News for Package 'Morpho'

Changes in Morpho version 2.13 (2025-09-04)

• NEW: inscribeEllipse/inscribeEllipseRot: fit a maximum area ellipse into a 2D outline. Published in Torres et al. (2025)

• NEW: ILDS, ILDSR2: functions to assess meaningful subsets of interlandmark distances (Cardini et al (2025) - under review).

• icpmat: add functionality to avoid excessive scaling in case of similarity transform.

• meshDist: fix heatmap colors for case matrix

Changes in Morpho version 2.12 (2023-12-06)

• Fixed compiler complaints by CRAN

• bindArr: check for input as array

Changes in Morpho version 2.11 (2023-01-26)

• crossProduct: added option normalize.

• Replace rgl.* calls with *3d calls. (#33)

• read.slicerjson: read undefined landmarks from json info instead of checking position values

• read.slicerjson: read orientation from file instead of generic lps2ras matrix

• read.slicerjson: allow to read undefined landmarks

• write.slicerjson: allow export of NA values for Slicer >=5.0

Changes in Morpho version 2.10 (2022-09-09)

• read.fcsv: optimize handling of fiducial names

• NEW: computeArea: function computing projected area enclosed by set of ordered landmarks.

• pls2B: fixed CV and permutest for univariate cases.

• pls2B: Added RV-coefficient (and permutation test)

• getPLSCommonShape: fixed common sd calculation in example

• procSym/align2procSym: support use.lm option in align2procSym

• restoreShapes: add option meanlogCS / procSym add meanlogCS as output in case sizeshape=TRUE

• restoreShapes: add option origsize.

• restoreShapes: add option sizeshape

• readallTPS: add scale to allow scaling by included scale factor.

Changes in Morpho version 2.9 (2021-09-01)

• deformGrid2d: added option lty

• read.slicerjson: add option to specify na values.

• rotonto: return correctly dimensioned matrices in NA cases.

• NEW: getPointAlongOutline and resampleCurve

• meshDist: added option titleplot for customizing heatmap axis.

• procSym: Add numbering to PC-Variance table.

• groupPCA: remove misleading combinedVar table from output

• mirror: added option to mirror on plane, using it as a wrapper for mirror2plane.

• fixed arguments in deprecated function showPC

• deprecated: showPC

• getSides: set default values for pcAlign and icpiter

• NEW: getSides to find bilateral landmarks.

• NEW: updateIndices: update a vector of indices after removel of some of the indexed items

• NEW: restoreFromPCA: retrieve data back from a pca space.

• slider3d: new option smoothnormals to obtain tangent plains from smoothed normals

• read.slicer.json: added option lps2ras to automatically convert lps 2 ras space on import

• read.fcsv: add option lps2ras to allow an automatic conversion to RAS space if coordinates are recorded in LPS (as of Slicer > 4.11).

Changes in Morpho version 2.8 (2020-03-04)

• classify: added option newdata to predict class affinity for new data

• NEW: added predict functions for CVA and groupPCA

• warpmovie3d: supports now colored meshes

• changed mesh coloring to new rgl default of per-vertex color vector

• deformGrid3d: fixed correct position of grid

• typprob: fix mean matrix for single cases

• computeTransform: fix checking for NA Landmarks in all transform types

• angleTest: if values exceed system max for doubles, set them to .Machine$double.xmax and issue warning

• mesh2obj: now simply a wrapper for Rvcg::vcgObjWrite. Fixes Issue #14.

• test-slider3d: correctly renamed test

• rotonto: readded accidentally commented line

• rotonto: fix case when x and y are missing different coordinates

• read.fcsv: adapted to latest 3D slicer fiducials format

Changes in Morpho version 2.7 (2019-05-16)

bugfixes and minor changes

• classify.bgPCA: fixed arrayhandling for non-landmark data

• deformGrid2d: significant speed up in grid generation

• slider3d: removed unnecessary print statement.

• export.meshDist: use vcgPlyWrite for export

• warpmovie: bug preventing to export to subfolder

• meshDist, render: set meshColor="legacy" for latest rgl-dev

• slider3d: check if number of meshes matches number of landmark configs

• mergeMeshes: fixed color handling in case color is a vector.

• getTrafoRotaxis: fixed critical bug

• checkLM: added option meshlist

• Docu fixes.

• classify.bgPCA: fix case for 3D arrays

• write.pts: fix cases with duplicate rownames (prohibited by R)

• read.pts: don't set rownames if there are duplicate namings in the pts file.

Changes in Morpho version 2.6 (2018-04-19)

New features

• virtualMeshScan, getOuterViewpoints: perform a virtual rescan of a mesh using defined POVs.

