correa Namespace Reference

Classes
class	Comp
class	Convex
class	Curvature
class	Ellipse
class	Frechet
class	INOUT
class	PersistenceDiagram
class	PersistencePoint
class	PH0
class	Polygon
class	PolygonBuilder
class	PyPolygon
class	Vector
class	Vector2D
class	Vertex

Typedefs
typedef std::vector< Vertex >::iterator	VertexIter
typedef std::vector< Vertex >::const_iterator	VertexCIter

Functions
	create_polygon (str poly_path, bool clean_points=True, bool scale_by_area=False, float convert_to_microns_factor=1.0)
	Read a polygon from file.
	create_polygon_focal_point (str poly_path, list[float] focal_point, bool clean_points=True, bool scale_by_area=False, float convert_to_microns_factor=1.0)
	Read a polygon from file, and specify a focal point.
	print_polygon (poly)
	Print information about the polygon.
	plot_polygon (_correa.PyPolygon poly)
	Plot a polygon.
	compare_polygons (_correa.PyPolygon poly1, _correa.PyPolygon poly2, q=2, verbose=False)
	Given two polygons (poly1, poly2), compare them.
	curv_ot_distance (_correa.PyPolygon poly1, _correa.PyPolygon poly2)
	Given two polygons (poly1, poly2), calculate the curv_ot distance between them.
	frechet_distance (_correa.PyPolygon poly1, _correa.PyPolygon poly2)
	Given two polygons (poly1, poly2), calculate the frechet distance between them.
	max_ellipse_distance (_correa.PyPolygon poly1, _correa.PyPolygon poly2)
	Given two polygons (poly1, poly2), calculate the max ellipse distance between them.
	min_ellipse_distance (_correa.PyPolygon poly1, _correa.PyPolygon poly2)
	Given two polygons (poly1, poly2), calculate the min ellipse distance between them.
	lsq_ellipse_distance (_correa.PyPolygon poly1, _correa.PyPolygon poly2)
	Given two polygons (poly1, poly2), calculate the least square ellipse distance between them.
	wasserstein_distance (_correa.PyPolygon poly1, _correa.PyPolygon poly2, q=2)
	Given two polygons (poly1, poly2), calculate the wasserstein distance between them via their persistence diagrams.
	willmore_distance (_correa.PyPolygon poly1, _correa.PyPolygon poly2)
	Given two polygons (poly1, poly2), calculate the willmore distance between them.
	plot_persistence_diagram (_correa.PyPolygon poly)
	Plot the persistence diagram of a polygon.
	only_persistence_polygon (str poly_path, list[float] focal_point, bool clean_points, bool scale_by_area, float convert_to_microns_factor=1.0)
	Given a polygon, calculate the persistence diagram.
	test_sensitivity_polygon (str poly_path, list[float] focal_point, bool scale_by_area=False, float convert_to_microns_factor=1.0)
auto	hera_wasserstein_distance (const std::vector< std::pair< double, double > > pd1, const std::vector< std::pair< double, double > > pd2, int q=2)
auto	initialise_polygon (std::string path_to_vertices, bool clean_points, bool scale_by_area, double convert_to_microns_factor)
auto	initialise_polygon (std::string path_to_vertices, std::string path_to_focal_point, bool clean_points, bool scale_by_area, double convert_to_microns_factor)
auto	initialise_polygon (std::string path_to_vertices, std::vector< double > focal_point, bool clean_points, bool scale_by_area, double convert_to_microns_factor)
auto	load_polygon (std::string file_path, bool clean_points, bool scale_by_area, double convert_to_microns_factor=1.0)
auto	load_polygon (std::string path_to_vertices, std::string path_to_focal, bool clean_points, bool scale_by_area, double convert_to_microns_factor)
auto	load_polygon (std::string path_to_vertices, std::vector< double > focal, bool clean_points, bool scale_by_area, double convert_to_microns_factor=1.0)
std::vector< double >	compare_polygons (PyPolygon poly1, PyPolygon poly2, int q, bool verbose)
double	wasserstein_distance (PyPolygon poly1, PyPolygon poly2, int q)
double	frechet_distance (PyPolygon poly1, PyPolygon poly2)
double	max_ellipse_distance (PyPolygon poly1, PyPolygon poly2)
double	min_ellipse_distance (PyPolygon poly1, PyPolygon poly2)
double	lsq_ellipse_distance (PyPolygon poly1, PyPolygon poly2)
double	willmore_distance (PyPolygon poly1, PyPolygon poly2)
double	curv_ot_distance (PyPolygon poly1, PyPolygon poly2)
void	print_polygon (PyPolygon P)
Vector	operator* (double s, const Vector &v)
double	dot (const Vector &u, const Vector &v)
Vector	cross (const Vector &u, const Vector &v)
double	dot (const Vector2D &u, const Vector2D &v)
void	dcopy_ (int *n, double *X, int *incx, double *Y, int *incy)
double	ddot_ (int *n, double *u, int *incu, double *v, int *incv)
double	dnrm2_ (int *n, double *X, int *incx)
void	daxpy_ (int *n, double *alpha, double *X, int *incx, double *Y, int *incy)
void	dscal_ (int *n, double *alpha, double *X, int *incx)
void	dgemv_ (char *trans, int *m, int *n, double *alpha, double *A, int *lda, double *X, int *incx, double *beta, double *Y, int *incy)
void	dgemm_ (char *transa, char *transb, int *m, int *n, int *k, double *alpha, double *A, int *lda, double *B, int *ldb, double *beta, double *C, int *ldc)
void	dgeev_ (char *JOBVL, char *JOBVR, int *N, double *A, int *LDA, double *WR, double *WI, double *VL, int *LDVL, double *VR, int *LDVR, double *WORK, int *LWORK, int *INFO)
void	dsyevd_ (char *JOBZ, char *UPLO, int *N, double *A, int *LDA, double *W, double *WORK, int *LWORK, int *IWORK, int *LIWORK, int *INFO)
void	dgetrf_ (int *M, int *N, double *A, int *LDA, int *IPIV, int *INFO)
void	dgetrs_ (char *Trans, int *N, int *Nrhs, double *A, int *LDA, int *IPIV, double *B, int *LDB, int *INFO)
void	dgetri_ (int *N, double *A, int *LDA, int *IPIV, double *WORK, int *LWORK, int *INFO)
bool	HeightComparison (tuple< int, double > &x, tuple< int, double > &y)

