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retistruct (version 0.5.9)

Retistruct - Retinal Reconstruction Program

Description

Program to reconstruct retinae from flattened retinae in which there are incisions and tears

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Version

Install

install.packages('retistruct')

Monthly Downloads

170

Version

0.5.9

License

CC BY-NC-SA 4.0

Maintainer

David Sterratt

Last Published

December 2nd, 2014

Functions in retistruct (0.5.9)

computeTearRelationships

Compute the parent relationships for a set of tears

flatplot.stitchedOutline

Flat plot of AnnotatedOutline

flatplot.reconstructedOutline

Flat plot of reconstructed outline

getDssMean.retinalReconstructedDataset

Get transformed spherical coordinates of Karcher mean of datapoints

Ecart

The deformation energy function

azimuthal.equalarea

Lambert azimuthal equal area projection

addClass

Add new class to class vector of object

StitchedOutline

Stitch together incisions and tears in an AnnotatedOutline

bary.to.sphere.cart

Convert barycentric coordinates of points in mesh on sphere to cartesian coordinates

circle

Return points on the unit circle

central.angle

Central angle between two points on a sphere

azel.to.sphere.colattitude

Convert azimuth-elevation coordinates to spherical coordinates

getGss

Get grouped variable with locations in spherical coordinates.

RetinalReconstructedDataset

RetinalReconstructedDataset constructor

Outline

Outline constructor

azimuthal.equidistant

Azimuthal equidistant projection

The deformation energy function

normalise.angle

Bring angle into range

labelTearPoints

Label three outline point indicies as apicies and vertices of tear

Piecewise smooth function used in area penalty

create.polar.cart.grid

Create grid on projection of hemisphere onto plane

lvsLplot

Plot the fractional change in length of mesh edges

fire

The FIRE algorithm

orthographic

Orthographic projection

kr.sscv

Cross validation estimate of the least squares error of the points mu given a particular value of the concentration kappa

The deformation energy gradient function

flipped.triangles.cart

Determine indicies of triangles that are flipped

getDssMean.reconstructedDataset

Karcher mean of datapoints in spherical coordinates

getKDE

Get kernel density estimate of data points

ReconstructedDataset

Constructor for RecontructedDataset object

remove.intersections

Remove intersections between adjacent segements in a closed path

flatplot.triangulatedOutline

Flat plot of TriangulatedOutline

TriangulatedOutline

Triangulate outline

getIDs.dataset

Get IDs of groups of data within a dataset

kde.L

Estimate of the log likelihood of the points mu given a particular value of the concentration kappa

getSssMean

Karcher mean of landmarks in spherical coordinates

getIDs

Get IDs of groups of data within a dataset

getDss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

Dataset

Constructor for a dataset object.

compute.intersections.sphere

Find the intersection of a plane with edges of triangles on a sphere

retistruct

Start the Retistruct GUI

getSss.reconstructedDataset

Get transformed spherical coordinates of landmarks.

mergePointsEdges

Merge stitched points and edges

getIDs.reconstructedDataset

Get IDs of groups of data within a ReconstructedDataset

read.datapoints

Read data points in CSV format

flipped.triangles

Determine indicies of triangles that are flipped

ensureFixedPointInRim

Ensure that the fixed point is in the rim, not a tear

flatplot.retinalDataset

Flat plot of retinal dataset

Fcart

The deformation energy gradient function

flatplot.dataset

Flat plot of Dataset

checkDatadir

Check the whether directory contains valid data

getStrains

Return strains edges are under in spherical retina

compute.kernel.estimate

Kernel estimate over grid

nameLandmark

Name a landmark in a Dataset

retistruct.batch

Batch operation using the parallel package

getTss

Get spherical coordinates of tears.

