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retistruct (version 0.5.9)
Retistruct - Retinal Reconstruction Program
Description
Program to reconstruct retinae from flattened retinae in which there are incisions and tears
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Install
install.packages('retistruct')
Monthly Downloads
81
Version
0.5.9
License
CC BY-NC-SA 4.0
Maintainer
David Sterratt
Last Published
December 2nd, 2014
Functions in retistruct (0.5.9)
Search functions
computeTearRelationships
Compute the parent relationships for a set of tears
flatplot.stitchedOutline
Flat plot of AnnotatedOutline
flatplot.reconstructedOutline
Flat plot of reconstructed outline
getDssMean.retinalReconstructedDataset
Get transformed spherical coordinates of Karcher mean of datapoints
Ecart
The deformation energy function
azimuthal.equalarea
Lambert azimuthal equal area projection
addClass
Add new class to class vector of object
StitchedOutline
Stitch together incisions and tears in an AnnotatedOutline
bary.to.sphere.cart
Convert barycentric coordinates of points in mesh on sphere to cartesian coordinates
circle
Return points on the unit circle
central.angle
Central angle between two points on a sphere
azel.to.sphere.colattitude
Convert azimuth-elevation coordinates to spherical coordinates
getGss
Get grouped variable with locations in spherical coordinates.
RetinalReconstructedDataset
RetinalReconstructedDataset constructor
Outline
Outline constructor
azimuthal.equidistant
Azimuthal equidistant projection
E
The deformation energy function
normalise.angle
Bring angle into range
labelTearPoints
Label three outline point indicies as apicies and vertices of tear
f
Piecewise smooth function used in area penalty
create.polar.cart.grid
Create grid on projection of hemisphere onto plane
lvsLplot
Plot the fractional change in length of mesh edges
fire
The FIRE algorithm
orthographic
Orthographic projection
kr.sscv
Cross validation estimate of the least squares error of the points mu given a particular value of the concentration kappa
dE
The deformation energy gradient function
flipped.triangles.cart
Determine indicies of triangles that are flipped
getDssMean.reconstructedDataset
Karcher mean of datapoints in spherical coordinates
getKDE
Get kernel density estimate of data points
ReconstructedDataset
Constructor for RecontructedDataset object
remove.intersections
Remove intersections between adjacent segements in a closed path
flatplot.triangulatedOutline
Flat plot of TriangulatedOutline
TriangulatedOutline
Triangulate outline
getIDs.dataset
Get IDs of groups of data within a dataset
kde.L
Estimate of the log likelihood of the points mu given a particular value of the concentration kappa
getSssMean
Karcher mean of landmarks in spherical coordinates
getIDs
Get IDs of groups of data within a dataset
getDss.retinalReconstructedDataset
Get transformed spherical coordinates of datapoints
Dataset
Constructor for a
dataset
object.
compute.intersections.sphere
Find the intersection of a plane with edges of triangles on a sphere
retistruct
Start the Retistruct GUI
getSss.reconstructedDataset
Get transformed spherical coordinates of landmarks.
mergePointsEdges
Merge stitched points and edges
getIDs.reconstructedDataset
Get IDs of groups of data within a ReconstructedDataset
read.datapoints
Read data points in CSV format
flipped.triangles
Determine indicies of triangles that are flipped
ensureFixedPointInRim
Ensure that the fixed point is in the rim, not a tear
flatplot.retinalDataset
Flat plot of retinal dataset
Fcart
The deformation energy gradient function
flatplot.dataset
Flat plot of Dataset
checkDatadir
Check the whether directory contains valid data
getStrains
Return strains edges are under in spherical retina
compute.kernel.estimate
Kernel estimate over grid
nameLandmark
Name a landmark in a Dataset
retistruct.batch
Batch operation using the parallel package
getTss
Get spherical coordinates of tears.
