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.

AuthorDavid C. Sterratt [aut, cre, cph], Daniel Lyngholm [aut, cph]
Date of publication2015-02-16 13:49:18
MaintainerDavid C. Sterratt <david.c.sterratt@ed.ac.uk>
LicenseCC BY-NC-SA 4.0
Version0.5.10
http://retistruct.r-forge.r-project.org/

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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