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
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
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
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
get number of meaningful Principal components
Obtain PC-scores for new landmark data
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
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
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
find vertices visible from a given viewpoints
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.
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
predict data from 2-Block PLS-scores
visualize an atlas defined by createAtlas
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
Compute the shape changes along the common axis of deformations
invert faces' orientation of triangular mesh
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
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
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 Landmarks from Slicer in Json format
import landmark data from csv files
projects the vertices of a mesh along its normals onto the surface of another one.
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
read dta files
symmetrize a bilateral landmark configuration
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
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.
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