Man pages for retistruct
Retinal Reconstruction Program

addClassAdd new class to class vector of object
addTearAdd tear to an AnnotatedOutline
AnnotatedOutlineConstructor for AnnotatedOutline object
azel.to.sphere.colattitudeConvert azimuth-elevation coordinates to spherical...
azimuthal.conformalAzimuthal conformal or stereographic or Wulff projection
azimuthal.equalareaLambert azimuthal equal area projection
azimuthal.equidistantAzimuthal equidistant projection
bary.to.sphere.cartConvert barycentric coordinates of points in mesh on sphere...
central.angleCentral angle between two points on a sphere
checkDatadirCheck the whether directory contains valid data
checkTearsCheck that tears are all in the correct direction
circleReturn points on the unit circle
compute.intersections.sphereFind the intersection of a plane with edges of triangles on a...
compute.kernel.estimateKernel estimate over grid
computeTearRelationshipsCompute the parent relationships for a set of tears
create.polar.cart.gridCreate grid on projection of hemisphere onto plane
csv.read.datasetRead a retinal dataset in CSV format
DatasetConstructor for a 'dataset' object.
dEThe deformation energy gradient function
EThe deformation energy function
EcartThe deformation energy function
ensureFixedPointInRimEnsure that the fixed point is in the rim, not a tear
fPiecewise smooth function used in area penalty
FcartThe deformation energy gradient function
fireThe FIRE algorithm
flatplotFlat plot of object
flatplot.annotatedOutlineFlat plot of AnnotatedOutline
flatplot.datasetFlat plot of Dataset
flatplot.outlineFlat plot of outline
flatplot.reconstructedOutlineFlat plot of reconstructed outline
flatplot.retinalDatasetFlat plot of retinal dataset
flatplot.stitchedOutlineFlat plot of AnnotatedOutline
flatplot.triangulatedOutlineFlat plot of TriangulatedOutline
flipped.trianglesDetermine indices of triangles that are flipped
flipped.triangles.cartDetermine indices of triangles that are flipped
fpPiecewise smooth function used in area penalty
getDssGet transformed spherical coordinates of datapoints
getDssHullareaGet area of convex hull around data points on sphere
getDssMeanKarcher mean of datapoints in spherical coordinates
getDssMean.reconstructedDatasetKarcher mean of datapoints in spherical coordinates
getDssMean.retinalReconstructedDatasetGet transformed spherical coordinates of Karcher mean of...
getDss.reconstructedDatasetGet transformed spherical coordinates of datapoints
getDss.retinalReconstructedDatasetGet transformed spherical coordinates of datapoints
getFlatRimLengthGet rim length of AnnotatedOutline
getGssGet grouped variable with locations in spherical coordinates.
getGss.reconstructedDatasetGet grouped variable with locations in spherical coordinates.
getGss.retinalReconstructedDatasetGet grouped variable with locations in spherical coordinates.
getIDsGet IDs of groups of data within a dataset
getIDs.datasetGet IDs of groups of data within a dataset
getIDs.reconstructedDatasetGet IDs of groups of data within a ReconstructedDataset
getImsGet coordinates of corners of pixels of image in spherical...
getIms.reconstructedOutlineGet coordinates of corners of pixels of image in spherical...
getKDEGet kernel density estimate of data points
getKRGet kernel regression estimate of grouped data points
getSssGet transformed spherical coordinates of landmarks.
getSssMeanKarcher mean of landmarks in spherical coordinates
getSss.reconstructedDatasetGet transformed spherical coordinates of landmarks.
getSss.retinalReconstructedDatasetGet transformed spherical coordinates of datapoints
getStrainsReturn strains edges are under in spherical retina
getTearReturn indices of tear in AnnotatedOutline
getTssGet spherical coordinates of tears.
identity.transformThe identity transformation
idt.read.datasetRead one of the Thompson lab's retinal datasets
ijroi.read.datasetRead a retinal dataset in IJROI format
invert.sphereInvert sphere about its centre
invert.sphere.to.hemisphereInvert sphere to hemisphere
karcher.mean.sphereKarcher mean on the sphere
kde.compute.concentrationFind the optimal concentration for a set of data
kde.fhatKernel density estimate on sphere using Fisherian density...
kde.fhat.cartKernel density estimate on sphere using Fisherian density...
kde.LEstimate of the log likelihood of the points mu given a...
kr.compute.concentrationFind the optimal concentration for a set of data
kr.sscvCross validation estimate of the least squares error of the...
kr.yhatKernel regression on sphere using Fisherian density with...
kr.yhat.cartKernel regression on sphere using Fisherian density with...
