retistruct: Retinal Reconstruction Program

Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the a standard retinal shape). It can estimate the position of a point on the intact adult retina to within 8 degrees of arc (3.6% of nasotemporal axis). The coordinates in reconstructed retinae can be transformed to visuotopic coordinates.

Author
David C. Sterratt [aut, cre, cph], Daniel Lyngholm [aut, cph]
Date of publication
2015-02-16 13:49:18
Maintainer
David C. Sterratt <david.c.sterratt@ed.ac.uk>
License
CC BY-NC-SA 4.0
Version
0.5.10
URLs

View on CRAN

Man pages

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

Files in this package

retistruct
retistruct/inst
retistruct/inst/CITATION
retistruct/inst/extdata
retistruct/inst/extdata/GM509
retistruct/inst/extdata/GM509/R-CONTRA
retistruct/inst/extdata/GM509/R-CONTRA/T.csv
retistruct/inst/extdata/GM509/R-CONTRA/P.csv
retistruct/inst/extdata/GM509/R-CONTRA/SYS.SYS
retistruct/inst/extdata/GM509/R-CONTRA/ALU.MAP
retistruct/inst/extdata/GM509/R-CONTRA/markup.csv
retistruct/inst/extdata/ijroi2
retistruct/inst/extdata/ijroi2/T.csv
retistruct/inst/extdata/ijroi2/datapoints.csv
retistruct/inst/extdata/ijroi2/outline.roi
retistruct/inst/extdata/ijroi2/P.csv
retistruct/inst/extdata/ijroi2/markup.csv
retistruct/inst/extdata/GM114-4-RC
retistruct/inst/extdata/GM114-4-RC/T.csv
retistruct/inst/extdata/GM114-4-RC/P.csv
retistruct/inst/extdata/GM114-4-RC/SYS.SYS
retistruct/inst/extdata/GM114-4-RC/ALU.MAP
retistruct/inst/extdata/GM114-4-RC/markup.csv
retistruct/inst/extdata/GM182-4
retistruct/inst/extdata/GM182-4/R-CONTRA
retistruct/inst/extdata/GM182-4/R-CONTRA/T.csv
retistruct/inst/extdata/GM182-4/R-CONTRA/P.csv
retistruct/inst/extdata/GM182-4/R-CONTRA/SYS.SYS
retistruct/inst/extdata/GM182-4/R-CONTRA/ALU.MAP
retistruct/inst/extdata/GM182-4/R-CONTRA/markup.csv
retistruct/inst/extdata/ijroi1
retistruct/inst/extdata/ijroi1/T.csv
retistruct/inst/extdata/ijroi1/datapoints.csv
retistruct/inst/extdata/ijroi1/outline.roi
retistruct/inst/extdata/ijroi1/P.csv
retistruct/inst/extdata/ijroi1/markup.csv
retistruct/inst/extdata/GMB530
retistruct/inst/extdata/GMB530/R-CONTRA
retistruct/inst/extdata/GMB530/R-CONTRA/T.csv
retistruct/inst/extdata/GMB530/R-CONTRA/P.csv
retistruct/inst/extdata/GMB530/R-CONTRA/SYS.SYS
retistruct/inst/extdata/GMB530/R-CONTRA/ALU.MAP
retistruct/inst/extdata/GMB530/R-CONTRA/markup.csv
retistruct/inst/extdata/smi32
retistruct/inst/extdata/smi32/image.png
retistruct/inst/extdata/smi32/T.csv
retistruct/inst/extdata/smi32/od.roi
retistruct/inst/extdata/smi32/outline.roi
retistruct/inst/extdata/smi32/P.csv
retistruct/inst/extdata/smi32/markup.csv
retistruct/inst/extdata/smi32-csv
retistruct/inst/extdata/smi32-csv/image.png
retistruct/inst/extdata/smi32-csv/T.csv
retistruct/inst/extdata/smi32-csv/od.csv
retistruct/inst/extdata/smi32-csv/P.csv
retistruct/inst/extdata/smi32-csv/outline.csv
retistruct/inst/extdata/smi32-csv/markup.csv
retistruct/inst/extdata/orange
retistruct/inst/extdata/orange/image.png
retistruct/inst/extdata/orange/T.csv
retistruct/inst/extdata/orange/outline.roi
retistruct/inst/extdata/orange/P.csv
retistruct/inst/extdata/orange/markup.csv
retistruct/tests
retistruct/tests/ijroi-format.R
retistruct/tests/ijroi-format.Rout.save
retistruct/tests/getFuns.Rout.save
retistruct/tests/getFuns.R
retistruct/tests/reconstruct.R
retistruct/tests/testthat.R
retistruct/tests/testthat
retistruct/tests/testthat/test-format-csv.R
retistruct/tests/testthat/test-karcher.R
