangularLaplaceBeltrami.html Element3DC0LinearTriangularLaplaceBeltrami]
#[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Element3DC0LinearTriangularMembrane.html Element3DC0LinearTriangularMembrane]

==itk::fem::MaterialLinearElasticity==
[http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1MaterialLinearElasticity.html MaterialLinearElasticity] is the only material type that currently exists in ITK. Several modifications were made to this class during the ITKv4 refactoring.

#Move the following class variables were moved from public to protected signatures: 
#*'''A''' - renamed to m_CrossSectionalArea
#*'''E''' - renamed m_YoungModulus
#*'''h'''  - renamed m_Thickness
#*'''I'''  - renamed m_MomentOfInertia
#*'''nu'''  - renamed m_PoissonRatio
#*'''RhoC'''   - renamed m_DensityHeatCapacity
#Add the following public class member functions to get/set the class variables.
#*void '''SetCrossSectionalArea'''(double) – Set the cross sectional area 
#*void '''SetYoungsModulus'''(double) – Set the Youngs Modulus 
#*void '''SetThickness'''(double) – Set the cross sectional thickness 
#*void '''SetMomentOfInertia'''(double) – Set the Moment of Inertia 
#*void '''SetPoissonsRatio'''(double) – Set the Poisson’s ratio
#*void '''SetDensityHeatProduct'''(double) – Set the Density - Heat Capacity product 
#*double '''GetCrossSectionalArea'''() – Get the cross sectional area
#*double '''GetYoungsModulus'''() – Get the Youngs Modulus
#*double '''GetThickness'''() – Get the cross sectional thickness
#*double '''GetMomentOfInertia'''() – Get the Moment of Inertia
#*double '''GetPoissonsRatio'''() – Get the Poisson’s ratio
#*double '''GetDensityHeatProduct'''() – Get the Density - Heat Capacity product


==itk::fem::Load==
This is the [http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Load.html load base class] for all specific implementations used in the itk::fem framework.


===itk::fem::LoadBC===
#The following class variables were from public to protected:
#*'''m_dof''' - renamed to m_DegreeOfFreedom
#*'''m_element''' - renamed to m_Element
#*'''m_value''' - renamed to m_Value
#The following class variable was removed
#*'''CLID''' 
#The following class functions were added, allowing the user to get and set the class variables:
#*void '''SetDegreeOfFreedom'''(unsigned int dof) – Set the degree of freedom for the local element for which the boundary condition is being applied.
#*void '''SetElement'''(Element::ConstPointer element) – Set the element for which the boundary condition is being applied.
#*void '''SetValue'''(vnl_vector< Element::Float > value) – Set the boundary condition using a vector representation. This can be used to restrict motion of an element in a particular direction.
#*unsigned int '''GetDegreeOfFreedom'''() – Returns the local degree of freedom for the element on which the boundary condition is being applied.
#*Element::ConstPointer '''GetElement'''() – Returns the element on which the boundary condition is being applied.
#*vnl_vector< Element::Float > '''GetValue'''() – Returns the assigned boundary condition.

===itk::fem::LoadBCMFC===
#The following class variables were from public to protected:
#*'''Index''' - renamed to m_Index
#*'''lhs''' - renamed to m_LeftHandSide
#*'''rhs''' - renamed to m_RightHandSide
#Add class methods to get and set the class variables.
#*void '''SetIndex'''(int) – Set the index variable for the multi freedom displacement constraint. This is used internally by the itk::Fem::Solver.
#*void '''AddLeftHandSideTerm'''(LoadBCMFC::MFCTerm) – Add terms to the right hand side of the multi freedom displacement constraint. Used to replace loadBCMFC.lhs.push_back().
#*void '''AddRightHandSideTerm'''(vnl_vector< Element::Float >) – Set the right hand side of the linear equation that defines the constraints. Replaces loadBCMFC.rhs = a;
#*int '''GetIndex''' – Get the index variable for the multi freedom displacement constraint.
#*int '''GetNumberOfLeftHandSideTerms'''() – Returns the number of terms used to define the left hand side of the multi freedom displacement constraint.
#*itk::LoadBFMC '''GetLeftHandSideTerm'''(int index) – Returns the specified left hand side term.
#*int '''GetNumberOfRightHandSideTerms'''()– Returns the number of terms used to define the left hand side of the multi freedom displacement constraint.
#*Element::Float '''GetRightHandSideTerm'''(int index) – Returns the specified right hand side term.
#*std::vector< MFCTerm >& '''GetLeftHandSideArray'''() - Get the left hand side of the FEM system
#*vnl_vector< Element::Float >& '''GetRightHandSideArray'''() - Get the right hand side of the FEM system

