Learn R Programming

⚠️There's a newer version (0.8.1) of this package.Take me there.

retistruct (version 0.5.10)

Retinal Reconstruction Program

Description

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.

Copy Link

Version

Install

install.packages('retistruct')

Monthly Downloads

234

Version

0.5.10

License

CC BY-NC-SA 4.0

Maintainer

David Sterratt

Last Published

February 16th, 2015

Functions in retistruct (0.5.10)

polar.cart.to.sphere.spherical

Convert polar projection in Cartesian coordinates to spherical coordinates on sphere

mergePointsEdges

Merge stitched points and edges

retistruct.export.matlab

Save reconstruction data in MATLAB format

Plot the fractional change in length of mesh edges

azimuthal.equidistant

Azimuthal equidistant projection

Flat plot of object

The deformation energy gradient function

TriangulatedOutline

Triangulate outline

The deformation energy function

Add new class to class vector of object

Return points on the unit circle

Ancillary function to place labels

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

getGss.retinalReconstructedDataset

Get grouped variable with locations in spherical coordinates.

invert.sphere.to.hemisphere

Invert sphere to hemisphere

kr.compute.concentration

Find the optimal concentration for a set of data

Kernel density estimate on sphere using Fisherian density with polar coordinates

RetinalReconstructedDataset

RetinalReconstructedDataset constructor

Put text on the polar plot

List datasets underneath a directory

Central angle between two points on a sphere

The deformation energy gradient function

line.line.intersection

Determine intersection between two lines

RetinalDataset constructor

recfile.version

Version of reconstruction file data format

flatplot.triangulatedOutline

Flat plot of TriangulatedOutline

StitchedOutline

Stitch together incisions and tears in an AnnotatedOutline

flatplot.reconstructedOutline

Flat plot of reconstructed outline

retistruct.cli.process

Process a dataset, saving results to disk

The FIRE algorithm

Get grouped variable with locations in spherical coordinates.

Remove tear from an AnnotatedOutline

Get spherical coordinates of tears.

getDssMean.reconstructedDataset

Karcher mean of datapoints in spherical coordinates

Add tear to an AnnotatedOutline

flatplot.dataset

Flat plot of Dataset

azimuthal.conformal

Azimuthal conformal or stereographic or Wulff projection

projectToSphere

Project mesh points in the flat outline onto a sphere

getIDs.reconstructedDataset

Get IDs of groups of data within a ReconstructedDataset

getSss.reconstructedDataset

Get transformed spherical coordinates of landmarks.

Kernel regression on sphere using Fisherian density with polar coordinates

Get transformed spherical coordinates of landmarks.

projection.reconstructedDataset

Plot projection of reconstructed dataset

computeTearRelationships

Compute the parent relationships for a set of tears

Kernel density estimate on sphere using Fisherian density with Cartesian coordinates

flatplot.outline

Flat plot of outline

ensureFixedPointInRim

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

Invert sphere about its centre

retistruct.batch.get.titrations

Get titrations from a directory of reconstructions

Name a landmark in a Dataset

retistruct.save.recdata

Save reconstruction data

bary.to.sphere.cart

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

Get transformed spherical coordinates of datapoints

getGss.reconstructedDataset

Get grouped variable with locations in spherical coordinates.

Get coordinates of corners of pixels of image in spherical coordinates

Return strains edges are under in spherical retina

projection.reconstructedOutline

Projection of a reconstructed outline

retistruct.batch.analyse.summaries

Extract statistics from a directory containing reconstruction directories.

Process a dataset with a time limit

Spherical plot of reconstructed outline

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

Karcher mean of datapoints in spherical coordinates

optimiseMapping

Optimise mapping

Return indicies of tear in AnnotatedOutline

getDssMean.retinalReconstructedDataset

Get transformed spherical coordinates of Karcher mean of datapoints

spherical.to.polar.area

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

retistruct.read.dataset

Read a retinal dataset

getDss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

retistruct.batch.analyse.summary

Extract statistics from the retistruct-batch.csv summary file

labelTearPoints

Label three outline point indicies as apicies and vertices of tear

ReconstructedDataset

Constructor for RecontructedDataset object

Get kernel density estimate of data points

sphere.tri.area

Area of triangles on a sphere

retistruct.reconstruct

Reconstruct a retina

sphere.cart.to.sphere.dualwedge

Convert from Cartesian to 'dualwedge' coordinates

sphericalplot.reconstructedOutline

Spherical plot of reconstructed outline

Constructor for a dataset object.

