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Morpho (version 2.10)

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

1,790

Version

2.10

License

GPL-2

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Repository

https://github.com/zarquon42b/Morpho

Maintainer

Stefan Schlager

Last Published

September 9th, 2022

Functions in Morpho (2.10)

Create Matrices necessary for Thin-Plate Spline

calculate common allometric component

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

Workhorse function for procSym, responsible for Procrustes registration

calulate regression scores for linear model

deprecated functions of Morpho

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

Test whether the direction of two vectors is similar

apply affine transformation to data

Canonical Variate Analysis

convert data from LPS to RAS space and back

Replace ID-strings of data and associated files.

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

calculate Centroid Size for a landmark configuration

concatenate multiple arrays/matrices

calculate mean of an array

Landmarks and a triangular mesh

align new data to an existing Procrustes registration

reverts list2array, converting an array to a list of matrices

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

correlation between a reduced space and the original space

compute the area of an n-dimensional hypersphere

Project coordinates onto a target triangular surface mesh.

calculate angle between two vectors

compute the area of an n-dimensional hypersphere cap

calculate Pseudo-inverse of a Matrix using RcppArmadillo

equidistantCurve

make a curve equidistant (optionally up/downsampling)

predefined colors for bone and skin

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

createMissingList

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

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

check for NA values in a matrix (of landmarks)

calculates the barycenters for all faces of a triangular mesh

computeTransform

calculate an affine transformation matrix

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

calculate the pooled within groups covariance matrix

Compute area enclosed within an irregular polygon

separate a 3D-pointcloud by a hyperplane

Create an atlas needed in placePatch

calculate variance of a distribution stemming from prediction models

getPointAlongOutline

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

estimate missing landmarks from their bilateral counterparts

try to identify bilateral landmarks and sort them by side

estimate missing landmarks

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

getPLSCommonShape

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

find indices of faces that contain specified vertices

calculates distances and PC-coordinates of covariance matrices

getMeaningfulPCs

get number of meaningful Principal components

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

getPLSfromScores

compute changes associated with 2-Block PLS-scores

get 4x4 Transformation matrix

fast kmeans clustering for 2D or 3D point clouds

compute 2-Block PLS scores for new data

plot histogram for multiple groups.

getTrafoRotaxis

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

visualise differences between two superimposed sets of 2D landmarks

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

getOuterViewpoints

Get viewpoints on a sphere around a 3D mesh

match two landmark configurations using iteratively closest point search

meshPlaneIntersect

get intersections between mesh and a plane

Obtain PC-scores for new landmark data

getVisibleVertices

find vertices visible from a given viewpoints

invert faces' orientation of triangular mesh

converts a list of matrices to an array

calculate the corners of a mesh's bouning box

find nearest neighbours for 2D and 3D point clouds

get intersection between a line and a plane

mirror points or mesh on an arbitrary plane

plot the result of slider3d

visualize an atlas defined by createAtlas

extract data from array names

plot lines between landmarks

Import 3D surface mesh files

Calculates the Riemannian distance between two superimposed landmark configs.

calculate average edge length of a triangular mesh

Perform PCA based of the group means' covariance matrix

projects a 3D coordinate orthogonally onto a plane

symmetrize a bilateral landmark configuration

visualise differences between two superimposed sets of 3D landmarks

predictPLSfromScores

predict data from 2-Block PLS-scores

merge multiple triangular meshes into a single one

retroDeformMesh

symmetrize a triangular mesh

predictRelWarps

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

convert a colored mesh to greyscale.

write fiducials in slicer4 format

predictShape.lm

Predict shapes based on linear models calculated from PCscores

calculate weights inverse to the distances from the specified observation.

plots the normals of a triangular surface mesh.

visualization of shape variation

performs permutation testing for group differences.

mirror landmarks or triangular mesh in place

fast Principal Component Analysis (PCA)

read.slicerjson

read Landmarks from Slicer in Json format

landmarks and a triangular mesh representing a human nose

export mesh objects to disk

Compute CV-scores from new data

Two-Block partial least square regression.

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

Get the shape changes from pls2B associated with each latent variable

readLandmarks.csv

import landmark data from csv files

exports a matrix containing landmarks into .pts format

plsCoVarCommonShape

Compute the shape changes along the common axis of deformations

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

Project points onto the closest point on a mesh

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

Q-Q plot to assess normality of data

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

calculate typicality probabilities

convert an 3D array into a matrix and back

some little helpers for vertex operations on triangular meshes

read fiducials from slicer4

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

Compute between-group-PC scores from new data

predictPLSfromData

predict 2 Block-PLS from new data

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

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

Procrustes ANOVA for structures with object symmetry

read.csv.folder

batch import data from files

plot or save the results of meshDist

Resample a curve equidistantly

Procrustes registration

create a perfectly symmetric version of landmarks

Read saved pick-points from meshlab

calculate relative Warp analysis

calculate the orthogonal complement of a 3D-vector

reads pts files

relax one specific landmark configuration against a reference

write.slicerjson

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

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

restore original data from PCA

restore shapes from PC-Scores or similar projections

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

rotate matrix of landmarks

scale a mesh of class "mesh3d"

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

virtualMeshScan

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

Export data to MorphoJ and Morphologika

Import landmarks and outlines from TPS files

correlation between shape space and tangent space

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

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

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

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

update a vector of indices after removal of some referenced items

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

sort curvepoints by using the subsequent neighbours

Compute face or vertex normals of a triangular mesh