# Retinal Reconstruction Program

## Documentation for package ‘retistruct’ version 0.5.12

- DESCRIPTION file.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F G I K L M N O P R S T V W

## -- A --

addClass | Add new class to class vector of object
addTear | Add tear to an AnnotatedOutline
AnnotatedOutline | Constructor for AnnotatedOutline object
azel.to.sphere.colattitude | Convert azimuth-elevation coordinates to spherical coordinates
azimuthal.conformal | Azimuthal conformal or stereographic or Wulff projection
azimuthal.equalarea | Lambert azimuthal equal area projection
azimuthal.equidistant | Azimuthal equidistant projection

## -- B --

bary.to.sphere.cart | Convert barycentric coordinates of points in mesh on sphere to cartesian coordinates

## -- C --

central.angle | Central angle between two points on a sphere
checkDatadir | Check the whether directory contains valid data
checkTears | Check that tears are all in the correct direction
circle | Return points on the unit circle
compute.intersections.sphere | Find the intersection of a plane with edges of triangles on a sphere
compute.kernel.estimate | Kernel estimate over grid
computeTearRelationships | Compute the parent relationships for a set of tears
create.polar.cart.grid | Create grid on projection of hemisphere onto plane
csv.read.dataset | Read a retinal dataset in CSV format

## -- D --

Dataset | Constructor for a 'dataset' object.
dE | The deformation energy gradient function

## -- E --

E | The deformation energy function
Ecart | The deformation energy function
ensureFixedPointInRim | Ensure that the fixed point is in the rim, not a tear

## -- F --

f | Piecewise smooth function used in area penalty
Fcart | The deformation energy gradient function
fire | The FIRE algorithm
flatplot | Flat plot of object
flatplot.annotatedOutline | Flat plot of AnnotatedOutline
flatplot.dataset | Flat plot of Dataset
flatplot.outline | Flat plot of outline
flatplot.reconstructedOutline | Flat plot of reconstructed outline
flatplot.retinalDataset | Flat plot of retinal dataset
flatplot.stitchedOutline | Flat plot of AnnotatedOutline
flatplot.triangulatedOutline | Flat plot of TriangulatedOutline
flipped.triangles | Determine indices of triangles that are flipped
flipped.triangles.cart | Determine indices of triangles that are flipped
fp | Piecewise smooth function used in area penalty

## -- G --

getDss | Get transformed spherical coordinates of datapoints
getDss.reconstructedDataset | Get transformed spherical coordinates of datapoints
getDss.retinalReconstructedDataset | Get transformed spherical coordinates of datapoints
getDssHullarea | Get area of convex hull around data points on sphere
getDssMean | Karcher mean of datapoints in spherical coordinates
getDssMean.reconstructedDataset | Karcher mean of datapoints in spherical coordinates
getDssMean.retinalReconstructedDataset | Get transformed spherical coordinates of Karcher mean of datapoints
getFlatRimLength | Get rim length of AnnotatedOutline
getGss | Get grouped variable with locations in spherical coordinates.
getGss.reconstructedDataset | Get grouped variable with locations in spherical coordinates.
getGss.retinalReconstructedDataset | Get grouped variable with locations in spherical coordinates.
getIDs | Get IDs of groups of data within a dataset
getIDs.dataset | Get IDs of groups of data within a dataset
getIDs.reconstructedDataset | Get IDs of groups of data within a ReconstructedDataset
getIms | Get coordinates of corners of pixels of image in spherical coordinates
getIms.reconstructedOutline | Get coordinates of corners of pixels of image in spherical coordinates
getKDE | Get kernel density estimate of data points
getKR | Get kernel regression estimate of grouped data points
getSss | Get transformed spherical coordinates of landmarks.
getSss.reconstructedDataset | Get transformed spherical coordinates of landmarks.
getSss.retinalReconstructedDataset | Get transformed spherical coordinates of datapoints
getSssMean | Karcher mean of landmarks in spherical coordinates
getStrains | Return strains edges are under in spherical retina
getTear | Return indices of tear in AnnotatedOutline
getTss | Get spherical coordinates of tears.

## -- I --

identity.transform | The identity transformation
idt.read.dataset | Read one of the Thompson lab's retinal datasets
ijroi.read.dataset | Read a retinal dataset in IJROI format
invert.sphere | Invert sphere about its centre
invert.sphere.to.hemisphere | Invert sphere to hemisphere

## -- K --

karcher.mean.sphere | Karcher mean on the sphere
kde.compute.concentration | Find the optimal concentration for a set of data
kde.fhat | Kernel density estimate on sphere using Fisherian density with polar coordinates
kde.fhat.cart | Kernel density estimate on sphere using Fisherian density with Cartesian coordinates
kde.L | Estimate of the log likelihood of the points mu given a particular value of the concentration kappa
kr.compute.concentration | Find the optimal concentration for a set of data
kr.sscv | Cross validation estimate of the least squares error of the points mu given a particular value of the concentration kappa
kr.yhat | Kernel regression on sphere using Fisherian density with polar coordinates
kr.yhat.cart | Kernel regression on sphere using Fisherian density with Cartesian coordinates