retistruct/tests/testthat/test-wedge.R
retistruct/tests/testthat/test-format-ijroi.R
retistruct/src
retistruct/src/energy.c
retistruct/NAMESPACE
retistruct/demo
retistruct/demo/smi32.R
retistruct/demo/orange.R
retistruct/demo/retistruct.method.R
retistruct/demo/low.high.R
retistruct/demo/00Index
retistruct/demo/wedge.R
retistruct/demo/retistruct.titrate.R
retistruct/NEWS
retistruct/R
retistruct/R/RetinalReconstructedOutline.R
retistruct/R/AnnotatedOutline.R
retistruct/R/RetinalReconstructedDataset.R
retistruct/R/transformations.R
retistruct/R/RetinalDataset.R
retistruct/R/projections.R
retistruct/R/spheristruct.R
retistruct/R/revision.R
retistruct/R/StitchedOutline.R
retistruct/R/retistruct-gui.R
retistruct/R/TriangulatedOutline.R
retistruct/R/retistruct-cli.R
retistruct/R/Dataset.R
retistruct/R/kernel-density.R
retistruct/R/Outline.R
retistruct/R/generics.R
retistruct/R/retistruct.R
retistruct/R/retistruct-batch.R
retistruct/R/plots.R
retistruct/R/geometry.R
retistruct/R/ReconstructedOutline.R
retistruct/R/format-idt.R
retistruct/R/format-ijroi.R
retistruct/R/format-common.R
retistruct/R/misc.R
retistruct/R/format-csv.R
retistruct/R/ReconstructedDataset.R
retistruct/R/zzz.R
retistruct/R/fire.R
retistruct/MD5
retistruct/DESCRIPTION
retistruct/man
retistruct/man/getDss.reconstructedDataset.Rd
retistruct/man/retistruct.batch.export.matlab.Rd
retistruct/man/retistruct.cli.process.Rd
retistruct/man/getKDE.Rd
retistruct/man/whichTear.Rd
retistruct/man/retistruct.potential.od.Rd
retistruct/man/invert.sphere.to.hemisphere.Rd
retistruct/man/getDssMean.Rd
retistruct/man/retistruct.cli.Rd
retistruct/man/addTear.Rd
retistruct/man/kr.yhat.cart.Rd
retistruct/man/dE.Rd
retistruct/man/sinusoidal.Rd
retistruct/man/nameLandmark.retinalDataset.Rd
retistruct/man/flatplot.Rd
retistruct/man/sphere.cart.to.sphere.spherical.Rd
retistruct/man/flatplot.stitchedOutline.Rd
retistruct/man/getIDs.Rd
retistruct/man/flipped.triangles.Rd
retistruct/man/sphere.wedge.to.sphere.cart.Rd
retistruct/man/azimuthal.equalarea.Rd
retistruct/man/retistruct.read.dataset.Rd
retistruct/man/flatplot.outline.Rd
retistruct/man/projection.reconstructedOutline.Rd
retistruct/man/name.list.Rd
retistruct/man/ensureFixedPointInRim.Rd
retistruct/man/kde.compute.concentration.Rd
retistruct/man/Outline.Rd
retistruct/man/sphericalplot.reconstructedDataset.Rd
retistruct/man/sphere.spherical.to.polar.cart.Rd
retistruct/man/retistruct.cli.figure.Rd
retistruct/man/strain.colours.Rd
retistruct/man/line.line.intersection.Rd
retistruct/man/panlabel.Rd
retistruct/man/getSssMean.Rd
retistruct/man/vecnorm.Rd
retistruct/man/E.Rd
retistruct/man/getGss.retinalReconstructedDataset.Rd
retistruct/man/kr.yhat.Rd
retistruct/man/kr.sscv.Rd
retistruct/man/RetinalReconstructedDataset.Rd
retistruct/man/retistruct.batch.get.titrations.Rd
retistruct/man/simplify.outline.Rd
retistruct/man/Dataset.Rd
retistruct/man/TriangulatedOutline.Rd
retistruct/man/lvsLplot.Rd
retistruct/man/retistruct.check.markup.Rd
retistruct/man/sphericalplot.Rd
retistruct/man/central.angle.Rd
retistruct/man/sphericalplot.reconstructedOutline.Rd
retistruct/man/getDssMean.retinalReconstructedDataset.Rd
retistruct/man/transform.image.reconstructedOutline.Rd
retistruct/man/ijroi.read.dataset.Rd
retistruct/man/retistruct.read.markup.Rd
retistruct/man/kde.fhat.Rd
retistruct/man/projection.Rd
retistruct/man/create.polar.cart.grid.Rd
retistruct/man/AnnotatedOutline.Rd
retistruct/man/retistruct.save.recdata.Rd
