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retistruct (version 0.5.11)

Retinal Reconstruction Program

Description

Reconstructs retinae by morphing a flat surface with cuts (a dissected flat-mount retina) onto a curvilinear surface (the 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.

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Install

install.packages('retistruct')

Monthly Downloads

285

Version

0.5.11

License

CC BY-NC-SA 4.0

Maintainer

David Sterratt

Last Published

July 15th, 2017

Functions in retistruct (0.5.11)

The deformation energy function

The deformation energy function

The deformation energy gradient function

Outline constructor

Restore points to spherical manifold

ReconstructedDataset

Constructor for RecontructedDataset object

ReconstructedOutline

Reconstruct outline into spherical surface

RetinalDataset constructor

AnnotatedOutline

Constructor for AnnotatedOutline object

Constructor for a dataset object.

RetinalReconstructedDataset

RetinalReconstructedDataset constructor

RetinalReconstructedOutline

RetinalReconstructedOutline constructor

Return points on the unit circle

compute.intersections.sphere

Find the intersection of a plane with edges of triangles on a sphere

azel.to.sphere.colattitude

Convert azimuth-elevation coordinates to spherical coordinates

azimuthal.conformal

Azimuthal conformal or stereographic or Wulff projection

bary.to.sphere.cart

Convert barycentric coordinates of points in mesh on sphere to cartesian coordinates

Central angle between two points on a sphere

Add new class to class vector of object

Add tear to an AnnotatedOutline

Check the whether directory contains valid data

Check that tears are all in the correct direction

azimuthal.equalarea

Lambert azimuthal equal area projection

azimuthal.equidistant

Azimuthal equidistant projection

create.polar.cart.grid

Create grid on projection of hemisphere onto plane

flatplot.reconstructedOutline

Flat plot of reconstructed outline

flatplot.retinalDataset

Flat plot of retinal dataset

Get area of convex hull around data points on sphere

Karcher mean of datapoints in spherical coordinates

csv.read.dataset

Read a retinal dataset in CSV format

flatplot.dataset

Flat plot of Dataset

flatplot.outline

Flat plot of outline

flipped.triangles

Determine indicies of triangles that are flipped

Piecewise smooth function used in area penalty

The FIRE algorithm

Piecewise smooth function used in area penalty

Get transformed spherical coordinates of datapoints

getDssMean.reconstructedDataset

Karcher mean of datapoints in spherical coordinates

getDssMean.retinalReconstructedDataset

Get transformed spherical coordinates of Karcher mean of datapoints

getIms.reconstructedOutline

Get coordinates of corners of pixels of image in spherical coordinates

Get kernel density estimate of data points

identity.transform

The identity transformation

idt.read.dataset

Read one of the Thompson lab's retinal datasets

mergePointsEdges

Merge stitched points and edges

Return a new version of the list in which any un-named elements have been given standardised names

normalise.angle

Bring angle into range

optimiseMapping

Optimise mapping

read.datapoints

Read data points in CSV format

StitchedOutline

Stitch together incisions and tears in an AnnotatedOutline

TriangulatedOutline

Triangulate outline

compute.kernel.estimate

Kernel estimate over grid

computeTearRelationships

Compute the parent relationships for a set of tears

flipped.triangles.cart

Determine indicies of triangles that are flipped

getIDs.reconstructedDataset

Get IDs of groups of data within a ReconstructedDataset

Get coordinates of corners of pixels of image in spherical coordinates

Get kernel regression estimate of grouped data points

Flat plot of object

flatplot.annotatedOutline

Flat plot of AnnotatedOutline

getDss.reconstructedDataset

Get transformed spherical coordinates of datapoints

getDss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

recfile.version

Version of reconstruction file data format

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

The deformation energy gradient function

ensureFixedPointInRim

Ensure that the fixed point is in the rim, not a tear

flatplot.stitchedOutline

Flat plot of AnnotatedOutline

getFlatRimLength

Get rim length of AnnotatedOutline

Get grouped variable with locations in spherical coordinates.

Return indicies of tear in AnnotatedOutline

Get spherical coordinates of tears.

