Geometric morphometrics operations in python
Project description
Welcome to Morphops!
Morphops implements common operations and algorithms for 2d and 3d geometric morphometrics, in python 3.
Some high-level operations in the current version are
Centering, rescaling data
Rigid Rotation, Ordinary and Generalized Procrustes alignment
Thin-plate spline warping
Reading from and writing to *.dta files
Dependencies
numpy
Installation
pip install morphops
Usage Examples
import morphops as mops
# Create 3 landmark sets, each having 5 landmarks in 2 dimensions.
A = [[0,0],[2,0],[2,2],[1,3],[0,2]]
B = [[0.1,-0.1],[2,0],[2.3,1.8],[1,3],[0.4,2]]
C = [[-0.1,-0.1],[2.1,0],[2,1.8],[0.9,3.1],[-0.4,2.1]]
# Perform Generalized Procrustes Alignment to align A, B, C.
# :func:`gpa` is in the procrustes module.
res = mops.gpa([A,B,C])
# res['aligned'] contains the aligned A, B, C.
# res['mean'] contains the mean of the aligned A, B, C.
# Create a Thin-plate Spline warp from A to B and warp C.
warped_C = mops.tps_warp(A, B, C)
# warped_C contains the image of the pts in C under the TPS warp.
Project details
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
morphops-0.1.9.tar.gz
(14.6 kB
view hashes)
Built Distribution
morphops-0.1.9-py3-none-any.whl
(16.2 kB
view hashes)