Morpho

calculate common allometric component

Canonical Variate Analysis

Create Matrices necessary for Thin-Plate Spline

deprecated functions of Morpho

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

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

correlation between a reduced space and the original space

Workhorse function for procSym, responsible for Procrustes registration

calulate regression scores for linear model

align new data to an existing Procrustes registration

calculate angle between two vectors

Test whether the direction of two vectors is similar

Replace ID-strings of data and associated files.

apply affine transformation to data

compute the area of an n-dimensional hypersphere

compute the area of an n-dimensional hypersphere cap

calculate Pseudo-inverse of a Matrix using RcppArmadillo

calculate mean of an array

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

calculates the barycenters for all faces of a triangular mesh

concatenate multiple arrays/matrices

Landmarks and a triangular mesh

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

calculate Centroid Size for a landmark configuration

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

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

Project coordinates onto a target triangular surface mesh.

predefined colors for bone and skin

calculate an affine transformation matrix

calculates distances and PC-coordinates of covariance matrices

calculate the pooled within groups covariance matrix

Create an atlas needed in placePatch

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

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

separate a 3D-pointcloud by a hyperplane

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

visualise differences between two superimposed sets of 2D landmarks

visualise differences between two superimposed sets of 3D landmarks

make a curve equidistant (optionally up/downsampling)

calculate variance of a distribution stemming from prediction models

fast kmeans clustering for 2D or 3D point clouds

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

estimate missing landmarks from their bilateral counterparts

estimate missing landmarks

find indices of faces that contain specified vertices

get number of meaningful Principal components

Get viewpoints on a sphere around a 3D mesh

Obtain PC-scores for new landmark data

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

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

compute changes associated with 2-Block PLS-scores

compute 2-Block PLS scores for new data

get 4x4 Transformation matrix

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

find vertices visible from a given viewpoints

Perform PCA based of the group means' covariance matrix

plot histogram for multiple groups.

match two landmark configurations using iteratively closest point search

invert faces' orientation of triangular mesh

Calculates the Riemannian distance between two superimposed landmark configs.

get intersection between a line and a plane

plot lines between landmarks

converts a list of matrices to an array

find nearest neighbours for 2D and 3D point clouds

merge multiple triangular meshes into a single one

convert a colored mesh to greyscale.

export mesh objects to disk

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

get intersections between mesh and a plane

calculate the corners of a mesh's bouning box

calculate average edge length of a triangular mesh

mirror landmarks or triangular mesh in place

mirror points or mesh on an arbitrary plane

extract data from array names

landmarks and a triangular mesh representing a human nose

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

visualization of shape variation

performs permutation testing for group differences.

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

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

plot the result of slider3d

visualize an atlas defined by createAtlas

plots the normals of a triangular surface mesh.

Two-Block partial least square regression.

Get the shape changes from pls2B associated with each latent variable

Compute the shape changes along the common axis of deformations

Import 3D surface mesh files

projects a 3D coordinate orthogonally onto a plane

fast Principal Component Analysis (PCA)

Compute CV-scores from new data

Compute between-group-PC scores from new data

predict 2 Block-PLS from new data

predict data from 2-Block PLS-scores

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

Predict shapes based on linear models calculated from PCscores

calculate weights inverse to the distances from the specified observation.

Procrustes ANOVA for structures with object symmetry

Procrustes registration

Project points onto the closest point on a mesh

Q-Q plot to assess normality of data

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

Export data to MorphoJ and Morphologika

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

batch import data from files

read fiducials from slicer4

read dta files

Read saved pick-points from meshlab

reads pts files

import landmark data from csv files

Import landmarks and outlines from TPS files

correlation between shape space and tangent space

calculate relative Warp analysis

relax one specific landmark configuration against a reference

plot or save the results of meshDist

symmetrize a bilateral landmark configuration

symmetrize a triangular mesh

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

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

rotate matrix of landmarks

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

scale a mesh of class "mesh3d"

convert PCs to landmark configuration

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.

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

sort curvepoints by using the subsequent neighbours

create a perfectly symmetric version of landmarks

calculate the orthogonal complement of a 3D-vector

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

calculate typicality probabilities

Compute face or vertex normals of a triangular mesh

convert an 3D array into a matrix and back

some little helpers for vertex operations on triangular meshes

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

write fiducials in slicer4 format

exports a matrix containing landmarks into .pts format