Class containing basic information about flat outlines
Construct an outline object. This sanitises the input points
P, as described below.
Superclass containing functions and data relating to sets of
features in flat Outline Subclass of FeatureSet The deformation energy function
Subclass of FeatureSet The deformation energy gradient function
Class containing functionality common to FeatureSet ReconstructedFeatureSet Class containing functions and data relating to annotating outlines
The deformation energy function
Restore points to spherical manifold
Class containing functions to reconstruct StitchedOutline s
and store the associated data Subclass of FeatureSet Class containing functionality common to flat and reconstructed outlines
Class containing functions and data relating to Stitching outlines
compute.intersections.sphere
Find the intersection of a plane with edges of triangles on
a sphere
Add point correspondences to the outline
Class to triangulate Fragment s Return points on the unit circle
Azimuthal conformal or stereographic or Wulff projection
Lambert azimuthal equal area projection
Convert an R6 object into a list, ignoring functions and
environments
Kernel estimate over grid
Flat plot of outline
Class containing functions and data to map CountSet s to
ReconstructedOutline s The FIRE algorithm
Create grid on projection of hemisphere onto plane
Class containing functions and data to map PointSet s to
ReconstructedOutline s Cross validation estimate of the least squares error of the
points mu given a particular value of the concentration kappa
Invert sphere about its centre
Plot "flat" (unreconstructed) representation of outline
invert.sphere.to.hemisphere
Invert sphere to hemisphere
Draw the "flat" outline in 3D with depth information
Class containing functions and data relating to Triangulation
azel.to.sphere.colatitude
Convert azimuth-elevation coordinates to spherical coordinates
Class containing functions and data relating to retinal outlines
RetinalReconstructedOutline
A version of ReconstructedOutline that is specific to
retinal datasets Read a retinal dataset in CSV format
Class containing functions and data to map FeatureSet s to
ReconstructedOutline s Kernel regression on sphere using Fisherian density with
polar coordinates
Determine indices of triangles that are flipped
Piecewise smooth function used in area penalty
The deformation energy gradient function
flatplot.AnnotatedOutline
Flat plot of AnnotatedOutline
Read a retinal dataset in IJROI format
Piecewise smooth function used in area penalty
Bring angle into range
Orthographic projection
kde.compute.concentration
Find the optimal concentration for a set of data
Interpolate values in image
flatplot.TriangulatedOutline
Plot the fractional change in length of mesh edges
Return a new version of the list in which any unnamed elements
have been given standardised names
Determine indices of triangles that are flipped
projection.RetinalReconstructedOutline
Plot projection of reconstructed dataset
Class containing functions and data to map LandmarkSet s to
ReconstructedOutline s Read data counts in CSV format
Convert barycentric coordinates of points in mesh on sphere
to cartesian coordinates
Inverse arc length of a parabola y=x^2/4f
Parse dependencies
Azimuthal equidistant projection
Read one of the Thompson lab's retinal datasets
The identity transformation
Put text on the polar plot
Determine intersection between two lines
polar.cart.to.sphere.spherical
Convert polar projection in Cartesian coordinates to
spherical coordinates on sphere
Kernel regression on sphere using Fisherian density with
Cartesian coordinates
Central angle between two points on a sphere
Check the whether directory contains valid data
flatplot.ReconstructedOutline
Flat plot of reconstructed outline
Retistruct check markup
Read a retinal dataset
Read the markup data
sphere.wedge.to.sphere.cart
Convert from 'wedge' to Cartesian coordinates
Extract summary data for a batch of reconstructions
Karcher mean on the sphere
Flat plot of AnnotatedOutline
retistruct.batch.analyse.summaries
Extract statistics from a directory containing
reconstruction directories.
Save markup
sphere.cart.to.sphere.spherical
Convert from Cartesian to spherical coordinates
Save reconstruction data in MATLAB format
Remove intersections between adjacent segments in a closed
path
Process a dataset, saving results to disk
sphere.cart.to.sphere.dualwedge
Convert from Cartesian to ‘dual-wedge’ coordinates
Reporting utility function
Save reconstruction data
retistruct.batch.analyse.summary
Extract statistics from the retistruct-batch.csv summary file
Estimate of the log likelihood of the points mu given a
particular value of the concentration kappa
Kernel density estimate on sphere using Fisherian density
with polar coordinates
Kernel density estimate on sphere using Fisherian density
with Cartesian coordinates
retistruct.batch.export.matlab
Export data from reconstruction data files to MATLAB
List datasets underneath a directory
Convert an list created by R6_to_list() into an R6 object.
Ancillary function to place labels
Arc length of a parabola y=x^2/4f
projection.ReconstructedOutline
Projection of a reconstructed outline
Find the optimal concentration for a set of data
Plot projection of a reconstructed outline
Plot figures for a batch of reconstructions
Convert latitude on sphere to radial variable in
area-preserving projection
Vector norm
Start the Retistruct GUI
Batch operation using the parallel package
Rotate axis of sphere
Simplify an outline object by removing short edges
sphere.spherical.to.sphere.cart
Convert from spherical to Cartesian coordinates
Area of triangles on a sphere
Stretch mesh
Generate colours for strain plots
retistruct.batch.get.titrations
Get titrations from a directory of reconstructions
Read data points in CSV format
remove.identical.consecutive.rows
Remove identical consecutive rows from a matrix
Process a dataset with a time limit
Print a figure to file
Read the reconstruction data from file
Reconstruct a retina
retistruct.batch.plot.titrations
Plot titrations
sphere.cart.to.sphere.wedge
Convert from Cartesian to 'wedge' coordinates
Simplify an outline object by removing short edges
Sinusoidal projection
sphere.spherical.to.polar.cart
Convert spherical coordinates on sphere to polar
projection in Cartesian coordinates
Area of triangles on a plane
Spherical plot of reconstructed outline
"Signed area" of triangles on a plane
sphericalplot.ReconstructedOutline
Spherical plot of reconstructed outline