• deformGrid3d: fixed indices starting with 0 for slices, add gridcol and gridwidth and added options to select subsets of slices.

• deformGrid2d: added options cex1,cex2,gridcol

• fixLMmirror: now allowing heavy abuse with loads of missing data and improved error handling

• plotNormals: allow for per vertex lenght vector and changed long=>length and deprecated old option

• checkLM: added possibility to view backwards

• slider3d: made function work in parallel on all OS

• pls2B: added CV (+ options)

• added plsCoVarCommonShape: Compute the shape changes along the common axis of deformations

• added getPLSCommonShape: Obtain linear combinations associated with the common shape change in each latent dimension of a pls2B

bugfixes and minor changes

• deformGrid3d: fixed indices starting with 0 for slices, add gridcol and gridwidth and added options to select subsets of slices.

• line2plane: fixed deprectated array multiplication warning

• changed Matrix::cBind to base::cbind

• Depend: > R 3.2.0

• GetPhi (retrodeform): set h to average between landmark distance (not the squared distance)

• CVA: add rownames and colnames to scores and CVs

Changes in Morpho version 2.5.1 (2017-04-19)

minor changes

• procSym: reverted to old behaviour, disabling orp if CSinit= FALSE

Changes in Morpho version 2.5 (2017-03-24)

New features

• added align2procSym to align new data to existing Procrustes aligned data.

• CVA: added option to specify prior probs

• fixLMtps, proc.weight: allow custom weight functions

• slider2d: public version of formerly private Semislide function

• procSym: added weights and centerweights to control Procrustes registration

• predictRelWarps: added prediction of uniform scores

• added support in predictRelWarps for alpha=0

• icpmat: added options for weights and centerweight

• deformGrid3d: allow exporting resulting 3D object as mesh

• cSize now also operates on mesh vertices

bugfixes and minor changes

• computeTransform: decreased singularity tolerance for type="tps"

• tps2d: added as alias of tps3d to avoid user confusion

• equidistantCurve: some minor improvements and fix for 2D case

• CreateL: fixed return of Lsubk3 if dim=2

• made read.mpp more generic

• applyTransform: more efficient normal handling for affine transform

• write.* functions: only append file suffix if missing in the filename

Changes in Morpho version 2.4.1 (2016-09-12)

bugfixes and minor changes

• fixed amount of covariance estimation

Changes in Morpho version 2.4 (2016-07-29)

New features

• added sortCurve and equidistantCurve

• added kappa statistic to print.classify

• added read/write.fcsv to read write landmark in 3DSlicer format

• added prcompfast, a faster and more memory efficient version of prcomp

• slider3d: now sliding without specifying surfaces is possible. Surface is estimated by computing normals from point clouds using vcgUpdateNormals

• added plot method for slider3d

• added fastKmeans a very fast and efficient way to compute kmeans-clustering for 2D and 3D data.

bugfixes and minor changes

• fixed c++14 standard requirements

• made index in rmVertex unique

• showPC: for single PCs vectors of length> 1 are coerced to matrix

• added option margin in deformGrid3d and deforGrid2d

• unified code for creating bending energy matrix

• made relWarps more memory and speed efficient and added option getBasis to disable (computationally expensive) calculation of vector basis.

• added dimnames from rownames in vecx

• returns Grandmean and Groupmeans as matrix/array for landmark data

• correct output in find.outliers if mahalanobis=TRUE and add probability

• added reflection=FALSE in find.outliers and corrected reported distances

• fixed read.lmdta for single configs

• slider3d: fixed case where all file infos are stored in sur.name

• fixed print.classify

• removed dependency yaImpute using vcgKDtree instead

• added unit testing for slider3d

• made CreateL and tps3d multi-threaded

• added options silent to slider3d and relaxLM

• ignore missing values when calculating quantiles and mindist in meshdist

• refactored CVA and added test for CVA

• fixed predictPLSfromScores for ncomp=1

• fixed correct lwd passing in deformGrid3d

• fixed procAOVsym for 2D case (correct df)

• added unit test for pls2B

• speed up pls2B by some orders of magnitude, now suitable for very large landmark configurations

• showPC: for single PCs vectors of length> 1 are coerced to matrix

Changes in Morpho version 2.3.1.1 (2016-01-22)

bugfixes and minor changes

• fixed c++14 standard requirements

• made index in rmVertex unique

Changes in Morpho version 2.3.1 (2015-12-15)

New features

• meshPlaneIntersect now also supports normals (as cutSpace)

