Calculations and Visualisations Related to Geometric Morphometrics
restore original data from PCA
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
reverts list2array, converting an array to a list of matrices
calculate mean of an array
Assess differences in amount and direction of asymmetric variation (on...
calculates the barycenters for all faces of a triangular mesh
concatenate multiple arrays/matrices
calculate common allometric component
extract information about fixed landmarks, curves and patches from and...
Visually browse through a sample rendering its landmarks and correspon...
check for NA values in a matrix (of landmarks)
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
Compute area enclosed within an irregular polygon
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 Matrices necessary for Thin-Plate Spline
create a list with empty entries to be used as missingList in slider3d
calculate Centroid Size for a landmark configuration
cut a mesh by a hyperplane and remove parts above/below that plane
separate a 3D-pointcloud by a hyperplane
Canonical Variate Analysis
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 landma...
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 consi...
Get the linear combinations associated with the common shape change in...
compute changes associated with 2-Block PLS-scores
compute 2-Block PLS scores for new data
Get a point along a line with a given distance from the start of the l...
try to identify bilateral landmarks and sort them by side
get 4x4 Transformation matrix
compute a 4x4 Transformation matrix for rotation around an arbitrary a...
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 sear...
invert faces' orientation of triangular mesh
Calculates the Riemannian distance between two superimposed landmark c...
get intersection between a line and a plane
plot lines between landmarks
converts a list of matrices to an array
convert data from LPS to RAS space and back
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
calculate the corners of a mesh's bouning box
calculates and visualises distances between surface meshes or 3D coord...
get intersections between mesh and a plane
calculate average edge length of a triangular mesh
mirror landmarks or triangular mesh in place
mirror points or mesh on an arbitrary plane
deprecated functions of Morpho
A toolbox providing methods for data-acquisition, visualisation and st...
extract data from array names
Estimate the shape by averaging the shape of the nearest neighbours.
align two 3D-pointclouds/meshes by their principal axes
visualization of shape variation
correlation between a reduced space and the original space
performs permutation testing for group differences.
perfom permutation testing on angles and distances between subgroups o...
Project semi-landmarks from a predefined atlas onto all specimen in a ...
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 between-group-PC scores from new data
Compute CV-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 observat...
Procrustes ANOVA for structures with object symmetry
Workhorse function for procSym, responsible for Procrustes registratio...
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...
Export data to MorphoJ and Morphologika
projects the vertices of a mesh along its normals onto the surface of ...
batch import data from files
read fiducials from slicer4
read dta files
Read saved pick-points from meshlab
reads pts files
read Landmarks from Slicer in Json format
Import landmarks and outlines from TPS files
import landmark data from csv files
correlation between shape space and tangent space
calulate regression scores for linear model
relax one specific landmark configuration against a reference
calculate relative Warp analysis
plot or save the results of meshDist
Resample a curve equidistantly
restore shapes from PC-Scores or similar projections
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 origi...
rotate ,scale and translate a mesh based on landmark information.
rotate matrix of landmarks
rotates, translates and scales one matrix onto an other using Procrust...
scale a mesh of class "mesh3d"
slides Semilandmarks along curves 2D by minimising bending energy of a...
slides Semilandmarks along curves and surfaces in 3D by minimising ben...
returns the solution space (basis and translation vector) for an equat...
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 m...
calculate typicality probabilities
update a vector of indices after removal of some referenced items
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 viewp...
Creates a sequence of images showing predefined steps of warping two m...
write fiducials in slicer4 format
exports a matrix containing landmarks into .pts format
Export landmarks (or any 3D coordinates) to the new slicer json format
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.