simplify.outline

Simplify an outline object by removing short edges

getFlatRimLength

Get rim length of AnnotatedOutline

Check the whether directory contains valid data

Orthographic projection

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

retistruct.batch.summary

Extract summary data for a batch of reconstructions

RetinalReconstructedOutline

RetinalReconstructedOutline constructor

read.datapoints

Read data points in CSV format

sphere.wedge.to.sphere.cart

Convert from 'wedge' to Cartesian coordinates

retistruct.batch.export.matlab

Export data from reconstruction data files to matlab

titrate.reconstructedOutline

Titrate values of phi0

compute.intersections.sphere

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

ijroi.read.dataset

Read a retinal dataset in IJROI format

Check that tears are all in the correct direction

csv.read.dataset

Read a retinal dataset in CSV format

retistruct.global.revision

Git short commit hash of Retistruct package

azimuthal.equalarea

Lambert azimuthal equal area projection

remove.identical.consecutive.rows

Remove identical consecutive rows from a matrix

Rotate axis of sphere

flatplot.annotatedOutline

Flat plot of AnnotatedOutline

Karcher mean of landmarks in spherical coordinates

retistruct.read.recdata

Read the reconstruction data from file

retistruct.check.markup

Retistruct check markup

Piecewise smooth function used in area penalty

sphere.spherical.to.polar.cart

Convert spherical coordinates on sphere to polar projection in Cartesian coordinates

retistruct.cli.figure

Print a figure to file

idt.read.dataset

Read one of the Thompson lab's retinal datasets

flatplot.retinalDataset

Flat plot of retinal dataset

solveMappingCart

Optimise mapping

Plot projection of an object

sphericalplot.reconstructedDataset

Spherical plot of reconstructed outline

Area of triangles on a plane

Kernel regression on sphere using Fisherian density with Cartesian coordinates

identity.transform

The identity transformation

Return index of tear

Get area of convex hull around data points on sphere

getDss.reconstructedDataset

Get transformed spherical coordinates of datapoints

normalise.angle

Bring angle into range

azel.to.sphere.colattitude

Convert azimuth-elevation coordinates to spherical coordinates

retistruct.batch.plot.ods

Superposed plot of ODs on polar axes

Start the Retistruct GUI

retistruct.read.markup

Read the markup data

getSss.retinalReconstructedDataset

Get transformed spherical coordinates of datapoints

flatplot.stitchedOutline

Flat plot of AnnotatedOutline

karcher.mean.sphere

Karcher mean on the sphere

transform.image.reconstructedOutline

Transform an image into the reconstructed space

Outline constructor

sphere.cart.to.sphere.wedge

Convert from Cartesian to 'wedge' coordinates

Get kernel regression estimate of grouped data points

compute.kernel.estimate

Kernel estimate over grid

Restore points to spherical manifold

retistruct.batch.plot.titrations

Plot titrations

Generate colours for strain plots

create.polar.cart.grid

Create grid on projection of hemisphere onto plane

flipped.triangles.cart

Determine indicies of triangles that are flipped

flipped.triangles

Determine indicies of triangles that are flipped

nameLandmark.retinalDataset

Name a landmark in a RetinalDataset

Set fixed point

sphere.cart.to.sphere.spherical

Convert from Cartesian to spherical coordinates

Get IDs of groups of data within a dataset

tri.area.signed

"Signed area" of triangles on a plane

kde.compute.concentration

Find the optimal concentration for a set of data

Get IDs of groups of data within a dataset

The deformation energy function

remove.intersections

Remove intersections between adjacent segements in a closed path

Sinusoidal projection

sphere.spherical.to.sphere.cart

Convert from spherical to Cartesian coordinates

AnnotatedOutline

Constructor for AnnotatedOutline object

ReconstructedOutline

Reconstruct outline into spherical surface

Piecewise smooth function used in area penalty

getIms.reconstructedOutline

Get coordinates of corners of pixels of image in spherical coordinates

retistruct.batch.figures

Plot figures for a batch of reconstructions

retistruct.batch

Batch operation using the parallel package

retistruct.potential.od

Test for a potential optic disc

retistruct.save.markup