azimuthal.conformal
Azimuthal conformal or stereographic or Wulff projection
kr.yhat
Kernel regression on sphere using Fisherian density with polar coordinates
invert.sphere.to.hemisphere
Invert sphere to hemisphere
retistruct.batch.export.matlab
Export data from reconstruction data files to matlab
getDssMean
Karcher mean of datapoints in spherical coordinates
RetinalReconstructedOutline
RetinalReconstructedOutline constructor
list.datasets
List datasets underneath a directory
retistruct.reconstruct
Reconstruct a retina
retistruct.batch.plot.ods
Superposed plot of ODs on polar axes
recfile.version
Version of reconstruction file data format
line.line.intersection
Determine intersection between two lines
retistruct.batch.summary
Extract summary data for a batch of reconstructions
optimiseMapping
Optimise mapping
projection.reconstructedDataset
Plot projection of reconstructed dataset
getIms.reconstructedOutline
Get coordinates of corners of pixels of image in spherical coordinates
projection
Plot projection of an object
simplify.outline
Simplify an outline object by removing short edges
setFixedPoint
Set fixed point
flatplot.annotatedOutline
Flat plot of AnnotatedOutline
sphericalplot
Spherical plot of reconstructed outline
retistruct.batch.analyse.summary
Extract statistics from the retistruct-batch.csv summary file
karcher.mean.sphere
Karcher mean on the sphere
flatplot.outline
Flat plot of outline
polartext
Put text on the polar plot
sphere.spherical.to.sphere.cart
Convert from spherical to Cartesian coordinates
AnnotatedOutline
Constructor for AnnotatedOutline object
retistruct.read.recdata
Read the reconstruction data from file
kr.yhat.cart
Kernel regression on sphere using Fisherian density with Cartesian coordinates
retistruct.cli.process
Process a dataset, saving results to disk
tri.area.signed
"Signed area" of triangles on a plane
retistruct.potential.od
Test for a potential optic disc
retistruct.batch.plot.titrations
Plot titrations
removeTear
Remove tear from an AnnotatedOutline
retistruct.batch.get.titrations
Get titrations from a directory of reconstructions
retistruct.global.revision
Git short commit hash of Retistruct package
sphericalplot.reconstructedOutline
Spherical plot of reconstructed outline
retistruct.read.dataset
Read a retinal dataset
spherical.to.polar.area
Convert lattitude on sphere to radial variable in area-preserving projection
ijroi.read.dataset
Read a retinal dataset in IJROI format
getDss.reconstructedDataset
Get transformed spherical coordinates of datapoints
getGss.reconstructedDataset
Get grouped variable with locations in spherical coordinates.
stretchMesh
Stretch mesh
getSss
Get transformed spherical coordinates of landmarks.
sphericalplot.reconstructedDataset
Spherical plot of reconstructed outline
retistruct.save.recdata
Save reconstruction data
idt.read.dataset
Read one of the Thompson lab's retinal datasets
polar.cart.to.sphere.spherical
Convert polar projection in Cartesian coordinates to spherical coordinates on sphere
kde.compute.concentration
Find the optimal concentration for a set of data
name.list
Return a new version of the list in which any un-named elements have been given standardised names
kde.fhat.cart
Kernel density estimate on sphere using Fisherian density with Cartesian coordinates
retistruct.read.markup
Read the markup data
projectToSphere
Project mesh points in the flat outline onto a sphere
remove.identical.consecutive.rows
Remove identical consecutive rows from a matrix
addTear
Add tear to an AnnotatedOutline
identity.transform
The identity transformation
checkTears
Check that tears are all in the correct direction
getIms
Get coordinates of corners of pixels of image in spherical coordinates
rotate.axis
Rotate axis of sphere
retistruct.save.markup
Save markup
retistruct.cli.figure
Print a figure to file
solveMappingCart
Optimise mapping
sphere.cart.to.sphere.dualwedge
Convert from Cartesian to 'dualwedge' coordinates
vecnorm
Vector norm
transform.image.reconstructedOutline
Transform an image into the reconstructed space
whichTear
Return index of tear
sinusoidal
Sinusoidal projection
titrate.reconstructedOutline
Titrate values of phi0
kde.fhat
Kernel density estimate on sphere using Fisherian density with polar coordinates
fp
Piecewise smooth function used in area penalty
sphere.cart.to.sphere.spherical
Convert from Cartesian to spherical coordinates
nameLandmark.retinalDataset
Name a landmark in a RetinalDataset
getDssHullarea
Get area of convex hull around data points on sphere
RetinalDataset
RetinalDataset constructor
tri.area
Area of triangles on a plane
retistruct.check.markup
Retistruct check markup
csv.read.dataset
Read a retinal dataset in CSV format
sphere.spherical.to.polar.cart
Convert spherical coordinates on sphere to polar projection in Cartesian coordinates
invert.sphere
Invert sphere about its centre
strain.colours
Generate colours for strain plots
getSss.retinalReconstructedDataset
Get transformed spherical coordinates of datapoints
panlabel
Ancillary function to place labels
projection.reconstructedOutline
Projection of a reconstructed outline
getTear
Return indicies of tear in AnnotatedOutline
ReconstructedOutline
Reconstruct outline into spherical surface
Rcart
Restore points to spherical manifold
getGss.retinalReconstructedDataset
Get grouped variable with locations in spherical coordinates.
retistruct.cli
Process a dataset with a time limit
sphere.cart.to.sphere.wedge
Convert from Cartesian to 'wedge' coordinates
sphere.wedge.to.sphere.cart
Convert from 'wedge' to Cartesian coordinates
flatplot
Flat plot of object
getDss
Get transformed spherical coordinates of datapoints
getFlatRimLength
Get rim length of AnnotatedOutline
getKR
Get kernel regression estimate of grouped data points
kr.compute.concentration
Find the optimal concentration for a set of data
retistruct.batch.analyse.summaries
Extract statistics from a directory containing reconstruction directories.
retistruct.batch.figures
Plot figures for a batch of reconstructions
retistruct.export.matlab
Save reconstruction data in MATLAB format
sphere.tri.area
Area of triangles on a sphere