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shapeworks::ParticleShapeStatistics

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#include <ParticleShapeStatistics.h>

Public Functions

Name
ParticleShapeStatistics()
ParticleShapeStatistics(std::shared_ptr< Project > project)
~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 )
Dimensionality of the domain of the particle system.
int ImportPoints(std::vector< Eigen::VectorXd > points, std::vector< int > group_ids)
Loads a set of point files and pre-computes some statistics.
int ReadPointFiles(const std::string & s)
Loads a set of point files and pre-computes some statistics.
int ReloadPointFiles()
Reloads a set of point files and recomputes some statistics.
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.
int WriteCSVFile2(const std::string & s)
int ComputeModes()
Computes PCA modes from the set of correspondence mode positions. Requires that ReadPointFiles be called first.
int PrincipalComponentProjections()
int FisherLinearDiscriminant(unsigned int numModes)
Computes fishers linear discriminant line for best group separation.
int SampleSize() const
Returns the sample size.
int Group1SampleSize() const
int Group2SampleSize() const
int NumberOfDimensions() const
Returns the number of dimensions (this is number of points times Dimension)
int GroupID(unsigned int i) const
Returns the group ids.
const std::vector< int > & GroupID() const
const Eigen::MatrixXd & Eigenvectors() const
Returns the eigenvectors/values.
const std::vector< double > & Eigenvalues() const
const Eigen::VectorXd & Mean() const
Returns the mean shape.
const Eigen::VectorXd & Group1Mean() const
const Eigen::VectorXd & Group2Mean() const
const Eigen::VectorXd & NormalizedGroupDifference() const
Returns group2 - group1 mean.
const Eigen::VectorXd & GroupDifference() const
int ComputeMedianShape(const int ID)
double L1Norm(unsigned int a, unsigned int b)
Returns the euclidean L1 norm between shape a and b.
Eigen::MatrixXd & PCALoadings()
Returns the component loadings.
const Eigen::VectorXd & FishersLDA() const
Returns the Fisher linear discriminant.
const Eigen::MatrixXd & ShapeMatrix() const
Returns the shape matrix.
const Eigen::MatrixXd & RecenteredShape() const
Returns the shape with the mean subtracted.
const std::vector< double > & PercentVarByMode() const
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

Detailed Description

class shapeworks::ParticleShapeStatistics;

This class computes various statistics for a set of correspondence positions and group ids.

Public Functions Documentation

function ParticleShapeStatistics

inline ParticleShapeStatistics()

function ParticleShapeStatistics

ParticleShapeStatistics(
    std::shared_ptr< Project > project
)

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< Eigen::VectorXd > 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 int SampleSize() const

Returns the sample size.

function Group1SampleSize

inline int Group1SampleSize() const

function Group2SampleSize

inline int Group2SampleSize() const

function NumberOfDimensions

inline int NumberOfDimensions() const

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

function GroupID

inline int GroupID(
    unsigned int i
) const

Returns the group ids.

function GroupID

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

function Eigenvectors

inline const Eigen::MatrixXd & Eigenvectors() const

Returns the eigenvectors/values.

function Eigenvalues

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

function Mean

inline const Eigen::VectorXd & Mean() const

Returns the mean shape.

function Group1Mean

inline const Eigen::VectorXd & Group1Mean() const

function Group2Mean

inline const Eigen::VectorXd & Group2Mean() const

function NormalizedGroupDifference

inline const Eigen::VectorXd & NormalizedGroupDifference() const

Returns group2 - group1 mean.

function GroupDifference

inline const Eigen::VectorXd & GroupDifference() const

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 Eigen::VectorXd & FishersLDA() const

Returns the Fisher linear discriminant.

function ShapeMatrix

inline const Eigen::MatrixXd & ShapeMatrix() const

Returns the shape matrix.

function RecenteredShape

inline const Eigen::MatrixXd & RecenteredShape() const

Returns the shape with the mean subtracted.

function PercentVarByMode

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

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;

Updated on 2022-07-23 at 17:50:03 -0600