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Morpho (version 2.2)

Calculations and visualisations related to Geometric Morphometrics

Description

A toolset for Geometric Morphometrics and mesh processing. This includes (among other stuff) mesh deformations based on reference points, permutation tests, detection of outliers, processing of sliding semi-landmarks and semi-automated surface landmark placement.

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Install

install.packages('Morpho')

Monthly Downloads

1,495

Version

2.2

License

GPL-2

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Repository

https://github.com/zarquon42b/Morpho

Homepage

http://sourceforge.net/projects/morpho-rpackage/

Maintainer

Stefan Schlager

Last Published

December 16th, 2014

Functions in Morpho (2.2)

Workhorse function for procSym, responsible for Procrustes registration

estimate missing landmarks from their bilateral counterparts

match two landmark configurations using iteratively closest point search

correlation between a reduced space and the original space

Estimate the shape by averaging the shape of the nearest neighbours.

Canonical Variate Analysis

separate a 3D-pointcloud by a hyperplane

deprecated functions of Morpho

Create Matrices necessary for Thin-Plate Spline

invert faces' orientation of triangular mesh

classify specimen based on between-group PCA or CVA

Graphical interface to find outliers and/or to switch mislabeld landmarks

Landmarks and a triangular mesh

computeTransform

calculate an affine transformation matrix

Replace ID-strings of data and associated files.

cut a mesh by a hyperplane and remove parts above/below that plane

calculates the barycenters for all faces of a triangular mesh

createMissingList

create a list with empty entries to be used as missingList in slider3d

predefined colors for bone and skin

calculate variance of a distribution stemming from prediction models

calculate mean of an array

calculate Centroid Size for a landmark configuration

calculate angle between two vectors

visualise differences between two superimposed sets of 2D landmarks

plots the normals of a triangular surface mesh.

Project semi-landmarks from a predefined atlas onto all specimen in a sample

align two 3D-pointclouds/meshes by their principal axes

Project coordinates onto a target triangular surface mesh.

get 4x4 Transformation matrix

extract information about fixed landmarks, curves and patches from and atlas generated by "landmark"

visualization of shape variation

fast calculation of a Matrix' per row/ per column mean - useful for very large matrices

Perform PCA based of the group means' covariance matrix

plot lines between landmarks

convert a colored mesh to greyscale.

concatenate multiple arrays/matrices

plot histogram for multiple groups.

A toolbox providing methods for data-acquisitiopn, visualisation and statistical methods related to Geometric Morphometrics and shape analysis

Procrustes registration

mirror landmarks or triangular mesh in place

visualise differences between two superimposed sets of 3D landmarks

Two-Block partial least square regression.

converts a mesh containing quadrangular faces into one only consisting of triangles

getTrafoRotaxis

compute a 4x4 Transformation matrix for rotation around an arbitrary axis

landmarks and a triangular mesh representing a human nose

symmetrize a bilateral landmark configuration

calculate the corners of a mesh's bouning box

projects a 3D coordinate orthogonally onto a plane

Calculates the Riemannian distance between two superimposed landmark configs.

find nearest neighbours for point clouds

Project points onto the closest point on a mesh

Creates a sequence of images showing predefined steps of warping two meshes or landmark configurations (2D and 3D) into each other

Export data to MorphoJ and Morphologika

extract data from array names

Q-Q plot to assess normality of data

perfom permutation testing on angles and distances between subgroups of two major groups.

Assess differences in amount and direction of asymmetric variation

visualize an atlas defined by createAtlas

Import landmarks and outlines from TPS files

rotate matrix of landmarks

returns the solution space (basis and translation vector) for an equation system

export mesh objects to disk

convert an 3D array into a matrix and back

rotates, translates and scales one matrix onto an other using Procrustes fitting

estimate missing landmarks

correlation between shape space and tangent space

reads pts files

calculate typicality probabilities

relax one specific landmark configuration against a reference

merge multiple triangular meshes into a single one

create a perfectly symmetric version of landmarks

readLandmarks.csv

import landmark data from csv files

calculate common allometric component

calculate a rotation matrix around an arbitrary axis through the origin in 3D

calulate regression scores for linear model

apply affine transformation to data

slides Semilandmarks along curves and surfaces in 3D by minimising bending energy of a thin-plate spline deformation.

projects the vertices of a mesh along its normals onto the surface of another one.

calculate average edge length of a triangular mesh

calculates distances and PC-coordinates of covariance matrices

performs permutation testing for group differences.

render.matrixDist

plot or save the results of meshDist

predictShape.lm

Predict shapes based on linear models calculated from PCscores

calculate the pooled within groups covariance matrix

thin plate spline mapping

Compute face or vertex normals of a triangular mesh

calculate weights inverse to the distances from the specified observation.

calculate relative Warp analysis

warping a mesh onto another configuration

meshDist.matrix

calculates and visualises distances between surface meshes or 3D coordinates and a surface mesh.

retroDeformMesh

symmetrize a triangular mesh

calculate the orthogonal complement of a 3D-vector

Procrustes ANOVA for structures with object symmetry

rotate ,scale and translate a mesh based on landmark information.

Create an atlas needed in placePatch

some little helpers for vertex operations on triangular meshes

read.csv.folder

batch import data from files

Read saved pick-points from meshlab

meshPlaneIntersect

get intersections between mesh and a plane

convert PCs to landmark configuration

scale a mesh of class "mesh3d"

Import 3D surface mesh files

Rotate an object (matrix or mesh) around an arbitrary axis in 3D

exports a matrix containing landmarks into .pts format

Visually browse through a sample rendering its landmarks and corresponding surfaces.

find indices of faces that contain specified vertices