This is Tweezepy, a Python package for calibrating forces in single-molecule force spectroscopy video-tracking experiments using the power spectral density (PSD), Allan variance (AV), and Hadamard variance (HV).
Read the documentation for Tweezepy. The usage of HV is the same as AV. You just need to replace every "AV" with "HV"
The simplest method of installing the Tweezepy package is via the Python Package Index (PyPI). To install from PyPI, you will need to be able to run python from the command line and make sure you have pip available.
However, HV is only available via setuptools, it will be added to PyPI soon.
Install from PyPI:
pip install tweezepy
An alternative method to install Tweezepy is with setuptools. Clone the repository onto a local machine, then navigate to the directory.
Using setuptools:
cd path/to/tweezepy
python setup.py install
The Tweezepy package includes the following modules:
- 'smmcalibration' - classes for calibration methods using the PSD and AV
- 'expressions' - functions with closed-form expressions for thermal motion in the PSD and AV
- 'MLE' - classes for maximum likelihood estimation (MLE) and Monte Carlo Markov chain (MCMC) sampling
- 'allanvar' - tools for calculating the AV and equivalent degrees of freedom
- 'hadamardvar' - tools for calculating the HV and equivalent degrees of freedom
- 'simulations' - tools to simulate bead thermal motion