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Morpho (version 2.12)

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

1,457

Version

2.12

License

GPL-2

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Repository

https://github.com/zarquon42b/Morpho

Maintainer

Stefan Schlager

Last Published

December 6th, 2023

Functions in Morpho (2.12)

calculate Pseudo-inverse of a Matrix using RcppArmadillo

reverts list2array, converting an array to a list of matrices

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

Project coordinates onto a target triangular surface mesh.

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

calculates the barycenters for all faces of a triangular mesh

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

check for NA values in a matrix (of landmarks)

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

createMissingList

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

calculate Centroid Size for a landmark configuration

Replace ID-strings of data and associated files.

calculate the pooled within groups covariance matrix

Create an atlas needed in placePatch

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

Landmarks and a triangular mesh

computeTransform

calculate an affine transformation matrix

calculates distances and PC-coordinates of covariance matrices

concatenate multiple arrays/matrices

fast kmeans clustering for 2D or 3D point clouds

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

equidistantCurve

make a curve equidistant (optionally up/downsampling)

separate a 3D-pointcloud by a hyperplane

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

visualise differences between two superimposed sets of 2D landmarks

visualise differences between two superimposed sets of 3D landmarks

predefined colors for bone and skin

find indices of faces that contain specified vertices

getMeaningfulPCs

get number of meaningful Principal components

Obtain PC-scores for new landmark data

getOuterViewpoints

Get viewpoints on a sphere around a 3D mesh

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

estimate missing landmarks

Compute area enclosed within an irregular polygon

estimate missing landmarks from their bilateral counterparts

converts a list of matrices to an array

find nearest neighbours for 2D and 3D point clouds

getPointAlongOutline

Get a point along a line with a given distance from the start of the line

try to identify bilateral landmarks and sort them by side

plot lines between landmarks

getTrafoRotaxis

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

export mesh objects to disk

get intersection between a line and a plane

get 4x4 Transformation matrix

Perform PCA based of the group means' covariance matrix

merge multiple triangular meshes into a single one

getVisibleVertices

find vertices visible from a given viewpoints

getPLSCommonShape

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

extract data from array names

mirror points or mesh on an arbitrary plane

mirror landmarks or triangular mesh in place

calculate average edge length of a triangular mesh

convert a colored mesh to greyscale.

visualization of shape variation

performs permutation testing for group differences.

compute 2-Block PLS scores for new data

calculate variance of a distribution stemming from prediction models

plot histogram for multiple groups.

getPLSfromScores

compute changes associated with 2-Block PLS-scores

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

plot the result of slider3d

predictPLSfromScores

predict data from 2-Block PLS-scores

visualize an atlas defined by createAtlas

predictRelWarps

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

plots the normals of a triangular surface mesh.

Two-Block partial least square regression.

match two landmark configurations using iteratively closest point search

landmarks and a triangular mesh representing a human nose

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

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

Get the shape changes from pls2B associated with each latent variable

plsCoVarCommonShape

Compute the shape changes along the common axis of deformations

invert faces' orientation of triangular mesh

meshPlaneIntersect

get intersections between mesh and a plane

Calculates the Riemannian distance between two superimposed landmark configs.

calculate the corners of a mesh's bouning box

fast Principal Component Analysis (PCA)

calculate weights inverse to the distances from the specified observation.

Compute CV-scores from new data

predictShape.lm

Predict shapes based on linear models calculated from PCscores

Compute between-group-PC scores from new data

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

Procrustes ANOVA for structures with object symmetry

Read saved pick-points from meshlab

Procrustes registration

predictPLSfromData

predict 2 Block-PLS from new data

reads pts files

Import 3D surface mesh files

projects a 3D coordinate orthogonally onto a plane

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

read.slicerjson

read Landmarks from Slicer in Json format

readLandmarks.csv

import landmark data from csv files

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

read.csv.folder

batch import data from files

Q-Q plot to assess normality of data

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

rotate matrix of landmarks

Project points onto the closest point on a mesh

calculate relative Warp analysis

relax one specific landmark configuration against a reference

restore original data from PCA

Import landmarks and outlines from TPS files

correlation between shape space and tangent space

read fiducials from slicer4

symmetrize a bilateral landmark configuration

retroDeformMesh

symmetrize a triangular mesh

Export data to MorphoJ and Morphologika

Resample a curve equidistantly

plot or save the results of meshDist

restore shapes from PC-Scores or similar projections

calculate typicality probabilities

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

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

sort curvepoints by using the subsequent neighbours

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

exports a matrix containing landmarks into .pts format

scale a mesh of class "mesh3d"

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

write fiducials in slicer4 format

write.slicerjson

Export landmarks (or any 3D coordinates) to the new slicer json format

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

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

virtualMeshScan

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

convert an 3D array into a matrix and back

create a perfectly symmetric version of landmarks

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

some little helpers for vertex operations on triangular meshes

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

calculate the orthogonal complement of a 3D-vector

Compute face or vertex normals of a triangular mesh

update a vector of indices after removal of some referenced items

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

convert data from LPS to RAS space and back

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

Create Matrices necessary for Thin-Plate Spline

Workhorse function for procSym, responsible for Procrustes registration

correlation between a reduced space and the original space

calulate regression scores for linear model

calculate common allometric component

Canonical Variate Analysis

compute the area of an n-dimensional hypersphere cap

deprecated functions of Morpho

apply affine transformation to data

align new data to an existing Procrustes registration

calculate angle between two vectors

calculate mean of an array

compute the area of an n-dimensional hypersphere

Test whether the direction of two vectors is similar