Retinal Reconstruction Program
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Documentation for package ‘retistruct’ version 0.8.1
- DESCRIPTION file.
- Code demos. Use demo() to run them.
- Package NEWS.
Help Pages
A B C D E F I K L M N O P R S T U V
-- A --
| AnnotatedOutline | Class containing functions and data relating to annotating outlines |
| azel.to.sphere.colatitude | Convert azimuth-elevation coordinates to spherical coordinates |
| azimuthal.conformal | Azimuthal conformal or stereographic or Wulff projection |
| azimuthal.equalarea | Lambert azimuthal equal area projection |
| azimuthal.equidistant | Azimuthal equidistant projection |
-- B --
| bary.to.sphere.cart | Convert barycentric coordinates of points in mesh on sphere to cartesian coordinates |
-- C --
| central.angle | Central angle between two points on a sphere |
| checkDatadir | Check the whether directory contains valid data |
| circle | Return points on the unit circle |
| compute.intersections.sphere | Find the intersection of a plane with edges of triangles on a sphere |
| compute.kernel.estimate | Kernel estimate over grid |
| CountSet | Subclass of 'FeatureSet' to represent counts centred on points |
| create.polar.cart.grid | Create grid on projection of hemisphere onto plane |
| csv.read.dataset | Read a retinal dataset in CSV format |
-- D --
| dE | The deformation energy gradient function |
| depthplot3D | Draw the "flat" outline in 3D with depth information |
| directories | File system directories used by shinyFiles |
-- E --
| E | The deformation energy function |
| Ecart | The deformation energy function |
-- F --
| f | Piecewise smooth function used in area penalty |
| Fcart | The deformation energy gradient function |
| FeatureSet | Superclass containing functions and data relating to sets of features in flat 'Outline's |
| FeatureSetCommon | Class containing functionality common to 'FeatureSet's and 'ReconstructedFeatureSet's |
| fire | The FIRE algorithm |
| flatplot | Plot "flat" (unreconstructed) representation of outline |
| flatplot.AnnotatedOutline | Flat plot of AnnotatedOutline |
| flatplot.Outline | Flat plot of outline |
| flatplot.ReconstructedOutline | Flat plot of reconstructed outline |
| flatplot.StitchedOutline | Flat plot of AnnotatedOutline |
| flatplot.TriangulatedOutline | Plot flat 'TriangulatedOutline'. |
| flipped.triangles | Determine indices of triangles that are flipped |
| flipped.triangles.cart | Determine indices of triangles that are flipped |
| fp | Piecewise smooth function used in area penalty |
| Fragment | Construct an outline object. This sanitises the input points 'P', as described below. |
-- I --
| identity.transform | The identity transformation |
| idt.read.dataset | Read one of the Thompson lab's retinal datasets |
| ijroi.read.dataset | Read a retinal dataset in IJROI format |
| ijroimulti.read.dataset | Read a retinal dataset in IJROI format |
| interpolate.image | Interpolate values in image |
| invert.sphere | Invert sphere about its centre |
| invert.sphere.to.hemisphere | Invert sphere to hemisphere |
-- K --
| karcher.mean.sphere | Karcher mean on the sphere |
| kde.compute.concentration | Find the optimal concentration for a set of data |
| kde.fhat | Kernel density estimate on sphere using Fisherian density with polar coordinates |
| kde.fhat.cart | Kernel density estimate on sphere using Fisherian density with Cartesian coordinates |
| kde.L | Estimate of the log likelihood of the points mu given a particular value of the concentration kappa |
| kr.compute.concentration | Find the optimal concentration for a set of data |
| kr.sscv | Cross validation estimate of the least squares error of the points mu given a particular value of the concentration kappa |
| kr.yhat | Kernel regression on sphere using Fisherian density with polar coordinates |
| kr.yhat.cart | Kernel regression on sphere using Fisherian density with Cartesian coordinates |
-- L --
| LandmarkSet | Subclass of 'FeatureSet' to represent points |
| line.line.intersection | Determine intersection between two lines |
| list.datasets | List datasets underneath a directory |
| list_to_R6 | Convert an list created by R6_to_list() into an R6 object. |
| lvsLplot | Plot the fractional change in length of mesh edges |
-- M --
| morph.dataset.to.parabola | Morph a flat dataset to a parabola for testing purposes |
-- N --
| name.list | Return a new version of the list in which any unnamed elements have been given standardised names |
| normalise.angle | Bring angle into range |
-- O --
