AFM-tools 2.0

A Python package for visualizing and analyzing Atomic Force Microscopy(AFM) and Piezoelectric Force Microscopy(PFM) experimental data, offering tools to process, visualize, and extract meaningful insights from AFM images and measurements.

AFM-tools is a Python package for loading, processing, and visualizing Atomic Force Microscopy (AFM) and Piezoelectric Force Microscopy (PFM) data.

Project Links

• Source: https://github.com/yig319/AFM-tools

• Issues: https://github.com/yig319/AFM-tools/issues

• PyPI: https://pypi.org/project/AFM-tools/

Installation

Install from PyPI:

pip install AFM-tools

Most users should use this pip install. It includes all core AFM/PFM features. 3D utilities in afm_tools.drawing_3d require mayavi (VTK/Qt stack), which is recommended via Conda.

Install from source:

git clone https://github.com/yig319/AFM-tools.git
cd AFM-tools
pip install -e .

Clone On A New Desktop (Core Pip Environment)

From a fresh machine, this is the recommended setup for core AFM-tools usage:

git clone https://github.com/yig319/AFM-tools.git
cd AFM-tools
python -m venv .venv
source .venv/bin/activate
pip install -U pip
pip install -r requirements-dev.txt
pip install -e .

Optional: 3D environment (Mayavi via Conda)

If you need drawing_3d/Mayavi features:

conda env create -f environment-mayavi.yml
conda activate afm-tools-3d

This Conda environment installs mayavi/vtk/pyqt plus AFM-tools dependencies. Use it when you need 3D visualization.

Quick Start

import numpy as np
from afm_tools.afm_viz import AFMVisualizer

# Example image array (replace with real AFM/PFM image data)
img = np.random.randn(256, 256)

viz = AFMVisualizer()
viz.viz(img=img, scan_size={"image_size": 256, "scale_size": 1, "units": "um"})

Features

• Read and parse AFM-related wave/image formats.

• 2D/3D visualization utilities for AFM/PFM datasets.

• Domain and morphology analysis helpers.

• Video and plotting utilities for time/scan series.

Documentation

Sphinx documentation is provided in the docs directory.

Build docs locally:

pip install -r docs/requirements.txt
pip install -e .
sphinx-build -b html docs docs/_build/html

License

This project is licensed under the MIT License. See LICENSE.txt.