Retinal Reconstruction Program

AnnotatedOutline | Class containing functions and data relating to annotating... |

azel.to.sphere.colatitude | Convert azimuth-elevation coordinates to spherical... |

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... |

central.angle | Central angle between two points on a sphere |

checkDatadir | Check the whether directory contains valid data |

circle | Return points on the unit circle |

compute.intersections.sphere | Find the intersection of a plane with edges of triangles on a... |

compute.kernel.estimate | Kernel estimate over grid |

CountSet | Subclass of 'FeatureSet' to represent counts centred on... |

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 |

depthplot3D | Draw the "flat" outline in 3D with depth information |

E | The deformation energy function |

Ecart | The deformation energy function |

f | Piecewise smooth function used in area penalty |

Fcart | The deformation energy gradient function |

FeatureSet | Superclass containing functions and data relating to sets of... |

FeatureSetCommon | Class containing functionality common to 'FeatureSet's and... |

fire | The FIRE algorithm |

flatplot | Plot "flat" (unreconstructed) representation of outline |

flatplot.AnnotatedOutline | Flat plot of AnnotatedOutline |

flatplot.Outline | Flat plot of outline |

flatplot.ReconstructedOutline | Flat plot of reconstructed outline |

flatplot.StitchedOutline | Flat plot of AnnotatedOutline |

flatplot.TriangulatedOutline | Plot flat '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 |

Fragment | Construct an outline object. This sanitises the input points... |

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 |

interpolate.image | Interpolate values in image |

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... |

kde.fhat.cart | Kernel density estimate on sphere using Fisherian density... |

kde.L | Estimate of the log likelihood of the points mu given a... |

kr.compute.concentration | Find the optimal concentration for a set of data |

kr.sscv | Cross validation estimate of the least squares error of the... |

kr.yhat | Kernel regression on sphere using Fisherian density with... |

kr.yhat.cart | Kernel regression on sphere using Fisherian density with... |

LandmarkSet | Subclass of 'FeatureSet' to represent points |

line.line.intersection | Determine intersection between two lines |

list.datasets | List datasets underneath a directory |

list_to_R6 | Convert an list created by R6_to_list() into an R6 object. |

lvsLplot | Plot the fractional change in length of mesh edges |

name.list | Return a new version of the list in which any unnamed... |

normalise.angle | Bring angle into range |

orthographic | Orthographic projection |

Outline | Class containing basic information about flat outlines |

OutlineCommon | Class containing functionality common to flat and... |

panlabel | Ancillary function to place labels |

parabola.arclength | Arc length of a parabola y=x^2/4f |

parabola.invarclength | Inverse arc length of a parabola y=x^2/4f |

parse.dependencies | Parse dependencies |

PathOutline | Add point correspondences to the outline |

PointSet | Subclass of 'FeatureSet' to represent points |

polar.cart.to.sphere.spherical | Convert polar projection in Cartesian coordinates to... |

polartext | Put text on the polar plot |

projection | Plot projection of a reconstructed outline |

projection.ReconstructedOutline | Projection of a reconstructed outline |

projection.RetinalReconstructedOutline | Plot projection of reconstructed dataset |

R6_to_list | Convert an R6 object into a list, ignoring functions and... |

Rcart | Restore points to spherical manifold |

read.datacounts | Read data counts in CSV format |

read.datapoints | Read data points in CSV format |

ReconstructedCountSet | Class containing functions and data to map CountSets to... |

ReconstructedFeatureSet | Class containing functions and data to map FeatureSets to... |

ReconstructedLandmarkSet | Class containing functions and data to map LandmarkSets to... |

ReconstructedOutline | Class containing functions to reconstruct StitchedOutlines... |

ReconstructedPointSet | Class containing functions and data to map PointSets to... |

remove.identical.consecutive.rows | Remove identical consecutive rows from a matrix |

remove.intersections | Remove intersections between adjacent segments in a closed... |

report | Reporting utility function |

RetinalOutline | Class containing functions and data relating to retinal... |

RetinalReconstructedOutline | A version of ReconstructedOutline that is specific to retinal... |

retistruct | Start the Retistruct GUI |

retistruct.batch | Batch operation using the parallel package |

retistruct.batch.analyse.summaries | Extract statistics from a directory containing reconstruction... |

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.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.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 |

simplifyFragment | Simplify an outline object by removing short edges |

simplifyOutline | Simplify an outline object by removing short edges |

sinusoidal | Sinusoidal projection |

sphere.cart.to.sphere.dualwedge | Convert from Cartesian to 'dual-wedge' 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... |

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 |

sphericalplot | Spherical plot of reconstructed outline |

sphericalplot.ReconstructedOutline | Spherical plot of reconstructed outline |

spherical.to.polar.area | Convert latitude on sphere to radial variable in... |

StitchedOutline | Class containing functions and data relating to Stitching... |

strain.colours | Generate colours for strain plots |

stretchMesh | Stretch mesh |

TriangulatedFragment | Class to triangulate Fragments |

TriangulatedOutline | Class containing functions and data relating to Triangulation |

tri.area | Area of triangles on a plane |

tri.area.signed | "Signed area" of triangles on a plane |

vecnorm | Vector norm |

Embedding an R snippet on your website

Add the following code to your website.

For more information on customizing the embed code, read Embedding Snippets.