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Funding Acknowledgements

The development of the initial version of Retistruct was supported by a Programme Grant from the UK Wellcome Trust (G083305) from 2008-2013.

Improvements to image handing and refactoring the code (released in v0.6.0) were supported by The Jackson Laboratory (Bar Harbor, ME, USA) Scientific Services Innovation Fund from 2016-2017 and an NIH R21 grant (EY027894–01A1) from 2018-2020 to Dr. Mark P. Krebs, The Jackson Laboratory.

For full details go to the home page: http://davidcsterratt.github.io/retistruct/

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Install

install.packages('retistruct')

Monthly Downloads

241

Version

0.6.1

License

CC BY-NC-SA 4.0

Maintainer

David Sterratt

Last Published

December 9th, 2019

Functions in retistruct (0.6.1)

The deformation energy function

The deformation energy function

Fragment constructor

FeatureSet class

The deformation energy gradient function

LandmarkSet class

AnnotatedOutline

AnnotatedOutline object

RetinalOutline class

RetinalReconstructedOutline

RetinalReconstructedOutline constructor

flatplot.AnnotatedOutline

Flat plot of AnnotatedOutline

azel.to.sphere.colatitude

Convert azimuth-elevation coordinates to spherical coordinates

The FIRE algorithm

TriangulatedOutline

TriangulatedOutline object

compute.kernel.estimate

Kernel estimate over grid

TriangulatedFragment

Triangulate outline Parameters to constructor: P Points to triangulate n Minimum number of points in the triangulation suppress.external.steiner If TRUE prevent the addition of points in the outline. This happens to maintain triangle quality. report Function to report progress

ReconstructedOutline

Reconstruct outline into spherical surface

StitchedOutline

Stitch together incisions and tears in an AnnotatedOutline

ReconstructedPointSet

ReconstructedPointSet class

Restore points to spherical manifold

ReconstructedCountSet

ReconstructedCountSet class

Add point correspondences to the outline

flatplot.ReconstructedOutline

Flat plot of reconstructed outline

create.polar.cart.grid

Create grid on projection of hemisphere onto plane

ReconstructedFeatureSet

ReconstructedFeatureSet class Initialised with a FeatureSet (fs) and an ReconstructedOutline (ro) object

line.line.intersection

Determine intersection between two lines

Piecewise smooth function used in area penalty

kr.compute.concentration

Find the optimal concentration for a set of data

flipped.triangles.cart

Determine indices of triangles that are flipped

parabola.invarclength

Inverse arc length of a parabola y=x^2/4f

Kernel regression on sphere using Fisherian density with Cartesian coordinates

Kernel density estimate on sphere using Fisherian density with Cartesian coordinates

ReconstructedLandmarkSet

ReconstructedLandmarkSet class

Convert an R6 object into a list, ignoring functions and environments

azimuthal.equidistant

Azimuthal equidistant projection

Draw the "flat" outline in 3D with depth information

Central angle between two points on a sphere

Check the whether directory contains valid data

Piecewise smooth function used in area penalty

parse.dependencies

Parse dependencies

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

kde.compute.concentration

Find the optimal concentration for a set of data

flatplot.StitchedOutline

Flat plot of AnnotatedOutline

Kernel density estimate on sphere using Fisherian density with polar coordinates

Start the Retistruct GUI

azimuthal.equalarea

Lambert azimuthal equal area projection

azimuthal.conformal

Azimuthal conformal or stereographic or Wulff projection

Return points on the unit circle

polar.cart.to.sphere.spherical

Convert polar projection in Cartesian coordinates to spherical coordinates on sphere

Kernel regression on sphere using Fisherian density with polar coordinates

retistruct.batch

Batch operation using the parallel package

read.datapoints

Read data points in CSV format

retistruct.cli.process

Process a dataset, saving results to disk

remove.identical.consecutive.rows

Remove identical consecutive rows from a matrix

Put text on the polar plot

retistruct.batch.get.titrations

Get titrations from a directory of reconstructions

flatplot.TriangulatedOutline

Plot flat TriangulatedOutline.

compute.intersections.sphere

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

flipped.triangles

Determine indices of triangles that are flipped

bary.to.sphere.cart

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

ijroi.read.dataset

Read a retinal dataset in IJROI format

Plot projection of a reconstructed outline

normalise.angle

Bring angle into range

Orthographic projection

projection.ReconstructedOutline

Projection of a reconstructed outline

interpolate.image

Interpolate values in image

The deformation energy gradient function

csv.read.dataset

Read a retinal dataset in CSV format

idt.read.dataset

Read one of the Thompson lab's retinal datasets

identity.transform

The identity transformation

retistruct.batch.plot.titrations

Plot titrations

retistruct.read.recdata

Read the reconstruction data from file

remove.intersections

Remove intersections between adjacent segments in a closed path

Invert sphere about its centre

Rotate axis of sphere

Generate colours for strain plots

Reporting utility function

retistruct.batch.summary

Extract summary data for a batch of reconstructions

retistruct.check.markup

Retistruct check markup

retistruct.reconstruct

Reconstruct a retina

retistruct.export.matlab

Save reconstruction data in MATLAB format

flatplot.Outline

Flat plot of outline

List datasets underneath a directory

projection.RetinalReconstructedOutline

Plot projection of reconstructed dataset

invert.sphere.to.hemisphere

Invert sphere to hemisphere

Convert an list created by R6_to_list() into an R6 object.

simplifyFragment

Simplify an outline object by removing short edges

Area of triangles on a plane

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

Sinusoidal projection

simplifyOutline

Simplify an outline object by removing short edges

sphere.wedge.to.sphere.cart

Convert from 'wedge' to Cartesian coordinates

retistruct.batch.analyse.summary

Extract statistics from the retistruct-batch.csv summary file

retistruct.batch.analyse.summaries

Extract statistics from a directory containing reconstruction directories.

read.datacounts

Read data counts in CSV format

Spherical plot of reconstructed outline

sphericalplot.ReconstructedOutline

Spherical plot of reconstructed outline

retistruct.batch.export.matlab

Export data from reconstruction data files to MATLAB

karcher.mean.sphere

Karcher mean on the sphere

Ancillary function to place labels

Plot the fractional change in length of mesh edges

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

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

Plot "flat" (unreconstructed) representation of outline

parabola.arclength

Arc length of a parabola y=x^2/4f

retistruct.read.dataset

Read a retinal dataset

retistruct.read.markup

Read the markup data

retistruct.save.markup

Process a dataset with a time limit

sphere.cart.to.sphere.dualwedge

Convert from Cartesian to ‘dual-wedge’ coordinates

sphere.spherical.to.sphere.cart

Convert from spherical to Cartesian coordinates

retistruct.batch.figures

Plot figures for a batch of reconstructions

retistruct.cli.figure

Print a figure to file

sphere.tri.area

Area of triangles on a sphere

sphere.cart.to.sphere.spherical

Convert from Cartesian to spherical coordinates

retistruct.save.recdata

Save reconstruction data

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