## -- L --

labelTearPoints | Label three outline point indices as apices and vertices of tear
line.line.intersection | Determine intersection between two lines
list.datasets | List datasets underneath a directory
lvsLplot | Plot the fractional change in length of mesh edges

## -- M --

mergePointsEdges | Merge stitched points and edges

## -- N --

name.list | Return a new version of the list in which any un-named elements have been given standardised names
nameLandmark | Name a landmark in a Dataset
nameLandmark.retinalDataset | Name a landmark in a RetinalDataset
normalise.angle | Bring angle into range

## -- O --

optimiseMapping | Optimise mapping
orthographic | Orthographic projection
Outline | Outline constructor

## -- P --

panlabel | Ancillary function to place labels
parse.dependencies | Parse dependencies
polar.cart.to.sphere.spherical | Convert polar projection in Cartesian coordinates to spherical coordinates on sphere
polartext | Put text on the polar plot
projection | Plot projection of an object
projection.reconstructedDataset | Plot projection of reconstructed dataset
projection.reconstructedOutline | Projection of a reconstructed outline
projectToSphere | Project mesh points in the flat outline onto a sphere

## -- R --

Rcart | Restore points to spherical manifold
read.datacounts | Read data counts in CSV format
read.datapoints | Read data points in CSV format
recfile.version | Version of reconstruction file data format
ReconstructedDataset | Constructor for RecontructedDataset object
ReconstructedOutline | Reconstruct outline into spherical surface
remove.identical.consecutive.rows | Remove identical consecutive rows from a matrix
remove.intersections | Remove intersections between adjacent segments in a closed path
removeTear | Remove tear from an AnnotatedOutline
RetinalDataset | RetinalDataset constructor
RetinalReconstructedDataset | RetinalReconstructedDataset constructor
RetinalReconstructedOutline | RetinalReconstructedOutline constructor
retistruct | Start the Retistruct GUI
retistruct.batch | Batch operation using the parallel package
retistruct.batch.analyse.summaries | Extract statistics from a directory containing reconstruction directories.
retistruct.batch.analyse.summary | Extract statistics from the retistruct-batch.csv summary file
retistruct.batch.export.matlab | Export data from reconstruction data files to matlab
retistruct.batch.figures | Plot figures for a batch of reconstructions
retistruct.batch.get.titrations | Get titrations from a directory of reconstructions
retistruct.batch.plot.ods | Superposed plot of ODs on polar axes
retistruct.batch.plot.titrations | Plot titrations
retistruct.batch.summary | Extract summary data for a batch of reconstructions
retistruct.check.markup | Retistruct check markup
retistruct.cli | Process a dataset with a time limit
retistruct.cli.figure | Print a figure to file
retistruct.cli.process | Process a dataset, saving results to disk
retistruct.export.matlab | Save reconstruction data in MATLAB format
retistruct.potential.od | Test for a potential optic disc
retistruct.read.dataset | Read a retinal dataset
retistruct.read.markup | Read the markup data
retistruct.read.recdata | Read the reconstruction data from file
retistruct.reconstruct | Reconstruct a retina
retistruct.save.markup | Save markup
retistruct.save.recdata | Save reconstruction data
rotate.axis | Rotate axis of sphere

## -- S --

setFixedPoint | Set fixed point
simplify.outline | Simplify an outline object by removing short edges
sinusoidal | Sinusoidal projection
solveMappingCart | Optimise mapping
sphere.cart.to.sphere.dualwedge | Convert from Cartesian to 'dualwedge' coordinates
sphere.cart.to.sphere.spherical | Convert from Cartesian to spherical coordinates
sphere.cart.to.sphere.wedge | Convert from Cartesian to 'wedge' coordinates
sphere.spherical.to.polar.cart | Convert spherical coordinates on sphere to polar projection in Cartesian coordinates
sphere.spherical.to.sphere.cart | Convert from spherical to Cartesian coordinates
sphere.tri.area | Area of triangles on a sphere
sphere.wedge.to.sphere.cart | Convert from 'wedge' to Cartesian coordinates
spherical.to.polar.area | Convert latitude on sphere to radial variable in area-preserving projection
sphericalplot | Spherical plot of reconstructed outline
sphericalplot.reconstructedDataset | Spherical plot of reconstructed outline
sphericalplot.reconstructedOutline | Spherical plot of reconstructed outline
StitchedOutline | Stitch together incisions and tears in an AnnotatedOutline
strain.colours | Generate colours for strain plots
stretchMesh | Stretch mesh

## -- T --

titrate.reconstructedOutline | Titrate values of phi0
transform.image.reconstructedOutline | Transform an image into the reconstructed space
tri.area | Area of triangles on a plane
tri.area.signed | "Signed area" of triangles on a plane
TriangulatedOutline | Triangulate outline

## -- V --

vecnorm | Vector norm

## -- W --

whichTear | Return index of tear