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Morpho (version 2.6)

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

1,401

Version

2.6

License

GPL-2

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Repository

https://github.com/zarquon42b/Morpho

Maintainer

Stefan Schlager

Last Published

April 24th, 2018

Functions in Morpho (2.6)

Assess differences in amount and direction of asymmetric variation (only object symmetry)

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

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

apply affine transformation to data

creates 3D shapes from data to be saved as triangular meshes

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

fast kmeans clustering for 2D or 3D point clouds

Replace ID-strings of data and associated files.

calculate Centroid Size for a landmark configuration

equidistantCurve

make a curve equidistant (optionally up/downsampling)

separate a 3D-pointcloud by a hyperplane

Project coordinates onto a target triangular surface mesh.

classify specimen based on between-group PCA or CVA or typprobClass

predefined colors for bone and skin

calculate variance of a distribution stemming from prediction models

plot histogram for multiple groups.

calculates the barycenters for all faces of a triangular mesh

determine the minimum ratio for two subsequent eigenvalues to be considered different

concatenate multiple arrays/matrices

match two landmark configurations using iteratively closest point search

getPLSCommonShape

Get the linear combinations associated with the common shape change in each latent dimension of a pls2B

Landmarks and a triangular mesh

get intersection between a line and a plane

plot lines between landmarks

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

Get the shape changes from pls2B associated with each latent variable

createMissingList

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

landmarks and a triangular mesh representing a human nose

getPLSfromScores

compute changes associated with 2-Block PLS-scores

calculate the pooled within groups covariance matrix

computeTransform

calculate an affine transformation matrix

compute 2-Block PLS scores for new data

Create an atlas needed in placePatch

plsCoVarCommonShape

Compute the shape changes along the common axis of deformations

predictPLSfromScores

predict data from 2-Block PLS-scores

calculates distances and PC-coordinates of covariance matrices

visualise differences between two superimposed sets of 2D landmarks

predictRelWarps

predict relative warps for data not included in the training data set

visualise differences between two superimposed sets of 3D landmarks

estimate missing landmarks from their bilateral counterparts

merge multiple triangular meshes into a single one

convert a colored mesh to greyscale.

visualization of shape variation

projects a 3D coordinate orthogonally onto a plane

performs permutation testing for group differences.

Import 3D surface mesh files

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

estimate missing landmarks

find indices of faces that contain specified vertices

read.csv.folder

batch import data from files

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

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

getMeaningfulPCs

get number of meaningful Principal components

Project points onto the closest point on a mesh

getOuterViewpoints

Get viewpoints on a sphere around a 3D mesh

Obtain PC-scores for new landmark data

scale a mesh of class "mesh3d"

calculate typicality probabilities

invert faces' orientation of triangular mesh

getVisibleVertices

find vertices visible from a given viewpoints

Compute face or vertex normals of a triangular mesh

Calculates the Riemannian distance between two superimposed landmark configs.

Perform PCA based of the group means' covariance matrix

export mesh objects to disk

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

Q-Q plot to assess normality of data

correlation between shape space and tangent space

calculate the corners of a mesh's bouning box

write fiducials in slicer4 format

calculate relative Warp analysis

meshPlaneIntersect

get intersections between mesh and a plane

calculate average edge length of a triangular mesh

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

fast Principal Component Analysis (PCA)

mirror landmarks or triangular mesh in place

rotate matrix of landmarks

exports a matrix containing landmarks into .pts format

calculate the orthogonal complement of a 3D-vector

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

plot the result of slider3d

predictPLSfromData

predict 2 Block-PLS from new data

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

get 4x4 Transformation matrix

Procrustes ANOVA for structures with object symmetry

thin plate spline mapping (2D and 3D) for coordinates and triangular meshes

Procrustes registration

visualize an atlas defined by createAtlas

getTrafoRotaxis

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

readLandmarks.csv

import landmark data from csv files

find nearest neighbours for 2D and 3D point clouds

predictShape.lm

Predict shapes based on linear models calculated from PCscores

converts a list of matrices to an array

Import landmarks and outlines from TPS files

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

extract data from array names

mirror points or mesh on an arbitrary plane

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

calculate weights inverse to the distances from the specified observation.

read fiducials from slicer4

plots the normals of a triangular surface mesh.

Two-Block partial least square regression.

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

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

relax one specific landmark configuration against a reference

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

plot or save the results of meshDist

Export data to MorphoJ and Morphologika

convert PCs to landmark configuration

slides Semilandmarks along curves 2D by minimising bending energy of a thin-plate spline deformation.

Read saved pick-points from meshlab

virtualMeshScan

remove all parts of a triangular mesh, not visible from a set of viewpoints

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

reads pts files

symmetrize a bilateral landmark configuration

retroDeformMesh

symmetrize a triangular mesh

sort curvepoints by using the subsequent neighbours

create a perfectly symmetric version of landmarks

convert an 3D array into a matrix and back

some little helpers for vertex operations on triangular meshes

calulate regression scores for linear model

Workhorse function for procSym, responsible for Procrustes registration

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

calculate common allometric component

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

deprecated functions of Morpho

align new data to an existing Procrustes registration

correlation between a reduced space and the original space

Canonical Variate Analysis

calculate mean of an array

Create Matrices necessary for Thin-Plate Spline

calculate Pseudo-inverse of a Matrix using RcppArmadillo

compute the area of an n-dimensional hypersphere

compute the area of an n-dimensional hypersphere cap

Test whether the direction of two vectors is similar

calculate angle between two vectors