Estimate of the log likelihood of the points mu given a particular value of the concentration kappa

kde.compute.concentration

Find the optimal concentration for a set of data

kr.compute.concentration

Find the optimal concentration for a set of data

Cross validation estimate of the least squares error of the points mu given a particular value of the concentration kappa

parse.dependencies

Parse dependencies

Get transformed spherical coordinates of landmarks.

invert.sphere.to.hemisphere

Invert sphere to hemisphere

karcher.mean.sphere

Karcher mean on the sphere

List datasets underneath a directory

flatplot.triangulatedOutline

Flat plot of TriangulatedOutline

getGss.reconstructedDataset

Get grouped variable with locations in spherical coordinates.

Karcher mean of landmarks in spherical coordinates

Return strains edges are under in spherical retina

Get IDs of groups of data within a dataset

Get IDs of groups of data within a dataset

getSss.reconstructedDataset

Get transformed spherical coordinates of landmarks.

getSss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

getGss.retinalReconstructedDataset

Get grouped variable with locations in spherical coordinates.

Kernel density estimate on sphere using Fisherian density with polar coordinates

Kernel density estimate on sphere using Fisherian density with Cartesian coordinates

labelTearPoints

Label three outline point indicies as apicies and vertices of tear

line.line.intersection

Determine intersection between two lines

Plot the fractional change in length of mesh edges

Name a landmark in a Dataset

nameLandmark.retinalDataset

Name a landmark in a RetinalDataset

polar.cart.to.sphere.spherical

Convert polar projection in Cartesian coordinates to spherical coordinates on sphere

remove.identical.consecutive.rows

Remove identical consecutive rows from a matrix

remove.intersections

Remove intersections between adjacent segements in a closed path

retistruct.batch.figures

Plot figures for a batch of reconstructions

projection.reconstructedOutline

Projection of a reconstructed outline

read.datacounts

Read data counts in CSV format

retistruct.batch.summary

Extract summary data for a batch of reconstructions

retistruct.check.markup

Retistruct check markup

Put text on the polar plot

projectToSphere

Project mesh points in the flat outline onto a sphere

Remove tear from an AnnotatedOutline

retistruct.batch.get.titrations

Get titrations from a directory of reconstructions

retistruct.reconstruct

Reconstruct a retina

retistruct.save.markup

Set fixed point

retistruct.cli.process

Process a dataset, saving results to disk

retistruct.export.matlab

Save reconstruction data in MATLAB format

sphere.cart.to.sphere.dualwedge

Convert from Cartesian to 'dualwedge' coordinates

sphere.cart.to.sphere.spherical

Convert from Cartesian to spherical coordinates

Start the Retistruct GUI

retistruct.batch.plot.ods

Superposed plot of ODs on polar axes

retistruct.batch.plot.titrations

Plot titrations

Process a dataset with a time limit

ijroi.read.dataset

Read a retinal dataset in IJROI format

Invert sphere about its centre

Kernel regression on sphere using Fisherian density with polar coordinates

simplify.outline

Simplify an outline object by removing short edges

sphericalplot.reconstructedOutline

Spherical plot of reconstructed outline

Generate colours for strain plots

Spherical plot of reconstructed outline

sphericalplot.reconstructedDataset

Spherical plot of reconstructed outline

retistruct.read.markup

Read the markup data

retistruct.read.recdata

Read the reconstruction data from file

sphere.cart.to.sphere.wedge

Convert from Cartesian to 'wedge' coordinates

retistruct.cli.figure

Print a figure to file

Sinusoidal projection

solveMappingCart

Optimise mapping

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

Kernel regression on sphere using Fisherian density with Cartesian coordinates

Orthographic projection

Ancillary function to place labels

Plot projection of an object

projection.reconstructedDataset

Plot projection of reconstructed dataset

retistruct.batch

Batch operation using the parallel package

retistruct.batch.analyse.summaries

Extract statistics from a directory containing reconstruction directories.

retistruct.potential.od

Test for a potential optic disc

retistruct.read.dataset

Read a retinal dataset

sphere.wedge.to.sphere.cart

Convert from 'wedge' to Cartesian coordinates

spherical.to.polar.area

Convert lattitude on sphere to radial variable in area-preserving projection

transform.image.reconstructedOutline

Transform an image into the reconstructed space

Area of triangles on a plane

retistruct.save.recdata

Save reconstruction data

Rotate axis of sphere

titrate.reconstructedOutline

Titrate values of phi0

tri.area.signed

"Signed area" of triangles on a plane

Return index of tear