===itk::fem::LoadEdge===
#The following member variables were moved from public to protected signatures:
#*'''m_Edge'''
#*'''m_Force''' 
#The following public membership functions are now provided to get/set class variables
#*void '''SetEdge'''(int) – Set the edge to apply the desired force.
#*void '''SetForce'''(vnl_matrix< Float >) – Set the force to be applied to an edge.
#*int '''GetEdge'''() – Get the edge for the applied force. 
#*vnl_matrix< Float > '''GetForce'''() – Get the force applied.
#*void '''ApplyLoad'''(Element::ConstPointer element, Element::VectorType & Fe) - Apply the load to the elements on which it is applied.

===itk::fem::LoadGravConst===
#The following member variables were moved from public to protected signatures: 
#*'''Fg_value''' - renamed m_GravityForce
#The following public membership functions are now provided to get/set class variables:
#*void '''SetForce'''(vnl_vector< Float >) – Set the constant force vector that exists for every point in space.
#*vnl_vector< Float > '''GetForce'''() – Return the constant force vector that exists for every point in space.
#*vnl_vector< Float > '''GetGravitationalForceAtPoint'''(vnl_vector< Float > ) - Return the force at the specified location. The same value is returned at every point.
#*void '''ApplyLoad'''(Element::ConstPointer element, Element::VectorType & Fe) - Apply the load to the specified element.

===itk::fem::LoadLandmark===
#The following member variables were moved from public to protected signatures: 
#*'''eta''' - renamed to m_Eta
#*'''m_force''' - renamed to m_Force
#*'''m_pt''' - renamed to m_Point
#*'''m_Solution'''
#*'''m_Source'''
#*'''m_Target''' 
#The following public membership functions are now provided to get/set class variables: 
#*void '''SetEta'''(double) – Set the square root of the variance.
#*double '''GetEta'''(double) – Get the square root of the variance.
#*void '''ApplyLoad'''(Element::ConstPointer element, Element::VectorType & Fe) - Apply load the specified element
#*itk::LightObject::Pointer '''CreateAnother'''(void) - Create a copy of the load

===itk::fem::LoadNode===
#The following member variables were moved from public to protected signatures: 
#*'''F''' - renamed m_Force
#*'''m_element''' - renamed m_Element
#*'''m_pt''' - renamed m_Point
#The following public membership functions are now provided to get/set class variables: 
#*void '''SetForce'''(vnl_vector< Float >) – Set the applied force to the node.
#*void '''SetElement'''(Element::ConstPointer) – Set the element in the system that contains the degrees of freedom on which the force is applied.
#*void '''SetNode'''(unsigned int) – Set the point on which the force is being applied.
#*vnl_vector< Float > &'''GetForce'''() – Get the applied force.
#*Element::ConstPointer '''GetElement'''() – Get the element in the system that contains the degrees of freedom on which the force is applied.
#*Unsigned int '''GetNode'''() – Get the point on which the force is being applied.
#*itk::LightObject::Pointer '''CreateAnother'''(void) - Create a copy of the load
#*void '''ApplyLoad'''(Element::ConstPointer element, Element::VectorType & Fe) - Apply load the specified element

===itk::fem::LoadPoint===
#Move the following class variables from public to protected signatures: 
#*'''Fp''' - renamed m_Point
#*'''point''' -renamed m_ForcePoint
#The following public membership functions are now provided to get/set class variables: 
#*void '''SetForce'''(vnl_vector<Float>) – Set the force to be applied to the specified point location.
#*void '''SetPoint'''(vnl_vector<Float>) – Set the point where the force is applied in global coordinates.
#*vnl_vector<Float> & '''GetForce'''(vnl_vector<Float>) – Get the applied force.
#*vnl_vector<Float> & '''GetPoint''' (vnl_vector<Float>) – Get the point where the force is applied.
#*itk::LightObject::Pointer '''CreateAnother'''(void) - Create a copy of the load
#*void '''ApplyLoad'''(Element::ConstPointer element, Element::VectorType & Fe) - Apply load the specified element

==itk::Solver==
The [http://www.itk.org/Doxygen/html/classitk_1_1fem_1_1Solver.html itk::fem::Solver] is a templated class over the problem dimension. This is now a proper ITK filter that inherits from [http://www.itk.org/Doxygen/html/classitk_1_1ProcessObject.html ProcessObject]. The filter takes as input a FEMObject and will generate an output FEMObject. To get the Solver to generate a solution, the '''RunSolver()''' method needs to be called.