azimuthal.conformal

Azimuthal conformal or stereographic or Wulff projection

kr.yhat

Kernel regression on sphere using Fisherian density with polar coordinates

invert.sphere.to.hemisphere

Invert sphere to hemisphere

retistruct.batch.export.matlab

Export data from reconstruction data files to matlab

getDssMean

Karcher mean of datapoints in spherical coordinates

RetinalReconstructedOutline

RetinalReconstructedOutline constructor

list.datasets

List datasets underneath a directory

retistruct.reconstruct

Reconstruct a retina

retistruct.batch.plot.ods

Superposed plot of ODs on polar axes

recfile.version

Version of reconstruction file data format

line.line.intersection

Determine intersection between two lines

retistruct.batch.summary

Extract summary data for a batch of reconstructions

optimiseMapping

Optimise mapping

projection.reconstructedDataset

Plot projection of reconstructed dataset

getIms.reconstructedOutline

Get coordinates of corners of pixels of image in spherical coordinates

projection

Plot projection of an object

simplify.outline

Simplify an outline object by removing short edges

setFixedPoint

Set fixed point

flatplot.annotatedOutline

Flat plot of AnnotatedOutline

sphericalplot

Spherical plot of reconstructed outline

retistruct.batch.analyse.summary

Extract statistics from the retistruct-batch.csv summary file

karcher.mean.sphere

Karcher mean on the sphere

flatplot.outline

Flat plot of outline

polartext

Put text on the polar plot

sphere.spherical.to.sphere.cart

Convert from spherical to Cartesian coordinates

AnnotatedOutline

Constructor for AnnotatedOutline object

retistruct.read.recdata

Read the reconstruction data from file

kr.yhat.cart

Kernel regression on sphere using Fisherian density with Cartesian coordinates

retistruct.cli.process

Process a dataset, saving results to disk

tri.area.signed

"Signed area" of triangles on a plane

retistruct.potential.od

Test for a potential optic disc

retistruct.batch.plot.titrations

Plot titrations

removeTear

Remove tear from an AnnotatedOutline

retistruct.batch.get.titrations

Get titrations from a directory of reconstructions

retistruct.global.revision

Git short commit hash of Retistruct package

sphericalplot.reconstructedOutline

Spherical plot of reconstructed outline

retistruct.read.dataset

Read a retinal dataset

spherical.to.polar.area

Convert lattitude on sphere to radial variable in area-preserving projection

ijroi.read.dataset

Read a retinal dataset in IJROI format

getDss.reconstructedDataset

Get transformed spherical coordinates of datapoints

getGss.reconstructedDataset

Get grouped variable with locations in spherical coordinates.

stretchMesh

Stretch mesh

getSss

Get transformed spherical coordinates of landmarks.

sphericalplot.reconstructedDataset

Spherical plot of reconstructed outline

retistruct.save.recdata

Save reconstruction data

idt.read.dataset

Read one of the Thompson lab's retinal datasets

polar.cart.to.sphere.spherical

Convert polar projection in Cartesian coordinates to spherical coordinates on sphere

kde.compute.concentration

Find the optimal concentration for a set of data

name.list

Return a new version of the list in which any un-named elements have been given standardised names

kde.fhat.cart

Kernel density estimate on sphere using Fisherian density with Cartesian coordinates

retistruct.read.markup

Read the markup data

projectToSphere

Project mesh points in the flat outline onto a sphere

remove.identical.consecutive.rows

Remove identical consecutive rows from a matrix

addTear

Add tear to an AnnotatedOutline

identity.transform

The identity transformation

checkTears

Check that tears are all in the correct direction

getIms

Get coordinates of corners of pixels of image in spherical coordinates

rotate.axis

Rotate axis of sphere

retistruct.save.markup

Save markup

retistruct.cli.figure

Print a figure to file

solveMappingCart

Optimise mapping

sphere.cart.to.sphere.dualwedge

Convert from Cartesian to 'dualwedge' coordinates

vecnorm

Vector norm

transform.image.reconstructedOutline

Transform an image into the reconstructed space

whichTear

Return index of tear

sinusoidal

Sinusoidal projection

titrate.reconstructedOutline

Titrate values of phi0

kde.fhat

Kernel density estimate on sphere using Fisherian density with polar coordinates

Piecewise smooth function used in area penalty

sphere.cart.to.sphere.spherical

Convert from Cartesian to spherical coordinates

nameLandmark.retinalDataset

Name a landmark in a RetinalDataset

getDssHullarea

Get area of convex hull around data points on sphere

RetinalDataset

RetinalDataset constructor

tri.area

Area of triangles on a plane

retistruct.check.markup

Retistruct check markup

csv.read.dataset

Read a retinal dataset in CSV format

sphere.spherical.to.polar.cart

Convert spherical coordinates on sphere to polar projection in Cartesian coordinates

invert.sphere

Invert sphere about its centre

strain.colours

Generate colours for strain plots

getSss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

panlabel

Ancillary function to place labels

projection.reconstructedOutline

Projection of a reconstructed outline

getTear

Return indicies of tear in AnnotatedOutline

ReconstructedOutline

Reconstruct outline into spherical surface

Rcart

Restore points to spherical manifold

getGss.retinalReconstructedDataset

Get grouped variable with locations in spherical coordinates.

retistruct.cli

Process a dataset with a time limit

sphere.cart.to.sphere.wedge

Convert from Cartesian to 'wedge' coordinates

sphere.wedge.to.sphere.cart

Convert from 'wedge' to Cartesian coordinates

flatplot

Flat plot of object

getDss

Get transformed spherical coordinates of datapoints

getFlatRimLength

Get rim length of AnnotatedOutline

getKR

Get kernel regression estimate of grouped data points

kr.compute.concentration

Find the optimal concentration for a set of data

retistruct.batch.analyse.summaries

Extract statistics from a directory containing reconstruction directories.

retistruct.batch.figures

Plot figures for a batch of reconstructions

retistruct.export.matlab

Save reconstruction data in MATLAB format

sphere.tri.area

Area of triangles on a sphere