| orthographic | Orthographic projection |
| Outline | Class containing basic information about flat outlines |
| OutlineCommon | Class containing functionality common to flat and reconstructed outlines |
-- P --
| panlabel | Ancillary function to place labels |
| parabola.arclength | Arc length of a parabola y=x^2/4f |
| parabola.invarclength | Inverse arc length of a parabola y=x^2/4f |
| parse.dependencies | Parse dependencies |
| PathOutline | Add point fullcuts to the outline |
| PointSet | Subclass of 'FeatureSet' to represent points |
| polar.cart.to.sphere.spherical | Convert polar projection in Cartesian coordinates to spherical coordinates on sphere |
| polartext | Put text on the polar plot |
| projection | Plot projection of a reconstructed outline |
| projection.ReconstructedOutline | Projection of a reconstructed outline |
| projection.RetinalReconstructedOutline | Plot projection of reconstructed dataset |
-- R --
| R6_to_list | Convert an R6 object into a list, ignoring functions and environments |
| Rcart | Restore points to spherical manifold |
| read.datacounts | Read data counts in CSV format |
| read.datapoints | Read data points in CSV format |
| ReconstructedCountSet | Class containing functions and data to map CountSets to ReconstructedOutlines |
| ReconstructedFeatureSet | Class containing functions and data to map FeatureSets to ReconstructedOutlines |
| ReconstructedLandmarkSet | Class containing functions and data to map LandmarkSets to ReconstructedOutlines |
| ReconstructedOutline | Class containing functions to reconstruct StitchedOutlines and store the associated data |
| ReconstructedPointSet | Class containing functions and data to map PointSets to ReconstructedOutlines |
| remove.identical.consecutive.rows | Remove identical consecutive rows from a matrix |
| remove.intersections | Remove intersections between adjacent segments in a closed path |
| report | Reporting utility function |
| RetinalOutline | Class containing functions and data relating to retinal outlines |
| RetinalReconstructedOutline | A version of ReconstructedOutline that is specific to retinal datasets |
| retistruct | Start the Retistruct GUI |
| retistruct.batch | Batch operation using the parallel package |
| retistruct.batch.export.matlab | Export data from reconstruction data files to MATLAB |
| retistruct.batch.figures | Plot figures for a batch of reconstructions |
| retistruct.batch.get.titrations | Get titrations from a directory of reconstructions |
| retistruct.batch.plot.titrations | Plot titrations |
| retistruct.batch.summary | Extract summary data for a batch of reconstructions |
| retistruct.check.markup | Retistruct check markup |
| retistruct.cli | Process a dataset with a time limit |
| retistruct.cli.figure | Print a figure to file |
| retistruct.cli.process | Process a dataset, saving results to disk |
| retistruct.export.matlab | Save reconstruction data in MATLAB format |
| retistruct.read.dataset | Read a retinal dataset |
| retistruct.read.markup | Read the markup data |
| retistruct.read.recdata | Read the reconstruction data from file |
| retistruct.reconstruct | Reconstruct a retina |
| retistruct.save.markup | Save markup |
| retistruct.save.recdata | Save reconstruction data |
| rotate.axis | Rotate axis of sphere |
-- S --
| server | Retistruct Shiny Server |
| simplifyFragment | Simplify an outline object by removing short edges |
| simplifyOutline | Simplify an outline object by removing short edges |
| sinusoidal | Sinusoidal projection |
| sphere.cart.to.sphere.dualwedge | Convert from Cartesian to 'dual-wedge' coordinates |
| sphere.cart.to.sphere.spherical | Convert from Cartesian to spherical coordinates |
| 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 |
| sphere.spherical.to.sphere.cart | Convert from spherical to Cartesian coordinates |
| sphere.tri.area | Area of triangles on a sphere |
| 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 |
| sphericalplot | Spherical plot of reconstructed outline |
| sphericalplot.ReconstructedOutline | Spherical plot of reconstructed outline |
| StitchedOutline | Class containing functions and data relating to Stitching outlines |
| strain.colours | Generate colours for strain plots |
| stretchMesh | Stretch mesh |
-- T --
| tri.area | Area of triangles on a plane |
| tri.area.signed | "Signed area" of triangles on a plane |
| TriangulatedFragment | Class to triangulate Fragments |
| TriangulatedOutline | Class containing functions and data relating to Triangulation |
-- U --
| ui | Retistruct UI |
-- V --
| vecnorm | Vector norm |