Outline: Class containing basic information about flat outlines

In retistruct: Retinal Reconstruction Program

Description

An Outline has contains the polygon describing the outline and an image associated with the outline.

Super class

retistruct::OutlineCommon -> Outline

Public fields

P

A N-by-2 matrix of points of the Outline arranged in anticlockwise order

scale

The length of one unit of P in arbitrary units

units

String giving units of scaled P, e.g. “um”

gf

For each row of P, the index of P that is next in the outline travelling anticlockwise (forwards)

gb

For each row of P, the index of P that is next in the outline travelling clockwise (backwards)

h

For each row of P, the correspondence of that point (which will be to itself initially)

im

An image as a raster object

Methods

Public methods

• Outline$new()

• Outline$getImage()

• Outline$replaceImage()

• Outline$mapFragment()

• Outline$mapPids()

• Outline$addPoints()

• Outline$getPoints()

• Outline$getPointsScaled()

• Outline$getRimSet()

• Outline$getOutlineSet()

• Outline$getOutlineLengths()

• Outline$addFeatureSet()

• Outline$clone()

Inherited methods

• retistruct::OutlineCommon$clearFeatureSets()

• retistruct::OutlineCommon$getFeatureSet()

• retistruct::OutlineCommon$getFeatureSets()

• retistruct::OutlineCommon$getFeatureSetTypes()

• retistruct::OutlineCommon$getIDs()

---

Method new()

Construct an outline object. This sanitises the input points P.

Usage

Outline$new(P = NULL, scale = NA, im = NULL, units = NA)

Arguments

P

An N-by-2 matrix of points of the Outline

scale

The length of one unit of P in arbitrary units

im

The image as a raster object

units

String giving units of scaled P, e.g. “um”

---

Method getImage()

Image accessor

Usage

Outline$getImage()

Returns

An image as a raster object

---

Method replaceImage()

Image setter

Usage

Outline$replaceImage(im)

Arguments

im

An image as a raster object

---

Method mapFragment()

Map the point IDs of a Fragment on the point IDs of this Outline

Usage

Outline$mapFragment(fragment, pids)

Arguments

fragment

Fragment to map

pids

Point IDs in Outline of points in Fragment

---

Method mapPids()

Map references to points

Usage

Outline$mapPids(x, y, pids)

Arguments

x

References to point indices in source

y

References to existing point indices in target

pids

IDs of points in point register

Returns

New references to point indices in target

---

Method addPoints()

Add points to the outline register of points

Usage

Outline$addPoints(P)

Arguments

P

2 column matrix of points to add

Returns

The ID of each added point in the register. If points already exist a point will not be created in the register, but an ID will be returned

---

Method getPoints()

Get unscaled mesh points

Usage

Outline$getPoints()

Returns

Matrix with columns X and Y

---

Method getPointsScaled()

Get scaled mesh points

Usage

Outline$getPointsScaled()

Returns

Matrix with columns X and Y which is exactly scale times the matrix returned by getPoints

---

Method getRimSet()

Get set of points on rim

Usage

Outline$getRimSet()

Returns

Vector of point IDs, i.e. indices of the rows in the matrices returned by getPoints and getPointsScaled

---

Method getOutlineSet()

Get points on the edge of the outline

Usage

Outline$getOutlineSet()

Returns

Vector of points IDs on outline

---

Method getOutlineLengths()

Get lengths of edges of the outline

Usage

Outline$getOutlineLengths()

Returns

Vector of lengths of edges connecting neighbouring points

---

Method addFeatureSet()

Add a FeatureSet, e.g. a PointSet or LandmarkSet

Usage

Outline$addFeatureSet(fs)

Arguments

fs

FeatureSet to add

---

Method clone()

The objects of this class are cloneable with this method.

Usage

Outline$clone(deep = FALSE)

Arguments

deep

Whether to make a deep clone.

Author(s)

David Sterratt

retistruct documentation built on April 4, 2020, 5:08 p.m.