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Morpho (version 2.11)

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

2.11

License

GPL-2

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Repository

https://github.com/zarquon42b/Morpho

Maintainer

Stefan Schlager

Last Published

January 27th, 2023

Functions in Morpho (2.11)

Canonical Variate Analysis

Create Matrices necessary for Thin-Plate Spline

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

calculate common allometric component

Workhorse function for procSym, responsible for Procrustes registration

convert data from LPS to RAS space and back

deprecated functions of Morpho

calulate regression scores for linear model

align new data to an existing Procrustes registration

calculate angle between two vectors

compute the area of an n-dimensional hypersphere cap

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

calculate mean of an array

reverts list2array, converting an array to a list of matrices

concatenate multiple arrays/matrices

check for NA values in a matrix (of landmarks)

calculate Centroid Size for a landmark configuration

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

compute the area of an n-dimensional hypersphere

apply affine transformation to data

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

calculate Pseudo-inverse of a Matrix using RcppArmadillo

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

Test whether the direction of two vectors is similar

Replace ID-strings of data and associated files.

Landmarks and a triangular mesh

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

computeTransform

calculate an affine transformation matrix

correlation between a reduced space and the original space

separate a 3D-pointcloud by a hyperplane

createMissingList

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

calculates the barycenters for all faces of a triangular mesh

calculates distances and PC-coordinates of covariance matrices

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

calculate the pooled within groups covariance matrix

getPLSfromScores

compute changes associated with 2-Block PLS-scores

Create an atlas needed in placePatch

compute 2-Block PLS scores for new data

fast kmeans clustering for 2D or 3D point clouds

get 4x4 Transformation matrix

calculate variance of a distribution stemming from prediction models

equidistantCurve

make a curve equidistant (optionally up/downsampling)

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

getTrafoRotaxis

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

predefined colors for bone and skin

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

getOuterViewpoints

Get viewpoints on a sphere around a 3D mesh

estimate missing landmarks from their bilateral counterparts

estimate missing landmarks

Obtain PC-scores for new landmark data

Calculates the Riemannian distance between two superimposed landmark configs.

getPLSCommonShape

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

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

invert faces' orientation of triangular mesh

Project coordinates onto a target triangular surface mesh.

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

visualise differences between two superimposed sets of 2D landmarks

meshPlaneIntersect

get intersections between mesh and a plane

visualise differences between two superimposed sets of 3D landmarks

converts a list of matrices to an array

calculate the corners of a mesh's bouning box

get intersection between a line and a plane

Perform PCA based of the group means' covariance matrix

getVisibleVertices

find vertices visible from a given viewpoints

performs permutation testing for group differences.

visualization of shape variation

mirror points or mesh on an arbitrary plane

find nearest neighbours for 2D and 3D point clouds

extract data from array names

convert a colored mesh to greyscale.

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

merge multiple triangular meshes into a single one

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

predictPLSfromScores

predict data from 2-Block PLS-scores

Compute between-group-PC scores from new data

predictRelWarps

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

plot lines between landmarks

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

Compute area enclosed within an irregular polygon

find indices of faces that contain specified vertices

Get the shape changes from pls2B associated with each latent variable

Two-Block partial least square regression.

export mesh objects to disk

plots the normals of a triangular surface mesh.

plsCoVarCommonShape

Compute the shape changes along the common axis of deformations

landmarks and a triangular mesh representing a human nose

predictPLSfromData

predict 2 Block-PLS from new data

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

Procrustes registration

Export data to MorphoJ and Morphologika

Procrustes ANOVA for structures with object symmetry

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

calculate relative Warp analysis

Import landmarks and outlines from TPS files

read.slicerjson

read Landmarks from Slicer in Json format

read fiducials from slicer4

Q-Q plot to assess normality of data

Project points onto the closest point on a mesh

match two landmark configurations using iteratively closest point search

calculate average edge length of a triangular mesh

plot histogram for multiple groups.

getMeaningfulPCs

get number of meaningful Principal components

mirror landmarks or triangular mesh in place

restore shapes from PC-Scores or similar projections

correlation between shape space and tangent space

restore original data from PCA

visualize an atlas defined by createAtlas

plot the result of slider3d

fast Principal Component Analysis (PCA)

Import 3D surface mesh files

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

relax one specific landmark configuration against a reference

read.csv.folder

batch import data from files

slides Semilandmarks along curves 2D 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.

projects a 3D coordinate orthogonally onto a plane

write fiducials in slicer4 format

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

readLandmarks.csv

import landmark data from csv files

create a perfectly symmetric version of landmarks

Compute CV-scores from new data

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

virtualMeshScan

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

calculate the orthogonal complement of a 3D-vector

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

rotate matrix of landmarks

Compute face or vertex normals of a triangular mesh

sort curvepoints by using the subsequent neighbours

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

Resample a curve equidistantly

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

plot or save the results of meshDist

some little helpers for vertex operations on triangular meshes

predictShape.lm

Predict shapes based on linear models calculated from PCscores

convert an 3D array into a matrix and back

symmetrize a bilateral landmark configuration

update a vector of indices after removal of some referenced items

calculate weights inverse to the distances from the specified observation.

retroDeformMesh

symmetrize a triangular mesh

Read saved pick-points from meshlab

reads pts files

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

calculate typicality probabilities

write.slicerjson

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