A B C D E F G I K L M N O P R S T V W
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 |
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 |
Dataset | Constructor for a 'dataset' object. |
dE | The deformation energy gradient function |
E | The deformation energy function |
Ecart | The deformation energy function |
ensureFixedPointInRim | Ensure that the fixed point is in the rim, not a tear |
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 |
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. |
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.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 |
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 |
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 |
Outline | Outline constructor |
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 |
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 |
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 |
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 |
vecnorm | Vector norm |
whichTear | Return index of tear |