#The following class variables were removed: 
#*'''node'''
#*'''el'''
#*'''load'''
#*'''mat'''


==itk::FEMObjectSpatialObject==
To support I/O we have developed a new spatial object, [http://www.itk.org/Doxygen/html/classitk_1_1FEMObjectSpatialObject.html FEMObjectSpatialObject], was created. A fairly simple conversion is used to convert a from FEMObjectSpatialObject to FEMObject and vice-versa. The public class methods provides this interface.
#void '''SetFEMObject'''( FEMObjectType * femobject ) 
#FEMObjectType * '''GetFEMObject'''( void )

The FEM objects can then be read and written using the [http://www.itk.org/Doxygen/html/classitk_1_1SpatialObjectReader.html itk::SpatialObjectReader] and [http://www.itk.org/Doxygen/html/classitk_1_1SpatialObjectWriter.html itk::SpatialObjectWriter] respectively.

==File Formats==
The only file format that is currently supported for FEM objects is the spatial object file format. The file format has header information that defines the object(s) stored within the file as well as other information such as the dimension, how the data is stored, etc. Comments are allowed in the file format. Any characters that follow a '''%''' symbol are defined as comments. The header contains the following elements:

*'''ObjectType =''' - Defines the type of object stored (e.g. Scene or FEMObject)
*'''NDims ='''  - Defines the dimension for the stored object
*'''NObjects =''' - Defines the number of objects if the object is a Scene
*'''BinaryData =''' - Defines if the data is binary or not. Binary data is not yet supported
*'''Offset =''' - Defines the position offset  - Currently ignored for FEMObject
*'''CenterOfRotation =''' - Defines center of rotation  - Currently ignored for FEMObject
*'''ElementSpacing =''' - Defines element spacing - Currently ignored for FEMObject
*'''ElementDataFile =''' - Defines where the data is stored ('''LOCAL''' means the data is stored within the same file.


Below the header the user can define the FEM Object using the following format. Typically the user will define the nodes for the FEM problem first. 

===Nodes===
Each node is denoted with a '''<Node>''' marker and then the global node number is specified followed by its position. The dimension of the position is defined by the '''Ndims''' field in the META spatial object header. After all of the nodes are defined there should be a '''<END>''' marker. Here is an example. 

 <Node>
  0	% Global node number
  2 0 0 % Nodal coordinates
 <Node>
  1	% Global node number
  2 1 0	% Nodal coordinates
 <Node>
  2	% Global node number
  2 1 2	% Nodal coordinates
 <END>	% End of nodes

===Materials===
Similar to Nodes, Materials are specified by a maker that defines the type of material being defined. Presently, there is only one material property type, '''MaterialLinearElasticity'''. The material marker is followed by all of the parameters that are used to define the material (Global Number, Young modulus, Cross-sectional area, Moment of inertia, Poisson's ratio, thickness, and Density Heat Capacity). Here is an example

 <MaterialLinearElasticity>
  0	% Global material number
  E  : 30000000	% Young modulus
  A  : 0	% Crossection area
  I  : 0	% Moment of inertia
  nu : 0.3	% Poisson's ratio
  h  : 1	% Thickness
  RhoC : 1	% Density Heat Capacity
 END:	% End of current material definition
 <END>  % End of materials

===Elements===
Elements define the type of element, the global number, the global number of the nodes used to define the element, and the global number for the material. The following element types are supported
*Element2DC1Beam
*Element2DC0LinearQuadrilateralStress
*Element2DC0LinearQuadrilateralStrain
*Element2DC0LinearQuadrilateralMembrane
*Element2DC0LinearTriangularStress
*Element2DC0LinearTriangularStrain
*Element2DC0LinearTriangularMembrane
*Element2DC0QuadraticTriangularStress
*Element2DC0QuadraticTriangularStrain
*Element3DC0LinearHexahedronMembrane
*Element3DC0LinearHexahedronStrain
*Element3DC0LinearTetrahedronMembrane
*Element3DC0LinearTetrahedronStrain
*Element3DC0LinearTriangularLaplaceBeltrami
*Element3DC0LinearTriangularMembrane 