• added default method for applyTransform for 2D and 3D vectors

bugfixes and minor changes

• removed bePCs with zero variance from output in relWarps

• improved error handling in placePatch

• set square=FALSE in qqmat

• added message if CSinit = F and orp = T, that orp is disabled

• fixed applyTransform for type="tps" and inverse = TRUE

• added testthat test for relWarps

• tweaked relWarps to work with large amounts of coordinates

• fixed wrong bracket position in ProcGPA leading to only a single iteration

• CVA: fixed calculation of posterior probs if cv=F

• fixed linewidth in CVA example to stop check complaints

• set p.adjust.method="none"

• only return significant scores in relWarps

• named output of plsCoVar

Changes in Morpho version 2.3.0 (2015-06-18)

New features

• added function line2plane to calculate intersection of a line and a plane

• added option pcAlign in function mirror to improve alignment to original object

• added option pcAlign in relWarps and procSym to allow alignment to first specimen rather than PC-axes.

• Gregory Jefferis added unit testing setup infrastructure

• added new functions getPLSfromScores, getPLSscores predictPLSfromScores,predictPLSfromData and plsCoVar for prediction and handling results from 2-Block PLS regression.

• made relaxLM an S3 function and added methods for mesh3d to relax two meshes with corresponding vertices. Added use.lm to specify subset of coordinates for alignment if bending =FALSE

• new option 'as.factor' in name2factor

• deprecated warp.mesh (use tps3d now for meshes and matrices)

• meshDist now allows custom colorramps

• added option wireframe in deformGrid2d

• added support for registered meshes in computeTransform

• added selection of transform type in icpmat

• added option use.lm to slider3d to specify subset for alignment if bending =FALSE

• added getMeaningfulPCs to determine meaningful Principal Components.

• made optimization in pcAlign and mirror run in parallel (not supported on Windows OS).

bugfixes and minor changes

• fixed normal handling in mergeMeshes

• fixed coefficient scaling in RegScore

• added update of normals in meshDist

• removed unnecessary function meanMat and replaced it with generic colMeans

• fixed calculation of loadings in pls2B

• set lambda (regularization) in all tps related functions to 1e-8 to avoid gross distortions in some cases

• fixed typo in pcAlign leading to misbehaviour if iterations < 1

Changes in Morpho version 2.2 (2014-12-16)

New features

• slider3d, relaxLM and procSym now allow minimizing Procrustes distance

• added orientation check in pcAlign to avoid reflections

• massive speed improvements in sliding semi-landmarks routines

• added options missing/missingList in relaxLM and slider3d to allow using semi-landmarks in "thin-air"

• added helper function createMissingList

• added function points2plane for projecting a point/pointcloud onto a plane.

• pcAlign with y missing now centers a shape and aligns it by its principal axes.

• added option pcAlign in procSym and ProcGPA to enable/disable alignment of sample by principal axes

bugfixes and minor changes

• renamed conv2backf to invertFaces

• renamed crossp to crossProduct

• renamed tanplan to tangentPlane

• reorient faces if reflections are involved in applyTransform

• made read.lmdta more versatile

• fixed an issue with argument "size" in deformGrid3d

• set default method to "vcg" in meshDist

Changes in Morpho version 2.1 (2014-09-25)

New features

• added new function mirror to mirror a landmark configuration or a mesh and registering onto the original one.

• added new functions retroDeform3d and retroDeformMesh for removing affine deformation from a 3D-meshes and pointclouds

• deformGrid3d now also accepts meshes

• added function classify for CVA and groupPCA for creating classification tables

• added new function getTrafo4x4, getTrafoRotaxis, computeTransform and applyTransform, for computing and applying affine transformations.

• new function pcAlign to align meshes and pointclouds by their principal axes

• added function meshPlaneIntersect to find intersection points between a mesh and a plane

• added function getFaces to get indices of faces that contain specified vertices

bugfixes and minor changes

• fixed issue with argument sep in typprobClass

• added option size in deformGrid3d

• fixed argument tol in ray2mesh

• fixed rhotol in placePatch if inflate=NULL

• fixed NA in colors from meshDist

• fixed rmVertex in case no faces remain

• changed relaxLM to accept 2D configs

• replaced workhorse function in projRead by the faster vcgClostKD

• made plotNormals to work with homogenous and non-homogeneous coordinates

• fixed issue in output of CVAdists (wrong attribution of p-value tables)

Changes in Morpho version 2.0.3 (2014-05-13)

• added support for objects stored in a list in bindArr

• made rotreverse an S3 function for matrices and mesh3d

• fixed bug in slider3d if pairedLM != 0

• fixed pooled within covariance matrix (covW) for single group entries

• speed up rotonto, rotonmat by vectorizing

• removed junk comments

• added fix for weighted Grandmean in CVA (thanks to Anne-Beatrice Defour)

