Libs/Optimize/ParticleSystem/itkParticleGeneralShapeGradientMatrix.h

Namespaces

Name
itk

Classes

	Name
class	itk::ParticleGeneralShapeGradientMatrix Each column describes a shape. A shape may be composed of m_DomainsPerShape domains (default 1). ALL DOMAINS ARE NOT ASSUMED TO HAVE THE SAME NUMBER OF PARTICLES!

Source code

#pragma once


#include "itkParticleAttribute.h"
#include "itkDataObject.h"
#include "itkWeakPointer.h"
#include "itkParticleContainer.h"
#include "vnl/vnl_matrix.h"

#include "ParticleImplicitSurfaceDomain.h"
#include "ParticleImageDomainWithGradients.h"
#include "ParticleImageDomainWithGradN.h"
#include "TriMesh.h"

#include "itkParticleSystem.h"

namespace itk
{
template <class T, unsigned int VDimension>
class ITK_EXPORT ParticleGeneralShapeGradientMatrix
        : public vnl_matrix<T>, public ParticleAttribute<VDimension>
{
public:
    typedef T DataType;
    typedef ParticleGeneralShapeGradientMatrix Self;
    typedef ParticleAttribute<VDimension> Superclass;
    typedef SmartPointer<Self>  Pointer;
    typedef SmartPointer<const Self>  ConstPointer;
    typedef WeakPointer<const Self>  ConstWeakPointer;

    typedef ParticleSystem ParticleSystemType;
    itkNewMacro(Self)


    itkTypeMacro(ParticleGeneralShapeGradientMatrix, ParticleAttribute)

    virtual void BeforeIteration() {}
    virtual void AfterIteration() {}

    void SetDomainsPerShape(int i)
    { m_DomainsPerShape = i;     }
    int GetDomainsPerShape() const
    { return m_DomainsPerShape;  }

    void SetAttributesPerDomain(const std::vector<int> &i)
    { m_AttributesPerDomain = i; }

    void SetAttributeScales( const std::vector<double> &s)
    { m_AttributeScales = s;     }

    void SetXYZ(int i, bool val)
    {
        if (m_use_xyz.size() != m_DomainsPerShape)
            m_use_xyz.resize(m_DomainsPerShape);
        m_use_xyz[i] = val;
    }
    void SetNormals(int i, bool val)
    {
        if (m_use_normals.size() != m_DomainsPerShape)
            m_use_normals.resize(m_DomainsPerShape);
        m_use_normals[i] = val;
    }

    virtual void SetMatrix(const vnl_matrix<T> &m)
    {
        vnl_matrix<T>::operator=(m);
    }

    virtual void ResizeMatrix(int rs, int cs)
    {
        vnl_matrix<T> tmp(*this); // copy existing  matrix

        // Create new column (shape)
        this->set_size(rs, cs);

        // Copy old data into new matrix.
        for (unsigned int c = 0; c < tmp.cols(); c++)
        {
            for (unsigned int r = 0; r < tmp.rows(); r++)
                this->operator()(r,c) = tmp(r,c);
        }
    }

    void SetValues(const ParticleSystemType *ps, int idx, int d)
    {
        const typename itk::ParticleSystem::PointType posLocal = ps->GetPosition(idx, d);

        unsigned int k = 0;
        int dom = d % m_DomainsPerShape;
        int num = 0;
        for (int i = 0; i < dom; i++)
        {
            if (m_use_xyz[i])
            {
                k += VDimension * ps->GetNumberOfParticles(i);
                num += VDimension;
            }
            if (m_use_normals[i])
            {
                k += VDimension * ps->GetNumberOfParticles(i);
                num += VDimension;
            }
            k += m_AttributesPerDomain[i]* ps->GetNumberOfParticles(i);
            num += m_AttributesPerDomain[i];
        }
        if (m_use_xyz[dom])
            k += idx * VDimension;
        if (m_use_normals[dom])
            k += idx * VDimension;
        k += idx * m_AttributesPerDomain[dom];



        int s = 0;
        if (m_use_xyz[dom])
        {
            for (unsigned int i = 0; i < VDimension; i++)
            {
                for (unsigned int j = 0; j < VDimension; j++)
                {
                    if (i == j)
                        this->operator()(i+k, j + 3* (d / m_DomainsPerShape)) = 1.0*m_AttributeScales[num+i];
                    else
                        this->operator()(i+k, j + 3* (d / m_DomainsPerShape)) = 0.0;
                }