Here is an example definition of two elements. 
 <Element2DC0LinearTriangularStress>
  0	% Global element number
  0	% Node 1 ID
  1	% Node 2 ID
  2	% Node 3 ID
  0	% MaterialLinearElasticity ID
 <Element2DC0LinearTriangularStress>
  1	% Global element number
  0	% Node 1 ID
  2	% Node 2 ID
  3	% Node 3 ID
  0	% MaterialLinearElasticity ID 
 <END>	% End of elements

===Loads===
Similar structures are used for Loads. Each load definition is slightly different depending on the type of load. Here are examples that show how to define each of the Load types in the Meta file. AT the end of the load section there should be a '''<END>''' marker to signal the end of loads.

 <LoadNode>
  0	% Global load number
  1	% GN of the element on which the load acts
  2	% Point number within the element
  2 0 -1000	% Force vector

 <LoadBC>
  1	% Global load number
  0	% GN of element
  0	% DOF# in element
  1 0	% rhs of MFC

 <LoadBCMFC>

  5	% Global object number

  2	% Number of DOFs in this MFC

  %==>

  0	% GN of element

  1	% DOF# in element

  1	% weight

  %==>

  1	% GN of element

  3	% DOF# in element

  -1	% weight

  %==>

  1 0	% rhs of MFC

 <LoadEdge>

  0	% Global load number

  0	% GN of the element on which the load acts

  1	% Edge number

  2 2 	% # Rows and Columns in force matrix
  10 0	% Force Matrix

  5 0   % Force Matrix

 <LoadGravConst>

  1	% Global load number

  1	% Number of elements on which the load acts

  1	% GN of the element on which the load acts

  2  0 -12.762	% Force vector	

 <LoadLandmark>
  0  % Global load number
  2 0. 0.   % Original point location
  2 0. 1.   % Deformed point location
  1.e-2     % Square root of landmark variance

==Other Formats==
*Netgen supports gmsh format
*tetgen supports VTK 
*VTK supports several additional formats

=Update the itk::FEMRegistrationFilter=
To make the FEMRegistrationFilter similar to the other registration filters the following changes will be made
#Remove these public member functions. The application programmer will be responsible for loading the images and setting the parameters for the filter. The configuration file will be removed.
#*'''GetConfigFileName''' ()
#*'''GetFixedFile''' ()
#*'''GetMovingFile''' ()
#*'''GetResultsFileName''' ()
#*'''GetWriteDisplacements''' ()
#*'''ReadConfigFile''' (const char *)
#*'''SetConfigFileName''' (const char *f)
#*'''SetDisplacementsFile''' (const char *r)
#*'''SetFixedFile''' (const char *t)
#*'''SetLandmarkFile''' (const char *l)
#*'''SetMovingFile''' (const char *r)
#*'''SetResultsFile''' (const char *r)
#*'''SetResultsFileName''' (const char *f)
#*'''WriteDisplacementField''' (unsigned int index)
#*'''WriteDisplacementFieldMultiComponent''' ()
#*'''WriteWarpedImage''' (const char *fn)
#Add these new public member functions
#*bool '''AddNextMovingLandmark'''(PointType) – Add another point for the moving image to the registration.
#*bool '''AddNextFixedLandmark'''(PointType) – Add another point from the fixed image to the registration.
#*void '''ClearMovingLandmarks'''() – Remove all of the existing landmarks for the moving image.
#*void '''ClearFixedLandmarks'''() – Remove all of the existing landmarks for the fixed image.
#*bool '''InsertMovingLandmark'''(PointType p, int index) – Insert the moving landmark at the specified index.
#*bool '''InsertFixedLandmark'''(PointType p, int index) – Insert the fixed landmark at the specified index.
#*bool '''RemoveMovingLandmark'''(int index)
#*bool '''RemoveFixedLandmark'''(int index)
#*void '''SetFEMesh'''() – Set the mesh to be used for the registration.
#*void '''GetFEMesh'''() – Get the mesh used in the registration.
#*void '''SetUserDefinedMesh'''(bool) – Specifies if the user will provide a custom mesh or if it will be generated based on the image.


=Data Structure=
*Spatial Objects - 
*ITK::Mesh - 
*VTK Unstructured Grids -


=Solvers=
*SuperLU
*PETSc