• added check for empty patches and curves in cExtract (thanks to M. Friess for pointing that out)

• added 'cutMeshPlane' and 'cutSpace' to cut a pointcloud into upper and lower part

• added function 'solutionSpace' to calculate the basis of the solution space for Ax=b, with det(A)=0

• minor changes in asymPermute (docu and table naming)

• enabled multigroup support in asymPermute

• added groupmean output in asymPermute

• updateNormals: if no faces are present, mesh will be returned unchanged now. quadric faces are converted to triangular ones

• add new function 'quad2trimesh' for converting quadric meshes into triangular meshes.

• made code in pcaplot3d easier to maintain by creating .pcaplot3d

• assigned additional attributes to output of procSym

• exposed armaGinv, a simple wrapper to call Armadillos pseudo-inverse function.

Changes in Morpho version 2.0.2 (2014-02-24)

• added function 'fixLMmirror' to estimate missing bilateral landmarks

• wrote C++ versions of some subroutines to speed up Procrustes registration.

• added function arrMean3 to calculate fast average of 3D-array

• reprojection onto surface in 'slider3d' now can run in parallel (only OS X and Linux)

Changes in Morpho version 2.0.1 (2014-02-07)

• 'createAtlas' has new option "keep.fix" to specifiy landmarks that should be kept from sliding in case corrCurves are defined.

Changes in Morpho version 2.0 (2014-02-06)

• wrote C++ implementation of 'covPCA' (much faster) and added bootstrapping option to compute confidence intervals for PC-scores (removed obsolete options "mc.cores" and "scores")

• all functions calling trimesh-tools are now wrappers for much faster implementations from Rvcg

• placePatch now runs in parallel

• warpmovie3d now allows make movie of deformed mesh AND landmarks

Changes in Morpho version 1.99 (2013-12-18)

R-code

• renamed 'adnormals' to 'updateNormals'

• 'permudist' is now massively faster by using C++ code for permutation. It can handle more than 2 groups now.

• as the new 'permudist' is now implemented in 'groupPCA', it gets a boost, too.

• added function 'RegScore' to calculate Regression scores as described in Drake & Klingenberg(2008)

• added 'CAC' (common allometric component)

• added functions 'asymPermute' (assessing directional asymmetry) and 'meanMat' (fast Matrix averaging)

• covPCA now returns the distances instead of squared distances

• added option to revert vecx to translate a matrix back into an array containing landmarks

• adapted 'ray2mesh' to work in parallel calls and added option "mc.cores" in 'placePatch' - even in Windows

• added optipn "add" in "meshDist" and "render" to add to existing rgl window.

• fixed error in in 'placePatch' in case "data" is a matrix

Package documentation

• switched to roxygen2

• fixed some docu and added examples in 'pcaplot3d' and 'rotonmat'

• added link to PDF-manual in Morpho's help page

• commented out the answers in find.outliers to be able to run run_examples(...,run=FALSE) without errors

• marked more examples as dontrun, as the usage of roxygen2 allows the detailed check of ALL examples by using run_examples(devtools package). This uses less checking time and keeps CRAN from complaining

Misc

• translated all FORTRAN routines into C++ using Rcpp/RcppArmadillo

Changes in Morpho version 1.0 (2013-11-04)

R-code

• added option "barycoords" in 'closemeshKD' and added normal weighting

• made reprojection ind 'slider3d' using multiple cores in case "meshlist" is specified

• added option "blockdiag" in 'CreateL' to supress returning blockdiagonal matrix containin Lsubk

• significant speedup in calcGamma (responsible for sliding)

• added option "meshlist" in 'slider3d' and fixed memory allocation problem for orthogonal projection with large amounts of landmarks in 'procSym' (underlying routine 'orp')

• added autonaming of output in write.pts

• 'mergeMeshes' now allows a list of meshes to merge

• fixed error in 'mcNNindex' in case k=1

• added landmark matrix to output of 'cExtract'

• set pointsize to 10 in 'deformGrid3d' in case "type="p""

• added options "silent"/"ignore.stdout" to 'ply2mesh', 'projRead', 'ray2mesh', 'slider3d' and 'warp.mesh' to supress terminal output

• added option "pt.size" instead of "radius" in 'checkLM' and 'plotAtlas' to control point/sphere size.

• added option "fixRepro" in 'slider3d' and 'relaxLM' to supress reprojection of fix landmarks onto the surface. This can be useful when some fix landmarks are in "thin air".

