shapeworks::ParticleShapeStatistics

Public Functions

	Name
	ParticleShapeStatistics()
	~ParticleShapeStatistics()
int	DoPCA(std::vector< std::vector< Point >> global_pts, int domainsPerShape =1)
int	DoPCA(ParticleSystem particleSystem, int domainsPerShape =1)
	itkStaticConstMacro(Dimension , unsigned int , VDimension )
int	ImportPoints(std::vector< vnl_vector< double >> points, std::vector< int > group_ids)
int	ReadPointFiles(const std::string & s)
int	ReloadPointFiles()
int	WriteCSVFile(const std::string & s)
int	WriteCSVFile2(const std::string & s)
int	ComputeModes()
int	PrincipalComponentProjections()
int	FisherLinearDiscriminant(unsigned int numModes)
const int	SampleSize()
const int	Group1SampleSize()
const int	Group2SampleSize()
const int	NumberOfDimensions()
const int	GroupID(unsigned int i)
const std::vector< int > &	GroupID()
const vnl_matrix< double > &	Eigenvectors()
const std::vector< double > &	Eigenvalues()
const vnl_vector< double > &	Mean()
const vnl_vector< double > &	Group1Mean()
const vnl_vector< double > &	Group2Mean()
const vnl_vector< double > &	NormalizedGroupDifference()
const vnl_vector< double > &	GroupDifference()
int	ComputeMedianShape(const int ID)
double	L1Norm(unsigned int a, unsigned int b)
Eigen::MatrixXd &	PCALoadings()
const vnl_vector< double > &	FishersLDA()
const vnl_matrix< double > &	ShapeMatrix()
const vnl_matrix< double > &	RecenteredShape()
std::vector< double >	PercentVarByMode()
int	SimpleLinearRegression(const std::vector< double > & y, const std::vector< double > & x, double & a, double & b) const
Eigen::VectorXd	get_compactness(std::function< void(float)> progress_callback)
Eigen::VectorXd	get_specificity(std::function< void(float)> progress_callback)
Eigen::VectorXd	get_generalization(std::function< void(float)> progress_callback)
Eigen::MatrixXd	get_group1_matrix()
Eigen::MatrixXd	get_group2_matrix()

Public Attributes

	Name
constexpr static int	VDimension

Public Functions Documentation

function ParticleShapeStatistics

inline ParticleShapeStatistics()

function ~ParticleShapeStatistics

inline ~ParticleShapeStatistics()

function DoPCA

int DoPCA(
    std::vector< std::vector< Point >> global_pts,
    int domainsPerShape =1
)

function DoPCA

int DoPCA(
    ParticleSystem particleSystem,
    int domainsPerShape =1
)

function itkStaticConstMacro

itkStaticConstMacro(
    Dimension ,
    unsigned int ,
    VDimension 
)

Dimensionality of the domain of the particle system.

function ImportPoints

int ImportPoints(
    std::vector< vnl_vector< double >> points,
    std::vector< int > group_ids
)

Loads a set of point files and pre-computes some statistics.

function ReadPointFiles

int ReadPointFiles(
    const std::string & s
)

Loads a set of point files and pre-computes some statistics.

function ReloadPointFiles

int ReloadPointFiles()

Reloads a set of point files and recomputes some statistics.

function WriteCSVFile

int WriteCSVFile(
    const std::string & s
)

Writes a text file in comma-separated format. Suitable for reading into excel or R or Matlab for analysis.

function WriteCSVFile2

int WriteCSVFile2(
    const std::string & s
)

function ComputeModes

int ComputeModes()

Computes PCA modes from the set of correspondence mode positions. Requires that ReadPointFiles be called first.

function PrincipalComponentProjections

int PrincipalComponentProjections()

Computes the principal component loadings, or projections onto the principal componenent axes for each of the samples. ComputeModes must be called first.

function FisherLinearDiscriminant

int FisherLinearDiscriminant(
    unsigned int numModes
)

Computes fishers linear discriminant line for best group separation.

function SampleSize

inline const int SampleSize()

Returns the sample size.

function Group1SampleSize

inline const int Group1SampleSize()

function Group2SampleSize

inline const int Group2SampleSize()

function NumberOfDimensions

inline const int NumberOfDimensions()

Returns the number of dimensions (this is number of points times Dimension)

function GroupID

inline const int GroupID(
    unsigned int i
)

Returns the group ids

function GroupID

inline const std::vector< int > & GroupID()

function Eigenvectors

inline const vnl_matrix< double > & Eigenvectors()

Returns the eigenvectors/values.

function Eigenvalues

inline const std::vector< double > & Eigenvalues()

function Mean

inline const vnl_vector< double > & Mean()

Returns the mean shape.

function Group1Mean

inline const vnl_vector< double > & Group1Mean()

function Group2Mean

inline const vnl_vector< double > & Group2Mean()

function NormalizedGroupDifference

inline const vnl_vector< double > & NormalizedGroupDifference()

function GroupDifference

inline const vnl_vector< double > & GroupDifference()

function ComputeMedianShape

int ComputeMedianShape(
    const int ID
)

Returns the median shape for the set of shapes with Group ID equal to the integer argument. For example, ComputeMedianShape(0) returns the median shape for the set of shapes with m_groupIDs == 0. The median shape is defined as the shape with the minimum sum of Euclidean L1 norms to all other shapes in that group. Arguments passed to this function are set to the index number of the median shape for Group A and Group B, respectively.

function L1Norm

double L1Norm(
    unsigned int a,
    unsigned int b
)

Returns the euclidean L1 norm between shape a and b

function PCALoadings

inline Eigen::MatrixXd & PCALoadings()

Returns the component loadings

function FishersLDA

inline const vnl_vector< double > & FishersLDA()

Returns the Fisher linear discriminant

function ShapeMatrix

inline const vnl_matrix< double > & ShapeMatrix()

Returns the shape matrix

function RecenteredShape

inline const vnl_matrix< double > & RecenteredShape()

Returns the shape with the mean subtracted

function PercentVarByMode

inline std::vector< double > PercentVarByMode()

function SimpleLinearRegression

int SimpleLinearRegression(
    const std::vector< double > & y,
    const std::vector< double > & x,
    double & a,
    double & b
) const

Computes a simple linear regression of the first list of values with respect to the second y=a + bx. Returns the estimated parameters a & b. Returns 0 on success and -1 on fail.

function get_compactness

Eigen::VectorXd get_compactness(
    std::function< void(float)> progress_callback
)

function get_specificity

Eigen::VectorXd get_specificity(
    std::function< void(float)> progress_callback
)

function get_generalization

Eigen::VectorXd get_generalization(
    std::function< void(float)> progress_callback
)

function get_group1_matrix

Eigen::MatrixXd get_group1_matrix()

function get_group2_matrix

Eigen::MatrixXd get_group2_matrix()

Public Attributes Documentation

variable VDimension

static constexpr static int VDimension = 3;

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Updated on 2022-03-31 at 09:51:18 -0600