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retistruct (version 0.5.12)

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

263

Version

0.5.12

License

CC BY-NC-SA 4.0

Maintainer

David Sterratt

Last Published

August 9th, 2017

Functions in retistruct (0.5.12)

The deformation energy function

The deformation energy function

The deformation energy gradient function

Outline constructor

ReconstructedOutline

Reconstruct outline into spherical surface

RetinalDataset constructor

Restore points to spherical manifold

ReconstructedDataset

Constructor for RecontructedDataset object

AnnotatedOutline

Constructor for AnnotatedOutline object

Constructor for a dataset object.

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 to cartesian coordinates

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

Central angle between two points on a sphere

flatplot.reconstructedOutline

Flat plot of reconstructed outline

flatplot.retinalDataset

Flat plot of retinal dataset

azel.to.sphere.colattitude

Convert azimuth-elevation coordinates to spherical coordinates

azimuthal.conformal

Azimuthal conformal or stereographic or Wulff projection

Return points on the unit circle

compute.intersections.sphere

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

RetinalReconstructedDataset

RetinalReconstructedDataset constructor

RetinalReconstructedOutline

RetinalReconstructedOutline constructor

create.polar.cart.grid

Create grid on projection of hemisphere onto plane

csv.read.dataset

Read a retinal dataset 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

flatplot.dataset

Flat plot of Dataset

flatplot.outline

Flat plot of outline

getDss.reconstructedDataset

Get transformed spherical coordinates of datapoints

getDss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

getIDs.reconstructedDataset

Get IDs of groups of data within a ReconstructedDataset

The deformation energy gradient function

ensureFixedPointInRim

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

flatplot.stitchedOutline

Flat plot of AnnotatedOutline

flatplot.triangulatedOutline

Flat plot of TriangulatedOutline

Get coordinates of corners of pixels of image in spherical coordinates

getIms.reconstructedOutline

Get coordinates of corners of pixels of image in spherical coordinates

Get kernel density estimate of data points

ijroi.read.dataset

Read a retinal dataset in IJROI format

flipped.triangles

Determine indices of triangles that are flipped

Get IDs of groups of data within a dataset

Get IDs of groups of data within a dataset

Piecewise smooth function used in area penalty

The FIRE algorithm

Piecewise smooth function used in area penalty

Get transformed spherical coordinates of datapoints

Invert sphere about its centre

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

flipped.triangles.cart

Determine indices of triangles that are flipped

normalise.angle

Bring angle into range

optimiseMapping

Optimise mapping

read.datapoints

Read data points in CSV format

recfile.version

Version of reconstruction file data format

getFlatRimLength

Get rim length of AnnotatedOutline

Get grouped variable with locations in spherical coordinates.

getSss.reconstructedDataset

Get transformed spherical coordinates of landmarks.

getSss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

Get kernel regression estimate of grouped data points

Get transformed spherical coordinates of landmarks.

invert.sphere.to.hemisphere

Invert sphere to hemisphere

karcher.mean.sphere

Karcher mean on the sphere

getGss.reconstructedDataset

Get grouped variable with locations in spherical coordinates.

getGss.retinalReconstructedDataset

Get grouped variable with locations in spherical coordinates.

Karcher mean of landmarks in spherical coordinates

Return strains edges are under in spherical retina

retistruct.batch.plot.ods

Superposed plot of ODs on polar axes

retistruct.batch.plot.titrations

Plot titrations

retistruct.reconstruct

Reconstruct a retina

retistruct.save.markup

sphere.cart.to.sphere.dualwedge

Convert from Cartesian to 'dualwedge' coordinates

Flat plot of object

flatplot.annotatedOutline

Flat plot of AnnotatedOutline

Get area of convex hull around data points on sphere

Karcher mean of datapoints in spherical coordinates

identity.transform

The identity transformation

idt.read.dataset

Read one of the Thompson lab's retinal datasets

labelTearPoints

Label three outline point indices as apices and vertices of tear

line.line.intersection

Determine intersection between two lines

parse.dependencies

Parse dependencies

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 segments in a closed path

retistruct.batch.summary

Extract summary data for a batch of reconstructions

mergePointsEdges

Merge stitched points and edges

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

Put text on the polar plot

projectToSphere

Project mesh points in the flat outline onto a sphere

projection.reconstructedOutline

Projection of a reconstructed outline

retistruct.check.markup

Retistruct check markup

retistruct.cli.process

Process a dataset, saving results to disk

retistruct.export.matlab

Save reconstruction data in MATLAB format

Set fixed point

getDssMean.reconstructedDataset

Karcher mean of datapoints in spherical coordinates

getDssMean.retinalReconstructedDataset

Get transformed spherical coordinates of Karcher mean of datapoints

Return indices of tear in AnnotatedOutline

Get spherical coordinates of tears.

read.datacounts

Read data counts in CSV format

retistruct.batch

Batch operation using the parallel package

retistruct.batch.analyse.summaries

Extract statistics from a directory containing reconstruction directories.

Process a dataset with a time limit

retistruct.cli.figure

Print a figure to file

retistruct.save.recdata

Save reconstruction data

Rotate axis of sphere

sphere.spherical.to.sphere.cart

Convert from spherical to Cartesian coordinates

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

Kernel regression on sphere using Fisherian density with polar coordinates

Kernel regression on sphere using Fisherian density with Cartesian coordinates

Name a landmark in a Dataset

nameLandmark.retinalDataset

Name a landmark in a RetinalDataset

Remove tear from an AnnotatedOutline

Start the Retistruct GUI

retistruct.batch.figures

Plot figures for a batch of reconstructions

sphere.tri.area

Area of triangles on a sphere

Kernel density estimate on sphere using Fisherian density with polar coordinates

Kernel density estimate on sphere using Fisherian density with Cartesian coordinates

List datasets underneath a directory

Plot the fractional change in length of mesh edges

Orthographic projection

Ancillary function to place labels

Plot projection of an object

projection.reconstructedDataset

Plot projection of reconstructed dataset

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.read.markup

Read the markup data

retistruct.read.recdata

Read the reconstruction data from file

sphere.cart.to.sphere.spherical

Convert from Cartesian to spherical coordinates

sphere.wedge.to.sphere.cart

Convert from 'wedge' to Cartesian coordinates

spherical.to.polar.area

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

tri.area.signed

"Signed area" of triangles on a plane

retistruct.batch.get.titrations

Get titrations from a directory of reconstructions

retistruct.read.dataset

Read a retinal dataset

Sinusoidal projection

solveMappingCart

Optimise mapping

simplify.outline

Simplify an outline object by removing short edges

Spherical plot of reconstructed outline

sphericalplot.reconstructedDataset

Spherical plot of reconstructed outline

transform.image.reconstructedOutline

Transform an image into the reconstructed space

retistruct.potential.od

Test for a potential optic disc

titrate.reconstructedOutline

Titrate values of phi0

Return index of tear

Area of triangles on a plane

sphere.cart.to.sphere.wedge

Convert from Cartesian to 'wedge' coordinates

sphere.spherical.to.polar.cart

Convert spherical coordinates on sphere to polar projection in Cartesian coordinates

sphericalplot.reconstructedOutline

Spherical plot of reconstructed outline

Generate colours for strain plots