• added support for point cloud export in 'mesh2ply' and 'mesh2obj'

• added option "silent" in 'rmUnrefVertex'

• fixed error in 'relWarps' preventing it to work for 2D configs

• added function 'checkLM'. Useful to visualize if projection by 'placePatch' was successful by browsing through sample.

• added functions 'placePatch', 'createAtlas' and 'plotAtlas' for defining templates and functions to project (semi-) landmarks from an atlas onto all specimen in a given sample

• fixed missing '-1' subtraction in 'covW'

• added function 'mergeMeshes' to concatenate multiple triangular meshes.

• made function 'procAOVsym' (procrustes Anova for object symmetry) public.

• made functions 'cSize', 'mcNNindex', 'meshcube', 'meshres', 'ProcGPA' public.

• added option 'info' in 'read.mpp'

• merged 'CreateL' and 'CreateL2D'

• rewrote large parts of 'CVA', 'groupPCA' and 'permudist' to make the code more efficient

• 'covPCA' now allows permutation tests to check if pairwise distances between covariance matrices are significant and reports rownames for two-group case

• removed unnecessary complicated check for empty groups by simply using function 'factor' in 'covW' and 'typprobClass'

• white space formatting in code

• added option "mshape" to function 'orp' to specify a custom pole for projection

• made function 'fx', 'PCAcrova' and 'calcTang_U' interntal-only by prefixing function name with '.'

• removed unnecessary sinus calculation in 'angle.calc'

Package documentation

• added docu and examples for all newly exposed functions (see above)

• added examples for 'find.outliers'

• added more examples for covPCA, performing permutation tests

• added docu for function 'barycenter'

• added a lot of examples to docu and documented data(nose)

• added documentation for 'angle.calc'

• added example in 'relaxLM'

• added section "details" in procSym, added example in slider3d

• added example for procAOVsym

• changed parameters in examples for 'pls2B' and 'relaxLM' to decrease completion time

Misc

• changed doParallel from Dependency to Import - needs 'doParallel' >= 1.06

• removed obsolete Fortran code

• added minimum version for imported package 'Matrix'(>= 1.0-1)

• changed foreach, parallel and rgl (needs rgl version >= 0.93.963) from 'Depends' to 'Imports' (affecting DESCRIPTION and NAMESPACE)

• massive NAMESPACE editing by switching to manual export instead of regular expression export

Changes in Morpho version 0.25-1 (2013-08-02)

R-code

• replaced abind with 'bindArr' in 'fixLMtps' and 'procSym'

• moved Distance calculation in 'CVA' to '.CVAdists' and radically cleaned code;

• removal of redundant variables in 'groupPCA'

• added option 'reflect' to 'procSym' (and underlying functions) and added copyright note for code copied from shapes package

Package documentation

• added docu for new data set "boneData"

• added examples in 'procSym'

• added example for 'tps3d'

Misc

• added additional example data (landmarks and a bone surface mesh)

• updated DESCRIPTION and README

• updated README added sourceforge and github download links

• added README.Rd

• added NEWS.Rd

Changes in Morpho version 0.25 (2013-07-24)

R-code

• simplified code in 'CVA' and 'CVA.crova'

• fixed issue when n-groups > n variables in 'CVA' and 'CVA.crova'

• replaced 'nn2' (RANN) with 'ann' (yaImpute) because RANN got (temporarily) banned from CRAN because of violation of policy

• added 'readLandmarks.csv' to read landmarks stored in spreadsheet text files (e.g. comma separated)

• added check for empty groups in 'typprobClass' and 'covW'

• changed cube creation in 'deformGrid3d' (much faster now).

• added options weights and centerweight in 'rotonmat'

• added confirmation for plotting spheres in 'deformGrid3d' when n > 1000 (can be slow)

• 'pcaplot3d' now works if data has only 1 PC

• removed useless code remains

• added 'bindArr' to concatenate matrices/arrays

• changed default core value in 'closemeshKD' from detectCores() to 1.

• added option 'keep' in 'rmVertex'

• changed default method in 'meshDist.mesh3d' from vcglib to morpho

• renamed 'regdist.raw' to 'regdist' and removed original 'regdist' (too prone to user error)

Package documentation

• finally mentioned Marta Rufino for providing all examples in docu for 'CVA' (sorry Marta, I simply forgot)

• fixed some docu and added examples in 'pcaplot3d' and 'rotonmat'

• added docu for 'anonymize', 'r2morphoj', 'r2morphologika', 'NNshapeReg', 'kendalldist'

Misc

• updated COPYRIGHT file

• switched from depends to import for colorRamps, MASS, RANN