AnnotatedOutline        Constructor for AnnotatedOutline object
Dataset                 Constructor for a 'dataset' object.
E                       The deformation energy function
Ecart                   The deformation energy function
Fcart                   The deformation energy gradient function
Outline                 Outline constructor
Rcart                   Restore points to spherical manifold
ReconstructedDataset    Constructor for RecontructedDataset object
ReconstructedOutline    Reconstruct outline into spherical surface
RetinalDataset          RetinalDataset constructor
RetinalReconstructedDataset
                        RetinalReconstructedDataset constructor
RetinalReconstructedOutline
                        RetinalReconstructedOutline constructor
StitchedOutline         Stitch together incisions and tears in an
                        AnnotatedOutline
TriangulatedOutline     Triangulate outline
addClass                Add new class to class vector of object
addTear                 Add tear to an AnnotatedOutline
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
bary.to.sphere.cart     Convert barycentric coordinates of points in
                        mesh on sphere to cartesian coordinates
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
dE                      The deformation energy gradient function
ensureFixedPointInRim   Ensure that the fixed point is in the rim, not
                        a tear
f                       Piecewise smooth function used in area penalty
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 indicies of triangles that are
                        flipped
flipped.triangles.cart
                        Determine indicies of triangles that are
                        flipped
fp                      Piecewise smooth function used in area penalty
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 indicies of tear in AnnotatedOutline
getTss                  Get spherical coordinates of tears.
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
karcher.mean.sphere     Karcher mean on the sphere
kde.L                   Estimate of the log likelihood of the points mu
                        given a particular value of the concentration
                        kappa
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
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
labelTearPoints         Label three outline point indicies as apicies
                        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
mergePointsEdges        Merge stitched points and edges
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
optimiseMapping         Optimise mapping
orthographic            Orthographic projection
panlabel                Ancillary function to place labels
polar.cart.to.sphere.spherical
                        Convert polar projection in Cartesian
                        coordinates to spherical coordinates on sphere
polartext               Put text on the polar plot
projectToSphere         Project mesh points in the flat outline onto a
                        sphere
projection              Plot projection of an object
projection.reconstructedDataset
                        Plot projection of reconstructed dataset
projection.reconstructedOutline
                        Projection of a reconstructed outline
read.datapoints         Read data points in CSV format
recfile.version         Version of reconstruction file data format
remove.identical.consecutive.rows
                        Remove identical consecutive rows from a matrix
remove.intersections    Remove intersections between adjacent segements
                        in a closed path
removeTear              Remove tear from an AnnotatedOutline
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.global.revision
                        Git short commit hash of Retistruct package
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
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 lattitude 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
strain.colours          Generate colours for strain plots
stretchMesh             Stretch mesh
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
vecnorm                 Vector norm
whichTear               Return index of tear
