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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

92

Version

0.6.3

License

CC BY-NC-SA 4.0

Maintainer

Last Published

April 4th, 2020

Functions in retistruct (0.6.3)

Class containing basic information about flat outlines

Construct an outline object. This sanitises the input points P, as described below.

Superclass containing functions and data relating to sets of features in flat Outlines

Subclass of FeatureSet to represent counts centred on points

The deformation energy function

Subclass of FeatureSet to represent points

The deformation energy gradient function

FeatureSetCommon

Class containing functionality common to FeatureSets and ReconstructedFeatureSets

AnnotatedOutline

Class containing functions and data relating to annotating outlines

The deformation energy function

Restore points to spherical manifold

ReconstructedOutline

Class containing functions to reconstruct StitchedOutlines and store the associated data

Subclass of FeatureSet to represent points

Class containing functionality common to flat and reconstructed outlines

StitchedOutline

Class containing functions and data relating to Stitching outlines

compute.intersections.sphere

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

Add point correspondences to the outline

TriangulatedFragment

Class to triangulate Fragments

Return points on the unit circle

azimuthal.conformal

Azimuthal conformal or stereographic or Wulff projection

azimuthal.equalarea

Lambert azimuthal equal area projection

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

compute.kernel.estimate

Kernel estimate over grid

flatplot.Outline

Flat plot of outline

ReconstructedCountSet

Class containing functions and data to map CountSets to ReconstructedOutlines

The FIRE algorithm

create.polar.cart.grid

Create grid on projection of hemisphere onto plane

ReconstructedPointSet

Class containing functions and data to map PointSets to ReconstructedOutlines

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

Invert sphere about its centre

Plot "flat" (unreconstructed) representation of outline

invert.sphere.to.hemisphere

Invert sphere to hemisphere

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

TriangulatedOutline

Class containing functions and data relating to Triangulation

azel.to.sphere.colatitude

Convert azimuth-elevation coordinates to spherical coordinates

Class containing functions and data relating to retinal outlines

RetinalReconstructedOutline

A version of ReconstructedOutline that is specific to retinal datasets

csv.read.dataset

Read a retinal dataset in CSV format

ReconstructedFeatureSet

Class containing functions and data to map FeatureSets to ReconstructedOutlines

Kernel regression on sphere using Fisherian density with polar coordinates

flipped.triangles.cart

Determine indices of triangles that are flipped

Piecewise smooth function used in area penalty

The deformation energy gradient function

flatplot.AnnotatedOutline

Flat plot of AnnotatedOutline

ijroi.read.dataset

Read a retinal dataset in IJROI format

Piecewise smooth function used in area penalty

normalise.angle

Bring angle into range

Orthographic projection

kde.compute.concentration

Find the optimal concentration for a set of data

interpolate.image

Interpolate values in image

flatplot.TriangulatedOutline

Plot flat TriangulatedOutline.

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

flipped.triangles

Determine indices of triangles that are flipped

projection.RetinalReconstructedOutline

Plot projection of reconstructed dataset

ReconstructedLandmarkSet

Class containing functions and data to map LandmarkSets to ReconstructedOutlines

read.datacounts

Read data counts in CSV format

bary.to.sphere.cart

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

parabola.invarclength

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

parse.dependencies

Parse dependencies

azimuthal.equidistant

Azimuthal equidistant projection

idt.read.dataset

Read one of the Thompson lab's retinal datasets

identity.transform

The identity transformation

Put text on the polar plot

line.line.intersection

Determine intersection between two lines

polar.cart.to.sphere.spherical

Convert polar projection in Cartesian coordinates to spherical coordinates on sphere

Kernel regression on sphere using Fisherian density with Cartesian coordinates

Central angle between two points on a sphere

Check the whether directory contains valid data

flatplot.ReconstructedOutline

Flat plot of reconstructed outline

retistruct.check.markup

Retistruct check markup

retistruct.read.dataset

Read a retinal dataset

retistruct.read.markup

Read the markup data

sphere.wedge.to.sphere.cart

Convert from 'wedge' to Cartesian coordinates

retistruct.batch.summary

Extract summary data for a batch of reconstructions

karcher.mean.sphere

Karcher mean on the sphere

flatplot.StitchedOutline

Flat plot of AnnotatedOutline

retistruct.batch.analyse.summaries

Extract statistics from a directory containing reconstruction directories.

retistruct.save.markup

sphere.cart.to.sphere.spherical

Convert from Cartesian to spherical coordinates

retistruct.export.matlab

Save reconstruction data in MATLAB format

remove.intersections

Remove intersections between adjacent segments in a closed path

retistruct.cli.process

Process a dataset, saving results to disk

sphere.cart.to.sphere.dualwedge

Convert from Cartesian to ‘dual-wedge’ coordinates

Reporting utility function

retistruct.save.recdata

Save reconstruction data

retistruct.batch.analyse.summary

Extract statistics from the retistruct-batch.csv summary file

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

Kernel density estimate on sphere using Fisherian density with polar coordinates

Kernel density estimate on sphere using Fisherian density with Cartesian coordinates

retistruct.batch.export.matlab

Export data from reconstruction data files to MATLAB

List datasets underneath a directory

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

Ancillary function to place labels

parabola.arclength

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

projection.ReconstructedOutline

Projection of a reconstructed outline

kr.compute.concentration

Find the optimal concentration for a set of data

Plot projection of a reconstructed outline

retistruct.batch.figures

Plot figures for a batch of reconstructions

spherical.to.polar.area

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

Start the Retistruct GUI

retistruct.batch

Batch operation using the parallel package

Rotate axis of sphere

simplifyFragment

Simplify an outline object by removing short edges

sphere.spherical.to.sphere.cart

Convert from spherical to Cartesian coordinates

sphere.tri.area

Area of triangles on a sphere

Generate colours for strain plots

retistruct.batch.get.titrations

Get titrations from a directory of reconstructions

read.datapoints

Read data points in CSV format

remove.identical.consecutive.rows

Remove identical consecutive rows from a matrix

Process a dataset with a time limit

retistruct.cli.figure

Print a figure to file

retistruct.read.recdata

Read the reconstruction data from file

retistruct.reconstruct

Reconstruct a retina

retistruct.batch.plot.titrations

Plot titrations

sphere.cart.to.sphere.wedge

Convert from Cartesian to 'wedge' coordinates

simplifyOutline

Simplify an outline object by removing short edges

Sinusoidal projection

sphere.spherical.to.polar.cart

Convert spherical coordinates on sphere to polar projection in Cartesian coordinates

Area of triangles on a plane

Spherical plot of reconstructed outline

tri.area.signed

"Signed area" of triangles on a plane

sphericalplot.ReconstructedOutline

Spherical plot of reconstructed outline