retistruct/man/projection.reconstructedDataset.Rd
retistruct/man/tri.area.Rd
retistruct/man/retistruct.batch.plot.ods.Rd
retistruct/man/invert.sphere.Rd
retistruct/man/getDssMean.reconstructedDataset.Rd
retistruct/man/getIms.Rd
retistruct/man/retistruct.save.markup.Rd
retistruct/man/getIDs.dataset.Rd
retistruct/man/polar.cart.to.sphere.spherical.Rd
retistruct/man/orthographic.Rd
retistruct/man/compute.intersections.sphere.Rd
retistruct/man/csv.read.dataset.Rd
retistruct/man/labelTearPoints.Rd
retistruct/man/bary.to.sphere.cart.Rd
retistruct/man/retistruct.Rd
retistruct/man/getFlatRimLength.Rd
retistruct/man/idt.read.dataset.Rd
retistruct/man/kde.fhat.cart.Rd
retistruct/man/retistruct.batch.Rd
retistruct/man/Ecart.Rd
retistruct/man/solveMappingCart.Rd
retistruct/man/normalise.angle.Rd
retistruct/man/Fcart.Rd
retistruct/man/kde.L.Rd
retistruct/man/flatplot.dataset.Rd
retistruct/man/retistruct.batch.analyse.summary.Rd
retistruct/man/checkTears.Rd
retistruct/man/list.datasets.Rd
retistruct/man/getGss.reconstructedDataset.Rd
retistruct/man/sphere.cart.to.sphere.wedge.Rd
retistruct/man/flatplot.reconstructedOutline.Rd
retistruct/man/retistruct.export.matlab.Rd
retistruct/man/optimiseMapping.Rd
retistruct/man/retistruct.batch.figures.Rd
retistruct/man/remove.identical.consecutive.rows.Rd
retistruct/man/ReconstructedOutline.Rd
retistruct/man/sphere.tri.area.Rd
retistruct/man/read.datapoints.Rd
retistruct/man/azimuthal.equidistant.Rd
retistruct/man/retistruct.read.recdata.Rd
retistruct/man/azimuthal.conformal.Rd
retistruct/man/retistruct.batch.plot.titrations.Rd
retistruct/man/Rcart.Rd
retistruct/man/setFixedPoint.Rd
retistruct/man/sphere.cart.to.sphere.dualwedge.Rd
retistruct/man/tri.area.signed.Rd
retistruct/man/getStrains.Rd
retistruct/man/flatplot.retinalDataset.Rd
retistruct/man/getSss.Rd
retistruct/man/projectToSphere.Rd
retistruct/man/addClass.Rd
retistruct/man/remove.intersections.Rd
retistruct/man/compute.kernel.estimate.Rd
retistruct/man/StitchedOutline.Rd
retistruct/man/RetinalDataset.Rd
retistruct/man/azel.to.sphere.colattitude.Rd
retistruct/man/getSss.retinalReconstructedDataset.Rd
retistruct/man/flatplot.annotatedOutline.Rd
retistruct/man/flatplot.triangulatedOutline.Rd
retistruct/man/retistruct.reconstruct.Rd
retistruct/man/titrate.reconstructedOutline.Rd
retistruct/man/retistruct.batch.summary.Rd
retistruct/man/flipped.triangles.cart.Rd
retistruct/man/kr.compute.concentration.Rd
retistruct/man/ReconstructedDataset.Rd
retistruct/man/nameLandmark.Rd
retistruct/man/getIDs.reconstructedDataset.Rd
retistruct/man/fp.Rd
retistruct/man/checkDatadir.Rd
retistruct/man/removeTear.Rd
retistruct/man/getSss.reconstructedDataset.Rd
retistruct/man/getDss.retinalReconstructedDataset.Rd
retistruct/man/spherical.to.polar.area.Rd
retistruct/man/getKR.Rd
retistruct/man/retistruct.global.revision.Rd
retistruct/man/f.Rd
retistruct/man/identity.transform.Rd
retistruct/man/retistruct.batch.analyse.summaries.Rd
retistruct/man/circle.Rd
retistruct/man/recfile.version.Rd
retistruct/man/getDss.Rd
retistruct/man/rotate.axis.Rd
retistruct/man/getTear.Rd
retistruct/man/polartext.Rd
retistruct/man/stretchMesh.Rd
retistruct/man/mergePointsEdges.Rd
retistruct/man/getGss.Rd
retistruct/man/computeTearRelationships.Rd
retistruct/man/sphere.spherical.to.sphere.cart.Rd
retistruct/man/getIms.reconstructedOutline.Rd
retistruct/man/fire.Rd
retistruct/man/getDssHullarea.Rd
retistruct/man/RetinalReconstructedOutline.Rd
retistruct/man/getTss.Rd
retistruct/man/karcher.mean.sphere.Rd