Variables
Convex	convexhull

Detailed Description

Correa 

Documentation for the Python functions in Correa.

Function Documentation

compare_polygons() [1/2]

correa.compare_polygons	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2,
			q = 2,
			verbose = False )

Given two polygons (poly1, poly2), compare them.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.
q	q for the Wasserstein distance,.
verbose	setting for verbose output.

Returns

dWasserstein, dFrechet, dMax, dMin, dLSQ, dWillmore, dCurvOT.

compare_polygons() [2/2]

std::vector< double > correa::compare_polygons	(	PyPolygon	poly1,
		PyPolygon	poly2,
		int	q,
		bool	verbose )

wrapper to compare pairs of polygons.

Has a variety of methods to calculate the distances between a pair of polygons.

Prints their comparisons

create_polygon()

correa.create_polygon	(	str	poly_path,
		bool	clean_points = True,
		bool	scale_by_area = False,
		float	convert_to_microns_factor = 1.0 )

Read a polygon from file.

This will recenter the polygon to the center of mass of the vertices, so be careful.

Parameters

poly_path

path to the file you want to read in.

Returns

PyPolygon object.

create_polygon_focal_point()

correa.create_polygon_focal_point	(	str	poly_path,
		list[float]	focal_point,
		bool	clean_points = True,
		bool	scale_by_area = False,
		float	convert_to_microns_factor = 1.0 )

Read a polygon from file, and specify a focal point.

Parameters

poly_path	path to the file containing the polygon.
focal_point	either a path to the file containing the focal point, or a list with the coordinates.

Returns

PyPolygon object

curv_ot_distance()

correa.curv_ot_distance	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2 )

Given two polygons (poly1, poly2), calculate the curv_ot distance between them.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.

Returns

distance.

frechet_distance()

correa.frechet_distance	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2 )

Given two polygons (poly1, poly2), calculate the frechet distance between them.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.

Returns

distance.

hera_wasserstein_distance()

auto correa::hera_wasserstein_distance	(	const std::vector< std::pair< double, double > >	pd1,
		const std::vector< std::pair< double, double > >	pd2,
		int	q = 2 )

Caculate the Wasserstein distance between two persistence diagrams using Hera.

Parameters

pd1	first persistence diagram
pd2	second persistence diagram
q	the qth power to use, default is 2

Returns

qth wasserstein distance between the two persistence diagrams

lsq_ellipse_distance()

correa.lsq_ellipse_distance	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2 )

Given two polygons (poly1, poly2), calculate the least square ellipse distance between them.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.

Returns

distance.

max_ellipse_distance()

correa.max_ellipse_distance	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2 )

Given two polygons (poly1, poly2), calculate the max ellipse distance between them.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.

Returns

distance.

min_ellipse_distance()

correa.min_ellipse_distance	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2 )

Given two polygons (poly1, poly2), calculate the min ellipse distance between them.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.

Returns

distance.

only_persistence_polygon()

correa.only_persistence_polygon	(	str	poly_path,
		list[float]	focal_point,
		bool	clean_points,
		bool	scale_by_area,
		float	convert_to_microns_factor = 1.0 )

Given a polygon, calculate the persistence diagram.

Parameters

poly_path	path to the file containing the polygon.
focal_point	either a path to the file containing the focal point, or a list with the coordinates.
clean_points	whether to clean the points.
scale_by_area	whether to scale by area.
convert_to_microns_factor	scale factor for pixel to micrometer conversion.

Returns

persistence diagram.

plot_persistence_diagram()

correa.plot_persistence_diagram

(

_correa.PyPolygon

poly

)

Plot the persistence diagram of a polygon.

Parameters

poly	the polygon you want to plot the persistence diagram of.

Returns

a plotly.express figure.

plot_polygon()

correa.plot_polygon

(

_correa.PyPolygon

poly

)

Plot a polygon.

Parameters

poly	the polygon you want to plot.

Returns

a matplotlib.pyplot figure.

print_polygon() [1/2]

correa.print_polygon

(

poly

)

Print information about the polygon.

Parameters

poly	the polygon you want information about.

print_polygon() [2/2]

void correa::print_polygon

(

PyPolygon

P

)

print the information about a PyPolygon

wasserstein_distance()

correa.wasserstein_distance	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2,
			q = 2 )

Given two polygons (poly1, poly2), calculate the wasserstein distance between them via their persistence diagrams.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.

Returns

distance.

willmore_distance()

correa.willmore_distance	(	_correa.PyPolygon	poly1,
		_correa.PyPolygon	poly2 )

Given two polygons (poly1, poly2), calculate the willmore distance between them.

Parameters

poly1	first polygon to compare.
poly2	second polygon to compare.

Returns

distance.