# Retinal Reconstruction Program

## Documentation for package ‘retistruct’ version 0.8.1

- DESCRIPTION file.
- Code demos. Use demo() to run them.
- Package NEWS.

## Help Pages

A B C D E F I K L M N O P R S T U V

## -- A --

AnnotatedOutline | Class containing functions and data relating to annotating outlines
azel.to.sphere.colatitude | 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

## -- B --

bary.to.sphere.cart | Convert barycentric coordinates of points in mesh on sphere to cartesian coordinates

## -- C --

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 sphere
compute.kernel.estimate | Kernel estimate over grid
CountSet | Subclass of 'FeatureSet' to represent counts centred on points
create.polar.cart.grid | Create grid on projection of hemisphere onto plane
csv.read.dataset | Read a retinal dataset in CSV format

## -- D --

dE | The deformation energy gradient function
depthplot3D | Draw the "flat" outline in 3D with depth information
directories | File system directories used by shinyFiles

## -- E --

E | The deformation energy function
Ecart | The deformation energy function

## -- F --

f | Piecewise smooth function used in area penalty
Fcart | The deformation energy gradient function
FeatureSet | Superclass containing functions and data relating to sets of features in flat 'Outline's
FeatureSetCommon | Class containing functionality common to 'FeatureSet's and 'ReconstructedFeatureSet's
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 'P', as described below.

## -- I --

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
ijroimulti.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

## -- K --

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

## -- L --

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

## -- M --

morph.dataset.to.parabola | Morph a flat dataset to a parabola for testing purposes

## -- N --

name.list | Return a new version of the list in which any unnamed elements have been given standardised names
normalise.angle | Bring angle into range

## -- O --

orthographic | Orthographic projection
Outline | Class containing basic information about flat outlines
OutlineCommon | Class containing functionality common to flat and reconstructed outlines

## -- P --

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 fullcuts to the outline
PointSet | Subclass of 'FeatureSet' to represent points
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 a reconstructed outline
projection.ReconstructedOutline | Projection of a reconstructed outline
projection.RetinalReconstructedOutline | Plot projection of reconstructed dataset

## -- R --

R6_to_list | Convert an R6 object into a list, ignoring functions and environments
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 ReconstructedOutlines
ReconstructedFeatureSet | Class containing functions and data to map FeatureSets to ReconstructedOutlines
ReconstructedLandmarkSet | Class containing functions and data to map LandmarkSets to ReconstructedOutlines
ReconstructedOutline | Class containing functions to reconstruct StitchedOutlines and store the associated data
ReconstructedPointSet | Class containing functions and data to map PointSets to ReconstructedOutlines
remove.identical.consecutive.rows | Remove identical consecutive rows from a matrix
remove.intersections | Remove intersections between adjacent segments in a closed path
report | Reporting utility function
RetinalOutline | Class containing functions and data relating to retinal outlines
RetinalReconstructedOutline | A version of ReconstructedOutline that is specific to retinal datasets
retistruct | Start the Retistruct GUI
retistruct.batch | Batch operation using the parallel package
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

## -- S --

server | Retistruct Shiny Server
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 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.ReconstructedOutline | Spherical plot of reconstructed outline
StitchedOutline | Class containing functions and data relating to Stitching outlines
strain.colours | Generate colours for strain plots
stretchMesh | Stretch mesh

## -- T --

tri.area | Area of triangles on a plane
tri.area.signed | "Signed area" of triangles on a plane
TriangulatedFragment | Class to triangulate Fragments
TriangulatedOutline | Class containing functions and data relating to Triangulation

## -- U --

ui | Retistruct UI

## -- V --

vecnorm | Vector norm