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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 |