Man pages for retistruct
Retinal Reconstruction Program

AnnotatedOutlineClass containing functions and data relating to annotating... azimuth-elevation coordinates to spherical...
azimuthal.conformalAzimuthal conformal or stereographic or Wulff projection
azimuthal.equalareaLambert azimuthal equal area projection
azimuthal.equidistantAzimuthal equidistant projection barycentric coordinates of points in mesh on sphere...
central.angleCentral angle between two points on a sphere
checkDatadirCheck the whether directory contains valid data
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
CountSetSubclass of 'FeatureSet' to represent counts centred on...
create.polar.cart.gridCreate grid on projection of hemisphere onto plane a retinal dataset in CSV format
dEThe deformation energy gradient function
depthplot3DDraw the "flat" outline in 3D with depth information
EThe deformation energy function
EcartThe deformation energy function
fPiecewise smooth function used in area penalty
FcartThe deformation energy gradient function
FeatureSetSuperclass containing functions and data relating to sets of...
FeatureSetCommonClass containing functionality common to 'FeatureSet's and...
fireThe FIRE algorithm
flatplotPlot "flat" (unreconstructed) representation of outline
flatplot.AnnotatedOutlineFlat plot of AnnotatedOutline
flatplot.OutlineFlat plot of outline
flatplot.ReconstructedOutlineFlat plot of reconstructed outline
flatplot.StitchedOutlineFlat plot of AnnotatedOutline
flatplot.TriangulatedOutlinePlot flat '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
FragmentConstruct an outline object. This sanitises the input points...
identity.transformThe identity transformation one of the Thompson lab's retinal datasets a retinal dataset in IJROI format
interpolate.imageInterpolate values in image
invert.sphereInvert sphere about its centre 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...
LandmarkSetSubclass of 'FeatureSet' to represent points
line.line.intersectionDetermine intersection between two lines
list.datasetsList datasets underneath a directory
list_to_R6Convert an list created by R6_to_list() into an R6 object.
lvsLplotPlot the fractional change in length of mesh edges
name.listReturn a new version of the list in which any unnamed...
normalise.angleBring angle into range
orthographicOrthographic projection
OutlineClass containing basic information about flat outlines
OutlineCommonClass containing functionality common to flat and...
panlabelAncillary function to place labels
parabola.arclengthArc length of a parabola y=x^2/4f
parabola.invarclengthInverse arc length of a parabola y=x^2/4f
parse.dependenciesParse dependencies
PathOutlineAdd point correspondences to the outline
PointSetSubclass of 'FeatureSet' to represent points polar projection in Cartesian coordinates to...
polartextPut text on the polar plot
projectionPlot projection of a reconstructed outline
projection.ReconstructedOutlineProjection of a reconstructed outline
projection.RetinalReconstructedOutlinePlot projection of reconstructed dataset
R6_to_listConvert an R6 object into a list, ignoring functions and...
RcartRestore points to spherical manifold
read.datacountsRead data counts in CSV format
read.datapointsRead data points in CSV format
ReconstructedCountSetClass containing functions and data to map CountSets to...
ReconstructedFeatureSetClass containing functions and data to map FeatureSets to...
ReconstructedLandmarkSetClass containing functions and data to map LandmarkSets to...
ReconstructedOutlineClass containing functions to reconstruct StitchedOutlines...
ReconstructedPointSetClass containing functions and data to map PointSets to...
remove.identical.consecutive.rowsRemove identical consecutive rows from a matrix
remove.intersectionsRemove intersections between adjacent segments in a closed...
reportReporting utility function
RetinalOutlineClass containing functions and data relating to retinal...
RetinalReconstructedOutlineA version of ReconstructedOutline that is specific to retinal...
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.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 a retinal dataset the markup data the reconstruction data from file
retistruct.reconstructReconstruct a retina markup reconstruction data
rotate.axisRotate axis of sphere
simplifyFragmentSimplify an outline object by removing short edges
simplifyOutlineSimplify an outline object by removing short edges
sinusoidalSinusoidal projection from Cartesian to 'dual-wedge' coordinates from Cartesian to spherical coordinates from Cartesian to 'wedge' coordinates spherical coordinates on sphere to polar projection... from spherical to Cartesian coordinates
sphere.tri.areaArea of triangles on a sphere from 'wedge' to Cartesian coordinates
sphericalplotSpherical plot of reconstructed outline
sphericalplot.ReconstructedOutlineSpherical plot of reconstructed outline latitude on sphere to radial variable in...
StitchedOutlineClass containing functions and data relating to Stitching...
strain.coloursGenerate colours for strain plots
stretchMeshStretch mesh
TriangulatedFragmentClass to triangulate Fragments
TriangulatedOutlineClass containing functions and data relating to Triangulation
tri.areaArea of triangles on a plane
tri.area.signed"Signed area" of triangles on a plane
vecnormVector norm
retistruct documentation built on April 4, 2020, 5:08 p.m.