            }
            k += VDimension;
            s += VDimension;
        }
        if (m_use_normals[dom])
        {

            if (ps->GetDomainFlag(d))
            {
                for (unsigned int c = s; c < s+VDimension; c++)
                {
                    for (unsigned int vd = 0; vd < VDimension; vd++)
                        this->operator()(c-s+k, vd + 3 * (d / m_DomainsPerShape)) = 0.0*m_AttributeScales[num+c];
                }
                s += VDimension;
                k += VDimension;
            }
            else
            {
                vnl_vector_fixed<float, DIMENSION> gradient = ps->GetDomain(d)->SampleGradientAtPoint(posLocal, idx);
                vnl_vector_fixed<float, DIMENSION> normal = gradient.normalize();
                float grad_mag = gradient.magnitude(); //TODO This is always 1.0. Fix when correcting image gradient of normals
                typename shapeworks::ParticleDomain::GradNType grad_n = ps->GetDomain(d)->SampleGradNAtPoint(posLocal, idx);

                typename shapeworks::ParticleImageDomainWithGradN<float>::VnlMatrixType mat1;
                mat1.set_identity();
                vnl_matrix<float> nrml(VDimension, 1);
                nrml.fill(0.0);
                nrml(0,0) = normal[0]; nrml(1,0) = normal[1]; nrml(2,0) = normal[2];
                typename shapeworks::ParticleImageDomainWithGradN<float>::VnlMatrixType mat2 = nrml * nrml.transpose();

                for (unsigned int x1 = 0; x1 < VDimension; x1++) {
                    for (unsigned int x2 = 0; x2 < VDimension; x2++) {
                        mat1(x1, x2) -= mat2(x1, x2);
                        grad_n(x1, x2)   /= grad_mag;
                    }
                }

                // mat3 = H/|grad_f| * (I - n*n');
                typename shapeworks::ParticleImageDomainWithGradN<float>::VnlMatrixType mat3 = grad_n * mat1;
                typename itk::ParticleSystem::VnlMatrixType tmp;
                tmp.set_size(VDimension, VDimension);
                tmp.fill(0.0);
                for (unsigned int c = 0; c<VDimension; c++)
                {
                    for (unsigned vd = 0; vd<VDimension; vd++)
                        tmp(c,vd) = mat3(c,vd);
                }

                tmp = ps->TransformNormalDerivative(tmp, ps->GetTransform(d) * ps->GetPrefixTransform(d));

                for (unsigned int c = s; c < s+VDimension; c++)
                {
                    for (unsigned int vd = 0; vd < VDimension; vd++)
                        this->operator()(c-s+k, vd + 3 * (d / m_DomainsPerShape)) = tmp(c-s, vd)*m_AttributeScales[num+c];
                }
                s += VDimension;
                k += VDimension;
            }
        }


        if (m_AttributesPerDomain[dom] > 0)
        {
            if (ps->GetDomainFlag(d))
            {
                for (int aa = 0; aa < m_AttributesPerDomain[dom]; aa++)
                {
                    for (unsigned int vd = 0; vd < VDimension; vd++)
                        this->operator()(aa+k, vd + 3 * (d / m_DomainsPerShape)) = 0.0*m_AttributeScales[num+aa+s];
                }
            }
            else
            {
              // TODO, figure out what is going on here
                point pt;
                pt.clear();
                pt[0] = posLocal[0];
                pt[1] = posLocal[1];
                pt[2] = posLocal[2];

