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Morpho 2.0.3-1

@zarquon42b zarquon42b released this · 348 commits to master since this release

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OSX version
Linux version (source code)

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

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Morpho 2.0.2

@zarquon42b zarquon42b released this · 392 commits to master since this release

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Changes in Morpho version 2.0.2 (2013-02-24)

  • 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)

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Morpho 2.0.1

@zarquon42b zarquon42b released this · 424 commits to master since this release

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Changes in Morpho version 2.0.1 (2013-02-07)

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

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Pre-release

Morpho 1.99 - codename "Morphodillo"

@zarquon42b zarquon42b released this · 516 commits to master since this release

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Changes in Morpho version 1.99 (2013-12-18)
All FORTRAN code is now replaced by C++ code using Rcpp/RcppArmadillo!!

  • 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 option "add" in "meshDist" and "render" to add to existing rgl window.
  • fixed error in in 'placePatch' in case "data" is a matrix

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Morpho 1.0-2

@zarquon42b zarquon42b released this · 569 commits to master since this release

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OSX version
Linux version (source code)

Caution: the latest version of rgl (>= 0.93.963) and doParallel (>= 1.0.6) is required

Changes in Morpho version 1.0-2 (2013-11-05)

  • 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'

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Morpho 1.0beta2 (a.k.a. 0.99.1)

@zarquon42b zarquon42b released this · 612 commits to master since this release

Windows version
OSX version
Linux version (source code)

Caution: the latest version of rgl (>= 0.93.963) is required

Changes in Morpho version 0.99.1 (2013-10-07)

  • 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'
  • 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
  • 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

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Pre-release

releasing v. 0.99 (1.0-alpha)

@zarquon42b zarquon42b released this · 632 commits to master since this release

Windows version
OSX version
Linux version (source code)

Caution: the latest version of rgl (>= 0.93.963) is required

Changes in Morpho version 0.99 (2013-09-20)

  • 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
  • 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

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