labelTearPointsLabel three outline point indices as apices and vertices of...
line.line.intersectionDetermine intersection between two lines
list.datasetsList datasets underneath a directory
lvsLplotPlot the fractional change in length of mesh edges
mergePointsEdgesMerge stitched points and edges
nameLandmarkName a landmark in a Dataset
nameLandmark.retinalDatasetName a landmark in a RetinalDataset
name.listReturn a new version of the list in which any un-named...
normalise.angleBring angle into range
optimiseMappingOptimise mapping
orthographicOrthographic projection
OutlineOutline constructor
panlabelAncillary function to place labels
parse.dependenciesParse dependencies
polar.cart.to.sphere.sphericalConvert polar projection in Cartesian coordinates to...
polartextPut text on the polar plot
projectionPlot projection of an object
projection.reconstructedDatasetPlot projection of reconstructed dataset
projection.reconstructedOutlineProjection of a reconstructed outline
projectToSphereProject mesh points in the flat outline onto a sphere
RcartRestore points to spherical manifold
read.datacountsRead data counts in CSV format
read.datapointsRead data points in CSV format
recfile.versionVersion of reconstruction file data format
ReconstructedDatasetConstructor for RecontructedDataset object
ReconstructedOutlineReconstruct outline into spherical surface
remove.identical.consecutive.rowsRemove identical consecutive rows from a matrix
remove.intersectionsRemove intersections between adjacent segments in a closed...
removeTearRemove tear from an AnnotatedOutline
RetinalDatasetRetinalDataset constructor
RetinalReconstructedDatasetRetinalReconstructedDataset constructor
RetinalReconstructedOutlineRetinalReconstructedOutline constructor
retistructStart the Retistruct GUI
retistruct.batchBatch operation using the parallel package
retistruct.batch.analyse.summariesExtract statistics from a directory containing reconstruction...
retistruct.batch.analyse.summaryExtract statistics from the retistruct-batch.csv summary file
retistruct.batch.export.matlabExport data from reconstruction data files to matlab
retistruct.batch.figuresPlot figures for a batch of reconstructions
retistruct.batch.get.titrationsGet titrations from a directory of reconstructions
retistruct.batch.plot.odsSuperposed plot of ODs on polar axes
retistruct.batch.plot.titrationsPlot titrations
retistruct.batch.summaryExtract summary data for a batch of reconstructions
retistruct.check.markupRetistruct check markup
retistruct.cliProcess a dataset with a time limit
retistruct.cli.figurePrint a figure to file
retistruct.cli.processProcess a dataset, saving results to disk
retistruct.export.matlabSave reconstruction data in MATLAB format
retistruct.potential.odTest for a potential optic disc
retistruct.read.datasetRead a retinal dataset
retistruct.read.markupRead the markup data
retistruct.read.recdataRead the reconstruction data from file
retistruct.reconstructReconstruct a retina
retistruct.save.markupSave markup
retistruct.save.recdataSave reconstruction data
rotate.axisRotate axis of sphere
setFixedPointSet fixed point
simplify.outlineSimplify an outline object by removing short edges
sinusoidalSinusoidal projection
solveMappingCartOptimise mapping
sphere.cart.to.sphere.dualwedgeConvert from Cartesian to 'dualwedge' coordinates
sphere.cart.to.sphere.sphericalConvert from Cartesian to spherical coordinates
sphere.cart.to.sphere.wedgeConvert from Cartesian to 'wedge' coordinates
sphere.spherical.to.polar.cartConvert spherical coordinates on sphere to polar projection...
sphere.spherical.to.sphere.cartConvert from spherical to Cartesian coordinates
sphere.tri.areaArea of triangles on a sphere
sphere.wedge.to.sphere.cartConvert from 'wedge' to Cartesian coordinates
sphericalplotSpherical plot of reconstructed outline
sphericalplot.reconstructedDatasetSpherical plot of reconstructed outline
sphericalplot.reconstructedOutlineSpherical plot of reconstructed outline
spherical.to.polar.areaConvert latitude on sphere to radial variable in...
StitchedOutlineStitch together incisions and tears in an AnnotatedOutline
strain.coloursGenerate colours for strain plots
stretchMeshStretch mesh
titrate.reconstructedOutlineTitrate values of phi0
transform.image.reconstructedOutlineTransform an image into the reconstructed space
TriangulatedOutlineTriangulate outline
tri.areaArea of triangles on a plane
tri.area.signed"Signed area" of triangles on a plane
vecnormVector norm
whichTearReturn index of tear
retistruct documentation built on Aug. 10, 2017, 1:03 a.m.