                for (int aa = 0; aa < m_AttributesPerDomain[dom]; aa++)
                {
                    point dc;
                    dc.clear();
                    const shapeworks::ParticleImplicitSurfaceDomain<float> * domain
                        = static_cast<const shapeworks::ParticleImplicitSurfaceDomain<float> *>(ps->GetDomain(d));
                    meshFIM *ptr = domain->GetMesh();
                    dc = ptr->GetFeatureDerivative(pt, aa);
                    for (int vd = 0; vd < VDimension; vd++)
                        this->operator()(aa+k, vd + 3 * (d / m_DomainsPerShape)) = dc[vd]*m_AttributeScales[num+aa+s];
                }
            }
        }
    }

    virtual void DomainAddEventCallback(Object *, const EventObject &e)
    {
        const itk::ParticleDomainAddEvent &event = dynamic_cast<const itk::ParticleDomainAddEvent &>(e);
        unsigned int d = event.GetDomainIndex();

        if ( d % m_DomainsPerShape  == 0 )
            this->ResizeMatrix(this->rows(), this->cols()+3); //3 columns for every shape
    }

    virtual void PositionAddEventCallback(Object *o, const EventObject &e)
    {
        // update the size of matrix based on xyz, normals and number of attributes being used
        const itk::ParticlePositionAddEvent &event = dynamic_cast<const itk::ParticlePositionAddEvent &>(e);
        const itk::ParticleSystem *ps= dynamic_cast<const itk::ParticleSystem *>(o);
        const int d = event.GetDomainIndex();
        const unsigned int idx = event.GetPositionIndex();

        int numRows = 0;
        for (int i = 0; i < m_DomainsPerShape; i++)
        {
            if (m_use_xyz[i])
                numRows += VDimension * ps->GetNumberOfParticles(i);
            if (m_use_normals[i])
                numRows += VDimension * ps->GetNumberOfParticles(i);
            numRows += m_AttributesPerDomain[i]* ps->GetNumberOfParticles(i);
        }

        if (numRows > this->rows())
            this->ResizeMatrix(numRows, this->cols());

        this->SetValues(ps, idx, d);
    }

    virtual void PositionSetEventCallback(Object *o, const EventObject &e)
    {
        // update xyz, normals and number of attributes being used
        const itk::ParticlePositionSetEvent &event = dynamic_cast<const itk::ParticlePositionSetEvent &>(e);
        const itk::ParticleSystem *ps= dynamic_cast<const itk::ParticleSystem *>(o);
        const int d = event.GetDomainIndex();
        const unsigned int idx = event.GetPositionIndex();

        this->SetValues(ps, idx, d);
    }

    virtual void PositionRemoveEventCallback(Object *, const EventObject &)
    {
        // NEED TO IMPLEMENT THIS
    }

protected:
    ParticleGeneralShapeGradientMatrix()
    {
        m_DomainsPerShape = 1;

        this->m_DefinedCallbacks.DomainAddEvent = true;
        this->m_DefinedCallbacks.PositionAddEvent = true;
        this->m_DefinedCallbacks.PositionSetEvent = true;
        this->m_DefinedCallbacks.PositionRemoveEvent = true;
    }
    virtual ~ParticleGeneralShapeGradientMatrix() {}

    void PrintSelf(std::ostream& os, Indent indent) const
    {  Superclass::PrintSelf(os,indent);  }

    int m_DomainsPerShape;
private:

    ParticleGeneralShapeGradientMatrix(const Self&); //purposely not implemented
    void operator=(const Self&); //purposely not implemented

    std::vector<bool> m_use_xyz;
    std::vector<bool> m_use_normals;
    std::vector<int> m_AttributesPerDomain;
    std::vector<double> m_AttributeScales;

}; // end class

} // end namespace

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Updated on 2022-07-23 at 17:50:04 -0600