Comp2DShapesFocal.h File Reference

#include <iostream>
#include <iomanip>
#include <sstream>
#include <string>
#include <cstring>
#include <stdlib.h>
#include <fstream>
#include <cmath>
#include <ctime>
#include <unistd.h>
#include <cstdlib>
#include <limits>
#include <assert.h>
#include "hera/wasserstein.h"
#include "InOut.h"
#include "PolygonBuilder.h"
#include "Polygon.h"
#include "Frechet.h"
#include "Ellipse.h"
#include "Curvature.h"
#include "PH0.h"

Macros
#define	NUM_THREADS   32

Typedefs
using	PersistenceDiagram = std::vector<std::pair<double,double>>

Functions
bool	parse_args (int argc, char **argv, std::string *file1, std::string *focal1, std::string *file2, std::string *focal2, int *disttype, double *microns_per_pixel1, double *microns_per_pixel2, bool *verbose)
	Parse command-line arguments for Comp2DShapesFocal.

Variables
int	threadids [NUM_THREADS]
pthread_t	threads [NUM_THREADS]
INOUT	inout
Polygon	poly
PolygonBuilder	pbuilder
Frechet	frechet
Ellipse	ellipse
Curvature	curv

Detailed Description

Author

Patrice Koehl

Yossi Bokor Bleile

Date

December 2025

Version

1.2

Copyright

BSD 3-Clause License.

Function Documentation

parse_args()

bool parse_args	(	int	argc,
		char **	argv,
		std::string *	file1,
		std::string *	focal1,
		std::string *	file2,
		std::string *	focal2,
		int *	disttype,
		double *	microns_per_pixel1,
		double *	microns_per_pixel2,
		bool *	verbose )

Parse command-line arguments for Comp2DShapesFocal.

Parses command-line arguments for the Comp2DShapesFocal program, extracting input files, focal points, distance type, microns per pixel settings, and verbose flag.

Parameters

	argc	Argument count from main()
	argv	Argument vector from main()
[out]	file1	Path to first input polygon file (set by -i1 flag)
[out]	focal1	Focal point for first polygon - file path or "x,y" format (set by -f1 flag)
[out]	file2	Path to second input polygon file (set by -i2 flag)
[out]	focal2	Focal point for second polygon - file path or "x,y" format (set by -f2 flag)
[out]	disttype	Distance type flag (set by -d flag): 0: Fréchet distance - measures similarity between curves, representing the minimum leash length needed for a person walking a dog along each curve 1: Ellipse-based distances - compares aspect ratios of inscribed, inscribing, and least-squares fitted ellipses 2: Curvature-based distances - includes Willmore energy (bending energy) and Wasserstein distance between curvature distributions 3: 2-Wasserstein distance between persistence diagrams - topological shape descriptor based on persistent homology 4: All distances - computes all of the above metrics
[out]	microns_per_pixel1	Microns per pixel conversion for polygon 1 (set by -mpp1 or -mpp flag, default: 1.0)
[out]	microns_per_pixel2	Microns per pixel conversion for polygon 2 (set by -mpp2 or -mpp flag, default: 1.0)
[out]	verbose	Enable verbose output (set by -v or –verbose flag, default: false)

Returns

true if arguments were parsed successfully, false otherwise